@article {pmid41372637, year = {2025}, author = {Kosmopoulos, JC and Pallier, W and Malik, AA and Anantharaman, K}, title = {Ecosystem health shapes viral ecology in peatland soils.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {41372637}, issn = {2058-5276}, support = {DBI2047598//National Science Foundation (NSF)/ ; 2137424//National Science Foundation (NSF)/ ; }, abstract = {Peatlands hold up to one-third of Earth's soil carbon but are increasingly turning from being carbon sinks to becoming carbon sources due to human impacts. Restoration efforts aim to reverse this trend, but viral influences on peatland recovery remain unclear, despite viruses being potent regulators of microbiomes and ecosystem function. Here we sequenced soil metagenomes to study viral communities across seven UK peatlands, each encompassing areas representing three peatland ecosystem health statuses: natural, damaged and restored. We found that viral diversity and community structure were shaped by both geography and ecosystem health. Viruses were geographically widespread, yet exhibited ecosystem health-specific endemism and functional adaptation, highlighting their sensitivity to restoration. Virus-host dynamics ranged from stable 'piggyback-the-winner' relationships to decoupled dynamics in those infecting keystone aerobes, sulfate reducers, carbohydrate degraders and fermenters. These findings position viruses as dynamic drivers of peatland ecosystem recovery and could unlock pathways to bolster carbon retention and accelerate climate mitigation.}, }
@article {pmid41372407, year = {2025}, author = {Asnicar, F and Manghi, P and Fackelmann, G and Baldanzi, G and Bakker, E and Ricci, L and Piccinno, G and Piperni, E and Mladenovic, K and Amati, F and Arrè, A and Ganesh, S and Giordano, F and Davies, R and Wolf, J and Bermingham, KM and Berry, SE and Spector, TD and Segata, N}, title = {Gut micro-organisms associated with health, nutrition and dietary interventions.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {41372407}, issn = {1476-4687}, abstract = {The incidence of cardiometabolic diseases is increasing globally, and both poor diet and the human gut microbiome have been implicated[1]. However, the field lacks large-scale, comprehensive studies exploring these links in diverse populations[2]. Here, in over 34,000 US and UK participants with metagenomic, diet, anthropometric and host health data, we identified known and yet-to-be-cultured gut microbiome species associated significantly with different diets and risk factors. We developed a ranking of species most favourably and unfavourably associated with human health markers, called the 'ZOE Microbiome Health Ranking 2025'. This system showed strong and reproducible associations between the ranking of microbial species and both body mass index and host disease conditions on more than 7,800 additional public samples. In an additional 746 people from two dietary interventional clinical trials, favourably ranked species increased in abundance and prevalence, and unfavourably ranked species reduced over time. In conclusion, these analyses provide strong support for the association of both diet and microbiome with health markers, and the summary system can be used to inform the basis for future causal and mechanistic studies. It should be emphasized, however, that causal inference is not possible without prospective cohort studies and interventional clinical trials.}, }
@article {pmid41371202, year = {2025}, author = {Xu, B and Zhang, H and Li, M and Lin, H and Wang, C}, title = {Application of metagenomic next-generation sequencing in diagnose the pulmonary infections caused by Aureobasidium melanogenum: A case report and review of the literature.}, journal = {Diagnostic microbiology and infectious disease}, volume = {114}, number = {3}, pages = {117213}, doi = {10.1016/j.diagmicrobio.2025.117213}, pmid = {41371202}, issn = {1879-0070}, abstract = {Aureobasidium melanogenum (A. melanogenum) is a black-yeast-like fungus widely present in nature that rarely causes human infections. We report a case of pulmonary infection caused by A. melanogenum in a 60-year-old male farmer, who initially presented with severe paroxysmal coughing and right-sided chest pain and was initially misdiagnosed with tuberculosis or lung cancer. While sputum cultures were negative, metagenomic next-generation sequencing (mNGS) detected A. melanogenum in bronchoalveolar lavage fluid, which was confirmed by PCR-Sanger sequencing. Susceptibility thresholds for Aureobasidium have not been established, and the optimal treatment requires further investigation. This case highlights that A. melanogenum infection should be considered even when lung lesions cannot be diagnosed by conventional methods. mNGS demonstrates potential advantages in detecting this pathogen, underscoring its value in diagnosing such rare fungal pulmonary infections.}, }
@article {pmid41371154, year = {2025}, author = {Tervo, S and Zalewski, A and Vauhkonen, H and Nieoczym, M and Kołodziej-Sobocińska, M and Lehikoinen, S and Aaltonen, K and Smura, T and Sironen, T and Pettersson, J}, title = {Virus circulation in native, introduced, and farmed mustelids in Poland.}, journal = {Virology}, volume = {615}, number = {}, pages = {110771}, doi = {10.1016/j.virol.2025.110771}, pmid = {41371154}, issn = {1096-0341}, abstract = {American mink (Neogale vison) are known carriers of various viruses, including many zoonoses. Their susceptibility to a wide range of pathogens and anatomical similarities to human lungs raise concerns about their potential role in facilitating interspecies transmission. Here we analysed viruses detected in tissue samples of native mustelids, and feral and farmed mink in Poland (2019-2022). The species included American mink, pine and stone marten (Martes martes, Martes foina), weasel (Mustela nivalis), European badger (Meles meles), European polecat (Mustela putorius), and Eurasian otter (Lutra lutra). Blood samples were tested for antibodies against SARS-CoV-2 (n = 270), and lung samples were subjected to genetic studies by PCR (n = 129) or metagenomics (n = 37). No evidence of SARS-CoV-2 was found in feral or wild populations, although two farmed mink tested positive for SARS-CoV-2 by PCR. Aleutian mink disease virus (AMDV) and mink Torque teno neovison virus (mTTV) were identified by metagenomics, and PCR analyses revealed frequent co-infection. AMDV was most prevalent in mink, while other mustelids showed serological evidence but were PCR-negative suggesting viral clearance. AMDV-DNA was found in 26.4 % and mTTV-DNA in 87.8 % of tissue samples. Two animals were co-infected with AMDV, mTTV, and SARS-CoV-2. Phylogenetic analysis revealed both local persistence and inter-farm transmission of AMDV, including transmission between feral and farmed mink. mTTV showed mixing of strains between Poland and China. The findings stress the need for improved surveillance and biosafety to monitor zoonotic threats and cross-species transmission.}, }
@article {pmid41371144, year = {2025}, author = {Zhao, K and Yang, L and Zhang, Y and Fang, H and Huang, Y and Hou, J and Wang, X and Liu, W and Luo, Y}, title = {Enrichment of a microbial consortium for 1,1,2-trichloroethane remediation: Insights into dechlorinators and community interactions.}, journal = {Journal of hazardous materials}, volume = {501}, number = {}, pages = {140716}, doi = {10.1016/j.jhazmat.2025.140716}, pmid = {41371144}, issn = {1873-3336}, abstract = {Chlorinated aliphatic hydrocarbons (CAHs), such as 1,1,2-trichloroethane (1,1,2-TCA), are persistent groundwater pollutants with high toxicity and carcinogenicity. Anaerobic reductive dechlorination by organohalide-respiring bacteria (OHRB) offers a promising remediation strategy. In this study, a stable microbial consortium, designated ZJGTCA, was enriched and shown to dechlorinate 1,1,2-TCA to ethene, achieving a complete dechlorination rate of 51.22 μM·day[-1] and a dihaloelimination rate of 2150 μM·day[-1] . Microbial succession analyses identified Trichlorobacter and Dehalococcoides as key dechlorinators, with qPCR quantifying their abundances as 2.82 × 10 [10] and 8.92 × 10 [11] copies·L[-1] , respectively. Network and metagenomic analyses revealed that Trichlorobacter and Citrobacter contribute critically to cofactor biosynthesis, including biotin, thiamine, and cobalamin pathways. Metagenome-assembled genome (MAG) analysis further established a microbial interaction model in which Trichlorobacter performs dihaloelimination, Dehalococcoides completes hydrogenolysis, and both Trichlorobacter and Citrobacter act as cofactor producers. Fermentative bacteria such as Sphaerochaeta metabolize lactate, propionate, and long-chain fatty acids into acetate and H2, supporting dechlorinators. These complementary functions highlight the ecological interactions sustaining efficient 1,1,2-TCA reductive dechlorination. The ZJGTCA consortium represents a promising bioaugmentation agent for CAHs-contaminated groundwater, offering insights into enhancing pollutant degradation and maintaining microbial community stability.}, }
@article {pmid41371128, year = {2025}, author = {Zeng, BH and Li, P and Zhang, HR and Xia, BH and Liu, B and Kong, LM and Liu, L and Li, ZH}, title = {The gut as a reservoir of drug-resistant pathogens: Mechanisms of ENR-driven horizontal gene transfer in aquaculture.}, journal = {Journal of hazardous materials}, volume = {501}, number = {}, pages = {140758}, doi = {10.1016/j.jhazmat.2025.140758}, pmid = {41371128}, issn = {1873-3336}, abstract = {Enrofloxacin (ENR), commonly used in aquaculture, plays a role in the development and dissemination of antibiotic resistance genes (ARGs). While most research on ARGs has focused on the environment, the gut, the host's largest microbial habitat, remains underexplored. Accordingly, this research investigates the gut microbiome, aiming to assess the potential mobility of ARGs after ENR exposure. Additionally, ENR exposure alters short-chain fatty acid (SCFAs) levels. Subsequent conjugation transfer experiments demonstrated that ENR exposure modifies SCFA levels, and this alteration facilitates the spread of ARGs. Both plasmid- and phage-mediated ARGs transmission were observed. ENR exerted selective pressure on the gut microbiota, significantly promoting plasmid-mediated conjugation as a key driver of ARGs dissemination. Simultaneously, environmental stress triggered the release of progeny phages carrying ARGs, further facilitating their spread. Conjugation experiments confirmed that ENR and SCFAs interact with bacterial outer membrane proteins, inducing the production of ROS. As a result of ROS production, membrane integrity is disrupted and membrane permeability is increased, ultimately causing an increase in the frequency of conjugative transfer and facilitating the horizontal delivery of ARGs. Therefore, ENR not only directly influences the transmission of ARGs but also indirectly promotes their transmission by altering SCFA levels. The study findings underscore the risks posed by excessive use of ENR in aquaculture to public health, providing scientific evidence to prevent food safety hazards from market entry of aquatic products carrying drug-resistant pathogens.}, }
@article {pmid41370957, year = {2025}, author = {Tian, H and Liu, J and Zhang, Y and Yang, T and Hao, G}, title = {Decoding the microplastic Micro-interface: a complex Web of gene transfer and pathogenic threats in wastewater.}, journal = {Environment international}, volume = {207}, number = {}, pages = {109971}, doi = {10.1016/j.envint.2025.109971}, pmid = {41370957}, issn = {1873-6750}, abstract = {The microplastic micro-interface (MPMI) in the municipal wastewater treatment system (MWTS) provides a new ecological niche for the microbiome (MGs) and potential pathogens (PPHs), facilitating both vertical and horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs). However, the distribution patterns and gene transfer events of PPHs, ARGs, and VFGs in MPMI remain unknown. This study examined three representative MPMIs (PET-MPMI, PE-MPMI, and PP-MPMI) colonized in the transverse gradient of MWTS using metagenomics. MGs, PPHs, ARGs, VFGs, and MGEs varied significantly across transverse gradients and horizontal interfaces. In MPMI, MGs/PPHs exhibited better connectivity and robustness (closeness centrality 19.51/21.45 and betweenness centricity 19.66/14.07), ARG hosts (mostly Escherichia coli and Salmonella enterica) demonstrated greater contig diversity and richness (6.44-7.36%), and adhesive VFGs provided superior competitive advantages. Additionally, MPMI shows a more complex and persistent coexistence pattern of MGs, ARGs, and VFGs (54.30-57.25%), increasing pathogenicity risk. MPMI accelerates the HGT of ARGs mediated by MGEs at the horizontal interface and transverse gradients through PPHs, with MGs, PPHs, MGEs, and VFGs directly influencing the alterations in ARGs within MPMI. This study developed a conceptual framework to understand MPMI gene co-occurrence and transfer across transverse gradients and interfaces, as well as the health risks of MPMI from ARG and VFG metastasis mediated by PPHs.}, }
@article {pmid41370178, year = {2025}, author = {Peto, L and Fawcett, N and Kamfose, MM and Scarborough, C and Peniket, A and Danby, R and Peto, TEA and Crook, DW and Llewelyn, MJ and Walker, AS}, title = {The impact of different antimicrobial exposures on the gut microbiome in the ARMORD observational study.}, journal = {eLife}, volume = {13}, number = {}, pages = {}, doi = {10.7554/eLife.97751}, pmid = {41370178}, issn = {2050-084X}, support = {NIHR200915//National Institute for Health and Care Research/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Male ; Female ; Adult ; Cross-Sectional Studies ; Middle Aged ; Aged ; *Anti-Bacterial Agents/pharmacology ; *Anti-Infective Agents/pharmacology ; Feces/microbiology ; Metagenomics ; United Kingdom ; *Bacteria/drug effects/classification/genetics ; Young Adult ; }, abstract = {Better metrics to compare the impact of different antimicrobials on the gut microbiome would aid efforts to control antimicrobial resistance (AMR). The Antibiotic Resistance in the Microbiome - Oxford (ARMORD) study recruited inpatients, outpatients, and healthy volunteers in Oxfordshire, UK, who provided stool samples for metagenomic sequencing. Data on previous antimicrobial use and potential confounders were recorded. Exposures to each antimicrobial were considered as factors in a multivariable linear regression, also adjusted for demographics, with separate analyses for those contributing samples cross-sectionally or longitudinally. Outcomes were Shannon diversity and relative abundance of specific bacterial taxa (Enterobacteriaceae, Enterococcus, and major anaerobic groups) and antimicrobial resistance genes (targeting beta-lactams, tetracyclines, aminoglycosides, macrolides, and glycopeptides). 225 adults were included in the cross-sectional analysis, and a subset of 79 patients undergoing haematopoietic cell transplant provided serial samples for longitudinal analysis. Results were largely consistent between the two sampling frames. Recent use of piperacillin-tazobactam, meropenem, intravenous co-amoxiclav, and clindamycin was associated with large reductions in microbiome diversity and reduced abundance of anaerobes. Exposure to piperacillin-tazobactam and meropenem was associated with a decreased abundance of Enterobacteriaceae and an increased abundance of Enterococcus and major AMR genes, but there was no evidence that these antibiotics had a greater impact on microbiome diversity than iv co-amoxiclav or oral clindamycin. In contrast, co-trimoxazole, doxycycline, antifungals, and antivirals had less impact on microbiome diversity and selection of AMR genes. Simultaneous estimation of the impact of over 20 antimicrobials on the gut microbiome and AMR gene abundance highlighted important differences between individual drugs. Some drugs in the WHO Access group (co-amoxiclav, clindamycin) had similar magnitude impact on microbiome diversity to those in the Watch group (meropenem, piperacillin-tazobactam) with potential implications for acquisition of resistant organisms. Metagenomic sequencing can be used to compare the impact of different antimicrobial agents and treatment strategies on the commensal flora.}, }
@article {pmid41369685, year = {2025}, author = {Mohammadi, R and Morovati, H and Safari, F}, title = {The human mycobiome: a critical yet understudied component of health and disease.}, journal = {Microbiology (Reading, England)}, volume = {171}, number = {12}, pages = {}, doi = {10.1099/mic.0.001631}, pmid = {41369685}, issn = {1465-2080}, mesh = {Humans ; *Mycobiome ; *Fungi/genetics/classification/isolation & purification/physiology ; COVID-19/microbiology/complications ; Dysbiosis/microbiology ; SARS-CoV-2 ; Metagenomics ; Neoplasms/microbiology ; }, abstract = {The human body hosts a complex and dynamic microbial community that is crucial for maintaining health. While bacteria dominate this system, fungal communities, collectively called the mycobiome, are increasingly recognized as vital contributors. However, fungi remain understudied due to challenges in culturing many species, limiting our understanding of their roles, interactions and effects on human biology. Advances in next-generation sequencing have transformed mycobiome research, revealing fungal diversity and its impact on health and disease. This review examines the mycobiome's composition and function across major body sites, including the gut, mouth, lungs, reproductive tract and skin. It also explores connections between fungal imbalances (dysbiosis) and diseases such as neurological disorders, cancer and post-COVID-19 complications. Despite progress, challenges persist, including the need for better culture-independent diagnostic tools and standardized research methods. Combining culturomics and metagenomics could help overcome these limitations and identify new treatment targets. By summarizing current knowledge and highlighting research gaps, this review aims to guide future studies on the mycobiome's role in human health.}, }
@article {pmid41369293, year = {2025}, author = {Liu, R and Wei, H and Xu, Z and Liu, Y and He, J and Wang, Z and Wang, L and Luo, M and Fang, J and Baltar, F and Xu, Y and Liang, Q and Huang, L}, title = {Extensive halogenated organic compound reservoirs and active microbial dehalogenation in Mariana Trench sediments.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf273}, pmid = {41369293}, issn = {1751-7370}, abstract = {The hadal trenches, the deepest regions of the ocean, serve as the final sinks for marine particles and "tunnels" for material exchange between the ocean and Earth's interior. Despite their extreme conditions, the trench sediments contain high content of organic carbon and active microbial carbon turnover, are hotspots for deep-sea organic carbon degradation and unique microbial processes. However, little is known about the organic carbon components and microbial metabolisms driving their degradation in trench sediments. This study provides the first comprehensive quantification of total halogenated organic compounds (organohalides) in Mariana Trench sediments. The measured bulk organic halogen concentrations exceeded all previously reported individual compounds by orders of magnitude, with a mean stoichiometric ratio of 1:49 (halogen:carbon) in the sedimentary organic carbon pool. These findings suggest the trench sediments may represent a significant reservoir for organohalides. Metagenomic analysis of global ocean data shows significant enrichment of the genes for organohalides biodegradation (dehalogenation) in trench microbiomes than those in other marine environments. Putative dehalogenating microorganisms in trench sediments encompassed 16 phyla and 52 orders, capable of metabolizing 18 structurally diverse organohalide compounds, revealing an unexpectedly broad phylogenetic distribution of organohalides metabolism and versatile substrate specificity among trench microbial communities. High pressure microcosm experiments demonstrated rapid degradation of typical organohalide compounds and transcription of genes related to organohalides metabolisms, confirming an active organohalides degradation by trench microorganisms. These findings underscore the role of organohalides metabolism in organic carbon remineralization in hadal trenches, advancing our understanding of deep-sea carbon cycling and microbial survival.}, }
@article {pmid41369187, year = {2025}, author = {Calderón-Osorno, M and Rojas-Jimenez, K}, title = {Depth-driven decline in viral diversity unveils potential novel viruses in global deep-sea ecosystems.}, journal = {Microbiology (Reading, England)}, volume = {171}, number = {12}, pages = {}, doi = {10.1099/mic.0.001632}, pmid = {41369187}, issn = {1465-2080}, mesh = {*Seawater/virology ; *Viruses/genetics/classification/isolation & purification ; *Biodiversity ; Ecosystem ; Metagenomics ; Phylogeny ; Microbiota ; Oceans and Seas ; Metagenome ; }, abstract = {Deep-sea ecosystems remain poorly understood due to exploration challenges. Despite the advancements metagenomics have brought to the understanding of the ocean microbiome, the diversity of marine viruses, particularly in the deep sea, is still not well characterized. In this study, we analysed the impact of depth on the composition and diversity of marine viruses in deep-sea waters at a global scale. Raw reads from deep-sea shotgun DNA sequences were retrieved from the Tara and Malaspina expeditions, encompassing depths from 270 to 4,005 m. A total of 80 samples containing viral reads were identified and analysed through a comprehensive bioinformatics pipeline, including quality assessment, taxonomic classification and metabolic annotation. The analysis reveals that microbial viral diversity significantly decreases with depth, with shallower waters exhibiting higher species richness. We determined that a substantial proportion of deep-sea viral sequences remains unclassified - up to 31.9% at depths of 270-1,000 m and 9.6% at 2,400-4,005 m. Additionally, a higher abundance of auxiliary metabolic genes was observed at shallower depths, indicating potential roles in host metabolism and adaptation. Our findings reveal the deep ocean as a vast, largely unexplored source of microbial viral diversity. This research emphasizes how depth influences viral diversity and community makeup in deep-sea environments, underscoring the need for further exploration to fully grasp their complexity and ecological roles.}, }
@article {pmid41369016, year = {2025}, author = {Southwood, LL and Long, A and Perez, J and Daniel, S and Bittinger, K and Aitken, M and Redding, L}, title = {Effect of surgical antimicrobial prophylaxis duration for colic surgery on complications and resistome.}, journal = {Equine veterinary journal}, volume = {}, number = {}, pages = {}, doi = {10.1002/evj.70137}, pmid = {41369016}, issn = {2042-3306}, support = {//Raymond Firestone Research Foundation/ ; }, abstract = {BACKGROUND: Based on human studies, surgical antimicrobial (AMD) prophylaxis (SAP) beyond 24 h is unnecessary and potentially detrimental.<br><br>OBJECTIVE: To compare clinical and microbiological outcomes in patients receiving 24- or 72-h of SAP for colic surgery.<br><br>STUDY DESIGN: Prospective randomised clinical trial.<br><br>METHODS: Horses that recovered from colic surgery were considered. Exclusion criteria were (1) age <2&#x2009;years; (2) Miniature Horses, pony, and draught breeds; (3) azotaemia; (4) recent hospitalisation, colic surgery, or AMDs; (5) local AMD administration. Eligible horses were randomly assigned to receive SAP with potassium penicillin and gentamicin for 24- or 72-h. Clinical data and complications were compared between SAP groups. Admission and discharge faecal samples from a subset of horses (N&#x2009;=&#x2009;49) underwent shotgun metagenomic sequencing on an Illumina platform. Host reads were filtered by aligning to reference genomes using the Burrows-Wheeler Aligner, and taxonomic classification was performed with kraken2. Sequencing reads were aligned to the Comprehensive Antimicrobial Resistance Database (CARD)5 and characterised using the AMR++ pipeline. The microbiome/resistome was characterised and compared between SAP groups over time.<br><br>RESULTS: One hundred and forty horses completed the study (24-h N&#x2009;=&#x2009;71 and 72-h N&#x2009;=&#x2009;69). The only clinical variable that was different between SAP groups was age (24-h median age 16 [IQR 9, 20] and 72-h 12 [6, 18] years, p&#x2009;=&#x2009;0.03). There was no significant difference between groups for any complications including incisional infection (24-h 17 [95% CI 10-27]% and 72-h 16 [9-26]%, p&#x2009;=&#x2009;0.9). Time was the main driver of changes in the microbiome/resistome: alpha diversity decreased while AMD resistance genes associated with administered AMD increased between admission and discharge. Discharge beta-lactam resistance genes were significantly higher in the 72-h than the 24-h group.<br><br>MAIN LIMITATIONS: Single hospital, small numbers for complications, clinicians not blinded to SAP group.<br><br>CONCLUSIONS: SAP for 24-h is recommended for horses undergoing colic surgery.}, }
@article {pmid41368664, year = {2025}, author = {Diaz, AJ and Centurioni, DA and Lasek-Nesselquist, E and Lapierre, P and Egan, CT and Perry, MJ}, title = {Whole genome sequencing of neurotoxin-producing Clostridium species in New York state to bolster epidemiological investigations and reveal patterns of diversity and distribution.}, journal = {Frontiers in public health}, volume = {13}, number = {}, pages = {1651032}, pmid = {41368664}, issn = {2296-2565}, mesh = {New York/epidemiology ; *Whole Genome Sequencing ; Humans ; *Clostridium/genetics/isolation &amp; purification/classification ; Phylogeny ; Polymorphism, Single Nucleotide ; Botulism/epidemiology ; *Neurotoxins ; Retrospective Studies ; Botulinum Toxins/genetics ; }, abstract = {Clostridia that produce neurotoxins are highly relevant organisms to public health. While cases of botulism [caused by C. botulinum and other organisms that produce botulinum neurotoxin (BoNT)] are rare, the severity of this disease necessitates robust epidemiologic surveillance to promptly identify and mitigate outbreaks. Next generation sequencing (NGS) can provide additional support to these investigations through single nucleotide polymorphism (SNP)-based analysis, phylogenetic reconstruction, toxin subtyping, and structural analysis. Until recently, testing for this disease was restricted to traditional culture or molecular methods such as polymerase chain reaction (PCR) to detect bont genes, while mouse bioassay and endopeptidase-mass spectrometry (Endopep-MS) methods confirmed the presence of enzymatically active toxin. The New York State Department of Health (NYSDOH) Wadsworth Center Biodefense Laboratory performed a retrospective whole genome sequence (WGS) analysis of approximately 240 Clostridium spp. isolates from the past 40 years to supplement traditional test results and further characterize these organisms. Genomic analyses identified seven BoNT serotypes/serotype combinations, including A4(B5), A5(B2'), and B5F2 that were uncharacteristic of samples typically received. Additionally, SNP-based analysis and de novo genome assemblies retrospectively validated several epidemiology links or differentiated samples previously tested with only traditional methods. Our work highlights the clinical utility of supplementing conventional data with NGS to further characterize BoNT-producing organisms and underscores the importance of incorporating WGS into laboratory workflows to support epidemiologic investigations. However, several obstacles still exist which may prevent implementation. These include the expertise needed to execute bioinformatic analyses and interpret the resulting data, a lack of standardized bioinformatic workflows, and difficulty in determining SNP-based thresholds to identify linked samples without incorporation of additional data and analyses. Supplementing or replacing short-read sequencing with long-read sequencing (LRS) and the use of metagenomic or capture-based enrichment for analysis of primary specimens could increase the leverage obtained from WGS in epidemiological investigations.}, }
@article {pmid41368641, year = {2025}, author = {He, J and Jia, J and Qu, W and Zhang, S and Fan, K and Lin, R and Zhao, W and Niu, Y and Huang, Y and Jia, L}, title = {Bacteroides ovatus-derived N-methylserotonin inhibit colorectal cancer via the HTR1D-mediated cAMP-PKA-NF-κB signaling axis.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1696701}, pmid = {41368641}, issn = {1664-3224}, mesh = {Humans ; *Colorectal Neoplasms/metabolism/pathology/drug therapy/microbiology ; Animals ; NF-kappa B/metabolism ; Mice ; Signal Transduction/drug effects ; Cyclic AMP/metabolism ; Gastrointestinal Microbiome ; Male ; *Serotonin/analogs &amp; derivatives/pharmacology/metabolism ; Female ; *Bacteroides/metabolism ; Cyclic AMP-Dependent Protein Kinases/metabolism ; Middle Aged ; Cell Line, Tumor ; Aged ; Disease Models, Animal ; }, abstract = {OBJECTIVE: To analyze differences in gut microbiota composition, metabolites, and metabolic pathways between healthy individuals and colorectal cancer (CRC) patients, and to investigate the inhibitory effects of N-methylserotonin (NMS) produced by Bacteroides ovatus (B.o) from orange fiber on CRC progression and its underlying mechanisms.<br><br>METHODS: (1) Fecal samples from CRC patients (n=26) and healthy controls (n=20) were collected for metagenomic sequencing and untargeted metabolomics analysis; (2) The ability of B.o to produce NMS from orange fiber was validated in vitro; (3) A CRC mouse model was established using azoxymethane (AOM)/dextran sulfate sodium (DSS) induction, followed by evaluation of body weight, rectal bleeding, colorectal length, tumor number, and intestinal barrier function; (4) Network pharmacology, molecular docking, and western blot analysis were combined to verify the mechanism of action; (5) 16S rRNA sequencing was performed to analyze gut microbiota changes.<br><br>RESULTS: (1) CRC patients showed significantly increased metabolic pathways including glycolysis, methane metabolism, beneficial amino acid degradation, and linoleic acid degradation, along with significantly decreased B.o abundance and NMS levels, which were positively correlated; (2) NMS significantly inhibited CRC cell proliferation, migration, and invasion, while promoting apoptosis; (3) Combined treatment with B.o and orange fiber or NMS alone reduced tumorigenesis and improved intestinal barrier function; (4) Mechanistic studies revealed that these effects could be mediated through downregulation of 5-hydroxytryptamine receptor 1D (HTR1D) expression and inhibition of the cAMP/PKA/I&#x3ba;B&#x3b1;/NF-&#x3ba;B pathway; (5) The treatments optimized gut microbiota structure and metabolite composition.<br><br>CONCLUSION: B.o and its metabolite NMS possibly inhibit CRC progression by modulating the HTR1D-mediated cAMP/PKA/NF-&#x3ba;B signaling pathway, while improving gut microbiota structure, providing a novel therapeutic target for CRC prevention and treatment.}, }
@article {pmid41368505, year = {2025}, author = {Di Leo, D and Nilsson, E and Krinos, A and Pinhassi, J and Lundin, D}, title = {The Nextflow nf-core/metatdenovo pipeline for reproducible annotation of metatranscriptomes, and more.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e20328}, pmid = {41368505}, issn = {2167-8359}, mesh = {*Software ; Reproducibility of Results ; Workflow ; *Transcriptome ; *Computational Biology/methods ; *Molecular Sequence Annotation/methods ; *Metagenomics/methods ; }, abstract = {Metatranscriptomics-the sequencing of community RNA-has become a popular tool in microbial ecology, proving useful for both in situ surveys and experiments. However, annotating raw sequence data remains challenging for many research groups with limited computational experience. Standardized and reproducible analyses are important to enhance transparency, comparability across studies, and long-term reproducibility. To simplify metatranscriptome processing for biologists, and to promote reproducible analyses, we introduce nf-core/metatdenovo, a Nextflow-based workflow. Nextflow pipelines run on different computing platforms, from standalone systems to high-performance computing clusters and cloud platforms (e.g., AWS, Google Cloud, Azure) and use container technology such as Docker or Singularity to reproducibly provision software. Biologists can access the pipeline using either the command line or the Seqera platform, which provides a web browser-based interface to Nextflow pipelines. Collaborating with nf-core ensures high-quality, documented, reproducible workflows. Our nf-core/metatdenovo pipeline adheres to these established standards, enabling FAIR metatranscriptome de novo assembly, quantification, and annotation.}, }
@article {pmid41368072, year = {2025}, author = {Bourquin, M and Peter, H and Michoud, G and Geers, A and ,  and Busi, SB and Battin, TI}, title = {Glacier influence shapes the genomic architecture of the downstream aquatic microbiome.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf076}, pmid = {41368072}, issn = {2730-6151}, abstract = {The factors and processes that shape microbial genomes and determine the success of microbes in different environments have long attracted scientific interest. Here, leveraging 2855 metagenome-assembled genomes sampled by the Vanishing Glacier Project from glacier-fed streams (GFSs), we shed light on the genomic architecture of the benthic microbiome in these harsh ecosystems-now vanishing because of climate change. Owing to glacial influence, the GFS benthic habitat is unstable, notoriously cold, and ultra-oligotrophic. Along gradients of glacial influence and concomitant variation in benthic algal biomass across 149 GFSs draining Earth's major mountain ranges, we show how genomes of GFS bacteria vary in terms of size, coding density, gene redundancy, and translational machinery. We develop a novel, phylogeny-rooted analytical framework that allows pinpointing the phylogenetic depth at which patterns in genomic trends occur. These analyses reveal both deep- and shallow-rooting phylogenetic patterns in genomic features associated with key GFS taxa and functional potential relevant to live in these ecosystems. Additionally, we highlight the role of several clades of Gammaproteobacteria in shaping community-level genomic architecture. Our work shows how genome architecture is shaped by selective environmental constraints in an extreme environment. These insights are important as they reveal putatively important adaptations to the GFS environment which is now changing at rapid pace due to climate change.}, }
@article {pmid41367710, year = {2026}, author = {He, M and Chen, F and Xian, X and Guo, Z}, title = {Diagnosis and treatment of invasive fungal disease in children with hematological malignancies after chemotherapy: Challenges and strategies (Review).}, journal = {Experimental and therapeutic medicine}, volume = {31}, number = {1}, pages = {21}, pmid = {41367710}, issn = {1792-1015}, abstract = {Invasive fungal disease (IFD) has a high incidence rate in pediatric patients with hematological malignancies and hematopoietic stem cell transplantation, markedly elevating mortality rates. Major pathogens include Aspergillus, Candida and emerging non-Aspergillus molds. Clinical manifestations such as persistent fever and dyspnea are frequently non-specific, complicating early diagnosis. Invasive candidiasis typically manifests as candidemia or hepatosplenic infection, whereas invasive aspergillosis predominantly involves the lower respiratory tract. Prophylactic antifungal therapy reduces IFD risk but may lead to breakthrough IFD, particularly during prolonged neutropenia (>14 days). Treatment strategies require individualized selection between monotherapy and combination regimens, incorporating patient status, local epidemiology, prior antifungal exposure, drug metabolism and socioeconomic factors; however, treatment strategies can be hindered by diagnostic challenges including age-specific biomarker thresholds. Emerging techniques such as metagenomic next-generation sequencing show promise for rapid pathogen identification. Central nervous system involvement occurs in a certain proportion of pediatric cases and requires multimodal intervention. Early diagnosis through optimized imaging and timely initiation of targeted therapy are key to overcome clinical challenges and improving prognosis in this vulnerable population. The present review aimed to systematically review the epidemiological characteristics, diagnostic challenges and therapeutic strategies of IFD in pediatric hematological malignancies post-chemotherapy. By collating current clinical evidence, the present review provides an evidence-based framework for optimizing management in this high-risk population.}, }
@article {pmid41367425, year = {2025}, author = {An, Y and Xu, M and Kang, Y and Fang, J and Zhang, X}, title = {Tripartite exacerbation stratification in AECOPD suggests a gradient of lower airway dysbiosis: a metagenomic transition from commensal taxa to pseudomonadota dominance.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1588029}, pmid = {41367425}, issn = {1664-302X}, abstract = {BACKGROUND: The frequency of acute exacerbations (AECOPD) is a critical predictor of disease progression in chronic obstructive pulmonary disease (COPD). However, the dynamics of the lower respiratory microbiome across a spectrum of exacerbation frequency remain poorly characterized, limiting insights into microbial drivers of susceptibility.<br><br>METHODS: We conducted a cross-sectional study of 39 hospitalized AECOPD patients, stratified into non-frequent (NFE, &#x2264; 1 event/year, n = 11), moderate (ME, 2 events/year, n = 13), and frequent exacerbators (FE, &#x2265;3 events/year, n = 15). Metagenomic next-generation sequencing (mNGS) was performed on bronchoalveolar lavage fluid (BALF) to profile the airway microbiome.<br><br>RESULTS: Microbial alpha diversity exhibited a significant, graded decline from NFE to FE groups (e.g., Shannon index: NFE 3.68 &#xb1; 0.34, ME 3.02 &#xb1; 1.02, FE 0.84 &#xb1; 0.54; p < 0.05). Beta diversity analysis revealed distinct community clustering by exacerbation phenotype (PERMANOVA R[2] = 0.19, p = 0.001). The FE group was characterized by a striking dominance of Pseudomonadota (relative abundance: 72.25%), which correlated positively with exacerbation frequency (r = 0.536, p < 0.001). In contrast, commensal taxa including Streptococcus (r = -0.814, p < 0.0001) and others within the Bacillota and Bacteroidota phyla were depleted in FE and were negatively associated with exacerbation frequency. Twelve exacerbation-resilient taxa (83.3% belonging to Bacillota/Bacteroidota) were positively correlated with FEV1% predicted (r = 0.322-0.483, p < 0.05). Alpha diversity indices showed a strong inverse association with exacerbation frequency (r = -0.84 to -0.86, p < 0.001) but not spirometric measures.<br><br>CONCLUSION: Our findings delineate a gradient of airway microbial dysbiosis along the exacerbation frequency spectrum in COPD. The exacerbation-prone phenotype is defined by a loss of microbial diversity, expansion of Pseudomonadota, and depletion of potentially protective commensals. These microbiome features represent promising biomarkers for identifying high-risk patients and may inform future microbiome-targeted therapeutic strategies.}, }
@article {pmid41367410, year = {2025}, author = {Tansirichaiya, S and Songsomboon, K and Wigand, J and Winje, E and Chaianant, N and Leartsiwawinyu, W and Al-Haroni, M}, title = {Geographic signatures in the oral resistome: a comparative metagenomic analysis of healthy individuals from Thailand and Norway.}, journal = {Journal of oral microbiology}, volume = {17}, number = {1}, pages = {2589656}, pmid = {41367410}, issn = {2000-2297}, abstract = {BACKGROUND: The oral cavity is an important yet understudied reservoir of antimicrobial resistance genes (ARGs), potentially shaped by geographic variation in antibiotic usage.<br><br>OBJECTIVE: To compare the oral resistomes of healthy adults from Thailand and Norway, two countries with contrasting antimicrobial use practices, using shotgun metagenomic sequencing.<br><br>DESIGN: Stimulated saliva samples were collected from healthy adults in Thailand (n&#x2009;=&#x2009;43) and Norway (n&#x2009;=&#x2009;50). ARGs were identified with AMRPlusPlus against the MEGARes database, and microbial taxonomy was profiled with KrakenUniq. Diversity metrics, ordination, and clustering analyses assessed resistome and microbiome structures.<br><br>RESULTS: Thai samples exhibited significantly greater ARG richness, evenness, and diversity (p&#x2009;<&#x2009;0.001), driven by higher abundances of multi-biocide, nucleoside, and copper resistance genes. Norwegian samples were enriched in aminoglycoside, sulfonamide, and quaternary ammonium compound resistance genes. Both cohorts shared core oral genera, but Thai samples showed greater taxonomic richness without differences in overall microbiome diversity. Non-metric multidimensional scaling and PERMANOVA revealed stronger geographic separation for resistomes (R&#xb2;&#x2009;=&#x2009;0.639) than microbiomes (R&#xb2;&#x2009;=&#x2009;0.382). Co-occurrence networks highlighted structured associations between ARG groups and bacterial genera, suggesting ecological influences beyond taxonomic composition.<br><br>CONCLUSIONS: These results reveal distinct geographic signatures in the oral resistome that are not fully explained by microbiome structure, reflecting the influence of local ecological and societal factors, including antimicrobial exposure. The findings highlight the oral cavity as a dynamic ARG reservoir and support its inclusion in regional antimicrobial resistance surveillance to inform public health strategies.}, }
@article {pmid41367394, year = {2025}, author = {Oke, OE and Fasasi, LO and Opowoye, IO and Akosile, OA}, title = {The role of gut microbiota-derived metabolites in modulating poultry immunometabolism.}, journal = {Frontiers in physiology}, volume = {16}, number = {}, pages = {1700406}, pmid = {41367394}, issn = {1664-042X}, abstract = {The poultry sector is crucial to global food security, but it faces increasing challenges from heat stress, viral diseases, and restrictions on antibiotic use. These stressors highlight immunometabolism, the junction of immune function and metabolic pathways, as a crucial factor in determining the productivity and health of poultry. There is growing evidence that the gut microbiota is a dynamic metabolic organ that produces a diverse range of bioactive metabolites in addition to its function in nutritional digestion. The immunometabolism of poultry is significantly influenced by these microbiota-derived metabolites, including short-chain fatty acids, bile acid derivatives, amino acid catabolites, vitamins, and polyamines. Disease resistance, vaccination responsiveness, and stress adaptability are shaped by their modulation of intestinal barrier integrity, energy balance, oxidative stress resilience, and immune cell activation. This review summarises what is currently known about the functional diversity and composition of the gut microbiota in poultry, describes the concept of immunometabolism in birds, and assesses the mechanisms by which microbial metabolites regulate metabolic and immunological crosstalk. Prebiotics, probiotics, synbiotics, postbiotics, phytochemicals, and other nutritional and managerial interventions that improve advantageous metabolite profiles are given particular consideration. Applications to enhance poultry health, alleviate heat stress, reduce reliance on antibiotics, and promote sustainable production are also discussed. For mapping metabolite-immune interactions, emerging methods such as germ-free models, metabolomics, metagenomics, and systems biology approaches are emphasised as revolutionary. Metabolites produced by the gut microbiota are crucial to poultry immunometabolism and offer promising opportunities for precision nutrition and healthcare. Bridging the existing research gaps using integrative, multidisciplinary methods to promote sustainable and resilient poultry production is needed. This review centres on the mechanistic axis linking gut microbiota-derived metabolites to host immunometabolic regulation, tracing the pathway from metabolite generation through receptor activation and immune-metabolic reprogramming to measurable phenotypic outcomes in poultry.}, }
@article {pmid41367385, year = {2025}, author = {Cavenaghi, A and Mallah, NEZ and Navarro, L and Martinón-Torres, F and Gómez-Carballa, A and Salas, A}, title = {Decoding the peripheral transcriptomic and meta-genomic response to music in autism spectrum disorder via saliva-based RNA sequencing.}, journal = {Frontiers in molecular biosciences}, volume = {12}, number = {}, pages = {1696704}, pmid = {41367385}, issn = {2296-889X}, abstract = {INTRODUCTION: Behavioral interventions for autism spectrum disorder show variable outcomes, highlighting the need for complementary therapies. Music-based interventions are promising, yet their molecular mechanisms remain unclear. Saliva-based RNA sequencing (RNA-seq) provides a non-invasive framework to monitor neuroimmune and metabolic dynamics, but its application in autism remains underexplored.<br><br>METHODS: We explored the buccal transcriptional effects of music exposure in five individuals with autism (8-37 years; 60% female). To overcome saliva-specific limitations, we combined Poly-A selection and Human-Enriched protocols preparation methods to enhance human transcript detection and reproducibility while capturing microbial signals.<br><br>RESULTS: Individually, each dataset revealed a few differentially expressed genes, but integrated analysis improved biological resolution. Consistently modulated genes included HERC6, TSPAN5, and REM2, involved in neurodevelopmental and immune functions. Enrichment analyses highlighted pathways associated with immune regulation, oxidative phosphorylation, and epithelial differentiation, hallmarks of autism, such as immune dysregulation and mitochondrial dysfunction. Co-expression network analysis identified modules correlated with music exposure. The AKNA module, previously linked to autism, was downregulated and enriched for Ras-related GTPase and immune pathways, suggesting modulation of intracellular signaling and inflammation. Conversely, upregulation of the UBE2D3 module indicated activation of endoplasmic reticulum stress responses, a contributor to autism. Exploratory metagenomics identified 15 microbial species responsive to music exposure, including Acidipropionibacterium acidipropionici and Propionibacterium freudenreichii, producers of propionic acid, a metabolite associated with autism-like behaviors and neuroinflammation.<br><br>CONCLUSION: Saliva-based RNA-seq can stably capture transcriptomic and microbial responses to behavioral stimuli. Music exposure modulates neuroimmune pathways relevant to autism, supporting the biological plausibility of music therapy and demonstrating saliva-based RNA-seq as a viable, non-invasive tool for monitoring intervention outcomes.}, }
@article {pmid41366867, year = {2025}, author = {Khaengraeng, C and Mhuantong, W and Chaiprom, U and Bunkoed, W and Kuncharoen, N and Kasem, S and Chatnaparat, T and Suwannarat, S}, title = {Fungal and Bacterial Communities Associated with Northern Corn Leaf Blight in Resistant and Susceptible Sweet Corn.}, journal = {The plant pathology journal}, volume = {41}, number = {6}, pages = {736-754}, doi = {10.5423/PPJ.OA.05.2025.0060}, pmid = {41366867}, issn = {1598-2254}, support = {FF(KU)2.66//Kasetsart University Research and Development Institute/ ; }, abstract = {Northern corn leaf blight (NCLB), caused by Exserohilum turcicum (Setosphaeria turcica), is a major disease that negatively impacts the yield and quality of sweet corn. Plant-associated microbes hold great potential for enhancing crop productivity and sustainability. This study investigated the fungal and bacterial communities associated with NCLB in resistant and susceptible sweet corn cultivars using amplicon metagenomic sequencing. The structural composition and diversity of the fungal community in symptomatic NCLB-susceptible cultivars differed significantly from those in asymptomatic NCLB-resistant cultivars. In contrast, the bacterial communities showed no significant differences between resistant and susceptible cultivars in both the phyllosphere and rhizosphere. Exserohilum and Alternaria were significantly more abundant in the phyllosphere of symptomatic NCLB-susceptible plants, while fungal genera such as Sporobolomyces and Aureobasidium, along with the order Dothideales and the bacteria Bacillus, were significantly more abundant in the phyllosphere of asymptomatic NCLB-resistant cultivars. Microbial metabolic functions related to sugar metabolism-including sucrose biosynthesis and the degradation of glucose and xylose, compounds abundant in plant cell walls-were enriched in the phyllosphere of symptomatic NCLB-susceptible plants. In contrast, functions associated with detoxification and defense responses to plant phenolic compounds were enriched in microbes from asymptomatic NCLB-resistant cultivars. Additionally, Bacillus, identified ash part of the core microbiome, and the epiphytic yeast Sporobolomyces, identified as a hub in the microbial network, exhibited antimicrobial activity that may suppress E. turcicum. These findings offer valuable insights into the role of microbial communities in plant health and disease resistance, with promising implications for developing microbiome-based strategies to manage NCLB.}, }
@article {pmid41366832, year = {2025}, author = {Wu, X and Yang, C and Qing, L and Yang, W and Zhou, K and Lu, G}, title = {Metagenomic Next-generation Sequencing Aids Diagnosis of Leishmania donovani-associated Hemophagocytic Lymphohistiocytosis in Infants: Case Report and Systematic Review.}, journal = {The Pediatric infectious disease journal}, volume = {}, number = {}, pages = {}, doi = {10.1097/INF.0000000000005078}, pmid = {41366832}, issn = {1532-0987}, abstract = {Diagnosing hemophagocytic lymphohistiocytosis (HLH) triggers in infants is challenging. In a 9-month-old boy with unresponsive fever and pancytopenia, conventional tests were negative. Metagenomic next-generation sequencing detected Leishmania donovani, confirming Leishmania donovani-associated HLH. Targeted antiparasitic therapy replaced empiric immunosuppression, leading to rapid recovery. This case demonstrates that metagenomic next-generation sequencing is crucial for rapid pathogen identification in critically ill infants with HLH of unknown cause.}, }
@article {pmid41366711, year = {2025}, author = {Rey Redondo, E and Xu, W and Xu, Y and Sun, R and Wan, SH and Leung, SKK and Yung, CCM}, title = {Multi-domain temporal patterns reveal stable community membership but dynamic interactions in the coastal microbiome.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-025-00803-5}, pmid = {41366711}, issn = {2524-6372}, support = {Hong Kong PhD Fellowship Scheme//Research Grants Council of Hong Kong/ ; 16102024//Research Grants Council of Hong Kong/ ; }, abstract = {BACKGROUND: Marine microbial communities drive global biogeochemical cycles and oceanic food webs, yet our understanding of their holistic temporal dynamics remains limited, particularly in the South China Sea. Most studies have focused on specific taxonomic groups or single temporal scales, leaving a gap in comprehensive, multi-domain, and multi-timescale analyses.<br><br>RESULTS: Using an integrated multi-omics approach that combined metagenomic, metatranscriptomic, and metaviromic analyses, we conducted time-series sampling over 48-h periods during winter and summer to investigate microbial community dynamics in the coastal South China Sea. Seasonal transitions were identified as the primary drivers of community shifts, with diel variations playing a secondary role across all taxonomic domains. Within seasons, diel changes followed a progressive trajectory rather than recurring cyclic patterns. Eukaryotic communities exhibited the most pronounced temporal fluctuations, while prokaryotic and viral communities displayed remarkable stability. Unlike previous coastal studies, viral communities maintained high similarity between seasons, suggesting the presence of a persistent viral reservoir in this region. Gene expression analysis revealed dynamic population shifts in photosynthetic microorganisms, with Mamiellophyceae green algae and their associated Prasinovirus displaying pronounced seasonal and diel rhythmicity.<br><br>CONCLUSIONS: This study provides novel insights into the temporal dynamics of microbial communities and host-virus interactions in the South China Sea. The stability of viral communities, coupled with synchronised host-virus activities, highlights potential mechanisms supporting ecosystem resilience in this coastal region. These findings enhance our understanding of marine ecosystem processes and establish a robust framework for exploring microbial responses to environmental changes on both diel and seasonal scales.}, }
@article {pmid41366428, year = {2025}, author = {Xiong, Z and Dodson, BP and Rogers, MB and Sneiderman, CT and Janesko-Feldman, K and Vagni, V and Manole, M and Li, X and Rajasundaram, D and Clark, RSB and Raphael, I and Morowitz, MJ and Mariño, E and Kochanek, PM and Jha, RM and Kohanbash, G and Simon, DW}, title = {Microbial production of short-chain fatty acids attenuates long-term neurologic impairment after traumatic brain injury.}, journal = {Journal of neuroinflammation}, volume = {22}, number = {1}, pages = {285}, pmid = {41366428}, issn = {1742-2094}, support = {R21 NS131689/NS/NINDS NIH HHS/United States ; R21 NS131689/NS/NINDS NIH HHS/United States ; R01NS 127372/NH/NIH HHS/United States ; }, mesh = {Animals ; *Brain Injuries, Traumatic/metabolism/complications ; Mice ; Mice, Inbred C57BL ; *Fatty Acids, Volatile/metabolism/biosynthesis ; *Gastrointestinal Microbiome/physiology ; Male ; }, abstract = {BACKGROUND: Traumatic brain injury (TBI) triggers persistent gut microbiome dysbiosis characterized by depletion of short-chain fatty acid (SCFA)-producing bacteria. However, the link between SCFA depletion and long-term neurologic impairment (LTNI) after TBI remains unclear. Previously, we and others noted the involvement of metabolite-sensing receptors and SCFA ligands in mouse models of neurodegenerative diseases, including Alzheimer's. Here, we further investigated SCFA-mediated neuroprotection in LTNI at both microbiome and single-cell resolution using the controlled cortical impact (CCI) model of TBI with a high-yielding SCFA diet to examine their mechanistic role in pathogenesis.<br><br>METHODS: C57BL6/J mice were randomized to CCI (6&#xa0;m/s, 2&#xa0;mm) or sham surgery. Following surgery, mice were randomized to a study diet based on a balanced modification of the AIN93-G diet containing either 15% high amylose maize starch (HAMS) control diet or acetylated and butyrylated HAMS (HAMSAB) for 6 months to model increased SCFA production by bacterial fermentation in the gut. Morris water maze test and nesting assessment were performed at 1, 3, and 6 months after injury. The longitudinal gut microbiome changes were investigated by 16&#xa0;S rRNA amplicon and metagenomic sequencing of fecal pellets at baseline, 1 month, and 6 months post-injury. At 6 months, pericontusional tissue was collected for single-cell RNA-sequencing following the 10X Genomics protocol or histologic analysis.<br><br>RESULTS: Compared to the HAMS control diet, HAMSAB diet remodeled the CCI murine gut microbiome at an early phase, increased various SCFA-producing taxa, and attenuated neurologic deficits up to 6 months after CCI. In mice fed HAMSAB diet, single-cell transcriptomics and pathway analysis identified the promotion of neurogenesis, including increased doublecortin-positive immature neurons. In myeloid cells, HAMSAB induced an anti-inflammatory phenotype, inhibiting pro-inflammatory signaling interaction such as midkine signaling, and promoted differentiation to disease-associated microglia (DAM). Simultaneously, SCFAs reduced neurodegenerative pathway activity in neurons and glial cells and reduced phosphorylated tau deposition in pericontusional cortex.<br><br>CONCLUSIONS: Diet-facilitated microbial production of acetate and butyrate attenuates behavioral deficits of LTNI after TBI and produces enduring benefits at the single-cell level on the neuro-inflammatory and neuro-progenitor responses. This therapeutic approach could have a broader potential to prevent neurodegenerative disease.}, }
@article {pmid41366253, year = {2025}, author = {Breselge, S and de Paula Dias Moreira, L and Skibinska, I and Yin, X and Brennan, L and Kilcawley, K and Porcellato, D and Cotter, PD}, title = {Water kefir multi-omics reveals functional redundancies despite taxonomic differences and the underappreciated contribution of yeast.}, journal = {NPJ science of food}, volume = {9}, number = {1}, pages = {265}, pmid = {41366253}, issn = {2396-8370}, support = {818368//European Union's Horizon 2020/ ; 818368//European Union's Horizon 2020/ ; SFI/12/RC/2273_P2/SFI_/Science Foundation Ireland/Ireland ; SFI/12/RC/2273_P2/SFI_/Science Foundation Ireland/Ireland ; USIRL-2019-1//HRB/SFI/ ; USIRL-2019-1//HRB/SFI/ ; SFI/16/RC/3835//Irish Department of Agriculture, Food and the Marine/ ; TC/2018/0025//Food for Health Ireland/ ; NA-AGFOODDEVELAUTH20201216//Institute for the Advancement of Food and Nutritional Sciences/ ; 101060218//European Union's Horizon Europe/ ; }, abstract = {Water kefir (WK) is a fermented beverage produced by a complex symbiotic community of microbes, including yeasts, lactic acid bacteria (LAB), and acetic acid bacteria (AAB). Here, we combined shotgun metagenomics, NMR metabolomics, GC-MS volatile organic compound (VOC) analysis, and metaproteomics to investigate microbial succession, functional dynamics, and the roles of yeasts and Zymomonas in WK fermentations representative of two WK types, i.e., one dominated by yeast-LAB-AAB and another by Zymomonas. Metagenomic profiling revealed that yeast-LAB-AAB communities exhibited dynamic microbial succession, whereas Zymomonas-dominated communities remained stable. Despite differing microbial compositions, both fermentations maintained consistent global metabolic functions, although specialized metabolic pathways and VOC profiles diverged. Metaproteomic analysis revealed a strong underappreciation of yeast contributions in metagenomic datasets, with yeasts representing a larger fraction of the proteome than predicted by DNA-based abundance. Lentilactobacillus hilgardii was enriched on WK grains, suggesting a specialized niche role. Our findings highlight the value of integrating multi-omics approaches to uncover microbial activity and community function in fermented foods and offer insights for the design of tailored WK starter cultures.}, }
@article {pmid41366061, year = {2025}, author = {Deng, JW and Zhou, YL and Zhang, YX and Zhou, CB and Fang, JY}, title = {The relationship between gut microbiota, lifestyle habits, and early-onset colorectal cancer: shedding light on early prediction.}, journal = {British journal of cancer}, volume = {}, number = {}, pages = {}, pmid = {41366061}, issn = {1532-1827}, support = {82203224, 81830081//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {BACKGROUND: The development of early-onset colorectal cancer (EO-CRC) is linked to environmental exposures and gut microbiota alterations. We aimed to discover the connection and develop prediction strategies.<br><br>METHODS: In the observational study, we performed 16S rRNA sequencing and metagenomic sequencing on 76 samples from discovery cohort and validation cohort, and qPCR analysis of selected microbiota, along with lifestyle and dietary assessment on 298 samples from validation cohort. Mediation analysis was employed to investigate the mediating role of gut microbiota. Logistic regression analysis evaluated the optimal prediction model for EO-CRC, with the area under the receiver operating characteristic curves (AUC) assessing diagnostic value.<br><br>RESULTS: Dysbiosis of the EO-CRC gut microbiota was characterised by evaluated abundance of F. nucleatum, P. micra, Pks[+] E. coli, and F. Plautii. Mediation analysis showed that Pks[+] E. coli mediated the relationship between fried food, processed meat and coffee to EO-CRC, while F. nucleatum mediated the adverse effects of snacks. A combination of three bacterial markers along with lifestyle and diet demonstrated strong diagnostic potential (AUC&#x2009;=&#x2009;0.95, 95% CI&#x2009;=&#x2009;0.92-0.98).<br><br>CONCLUSIONS: Our data suggested that the EO-CRC-enriched bacteria may mediate the effects of lifestyle and dietary factors on disease development. A predictive model combining diet, lifestyle, and gut bacteria demonstrated promising early predictive capabilities.}, }
@article {pmid41365917, year = {2025}, author = {Duarte, VDS and Franklin, FV and Krysmann, A and Porcellato, D}, title = {Longitudinal study of the udder microbiome using genome-centric metagenomics uncovers pathogen-driven adaptation and succession.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {227}, pmid = {41365917}, issn = {2055-5008}, support = {314733//Norges Forskningsr&#xe5;d/ ; 314733//Norges Forskningsr&#xe5;d/ ; 314733//Norges Forskningsr&#xe5;d/ ; 314733//Norges Forskningsr&#xe5;d/ ; }, mesh = {Animals ; Female ; *Mammary Glands, Animal/microbiology ; Cattle ; *Mastitis, Bovine/microbiology ; Longitudinal Studies ; *Metagenomics/methods ; *Microbiota ; *Bacteria/genetics/classification/isolation &amp; purification/pathogenicity ; Lactation ; RNA, Ribosomal, 16S/genetics ; Genome, Bacterial ; }, abstract = {Bovine mastitis remains a major disease affecting dairy herds globally due to its complex and multi-etiological nature. To address gaps in microbial and immunological understanding, this longitudinal study examined the udder microbiome across lactation in 24 Norwegian Red cows. Somatic cell count (SCC) and microbiota composition varied by lactation stage, with low SCC (< 100,000 cells/mL) more frequent in early (80%) and middle (78.9%) than late lactation (53%) and dry-off (53.1%). Microbial diversity was shaped by SCC, lactation stage, and individual variability. Temporal profiling identified persistent infections involving Staphylococcus aureus and Staphylococcus chromogenes, while samples with low SCC were enriched in beneficial genera including Corynebacterium, Bradyrhizobium, and Lactococcus. Shotgun metagenomics revealed pathogen-specific metabolic traits, and genome-centric analysis recovered 142 MAGs characterized via sequence typing, virulence, and resistance profiling. These findings offer valuable insights into microbial adaptation and succession, informing strategies to better manage and prevent mastitis.}, }
@article {pmid41279710, year = {2025}, author = {Joshi, B and Zulk, JJ and Serchejian, C and Hameed, ZA and Larson, AB and Terwilliger, AL and Kumar, D and Mysorekar, IU and Britton, RA and Maresso, AW and Patras, KA}, title = {Bacteriophage-mediated reduction of uropathogenic E. coli from the urogenital epithelium.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41279710}, issn = {2692-8205}, abstract = {Urinary tract infections (UTIs), primarily caused by uropathogenic Escherichia coli (UPEC), affect millions annually. UPEC gains access to the urinary tract through mucosal reservoirs including the vaginal tract. With rising antibiotic resistance and frequent recurrence, alternative non-antibiotic strategies like bacteriophage (phage) therapy are gaining attention. We explored the potential of a lytic phage, ΦHP3, as well as a phage cocktail to decolonize UPEC from the urogenital tract using in vitro and in vivo models. Phage significantly inhibited UPEC growth in both bacteriologic medium and simulated vaginal fluid. Pretreatment of human vaginal epithelial cells (VK2/E6E7) and bladder carcinoma cells (HTB-9) with phage reduced adhesion and invasion of UPEC compared with controls. Phage treatment was further able to reduce intracellular UPEC in VK2 cells. Notably, phage pretreatment did not impact phage resistant UPEC strains, indicating that phage lysis was the primary driver of phenotypes. Live confocal microscopy confirmed interaction of phage particles with UPEC and with both epithelial cell lines. In vivo, daily intravaginal ΦHP3 administration in humanized microbiota mice significantly reduced vaginal UPEC burden after 4 days. Treatment with a phage cocktail also reduced vaginal and cervical tissue burdens by day 7 post-treatment. UPEC dissemination was observed to uterine and kidney tissues, but burdens were not different between phage and mock-treated groups. In conclusion, we demonstrate that phage and phage cocktails can modestly reduce UPEC urogenital colonization, highlighting the potential of phage therapy as a viable treatment option for UTI prevention.}, }
@article {pmid41055130, year = {2025}, author = {Henson, LH and Christensen, KA and Sutherland, BJG and Johnson, HA and vonHoldt, B and Stronen, AV and Paquet, PC and Moody, J and Koop, BF and Darimont, CT}, title = {Grizzly bear population genomics across a coastal-interior ecotone in British Columbia, Canada.}, journal = {G3 (Bethesda, Md.)}, volume = {15}, number = {12}, pages = {}, doi = {10.1093/g3journal/jkaf237}, pmid = {41055130}, issn = {2160-1836}, support = {GEN013//Genome BC GeneSolve/ ; //LHH/ ; IT07676//MITACS Accelerate/ ; //Raincoast Chair of Applied Conservation Science/ ; }, mesh = {Animals ; British Columbia ; *Ursidae/genetics ; Polymorphism, Single Nucleotide ; *Genetics, Population ; *Metagenomics/methods ; Genotype ; *Ecosystem ; *Genomics/methods ; }, abstract = {Local adaptation research often focuses on discrete populations without extensive gene flow that are under differential selective pressures. By contrast, grizzly bears Ursus arctos in British Columbia (BC) are wide-ranging omnivores that span an environmental and resource ecotone from the coastal, salmon-enriched rainforest to dry interior plateau. This ecotone has been associated with local adaptation in other species and the different regions to morphological variation in grizzly bears. To understand genome-wide population genetic patterns across the ecotone and to identify loci or genomic regions associated with these different environments, here we use whole-genome resequencing to characterize 3.9 M SNPs in 31 grizzly bears spanning from central to northern latitudes in coastal and interior regions (to the west and east of the coastal mountain range [CMR], respectively). Clustering grizzly samples by genotypes identified 3 groups that generally correspond to the source geographic regions, with the greatest variation occurring from north to south. The data were best explained by a single ancestry cluster, but K = 3 recovered the 3 geographic groupings and were used to identify putative nonmigrant individuals. The presence of individuals with mixed ancestry (using K = 3) provides evidence for travel across the CMR, but significant differentiation between clusters (mean FST = 0.015 to 0.036) suggests some genetic separation between the regions, supporting an isolation-by-distance or clinal variation model. Putative close-kin were identified and removed, then multiple supervised outlier SNP detection methods were applied to identify regions of the genome consistently segregating between coastal and interior regions. Several associated genomic regions and candidate genes were identified, including a consistently identified outlier region near the gene creatine kinase, m-type. This work provides the first genome-wide analysis of grizzly bears in the studied region. These findings will be useful for connectivity planning and research on the adaptability of coastal and interior grizzlies to future climate change scenarios.}, }
@article {pmid41365804, year = {2025}, author = {Thompson, AR and Adams, BJ and Hogg, ID and Yooseph, S}, title = {Evidence for Trace Gas Metabolism and Widespread Antibiotic Synthesis in an Abiotically Driven, Antarctic Soil Ecosystem.}, journal = {Environmental microbiology reports}, volume = {17}, number = {6}, pages = {e70249}, doi = {10.1111/1758-2229.70249}, pmid = {41365804}, issn = {1758-2229}, support = {ANT 2133685//National Science Foundation/ ; OPP-2224760//National Science Foundation/ ; DBI-2400009//National Science Foundation/ ; OAC-2408259//National Science Foundation/ ; OPP-1043681//National Science Foundation/ ; OPP-1559691//National Science Foundation/ ; OPP-2129685//National Science Foundation/ ; //Antarctica New Zealand (Event K024)/ ; //New Zealand Antarctic Research Institute (Event K024)/ ; //Monte L. Bean Life Science Museum, the Department of Biology, Brigham Young University/ ; //Kravis Department of Integrated Sciences, Claremont McKenna College/ ; }, mesh = {Antarctic Regions ; *Soil Microbiology ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; Metagenome ; *Anti-Bacterial Agents/biosynthesis ; Ecosystem ; Soil/chemistry ; *Gases/metabolism ; }, abstract = {The McMurdo Dry Valleys (MDVs) of Antarctica are a uniquely pristine, low-biodiversity model system for understanding fundamental ecological phenomena, the impact of a warming climate on ecosystem functioning, community structure and composition and the dynamics of adaptation. Despite the scientific value of this system, we still know little about the functional ecology of its biota, especially the bacteria. Here, we analysed the bacterial taxonomic and functional diversity of 18 shotgun metagenomes using the VEBA metagenome processing pipeline. We recovered 701 medium-to-high quality metagenome-assembled genomes (MAGs) (≥ 50% completeness and contamination < 10%) and 201 high-quality MAGs (≥ 80% completeness and < 10% contamination), almost 50% more than found in similar sites previously. We found that: (1) community composition shifts along environmental gradients correlated with soil moisture, elevation and distance to the coast; (2) many MDV bacteria are capable of performing trace gas metabolism; (3) genes associated with antibiotic-mediated competitive interactions (e.g., antibiotic biosynthesis and antibiotic resistance genes) are widespread; and (4) MDV bacteria employ survival strategies common to bacteria in similarly extreme environments. This study provides novel insight into microbial survival strategies in extreme environments and lays the groundwork for a more comprehensive understanding of the autecology of MDV bacteria.}, }
@article {pmid41365463, year = {2025}, author = {Xi, L and Chen, J and Chen, Y and Lai, K and Xu, S}, title = {Nonthyroidal illness syndrome and diagnostic utility of CSF mNGS: insights from a case series of neurological scrub typhus.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {}, number = {}, pages = {108291}, doi = {10.1016/j.ijid.2025.108291}, pmid = {41365463}, issn = {1878-3511}, abstract = {We describe five cases of neurological scrub typhus that highlight two critical, underrecognized aspects of this disease. First, cerebrospinal fluid metagenomic next-generation sequencing (CSF mNGS) accurately identified Orientia tsutsugamushi in all three patients tested, while the conventional Weil-Felix test was negative in every case, establishing mNGS as a pivotal diagnostic tool. Second, we uncovered a high prevalence of thyroid dysfunction, with nonthyroidal illness syndrome (NTIS) present in three of four patients tested, a novel systemic complication linked to severe inflammatory stress. Additional notable findings included frequent hypokalemia, at times severe enough to mimic periodic paralysis, and urban acquisition in two cases, suggesting an expanding epidemiological footprint. All patients improved on doxycycline-based regimens. This series underscores the diagnostic superiority of CSF mNGS and reveals NTIS as a key endocrine manifestation in neurological scrub typhus, urging greater clinical vigilance.}, }
@article {pmid41365368, year = {2025}, author = {Cheng, T and Zhou, P and Zhang, M and Huang, T and Wu, B and Zhuang, J and Wang, B and Xu, X}, title = {Synergistic division of labor in a bacterial consortium for enhanced phenanthrene mineralization under cadmium stress: mechanisms of degradation-detoxification coordination.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {133782}, doi = {10.1016/j.biortech.2025.133782}, pmid = {41365368}, issn = {1873-2976}, abstract = {The remediation of co-contamination by polycyclic aromatic hydrocarbons (PAHs) and heavy metals poses a significant challenge. Although microbial consortia present a promising approach, their synergistic mechanisms under stress conditions are not fully understood. To address this gap, we constructed a functionally specialized bacterial consortium (KZ) by assembling Klebsiella sp. CW-D3T and Arthrobacter sp. SZ-3, which synergistically enhanced phenanthrene (PHE) degradation and mineralization under cadmium stress (25 mg/L Cd[2+]), outperforming monocultures by 1.2-1.9-fold. Through biomass-normalized enzyme activity assays, we uncovered a structured division of labor: SZ-3 exhibited superior upstream catalytic activity (50 % higher 2H1N conversion), while CW-D3T dominated downstream mineralization (>80 % contribution). Mechanistic investigations via metagenomics revealed that CW-D3T utilized high-expression efflux pumps (ZntA/zinT) and antioxidant genes (yhcN) to mitigate cadmium toxicity, whereas SZ-3 employed the frnE-mediated oxidative stress response and limited Cd[2+] uptake via mntH. This study elucidates a synergistic mechanism for concurrent PAH degradation and heavy metal detoxification, offering a novel bioresource for remediating co-contaminated environments.}, }
@article {pmid41365245, year = {2025}, author = {De Koch, MD and Kraberger, S and Fielding, R and Smith, K and Schiavone, K and Hall, KR and Reid, VS and Boyea, D and Smith, EL and Schmidlin, K and Fontenele, RS and Martin, DP and Krupovic, M and Varsani, A}, title = {Novel circoviruses identified in short-finned pilot whale and orca from the North Atlantic Ocean.}, journal = {Virology}, volume = {615}, number = {}, pages = {110768}, doi = {10.1016/j.virol.2025.110768}, pmid = {41365245}, issn = {1096-0341}, abstract = {The family Circoviridae comprises viruses with small single-stranded DNA genomes that are known to infect various animals, resulting in considerable morbidity and mortality in some hosts. Circoviruses have been recently identified through metagenomic sequencing in diverse terrestrial vertebrate species, but their distribution and diversity in marine vertebrates remains underexplored. Here, we use high-throughput sequencing (HTS) to identify circoviruses from archived tissue samples of delphinids (order Artiodactyla, infraorder Cetacea, family Delphinidae). Based on the HTS data, we designed specific abutting primer pairs to recover seven complete circovirus genomes from individual delphinid hosts, namely, the short-finned pilot whale (Globicephala macrorhynchus, n = 5) and the orca (Orcinus orca, n = 2). The circoviruses from the two delphinid species share <65.4 % genome-wide pairwise nucleotide identity with all classified circovirus representative sequences and 66 % amongst themselves. Accordingly, these viruses, which we have named shofin circovirus and orcin circovirus, respectively, represent two novel species. This report also marks the first detection of cetacean circoviruses in the North Atlantic Ocean (near St. Vincent, Caribbean). Notably, analysis of the capsid protein sequences and structures of the delphinid circoviruses revealed notable elaborations within the surface exposed loops that have been previously shown to be a major antigenic epitope in porcine circovirus 2. Collectively, the delphinid circovirus genomes expand the known diversity of circoviruses of marine vertebrates and suggest similar evolutionary pressures exerted by the immune systems of cetacean and suina hosts, both members of the order Artiodactyla.}, }
@article {pmid41365225, year = {2025}, author = {Jin, W and Zhang, Y and Li, Y and Li, R and Su, X and Jing, S and Wang, R and Qiu, Y and Xie, X and Guo, Z and Zhao, X}, title = {Polyethylene microplastics induce microbial functional reprogramming via rhizosphere network disruption, accelerating soil decline.}, journal = {Journal of environmental management}, volume = {397}, number = {}, pages = {128236}, doi = {10.1016/j.jenvman.2025.128236}, pmid = {41365225}, issn = {1095-8630}, abstract = {Polyethylene microplastics (PE-MPs) are emerging soil pollutants with unclear mechanisms of impact on rhizosphere ecosystem functions. Using Angelica sinensis, a medicinal plant valued for its root use, as a model, this study integrated untargeted metabolomics, metagenomic sequencing, and PLS-PM modeling to investigate rhizosphere responses to different PE-MPs concentrations (250, 500, 1000 mg/kg). With increasing PE-MPs dosage, rhizosphere metabolic pathways shifted toward stress adaptation, featuring functional homeostasis and energy reprogramming. Exposure to PE-MPs significantly altered microbial community structure: bacterial and viral shannon, richness, and pielou evenness indices increased, fungal dominance and reduced evenness were observed, and archaeal diversity indices declined. Microbial network stability and functional redundancy weakened, increasing ecosystem sensitivity. Metabolite-microbe association analysis revealed synergistic enrichment patterns, suggesting that plants may recruit beneficial microbes through metabolite regulation. The PLS-PM modeling results indicated that metabolite changes regulate the expression of C/N/S/P cycling functional genes through shifts in bacterial and viral community compositions, where bacteria serve as the primary regulatory hubs and viruses play a key role in amplifying microbial signaling by influencing the microbial community. The expression of these functional genes was negatively correlated with the Soil Quality Index (SQI), indicating that PE-MPs-induced metabolic stress accelerates soil functional degradation. This study provides new insights into microplastic-driven rhizosphere disruption and offers a theoretical basis and biomarkers for microbial regulation and soil ecological restoration.}, }
@article {pmid41365051, year = {2025}, author = {Wang, H and Congzhu,  and Wang, J and Lin, X and Guo, Y and Kiani, FA and Zhou, X and Ding, Y}, title = {Clostridium perfringens can promote the formation of fatty liver in cows.}, journal = {Veterinary microbiology}, volume = {312}, number = {}, pages = {110826}, doi = {10.1016/j.vetmic.2025.110826}, pmid = {41365051}, issn = {1873-2542}, abstract = {During the periparturient period, reduced feed intake often causes negative energy balance in dairy cows, leading to fat mobilization, hepatic lipid accumulation, and fatty liver disease (FLD), ultimately compromising health and milk production. This study investigated the association between FLD and gut microbiota dysbiosis, with a particular focus on the role of Clostridium perfringens within the gut-liver axis. Metagenomic sequencing of ileal contents revealed a marked decrease in microbial diversity in cows with FLD, along with increased abundances of potential pathogens such as C. perfringens, Enterobacter cloacae, and Vibrio alginolyticus. Functional annotation indicated elevated expression of virulence factors (e.g., Hsp60, flagella, mu-toxin), antibiotic resistance genes (e.g., otrA, lsaC), and pathways related to lipopolysaccharide (LPS) biosynthesis and mitogen-activated protein kinase (MAPK) signaling pathways, suggesting enhanced pro-inflammatory potential. qPCR analysis of ileal tissue demonstrated reduced expression of tight junction proteins (zona occludens 1 (ZO-1), Claudin-1, and Occludin) and increased levels of pro-inflammatory cytokines (Interleukin-1 beta (IL-1β), Interleukin-6 (IL-6), Tumour necrosis factor-alpha (TNF-α)), alongside a decrease in the anti-inflammatory cytokine interleukin-10 (IL-10), indicating compromised intestinal barrier function and local inflammation. Given the significant enrichment of C. perfringens in the ileum of FLD cows, we hypothesized its involvement in disease pathogenesis. To test this, C. perfringens was isolated and orally administered to antibiotic-pretreated mice fed a high-fat diet. These mice developed exacerbated hepatic steatosis, metabolic disturbances, and heightened inflammatory responses. Moreover, Western blot analysis revealed reduced expression of intestinal tight junction proteins (ZO-1, Claudin-1, Occludin), indicating increased intestinal permeability. Quantitative PCR confirmed upregulation of pro-inflammatory cytokines (IL-1β, IL-6, TNF-α) and downregulation of IL-10 in both intestinal and hepatic tissues. These findings indicate that C. perfringens may promote FLD by impairing gut barrier integrity and enhancing inflammatory responses. In conclusion, our findings suggest that C. perfringens may contribute to the development of FLD in dairy cows by impairing intestinal barrier integrity and promoting systemic inflammation.}, }
@article {pmid41364992, year = {2025}, author = {Alharbi, M and Nguyen-Dinh, T and Wong, WW and Leung, PM and Kessler, AJ and Greening, C and Cook, PLM}, title = {Dissimilatory nitrate reduction to ammonium driven by iron tolerant Lutibacter in coastal sediments.}, journal = {The Science of the total environment}, volume = {1010}, number = {}, pages = {181095}, doi = {10.1016/j.scitotenv.2025.181095}, pmid = {41364992}, issn = {1879-1026}, abstract = {The processes of denitrification and dissimilatory NO3[-] reduction to ammonium (DNRA) occupy a competing pivotal point in the nitrogen cycle. Denitrification leads to a loss of fixed nitrogen, while DNRA recycles NO3[-] as bioavailable ammonium. Iron (II) is known to enhance DNRA, by acting as an electron donor, however, the organisms responsible for iron driven DNRA remain poorly understood. Here we undertook incubations of sediment with NO3[-] and Fe[2+] additions followed by process measurements and metagenomic analysis to measure DNRA and microbial community structure. Addition of Fe[2+] stimulated DNRA, and greatly increased the relative abundance of flavobacteria (Lutibacter) in slurries over a period of 12-24 days compared to controls. We isolated a strain of Lutibacter from these slurries which mediated organotrophic and mixotrophic DNRA (while oxidising sulphide). No genes capable of Fe[2+] oxidation were detected in agreement with experiments that showed this strain had no ability to oxidise Fe[2+]. The addition of Fe[2+] to pure cultures had no significant effect on DNRA, suggesting these bacteria are not stimulated nor inhibited by the presence of Fe[2+]. As such, in contrast to previous studies, we find Fe[2+] addition to sediments enhances DNRA by favouring Fe tolerant Lutibacter and is uncoupled Fe[2+] oxidation in coastal sediments. This has implications for how pollutants such as higher Fe[2+] concentrations and disturbance can lead to bacterial community shifts that enhance nitrogen retention within ecosystems. Isolates of these robust bacteria have the potential to help recover NO3[-] as NH4[+] in novel water treatment systems.}, }
@article {pmid41364990, year = {2025}, author = {Shen, S and Shimotori, K and Tsuchiya, K and Shigeta, S and Sueyoshi, M and Matsuda, T and Shimizu, Y}, title = {Carrier-resolved metagenomics suggests the dual "filter-hub" function of a large freshwater lake toward incoming antibiotic resistance genes.}, journal = {The Science of the total environment}, volume = {1010}, number = {}, pages = {181145}, doi = {10.1016/j.scitotenv.2025.181145}, pmid = {41364990}, issn = {1879-1026}, abstract = {Rivers and wastewater-treatment plants (WWTPs) convey antibiotic resistance genes (ARGs) to lakes. Studies simultaneously profiling ARGs and their carriers and tracking their persistence in lakes remain scarce. We collected cell- and virus-size fractions from Lake Biwa, Japan, 11 in-flowing rivers, and one WWTP for shotgun metagenomic sequencing. We reconstructed 326 bacterial metagenome-assembled genomes, 7917 plasmid contigs (472 harboring conjugation genes), and 32,375 viral contigs. The chromosomes contained 1502 ARGs (predominantly fluoroquinolone and glycopeptide resistance). The plasmids encoded efflux- and target-alteration determinants spanning 25 drug classes. Only 3.6 % of the viral genomes carried ARGs, chiefly qnr and dfr. ARG class composition differed among carriers, forming a spatial mosaic unrelated to land use or livestock density. Of the ARG-carrying cells and viruses, 85-97 % were undetectable in the lake, suggesting dilution and adaptation failure. Chromosome comparison identified 1809 putative horizontal gene transfer events, 2.1 % of which bridged lake-resident and external taxa. ARG profiles differed according to carrier type. Thus, Lake Biwa might function simultaneously as a filter, removing incoming ARG-carrying cells and viral particles, and as a "silent hub," potentially integrating external ARGs into lake-resident bacteria through horizontal gene transfer. These data provide a foundation for assessing and managing antimicrobial resistance in large freshwater ecosystems.}, }
@article {pmid41364878, year = {2025}, author = {Yoon, SE and Kang, W and Cho, J and Cho, HJ and Chalita, M and Oh, HS and Hyun, DW and Han, S and Kim, H and Sung, H and Lee, JY and Park, B and Ryu, KJ and Kim, HY and Cho, D and Kim, WS and Kim, SJ}, title = {Microbiome and metabolite biomarkers of CAR T-cell therapy outcomes in relapsed/refractory diffuse large B cell lymphoma.}, journal = {Blood advances}, volume = {}, number = {}, pages = {}, doi = {10.1182/bloodadvances.2025016858}, pmid = {41364878}, issn = {2473-9537}, abstract = {CD19 CAR T-cell therapy has revolutionized treatment for relapsed/refractory diffuse large B-cell lymphoma (RR-DLBCL), but challenges like post-treatment failure and immune-related adverse events (AEs) persist. This study explores the gut microbiome as a predictive biomarker for CAR T-cell therapy outcomes and toxicity. Stool and serum samples from RR-DLBCL patients were analyzed at apheresis (47 samples) and one month post-infusion (32 samples) using whole-genome sequencing metagenomics. When compared with healthy controls and newly diagnosed DLBCL, RR-DLBCL showed significant gut dysbiosis, characterized by increased Proteobacteria and Enterobacteriaceae. Responders to treatment had higher levels of Bacteroides fragilis, while non-responders exhibited higher levels of Faecalibacterium prausnitzii. Functional metagenomic analysis suggested enrichment of inosine biosynthesis pathways in responders, and elevated serum inosine demonstrated an exploratory association with improved progression-free survival. Distinct microbial taxa and serum fatty acid profiles were also linked to CAR T-cell-related AEs, with higher acetate and butyrate levels in patients without AEs, and increased isovalerate in those with AEs. These findings indicate that gut microbiome features-particularly Bacteroides fragilis and inosine metabolism-may serve as candidate biomarkers for CAR T-cell therapy outcomes and toxicity. However, given the exploratory nature of these analyses and the limited cohort size, results should be interpreted cautiously. Larger, prospective studies will be required to validate these observations and to assess the potential of microbiome-based strategies to optimize CAR T-cell therapy in RR-DLBCL.}, }
@article {pmid41364497, year = {2025}, author = {Saroff, MJ and Haile, AA and Baniel, A and Kraberger, S and Regney, M and Harrach, B and Kaján, GL and Lu, A and Beehner, JC and Bergman, TJ and Snyder-Mackler, N and Varsani, A and Schneider-Crease, IA}, title = {Early-life infection dynamics and genomic diversity of adenoviruses in a wild primate (Theropithecus gelada).}, journal = {Microbial genomics}, volume = {11}, number = {12}, pages = {}, doi = {10.1099/mgen.0.001595}, pmid = {41364497}, issn = {2057-5858}, mesh = {Animals ; Feces/virology ; *Theropithecus/virology ; Ethiopia ; *Adenoviridae Infections/virology/veterinary ; Phylogeny ; Genome, Viral ; *Adenoviruses, Simian/genetics/classification ; *Adenoviridae/genetics/classification ; Genetic Variation ; Female ; Male ; }, abstract = {In humans, adenoviruses (AdVs) are frequently associated with respiratory illnesses, posing risks to children with developing immune systems and immunocompromised individuals. Outbreaks and epidemics are generally centred in close-contact settings, such as childcare facilities, and transmission occurs through faecal-oral and airborne pathways. AdVs have coevolved across the primate lineage, but very little is known about whether the early-life dynamics in non-human primates mirror those in humans. Here, we leverage longitudinal data collected on a population of geladas (Theropithecus gelada) in the Simien Mountains National Park, Ethiopia, to evaluate AdV dynamics across the gelada lifespan. We identified ten coding-complete AdV genomes representing seven unique simian adenovirus (SAdV) types, four of which are adequately different from the known ones to establish new species. We assessed behavioural and seasonal drivers of SAdV presence and richness across repeated faecal samples from known individuals. Contrary to our expectation that the highest risk would occur after the initiation of play behaviour in infancy (~6 months of age), when peer-to-peer transmission risk is expected to increase, SAdV likelihood was highest in infants under 6 months of age. Risk and richness declined over the lifespan, with very few adults infected, and higher minimum temperatures were weakly but significantly negatively associated with richness. Our results suggest that, unlike in humans, SAdV exposure occurs prior to the initiation of close-contact play behaviours and likely results from the close spatial proximity of conspecifics throughout the dependent period. Like AdVs in humans, SAdVs in geladas maintain low levels in adulthood, with early infections potentially conferring life-long immunity.}, }
@article {pmid41364398, year = {2025}, author = {Han, N and Peng, X and Zhang, T and Qiang, Y and Li, X and Zhang, W}, title = {Strain-level dynamics of Akkermansia muciniphila in the human gut microbiota.}, journal = {AMB Express}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13568-025-01982-7}, pmid = {41364398}, issn = {2191-0855}, support = {2018YFC1200100//National Key Research and Development Program of China/ ; }, abstract = {Akkermansia muciniphila (Akk), a mucin-degrading bacterium residing in the human gut, plays a pivotal role in intestinal health. This study investigated its temporal dynamics, strain-level diversity, and cross-regional transmission using longitudinal metagenomic data from the Chinese Microbiome Project (CMP). We observed significant fluctuations in Akk relative abundance across 52 time points in 7 healthy individuals, with detection rates of 56.9% (16S rRNA gene sequencing) and 33.3% (whole-genome sequencing, WGS). Notably, "short-term blooms"--rapid increases followed by declines in relative abundance--were identified in multiple subjects. Genomic analysis of 39 Akkermansia metagenome-assembled genomes (MAGs), combined with 89 publicly available strains with complete genome, revealed phylogenetically distinct clusters (average nucleotide identity, ANI < 98% between clusters). Strikingly, individuals harbored different clusters at varying time points (e.g., AmII replaced by AmIb and later AmIa in subject P4), suggesting strain replacement and recurrent colonization. Furthermore, high-similarity strains (ANI > 99%) were shared between individuals with close contact (e.g., cohabiting subjects P2 and P4) and across geographically distant regions (China, South Korea, and the United States), implicating human-mediated or environmental transmission pathways. These findings underscore the dynamic nature of Akk within the gut microbiota and highlight the need to explore factors driving its colonization, strain competition, and ecological dissemination.}, }
@article {pmid41363757, year = {2025}, author = {Li, J and Pang, Y and Yu, H}, title = {Robot-Assisted Stereotactic Aspiration of a Parietal Brain Abscess With Metagenomic Identification of Fusobacterium nucleatum.}, journal = {The Journal of craniofacial surgery}, volume = {}, number = {}, pages = {}, doi = {10.1097/SCS.0000000000012287}, pmid = {41363757}, issn = {1536-3732}, abstract = {Robot-assisted stereotactic aspiration offers a minimally invasive approach to brain abscesses near the eloquent cortex. We report a rare case of a left parietal abscess caused by Fusobacterium nucleatum in an immunocompetent adult, managed successfully with this approach. The patient, a 52-year-old man, presented with right-sided limb numbness. MRI and contrast-enhanced CT revealed a cystic, ring-enhancing lesion with diffusion restriction in the left parietal lobe. Despite empiric broad-spectrum antibiotics, neurological deterioration occurred due to progressive mass effect. Robot-assisted stereotactic aspiration enabled single-stage, precise drainage of the abscess. Metagenomic next-generation sequencing identified F. nucleatum, prompting adjustment of antibiotics to ceftriaxone plus metronidazole, followed by metronidazole monotherapy. The patient improved clinically, and a 6-month MRI confirmed complete resolution, underscoring the precision of robotic stereotaxy for eloquent-region abscesses and highlighting the diagnostic value of metagenomic sequencing in detecting anaerobic pathogens.}, }
@article {pmid41363534, year = {2025}, author = {Ren, M and Liu, Y and Wang, Y and Tu, Y and Guo, Y and Sun, X and Niu, G and Wang, Y}, title = {Virome diversity and molecular characterization of two emerging RNA viruses in mosquito populations from Yantai, China.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0053925}, doi = {10.1128/msphere.00539-25}, pmid = {41363534}, issn = {2379-5042}, abstract = {Mosquito-borne viruses represent a major global public health threat, with transmission dynamics governed by climatic, ecological, and anthropogenic factors. Yantai City, Shandong Province, situated in a warm-temperate monsoon climate zone, shares geographical and ecological characteristics with regions where mosquito-borne viruses are endemic, creating potential for virus introduction. We used metagenomics to systematically analyze viral communities in mosquitoes from the Yantai region. We collected 8,111 mosquitoes representing four genera and six species, with Culex being predominant (89.8%). High-throughput sequencing revealed 11 viral species spanning 9 families, including Peribunyaviridae and Picornaviridae. Notably, Serbia mononega-like virus 1 and Biggievirus Mos11 represent the first reports from China, with quantitative reverse transcription PCR revealing minimum infection rates of 0.34% and 0.68%, respectively. Phylogenetic analysis revealed close relationships to known viral strains, with several isolates potentially representing novel genera or species. Analysis revealed that Culex quinquefasciatus harbored the greatest viral diversity (five species), with significantly higher viral diversity in agricultural versus urban areas (P < 0.001). Several viruses demonstrated cross-species transmission potential, including Zhee mosquito virus, Zhejiang mosquito virus 3, and Culex tritaeniorhynchus rhabdovirus, all detected across multiple mosquito species. While most viruses appear mosquito-specific, several show close phylogenetic relationships to known pathogens, potentially posing public health risks warranting surveillance. This study addresses knowledge gaps regarding mosquito-borne viruses in the Bohai Rim region and provides a scientific foundation for regional viral surveillance and early warning systems.IMPORTANCEMosquito-borne viruses are a significant global health threat, with the potential to cause widespread disease outbreaks. This study investigated the viral diversity within mosquito populations in Yantai, China, and characterized the molecular features of two emerging RNA viruses. These findings highlight the remarkable viral diversity harbored by Culex mosquitoes and reveal higher viral diversity in agricultural areas compared to urban settings. Several identified viruses exhibit cross-species transmission potential and close phylogenetic relationships to known pathogens, suggesting that they may pose public health risks. Understanding these interactions is essential for predicting how environmental changes may affect virus transmission and the resilience of surveillance and control strategies.}, }
@article {pmid41362850, year = {2025}, author = {Shu, H and Li, X and Chen, Y and Wang, W}, title = {Hemophagocytic lymphohistiocytosis secondary to disseminated histoplasmosis in an HIV-negative patient: A case of misdiagnosis.}, journal = {Medical mycology case reports}, volume = {50}, number = {}, pages = {100752}, pmid = {41362850}, issn = {2211-7539}, abstract = {Hemophagocytic lymphohistiocytosis (HLH) secondary to disseminated histoplasmosis (DH) is rare and often misdiagnosed, especially in non-endemic areas. We present a case of a 70-year-old Chinese man who was admitted with fever, nausea, and vomiting, initially misdiagnosed with pulmonary tuberculosis. The use of metagenomic next-generation sequencing (mNGS) played a crucial role in the early and accurate diagnosis, highlighting its potential as a valuable diagnostic tool for rare infections.}, }
@article {pmid41362398, year = {2025}, author = {Xu, X and Li, J and Pan, L and Yu, H and Huang, J}, title = {Gastropleural Fistula Following Combined TACE, Immunotherapy, and Bevacizumab in HCC: A Case Report.}, journal = {Journal of hepatocellular carcinoma}, volume = {12}, number = {}, pages = {2671-2677}, pmid = {41362398}, issn = {2253-5969}, abstract = {Gastropleural fistula (GPF) is an extremely rare complication after treatment for liver cancer. We report a case of a 54-year-old man with hepatitis B virus (HBV)-related liver cancer who developed a GPF after multiple sessions of transarterial chemoembolization (TACE) combined with immunotherapy and targeted therapy. During the third treatment, because of arterial remodeling and changes in tumor vascular supply, the embolization route was changed to the left inferior phrenic artery. After the procedure, the patient presented with abdominal pain, chest pain, and fever. Metagenomic next-generation sequencing (mNGS) of the pleural effusion identified Porphyromonas endodontalis, and Pneumocystis jirovecii was also detected in the sputum. Upper gastrointestinal endoscopy and water-soluble contrast radiography confirmed a gastric fundus perforation with a fistulous communication to the pleural cavity. After multidisciplinary evaluation, the patient underwent laparoscopic fistula repair and had a favorable postoperative recovery. This case highlights that, while the combination of TACE, immunotherapy, and targeted agents may provide synergistic antitumor benefits, it also carries a potential risk of serious gastric complications.}, }
@article {pmid41362143, year = {2025}, author = {Gao, WJ and Wan, YQ and Bian, WJ and Sun, KK and Gao, ZC}, title = {[A case of pulmonary alveolar proteinosis secondary to GATA2 deficiency combined with splenic M. kansasii infection and literature review].}, journal = {Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases}, volume = {48}, number = {12}, pages = {1153-1161}, doi = {10.3760/cma.j.cn112147-20250527-00287}, pmid = {41362143}, issn = {1001-0939}, mesh = {Humans ; *Pulmonary Alveolar Proteinosis/etiology ; Male ; *Mycobacterium Infections, Nontuberculous/complications ; *GATA2 Deficiency/complications ; Young Adult ; *GATA2 Transcription Factor/genetics/deficiency ; Mycobacterium kansasii ; Spleen/microbiology ; }, abstract = {Objective: To enhance the understanding of the rare disease GATA2 deficiency syndrome leading to pulmonary alveolar proteinosis (PAP) and non-tuberculous mycobacterial (NTM) disease. Methods: The clinical data of a patient with GATA2 deficiency-associated PAP and splenic M. kansasii disease admitted to Peking University People's Hospital were summarized. Relevant literature from January 1, 2010 to March 31, 2025 was retrieved and reviewed through Wanfang Data, China National Knowledge Infrastructure, and the National Center for Biotechnology Information database. Results: The patient was a 19-year-old male. The clinical manifestations included recurrent fever for 7 years. The peripheral blood routine test showed peripheral blood pancytopenia accompanied by monocytopenia. The serum granulocyte-macrophage colony-stimulating factor (GM-CSF) antibody was negative. Chest CT revealed diffuse interstitial lung changes, while [18]F-fluorodeoxyglucose positron emission tomography-computed tomography (FDG PET-CT) demonstrated splenomegaly with multiple focal FDG-avid lesions. Bone marrow biopsy indicated marrow failure. Histopathological examination of lung biopsy specimens was consistent with alveolar proteinosis, whereas histopathology of the spleen biopsy revealed granuloma and patellar necrosis. Metagenomic next-generation sequencing (mNGS) of the splenic specimen detected M. kansasii, and genetic testing identified a germline GATA2 mutation(c.1128del, p.Y377fs). Based on these findings, a diagnosis of GATA2 deficiency with secondary PAP and splenic M. kansasii infection was established. Following anti-NTM treatment, the patient's infection was controlled; however, hematopoietic stem cell transplantation was planned due to bone marrow failure. Literature search revealed 4 cases of GATA2 deficiency syndrome with bone marrow dysplasia. Three cases developed PAP. All 4 cases had NTM infection, including 1 case with disseminated NTM infection in the lungs, spleen, and bone marrow. GATA2 deficiency syndrome patients are prone to decreased numbers and functional defects of cells such as monocytes and NK cells, resulting in immune dysfunction and pulmonary alveolar macrophage dysfunction, reduced ability to resist NTM, leading to the patient being prone to NTM infection, namely MonoMAC syndrome, and can cause secondary PAP. Early identification and timely completion of genetic testing are beneficial for clear diagnosis and establishment of precise intervention strategies. Conclusion: GATA2 deficiency is a rare autosomal dominant genetic disorder caused by mutations in the GATA2 gene. Patients with cytopenia, GM-CSF antibody-negative PAP accompanied by NTM infection should be considered to have the possibility of this disease. Those patients should undergo GATA2 gene screening. Hematopoietic stem cell transplantation is currently the only possible method for curing GATA2 deficiency.}, }
@article {pmid41361579, year = {2025}, author = {Anunobi, OO and Abiola, RB and Ogah, CF}, title = {In silico pathogenomics of draft metagenome-assembled genome of gut Enterobacter cloacae from a gastroenteritis patient exhibiting potential determinants of multi-drug resistance and virulence.}, journal = {Antonie van Leeuwenhoek}, volume = {119}, number = {1}, pages = {6}, pmid = {41361579}, issn = {1572-9699}, mesh = {*Enterobacter cloacae/genetics/pathogenicity/drug effects/isolation &amp; purification ; Humans ; *Gastroenteritis/microbiology ; *Genome, Bacterial ; *Drug Resistance, Multiple, Bacterial/genetics ; Virulence/genetics ; Enterobacteriaceae Infections/microbiology ; *Metagenome ; Anti-Bacterial Agents/pharmacology ; Virulence Factors/genetics ; Computer Simulation ; Computational Biology ; Gastrointestinal Microbiome ; Phylogeny ; }, abstract = {Antimicrobial resistance (AMR) is considered one of the top 10 threats to global public health and development. Opportunistic bacteria such as Enterobacter cloacae have been reported to acquire resistance determinants, making them pathogenic reservoirs and a threat to health and most are on the path of becoming superbugs. These bacteria are commonly isolated along with pathogens from the stool and urine of patients diagnosed with typhoid fever, paratyphoid fever, gastroenteritis, urinary tract infection, and bloodstream infection or sepsis. The E. cloacae strain EC78 studied here is a metagenomic-assembled genome that was binned from sequenced data of a mixed bacterial culture taken from a patient diagnosed with gastroenteritis. The isolate was sequenced with Illumina Novaseq 6000 platform and analysed with various bioinformatics tools. EC78 origin strain contained antibiotics resistance genes, insertion sequences, phages, and virulence factors. Notable virulence genes responsible for immune modulation, efflux of drugs, invasion and nutritional virulence previously reported in Klebsiella pneumoniae., Escherichia coli, Shigella sp., and Salmonella sp. etc., were identified in EC78. Genetic characteristics that could contribute to pathogenicity, virulence, and antibiotic resistance, not commonly associated with E. cloacae, were identified in gut-domiciled EC78, suggesting the evolution of counter-therapy in the bacteria, probably driven by its quest for survival in an otherwise competitive biome.}, }
@article {pmid41361265, year = {2025}, author = {Wang, C and Wang, C and Chen, S and Shi, K and Yu, J and Ding, Y and Yue, Y and Hua, Y and Wang, H and Chen, J}, title = {Global landscape of antibiotic resistance genes in the human gut microbiome metagenome-assembled genomes.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-025-04586-0}, pmid = {41361265}, issn = {1471-2180}, support = {No.202524//the Scientific Research Program of the Bozhou University/ ; No. W2412100//International Cooperation and Exchanges NSFC-ASRT/ ; No. 42276137//National Natural Science Foundation of China/ ; No. 2022YFC2804205//National Key Research and Development Program of China/ ; No. 2022YFC2804104//National Key Research and Development Program of China/ ; }, }
@article {pmid41361202, year = {2025}, author = {Korzekwa, K and Lepionka, T and Bisak, A and Obuch-Woszczatyńska, O and Bylińska, K and Kauc, A and Skuza, K and Zaborski, B and Krzyżowska, M}, title = {Long-term biological surveillance of SARS-CoV-2 in critical points for municipal sewage catchment in light of wastewater-based epidemiology, public health and environmental hygiene.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {43320}, pmid = {41361202}, issn = {2045-2322}, support = {National Health Program for 2021-2025" no 357/2021/DA//Ministry of National Defence, Poland/ ; National Health Program for 2021-2025" no 357/2021/DA//Ministry of National Defence, Poland/ ; National Health Program for 2021-2025" no 357/2021/DA//Ministry of National Defence, Poland/ ; National Health Program for 2021-2025" no 357/2021/DA//Ministry of National Defence, Poland/ ; National Health Program for 2021-2025" no 357/2021/DA//Ministry of National Defence, Poland/ ; National Health Program for 2021-2025" no 357/2021/DA//Ministry of National Defence, Poland/ ; National Health Program for 2021-2025" no 357/2021/DA//Ministry of National Defence, Poland/ ; National Health Program for 2021-2025" no 357/2021/DA//Ministry of National Defence, Poland/ ; National Health Program for 2021-2025" no 357/2021/DA//Ministry of National Defence, Poland/ ; }, mesh = {*SARS-CoV-2/genetics/isolation &amp; purification ; *Sewage/virology ; *COVID-19/epidemiology/virology ; Humans ; *Wastewater/virology ; Public Health ; *Wastewater-Based Epidemiological Monitoring ; Poland/epidemiology ; Hygiene ; Environmental Monitoring ; }, abstract = {Routine monitoring and wastewater-based bio-surveillance represents a strong supporting tool for following and understanding SARS-CoV-2 endemicity or epidemic dynamics in society. The main objective of the research was a two-year qualitative and quantitative monitoring program of SARS-CoV-2 in sewage in a model urban agglomeration (the capital city), including the development of an algorithm for action in this area and a joint evaluation of procedures with a water and sewage company (public administration sector). To resolve problems, we continuously investigated inflows and outflows of four wastewater treatment plants and raw sewage of the whole catchment (including healthcare units, airport and military areas) within the Warsaw capital city for SARS-CoV-2, during two waves of COVID-19 in 2023 and 2024. The screening was performed by RT-qPCR (N1, N2, E probes) and NGS metagenomics analysis. The average cumulative load of the virus in sewage for the whole tested period was 3.5 × 10[5] genomic copies per litre. The highest load was found for wastewater inflows and the lowest one was found for housing estates and wastewater outflows. Higher viral concentrations in the wastewater than expected in medical records suggested a higher number of undiagnosed COVID-19 infections within the community. The obtained genotypes segregated within 11 clades (21I to 24 F), making '23 and '24 waves distinguishable. We consider our results and methodological approaches hold significant potential for public health, with particular emphasis on the needs of the Directive (EU) 2024/3019 of the European Parliament and of the Council.}, }
@article {pmid41360901, year = {2025}, author = {Lima, J and McNeilly, TN and Auffret, MD and Steele, P and Frew, D and Martínez-Álvaro, M and Dewhurst, RJ and Watson, M and Roehe, R}, title = {Rumen microbiome profiles of dairy cattle are affected by the presence of, and vaccination against, the abomasal parasitic nematode Ostertagia ostertagi.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-025-30604-2}, pmid = {41360901}, issn = {2045-2322}, support = {BB/N016742/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/N01720X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 10045515//Innovate UK/ ; }, abstract = {Ostertagia ostertagi is a highly prevalent nematode that affects grazing cattle and impacts performance and welfare by reducing appetite and hindering weight gain. Despite its economic significance, the influence of the abomasal parasite O. ostertagi on the rumen microbiome remains unexplored. We examined the effects of subclinical O. ostertagi infection and vaccination on the rumen microbiome at taxonomic and functional levels. In an experimental trial, calves treated with vaccine or adjuvant-only were orally challenged with O. ostertagi larvae daily for 25 days; 4 groups of animals (UNF: unvaccinated, unchallenged; VAC: vaccinated, challenged; CHE: unvaccinated, challenged, high cumulative faecal egg counts (cFEC), and CLE: unvaccinated, challenged, low cFEC) were selected for whole shotgun metagenomic sequencing. Using a rigorous permutation test based on partial least squares discriminant analyses, we identified 36 (91), 38 (31), 21 (57), 41 (64) and 29 (57) microbial genera (genes) that distinguished VAC, CHE and CLE from UNF, CHE from CLE, and CHE from VAC, respectively. The subclinical infection reshaped the rumen microbiome; enrichment of opportunistic pathogens such as Listeria, and depletion of Filifactor in infected animals were identified as potential biomarkers for host immune response, whereas Actinomyces and Microspora were potential biomarkers of resistance to infection. Microbial biochemical pathways like acetogenesis (e.g., Elusimicrobium, nrfA), pectin and hemicellulose degradation (e.g., Sphaerochaeta), and phosphorus and sulphur metabolism (e.g., Candidatus Accumulibacter and Desulfatibacillum) were also affected by parasitism. Both infection and vaccination altered methanogens, methanotrophs and the methane metabolism pathway, highlighted by distinct gene clustering patterns between infected and uninfected animals. Clustering patterns of infected and vaccinated animals exhibited some similarities, which may reflect immune system modulation of the ruminal microbiome as a result of an abomasal infection. This study unveils critical changes in the rumen microbiome due to the infection by and vaccination against the abomasal parasite O. ostertagi. Our results highlight the importance of monitoring microbial dynamics in the development of effective anthelmintic treatments and vaccines.}, }
@article {pmid41360540, year = {2026}, author = {Zhang, M and Jiang, Z and Li, J and Marie-Colette, AK and Liu, Q and Hao, N and Wang, J}, title = {Analyzing the contribution of functional microorganism to volatile flavor compounds in Semillon wine and predicting their metabolic roles during natural fermentation.}, journal = {Food research international (Ottawa, Ont.)}, volume = {223}, number = {Pt 2}, pages = {117842}, doi = {10.1016/j.foodres.2025.117842}, pmid = {41360540}, issn = {1873-7145}, mesh = {*Fermentation ; *Wine/analysis/microbiology ; *Volatile Organic Compounds/analysis/metabolism ; *Vitis/microbiology ; Gas Chromatography-Mass Spectrometry ; Taste ; Odorants/analysis ; China ; Microbiota ; Food Microbiology ; *Flavoring Agents/analysis ; *Bacteria/metabolism/classification ; Solid Phase Microextraction ; Hanseniaspora/metabolism ; }, abstract = {Indigenous microorganism plays a pivotal role in natural wine fermenting and its distinctive qualities shaping. However, the contributions of functional microbial taxa to wine flavor formation remain underexplored. This study focuses on the natural fermentation systems of Semillon grapes from Wuwei and Zhangye Gansu sub-regions within the Hexi Corridor of China. We characterized the dynamics of microbial community succession during fermentation using a combination of metagenomic sequence and culture-dependent analysis. Concurrently, volatile compounds were quantified using headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry. The mechanistic of functional microorganisms in wine flavor formation were unveiled by constructing KEGG metabolic network. The results revealed distinct microbial succession patterns between the two regions. In Zhangye, Hanseniaspora dominated the early fermentation stage, succeeded by Saccharomyces, Fructobacillus, and Brachyspira in middle and late stages. Conversely, in Wuwei, Pichia prevailed initially, with Brachyspira becoming stably enriched. Volatile esters and higher alcohols were identified as the major flavor components, contributing aroma notes of flowers, fresh greens, and stone fruits to the Semillon wine. Correlation analysis indicated positive associations between most key volatile aroma compounds and Saccharomyces, Brachyspira, Hanseniaspora, and Acetobacter. Metagenomic functional prediction highlighted carbohydrate and amino acid metabolic as the predominant pathways, with key processes involving glycolysis, fatty acid biosynthesis, and esterification. Core microbial taxa (Saccharomyces, Hanseniaspora, Starmerella, etc.) regulated flavor compound synthesis through a synergistic metabolic network. This study elucidates the succession of functional microorganisms and the development of flavor profiles during the natural fermentation of Semillon in the Hexi Corridor providing a reference for the development and application of functional microorganisms.}, }
@article {pmid41360290, year = {2025}, author = {Obermeier, PE and Alchikh, M and Ma, X and Reiche, J and Schweiger, B and Rath, BA}, title = {Digital severity scoring and viral metagenomics: A feasibility study on integrated diagnosis of pediatric influenza-like illness.}, journal = {Infectious diseases now}, volume = {}, number = {}, pages = {105223}, doi = {10.1016/j.idnow.2025.105223}, pmid = {41360290}, issn = {2666-9919}, abstract = {INTRODUCTION: Metagenomic next-generation sequencing (mNGS) holds promise for identifying diverse pathogens in complex cases of influenza-like illness (ILI). Interpreting results requires comprehensive clinical context. We aimed to explore the feasibility of an integrated diagnostic approach by linking shotgun viral mNGS with standardized clinical data for unbiased ascertainment and hypothesis generation in pediatric ILI patients.<br><br>PATIENTS AND METHODS: We studied a cohort of 6,073 pediatric ILI patients (mean age 3.1&#x202f;years, range 0-18.8&#x202f;years), assessed using the VIVI ScoreApp for immediate computation of Disease Severity and Risk Factor Scores. Nasopharyngeal samples were tested for nine respiratory viruses by PCR. In a nested pilot feasibility study, we linked the clinical dataset of 100 ILI patients with neurological complications (mean age 3.9&#x202f;years, range 0-17.8&#x202f;years) to additional viral mNGS. PCR and mNGS were compared by agreement rates and Cohen's &#x3ba; for inter-method reliability.<br><br>RESULTS: In the pilot feasibility study, the mean VIVI Disease Severity Score was above the cohort average (>67th percentile, p&#x202f;<&#x202f;0.0001), with 'age&#x202f;<&#x202f;2 years' as the most prevalent risk factor (n&#x202f;=&#x202f;44/100). mNGS identified 15 viruses, expanding the range of viral identifications by six viruses compared to PCR. Linking VIVI Scores with mNGS-discovered viruses suggested high disease severity. Sensitivity of mNGS was relatively low; overall agreement with PCR was 77-98&#x202f;% and overall reliability was 'moderate' (&#x3ba; scores of 0.1-0.85).<br><br>CONCLUSIONS: Digital surveillance tools can successfully integrate with mNGS to capture complex clinical patterns and generate data-driven hypotheses. Large-scale investigation and technical refinement are warranted.}, }
@article {pmid41359546, year = {2025}, author = {Provatas, K and Mouratidis, I and Georgakopoulos-Soares, I}, title = {KmerCrypt: private k-mer search with homomorphic encryption.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {6}, pages = {}, doi = {10.1093/bib/bbaf648}, pmid = {41359546}, issn = {1477-4054}, support = {//University of Texas at Austin/ ; }, mesh = {*Computer Security ; Humans ; Cloud Computing ; *Software ; Algorithms ; *Genomics/methods ; Databases, Genetic ; }, abstract = {Outsourcing the storage and analysis of genomic data to third-party servers is often necessary due to the scale of modern datasets, but it introduces significant privacy challenges that must be addressed to ensure secure handling. K-mer-based analyses offer broad applications across genomics research, clinical diagnostics, pathogen surveillance, and metagenomic classification, though implementation requires careful ethical and technical considerations, particularly when processing human genomic data in clinical settings. We present a novel protocol utilizing homomorphic encryption that enables a client to store a fully encrypted version of a genome on an untrusted server and perform private k-mer searches. The protocol ensures the server never gains access to the client's non-encrypted genome sequence, nor does it learn the content of any k-mer query. After a one-time client-side encryption of the genome, the server performs all computations on ciphertext, returning only encrypted results that can be decrypted solely by the data owner. This framework transforms an honest but curious cloud server into a secure storage and computation system, enabling practical and confidential querying of encrypted, client-owned genomic data. The system supports exact k-mer searches on genomic data, as well as position weight matrix searches. Finally, we provide KmerCrypt, a private k-mer search toolkit that implements this protocol, offering researchers an efficient and secure solution for querying encrypted genomic datasets without compromising privacy.}, }
@article {pmid41359366, year = {2025}, author = {Cheah, S and Burke, J and Bruinsma, FJ and Evans, M and Tsimiklis, H and Hodge, AM and Lynch, BM and Giles, GG and Sinha, R and Southey, MC and Milne, RL}, title = {Faecal sample collection for gut microbiome research in a prospective cohort: a pilot study within the Australian Breakthrough Cancer Study.}, journal = {Cancer research communications}, volume = {}, number = {}, pages = {}, doi = {10.1158/2767-9764.CRC-25-0445}, pmid = {41359366}, issn = {2767-9764}, abstract = {Large prospective analyses of human gut microbiome profiles are needed to elucidate the role of microbiome variation in the development of disease. We conducted a pilot study to assess the feasibility of home faecal sample collection within a cohort study. A subset of cohort study participants was randomly selected and randomised into four groups defined by faecal sample collection method and questionnaire components. Of 1,093 invited participants, 610 (56%) opted in and, of those, 88% returned a sample. Of those asked to provide a faecal sample via faecal occult blood test card (FOBT) and complete a short "day of sample" questionnaire (dosQ), 49% returned a sample. Sample return was comparable for participants additionally asked to provide a sample via ethanol tube (51%), complete a food frequency questionnaire (48%), or complete both additional activities (49%). Whole genome sequencing and metagenomic analysis on paired FOBT and ethanol samples showed that both collection methods provided sufficient quality and quantity of DNA for downstream metagenomic analyses and displayed highly concordant microbiome profiles. Home faecal sample collection for microbiome analysis is feasible in a large prospective cohort. Including additional components did not reduce the likelihood of participants completing all requested items.}, }
@article {pmid41359148, year = {2025}, author = {Rao, PM and Radha, P}, title = {Pioneering approaches to plastic biodegradation and upcycling for sustainability.}, journal = {Environmental monitoring and assessment}, volume = {198}, number = {1}, pages = {23}, pmid = {41359148}, issn = {1573-2959}, mesh = {*Biodegradation, Environmental ; *Plastics/metabolism/analysis ; Waste Management/methods ; }, abstract = {Plastic pollution has become one of the most significant threats to the environment and human health of the twenty-first century, with more than 300 million tons of waste generated annually, and conventional disposal methods are inadequate. To address this challenge, recent research has increasingly shifted toward biodegradation and upcycling as sustainable alternatives. Microbial degradation of synthetic plastics has shown advancement. This includes the introduction of novel strains like Aspergillus niger MG654699 for the 3.6% and 5% degradation of polyethylene terephthalate and polystyrene, respectively. Also, Streptomyces sp., Methylobacterium, Arthrobacter, and Sphingomonas have been studied to be responsible for mulch film degradation. Advances in metagenomics have further revealed the complexity of microbial consortia for driving these processes, whereas kinetic modeling has provided insights into degradation rates and conditions. Building on this foundation, artificial intelligence and machine learning are now expediting enzyme discovery, optimizing degradation pathways, and enabling intelligent waste management systems. Similarly, biosensors based on Vibrio fischeri and Escherichia coli improve monitoring by detecting plastic monomers. Beyond degradation, the integration of microbial and chemical processes has enabled the upcycling of plastic monomers into value-added products such as polyhydroxyalkanoates, vanillin, bacterial nanocellulose, fuels, and biochemicals, promoting a circular bioeconomy. These advances highlight a paradigm shift from waste accumulation to resource recovery, underscoring the potential of biotechnology and engineering innovations to transform plastic management. The review concludes by highlighting the challenges of scalability, environmental variability, and policy support while positioning biodegradation and upcycling as integrated strategies for a sustainable and resilient future.}, }
@article {pmid41358839, year = {2025}, author = {Li, Y and Fu, X and Sun, F and Dong, M and Wang, Y and Wang, Y and Liu, Q}, title = {Metabolomic and metagenomic insights into WFBG-mediated regulation of gut microbiota and metabolism in broilers.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0189025}, doi = {10.1128/aem.01890-25}, pmid = {41358839}, issn = {1098-5336}, abstract = {UNLABELLED: The steady state of gut microbiota is a key factor in regulating the growth of broilers. The regulatory role of wet-fermented brewer's grain (WFBG) in broiler gut development and microbiota is still elusive. In this study, non-targeted metabolomics and 16S rRNA sequencing analysis were used to investigate the effects of WFBG supplementation on serum metabolites and gut microbiota in 42-day-old broilers. Serum metabolomic analysis identified 546 differentially expressed metabolites (DEMs), with GO and KEGG enrichment analyses showing that specific DEMs were enriched in intestinal development-related pathways, including phenylalanine, tyrosine, tryptophan biosynthesis, and alpha-linolenic acid metabolism. 16S rRNA sequencing analysis showed significant intergroup differences in the relative abundances of Ligilactobacillus, Olsenella, Erysipelatoclostridium, and Blautia at the genus level in broiler gut microbiota between the control and WFBG groups. Integrative analysis of 16S rRNA sequencing and non-targeted metabolomics demonstrated that bacterial genera, including Streptococcus and Proteus, were positively correlated with N6,N6-dimethyllysine and quercetin but negatively associated with 18 DEMs, such as 4-methylbenzenesulfonic acid and deoxycholic acid derivatives. Furthermore, we identified potential biomarkers associated with intestinal development induced by 20% WFBG supplementation. Our findings suggest that the maximum recommended inclusion level of WFBG in broiler feed should not exceed 20%. This study provides novel insights into the molecular mechanisms underlying fiber utilization and intestinal maturation in broilers.<br><br>IMPORTANCE: This study investigated the regulatory mechanism of wet-fermented brewer's grain (WFBG) on gut development and microbiota in commercial broilers. Through integrated 16S rRNA sequencing and non-targeted metabolomic analysis, the study not only identified differential gut microbiota, serum metabolites, as well as their correlations, but also discovered potential biomarkers associated with intestinal development induced by 20% WFBG and clarified the maximum recommended inclusion level of WFBG (&#x2264;20%). This not only filled the gap in the molecular mechanism underlying WFBG-mediated regulation of fiber utilization and intestinal maturation in broilers but also provided a theoretical basis and practical guidance for the resource utilization of agricultural by-products, precision feeding of broilers, and intestinal health monitoring.}, }
@article {pmid41358761, year = {2025}, author = {Xu, S and Ding, Y and Li, M and Lin, Y and Wang, X and Liu, N and Zhang, L and Xu, T}, title = {Metagenomic next-generation sequencing diagnoses Talaromyces marneffei infections: case report and review.}, journal = {Journal of infection in developing countries}, volume = {19}, number = {11}, pages = {1727-1736}, doi = {10.3855/jidc.20367}, pmid = {41358761}, issn = {1972-2680}, mesh = {Humans ; *Talaromyces/genetics/isolation &amp; purification ; Male ; *High-Throughput Nucleotide Sequencing/methods ; *Mycoses/diagnosis/drug therapy/microbiology ; *Metagenomics/methods ; Antifungal Agents/therapeutic use ; Amphotericin B/therapeutic use ; Adult ; China ; }, abstract = {INTRODUCTION: Talaromyces marneffei is a pathogenic dimorphic fungus known for causing severe opportunistic infections that can be life-threatening. The fungus is most commonly found in Southeast Asia and southern China.<br><br>CASE REPORT: This case report describes the case of a young male patient infected with T. marneffei who was neither human immunodeficiency virus (HIV)-positive nor possessed anti-IFN-&#x3b3; antibodies, and who resided outside the typical endemic regions. The patient developed cough and sputum three months after the removal of the left arm fracture fixator, and was initially misdiagnosed with tuberculosis; however, the response to anti-tuberculosis treatment was not good. The diagnosis of subsequent recurrence was unknown. The condition recurred during the illness, and he was ultimately diagnosed with talaromycosis via metagenomic next-generation sequencing (mNGS). The patient's condition improved after appropriate treatment with liposomal amphotericin B.<br><br>CONCLUSIONS: Previous studies have found that T. marneffei infections are concentrated in patients with acquired immunodeficiency syndrome due to HIV infection, and in anti-IFN-&#x3b3; antibody-positive patients. However, infections are increasing in individuals who are not immunosuppressed and are often misdiagnosed and underdiagnosed during the initial course of the disease. Therefore, clinicians should be aware that mNGS is an effective technique for detecting T. marneffei infection in non-endemic areas where they encounter non-HIV infected patients. This case report aims to raise the awareness of physicians regarding this rare disease in non-endemic areas and non-HIV patients.}, }
@article {pmid41358744, year = {2025}, author = {Li, Y and Lin, W and Li, Z and Tran, T and Metcalf, BJ and Velusamy, S and Gross, A and Snippes Vagnone, P and Lynfield, R and Beall, B and McGee, L and Chochua, S}, title = {Whole-genome sequencing-based pathogen characterization for streptococcal infection directly from positive blood culture samples.}, journal = {Journal of clinical microbiology}, volume = {}, number = {}, pages = {e0112625}, doi = {10.1128/jcm.01126-25}, pmid = {41358744}, issn = {1098-660X}, abstract = {Clinical laboratories are increasingly using diagnostic tests directly on positive blood cultures, which may lead to fewer attempts to recover bacterial isolates. Consequently, public health laboratories can benefit from assays that directly process blood culture samples without requiring submission of clinical isolates to determine additional pathogen features not identified by clinical tests, such as vaccine serotype and bacterial genomic relatedness, for surveillance and outbreak response purposes. In partnership with the Minnesota Active Bacterial Core surveillance (ABCs) site, we identified blood culture samples positive for ABCs streptococcal pathogens and characterized them by a direct whole-genome sequencing from blood culture (dWGS) assay. The dWGS results were compared with the results of a reference method (WGS of isolates from the same cultures) to evaluate concordance in pathogen features and genome assemblies. Of the 97 eligible blood culture samples, 83 (86%) passed dWGS quality control criteria and were subjected to a total of 655 dWGS-based tests, which yielded 651 (99.3%) evaluable results. The percent agreement with reference results was 100% (83/83) for M protein gene (emm)/capsular types and 100% (81/81) for multilocus sequencing types. For genotypic antimicrobial susceptibility testing prediction, the percent prediction agreement was 100% (487/487), false resistant prediction rate was 0% (0/417), and the false susceptible prediction rate was 0% (0/66). Assemblies of pathogen genomes from the same patient differed by 1.08 ± 1.68 (mean ± SD) sites per genome. The dWGS assay can extract high-quality, important streptococcal strain characteristics directly from positive blood culture samples to support evolving public health needs.IMPORTANCEWhole-genome sequencing (WGS) technologies have emerged as a transformative toolkit used by public health microbiology laboratories to detect and characterize pathogens. The surveillance of bacterial diseases often relies on clinical laboratories to submit pathogen isolates to regional or national public health laboratories, which have the capacity to routinely conduct WGS-based strain characterization. Clinical laboratories are increasingly using diagnostic tests directly on positive blood cultures, which may lead to fewer attempts to recover bacterial isolates. The study evaluated a direct whole-genome sequencing from blood culture (dWGS) assay that directly processes blood culture samples. The dWGS assay recovered high quality, important streptococcal strain characteristics, including vaccine serotypes and whole-genome assemblies, without requiring submission of clinical isolates. Thus, the dWGS assay represents a promising tool for addressing the evolving needs of public health laboratories in the metagenomics era.}, }
@article {pmid41358671, year = {2025}, author = {Ngwese, MM and Adegbite, BR and Zinsou, JF and Fitzstevens, JL and Schmidt, VT and Moure, PAN and Maloum, MN and Tyakht, AV and Huus, KE and Youngblut, ND and Kremsner, PG and Adegnika, AA and Ley, RE}, title = {Infection with gut parasites correlates with gut microbiome diversity across human populations in Africa.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2587966}, doi = {10.1080/19490976.2025.2587966}, pmid = {41358671}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Feces/parasitology/microbiology ; Animals ; Gabon/epidemiology ; Female ; Male ; Child ; *Helminthiasis/parasitology/epidemiology/microbiology ; Metagenomics ; *Helminths/isolation &amp; purification/classification/genetics ; Child, Preschool ; Rural Population ; Bacteria/classification/genetics/isolation &amp; purification ; Metagenome ; Ascaris lumbricoides/isolation &amp; purification ; Strongyloides stercoralis/isolation &amp; purification ; Necator americanus/isolation &amp; purification ; Trichuris/isolation &amp; purification ; Biodiversity ; }, abstract = {Soil-transmitted helminths (STH) are common in (sub)tropical regions and primarily affect impoverished populations. These parasites reside in the gut, where they interact with both the microbiota and host immunity. Clinical STH detection is laborious and often not performed within the context of gut microbiome studies. Here, we present a proof-of-concept study assessing whether fecal metagenome data could be used to assess STH infection, and to relate STH infection to microbiome features. We leveraged 310 gut metagenomes obtained from mother-child pairs in two different locations in Gabon: one rural and one semi-urban, and assessed the presence of four STH species (Ascaris lumbricoides, Strongyloides stercoralis, Trichuris trichiura, and Necator americanus) using qPCR. Sequence data were used to characterize the microbiomes and to detect these parasites. Metagenomic read mapping and genome coverage metrics closely matched qPCR detection patterns. Within-location analyses revealed that parasite species richness was associated with microbiome diversity and taxonomic composition, with the strongest associations observed in children from the rural site. Applying this approach to published data from five additional African cohorts identified context-specific parasite-microbiome associations, as well as a modest but reproducible association between microbiome alpha diversity and parasite infection. These findings highlight the potential of shotgun metagenomics for concurrent parasite detection and microbiome profiling across diverse geographic and demographic contexts.}, }
@article {pmid41358536, year = {2025}, author = {Amornloetwattana, R and Eiamthong, B and Meesawat, P and Bunkum, P and Royer, B and Zeballos, N and Valenzuela-Ortega, M and Robinson, RC and Wallace, S and Uttamapinant, C}, title = {Cellular Upcycling of Polyethylene Terephthalate (PET) With an Engineered Human Saliva Metagenomic PET Hydrolase.}, journal = {ChemSusChem}, volume = {}, number = {}, pages = {e202502560}, doi = {10.1002/cssc.202502560}, pmid = {41358536}, issn = {1864-564X}, support = {B42G670039//National Science Research and Innovation Fund (NSRF) via the Program Management Unit for Human Resources &amp; Institutional Development, Research and Innovation/ ; MR/S033882/1//UK Research and Innovation/ ; BB/Y007972/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {Recent advances in biocatalytic recycling of polyethylene terephthalate (PET) using PET hydrolase enzymes have sparked interest in integrating PET degradation capabilities into living systems. Although cell-based strategies are limited by the mesophilic temperature constraints of microbial hosts, they offer a unique opportunity to couple PET depolymerization with biological upcycling into value-added chemicals. Here, a comprehensive approach for the cellular degradation and valorization of PET is reported. The crystal structure of MG8, a PET hydrolase identified from the human saliva metagenome is solved, and molecular dynamics simulations are used to pinpoint loop regions for targeted mutagenesis aimed at enhancing activity under moderate temperatures. Over 1000 MG8 loop variants are evaluated with a high-throughput mass spectrometric screening platform. Two catalytically improved mutants-MG8[G127Y/F250A] and MG8[N125S/G127Y/F250A]-exhibit significantly enhanced PET hydrolysis at 37°C. To enable whole-cell PET valorization, a two-strain Escherichia coli system called PETCAT is constructed: one strain is engineered to secrete MG8[G127Y/F250A] for PET degradation, and the other harbors a synthetic pathway comprising seven heterologous genes for the conversion of terephthalic acid (TPA) into catechol, a versatile intermediate used in pharmaceuticals and fragrances. This study establishes a modular, one-pot microbial platform for PET recycling and upcycling under physiologically relevant conditions.}, }
@article {pmid41358162, year = {2025}, author = {Nicolas-Asselineau, L and Speth, DR and Zeller, LM and Woodcroft, BJ and Singleton, CM and Liu, L and Dueholm, MKD and Milucka, J}, title = {Occurrence and temporal dynamics of denitrifying protist endosymbionts in the wastewater microbiome.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf209}, pmid = {41358162}, issn = {2730-6151}, abstract = {Effective wastewater treatment is of critical importance for preserving public health and protecting natural environments. Key processes in wastewater treatment, such as denitrification, are performed by a diverse community of prokaryotic and eukaryotic microbes. However, the diversity of the microbiome and the potential role of the different microbial taxa in some wastewater treatment plant setups is not fully understood. We aimed to investigate the presence and diversity of denitrifying bacteria of the candidate family Azoamicaceae that form obligate symbioses with protists in wastewater treatment plants. Our analyses showed that denitrifying endosymbionts belonging to the Ca. Azoamicus genus are present in 20%-50% of wastewater treatment plants worldwide. Time-resolved amplicon data from four Danish WWTPs showed high temporal fluctuations in the abundance and composition of the denitrifying endosymbiont community. Twelve high-quality metagenome-assembled genomes of denitrifying endosymbionts, four of which were circular, were recovered. Genome annotation showed that a newly described, globally widespread species, Ca. Azoamicus parvus, lacked a nitrous oxide reductase, suggesting that its denitrification pathway is incomplete. This observation further expands the diversity of metabolic potentials found in denitrifying endosymbionts and indicates a possible involvement of microbial eukaryote holobionts in wastewater ecosystem dynamics of nitrogen removal and greenhouse gas production.}, }
@article {pmid41357797, year = {2025}, author = {Yang, C and Li, M and Yang, S and Pan, J and Ding, Y and Yang, J}, title = {Channel selection of metagenomic next-generation sequencing in infants pathogen detection: a multicenter cross-sectional study.}, journal = {Frontiers in pediatrics}, volume = {13}, number = {}, pages = {1632123}, pmid = {41357797}, issn = {2296-2360}, abstract = {In the neonatal period, infectious diseases associated with high morbidity (e.g., neonatal sepsis and meningitis) are preliminarily assessed using indicators like C-reactive protein (CRP) and procalcitonin, but definitive diagnosis relies on pathogen detection through methods such as blood culture, which is time-consuming and has low sensitivity. To improve diagnostic efficiency, metagenomic next-generation sequencing (mNGS) is increasingly utilized, offering three testing modalities: DNA-only, RNA-only, and combined DNA+RNA channels. This retrospective study analyzed 894 clinical samples (peripheral blood, sputum, bronchoalveolar lavage fluid) to compare detection rates across channels. The overall mNGS positivity rate was 51.9% (464/894), with no significant differences among DNA-only (50.8%), RNA-only (55.7%), and combined channels (49.6%) (p > 0.05). Notably, bronchoalveolar lavage fluid samples exhibited the highest positivity rate (84.57%, 148/175), reaching 97.33% (73/75) with dual-channel testing. Sputum samples showed a 53.7% positivity rate (87/172), increasing to 82.35% (14/17) with dual-channel detection. Conversely, peripheral blood had an overall positivity rate of 43.14% (132/306), with the DNA-only channel outperforming RNA-only and dual channels (45.34% 5s. 43.00% and 34.21%). These findings underscore the importance of channel selection based on sample type to optimize diagnostic accuracy and cost-effectiveness.}, }
@article {pmid41357776, year = {2025}, author = {Yoshino, N and Matsumoto, K and Ishikawa, M and Nishio, J and Matsuzawa, T}, title = {Identity of Carbohydrate-Responsive Genes in a Cultured Microbial Community Using Metagenomic and Metatranscriptomic Approaches.}, journal = {Journal of applied glycoscience}, volume = {72}, number = {4}, pages = {7204201}, pmid = {41357776}, issn = {1880-7291}, abstract = {Metagenomics can be used to obtain sequence information on putative genes in a microbial community. However, it is difficult to identify genes with specific functions among the numerous predicted genes. In this study, we attempted to identify genes induced in cultured microbes by the addition of saccharides using metagenomic and metatranscriptomic analyses. A mixture of arabinoxylan and its derived oligosaccharides was used as the inducer in this study. Some genes were highly induced in the presence of additive saccharides and formed gene clusters for the utilization of additive saccharides, suggesting that metatranscriptomic and metagenomic analyses are useful for analyzing carbohydrate-responsive genes in microbial communities and screening novel carbohydrate-active enzymes.}, }
@article {pmid41357502, year = {2025}, author = {He, Y and Liang, L and Wei, S}, title = {Giant intracranial Brucella abscess after head trauma: a Case Report of neurobrucellosis in an urban elderly male without exposure history.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1676548}, pmid = {41357502}, issn = {2296-858X}, abstract = {Giant intracranial Brucella abscess is a severe and rare central nervous system infection whose pathogenesis remains incompletely understood. We detail the case of a 75-years-old urban male without Brucella exposure history who presented with fever and headache. Initial attribution of cephalgia to head trauma delayed diagnosis and treatment. Magnetic resonance imaging, metagenomic next-generation sequencing, and cerebrospinal fluid culture confirmed rapid development of a giant Brucella abscess (31 mm × 58 mm) within 2 weeks after head trauma. Head trauma may be potentially associated with the formation of Brucella brain abscess. Consequently, brucellosis patients with recent head trauma may warrant vigilant monitoring for this rare complication. It is imperative to avoid the premature attribution of headache to head trauma in such patients, as such an oversight risks delaying the diagnosis and management of a Brucella brain abscess.}, }
@article {pmid41357037, year = {2025}, author = {Syromyatnikov, MY and Burakova, IY and Smirnova, YD and Morozova, PD and Pogorelova, SV and Chirkin, EA and Tolkacheva, AA}, title = {Study of Akkermansia muciniphila Effect on the Gut Microbiome of Mice Under LPS-Induced Systemic Inflammation.}, journal = {International journal of inflammation}, volume = {2025}, number = {}, pages = {8695182}, pmid = {41357037}, issn = {2090-8040}, abstract = {Probiotics are strains of living bacteria and yeast that play an important role in regulating the gut microbiota and enhancing host immunity. In the last decade, the bacterial species Akkermansia muciniphila has attracted great interest due to its possible probiotic properties, which play an important role in human health. However, the mechanisms of action of A. muciniphila are still poorly understood. The effect of the A. muciniphila on the intestinal microbiome of model animals with systemic inflammation induced by lipopolysaccharide (LPS) is unexplored. This study aims to investigate the impact of A. muciniphila on the microbiological composition of the mouse gut under LPS-induced systemic inflammation using high-throughput sequencing. The study used a new generation sequencing method aimed at genome-wide sequencing of microorganisms, which makes it possible to study changes in the composition of the microbiome at the bacterial species level, as well as to identify the genes of the metabolic pathways of intestinal bacteria in the studied mice. Our analysis revealed statistically significant differences across all studied groups, with a notable predominance of members from the families Muribaculaceae, Rikenellaceae, and Oscillospiraceae. Consumption of A. muciniphila increased the alpha diversity of gut bacteria (Shannon index) in the context of induced inflammation. Evaluation of the effect of LPS and A. muciniphila on metabolic pathways showed statistically significant differences for the pathways of synthesis and degradation of amino acids, transforming folic acid, and synthesis of sugars. Genetic analysis showed that the probiotic bacterium A. muciniphila reduced the degree of negative effects of LPS on the mouse gut microbiome under systemic inflammation.}, }
@article {pmid41356787, year = {2025}, author = {Chatterjee, T and Roy, M and Almoujahed, MO and Ahmad, S}, title = {Aspergillus calidoustus: An Emerging Cause of Invasive Aspergillosis and the Role of Metagenomic Next-Generation Sequencing Test in Its Diagnosis.}, journal = {Case reports in infectious diseases}, volume = {2025}, number = {}, pages = {3221057}, pmid = {41356787}, issn = {2090-6625}, abstract = {Transplant recipients have a high risk of infection with opportunistic pathogens. The type, dose, and duration of immunosuppression and use of prior broad-spectrum antimicrobials contribute to overall risk of infections. Aspergillosis is a known opportunistic infection that can occur as mid or late infection after visceral transplant. Aspergillus fumigatus is the commonly isolated species, but with the use of prophylactic broad-spectrum antifungals, other species such as Aspergillus calidoustus are emerging. We report a case of invasive sinusitis and brain mass due to this species of Aspergillus that was identified using next-generation sequencing (NGS). Use of NGS early in clinical presentation may help in effective management of opportunistic infections in immunocompromised hosts.}, }
@article {pmid41356481, year = {2025}, author = {Rao, AV and Ghare, SS and Gautam, V and Hoffman, KL and Petrosino, J and So-Armah, K and Samet, JH and Patts, GJ and Cheng, DM and Blokhina, E and Krupitsky, EM and Lioznov, D and Zvartau, E and McClain, CJ and Tindle, H and Freiberg, MS and Barve, SS}, title = {Sex differences in beneficial and pathogenic bacteria in People With HIV (PWH) with a history of heavy alcohol drinking.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1632949}, pmid = {41356481}, issn = {1664-302X}, abstract = {BACKGROUND: HIV-1 infection and hazardous levels of alcohol consumption have been independently linked to gut dysbiosis affecting beneficial butyrate-producing bacteria. However, sex-based differences in the composition and function of gut microbiome of People With HIV (PWH) with a history of heavy alcohol drinking remain undetermined, which is the focus of this study.<br><br>METHODS: Cross-sectional study examining structural and functional features of the gut microbiome in PWH between men and women with a history of hazardous alcohol drinking recruited at St. Petersburg, Russia. 16S rDNA sequencing information was used for metataxonomic, Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) and Linear Discriminant Analysis Effect Size (LEfSe) analyses. Group-wise comparisons were done using Mann-Whitney U-test. Further, linear and logistic regression models were used to evaluate the association between sex and measures of gut microbial dysbiosis and Firmicutes/Bacteroidota (F/B) ratio, respectively. Data were adjusted for confounding covariates particularly, HIV-viral load, Anti-retroviral Therapy (ART) and alcohol usage.<br><br>RESULTS: Metataxonomic analysis demonstrated that women depicted significantly higher microbial diversity (Operational Taxonomic Units, OTUs and Shannon Index), higher percent relative abundance (%RA) of Firmicutes, lower %RA of Bacteroidota and higher F/B ratio. Importantly, logistic regression revealed that women had twice the odds of having F/B ratio > 1. Notably, women demonstrated significantly higher %RA of butyrate-producing bacterial families, i.e., Lachnospiraceae, Oscillospiraceae, Rikenellaceae and Marinifilaceae and genera. Correspondingly, significantly greater expression of bacterial genes involved in butyrate synthesis in women was demonstrated by PICRUSt2 analysis. Additionally, women depicted lower %RA of pathobiont, Prevotellaceae particularly, Prevotella_9 genus.<br><br>CONCLUSION: Overall, we observed significant sex-based differences in the relative abundances of beneficial bacterial communities such as butyrate producers and potential pathogenic Prevotella community in the gut microbiome of PWH with a history of heavy alcohol consumption. The observed sex-based differences are clinically relevant and could inform therapeutic strategies with evidence-based probiotics.}, }
@article {pmid41356476, year = {2025}, author = {Chen, Q and Guan, J and Yang, L and Lv, J and Gui, G and Xu, J and Yang, Z and Wang, X and Sun, B}, title = {Exploring the characteristics of gut microbiota in the development and progression of early-stage colorectal cancer based on metagenomic sequencing.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1658160}, pmid = {41356476}, issn = {1664-302X}, abstract = {INTRODUCTION: Colorectal cancer (CRC), a leading cause of cancer-related morbidity and mortality worldwide, often presents asymptomatically, resulting in late diagnosis. Accumulating evidence links gut microbiota dysbiosis to CRC initiation and progression.<br><br>OBJECTIVE: This study aimed to investigate the differences in gut microbiota composition and diversity among healthy controls (HC) and patients with colorectal lesions-including common colorectal polyps, small colorectal adenomas (SCRA), large colorectal adenomas (LCRA), and intramucosal carcinoma (IMC)-to identify bacterial species associated with disease progression and provide novel insights into the diagnosis and treatment of CRC based on the "polyp-adenoma-carcinoma" sequence.<br><br>METHODS: A total of 250 participants were recruited from the First Affiliated Hospital of Anhui Medical University between July 2023 and June 2024. The cohort included 30 HC, 52 with common colorectal polyps, 58 with SCRA, 56 with LCRA, and 54 with IMC. Fecal samples were collected for bacterial DNA extraction, followed by metagenomic sequencing to analyze microbial diversity. Differential microbiota analysis was performed using the R package microbiomeMarker and LEfSe. Group classification and feature identification were conducted using a random forest model. Functional profiling was performed using DIAMOND against the KEGG and MetaCyc databases.<br><br>RESULTS: No significant differences in &#x3b1;-diversity were observed across the groups. &#x3b2;-diversity analysis revealed significant differences in Bray-Curtis and Jaccard distances among the groups. The composition and abundance of gut microbiota at the phylum, class, order, family, genus, and species levels were significantly altered. LEfSe analysis identified specific bacterial species with significant differences in IMC compared to other groups. Furthermore, the random forest model effectively distinguished patients with IMC from other groups based on distinct microbial signatures. Functional profiling revealed that the gut microbiota undergoes metabolic reprogramming from a homeostatic to a pro-tumorigenic phenotype during CRC progression as well as reduced protective pathway abundance and impaired energy/biosynthetic metabolism in CRC-associated microbiota.<br><br>CONCLUSION: Gut microbiota profiles varied significantly among HC, polyp, SCRA, LCRA, and IMC groups. Specific microbial signatures were able to effectively differentiate IMC from both HC and non-malignant colorectal lesions, highlighting their potential as diagnostic biomarkers.}, }
@article {pmid41356466, year = {2025}, author = {Han, X and Sun, QG and Zang, D and Chen, J}, title = {Comprehensive fecal metagenomic and metabolomic analysis reveals the role of gut microbiota and metabolites in detecting brain metastasis of small cell lung cancer.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1673983}, pmid = {41356466}, issn = {1664-302X}, abstract = {BACKGROUND: Brain metastasis (BM) is a common and highly lethal complication in patients with small cell lung cancer (SCLC). People have paid great attention to exploring the relationship between gut microbiota and the occurrence and development of cancer. This study investigated the relationship between brain metastasis, gut microbiota, and their metabolites in SCLC, providing new insights for the prevention and diagnosis of brain metastasis in SCLC.<br><br>METHODS: Baseline fecal samples were collected from 45 participants, including 15 patients with BM and 30 patients with no distant metastasis who were newly diagnosed with SCLC. The gut microbiota and metabolite levels were analyzed using metagenomics and untargeted metabolomics, and machine learning models were utilized to identify differences and potential biomarkers.<br><br>RESULTS: Gut microbiota composition varied significantly between the two groups. Genus such as Alistipes and Streptococcus were more abundant in the brain metastasis group, while Bacteroides and Prevotella predominated in patients without distant spread. Metabolomic profiling identified several metabolites inversely associated with brain metastasis, including leukotriene F4, benzoic acid, velnacrine, piperidine, and an unidentified compound labeled C20916. KEGG pathway analysis linked multiple key physiological processes, such as aminobenzoate degradation, carbapenem biosynthesis, toluene degradation, dioxin degradation, and benzoate degradation, underscoring the complex role of gut microbial metabolites in cancer progression. Furthermore, machine learning models identified key biomarkers, including the genus Marvinbryantia and the metabolites benzoic acid, which showed strong discriminatory ability for brain metastasis. After robust validation, the model demonstrated good performance with excellent discriminative power (AUC&#x202f;=&#x202f;0.80).<br><br>CONCLUSION: Compared to patients without distant metastasis, SCLC patients with BM exhibit distinctive gut microbial and metabolite profiles. These findings suggest that specific gut microbes and their metabolic products may serve as valuable biomarkers for diagnosing and stratifying treatment in brain metastatic SCLC.}, }
@article {pmid41355980, year = {2025}, author = {Wu, X and Wang, W and Xu, L and Zhou, W and Zhou, J and Zhou, H}, title = {Value of plasma metagenomic next-generation sequencing for the diagnosis of invasive aspergillosis: a multicenter-center retrospective study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1656233}, pmid = {41355980}, issn = {2235-2988}, mesh = {Humans ; Retrospective Studies ; Male ; Female ; *High-Throughput Nucleotide Sequencing/methods ; Middle Aged ; Aged ; *Metagenomics/methods ; *Aspergillus/genetics/isolation &amp; purification/classification ; Adult ; Risk Factors ; Aged, 80 and over ; Young Adult ; China ; *Aspergillosis/diagnosis/microbiology ; *Plasma/microbiology ; }, abstract = {INTRODUCTION: Invasive aspergillosis (IA) is a severe fungal infection. Metagenomic Next Generation Sequencing (mNGS) is abroad and highly sensitive pathogen detection method that can accurately differentiate fungi to the species, and even subspecies level.<br><br>METHODS: To explore the value of plasma mNGSs in the diagnosis of invasive aspergillosis, a retrospective analysis was conducted on the clinical data of 334 patients with findings of Aspergillus spp. From mNGS from plasma at 4 hospitals, Zhejiang, from February 2021 to December 2022. The study analyzed risk factors, clinical manifestations, imaging features, microbiological results, and treatment outcomes of patients with Aspergillus infection.<br><br>RESULTS AND DISCUSSION: According to the diagnostic criteria for IA, among the 334 patients, there were 4 confirmed cases, 62 probable cases, 134 possible cases, and 134 false-positive cases. All 196 probable and possible cases exhibited risk factors, clinical manifestations, imaging features, and treatment outcomes consistent with Aspergillus infection. In 18 out of the 62 probable cases, the same Aspergillus nucleic acid was found in 2-4 peripheral blood mNGS samples collected at intervals of 17 days. The remaining 134 patients had detectable Aspergillus in plasma mNGS but lacked high-risk factors and clinical characteristics of Aspergillus infection, and there was a lack of other microbiological evidence, determined as false positives. Among the cases included in this study, the positive predictive value of plasma mNGS for diagnosing invasive aspergillosis was 59.9%. Plasma mNGS detection has significant reference value for diagnosing IA. However, comprehensive judgment should still be made in conjunction with clinical features.}, }
@article {pmid41355608, year = {2026}, author = {Chong, SY and Ilham, Z and Wan-Mohtar, WAAQI and Cheng, A}, title = {The Road to Sustainable Soy Sauce Production and Consumption.}, journal = {Comprehensive reviews in food science and food safety}, volume = {25}, number = {1}, pages = {e70352}, doi = {10.1111/1541-4337.70352}, pmid = {41355608}, issn = {1541-4337}, support = {//Universiti Malaya/ ; }, mesh = {Fermentation ; *Soy Foods/microbiology/analysis ; Food Microbiology ; Humans ; }, abstract = {Soy sauce (SS), a fermented condiment integral to various global cuisines, has undergone considerable technological advancements while preserving its traditional microbiological processes. This systematic review, adhering to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, synthesized findings from 181 peer-reviewed articles to examine trends in SS production and consumption. Our descriptive statistics and thematic analysis revealed five key focus areas: process optimization, microbial fermentation, safety, waste management, and evolving analytical technologies. Advances, such as metagenomics, synthetic biology, and enzyme engineering, have refined fermentation dynamics, improving flavor and production efficiency. Concurrently, sustainability-orientated innovations, including by-product bioconversion, low-sodium formulations, and traceable packaging, support both environmental goals and health-conscious consumption. The integration of multi-omics approaches (e.g., metabolomics, genomics, and transcriptomics) and high-resolution analytical tools (e.g., spectroscopy and sensor-based systems) has further strengthened quality control by enhancing authenticity, safety, and traceability. However, integrating traditional methods with emerging technologies such as precision fermentation, which facilitates targeted microbial control to improve product consistency, remains challenging due to microbial strain incompatibility, scalability issues, and the necessity to maintain cultural authenticity and sensory attributes. It is essential to implement scalable and sustainable solutions that improve microbial function while minimizing hazardous by-products and environmental effects. This review presents an integrated framework connecting five key thematic areas with the core pillars of sustainability: environment, economy, society, technology, and nutrition, offering a foundation for directing future research, policymaking, and industrial practices. Key priorities include the development of salt-tolerant microbial consortia, the valorization of fermentation by-products via circular economy strategies, and the standardization of sustainability certification criteria to facilitate practical implementation.}, }
@article {pmid41355553, year = {2025}, author = {Kim, MJ and Park, JH and Eom, YB}, title = {The Transmissibility of the Human Skin Virome: Potential Forensic Implications.}, journal = {MicrobiologyOpen}, volume = {14}, number = {6}, pages = {e70197}, doi = {10.1002/mbo3.70197}, pmid = {41355553}, issn = {2045-8827}, support = {//Soonchunhyang University (SCH-20130328), Ministry of Science and ICT, South Korea, RS-2023-NR076438 (NRF-2023R1A2C1003486)/ ; //Ministry of Science and ICT, South Korea, RS-2023-NR076438 (NRF-2023R1A2C1003486)/ ; }, mesh = {Humans ; *Virome ; *Skin/virology ; Adult ; *Viruses/classification/genetics/isolation &amp; purification ; Male ; Female ; Young Adult ; Republic of Korea ; Metagenome ; }, abstract = {The objective of this study was to evaluate the temporal stability and object-to-skin transferability of the skin virome in a Korean population. Skin virus metagenomes were collected from the anatomical locations (forehead, left hand, and right hand) of eight healthy adults and monitored over 3 months at intervals of 6 weeks. To assess the potential transfer of virome between skin and objects, subjects were instructed to contact four types of objects (cell phones, door handles, fabric, and plastic). Virome samples were then collected from the surfaces of these objects. Viruses were identified using databases and viral annotation bioinformatics tools. Fifteen viral families were consistently found to be stable and well-transmissible across anatomical locations and four types of objects. Furthermore, the presence/absence profiles of 54 viral species belonging to these 15 viral families exhibited significant individual specificity on both the skin (p < 0.01) and the objects handled by each subject (p < 0.05). We confirmed that these 54 viral markers remain stable over time within individuals and are transferable to contacted surfaces. Additionally, we explored the potential of using the virome as an individual identification marker, which may suggest new approaches for forensic applications.}, }
@article {pmid41355481, year = {2025}, author = {Becerra, D and Rodríguez-Caballero, G and Marhuenda-Egea, FC and Olaya-Abril, A and Moreno-Vivián, C and Sáez, LP and Luque-Almagro, VM and Roldán, MD}, title = {Microbial Diversity of the Surface of Polypropylene and Low Density Polyethylene-Based Materials (Plastisphere) From an Area Subjected to Intensive Agriculture.}, journal = {MicrobiologyOpen}, volume = {14}, number = {6}, pages = {e70121}, doi = {10.1002/mbo3.70121}, pmid = {41355481}, issn = {2045-8827}, support = {//This study was supported by Ministerio de Ciencia e Innovaci&#xf3;n, Spain (grant PID2021-124174OB-I00)./ ; }, mesh = {*Polypropylenes/metabolism ; *Polyethylene/metabolism ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Soil Microbiology ; RNA, Ribosomal, 16S/genetics ; Agriculture ; *Biodiversity ; Biodegradation, Environmental ; Phylogeny ; }, abstract = {Accumulation of synthetic plastics in the biosphere has led to global pollution, provoking serious consequences for the environment and human health. Uncontrolled agricultural plastic landfills have the risk of becoming a source of agrochemicals and microplastics. Biotechnological approaches to solve plastic pollution include the removal of these polymers through biological degradation, which is a friendly environmental method. The microbial communities colonizing plastic debris (plastisphere) are considered as a potential source of plastic-degrading microorganisms. In this study, a bacterial biodiversity analysis, based on 16S rRNA gene-targeted metagenomic sequencing, was achieved in the plastisphere of low-density polyethylene (LDPE) and polypropylene (PP) polymers from an agricultural landfill. The α-diversity analysis did not show significant differences between LDPE and PP plastispheres and the plastic-free bulk soil, while LDPE and PP bacterial communities clustered close, but separately from the bulk soil in a β-diversity analysis. Although the taxonomic composition of both plastispheres was different, they shared a significantly higher proportion of Cyanobacteria and Deinococcota than the bulk soil. Additional analyses showed different indicator families, genera and species that can be associated with plastispheres. A predictive functional analysis suggests that degradation of plastic additives in both plastispheres is probably occurring. In addition, the existence of degradation processes for specific herbicides in each plastisphere is highlighted, and the possible exposure of LDPE to both physical and biological degradation processes is also described. These results will contribute to characterize the soil plastisphere exposed to different environmental conditions, and to understand the specific biological niches where plastic-degrading microorganisms could survive.}, }
@article {pmid41354995, year = {2025}, author = {Li, J and Jiang, E and Zhang, M and Pan, C and Lei, C and Han, L and Lan, X}, title = {Phloretin inhibits ferroptosis by restoring the antioxidant capacity of bovine adipose and muscle cells via the AMPK-PPAR signaling pathway.}, journal = {Stress biology}, volume = {5}, number = {1}, pages = {74}, pmid = {41354995}, issn = {2731-0450}, support = {No.32372852//National Natural Science Foundation of China/ ; No.32402726//National Natural Science Foundation of China/ ; Innovative Exploration Category//Natural Science Basic Research Program of Shaanxi Province, Key Project on Frontier Exploration/ ; No.2025JC-QYCX-027//Natural Science Basic Research Program of Shaanxi Province, Key Project on Frontier Exploration/ ; No. 2024JC-JCQN-30//Science Fund for Distinguished Young Scholars of Shaanxi Province/ ; No.2023SR205//Shaanxi Provincal Innovation Leadership Program in Sciences and Technologies for Young and Middle-aged Scientists/ ; }, abstract = {Ferroptosis has been increasingly implicated in adipose and muscle dysfunction, systemic metabolic disturbances, and several diseases in livestock, which necessitates effective and side-effect-free inhibition strategies. Phloretin, a dihydrochalcone with excellent antioxidant and anti-inflammatory properties, may have the potential to restrain cell ferroptosis. Herein, phloretin was verified to significantly inhibit (1S,3R)-RSL3-induced ferroptosis by reducing intracellular MDA, Fe[2][+], and ROS levels and restoring cell total antioxidant capacity in bovine and mouse preadipocytes or myoblasts. It also alleviated oxidative stress (OS), a vital inducer of ferroptosis, by restoring antioxidant enzyme activity in the above cells and obese mice. In vivo, phloretin gavage significantly reversed the trend where high-fat diet (HFD)-induced OS promoted the expression of ferroptosis-promoting genes and proteins (e.g., ACSL4 and PTGS2) while inhibiting the expression of ferroptosis-negative regulators (e.g., Fth1 and Gpx4). Unlike most flavonoids that exert anti-inflammatory or antioxidant activities by altering the gut microbiota composition, metagenomic sequencing analysis of cecal contents from phloretin-gavaged and HFD mice revealed that phloretin exerts its antioxidative and ferroptosis-inhibitory effects independent of modulating gut microbiota diversity. Further transcriptomic analyses of mouse adipose tissues revealed that phloretin alleviated ferroptosis in adipocytes by modulating the transcription of genes enriched in AMPK and PPAR signaling pathways, such as Camkk2. Hence, based on multi-omics analysis combined with in vivo and in vitro verification, phloretin effectively alleviated the OS to further inhibit ferroptosis of adipose or muscle cells through the AMPK-PPAR pathway, which can provide new research ideas for ameliorating adipose or myocyte dysfunction induced by ferroptosis in animals.}, }
@article {pmid41354993, year = {2025}, author = {Zhang, W and Zhang, M and Xie, J and Huang, H and Schmitz-Esser, S and Li, W and Liu, H and Li, D}, title = {Dynamics of the gut microbiome and resistome in response to prophylactic antibiotic treatment in post-surgical giant pandas.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-025-25645-6}, pmid = {41354993}, issn = {2045-2322}, support = {2023NSFSC0011//Natural Science Foundation of Sichuan Province/ ; 2023NSFSC0011//Natural Science Foundation of Sichuan Province/ ; QD2023A46//Mianyang Teachers' College/ ; QD2023A46//Mianyang Teachers' College/ ; 2022 CPB-B09//the grants from the independent project of Chengdu Research Base of Giant Panda Breeding/ ; }, abstract = {For giant pandas, the ecological impact of prophylactic postoperative antibiotics on their gut microbial communities and resistome is not well characterized. Here, we assessed the impact of intravenous cefotaxime administration by analyzing longitudinal fecal samples from five giant pandas via 16 S rRNA sequencing (n = 304 samples) and shotgun metagenomics (n = 22 samples). 16 S-based analysis revealed that antibiotic exposure significantly altered bacterial community structure, resulting in a pronounced increase in the abundance of Pseudomonadota (from 50% ± 24% to 60% ± 38%; P < 0.001) and a reduction in Shannon diversity (from 2.8 ± 0.4 to 2.4 ± 1.3; P < 0.05). In contrast, metagenomic analysis indicated that cefotaxime exposure did not significantly increase the overall diversity of antimicrobial resistance genes (ARGs) or virulence factor genes (VFGs). However, we observed a marked expansion in the diversity of the CTX-M β-lactamase family (blaCTX-M), which persisted into the recovery phase. We also recovered 10 metagenome-assembled genomes (MAGs) harboring both ARGs and VFGs, identifying them as potential antibiotic-resistant pathogens (ARPs). Their abundance, however, remained unchanged throughout treatment. These findings provide new insights into the effects of short-term antibiotic exposure in giant pandas, highlighting its transient effect on microbial community structure and a limited effect on resistome diversity.}, }
@article {pmid41354859, year = {2025}, author = {Robas-Mora, M and Fernández-Pastrana, VM and González-Reguero, D and Probanza, A and Jiménez-Gómez, PA}, title = {Effect of PGPB-enriched organic fertilizer ORGAON[®]PK on the rhizospheric microbiota and biomass of Lupinus albus (L.): a sustainable alternative to chemical fertilizer.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-025-00827-x}, pmid = {41354859}, issn = {2524-6372}, support = {TED2021-132285A-I00//European Union NextGenerationEU/PRTR/ ; TED2021-132285A-I00//European Union NextGenerationEU/PRTR/ ; TED2021-132285A-I00//European Union NextGenerationEU/PRTR/ ; TED2021-132285A-I00//European Union NextGenerationEU/PRTR/ ; TED2021-132285A-I00//European Union NextGenerationEU/PRTR/ ; }, abstract = {The intensive use of agrochemicals is essential to maintain crop yields, but it has led to overexploitation of land and environmental deterioration. To promote more sustainable agriculture, this study evaluates the novel effects of biofertilizers enriched with plant growth promoting bacteria, such as Bacillus pretiosus and Pseudomonas agronomica, on Lupinus albus var. Orden Dorado, to improve the rhizospheric soil health and plant biomass as well as reducing dependence on chemical fertilizers. The organic matrix ORGAON[®]PK and its sterilized version, both derived from horticultural waste, were tested compared with a traditional chemical fertilizer and a water control. After three months of treatment, metagenomic analyses (16 S rRNA gene amplicons) indicated that the strains remained in the rhizosphere, increasing metabolic diversity without altering the microbial structure (Shannon index). In addition, a significant reduction in the minimum inhibitory concentration against clinical antibiotics (p < 0.05) was observed, highlighting the potential of biofertilizers to decrease microbial resistance in the soil. Principal component analysis showed clear differences between treated and control groups, and ANCOM-BC revealed changes in non-culturable bacteria. Biometric analyses revealed increases of 70-88% in shoot weight, ~ 80% in total biomass, and up to 36% in shoot elongation compared with the control. Biofertilizers improved nutritional quality and plant biomass, suggesting their potential as a sustainable and efficient alternative to the use of chemical fertilizers.}, }
@article {pmid41354765, year = {2025}, author = {Su, H and Han, P and Yan, H and Wu, C and Zeng, S and Zhang, P and Wang, Z and Dong, J and Liang, M and Jing, H and Zhang, D and Yang, C and Xie, N and Liu, X and Weng, S and Dong, G and He, J}, title = {Age-dependent patterns of the gut microbiome, antibiotic resistome, and pathogenicity in captive koalas (Phascolarctos cinereus).}, journal = {Communications biology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s42003-025-09302-2}, pmid = {41354765}, issn = {2399-3642}, abstract = {Gut microbiome has a profound influence on koalas' health. Yet, the relationships among the gut bacteriome, virome, antibiotic resistome, and pathogenicity throughout different stages in koala's life remain elusive. Here, we presented a metagenome-resolved survey of gut microbiome utilizing 75 fecal samples from three groups of captive koalas. The diversity of bacteriome and virome were age-dependent, predominating in adult koalas. Lytic viruses increased with age as lysogenic viruses and bacterial hosts declined, and virus-to-microbe ratios rose, revealing concomitant age-related shifts in microbial communities, though causality remains unresolved. Antibiotic resistance genes (ARGs) were more prevalent in young koalas, unlike in humans, where they accumulate with age. Two ARG-carrying pathogens, Klebsiella pneumoniae and Escherichia coli, were identified and cultured, with K. pneumoniae and E. coli predominating in young koalas. One age-dependent lytic virus infecting K. pneumoniae only detected in young koalas, and two lysogenic viruses infecting E. coli identified the in young and adult koalas. Analyses showed a positive correlation between mobile genetic elements (MGEs) and virulence factors (VFs), which facilitated the widespread dissemination of VFs and impacted health. Collectively, this study advances the understanding of gut microbiome in health, providing solutions to the treatment and management of captive koalas.}, }
@article {pmid41354674, year = {2025}, author = {Yang, S and Deng, W and Yang, T and Liu, C and Li, C and Li, G and Wei, R and Li, D and Huang, Y and Zhao, K and Zou, L}, title = {Enriched Streptococcus alactolyticus in non-cub giant panda gut contributes to the regulation of tryptophan and its neuromodulatory derivatives.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-025-00879-4}, pmid = {41354674}, issn = {2055-5008}, support = {031-2222996053//the Scientific Research Foundation from Sichuan Agricultural University/ ; The Giant Panda Microbiome Research and Biobank Establishment//the International Cooperation Funding Project for Giant Pandas/ ; }, abstract = {Despite feeding on a high-lignocellulose bamboo diet, the giant panda (Ailuropoda melanoleuca) retains a typical gut microbiome of Carnivora. We conducted shotgun metagenomic sequencing and functional validation of the giant panda's gut microbiome to elucidate its physiological roles and explore its functional adaptation to the species' specialized diet. Our results revealed that Streptococcus alactolyticus significantly increased in the guts of subadult, adult, and elderly individuals versus that in cubs. The gut microbiome of these non-cub giant pandas was significantly enriched in pathways and modules associated with tryptophan biosynthesis. Whole-genome sequencing and in vitro fermentation of S. alactolyticus demonstrated its ability to biosynthesize tryptophan. Gavage of S. alactolyticus in mice led to the enrichment of aromatic amino acid metabolism pathways in gut microbiome, accompanied by significantly elevated levels of 5-hydroxyindole acetic acid and kynurenine in fecal and/or serum samples (p < 0.05). Transcriptome sequencing of colons from mice revealed that most significant upregulated Gene Ontology (GO) terms mainly were related to spindle checkpoint signaling and chromosome segregation, while most significant downregulated GO terms mainly involved synaptic functional regulation. These findings suggest that S. alactolyticus enriched in the non-cub giant panda gut can regulate tryptophan, influencing host gut physiology via tryptophan metabolites.}, }
@article {pmid41354462, year = {2025}, author = {Wang, X and Liu, Y and Sun, Z and Li, J and Lu, Z and Huang, J and Hu, S and Cao, P and Cao, X and Li, S and Ruan, J and Liu, J and Xie, J and Sun, H and Chen, T and Li, S and Zhu, Z and Wen, Z and Tuan, RS and Hunter, DJ and Li, ZA and Shi, D and Ding, C}, title = {Multi-Omics Reveal the Dysregulated Gut-Joint Axis in Knee Synovitis: Data from Two Osteoarthritis Studies in China.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e12020}, doi = {10.1002/advs.202512020}, pmid = {41354462}, issn = {2198-3844}, support = {2023YFE0209700//National Key Research and Development Program of China/ ; GZC20231059//Postdoctoral Fellowship Program of CPSF/ ; 2024M761326//China Postdoctoral Science Foundation/ ; 2023A1515110748//Guangdong Basic and Applied Basic Research Foundation/ ; 2024A1515011794//Guangdong Basic and Applied Basic Research Foundation/ ; 82373653//National Science Foundation of China/ ; 82572825//National Science Foundation of China/ ; 2024A04J5169//Science and Technology Projects in Guangzhou/ ; A2401031//Shenzhen Medical Research Funds/ ; 1194737//Arthritis Australia and an NHMRC Investigator Grant Leadership 2/ ; 82325035//National Natural Science Foundation of China for Distinguished Young Scholars/ ; 82530083//Key Project of the National Science Foundation of China/ ; }, abstract = {Gut microbiota dysbiosis and associated host immuno-metabolic disorders may play a role in knee synovitis. Herein, integrated multi-omics analyses of stool and blood samples from subjects from Pearl River Osteoarthritis Cohort (PROC, N = 207) are conducted to explore the potential gut-joint axis. Specifically, gut metagenomics, serum metabolomics and plasma proteomics are carried out. Knee synovitis is identified by magnetic resonance imaging. A total of 87 synovitis cases are identified in PROC, which are characterized by increased Firmicutes/Bacteroidetes (F/B) ratio. Alterations in microbial functions of both leucine and geraniol degradation are closely associated with increased serum 3-hydroxyisovaleric acid and decreased geranic acid. These perturbations are significantly correlated with F/B ratio and down-regulated plasma TWEAK. Building upon these, the potential synovial targets are explored using a synovial single-cell dataset and the Nanjing Osteoarthritis Cohort (NOC, N = 22). Synovial fluid proteomics, histological analysis, and in vitro experiments with human fibroblast-like synoviocytes (FLS) are conducted for NOC subjects with different synovitis grades. An upregulated TWEAK receptor is found in higher grade of synovitis. In vitro, higher TWEAK induced down-regulated TWEAK receptor in FLS. The study for the first time revealed the gut-joint axis in knee synovitis, providing new insight into potential targets for synovitis treatment.}, }
@article {pmid41354223, year = {2025}, author = {Adhikary, P and Maddheshiya, A and Takkar, B and Das, T and Mukherjee, S}, title = {Differential gut microbiome profiles in diabetic retinopathy: A comparative study across continental populations.}, journal = {Diabetes research and clinical practice}, volume = {}, number = {}, pages = {113043}, doi = {10.1016/j.diabres.2025.113043}, pmid = {41354223}, issn = {1872-8227}, abstract = {Gut dysbiosis damages gut barrier, stimulates inflammation, endotoxemia, and breakdown of blood-retina barrier, promoting diabetic retinopathy (DR). Most microbiome studies on DR relied on 16S rRNA gene sequencing, documenting altered microbial richness, diversity, and shifts in dominant phyla and genera, though these findings remain inconsistent across populations. The only shotgun metagenomic study to date identified species Eubacterium hallii, Firmicutes bacterium and Alistipes finegoldii enriched in DR, with altered metabolic pathways. The β-diversity showed distinct inter-individual variations in diseased individuals compared to healthy controls (HC). The objective of this narrative review is to highlight the key microbial biomarkers, metabolic pathways, and putative microbiota-gut-retina axis integrating both 16S rRNA and shotgun data to compare microbial alterations across HC, T2DM, and DR. The review concludes with a comprehensive understanding of dysbiotic gut taxa associated with DM and DR in different populations showing wide variability in results mostly due to small sample size, geography, antidiabetic medications, lack of demographic and clinical data and limited taxonomic classification by 16S sequencing. This emphasizes the need of a large scale, multi-ethnic shotgun metagenomic sequencing study with systematically collected medical data and dietary information to understand the contributions of gut microbiome in the progression of DR.}, }
@article {pmid41354039, year = {2025}, author = {Meng, Y and Zhou, JX}, title = {Beyond technical feasibility: addressing practical hurdles for equitable wastewater metagenomic surveillance.}, journal = {The Lancet. Microbe}, volume = {}, number = {}, pages = {101311}, doi = {10.1016/j.lanmic.2025.101311}, pmid = {41354039}, issn = {2666-5247}, }
@article {pmid41353953, year = {2025}, author = {Pan, Y and Tan, T and Meng, J and Guo, H and Dong, Y and Cui, Y and Yu, N and Jin, X and Zhang, Y and Zou, H and Bolan, N and Siddique, KHM}, title = {Biochar and moisture variability shape soil carbon pools via microbial carbon-degrading genes.}, journal = {Journal of environmental management}, volume = {397}, number = {}, pages = {128157}, doi = {10.1016/j.jenvman.2025.128157}, pmid = {41353953}, issn = {1095-8630}, abstract = {Microbially derived organic carbon is a key component of the soil carbon pool. Shifts in microbial communities and their associated functional genes-triggered by moisture variability and biochar addition-can influence the composition and stability of soil organic carbon (SOC). However, the microbial processes involved in SOC formation and degradation under different biochar levels and moisture variability intensities remain clear. To address this, we conducted a 90-day microcosmic incubation using three levels of biochar addition (C0: 0, C1: 1 %, C2: 2 %, w/w) and three moisture regimes (W0: constant moisture, W1: high-intensity variability, W2: low-intensity variability) to analyzed microbial communities, carbohydrase activity, C-degrading genes, and C, N, and P enzyme activities to trace and characterize microbial contributions to SOC formation. The results showed a shift in the dominant soil microbial community from Actinomycetes to Ascomycetes with increasing moisture variability. Microbial biomass carbon increased by 158-900 % relative to C0W0, peaking under C2W1. This stimulation enhanced microbial carbon sequestration under high moisture variability while simultaneously accelerating the decomposition of both plant- and microbial-derived carbon. Biochar addition exerted only a marginal, non-significant inhibitory effect on the decomposition either carbon source (P > 0.05). Functional gene analysis revealed that 62 % of carbohydrate-active enzymes (CAZymes) targeted plant-derived components significantly exceeding the 38 % targeting microbial-derived components, indicating a significantly stronger degradation potential for plant residues under varying moisture conditions. This process was genetically regulated, as shown by the concurrent increase in of carbon-degrading gene abundance and corresponding enzyme activities. Consequently, microbial activity was efficiently modulated, with carbon use efficiency increasing by up to 767 % compared with the C0W0. Moisture variability and its interaction with biochar significantly (P < 0.05) or highly significantly (P < 0.01) affected these microbial indicators. This study reveals a moisture-driven microbial "carbon pump" operating through coordinating gene-enzyme-community regulation. Within this framework, up-regulated carbon-degrading genes align with enzyme activities to channel plant-derived carbon into stable SOC. The C2W1 treatment achieved the highest SOC stabilization, offering a theoretical basis for managing SOC under extreme climate conditions and advancing mechanistic understanding of microbe-mediated carbon dynamics.}, }
@article {pmid41353697, year = {2025}, author = {Pandey, AK}, title = {Computational approach for identification and characterization of a glucose-tolerant thermostable β-glucosidase from marine metagenome.}, journal = {Molecular diversity}, volume = {}, number = {}, pages = {}, pmid = {41353697}, issn = {1573-501X}, abstract = {Cellulase enzymes comprising endo-1,4-β-glucanase, exo-1,4-β-glucanase, and β-glucosidase mediate the degradation of cellulosic biomass and are frequently used in biofuel production from lignocellulose. β-glucosidases that convert cellobiose to glucose are sensitive to temperature and glucose concentration and thus often show limited catalytic efficiency. Several β-glucosidases having high temperature or glucose tolerance have been evaluated, but a potential candidate having high efficiency along with thermostability and glucose tolerance is yet to be identified. The present study focuses on marine metagenome investigation for the identification of high-potential β-glucosidase. Nine β-glucosidases of the GH 1 family having (β/α)8 barrel domains were observed. Six β-glucosidases were predicted to have a Tm value higher than 65 ℃, including ECV39653.1 β-glucosidase. Molecular docking of all identified β-glucosidases with cellobiose and glucose revealed that ECV39653.1 β-glucosidase has the highest negative binding energy of - 7.4 kcal/mol for cellobiose at the active site, while having insignificant binding of glucose with binding energy of -5.4 kcal/mol at a site different from the active site. The structural analysis showed an effective similarity of ECV39653.1 β-glucosidase with known thermostable and glucose-tolerant β-glucosidases. The prediction of kinetic parameters gave kcat/Km value of 989.08163 sec[-1] mM[-1] for cellobiose. In-depth MD simulation and free binding energy analysis showed highly effective binding of cellobiose over the 100 ns trajectory with an average total binding energy of - 17.45 kcal/mol. The PCA and analysis of free energy landscape showed less variance and conformational changes in ECV39653.1 β-glucosidase cellobiose complex form in comparison to apo-form and disclosed attainment of global minima, thus proving the high ECV39653.1 β-glucosidase-cellobiose complex stability. The analysis of the simulation trajectory revealed that glucose left the binding cavity during simulation, thus disclosing weak binding and, hence, effective glucose tolerance. Therefore, the present in-silico investigation provides a promising high-efficiency, thermostable, and glucose-tolerant ECV39653.1 β-glucosidase. Further studies can provide scope for its utilization in the development of effective technologies for large-scale biofuel production.}, }
@article {pmid41353545, year = {2025}, author = {Briggs, P and Trimmell, L and Stiemsma, LT and Monzón, J}, title = {Sexual and regional differences in the microbiome and functional metagenome of the lone star tick, Amblyomma americanum.}, journal = {Animal microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42523-025-00498-6}, pmid = {41353545}, issn = {2524-4671}, }
@article {pmid41353522, year = {2025}, author = {Mugwanya, M and Mpingirika, EZ and AbdelMaksoud, Y and Eissa, RA and Sewilam, H}, title = {Assessment of sediment physiochemical properties, microbial and predicted functional diversity in mangrove eco-restoration sites of Hamata, Mangrove Bay, and Saffaga along the Egyptian Red Sea coast.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {41353522}, issn = {1614-7499}, abstract = {Microbial communities perform important roles in nutrient cycling, degradation of environmental pollutants, and support of various life forms on Earth. Mangroves live in very harsh environments, and if not for the existence of several microbial species in their ecosystems, they would not survive. The Egyptian Red Sea coast is dominated by two mangrove species, Avicennia marina and Rhizophora mucronata, which serve as breeding grounds for marine organisms and aid in carbon sequestration. Despite their ecological significance, comparative studies examining the physiochemical properties and heavy metal concentration of mangrove sediments of two dominant species along the Egyptian Red Sea coast (Hamata, Mangrove Bay, and Saffaga) and their relationship to microbial and functional diversity are scarce. Our findings revealed significant differences in sodium ions, potassium ions, organic carbon, and bulk density at 30-50 cm depth across the locations. Heavy metal analysis revealed significantly lower concentrations of zinc and manganese and high concentrations of copper in sediment samples collected from Mangrove Bay at all sampling depths. Metagenomics analysis revealed that the dominant phyla across the three sites were Pseudomonadota, Bacillota, and Bacteroidota, along with Actenomycetota, and Chloroflexota, and unclassified bacteria. Within the phylum Bacillota, several major classes were identified, including Bacillota_A_368345, Bacillota_I, and Bacillota_C. Functional prediction revealed a higher abundance of microbes involved in energy metabolism and carbon cycle, whereas a lower abundance of microbes involved in sulfur and nitrogen cycles was noted across the sites. In conclusion, the identification of different microbial communities in sediments collected along the Egyptian Red Sea coastal areas suggests the role of different mangrove species and human activities in recruiting unique microbial species involved in promoting their survival under different environmental factors.}, }
@article {pmid41353382, year = {2025}, author = {Kacnik, S and MacIntyre, C and Guarido, M and Venter, M}, title = {Identification of insect-specific viruses in mosquitoes collected from wildlife and rural areas in north-eastern parts of South Africa using a metagenomic RNA sequencing approach.}, journal = {One health outlook}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42522-025-00185-1}, pmid = {41353382}, issn = {2524-4655}, }
@article {pmid41353361, year = {2025}, author = {France, MT and Chaudry, I and Rutt, L and Quain, M and Shirtliff, B and McComb, E and Maros, A and Alizadeh, M and Hussain, FA and Elovitz, MA and Relman, DA and Rahman, A and Brotman, RM and Price, JT and Kassaro, MP and Holm, JB and Ma, B and Ravel, J}, title = {VIRGO2: an enhanced gene catalog of the vaginal microbiome provides insights into its functional and ecology complexity.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-025-67136-2}, pmid = {41353361}, issn = {2041-1723}, support = {UH2AI083264//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; T32AI162579//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; OPP1189217//Bill and Melinda Gates Foundation (Bill &amp; Melinda Gates Foundation)/ ; INV048956//Bill and Melinda Gates Foundation (Bill &amp; Melinda Gates Foundation)/ ; INV048982//Bill and Melinda Gates Foundation (Bill &amp; Melinda Gates Foundation)/ ; }, abstract = {Despite the importance of the cervicovaginal microbiome, the mechanisms that govern its composition and drive its impact on host physiology remain poorly understood. With the aim to expand our understanding of the function and ecology of the vaginal microbiome, we present VIRGO2, an enhanced non-redundant gene catalog comprising over 1.7 million well-annotated genes from body-site specific microbes and viruses. Analyses using VIRGO2 reveal insights such as including the identification of previously uncharacterized vaginal bacteria, features of the vaginal mycobiome and phageome, and differential expression of bacterial carbohydrate catabolic genes. Constructed from over 2500 metagenomes and 4000 bacterial genomes, VIRGO2 broadens geographic representation and microbial diversity compared to its predecessor. This updated catalog enables more precise profiling of taxonomic and functional composition from metagenomic and metatranscriptomic datasets. VIRGO2 is a critical resource for integrative analyses of vaginal microbial communities and their interactions with host tissues, thereby enhancing our mechanistic understanding of vaginal health and disease.}, }
@article {pmid41353034, year = {2025}, author = {McCone, N and Hosokawa, M}, title = {Recovering genomes from uncultured fungi with single-cell genomics.}, journal = {Journal of bioscience and bioengineering}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jbiosc.2025.11.004}, pmid = {41353034}, issn = {1347-4421}, abstract = {Single-cell genomics (SCG) complements culture-independent metagenomics for accessing fungal genomes, particularly from lineages that remain uncultured. We contrast metagenomics, which excels when profiling community composition and metabolic potential but often underrepresents low-abundance fungi, with SCG, which first isolates individual cells or nuclei to generate single-amplified genomes (SAGs) and can recover rare or microdiverse taxa. We then organize existing fungal SCG applications into three subgroups: spore-level sequencing from host-enriched or environmental material; single-nucleus genomics for multinucleate fungi; and single-spore sequencing of haploid progeny for diploid linkage and chromosome phasing. Across studies, pooling and co-assembly of cognate cells improves completeness; key hurdles persist in wall lysis, whole-genome amplification bias, and contamination control. Practical advances include shallow sequencing for QC triage, nuclei pooling with normalized co-assembly, and hybrid long- and short-read assembly. SCG adds unique value where strain resolution and genotypic context matter, including host-to-mobile-element linkage, recovery of large biosynthetic gene clusters, and karyotype validation against telomere-to-telomere references. Used alongside metagenomics, SCG enables a strain-resolved view of fungal biodiversity and function, with incremental improvements across the SCG pipeline promising routine access to genomes from early-diverging and other environmentally embedded fungi.}, }
@article {pmid41352820, year = {2026}, author = {Chen, X and Tie, Y and Yang, Q and Wu, Z and Xu, W and Zhang, Z and Ju, F and Takamine, K and Zhang, W}, title = {Temporal metabolomic dynamics and microbial functional mechanisms unravel biomarkers for distinguishing maturation stages and types in medium- and high-temperature daqu.}, journal = {Food research international (Ottawa, Ont.)}, volume = {223}, number = {Pt 1}, pages = {117916}, doi = {10.1016/j.foodres.2025.117916}, pmid = {41352820}, issn = {1873-7145}, mesh = {Biomarkers/analysis ; *Metabolomics/methods ; *Hot Temperature ; *Wine/analysis/microbiology ; *Bacteria/metabolism/classification/genetics ; *Alcoholic Beverages/microbiology/analysis ; }, abstract = {Daqu maturation is essential for developing the characteristic flavor profiles of Chinese Baijiu, yet the underlying microbial metabolic mechanisms remain incompletely understood. This study employed an integrated multi-omics approach to investigate metabolic heterogeneity and identify differential biomarkers during the aging of medium-temperature (MD) and high-temperature (HD) Daqu. Physicochemical analysis revealed MD exhibited higher saccharifying power, whereas HD showed increased esterifying power and dynamic acidity changes. Microbial succession and metagenomic analysis uncovered distinct succession patterns: MD was dominated by Saccharopolyspora and Bacillus, while HD featured thermophilic genera including Kroppenstedtia and Virgibacillus. Co-occurrence network analysis demonstrated higher connectivity and reduced modularity in HD, indicating functional adaptation to high temperatures. Combined VIP and OAV analysis identified key aroma biomarkers that distinctly define both Daqu type and maturation stage. Tetramethylpyrazine and acetic acid characterized MD, while benzaldehyde and methyl hexadecanoate marked HD. Non-targeted metabolomics further indicated MD was enriched in phenylpropanoids and branched-chain amino acid derivatives, whereas HD accumulated peptides and steroid-related compounds. Crucially, integrated analysis demonstrated that these metabolic shifts were directly driven by microbial enzymatic activities (e.g., EC 4.1.1.5, EC 3.1.1.3). These findings establish a causal link between temperature-driven microbial functional specialization and metabolic output, and provide a biomarker framework for precise quality assessment of Daqu.}, }
@article {pmid41352612, year = {2025}, author = {Fishman, JA}, title = {Assuring Microbiological Safety in Clinical Xenotransplantation.}, journal = {American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ajt.2025.11.027}, pmid = {41352612}, issn = {1600-6143}, }
@article {pmid41352476, year = {2025}, author = {Su, J and Zhao, K and Zhou, X and Pan, Z and Xia, C}, title = {Early-life exposure to linezolid caused gut microbiota dysbiosis can be inherited from parents to offspring.}, journal = {Chemico-biological interactions}, volume = {}, number = {}, pages = {111863}, doi = {10.1016/j.cbi.2025.111863}, pmid = {41352476}, issn = {1872-7786}, abstract = {BACKGROUND AND OBJECTIVES: Linezolid is a broad-spectrum antibiotic against Gram-positive bacterial infections. Widespread use of linezolid has brought about significant adverse effects and potential reproductive toxicity, but there is not yet any study regarding to the transgenerational impact.<br><br>METHODS: Gut microbiota and metabolites from the 12-weeks old male mice who were treated with one-week linezolid at 4 weeks of age, as well as those from their offsprings, were analyzed by metagenomics and metabolomics, respectively. Reproductivity of the male parents were monitored, including fertility, litter size, survival and weight gain of offsprings.<br><br>RESULTS: Offsprings survival from the linezolid-treated male parents was obviously decreased, although fertilities, litter size, or weight gain was not affected. The linezolid-induced gut microbiota perturbation in male parents was manifested as lower alpha diversity, distinguishing beta diversity, and the dramatically altered profiles of function genes and metabolites. Especially, linezolid exposure reversed the relationship between Dysosmobacter and butyrogenic species, and that between Dysosmobacter and inflammation-associated species. Interestingly, gut microbiota dysbiosis also existed in both female and male offsprings from the treated male parents. Moreover, it was found that the differential metabolites enriched in ABC transporter pathway were found male parents and offsprings, while those enriched in sphingolipid signaling pathway were only found in offsprings of both sexes CONCLUSIONS: The early-life short-term exposure to linezolid make long-term gut microbiota dysregulation, which was even inherited from parents to offsprings. These findings raised critical concern about the ecological consequences of early-life antibiotic exposure and clinical safety evaluations.}, }
@article {pmid41352467, year = {2025}, author = {Nalladiyil, A and Khuntia, HK and Chanakya, HN and Babu, GLS}, title = {Treatment of ultra-high-strength compost leachate using an anaerobic biomass biofilm reactor.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {133774}, doi = {10.1016/j.biortech.2025.133774}, pmid = {41352467}, issn = {1873-2976}, abstract = {Leachate produced during the composting of the organic fraction of municipal solid waste (OFMSW) is highly concentrated and acidic (chemical oxygen demand (COD) -125 g/L, pH 3-5). Its recalcitrant nature necessitates long hydraulic retention times for effective digestion, which, in turn, leads to high organic loads and, consequently, large reactor footprints. This study evaluated the treatment performance, bioenergy potential, and microbial ecology of the Anaerobic Biomass Biofilm Reactor (ABBR) for ultra-high strength leachate treatment. The reactor employed lignocellulosic wastes such as coir, ridge gourd, and dried acacia leaves as natural biofilm supports. Operated over 180 days with a gradually increasing organic loading rate from 1.1 to 11.2 kg COD/m[3]/d, the reactor achieved 92.9 % COD removal and a methane yield of 0.357 NL/g COD removed at the maximum loading rate. Moreover, the reactor also exhibited exceptionally high space utilization efficiency (3.5-4 L CH4/L/d), highlighting its enhanced volumetric productivity and effectiveness in treating high-strength leachate. Metagenomic analysis revealed a diverse microbial community, with Methanospirillum (3 %) and Methanosaeta (2.6 %) identified as dominant archaea contributing to methanogenesis. The high moisture content of OFMSW, coupled with tropical climatic conditions, leads to rapid fermentation and the generation of large volumes of leachate. Therefore, the ABBR represents a sustainable and high-rate alternative to conventional anaerobic systems, enabling efficient leachate treatment and enhanced bioenergy recovery in windrow composting facilities.}, }
@article {pmid41352466, year = {2025}, author = {Liu, Z and Gao, Y and Wang, J and Jing, X and Chen, X and Hu, W and Lu, X and Liu, M and He, X and Kumar, G and Zhen, G}, title = {Perfluorooctane sulfonate (PFOS) inhibits methane production during sludge anaerobic digestion by breaking the carbon-transfer bridge between methanogenesis and acidogenesis.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {133775}, doi = {10.1016/j.biortech.2025.133775}, pmid = {41352466}, issn = {1873-2976}, abstract = {Per- or polyfluoroalkyl compounds (PFASs) are recognized as emerging contaminant, with perfluorooctane sulfonate (PFOS) being one of the most extensively utilized PFASs due to its great chemical stability. However, knowledge of the bio-chemical behavior, the toxicity of PFOS and its mechanisms of interfacial binding to microorganisms remain inadequately validated. In this study, the biotoxicity of PFOS and its molecular interfacial adsorption mechanism in anaerobic digestion were investigated. The results showed that the tightly bound EPS (TB-EPS) of anaerobic microorganisms could defend against the biotoxicity of PFOS to some extent by physical adsorption and chemical binding, the exposure to PFOS might produce a greater disturbance to methanogenic archaea. With the increase of PFOS, acid-producing bacteria (APB) and methanogenic archaea showed different resistance to PFOS, suppressing cumulative methane production by up to 91.64 %. On the contrary, APBs were more tolerant, and fatty acids accumulated up to 2194.27 mg/L. Metagenomics analysis further confirmed that functional genes associated with fatty acid biosynthesis (fas, FAS2, fabK, etc.) were significantly enriched (approximately 85.29 %) whereas the relative abundance of genes associated with methanogenesis (acs, comA, mcrB, etc.) were decreased (up to 65.96 %). Molecular docking results suggested a potential route for PFOS cellular entry, as it was observed to bind to the substrate-binding protein of the ATP-binding cassette (ABC) transporter and interact with key functional enzymes, which led to the inhibition of methanogens. This study provides novel insights into the molecular blocking mechanism by which PFOS disrupts carbon metabolic flux through the selective inhibition of methanogenic archaea, rather than through a general suppression of acidogenic bacteria.}, }
@article {pmid41352108, year = {2025}, author = {Zeng, Z and Lei, T and Zhou, M and Wen, H and Li, S}, title = {Ciprofloxacin removal and antibiotic resistance genes response in the EGSB-AnMBR system treating swine wastewater: Performance, mechanism, and metagenomics.}, journal = {Journal of environmental management}, volume = {397}, number = {}, pages = {128233}, doi = {10.1016/j.jenvman.2025.128233}, pmid = {41352108}, issn = {1095-8630}, abstract = {Ciprofloxacin (CIP), a veterinary antibiotic in swine wastewater is an emerging contaminant with low concentration but significant environmental risk. Its inhibitory effects on biological treatment systems and the proliferation of antibiotic resistance genes have raised widespread public concern. An expanded granular sludge bed reactor was coupled with an anaerobic membrane bioreactor (EGSB-AnMBR) to treat swine wastewater containing CIP. During 320 days operation, the EGSB-AnMBR system achieved over 98.6 % chemical oxygen demand (COD) removal efficiency and 61.4 %-100 % CIP removal efficiency. During the initial operation phase, sludge adsorption served as the primary mechanism for CIP removal, whereas biodegradation became dominant in the last operational phase. 16S rRNA gene high-throughput sequencing analysis revealed that under CIP stress, the abundance of CIP-resistant Spirochaetota increased from 4.7 % to 9.5 %, whereas Patescibacteria abundance progressively decreased from 72.7 % to 15.7 %. Metagenomic analysis demonstrated microbes in anaerobic granular sludge (AnGS) achieved "defense-efflux" by activating macB/evgS efflux pumps while suppressing tetA, whereas membrane biofilm (MB) developed a "storage-retention" strategy through synergistic effects of tetA and evgS. This EGSB-AnMBR system exhibits promising application potential for swine wastewater treatment and antibiotic control, providing significant support for livestock pollution management.}, }
@article {pmid41352011, year = {2025}, author = {Yang, K and Zhang, L and Zhao, K and Liu, W and Tiehm, A and Zhang, X}, title = {Metabolism regulates spatial distribution patterns of different microbial taxonomic groups in chlorinated aliphatic hydrocarbons contaminated soil.}, journal = {Journal of hazardous materials}, volume = {501}, number = {}, pages = {140640}, doi = {10.1016/j.jhazmat.2025.140640}, pmid = {41352011}, issn = {1873-3336}, abstract = {A mechanistic understanding of the distribution and role of subsurface microbial communities is crucial for sustainable environmental management. Bioremediation of chlorinated solvents relies on the bioactivity of organohalide-respiring bacteria and their interaction with syntrophic members. However, the spatial distribution pattern and its influencing factors of these members remain poorly understood. In this study, Distance-decay relationship (DDR) models and Sloan's neutral community models (NCM) were employed to quantify spatial turnover rates and stochastic processes of different taxa in chlorinated aliphatic hydrocarbon-contaminated soil. Incorporating metagenomic analysis and machine learning, this study highlights the contribution of genomic information and reveals how genetic potential for functional mechanisms may relate to distinct spatial distribution patterns. Findings indicate that metabolic potential, rather than environmental preference, primarily governs the heterogeneous distribution of different taxa. Archaeal syntrophic members, Bathyarchaeia, was identified as a potential reliable target for improving bioremediation efficiency. Correlation between parameters of different models suggests that dispersal ability plays an important role in the variation of spatial turnover rate. This was further supported by LASSO regression models in which genomic features relevant to biofilm formation, dormancy, and DNA repair pathways were identified as key predictors of spatial turnover. These findings not only offer actionable insights for enhancing bioremediation strategies at chlorinated solvent-contaminated sites but also demonstrate the potential of incorporating genomic features to understand microbial biogeography.}, }
@article {pmid41351981, year = {2025}, author = {Li, A and Ju, Z and Zhang, X and Wang, M and Xing, J and Liu, G and Qin, X}, title = {Fangji Huangqi Tang alleviated chronic kidney disease by regulating intestinal bacteria to inhibit the AHR/ROS pathway.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {150}, number = {}, pages = {157610}, doi = {10.1016/j.phymed.2025.157610}, pmid = {41351981}, issn = {1618-095X}, abstract = {BACKGROUND: Fangji Huangqi Tang (FHT) is a traditional Chinese herbal formula that is clinically effective and safe for chronic kidney disease (CKD). However, the mechanism of action of FHT remains unclear.<br><br>PURPOSE: In this study, we investigated the mechanism of the targeted regulation of intestinal flora by Fangji Huangqi Tang to delay CKD.<br><br>METHOD: A CKD model was established in rats and mice by tail vein injection of doxorubicin, and the rats and mice were administered FHT orally. Metagenomic sequencing analysis was employed to screen and identify FHT-regulated key gut bacteria in CKD model rats and mice. In vitro bacterial co-cultures of these taxa were analyzed for metabolite discovery. Oral supplementation of key bacteria in CKD mice was evaluated the therapeutic effects and validated the metabolic changes observed in vitro. Cellular Aryl Hydrocarbon Receptor (AHR) overexpression was conducted to clarify the mechanistic of the metabolite derived from microbiota.<br><br>RESULTS: FHT significantly enriched Corynebacterium stationis (C. stationis) in both CKD rat and mice models. In vitro, C. stationis metabolized tryptophan into Indole-3-Carbinol (I3C) while reducing indole levels. Oral administration of C. stationis in CKD mice attenuated renal dysfunction and elevated systemic I3C. Additionally, it downregulated AHR expression and diminished the expression of ROS-related inflammatory factors, thereby ameliorating CKD. Crucially, AHR overexpression reversed I3C's cytoprotective effects in MPC5 injury models.<br><br>CONCLUSIONS: This study reveals that FHT targets the enrichment of the gut bacterium C. stationis, driving tryptophan metabolism toward I3C conversion. This process suppresses AHR expression, reduces ROS levels and inflammatory injury, and ultimately retards the progression of CKD.}, }
@article {pmid41351872, year = {2025}, author = {Mukherjee, I and Bulzu, PA and Boukheloua, R and Asghar, U and Park, H and Vieira, HH and Chiriac, MC and Kasalický, V and Znachor, P and Rychtecký, P and Šimek, K and Salcher, MM and Haber, M and Ghai, R}, title = {Cultivation, genomics, and giant viruses of a ubiquitous and heterotrophic freshwater cryptomonad.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf271}, pmid = {41351872}, issn = {1751-7370}, abstract = {Heterotrophic nanoflagellates are the chief agents of bacterivory in the aquatic microbial loop but remain underrepresented in culture collections and in genomic databases. We isolated and characterised a representative of the previously uncultured freshwater Cryptomonad Group 1 (CRY1a) lineage using a genome-streamlined, ultrasmall and abundant microbe Planktophila versatilis as a prey and CARD-FISH probe-based screening. This isolate, Tyrannomonas regina, is one of the most dominant ubiquitous heterotrophic cryptomonads in freshwaters. It is a small heterotrophic nanoflagellate (ca. 3-5 μm) and has the smallest genome of any cryptomonad sequenced thus far. The compact genome (ca. 69 Mb) revealed no traces of a photosynthetic lifestyle, consistent with its phylogenomic placement as a sister-clade to cryptophytes that are characterised by the acquisition of a red-algal symbiont. Moreover, in comparison to its photosynthetic counterparts, its genome presents substantially lower repeat content and endogenous viral elements. Genomes of two giant viruses, Tyrannovirus reginensis GV1 and GV2, were also recovered from the same culture and represent a viral genus that has been described so far solely by metagenome-recovered genomes. Collectively, these findings provide insights into genomic ancestry and evolution, widespread ecological impact and interactions of an elusive protist lineage and illustrate the advantages of culture-centric approaches towards unfolding complex tapestries of life in the microbial world.}, }
@article {pmid41351776, year = {2025}, author = {Hussain, B and Javed, K and Ali, M and Ullah, S and Sun, S and Idris, AM and Singh, S}, title = {Impact of nanoparticles on biogeochemical processes in soil-plant system under heavy metals stress; exploring remediation mechanism and plant health status.}, journal = {Environmental geochemistry and health}, volume = {48}, number = {1}, pages = {31}, pmid = {41351776}, issn = {1573-2983}, mesh = {*Metals, Heavy/toxicity/metabolism ; *Soil Pollutants/toxicity/metabolism/chemistry ; Soil/chemistry ; *Plants/drug effects/metabolism ; *Environmental Restoration and Remediation ; Biodegradation, Environmental ; Stress, Physiological ; *Metal Nanoparticles/chemistry/toxicity ; }, abstract = {Although, NPs have potential to improved plant resistance against abiotic stress, increased nutrient usage efficiency, and sustenance of agricultural production. However, reactions of NPs in soil matrices, particularly their movement, perseverance, and biogeochemical reactions in soil-plant system under heavy metals (HMs) were not well understood. Therefore, this review presents the latest research in order to clarify the molecular interactions, beneficial transformations, and detoxification processes of NPs in plants and evaluates their roles in these processes. It further aims to quantify the benefits and risks, and give future directions for NPs design and applications in environmental remediation and agriculture. NPs significantly enhanced agricultural outcomes through mechanisms such as regulating HMs uptake, boosting antioxidant enzyme activity (up to a 60% increase), altering soil properties, and optimizing physiological metabolism. NPs amendments raised crop output by 20-55% while reducing disease and nutrient leaching to 50% and 30%, respectively, and improving the soil's carbon sink by 15%. Meanwhile, green-synthesized nanomaterials offer eco-friendly alternatives in remediation through processes like adsorption, oxidation, coprecipitation, ion-exchange, photocatalysis, and nanophytoremediation, achieving 100% pollutant removal efficiency for elements like hexavalent chromium using iron NPs. However, challenges such as NPs accumulation in food chains, potential toxicity to non-target species, and physiological disruptions necessitate solutions like microbiome co-delivery and stimuli-responsive systems to balance safety and effectiveness. In order to increase the available resources and address the worldwide food safety issue, the use of NPs in agroecosystems might be a crucial step towards sustainable farming. Therefore, the influence of NPs on soil, and plant antioxidant defense systems and oxidative stress activation under HMs should be studied using molecular, physiological, and biochemical techniques. For this purpose, real-time polymerase chain reaction (RT-PCR) analysis, illumina MiSeq sequencing, pyrosequencing analysis, metagenomics, metabolomics, proteomics, and functional assays etc. could be most useful for NPs risk/benefit evaluation.}, }
@article {pmid41351708, year = {2025}, author = {Campbell, KL and Armitage, AR and Labonté, JM}, title = {Microbial Communities Display Key Functional Differences between Reference and Restored Salt Marshes.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02661-7}, pmid = {41351708}, issn = {1432-184X}, abstract = {Salt marshes, despite their ecological importance (i.e., carbon sequestration) and rapid decline due to climate change and sea-level rise. Salt marsh ecosystems provide essential services such as removal of pollutants, carbon sequestration, and protection of coastal lands from storm surges. These services are strongly influenced by plant productivity, which is closely linked to microbial processes such as biogeochemical cycling of carbon, nitrogen, and sulfur. To retain carbon sequestration and other ecological functions, substantial efforts are currently directed towards coastal marsh restoration. Restoration efforts often lack comprehensive assessments of ecosystem functioning. Here, in an effort to assess ecosystem functions, we compared the microbial and viral community composition, as well as the genetic potential between reference and 10-year-old restored marshes in Galveston Bay, TX, USA. Duplicate bulk surface sediment in stands of Spartina alterniflora were sampled for metagenomic analysis. Metagenome assembled genomes analysis showed that while the microbial community composition was largely similar among sites, the overall metabolic potential was dissimilar. Restored sites displayed a higher abundance of carbon and nitrogen cycling functions compared to reference sites, which mainly consisted of sulfur cycling. Although the restored sites developed sediment microbial communities that approached reference microbial composition, the differences in the metabolic functions suggest that even after 10 years, the restored sites were still in a transitional stage of development. The differences between the reference and restored sites were even more differentiated in the viral community's predicted host composition. Additionally, viruses potentially play a variety of roles within the sediment community, including population control and biogeochemical cycles participation through auxiliary metabolic genes. These results highlight the prolonged timeline of functional development in restored salt marshes and highlight the need to develop approaches to boost the development of soil microbial communities in newly created habitats.}, }
@article {pmid41351628, year = {2025}, author = {Liu, S and Liu, P and Deng, J and He, J and Xiang, Y and Chen, H and Liao, S and Lu, Y and Zhang, Z and Xu, J and Zhang, Z}, title = {C-arm-guided percutaneous biopsy combined with mNGS: a dual-modality strategy for op timizing diagnosis and targeted management of spinal infections.}, journal = {European spine journal : official publication of the European Spine Society, the European Spinal Deformity Society, and the European Section of the Cervical Spine Research Society}, volume = {}, number = {}, pages = {}, pmid = {41351628}, issn = {1432-0932}, support = {2025ZDXM002//Chongqing Science and Health Joint Medical Research(CN)/ ; 2025ZDXM002//Chongqing Science and Health Joint Medical Research(CN)/ ; 2025ZDXM002//Chongqing Science and Health Joint Medical Research(CN)/ ; 2025ZDXM002//Chongqing Science and Health Joint Medical Research(CN)/ ; 2025ZDXM002//Chongqing Science and Health Joint Medical Research(CN)/ ; 2025ZDXM002//Chongqing Science and Health Joint Medical Research(CN)/ ; 2025ZDXM002//Chongqing Science and Health Joint Medical Research(CN)/ ; 2025ZDXM002//Chongqing Science and Health Joint Medical Research(CN)/ ; 2025ZDXM002//Chongqing Science and Health Joint Medical Research(CN)/ ; 2025ZDXM002//Chongqing Science and Health Joint Medical Research(CN)/ ; 2025ZDXM002//Chongqing Science and Health Joint Medical Research(CN)/ ; }, }
@article {pmid41351142, year = {2025}, author = {Sharko, F and Busova, V and Boulygina, E and Burakova, A and Pankova, S and Nedoluzhko, A}, title = {Ancient DNA sheds light on the historical distribution of the rare and ephemeral plant Coleanthus subtilis in Southern Siberia.}, journal = {BMC genomics}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12864-025-12365-4}, pmid = {41351142}, issn = {1471-2164}, abstract = {BACKGROUND: Ancient DNA is a valuable source of information about the distant past of our planet. Reconstructing the past ecosystems is essential for understanding many aspects of life in the steppes of southern Siberia and Central Asia, where numerous human societies representing different archaeological cultures have lived. The remains of their activities, revealed by archaeological excavations, provide a wide range of sources for the cultural and natural/biological history of the region. One of the most enigmatic Iron Age archaeological cultures in southern Siberia is the Tashtyk culture, which dates back to the 1st - 7th centuries AD. The people of this culture inhabited the Minusinsk Basin and practiced different burial rites, including cremation. Thanks to the exceptional preservation of organic remains in individual Tashtyk burials we know of quite an unusual phenomenon: the placement of cremains into the human-like mannequins made from animal skin and filled with herbaceous plants. This study analyses ancient DNA extracted from the grass stuffing of a mannequin found in 2023 at the Oglakhty cemetery, which dates back to 250-300 AD. Our aim is to identify the plant species that were used to stuff the mannequin approximately 1,700 years ago, and to compare their diversity with that of modern-day plant species. This is particularly significant given that the Oglakhty region is part of the Khakassky State Nature Reserve, which was added to the UNESCO Tentative List in 2016 due to its biodiversity and concentration of archaeological sites.<br><br>RESULTS: We sequenced the ancient DNA of a dried historical grass mixture in order to reconstruct the nearly complete chloroplast genomes of several apparent Poaceae species. Our analysis showed that, 1,700 years ago, the diversity of plant species in the Oglakhty area was similar to the modern meadow flora of the Minusinsk Basin. These included typical steppe and forest-steppe zone plant genera of Siberia, such as Holcus, Phleum, Poa, and Stipa. Interestingly, alongside the species commonly found in modern southern Siberian steppes and meadows, we discovered the rare, ephemeral, and protected moss grass, Coleanthus subtilis (Tratt.) Seidel ex Roem. et Schult. whose current distribution range spans highly fragmented areas of northern Eurasia and North America but not the Minusinsk Basin.<br><br>CONCLUSION: The herbaceous plant C. subtilis, whose DNA fragments were obtained through the metagenomic profiling of the human-like mannequin's stuffing at the Oglakhty cemetery, provides new insights into the cultural and natural history of Siberia. Firstly, we identified several grass taxa in the mannequin's stuffing. Most of them are characteristic for the steppe zone; the only exception is C. subtilis, which usually inhabits riverbanks. Therefore, we assume that, despite being primarily stuffed with the steppe plants, the Oglakhty mannequin was crafted on a riverbank, where C. subtilis might have got inside likely by chance. It is important to note that the stuffing process apparently took place after the vegetation season of C. subtilis in second half of summer and the beginning of autumn. Secondly, our research suggests that a population of C. subtilis, which is currently absent from the documented flora of southern Siberia, previously grew in the Minusinsk Basin wetlands. Our study highlights the need for field expeditions aimed to identify endemic populations of C. subtilis in the Yenisei River valley.}, }
@article {pmid41351056, year = {2025}, author = {Stach, TL and Starke, J and Bouderka, F and Bornemann, TLV and Soares, AR and Wilkins, MJ and Goldman, AE and Stegen, JC and Borton, MA and Probst, AJ}, title = {Conserved environmental adaptations of stream microbiomes in the hyporheic zone across North America.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-025-02236-1}, pmid = {41351056}, issn = {2049-2618}, support = {426547801//Deutsche Forschungsgemeinschaft/ ; DE-AC05-76RL01830//U.S. Department of Energy/ ; }, abstract = {BACKGROUND: Stream hyporheic zones represent a unique ecosystem at the interface of stream water and surrounding sediments, characterized by high heterogeneity and accelerated biogeochemical activity. These zones-represented by the top sediment layer in this study-are increasingly impacted by anthropogenic stressors and environmental changes at a global scale, directly altering their microbiomes. Despite their importance, the current body of literature lacks a systematic understanding of active nitrogen and sulfur cycling across stream sediment and surface water microbiomes, particularly across geographic locations and in response to environmental factors.<br><br>RESULTS: Based on previously published and unpublished datasets, 363 stream metagenomes were combined to build a comprehensive MAG and gene database from stream sediments and surface water including a full-factorial mesocosm experiment which had been deployed to unravel microbial stress response. Metatranscriptomic data from 23 hyporheic sediment samples collected across North America revealed that microbial activity in sediments was distinct from the activity in surface water, contrasting similarly encoded metabolic potential across the two compartments. The expressed energy metabolism of the hyporheic zone was characterized by increased cycling of sulfur and nitrogen compounds, governed by Nitrospirota and Desulfobacterota lineages. While core metabolic functions like energy conservation were conserved across sediments, temperature and stream order change resulted in differential expression of stress response genes previously observed in mesocosm studies.<br><br>CONCLUSIONS: The hyporheic zone is a microbial hotspot in stream ecosystems, surpassing the activity of overlaying riverine surface waters. Metabolic activity in the form of sulfur and nitrogen cycling in hyporheic sediments is governed by multiple taxa interacting through metabolic handoffs. Despite the spatial heterogeneity of streams, the hyporheic sediment microbiome encodes and expresses conserved stress responses to anthropogenic stressors, e.g., temperature, in streams of separate continents. The high number of uncharacterized differentially expressed genes as a response to tested stressors is a call-to-action to deepen the study of stream systems. Video Abstract.}, }
@article {pmid41350884, year = {2025}, author = {De Sanctis, B and Mirchandani, C and Dong, H and Macleod, R and Corbett-Detig, R and Wang, Y}, title = {Bamdam: a post-mapping authentication toolkit for ancient metagenomics.}, journal = {Genome biology}, volume = {26}, number = {1}, pages = {413}, pmid = {41350884}, issn = {1474-760X}, support = {35GM128932./NH/NIH HHS/United States ; 35GM128932./NH/NIH HHS/United States ; 4198810//National Natural Science Foundation of China-China Academy of General Technology Joint Fund for Basic Research/ ; 4198810//National Natural Science Foundation of China-China Academy of General Technology Joint Fund for Basic Research/ ; G10144//Social Sciences and Humanities Research Council of Canada/ ; }, mesh = {*Metagenomics/methods ; *Software ; Humans ; }, abstract = {Ancient metagenomic studies using capture or shotgun sequencing often perform pairwise alignment of individual reads against large reference databases followed by lowest common ancestor assignment for taxonomic identification. Here, we present bamdam, a lightweight post-mapping, post lowest common ancestor toolkit for eukaryotic or microbial metagenomics. Bamdam can shrink large metagenomics bam files, often by a factor of 10x or more, while retaining all informative reads and alignments, compute a suite of authentication metrics for each taxonomic node including k-mer duplicity, postmortem damage, and mean read complexity, and generate various visualizations including multi-sample deamination plots and damage-colored interactive Krona plots.}, }
@article {pmid41350579, year = {2025}, author = {Tarracchini, C and Longhi, G and Gennaioli, E and Muscò, A and Rizzo, SM and Viappiani, A and Vitale, SG and Mancabelli, L and Lugli, GA and Angioni, S and Turroni, F and van Sinderen, D and Milani, C and Ventura, M}, title = {Compiling an early life human gut microbiome atlas and identification of key microbial drivers.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-025-00868-7}, pmid = {41350579}, issn = {2055-5008}, abstract = {During the first year after birth, the infant gut microbiome undergoes a rapid and profound compositional and functional transformation, impelled by an intricate network of intrinsic and extrinsic factors. This process results in increased taxonomic and functional diversification, alongside greater interindividual variability. To better understand this early-life ecosystem, this study assessed the interindividual variability of the infant gut microbiome using a comprehensive infant gut microbiome database of 5288 fecal metagenomic data from healthy, full-term infants across various geographical locations. Our study identified six reference microbial communities, termed Early-Life Community State Types (ELi-CSTs), which not only capture specific compositional profiles and heterogeneity of the infant gut microbiome, but also record the extensive transformation experienced by this developing microbial community during the first year of human life. Indicative Species analysis and Random Forest modeling assisted the precise identification of unique, key taxonomic signatures that are critical to the structure of each ELi-CST, highlighting microbial taxa with pivotal roles in shaping the infant gut microbiota. To complement these findings, we established a bacterial biobank through dedicated cultivation efforts of the infant microbiota, comprising 182 genome-sequenced isolates corresponding to key taxa involved in early life gut microbiota assembly. This biobank provided the basis for co-cultivation experiments combined with transcriptome analyses, thereby enabling in vitro investigations into microbial cross-talk among key modulators, and yielding novel insights into the molecular interactions and cooperative dynamics behind early microbiome development.}, }
@article {pmid41350543, year = {2025}, author = {Nickodem, CA and Tran, PQ and Neeno-Eckwall, E and Congdon, AG and Sanford, GR and Silva, EM and Hite, JL}, title = {Soil management strategies drive divergent impacts on pathogens and environmental resistomes.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {43215}, pmid = {41350543}, issn = {2045-2322}, support = {AD00001395//U.S. Department of Agriculture/ ; 58-5090-2-035//U.S. Department of Agriculture/ ; AD00001395//U.S. Department of Agriculture/ ; }, mesh = {*Soil Microbiology ; Manure/microbiology ; Fertilizers ; *Soil/chemistry ; Animals ; Agriculture/methods ; Poultry ; Microbiota ; Metagenomics ; *Drug Resistance, Bacterial/genetics ; Humans ; Gene Transfer, Horizontal ; }, abstract = {Antimicrobial resistance (AMR) is a growing global health threat, and the genes that confer drug resistance are increasingly recognized as widespread environmental contaminants. Livestock manure, widely used as a non-synthetic fertilizer, is a potential source of AMR contamination in the environment. Manure fertilizers are well-documented reservoirs of AMR genes (ARGs) and drug-resistant pathogens. However, the role of soil management practices in shaping the persistence and spread of these genes after manure application remains poorly understood. We conducted a large-scale field experiment to evaluate how soil management practices influence the resistome (the genomic content involved in resistance to antimicrobial agents) and the overall microbiome of agricultural soils. Specifically, we ask: Does the use of composted poultry manure in organic soil management practices increase the risk of transmitting ARGs and drug-resistant pathogens? We integrated metagenomic sequencing with risk score analyses to assess the abundance, diversity, and mobility of resistance genes. Contrary to expectations, our results indicate that non-organic practices, despite not applying poultry manure, posed greater risks for transmitting AMR genes and human pathogens - due to significantly higher co-occurrence of ARGs with mobile genetic elements (MGEs), which facilitate horizontal gene transfer. In contrast, organic practices, that applied composted poultry manure, increased overall ARG and metal resistance gene (MRG) abundance, but the genes were less diverse and less mobile. These findings show that focusing solely on ARG and MRG abundance can misrepresent AMR risks and underscore the importance of evaluating gene mobility and management context when assessing AMR hazards. Our study highlights how soil management can be strategically leveraged to mitigate AMR transmission, offering actionable insights for sustainable agriculture, environmental stewardship, and public health protection.}, }
@article {pmid41350329, year = {2025}, author = {Sato, Y and Kumagai, H and Hirooka, H and Yoshida, T}, title = {Differences in prokaryotic and viral community between rumen and feces.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {43232}, pmid = {41350329}, issn = {2045-2322}, mesh = {*Feces/microbiology/virology ; Animals ; *Rumen/microbiology/virology ; Metagenomics/methods ; *Viruses/genetics/classification ; Metagenome ; Bacteria/genetics ; Virome ; *Prokaryotic Cells/virology ; Genome, Viral ; Gastrointestinal Microbiome ; }, abstract = {Ruminants harbor diverse microbial communities, including prokaryotes and viruses, across their digestive tract. Rumen viruses contribute to carbohydrate metabolism; however, their persistence and host interactions in the lower gastrointestinal tract remain unclear. In this study, we investigated the prokaryotic and viral communities in the rumen and feces of the same wethers using whole-metagenomic and virus-like particle metagenomic sequencing. For prokaryotic community analysis, we reconstructed over 300 metagenome-assembled genomes, most of which were novel. These revealed strong site specificity, with distinct prokaryotic community compositions between the rumen and feces. Virome analysis recovered more than 6,000 viral genomes, including many novel viruses. Unlike prokaryotes, several viruses were found to be shared between the rumen and feces. Auxiliary metabolic genes encoding glycoside hydrolases were identified in several rumen-associated viral genomes, whereas fecal-associated viral genomes did not harbor such genes. Host-virus interaction analysis predicted that viruses predominantly infect dominant bacterial taxa and methanogens within each gastrointestinal site, although some viruses may interact with hosts across different sites. These findings highlight the strong site specificity of the prokaryotic communities and the comparatively broader distribution of viruses within the ruminant gastrointestinal tract. These insights advance understanding of virus-prokaryote-host interactions with implications for animal productivity.}, }
@article {pmid40691354, year = {2026}, author = {Roux, S and Coclet, C}, title = {Viromics approaches for the study of viral diversity and ecology in microbiomes.}, journal = {Nature reviews. Genetics}, volume = {27}, number = {1}, pages = {32-46}, pmid = {40691354}, issn = {1471-0064}, mesh = {*Microbiota/genetics ; *Viruses/genetics/classification ; *Virome/genetics ; Humans ; Metagenomics/methods ; Ecosystem ; Genetic Variation ; Biodiversity ; Animals ; Genome, Viral ; }, abstract = {Viruses are found across all ecosystems and infect every type of organism on Earth. Traditional culture-based methods have proven insufficient to explore this viral diversity at scale, driving the development of viromics, the sequence-based analysis of uncultivated viruses. Viromics approaches have been particularly useful for studying viruses of microorganisms, which can act as crucial regulators of microbiomes across ecosystems. They have already revealed the broad geographic distribution of viral communities and are progressively uncovering the expansive genetic and functional diversity of the global virome. Moving forward, large-scale viral ecogenomics studies combined with new experimental and computational approaches to identify virus activity and host interactions will enable a more complete characterization of global viral diversity and its effects.}, }
@article {pmid41350265, year = {2025}, author = {Tang, H and Liu, H and Yuan, L and Xie, M and Zheng, J and Wang, J and Zhou, J and Yang, B and Lou, B and Han, D}, title = {Bronchoalveolar lavage fluid metagenomic datasets: a multidimensional clinical biomolecular resource.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1919}, pmid = {41350265}, issn = {2052-4463}, support = {82472371//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Humans ; *Metagenomics ; *Bronchoalveolar Lavage Fluid/microbiology ; High-Throughput Nucleotide Sequencing ; *Metagenome ; DNA Copy Number Variations ; }, abstract = {Metagenomic Next-Generation Sequencing (mNGS) enables simultaneous sequencing of both microbial and host nucleic acids in clinical samples. However, analytical approaches for interpreting complex mNGS datasets are seldom disclosed, limiting advancements in multimodal analysis and omics-driven research models built upon mNGS results. We present 402 high-quality bronchoalveolar lavage fluid mNGS DNA and RNA sequencing datasets for developing combined microbial-host metagenomic diagnostic approaches. Only the microbial (non-host) sequence reads have been deposited. We provide comprehensive descriptions of methods, tools, and pipelines used for mining microbial features (DNA/RNA microbial composition and bacteriophage abundances) and host response features (differential expression genes, transposable elements, cell-type composition, and copy number variation). These data processing pipelines set a standard for future multimodal omics diagnostic research, promoting the adoption of standardized practices in omics-based studies that integrate clinical data.}, }
@article {pmid41350118, year = {2025}, author = {Fukase, S and Kouketsu, A and Tamahara, T and Saito, T and Ito, A and Higashi, Y and Kajita, T and Kurobane, T and Miyakoshi, M and Iikubo, M and Shimizu, R and Takahashi, T and Yamauchi, K and Sugiura, T}, title = {Differences in the Oral Microbiome Between Patients With and Without Oral Squamous Cell Carcinoma.}, journal = {Journal of oral pathology &amp; medicine : official publication of the International Association of Oral Pathologists and the American Academy of Oral Pathology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jop.70099}, pmid = {41350118}, issn = {1600-0714}, abstract = {BACKGROUND: Although studies have demonstrated a relationship between pathogenic microorganisms and oral cancer, no study has demonstrated a relationship between changes in bacterial flora and oral squamous cell carcinoma (OSCC). Therefore, we investigated the association between oral microbiota and oral squamous cell carcinoma using metagenomic analysis.<br><br>METHODS: Saliva samples from 64 patients with OSCC and 50 healthy controls who visited the Department of Oral Surgery, Tohoku University Hospital, were collected, and bacterial genomic DNA was extracted using polymerase chain reaction amplification. Single-end sequencing was performed using the Illumina MiSeq platform, and sequence data were analyzed using the Quantitative Insights Into Microbial Ecology 2 platform. The Steel-Dwass test was used for between-group comparisons, and Analysis of Compositions of Microbiomes with Bias Correction was used to detect significant differences in microbiome composition.<br><br>RESULTS: Significant differences were observed in alpha-diversity indices of bacterial flora (richness, Faith- phylogenetic diversity, Shannon index) in the OSCC group compared to those in the control group. Among the OSCC group, patients with larger tumor diameters and lymph node metastases (T3/T4, N1 or greater) formed independent clusters in the beta diversity analysis of the bacterial flora. Bacteria of the Actinomycetia phylum, such as Actinomyces and Rothia, were significantly reduced in patients with higher stage and pathological grade. Conversely, bacteria of the phylum Spirochaetia and Proteobacteria, particularly those of the genus Treponema, were significantly elevated in advanced cancer cases.<br><br>CONCLUSIONS: Our results suggest that changes in the oral microbiota may play a role in OSCC development and progression.}, }
@article {pmid41349993, year = {2026}, author = {Zepernick, BN and Niknejad, DJ and Chase, EE and Abiodun, BA and Adler, MJ and Houghton, KA and Olavesen, JL and Sarumi, Q and Truchon, AR and Walton, JL and Cheshire, JH and Stanislawczyk, K and Hart, LN and Paerl, HW and Chaffin, JD and Boyer, GL and Castro, HF and Campagna, SR and Bullerjahn, GS and Wilhelm, SW}, title = {The ornithine-arginine cycle supported a toxic, metalimnic Planktothrix rubescens bloom.}, journal = {Harmful algae}, volume = {151}, number = {}, pages = {103008}, doi = {10.1016/j.hal.2025.103008}, pmid = {41349993}, issn = {1878-1470}, mesh = {*Cyanobacteria/metabolism/physiology/genetics ; *Arginine/metabolism ; *Ornithine/metabolism ; *Harmful Algal Bloom ; Metagenomics ; }, abstract = {Planktothrix rubescens is distinct from other cyanobacterial harmful algal bloom (cHAB) genera: the crimson-red cHAB thrives in the cold, low-light, nutrient-limited metalimnion. Studies have attributed this ecological success to buoyancy regulation, low-light adaptations, and the uptake of nitrogen-rich amino acids. Yet, it remains to be mechanistically determined how this cHAB maintains physiological nutrient quotas in the metalimnion due to limited in situ molecular studies. We employed metagenomics and metabolomics to generate hypotheses concerning a toxigenic P. rubescens bloom in Mead's Quarry (Knoxville, TN, USA) observed in two separate years. Our results suggest a perennial, metalimnic P. rubescens population may exist, with spring turnover facilitating seasonal migration to the epilimnion. Although P. rubescens dominated the epilimnion and metalimnion, intracellular metabolite pools grouped by depth and suggested depth-discrete partitioning of the arginine deiminase-mediated ornithine-arginine cycle (OAC, i.e., urea cycle) - while further indicating the presence of the arginine catabolic pathway. Though the arginine influx driving the OAC is unclear, we hypothesize this input is provided via the uptake of urea or nitrogen-rich amino acids. Further, we demonstrate arginine deiminase (agrE/argZ) is broadly distributed in Planktothrix genera and known microcystin producers, suggesting agrE/argZ-mediated arginine metabolism and the OAC may influence the fitness of toxigenic cHAB genera which require ample nitrogen to synthesize microcystins. Cumulatively, our results serve as a case study to provide insight on the metabolic pathways driving the ecological success of metalimnic P. rubescens blooms. On a broader scale, this work strengthens the case that alternative nitrogen metabolism - including urea utilization, amino acid catabolism, and the OAC - is a driver of toxigenic cHABs in fresh waters.}, }
@article {pmid41349311, year = {2025}, author = {Manfreda, C and Ghidini, S and Fuschi, A and Remondini, D and Guarneri, F and Alborali, GL and Fernández-Trapote, E and Cobo-Dìaz, JF and Alvarez-Ordóñez, A and Ianieri, A}, title = {In-depth characterization of microbiome and resistome of carcasses and processing environments in a swine slaughterhouse.}, journal = {Veterinary microbiology}, volume = {312}, number = {}, pages = {110820}, doi = {10.1016/j.vetmic.2025.110820}, pmid = {41349311}, issn = {1873-2542}, abstract = {Antimicrobial resistance represents a critical global health challenge. Within the swine production chain, all stages have been identified as potential reservoirs for antimicrobial resistance genes. In the present study whole metagenomic sequencing technology was applied in a swine slaughterhouse and pig carcasses to investigate microbial communities and their associated antimicrobial resistance genes. Actinomycetota and Pseudomonadota were the dominant phyla across all samples, while Bacillota, Bacteroidota, and Campylobacteriota were more prevalent in the dirty zone and carcass samples than in the clean zone. Key antimicrobial-resistant bacteria included genera such as Acinetobacter, Aeromonas, and Streptococcus, with Acinetobacter spp., Streptococcus suis, and Aliarcobacter cryaerophilus identified as high-priority species for food safety due to their persistence and antimicrobial resistance genes associations. Several genera showed strong correlations with resistance to macrolides, lincosamides, and beta-lactams. Moreover, the plasmid-borne and lateral gene transfer events were associated with dirty zone and carcass samples in comparison to clean zone samples, suggesting the potential dissemination of antimicrobial resistance genes, especially for macrolides and sulphonamides resistance genes. Tetracycline, beta-lactam, and aminoglycoside resistance genes were the most abundant antimicrobial resistance genes across all samples, consistent with a pig slaughterhouse environment. This study highlights distinct microbiome profiles across environmental zones of a pig slaughterhouse, reflecting the adaptation of bacterial taxa to specific processing conditions. The findings have significant implications for food business operators who have to apply appropriate hygienic measures to reduce the dissemination of bacterial food-borne pathogens and to mitigate the risk of antimicrobial resistance transfer along the food chain.}, }
@article {pmid41348832, year = {2025}, author = {Cervantes-Echeverría, M and Jimenez-Rico, MA and Manzo, R and Hernández-Reyna, A and Cornejo-Granados, F and Bikel, S and González, V and Hurtado Ramírez, JM and Sánchez-López, F and Salazar-León, J and Pedraza-Alva, G and Perez-Martinez, L and Ochoa-Leyva, A}, title = {Human-derived fecal virome transplantation (FVT) reshapes the murine gut microbiota and virome, enhancing glucose regulation.}, journal = {PloS one}, volume = {20}, number = {12}, pages = {e0337760}, doi = {10.1371/journal.pone.0337760}, pmid = {41348832}, issn = {1932-6203}, mesh = {Animals ; *Gastrointestinal Microbiome ; Humans ; Mice ; *Fecal Microbiota Transplantation/methods ; *Virome ; Male ; Diet, High-Fat/adverse effects ; Obesity/therapy/microbiology ; *Feces/virology ; Mice, Inbred C57BL ; *Glucose/metabolism ; Metabolic Syndrome/therapy/microbiology ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; }, abstract = {The gut microbiome, comprising bacteria, viruses, archaea, fungi, and protists, plays a crucial role in regulating host metabolism and health. This study explored the effects of fecal virome transplantation (FVT) from healthy human donors on metabolic syndrome (MetS) in a diet-induced obesity (DIO) mouse model, without diet change. Mice received a single oral dose of human-derived virus-like particles (VLPs) and continued on a high-fat diet (HFD) for 17 weeks. Despite persistent dietary stress, FVT significantly improved glucose tolerance. Longitudinal profiling by virome shotgun metagenomics and bacterial 16S rRNA sequencing revealed marked, durable shifts in both viral and bacterial community composition. Notable bacterial changes included a decrease in Akkermansia muciniphila and Peptococcaceae and increases in Allobaculum and Coprococcus; A. muciniphila positively correlated with glucose levels and negatively correlated with body weight. Together, these results suggests that human-derived virome can durably reshape gut microbial ecology and improve glucose metabolism in mice with obesity, even without dietary modification, offering a novel avenue for developing phage-based therapies. This proof-of-concept study provides foundational observations for using human-derived VLPs for FVT in standard laboratory mouse models, and provides a foundation for elucidating bacteria-phage interactions and their role in host metabolic health.}, }
@article {pmid41348596, year = {2025}, author = {Hernández-Velázquez, R and Ziemski, M and Bokulich, NA}, title = {ViromeXplore: integrative workflows for complete and reproducible virome characterization.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {6}, pages = {}, doi = {10.1093/bib/bbaf638}, pmid = {41348596}, issn = {1477-4054}, support = {22.00210//Swiss State Secretariat for Education, Research and Innovation/ ; //European Union nor European Research Executive Agency/ ; }, mesh = {*Virome ; *Workflow ; *Metagenomics/methods ; *Software ; High-Throughput Nucleotide Sequencing ; *Computational Biology/methods ; *Viruses/genetics/classification ; Metagenome ; Microbiota ; Genome, Viral ; Reproducibility of Results ; }, abstract = {Viruses play a crucial role in shaping microbial communities and global biogeochemical cycles, yet their vast genetic diversity remains underexplored. Next-generation sequencing technologies allow untargeted profiling of metagenomes from viral communities (viromes). However, existing workflows often lack modularity, flexibility, and seamless integration with other microbiome analysis platforms. Here, we introduce "ViromeXplore," a set of modular Nextflow workflows designed for efficient virome analysis. ViromeXplore incorporates state-of-the-art tools for contamination estimation, viral sequence identification, taxonomic assignment, functional annotation, and host prediction while optimizing computational resources. The workflows are containerized using Docker and Singularity, ensuring reproducibility and ease of deployment. Additionally, ViromeXplore offers optional integration with QIIME 2 and MOSHPIT, facilitating provenance tracking and interoperability with microbiome bioinformatics pipelines. By providing a scalable, user-friendly, and computationally efficient framework, ViromeXplore enhances viral metagenomic analysis and contributes to a deeper understanding of viral ecology. ViromeXplore is freely available at https://github.com/rhernandvel/ViromeXplore.}, }
@article {pmid41348453, year = {2025}, author = {Li, C and Ge, H and Huang, W and Zilda, DS and Radjasa, OK and Zhao, L and Cong, B and Liu, S and Zhang, Z}, title = {Vertically stratified microbial diversity and keystone species driving element cycling in the Magellan seamount sediments.}, journal = {Microbial genomics}, volume = {11}, number = {12}, pages = {}, doi = {10.1099/mgen.0.001493}, pmid = {41348453}, issn = {2057-5858}, mesh = {*Geologic Sediments/microbiology/chemistry ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/metabolism ; Metagenomics/methods ; Archaea/genetics/classification ; Phylogeny ; Biodiversity ; Microbiota ; }, abstract = {Deep-sea polymetallic nodules, rich in cobalt, nickel and titanium, are valuable for electronics, aerospace and energy industries. However, the vertical distribution and ecological functions of prokaryotic communities in sediments beneath nodules from the Magellan seamounts, a unique microbial habitat characterized by ultra-slow sedimentation rates (0.4-4 mm ky[-1]) and heterogeneous metal gradients, remain poorly characterized. In our research, 16S rRNA gene amplicon sequencing and metagenomic analyses of sediment cores (0-20 cm) from the western Pacific polymetallic nodule province revealed statistically significant decreases in prokaryotic diversity (Shannon index: 9.446 to 2.288; P<0.001). Proteobacteria, Crenarchaeota, Chloroflexi and Bacteroidota were the dominant taxa. The microbial co-occurrence network in the surface layer had a longer mean path length (2.11 vs 1 in the bottom layer) and a larger network diameter (11 vs 1), indicating a loose community structure and greater resistance to disturbance, while the bottom microbial network had a higher density (0.037 vs 0.01) and clustering coefficient (0.32 vs 1), suggesting tight microbial interactions. The concentrations of MnO (6.96-9.41 µg g[-1]) and P2O5 (2.55-3.89 µg g[-1]) gradually decreased with increasing depth. The concentrations of Co and Pb were relatively high in the surface sediments (0-8 cm) but decreased significantly below 8 cm. In contrast, the concentrations of Fe2O3 and As increased with depth. The environmental factors depth, MnO, Fe2O3 and heavy metals (Cr, Zn and Cu) were found to be the main drivers of the microbial community structure. We assembled 122 metagenome-assembled genomes from the metagenomic data. Gene abundance analysis revealed that sox genes (soxB/C/D/X/Y/Z) and assimilatory sulphate reduction genes (cysC and cysH) were highly abundant in the surface sediment, whereas the abundance of dissimilatory sulphate reduction genes (dsrA and dsrB) was enhanced in the bottom layer, reflecting a hierarchical adaptive strategy for sulphur metabolism. Our study expands current knowledge on the vertical variations of microbial diversity and microbially driven biogeochemical cycling in deep-sea settings underneath polymetallic nodules. Characterizing the microbial community underneath those nodules may provide insights into microbial resilience in extreme oligotrophic environments and valuable insights for future deep-sea mining activities.}, }
@article {pmid41348443, year = {2025}, author = {Luu, LDW and Bryant, C and Brown, J and Turner, M and Pham, TH and Mazraani, R and Burke, C and Jury, B and Shrestha, M and Fleming, K and Bateson, D and Russell, D and Bassett, F and Ong, E and Hocking, JS and Sweeney, S and Huston, WM}, title = {Cervicovaginal microbiome composition and absolute quantity are associated with pelvic inflammatory disease.}, journal = {Microbial genomics}, volume = {11}, number = {12}, pages = {}, doi = {10.1099/mgen.0.001574}, pmid = {41348443}, issn = {2057-5858}, mesh = {Humans ; Female ; *Pelvic Inflammatory Disease/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Case-Control Studies ; *Vagina/microbiology ; Adult ; *Cervix Uteri/microbiology ; Vaginosis, Bacterial/microbiology ; Gardnerella vaginalis/genetics ; Metagenomics ; *Bacteria/genetics/classification/isolation &amp; purification ; Young Adult ; }, abstract = {Pelvic inflammatory disease (PID), which involves infection and inflammation of the female reproductive tract, can lead to sequelae including chronic pelvic pain, ectopic pregnancy and tubal factor infertility. A causative pathogen is not identified in many PID cases (idiopathic PID) and does not develop in all women with a sexually transmitted infection or bacterial vaginosis. Therefore, there is a need to better understand the pathogenesis of PID. A case-control study was conducted to explore microbiome, antibiotic resistance and immune gene expression in PID. Microbial profiling using both 16S rRNA gene amplicon and metagenomic approaches revealed that bacterial vaginosis-associated bacteria such as Gardnerella vaginalis, Fannyhessea vaginae, Ureaplasma parvum and members of the Prevotella spp. were significantly enriched in PID cases, while healthy controls were associated with Lactobacillus (L.) crispatus. Quantitative analysis with species-specific quantitative real-time PCR (qPCR) indicated that a high copy number of L. crispatus (measured using calibrated copy estimates by qPCR) was strongly associated with cervical samples from women in the control group, whereas PID cases with this organism had low copies when measured using qPCR. Antibiotic resistance to tetracyclines was more frequently predicted in metagenome-assembled genomes from PID cases, and corresponding isolates cultured from cases were less susceptible to doxycycline (L. iners). Overall, this study supports that PID is associated with cervicovaginal dysbiosis and an absence or low quantity of L. crispatus.}, }
@article {pmid41347789, year = {2025}, author = {Malina, N and Tollerson, R and Monami, SJ and Rivera, E and Lee, M-K and Bilenker, LD and Ojeda, AS}, title = {Microbial community diversity and geochemistry inform bioremediation of molybdenum-contaminated groundwater.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0098825}, doi = {10.1128/aem.00988-25}, pmid = {41347789}, issn = {1098-5336}, abstract = {In situ remediation of groundwater at coal combustion product (CCP) sites can be challenging for elements such as molybdenum (Mo), which do not respond well to commonly used treatment. This research was initiated to improve the understanding of geochemistry and microbial diversity associated with a Mo plume at a CCP site toward the development of an in situ treatment scheme. Diffusive microbial samplers were designed and deployed at the study site for 9 weeks. Afterward, geochemical and community analyses were used as the basis to understand how microbial communities respond to elevated Mo concentrations within a plume. Our results show that the Mo and other constituents within the plume do not reduce the diversity of the community, in contrast to trends observed at other industrial sites with metals and metalloids in groundwater. Interestingly, bacteria of the order Burkholderiales were higher in abundance in wells where Mo >0.3 mg/L, and several sulfate-reducing bacteria were less abundant but not absent. Molybdenum sequestration experiments were also performed with sulfate-reducing bacteria enriched from groundwater samples collected at the site. The results show that Desulfomicrobium escambiense played a major role in Mo sequestration and activated a detoxification mechanism. This process involved the sequential activation of periplasmic heavy metal sensors, followed by the activation of atpE ATP synthase, which may function as an exporter of Mo to form Mo-S species in the periplasm of the cell. The results provide important considerations for bioremediation potential in groundwater settings impacted by Mo, especially those who seek to stimulate sulfate-reducing bacteria for Mo sequestration in biogenic sulfide solids.IMPORTANCEBioremediation of contaminated sites has become popular for chlorinated hydrocarbons, but it has not been widely applied to inorganic constituents outside of arsenic. Here, we show the potential for the development of geochemistry-informed bioremediation technologies of Mo-contaminated groundwater by leveraging Mo-tolerant communities despite the suppression of sulfate reduction by Mo.}, }
@article {pmid41347294, year = {2026}, author = {McCaughan, KJ and Kniel, KE}, title = {Current Knowledge and Future Directions for Cyclospora cayetanensis Research and Its Surrogates.}, journal = {Comprehensive reviews in food science and food safety}, volume = {25}, number = {1}, pages = {e70327}, doi = {10.1111/1541-4337.70327}, pmid = {41347294}, issn = {1541-4337}, support = {//National Institute of Food and Agriculture/ ; }, mesh = {*Cyclospora/genetics/isolation &amp; purification/physiology ; *Cyclosporiasis/parasitology/transmission ; Humans ; Animals ; Host-Parasite Interactions ; Oocysts ; Food Parasitology ; Cryptosporidium parvum ; }, abstract = {Cyclospora cayetanensis is a foodborne protozoan parasite that causes cyclosporiasis, a disease transmitted by the consumption of sporulated oocysts, often via contaminated produce. Since 2018, outbreaks traced back to domestically grown produce in the United States have raised growing concern. Despite its public health significance, research is hindered by methodological challenges, including inability to culture in vitro/in vivo and limited genomic characterization. This review examines current knowledge on its occurrence and transmission, detection methods, host-parasite interactions, genetics, and remediation strategies, while also evaluating use of surrogate organisms (Eimeria spp. and Cryptosporidium parvum) to address research gaps. Detection remains challenging due to low oocyst concentrations in environmental and food matrices, requiring highly sensitive molecular assays. Additionally, the lack of standardized sampling methods that are representative of an entire batch of produces further complicates reliable detection and surveillance efforts. The recently implemented Food and Drug Administration (FDA) Bacteriological Analytical Manual (BAM) Chapter 19c method has improved sensitivity but still requires refinement. Although Eimeria spp. offer insight into sporulation and environmental behaviors and C. parvum has supported methodological development, neither fully replicates C. cayetanensis biology; limiting the translatability of surrogate-based research. Remediation strategies are underexplored, though research on related coccidia suggests significant resistances to conventional sanitizers. Genomic advancements, including the identification of distinct C. cayetanensis lineages, provide useful insights, though gaps in genome assemblies limit phylogenetic and functional analyses. Emerging tools, such as metagenomics, single-cell sequencing, and AI-driven bioinformatics, may overcome persistent barriers. Addressing these challenges is essential for improving detection, risk assessment, and guiding policy, all of which will mitigate the public health burden of cyclosporiasis.}, }
@article {pmid41346779, year = {2025}, author = {Orsud, H and Zoughbor, S and AlDhaheri, F and Hajissa, K and Refaey, M and Ajab, S and Alswaider, K and Mohamed, N and Alkaabi, O and Al Rasbi, Z}, title = {Multi-marker comparative analysis of 18S, ITS1, and ITS2 primers for human gut mycobiome profiling.}, journal = {Frontiers in bioinformatics}, volume = {5}, number = {}, pages = {1690766}, pmid = {41346779}, issn = {2673-7647}, abstract = {BACKGROUND: Gut fungi play crucial roles in human health. The profiling of the human gut mycobiome continues to progress. However, adjustments in the selection of ribosomal DNA marker regions can substantially affect the taxonomic resolution of a population. In particular, the impact of using primers' combinations is insufficiently defined. In this study, we investigated the performance of three targeted sequencing regions, ITS1, ITS2 and 18S rRNA, separately and in combination.<br><br>METHODS: Eight fecal samples from healthy individuals (n = 4) and cancer patients (n = 4) were selected as proof of principle for amplicon-based sequencing conducted with the DNBSEQ&#x2122; sequencing system. Quality-filtered reads were grouped into operational taxonomic units (OTUs) via USEARCH and categorized using the SILVA (18S) and UNITE (ITS) databases. Downstream bioinformatics encompassed diversity analyses, principal component analysis (PCA), and biomarker detection via linear discriminant analysis effect size (LEfSe). To improve taxonomic coverage and compositional understanding, data were examined using ALDEx2 with centered log-ratio (CLR) transformation, facilitating reliable differential abundance and effect size assessment in small sample metagenomic contexts.<br><br>RESULTS AND DISCUSSION: Among primers, ITS2 and ITS1 enhanced the coverage of identified taxa, with operational taxonomic unit quantities of 183 and 158, respectively, compared to 58 OTUs of 18S. Accordingly, among primer combinations tested, the triple integration of ITS1-ITS2-18S produced the highest fungal richness, while the dual ITS1-ITS2 combined datasets enhanced group discrimination analysis, showing enrichment of Candida albicans and scarcity of Penicillium sp. in cancer patients. Our findings based on ITS sequencing and the combination of ITS1 and ITS2 provide instructive information on the composition and dynamics of gut fungi in our initial test subjects, enhancing our understanding of their roles in gut homeostasis and the microbial shifts associated with cancer. Despite our approach being conducted with a limited cohort to establish methodological feasibility, it brings attention to multi-marker strategies, demonstrating that integrated primer datasets surpass traditional single-marker methods in both taxonomic coverage and biomarker detection sensitivity in low-biomass fecal samples. Our research provides a reliable starting point for future studies on gut mycobiome in both healthy and diseased individuals, which could lead to better diagnostics and treatments based on microbiome profiles.}, }
@article {pmid41346662, year = {2025}, author = {Ren, M and Liao, Q}, title = {Diagnosis of Salmonella enterica-induced septic arthritis in a healthy child using metagenomic next-generation sequencing: a case report.}, journal = {Frontiers in pediatrics}, volume = {13}, number = {}, pages = {1704234}, pmid = {41346662}, issn = {2296-2360}, abstract = {Salmonella enterica-induced arthritis frequently manifests in children with malignancies, sickle cell disease, immunodeficiency, or undergoing immunosuppressive therapy; however, its incidence in healthy children is rare. Here, we present a case of septic arthritis resulting from S. enterica infection in a previously healthy child, diagnosed utilizing metagenomic next-generation sequencing (mNGS). This case underscores the utility of mNGS in the clinical identification of S. enterica arthritis. Particularly in scenarios where the causative pathogen remains unidentified, mNGS emerges as a pivotal adjunctive diagnostic modality for uncommon pathogens.}, }
@article {pmid41346360, year = {2025}, author = {Huang, J and Li, S and Jiang, C and Wang, L and Pan, Z and Zhang, Z and Zhu, J and Chen, W and Hu, X}, title = {Targeted next-generation sequencing for respiratory infections in patients with haematological malignancies.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1678858}, pmid = {41346360}, issn = {2235-2988}, mesh = {Humans ; *Hematologic Neoplasms/complications ; *Respiratory Tract Infections/diagnosis/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; Middle Aged ; Female ; Male ; Adult ; Aged ; Immunocompromised Host ; Sensitivity and Specificity ; Metagenomics/methods ; Young Adult ; Aged, 80 and over ; Adolescent ; Bacteria/genetics/isolation &amp; purification/classification ; }, abstract = {BACKGROUND: Patients with haematological malignancies are immunocompromised and prone to respiratory infections, but identification of causative pathogens is challenging. The aim of this study was to analyse the ability of targeted next-generation sequencing (tNGS) to detect pathogens in immunocompromised patients.<br><br>METHODS: tNGS and conventional microbiological tests (CMT) were performed on samples from the respiratory tract of 99 patients with suspected respiratory infections. Metagenomic next-generation sequencing (mNGS) was conducted in parallel in 43 patients. Comparative analysis was conducted using the Pearson &#x3c7;2 test and Fisher's exact test, as appropriate.<br><br>RESULTS: The overall microbial detection rates for tNGS were 100% (23/23) in the upper respiratory tract and 96.1% (99/103) in the lower respiratory tract. Microorganism colonization was detected by tNGS in 80.8% (97/120) of cases. The sensitivity of tNGS was approximately 30% higher than that of CMT (87.7% vs. 52.5%; P <&#xa0;0.001), but tNGS had a lower specificity (33.3% vs. 83.3%; P&#xa0;=&#xa0;0.242). tNGS improved the overall treatment success rate by 69.7% (69/99 cases) in CMT true-negative or CMT-partially matched cases. In the paired respiratory tNGS and mNGS cases, tNGS verified 73.3% (11/15) cases of infection, while mNGS only verified 40% (P&#xa0;=&#xa0;0.139).<br><br>CONCLUSIONS: Most immunosuppressed patients are colonized by microorganisms, and require prompt identification of the cause of any infections. tNGS has promising diagnostic potential and offers valuable information for optimizing antibiotic therapy, especially when compared to CMT.}, }
@article {pmid41346331, year = {2025}, author = {Preenanka, R and Sivam, V and Sasikala, R and Koombankallil, R and Raveendran, K and Jacob, J and Devadas, AL and Ravikumar, NK and Anbalakan, M and Chigilipalli, H and Thangaraj, RS and Basha, AK and Joseph, TC and Badireddy, MR and Vaiyapuri, M}, title = {Muscle Microbiome Analysis of Indian Mackerel (Rastrelliger kanagurta) Delineated Classical and Novel Spoilage Bacteria.}, journal = {Journal of food science}, volume = {90}, number = {12}, pages = {e70751}, doi = {10.1111/1750-3841.70751}, pmid = {41346331}, issn = {1750-3841}, support = {BT/PR46349/AAQ/3/1063/2022//&#x2003;Department of Biotechnology/ ; //&#x2003;Department of Biotechnology, Ministry of Science and Technology, India/ ; }, mesh = {Animals ; *Perciformes/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota ; *Seafood/microbiology ; Food Packaging/methods ; Food Microbiology ; RNA, Ribosomal, 16S/genetics ; *Muscles/microbiology ; Vacuum ; Metagenomics ; Food Storage ; }, abstract = {Metagenomics allows a comprehensive insight into the spoilage-associated muscle microbiome shifts in the air-packed and vacuum-packed Indian mackerel. This study explored the microbial composition and diversity of spoilage flora in air-packed (T1M, T2M, and T3M) and vacuum-packed (T4M, T5M, and T6M) Indian mackerel (Rastrelliger kanagurta) stored at 0 ± 2°C (iced), 5 ± 2°C (chilled), and 30 ± 2°C (abused) temperatures through metagenomics, targeting the V1-V9 region of 16s rRNA. Total Volatile Base Nitrogen and Thiobarbituric Acid were analyzed to confirm the spoilage threshold limit, and accordingly, the fish muscle tissue on the spoilage day was selected for microbiome analysis. Metagenomic analysis revealed distinct variation in the relative abundance and spoilage microbiome between the air-packed and vacuum-packed Indian mackerel stored at iced, chilled, and abused temperatures. The predominant bacterial species responsible for spoilage were Cetobacterium ceti, Clostridium polyendosporum, and Gilliamella apicola in vacuum-packed mackerel, whereas Shewanella arctica, S. aquimarina, S. baltica, Staphylococcus xylosus, and Burkholderia cepacia played a major role in the spoilage of air-packed samples. The observed bacterial population dynamics across different temperatures and packaging significantly influenced the microbiome diversity in Indian mackerel. Summing up, this study emphasizes the unique and diverse microbes contributing to spoilage and provides a valuable guide for the flora that need to be controlled for extending the shelf life of Indian mackerel.}, }
@article {pmid41346299, year = {2025}, author = {Zhang, C and Zhao, Z and Zhou, F and Shi, C and Zhai, X and Sha, Z and Chu, Q and Liu, H and Liu, S and Pan, Z and Wang, X and Pan, X and Fang, M and Rillig, MC and Wang, Z}, title = {Conventional and Biodegradable Microplastics Both Impair Soil Phosphorus Cycling and Availability via Microbial Suppression.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c11806}, pmid = {41346299}, issn = {1520-5851}, abstract = {Microplastics (MPs) are emerging soil pollutants that can disrupt essential biogeochemical processes, yet their effects on phosphorus (P) cycling remain underexplored. Here, we conducted a 150-day incubation experiment using agricultural soil amended with either polyethylene (PE, conventional) or polylactic acid (PLA, biodegradable) MPs to investigate their impact on microbially mediated P cycling. MPs altered soil P cycling and decreased available phosphorus (AP) by ∼15% after 90 days. Fourier transform infrared spectroscopy revealed weakened AP-associated functional groups (P-O-P, P-O, and P═O), most pronounced under PLA treatment. These shifts were accompanied by reduced abundances of key P-cycling taxa (Bacillus, Paenibacillus, and Sphingomonas) and downregulation of phosphatase gene abundance (phoA/D/X: -65.4% in PE, -59.8% in PLA). Correspondingly, the activities of acid, neutral, and alkaline phosphatases were all suppressed, with alkaline phosphatase in PE-treated soil reduced by 34.1%. Together, these results demonstrate that MPs disturb biotic transformation pathways, leading to subsequent alterations in the chemical speciation of soil P and decreased AP content. Notably, significant disruption was observed for both conventional and biodegradable types. Our findings challenge the prevailing assumption of environmental benignity for biodegradable plastics and underscore the urgent need for mechanistic assessments of their byproducts. Such disruption may hinder microbial P mobilization and decrease fertilizer use efficiency, ultimately threatening soil health and agricultural sustainability.}, }
@article {pmid41345980, year = {2025}, author = {Jiang, Y and Che, L and Li, SC}, title = {Deciphering the personalized functional redundancy hierarchy in the gut microbiome.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-025-02273-w}, pmid = {41345980}, issn = {2049-2618}, support = {JCYJ20220818101201004//Shenzhen Science and Technology Innovation Program/ ; JCYJ20220818101201004//Shenzhen Science and Technology Innovation Program/ ; JCYJ20220818101201004//Shenzhen Science and Technology Innovation Program/ ; }, abstract = {BACKGROUND: Functional redundancy (FR) in the human gut microbiome is crucial for maintaining stability and resilience, exhibiting a hierarchical structure. However, the precise configuration and functional implications of this hierarchy remain elusive and limited by single-metric measurements. We aimed to develop a method that comprehensively characterizes the hierarchical organization of functional redundancy in personalized microbiomes.<br><br>RESULTS: We represented functional redundancy as a network and developed a structural entropy (SE)-based approach to elucidate FR hierarchy, revealing functional redundancy clusters (FRCs)-groups of species capable of independently executing specific metabolic pathways. Through controlled simulations and cross-cohort analyses spanning 4912 gut metagenomes across 28 disease cohorts, we established that our approach offers higher resolution, more comprehensive measurement, and greater robustness in detecting disease-associated functional patterns than traditional FR methods. In healthy individuals, we observed FR network polycentric structure, which shifted to monocentric structure in non-alcoholic steatohepatitis patients. Vitamin biosynthesis FRCs correlated with microbiota transplantation efficiency, while FRCs specialized in short-chain fatty acid production predicted immunotherapy response and patient survival. Permutation tests validated the causal relationship between SE differences and disease phenotypes, while perturbation experiments revealed that FR keystone species exert disproportionate influence on the system's resilience.<br><br>CONCLUSIONS: Our SE-based approach to functional redundancy analysis provides superior sensitivity compared to conventional metrics by integrating multiple hierarchical levels of functional organization. This methodology establishes a novel perspective for understanding microbiome stability through personalized FR networks, positioning FRCs as promising diagnostic markers and therapeutic targets for microbiome-associated diseases. Video Abstract.}, }
@article {pmid41345979, year = {2025}, author = {Sakanaka, A and Furuno, M and Ishikawa, A and Katakami, N and Inoue, M and Mayumi, S and Kurita, D and Nishizawa, H and Omori, K and Taya, N and Isomura, ET and Kudoh, M and Takeuchi, H and Amano, A and Shimomura, I and Fukusaki, E and Kuboniwa, M}, title = {Diabetes alters the supragingival microbiome through plasma-to-saliva migration of glucose and fructose.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-025-02256-x}, pmid = {41345979}, issn = {2049-2618}, support = {22H03300, 22H00487, 22K10311, 21K18281//Japan Society for the Promotion of Science/ ; JP16gm0710005//Japan Agency for Medical Research and Development/ ; }, abstract = {BACKGROUND: Dental caries, a dysbiotic biofilm disease driven by polymicrobial acidogenesis, often coexists with type 2 diabetes (T2D). Previous studies suggest covarying relationships between circulating and salivary metabolites in patients with T2D. However, the role of hyperglycemia-induced saccharide migration from plasma to saliva in caries pathogenesis remains unclear. Here, we developed a novel method for untargeted metabolomics profiling of trace saliva from sublingual and submandibular glands, comparing this profile with those of plasma and whole saliva in participants with T2D (n = 31) and those with normoglycemia (n = 30). This comparison aimed to determine how circulating saccharide migration into the oral cavity and its subsequent microbial consumption are linked to dental caries. Additionally, shotgun metagenomic sequencing was combined with this analysis to investigate the cariogenic impact of circulating saccharide migration on the composition and function of supragingival biofilm using MetaPhlAn4 and HUMAnN3 pipelines.<br><br>RESULTS: The metabolomics profiles of glandular saliva showed intermediate dissimilarity between plasma and whole saliva, reflecting cardiometabolic traits more sensitively than whole saliva. Glucose and fructose showed a decreasing positive correlation with glycemic parameters in the order of plasma, glandular saliva, and whole saliva, suggesting systemic-to-oral migration and subsequent microbial consumption. Saccharide migration was more pronounced in participants with dental caries and plaque accumulation, coinciding with shifts in supragingival microbiota, including depletion of Streptococcus sanguinis, Corynebacterium durum, and Rothia aeria, and enrichment of Streptococcus mutans, Veillonella parvula, and Actinomyces sp. oral taxon 448. Glycolytic potential increased at the community level. Improved glycemic control reduced fructose migration and mitigated dysbiosis, decreasing fructose phosphotransferase abundance and shifting the S. mutans-S. sanguinis balance. Experimental validation demonstrated that fructose promotes S. mutans dominance over S. sanguinis in dual-species biofilms.<br><br>CONCLUSIONS: This study establishes saccharide migration as a metabolic driver of supragingival dysbiosis in T2D. The findings highlight the role of both glucose and fructose in caries pathogenesis and suggest that glycemic control could serve as an effective strategy as part of caries control. Video Abstract.}, }
@article {pmid41345977, year = {2025}, author = {Saati-Santamaría, Z and González-Dominici, LI and Jiménez-Gómez, A and Morais, D and Tláskal, V and Frontela, I and Benada, O and Qi, L and Sheng, Y and Rivas, R and Baldrian, P and García-Fraile, P}, title = {Transcriptome-guided discovery of novel plant-associated genes in a rhizosphere Pseudomonas.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-025-02277-6}, pmid = {41345977}, issn = {2049-2618}, support = {101090267//HORIZON-TMA-MSCA-PF-EF/ ; PID2023-150384NB-I00//European Union NextGenerationEU/PRTR/ ; TED2021-129157B-100//MICIU/AEI/10.1309/501100011033/ ; CLU-2025-2-04//Escalera de Excelencia - Consejer&#xed;a de Educaci&#xf3;n de Castilla y Le&#xf3;n - ERDF/ ; RYC2023-045204-I//MCIU/AEI/10.13039/501100011033 and ESF+/ ; 750795//EUROPEAN UNION'S HORIZON 2020/ ; }, abstract = {BACKGROUND: Microorganisms play important ecological roles during interactions with plants, with some strains promoting plant performance. However, the molecular basis of bacterial adaptation to the plant environment remains poorly understood. Microbial plant growth promotion is a complex process that likely involves numerous bacterial genes, many of which remain uncharacterized. In this study, we aimed to identify genes tightly associated with the bacterial adaptation to plant hosts by integrating transcriptomic data from bacteria colonizing roots with comparative genomic and metagenomic analyses.<br><br>RESULTS: Here, we identified a set of bacterial genes that were significantly upregulated during root colonization and are more abundant in rhizosphere communities than in bulk soils. Many of these genes had not been previously linked to plant-bacteria interactions. Comparative genomic analyses revealed some of these genes as more prevalent in plant-associated Pseudomonas genomes than in genomes from other environments. We argue that these genes may play relevant biological roles in this host, although only a few have been previously associated with plant colonization. Among them, we focused on a gene homologous to yafL, which encodes a cysteine peptidase of the NlpC/P60 family, known for its role in peptidoglycan remodelling. This gene is more abundant in rhizosphere microbiomes than in bulk soils, and it showed induced expression on the root surface, supporting its ecological relevance in root-associated environments. Functional validation using a knockout mutant confirmed its contribution to plant-bacteria interactions by affecting root architecture and plant growth.<br><br>CONCLUSIONS: This study provides new insights into the genetic basis of bacterial adaptation to the plant root environment. By integrating transcriptomic and comparative genomic analyses, we identified numerous genes upregulated during root colonization that are enriched in plant-associated Pseudomonas genomes. Our findings highlight previously overlooked bacterial functions with potential roles in plant-microbe interactions. The functional validation of a protein of the NlpC/P60 family supports its involvement in plant-bacteria interactions and underscores the importance of uncharacterized genes in shaping beneficial associations in the rhizosphere. Video Abstract.}, }
@article {pmid41345889, year = {2025}, author = {Bessière, P and Hayes, B and Fusade-Boyer, M and Sécula, A and Rous, G and Brun, J and Marchand, A and Croville, G and Cadiergues, MC and Guérin, JL}, title = {Seroprevalence and genetic diversity of feline immunodeficiency virus in outdoor cats in France.}, journal = {Veterinary research}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13567-025-01672-z}, pmid = {41345889}, issn = {1297-9716}, abstract = {Feline immunodeficiency virus (FIV) is a retrovirus that causes lifelong infections in cats and may lead to immune dysfunction. Despite its importance for feline health, there is limited FIV data from France. This study investigated samples collected from stray and owned cats with outdoor access across France between December 2023 and January 2025 to estimate FIV seroprevalence, identify seropositivity predictors and analyse the genetic diversity of circulating strains. Serological screening was performed using a commercial ELISA. Polymerase chain reaction (PCR) was conducted on ELISA-positive sera, with selected samples analysed by Sanger sequencing for phylogenetic inference. One sample underwent metagenomic shotgun sequencing using Oxford Nanopore technology. The national seroprevalence, estimated using a Bayesian hierarchical model, was 16% (95% credible interval: 8.4-20%) overall, then 31% (21-42%) among intact male cats, 18% (CrI: 10.6-25.2%) among neutered male cats and 8.4% (CrI: 1.8-14%) among female cats. Outdoor exposure, sex and neuter status were strong predictors of seropositivity. Among strays, predicted probability of seropositivity exceeded 50% by 5 years of age. All sequenced viruses were classified as subtype A. However, the phylogenetic analysis revealed notable genetic variability, indicating at least two independent introductions of FIV into France. While related to other European strains, several isolates appeared to share distinct ancestral lineages. The metagenomic dataset yielded approximately 100,000 FIV reads among 2 million total reads, enabling full genome recovery. These findings highlight the ongoing circulation of FIV in France and provide valuable data for veterinary practitioners and future surveillance efforts in Europe.}, }
@article {pmid41345831, year = {2025}, author = {Bu, Y and Sun, F and Liu, L and He, X and Wang, H and Chen, Z and He, T and Xu, S and Zhao, X and Meng, X}, title = {Comparative study on the rumen microbial communities and functions between Wagyu and Holstein calves.}, journal = {BMC genomics}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12864-025-12392-1}, pmid = {41345831}, issn = {1471-2164}, support = {CX23YQ31//Heilongjiang Agricultural Science and Technology Innovation Leapfrog Project/ ; CARS-37//Supported by China Agriculture Research System of MOF and MARA/ ; }, abstract = {BACKGROUND: Understanding the rumen microbiota's development in calves is essential for optimizing breed-specific feeding strategies. This study aimed to comparatively investigate the dynamic changes in the rumen microbial community structure and function in Wagyu and Holstein calves.<br><br>METHODS: Five 3-month-old Wagyu calves and five age-matched Holstein calves were selected. All animals received the same diet consisting of concentrate and hay, with free access to feed and water. Rumen fluid samples were collected monthly from 3 to 6 months of age. Metagenomic sequencing was performed to assess microbial composition (phylum and genus levels), alpha diversity (Shannon, Simpson, ACE, and Chao1 indices), and functional pathway (KEGG-based).<br><br>RESULTS: The cumulative relative abundance of dominant taxa at both phylum and genus levels declined with age in both breeds, more markedly in Wagyu calves than in Holsteins. From 3 to 6 months of age, the top five phyla combined dropped by 3.25% in Wagyu and 0.87% in Holstein calves, whereas the top ten genera combined decreased by 1.63% and 0.63%, respectively. Alpha diversity in Wagyu calves increased significantly with age. At 5 and 6 months, the Shannon, ACE, and Chao1 indices were significantly higher than those at 3 months (P&#x2009;<&#x2009;0.05). Moreover, from 4 to 6 months, Wagyu calves consistently exhibited significantly higher diversity indices than Holsteins (P&#x2009;<&#x2009;0.05). At 6 months, Wagyu calves showed a significant reduction in metabolism-related microbial genes and an increase in genes related to cellular processes and genetic information processing compared to earlier ages and Holstein calves (P&#x2009;<&#x2009;0.05).<br><br>CONCLUSIONS: These findings suggest potential breed-specific differences in the succession and functional maturation of rumen microbiota. Holstein calves developed earlier and more stable metabolic functions, while Wagyu calves underwent a more dynamic microbial selection process.<br><br>CLINICAL TRIAL NUMBER: Not applicable.}, }
@article {pmid41345737, year = {2025}, author = {Li, F and Yan, M and Su, D and Peng, J and Wang, X and Hao, J and Ma, T and Lin, Y and Shi, H}, title = {Integrated meta-omics reveals AFB1 dose-dependent remodeling of the rumen microbiome-virome-metabolome axis driving metabolic impairment in goats.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-025-02291-8}, pmid = {41345737}, issn = {2049-2618}, support = {grant no. 31902187//National Natural Science Foundation of China/ ; SCCXTD-2024-14//Innovation Team Development Funds for Sichuan Meat Goat and Sheep/ ; }, abstract = {BACKGROUND: Aflatoxin B1 (AFB1), a highly carcinogenic and hepatotoxic mycotoxin frequently contaminating animal feed, presents serious health risks to both humans and livestock. Although AFB1's hepatotoxicity and other organ damage are extensively characterized, how this mycotoxin influences ruminal microbiota dynamics and functional activities in ruminants remains underexplored. Although some studies suggest that AFB1 reduces nutrient digestibility and performance in ruminants, the underlying mechanisms are unclear. To aid in developing effective mitigation strategies for aflatoxicosis in ruminants, this study randomly divided Saanen goats into three groups. The CON group received the standard ration without additives, whereas LD and HD groups were provided identical basal diets fortified with 50 or 500 μg/kg AFB1. Throughout the study, alterations in ruminal fermentation parameters, microbiome, and metabolome profiles were analyzed.<br><br>RESULTS: With increasing AFB1 levels, ruminal pH, the concentration of total volatile fatty acids (VFA), acetate, and propionate decreased quadratically, while butyrate decreased linearly. Metagenomic profiling indicated suppressed populations of Pelagibacter and Flavobacterium following AFB1 exposure, contrasting with promoted growth of Cryptobacteroides. Additionally, seven carbohydrate-active enzymes (CAZymes), specifically GT92, GT20, CE7, GT32, GT35, GT57, and GT50, were found to be more prevalent in the rumen of the CON group. Statistically higher viral loads characterized the HD group when benchmarked against CON group. Metabolomics analysis identified 1197 differential metabolites among the CON, LD, and HD groups, including cytochalasin Ppho and chrysophanol, both known for their teratogenic properties and their ability to induce cell death.<br><br>CONCLUSIONS: This study indicates that dietary AFB1 exposure can alter the ruminal microbial and metabolomic profiles, induce prophage activation, and impact carbohydrate degradation and microbial protein turnover. These alterations may contribute to reductions in ruminal pH and volatile fatty acid concentrations, thereby impairing feed digestibility and animal performance. The findings provide valuable insights into AFB1's effects on rumen health, and further investigations of these metabolic pathways may help develop precision interventions to mitigate AFB1-induced rumen dysfunction and productivity losses. Video Abstract.}, }
@article {pmid41345617, year = {2025}, author = {Franco-Duarte, R and Saati-Santamaría, Z and Choowong, P and Dharmarathne, G and Menéndez, E and Soares, P and Rito, T and Cheung, W and Spahr, A and Eberhard, J and Jayasinghe, TN}, title = {Oral-associated bacteria in the gut microbiome of individuals with type 2 diabetes: a secondary analysis of metagenomic data.}, journal = {BMC oral health}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12903-025-07285-4}, pmid = {41345617}, issn = {1472-6831}, }
@article {pmid41345487, year = {2025}, author = {Karnachuk, OV and Panova, IA and Rusanov, II and Avakyan, MR and Lukina, AP and Ikkert, OP and Kijar, N and Kadnikov, VV and Beletsky, AV and Danilova, EV and Kopitsyn, DS and Pimenov, NV and Shcherbakova, VA and Ravin, NV}, title = {Thermophilic and mesophilic sulfate reduction by rare biosphere bacteria in acidic metal-bearing mine wastes from the temperate climate zone.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-025-28271-4}, pmid = {41345487}, issn = {2045-2322}, support = {24-14-00396//Russian Science Foundation/ ; 24-14-00396//Russian Science Foundation/ ; 24-14-00396//Russian Science Foundation/ ; 24-14-00396//Russian Science Foundation/ ; 24-14-00396//Russian Science Foundation/ ; 24-14-00396//Russian Science Foundation/ ; 22-14-00178-&#x420;//Russian Science Foundation/ ; 22-14-00178-&#x420;//Russian Science Foundation/ ; 22-14-00178-&#x420;//Russian Science Foundation/ ; }, abstract = {Dissimilatory sulfate reduction is the main microbial process that detoxifies metals and increases pH in acid mine drainage. Acidophilic, copper-resistant Desulfosporosinus sp. BG and Desulfosporosinus sp. OT were previously isolated from acidic metalliferous tailings of the Bom-Gorkhon mine in Transbaikalia and Norilsk, respectively. To understand the role of sulfate-reducing bacteria (SRB) in mine tailings, we returned to the Bom-Gorkhon site to measure sulfate-reduction rate (SRR) with radioactive tracer and to estimate the proportion of SRB in the microbial community using 16 SrRNA gene profiling and metagenomic analysis. The SRR measured under ambient temperature conditions was high, reaching 9.86 ± 0.89 µmol SO4 cm[- 3] day[- 1]. Unexpectedly for a temperate biotope, SRR values of the same order of magnitude were recorded at 60 °C. Thermophilic spore-forming Desulfotomaculum and Desulfofundulus are likely involved in the thermophilic process. The spores of thermophilic Desulfofundulus germinating at 20 °C may input into sulfate reduction at in-situ temperature conditions. Metagenomic analysis by dsr gene mapping and 16 S rRNA gene profiling revealed low abundance of Desulfosporosinus and other SRBs, indicating that geochemically important active sulfate reduction in acidic wetland sediments is carried out by a "rare biosphere" consortium. The cultivated BG[T] and OT strains are described as Desulfosporosinus cupriresistens sp. nov.}, }
@article {pmid41345261, year = {2025}, author = {Ma, J and Kim, N and Cha, JH and Kim, W and Kim, CY and Lee, YH and Kim, HS and Han, YD and Yong, D and Han, E and Yang, S and Beck, S and Lee, I}, title = {A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {41345261}, issn = {2058-5276}, support = {2022M3A9F3016364//National Research Foundation of Korea (NRF)/ ; 2022R1A2C1092062//National Research Foundation of Korea (NRF)/ ; }, abstract = {Understanding the human gut microbiome requires comprehensive genomic catalogues, yet many lack geographic diversity and contain medium-quality metagenome-assembled genomes (MAGs) missing up to 50% of genomic regions, potentially distorting functional insights. Here we describe an enhanced Human Reference Gut Microbiome (HRGM2) resource, a catalogue of near-complete MAGs (≥90% completeness, ≤5% contamination) and isolate genomes. HRGM2 comprises 155,211 non-redundant near-complete genomes from 4,824 prokaryotic species across 41 countries, representing a 66% increase in genome count and a 50% boost in species diversity compared to the Unified Human Gastrointestinal Genome catalogue. It enabled improved DNA-based species profiling, resolution of strain heterogeneity and survey of the human gut resistome. The exclusive use of these genomes improved metabolic capacity assessment, enabling high-confidence, automated genome-scale metabolic models of the entire microbiota and revealing disease-associated microbial metabolic interactions. This resource will facilitate reliable functional insights into gut microbiomes.}, }
@article {pmid41345243, year = {2025}, author = {Ste Marie, J and Mays, C and Guo, B and Radniecki, TS and Waite-Cusic, J and Navab-Daneshmand, T}, title = {Longitudinal replicated metagenomic analysis of biosolids-amended soils reveals enrichment of ARGs, virulence factors, and ESKAPE pathogens.}, journal = {npj antimicrobials and resistance}, volume = {3}, number = {1}, pages = {96}, pmid = {41345243}, issn = {2731-8745}, support = {2018-67017-27631//USDA National Institute of Food and Agriculture, Agricultural and Food Research Initiative Competitive Program, Agriculture Economics and Rural Communities/ ; }, abstract = {Biosolids land application introduces antibiotic resistance genes (ARGs) and clinically relevant pathogens into agricultural soils, raising concerns about long-term environmental and public health impacts. Despite growing interest in biosolids reuse, there remains a critical need for replicated, longitudinal studies to assess how biosolids amendments shape soil microbiomes and resistomes during crop cultivation. In this replicated longitudinal greenhouse study, we used shotgun metagenomics to characterize the impact of biosolids amendment on the soil microbiome, resistome, virulence factors, and ESKAPE pathogens during carrot cultivation. Biosolids-amended soils exhibited increased richness of microbial genera (e.g., Rhodanobacter, Dyella, and Thermomonas), ARG subtypes (resistance to sulfonamide, tetracycline, fosmidomycin, and macrolides), and virulence factors compared to pristine controls. Notably, all six ESKAPE pathogens, including Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp., were detected at elevated relative abundances (1.4- and 3.4-fold) in biosolids-amended soils and remained detectable throughout the 11-week cultivation period. Network analysis revealed statistically supported co-occurrences between microbial taxa and ARGs (with resistance to tetracyclines, beta-lactams, chloramphenicol, and multidrugs), suggesting possible host associations. These findings underscore the ecological and clinical relevance of biosolids amendment and highlight the need for integrated surveillance frameworks to mitigate antimicrobial resistance dissemination in agricultural environments.}, }
@article {pmid41345146, year = {2025}, author = {Kar, S and Reddy, MK and Asthana, R and Srivastava, P and Dhaarani, R and Reddy, KVNS and Meghamala, V and Koduru, JR and Karri, RR}, title = {Synergistic effects of syzygium cumini sawdust biochar and poultry manure on soil quality enhancement, nitrogen, organic carbon dynamics, and Amaranthus cruentus growth.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-025-25003-6}, pmid = {41345146}, issn = {2045-2322}, support = {Ref. No-2022/0149//GITAM Research Seed Grants/ ; }, abstract = {The study aimed to evaluate the potential of incorporating biochar with poultry manure to address the constant challenges of sandy, loam soils due to poor water retention and low soil fertility, and their influence on the growth and yield of Amaranthus cruentus during the Rabi and Kharif seasons. The combined effect of manures on soil health over different seasons was unexplored, so the current research has been taken up to understand the impact of different treatments on physical, chemical, and microbial dynamics in the Rabi and Kharif seasons. Advanced statistical analysis was used to measure the soil and plant factor variations across seasons. Pre- and post-harvest results showed substantial progress in the soil bulk density, water-holding capacity (WHC), and nutrient retention in KR5 (biochar + poultry manure) treatment, where WHC displayed a strong positive correlation with organic matter (r > 0.82). Even chemical analysis indicated increased soil nitrogen, phosphorus, potassium, and carbon levels. Metagenomic analysis implied microbial diversity and abundance promoting nitrogen fixation and decomposition of organic matter. FTIR and SEM also revealed structural improvements that are beneficial for microbial colonization and nutrient retention. The combination of biochar and poultry manure showed higher growth, increasing plant height by 40 cm and yielding over 550 g/m[2] during the Kharif season. The results have revealed that the combination of biochar and poultry manure has improved soil fertility, microbial diversity, and yield of Amaranthus cruentus grown in sandy loam soils.}, }
@article {pmid41345123, year = {2025}, author = {Tucker, SJ and Füssel, J and Freel, KC and Kiefl, E and Freel, EB and Ramfelt, O and Sullivan, CES and Gajigan, AP and Mochimaru, H and de Souza, MR and Quinn, M and Ratum, C and Tran, LL and Sobczyk, M and Miller, SE and Trigodet, F and Lolans, K and Morrison, HG and Fallon, B and Huettel, B and Pan, T and Rappé, MS and Eren, AM}, title = {A high-resolution diel survey of surface ocean metagenomes, metatranscriptomes, and transfer RNA transcripts.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1913}, pmid = {41345123}, issn = {2052-4463}, support = {687269//Simons Foundation/ ; 989028//Simons Foundation/ ; 989028//Simons Foundation/ ; 2019589//NSF | GEO | Division of Ocean Sciences (OCE)/ ; }, mesh = {*Metagenome ; Pacific Ocean ; *Transcriptome ; *RNA, Transfer/genetics ; *Seawater/microbiology ; Ecosystem ; Microbiota ; }, abstract = {The roles of marine microbes in ecosystem processes are inherently linked to their ability to sense, respond, and ultimately adapt to environmental change. Capturing the nuances of this perpetual dialogue and its long-term implications requires insight into the subtle drivers of microbial responses to environmental change that are most accessible at the shortest scales of time. Here, we present a multi-omics dataset comprising surface ocean metagenomes, metatranscriptomes, tRNA transcripts, and biogeochemical measurements, collected every 1.5 hours for 48 hours at two stations within coastal and adjacent offshore waters of the tropical Pacific Ocean. We expect that this integrated dataset of multiple sequence types and environmental parameters will facilitate novel insights into microbial ecology, microbial physiology, and ocean biogeochemistry and help investigate the different mechanisms of adaptation that drive microbial responses to environmental change.}, }
@article {pmid41345120, year = {2025}, author = {Abad-Recio, IL and Rubel, V and Filker, S and Garate, L and Stoeck, T and Logares, R and Lanzén, A}, title = {The Basque Coast Estuarine Sediment Gene Catalogue.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1909}, pmid = {41345120}, issn = {2052-4463}, support = {Fi 2089/3-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; STO 414/19-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, mesh = {*Estuaries ; *Geologic Sediments/microbiology ; Archaea/genetics ; Metagenomics ; Bacteria/genetics ; Biodiversity ; Ecosystem ; Eukaryota/genetics ; Viruses/genetics ; }, abstract = {Estuaries are critical transition zones that link marine, riverine, and terrestrial ecosystems, including habitats like intertidal mudflats and tidal marshes. These ecosystems are biodiversity hotspots providing essential ecological functions such as nutrient cycling and pollutant removal. Despite their importance, there is a significant knowledge gap regarding the ecological functioning of these habitats and how they are impacted by anthropogenic pressures. From intertidal estuarine benthos along the Basque Coast 92 microbial metagenomic assemblies were retrieved that allowed us to reconstruct 390 medium plus 81 high quality MAGs, along with 108 million putative genes from bacteria, archaea, eukaryotes, and viruses. This unique dataset will enhance our understanding of ecosystem functioning, biodiversity, and be useful to reveal biogeochemical processes and the role of unculturable biomass.}, }
@article {pmid41345102, year = {2025}, author = {Pope, R and Visconti, A and Zhang, X and Louca, P and Baleanu, AF and Lin, Y and Asnicar, F and Bermingham, K and Wong, KE and Michelotti, GA and Wolf, J and Segata, N and Berry, SE and Spector, TD and Leeming, ER and Gibson, R and Menni, C and Falchi, M}, title = {Faecal metabolites as a readout of habitual diet capture dietary interactions with the gut microbiome.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {10051}, pmid = {41345102}, issn = {2041-1723}, support = {27/2023//Chronic Disease Research Foundation (CDRF)/ ; }, mesh = {Humans ; *Feces/chemistry/microbiology ; *Gastrointestinal Microbiome/physiology ; *Diet ; Male ; Female ; Metabolome ; Middle Aged ; Metabolomics/methods ; Aged ; Metagenomics ; Adult ; Machine Learning ; }, abstract = {The interplay between diet and gut microbiome composition is complex. Faecal metabolites, the end products of human and microbial metabolism, provide insights into these interactions. Here, we integrate faecal metabolomics, metagenomics, and habitual dietary data from 1810 individuals from the TwinsUK and 837 from the ZOE PREDICT1 cohorts. Using machine learning models, we find that faecal metabolites accurately predict reported intakes of 20 food groups (area under the curve (AUC) > 0.80 for meat, nuts and seeds, wholegrains, tea and coffee, and alcohol) and adherence to seven dietary patterns (AUC from 0.71 for the Plant-based Diet Index to 0.83 for the Dietary Approaches to Stop Hypertension score). Notably, the faecal metabolome is a stronger predictor of atherosclerotic cardiovascular disease risk (AUC = 0.86) than the Dietary Approaches to Stop Hypertension score (AUC = 0.66). We identify 414 associations between 19 food groups and 211 metabolites, that significantly correlate with microbial α-diversity and 217 species. Our findings reveal that faecal metabolites capture mediations between diet and the gut microbiome, advancing our understanding of diet-related disease risk and informing metabolite-based interventions.}, }
@article {pmid41344778, year = {2026}, author = {Li, Z and Zhao, C and Mao, Z and Zhao, L and Penttinen, P and Zhang, S}, title = {Metagenomics insights into bacterial community, viral diversity and community-scale functions in fermented red pepper.}, journal = {Food microbiology}, volume = {135}, number = {}, pages = {104986}, doi = {10.1016/j.fm.2025.104986}, pmid = {41344778}, issn = {1095-9998}, mesh = {Fermentation ; *Capsicum/microbiology/virology ; Metagenomics ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism/virology ; *Fermented Foods/microbiology/virology ; Gene Transfer, Horizontal ; *Viruses/genetics/classification/isolation &amp; purification ; Bacteriophages/genetics/classification/isolation &amp; purification ; *Microbiota ; Food Microbiology ; }, abstract = {Fermented red peppers (FRPs) provide distinct flavor and possible health benefits, but understanding of their microbial functions, viral diversity, pathogenicity, and horizontal gene transfer (HGT) patterns remains limited. Integrated multi-method analysis revealed FRP's bacterial community was dominated by Bacillus (21.52 %), Lactobacillus sensu lato (14.27 %), and Pantoea (13.60 %). Bacillus drove core fermentation with an over 40 % contribution to carbon degradation and iron reduction. The virome was dominated by Caudoviricetes phages, yet 25.5 % of the functions of viral genes remained unknown. Critically, multidrug resistance genes were the most abundant ARGs, and beneficial bacteria served as major reservoirs for ARGs, co-occurring with potential opportunistic pathogens. Despite inhibitory conditions, these last dominated key metabolic nodes hydrogen generation and acetate oxidation. Counterintuitively, ARG profiles correlated with bacterial composition but not with mobile genetic elements or detected HGT events, challenging HGT as the primary ARG driver. These findings necessitate dual strategies: leveraging key microbes for fermentation efficiency while implementing stringent monitoring to mitigate pathogen and ARG related risks.}, }
@article {pmid41344758, year = {2026}, author = {Okoye, CO and Ezenwanne, BC and Olalowo, OO and Ajanwachukwu, OJ and Chukwudozie, KI}, title = {Microbial-mycotoxin interactions in food: A review of ecotoxicological implications and omics approaches for understanding detoxification mechanisms.}, journal = {Food microbiology}, volume = {135}, number = {}, pages = {104955}, doi = {10.1016/j.fm.2025.104955}, pmid = {41344758}, issn = {1095-9998}, mesh = {*Mycotoxins/metabolism/toxicity ; *Food Contamination/analysis ; *Fungi/metabolism/genetics ; *Food Microbiology ; Ecotoxicology ; Inactivation, Metabolic ; Animals ; Humans ; Genomics ; }, abstract = {Mycotoxins, toxic secondary metabolites produced by fungi such as Aspergillus, Fusarium, and Penicillium, frequently contaminate food supplies, posing risks to human health, animal welfare, and ecosystem stability. Mycotoxins like aflatoxins, ochratoxin A, fumonisins, trichothecenes, and zearalenone disrupt microbial communities, food chains, and environmental matrices, with synergistic interactions amplifying their toxicity. This review explores microbial-mycotoxin interactions in food systems, focusing on ecotoxicological implications and omics approaches for elucidating detoxification mechanisms. Microbial detoxification, through adsorption by cell wall components (e.g., β-glucans) or enzymatic biodegradation (e.g., lactonases, oxidoreductases), offers a sustainable alternative to physical and chemical methods. However, challenges include variable detoxification efficiency, mechanistic uncertainties, regulatory hurdles, and the detection of masked mycotoxins in complex food matrices. Omics technologies such as metagenomics, genomics, transcriptomics, and their integration provide comprehensive insights into microbial diversity, gene expression, enzyme activity, and metabolite transformations. In addition, omics integration enhances understanding of microbial-mycotoxin dynamics, supporting targeted biocontrol strategies. Future prospects include leveraging synthetic biology, CRISPR-based gene editing, and machine learning-assisted bioinformatics to optimize microbial strains and predict detoxification outcomes. By addressing these challenges, omics-driven approaches can mitigate mycotoxin contamination, ensure food safety, and reduce ecotoxicological impacts across global food systems.}, }
@article {pmid41344333, year = {2025}, author = {Cao, Y and Bowker, MA and Feng, Y and Delgado-Baquerizo, M and Xiao, B}, title = {The Great Wall of China harbors a diverse and protective biocrust microbiome.}, journal = {Current biology : CB}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cub.2025.10.087}, pmid = {41344333}, issn = {1879-0445}, abstract = {The Great Wall of China, one of the most emblematic human heritage sites ever built, is largely covered by a living skin that has a potentially distinct microbiome compared with bare wall surfaces. However, the structure and function of this microbiome remain virtually unknown, which hampers any effort to understand the impacts of this microbiome on the long-term conservation of the Great Wall. Here, we investigated the microbiome of the Great Wall at six sampling sites along a 600-km section, which stretches across arid and semiarid climates and is covered by a mosaic of biological soil crusts (biocrusts) and exposed wall surfaces. We hypothesized that these biocrusts could establish a unique microhabitat and support a microbiome with a community structure and function potentially distinct from those on bare walls, thereby modulating the biodeterioration processes affecting the Great Wall. Our findings revealed that biocrust-covered sections exhibited a 12%-62% increase in abundance, diversity, and co-occurrence network complexity for bacterial and fungal communities compared with bare walls. Further metagenomic analyses indicated that the biocrust cover enhanced the abundance of overall functional genes and stress-resistance pathways within the microbiome by 4%-15%, while decreasing the metabolic pathways linked to heritage biodeterioration. Aridity was an additional determinant of the microbiome. Our work serves as a critical step toward understanding the microbiome of the Great Wall, which contributes to conserving this unparalleled human monument for future generations.}, }
@article {pmid41344255, year = {2025}, author = {Chen, X and Wu, Y and Xue, B and You, Y and Yin, L and Wang, S and Zheng, J}, title = {Mechanism of flavor formation in Suansun fermented by Lactiplantibacillus plantarum during a three-stage flavor formation model.}, journal = {Food chemistry}, volume = {499}, number = {}, pages = {147316}, doi = {10.1016/j.foodchem.2025.147316}, pmid = {41344255}, issn = {1873-7072}, abstract = {This study employed an integrated multi-omics approach-metagenomics, metatranscriptomics, and metabolomics-to elucidate the flavor formation mechanism in Suansun, leading to the proposal of a three-stage flavor formation model. In the initial stage, Lactiplantibacillus plantarum dominates pyruvate metabolism, rapidly producing lactic acid and creating an acidic environment that drives microbial succession. This pH shift initiates the key flavor-forming stage, during which peak levels of Weissella cibaria align with linalool biosynthesis, suggesting strong temporal coordination. During the mid-to-late stages, the abundance of Clostridium species was strongly correlated with p-cresol generation via tyrosine catabolism, while Lactococcus and related taxa produce nonanal and ketones through fatty acid β-oxidation. Overall, the starter culture actively restructures the fermentation niche, sequentially activating metabolic pathways in successive microbial communities to shape a stable flavor profile. This staged model of flavor evolution provides a scientific foundation for optimizing and controlling Suansun fermentation quality.}, }
@article {pmid41344131, year = {2025}, author = {Liu, T and Li, L and Chen, J and Cai, G and Meng, F and Jiao, Y and Mao, Y and Wang, Z and Zuo, W and Tian, Y and Sun, H}, title = {Real-world aged microplastics exacerbate antibiotic resistance genes dissemination in anaerobic sludge digestion via enhancing microbial metabolite communication-driven pilus conjugative transfer.}, journal = {Water research}, volume = {290}, number = {}, pages = {125056}, doi = {10.1016/j.watres.2025.125056}, pmid = {41344131}, issn = {1879-2448}, abstract = {The dissemination of antibiotic resistance genes (ARGs) facilitated by coexisting microplastics (MPs) in the "source-sink" hotspots of waste activated sludge (WAS) raises great concern. Despite real-world MPs undergoing aging, whether and how naturally aged microplastics (AMPs) affect ARG dissemination during sludge treatment remains largely unknown. Herein, we systematically explored the evolved effects and underlying mechanisms of environmentally relevant MPs (0, 3, and 30 mg/kg TS) aging on ARG propagation in anaerobic sludge digestion via multi-omics analyses. Specifically, microplastic exposure increased total ARG abundance by 2.59-15.31 % with enriched mobile genetic elements (MGEs, 0.22-16.71 %). These effects were escalated at higher microplastic dosages and aging degrees. Mechanistically, metagenomic and metaproteomic analyses revealed the drivers for ARG amplification in the sludge digester evolved from the pristine microplastics (PMPs)-induced higher oxidative stress and membrane permeability to AMPs-induced higher multidrug efflux coupled with pilus-mediated conjugation. Subsequently, metagenomic binning identified key multidrug-resistant hosts of Sedimentibacter, Alicycliphilus, and Sulfuricurvum genera. Moreover, high-resolution metabolomics and reactomics network analysis uncovered that AMPs stimulated microbial metabolite turnover, particularly of nitrogenous and sulfurous compounds, and enhanced the complexity and communication frequency of molecular transformation networks centered on lignin and protein nodes, thereby promoting ARG exchange. Finally, Mantel tests reconfirmed that reactive oxygen species level (Mantel's r = 0.93, p = 0.04) and metabolite network connectivity (Mantel's r = 0.82, p = 0.04) are paramount drivers of ARG spread. These findings offer novel insights into the ARG amplification risk driven by MPs aging, guiding targeted strategies to mitigate ARG spread and improve resource recovery in sludge bioengineering systems.}, }
@article {pmid41344128, year = {2025}, author = {Xie, X and Li, E and Jiang, H and Pi, K and Yan, L and Shen, S}, title = {Methane biogeochemical turnover constrains arsenic transformation in groundwater systems: Organic molecular signatures and microbial functional networks.}, journal = {Water research}, volume = {290}, number = {}, pages = {125083}, doi = {10.1016/j.watres.2025.125083}, pmid = {41344128}, issn = {1879-2448}, abstract = {Arsenic (As) contamination of groundwater is primarily driven by microbially mediated redox processes and the dynamic evolution of dissolved organic matter (DOM). The influence of cycled methanogenesis and methane oxidation processes on As species transformation in geogenic As-contaminated groundwater, however, remain mechanistically elusive. In this study, quantitative relationships among DOM molecular characteristics, microbial functional networks, and As speciation were established using sediment microcosm experiments, Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), and metagenomic sequencing. The results indicate that rates of methanogenesis and methane oxidation are regulated by thermodynamic properties of DOM. Labile DOM promoted As(III) mobilization at a rate of 1.04 μg kg[-1] d[-1] through methyl-related metabolism. Remarkably, enhanced methane oxidation further elevated the As(III) generation rate to 3.30 μg kg[-1] d[-1], underscoring the accelerating effect of methane cycling on As release. In contrast, humified DOM decoupled the geochemical linkage between iron and As. Microbial succession governed the redox transitions, as the proliferation of methanogens substantially increased methane production (up to 7.23 mg kg[-1] d[-1]), while methanotrophs enhanced oxidation rates from 94.99 to 190.76 mg kg[-1] d[-1]. This microbial progression coupled sulfate and As(V) reduction through the up-regulation of key functional genes (dsrAB, arsC). Energy conversion during DOM biodegradation governs As migration stages. These findings highlight the interactive constraints on As speciation dynamics by molecular characteristics of DOM and microbial functional networks during methane biotransformation processes in groundwater systems. This research provides new mechanistic insights into As biogeochemical cycling in geogenic contaminated groundwater.}, }
@article {pmid41342600, year = {2025}, author = {Bauchinger, F and Berry, D}, title = {Metatranscriptomic-driven insights into mucosal glycan degradation by the human gut microbiota.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaf118}, pmid = {41342600}, issn = {1574-6941}, abstract = {The secreted mucus layer in the human gastrointestinal tract constitutes both a protective boundary between gut lumen and epithelium as well as an important nutrient source for members of the gut microbiota. While many gut microbes possess the genetic potential to degrade mucin it is still unclear which species transcribe the respective genes. Here, we systematically analyzed publicly available metagenome and metatranscriptome datasets to characterize the gut microbial community involved in mucosal glycan degradation. We utilized co-occurrence network analysis and linear regression to elucidate the ecological strategies of, and relationship between, mucus degraders. We found that although approximately 60% of species carrying genes encoding for mucosal-glycan-degrading enzymes have detectable transcription of these genes, only 21 species prevalently transcribe more than 1 gene. Furthermore, the transcription of individual genes was frequently dominated by single species in individual samples. Transcription patterns suggested the presence of competitive mucosal glycan degraders characterized by abundance-driven transcription that were negative predictors for the transcription of other degraders as well as opportunistic species with decoupled abundance and transcription profiles. These findings provide insights into the ecology of the mucosal glycan degradation niche in the human gut microbiota.}, }
@article {pmid41341964, year = {2025}, author = {Yao, J and Zhang, J and Zheng, L and Fang, W and Lang, Y}, title = {Coxiella burnetii Should Not Be Ignored: Two Cases of Q Fever Pneumonia Diagnosed by Metagenomic Next-Generation Sequencing.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {6227-6239}, pmid = {41341964}, issn = {1178-6973}, abstract = {BACKGROUND: Q fever is a globally distributed zoonotic disease caused by Coxiella burnetii (C. burnetii). As an obligate intracellular bacterium, C. burnetii is primarily transmitted from domestic animals to humans, with ticks also serving as potential vectors. The clinical manifestations of Q fever are often nonspecific and highly variable, making its diagnosis particularly challenging.<br><br>CASE PRESENTATION: Two male pneumonia patients were hospitalized in Deqing People's Hospital, one was 73 years old, and the other one was 30 years old, both of them presented with hyperpyrexia without a clear epidemiological history. However, initial empirical treatment was ineffective and microbiological cultures were all negative, then bronchoscopy was conducted for them and bronchoalveolar lavage fluid (BALF) was sent for metagenomic next-generation sequencing (mNGS) test. Ultimately, two patients were diagnosed with Q fever pneumonia, and the symptoms of patients were significantly improved after timely treatment with the special drug doxycycline and moxifloxacin, and lung inflammation in both patients were effectively absorbed in the subsequent follow-up examination.<br><br>CONCLUSION: Two cases of Q fever pneumonia were diagnosed through mNGS. As a new detection method, mNGS has advantages in the diagnosis of unknown infectious pathogens. As a zoonotic pathogen, C. burnetii should not be ignored. The One Health approach may be suitable for Q fever prevention and control.}, }
@article {pmid41341958, year = {2025}, author = {Chaves, M and Hashish, A and Goraichuk, IV and Casserta, LC and Mears, MC and Gadu, E and Bakre, A and Alexander Morris, ER and Shelkamy, MMS and Nadendla, S and Perez, DR and El-Gazzar, M}, title = {Nanopore sequencing in veterinary medicine: from concepts to clinical applications.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1701570}, pmid = {41341958}, issn = {2235-2988}, mesh = {*Nanopore Sequencing/methods/veterinary ; Animals ; *Veterinary Medicine/methods ; Computational Biology/methods ; *High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; Nanopores ; Genomics/methods ; }, abstract = {Oxford Nanopore Technologies (ONT) stands at the forefront of third-generation sequencing, utilizing a nanopore sequencing approach to achieve high-throughput DNA and RNA sequencing. This technology offers several key advantages, including real-time data generation, portability, and long-read capabilities, making it an increasingly valuable tool for a wide range of applications. This review will focus on the use of ONT in veterinary diagnostics exploring the evolving applications of ONT in veterinary medicine and its use in detecting viral and bacterial pathogens, antimicrobial resistance profiling, foodborne disease surveillance, and metagenomic analysis. We provide an overview of the diverse sequencing workflows available, from sample preparation to bioinformatics analysis, and highlight their advantages over traditional sequencing methods. While powerful, nanopore sequencing does present challenges such as error rates, barcode crosstalk, and workflow complexities. This review will address these issues and discuss potential future developments, as well as the long-term impact of ONT on the field of genomics. As nanopore sequencing technology continues to advance, its role in veterinary diagnostics is expected to expand significantly, leading to improvements in disease surveillance, outbreak response, and contributions to crucial One Health initiatives.}, }
@article {pmid41341954, year = {2025}, author = {Fang, XZ and Liu, ZH and Duan, LM and Yao, L and Xu, JQ and Yang, XB and Ren, LH and Jiang, YX and Sun, SW and Shang, Y and Yuan, Y}, title = {Clinical features, pathogens, and prognosis of immunocompromised host pneumonia in patients with malignancies.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1646513}, pmid = {41341954}, issn = {2235-2988}, mesh = {Humans ; *Immunocompromised Host ; Male ; *Neoplasms/complications ; Female ; Middle Aged ; Prospective Studies ; Aged ; Prognosis ; Bronchoalveolar Lavage Fluid/microbiology/virology ; *Pneumonia/microbiology/mortality/diagnosis ; Coinfection/microbiology ; Adult ; Bacteria/isolation &amp; purification/classification ; Metagenomics ; COVID-19 ; Aged, 80 and over ; SARS-CoV-2 ; }, abstract = {BACKGROUND: Cancer patients face elevated risks of severe pulmonary infections due to malignancy-related immunosuppression and anti-neoplastic therapy. Comprehensive data on the etiology and prognostic factors remain limited.<br><br>METHODS: This prospective cohort study enrolled 115 patients with malignancies and immunocompromised host pneumonia (ICHP) from July 2023 to July 2024. Pathogens were identified using clinical metagenomics of bronchoalveolar lavage fluid (BALF), supported by CT imaging and clinical evaluation.<br><br>RESULTS: Pathogens were detected in 92 patients (80.0%), with 158 potential pathogens detected. Etiologic diagnoses were established by BALF mNGS alone in 68 (73.9%), by combined mNGS plus standard microbiologic testing (SMT) in 24 (26.1%), and by SMT alone in 1 (1.1%). Pneumocystis jirovecii (32, 20.3%), SARS-CoV-2 (14, 8.9%), Aspergillus fumigatus (13, 8.2%), Klebsiella pneumoniae (12, 7.6%) and Haemophilus influenzae (10, 6.3%) were the five most common pathogens. Coinfections occurred in 36.5% of all enrolled patients. Death at 28 days, ICU admission, Death at ICU was more frequent among patients with polymicrobial infections than single pathogen infection, though this difference was not statistically significant. Use rate of vasoactive drugs was significantly higher in patients with coinfection than in patients with single-pathogen infection (39.1% vs. 16.0%). invasive mechanical ventilation (IMV) (OR = 22.86, p=0.047), vasopressor use (OR = 72.69, p=0.039), and higher Acute Physiology and Chronic Health Evaluation II (APACHE II) scores (OR = 1.46, p=0.016) were associated with increased 28-day all-cause mortality.<br><br>CONCLUSION: Patients with malignancies and evaluated for pulmonary infection were found to have unique microbiological profiles detected by BAL metagenomic sequencing. Co-detection of potential pathogens was high, and associated with high 28-day all-cause mortality.}, }
@article {pmid41341823, year = {2025}, author = {Huang, W and Lai, HP and Yu, L and Jin, L and Lei, W}, title = {Case Report: Chronic Q fever mimicking malignancy and tuberculosis in a hemodialysis patient: multidisciplinary diagnosis guided by metagenomic next-generation sequencing.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1656891}, pmid = {41341823}, issn = {2296-858X}, abstract = {BACKGROUND: Q fever, caused by Coxiella burnetii, is a rare zoonosis whose clinical presentation is highly heterogeneous. Chronic Q fever can present with atypical systemic masses, creating significant diagnostic challenges as it lacks distinctive imaging features, often leading to misdiagnosis.<br><br>CASE PRESENTATION: We report a case of a 50-year-old woman on maintenance hemodialysis who presented with a one-month history of generalized myalgia and abdominal discomfort. Initial PET-CT imaging revealed multiple hypermetabolic abdominal lesions (SUV&#x223c;max&#x223c; 7.1), mimicking metastatic malignancy. Histopathology of abdominal biopsies showed granulomatous inflammation with necrosis but lacked definitive microbiological evidence. Empirical anti-tuberculosis therapy was initiated based on clinical suspicion. Despite initial clinical improvement, the patient experienced recurrence of symptoms and radiological progression after 1 year. Re-evaluation with transesophageal echocardiography suggested the possibility of infective endocarditis. Crucially, metagenomic next-generation sequencing (mNGS) of a repeat biopsy identified Coxiella burnetii, confirming chronic Q fever. Targeted doxycycline therapy resulted in sustained clinical and radiological improvement, with lesion resolution confirmed at the 14-month follow-up.<br><br>CONCLUSION: This case underscores the diagnostic difficulty of chronic Q fever due to its non-specific presentation and imaging characteristics. PET-CT may suggest malignancy, but incorporating advanced molecular diagnostics such as mNGS is critical for accurate pathogen identification. Recognizing atypical manifestations and utilizing integrative diagnostic approaches can facilitate timely, targeted therapy, improving clinical outcomes in rare infectious diseases like Q fever.}, }
@article {pmid41341819, year = {2025}, author = {Kong, M and Sun, J}, title = {Case Report: A case of Nocardia otitidiscaviarum pneumonia diagnosed by application of metagenome next-generation sequencing and a narrow literature review.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1646940}, pmid = {41341819}, issn = {2296-858X}, abstract = {Nocardia is an opportunistic pathogen with relatively low incidence but high mortality. Recently, reports of Nocardia infections have increased; however, infections caused by Nocardia otitidiscaviarum (N. otitidiscaviarum) remain relatively rare. Due to its non-specific clinical manifestations and imaging features, N. ototidiscaviarum infections are frequently misdiagnosed or underdiagnosed, and no standardized guidelines currently exist for their diagnosis and treatment. In this study, we report a case of pulmonary infection caused by N. otitidiscaviarum, which was diagnosed using a combination of traditional microbial morphology and second-generation sequencing, and subsequently showed improvement following treatment with trimethoprim-sulfamethoxazole (TMP-SMZ) and linezolid. Additionally, we conducted a comprehensive literature review using PubMed to provide insights for improving the diagnosis and treatment of N. otitidiscaviarum infections.}, }
@article {pmid41341716, year = {2025}, author = {Leutert, A and Zeckanovic, A and Huber, M and Meyer Sauteur, PM and Morscher, RJ}, title = {Recurrent vaccine-strain varicella zoster virus reactivation in a child with acute lymphatic leukemia.}, journal = {IDCases}, volume = {42}, number = {}, pages = {e02422}, pmid = {41341716}, issn = {2214-2509}, abstract = {This case illustrates recurrent herpes zoster (HZ) in a child with acute lymphatic leukemia. Interestingly, vaccine-strain HZ was confirmed by identifying the live-attenuated Oka vaccine strain (vOka) using metagenomic sequencing and sequence comparison at three loci that distinguish vOka from wild-type varicella zoster virus (VZV). Although vaccine-strain HZ is generally milder than HZ caused by wild-type VZV, prompt recognition and initiation of antiviral treatment is essential in immunocompromised patients, as fatal varicella due to disseminated vaccine-strain VZV has been reported in this high risk group.}, }
@article {pmid41341658, year = {2025}, author = {Kriem, LS and King, N and Niemann, S and Vainshtein, Y and Sonntag, M}, title = {Molecular Identification of Human and Plant Pathogens in Municipal Domestic Wastewater for Hydroponic System Applications.}, journal = {International journal of microbiology}, volume = {2025}, number = {}, pages = {6958575}, pmid = {41341658}, issn = {1687-918X}, abstract = {Water is essential for human survival and socioeconomic development, yet its overconsumption threatens global food security and ecosystem integrity. This necessitates a 60% increase in food production, further straining water resources. Hydroponic systems represent a promising solution, utilizing up to 90% less water than traditional methods while providing optimal growing conditions for crops. This study was aimed at developing a PCR-based detection system for main human and plant pathogens in hydroponic systems using treated domestic wastewater. Metagenomic analysis of wastewater samples revealed significant microbial diversity, identifying human pathogens such as Pseudomonas aeruginosa and Yersinia enterocolitica, alongside plant pathogens including Rhodococcus fascians. Specific primer pairs for the most abundant species found in a domestic municipal wastewater sample of target pathogens (Streptococcus mutans, P. aeruginosa, Acinetobacter baumannii, Y. enterocolitica, Enterococcus faecalis, Pseudomonas viridiflava, R. fascians, Xanthomonas vesicatoria, and Pseudomonas syringae) were designed and validated, ensuring high specificity and efficiency. Future research should focus on enhancing detection methods and optimizing DNA extraction techniques to improve pathogen quantification and management in hydroponic systems. This approach is crucial for sustainable agricultural practices that minimize water usage while ensuring food safety and environmental health.}, }
@article {pmid41341495, year = {2025}, author = {Rana, TS and Bansode, RR and Rana, JP and Williams, LL}, title = {A systematic review: polyphenol's effect on food allergy via microbiome modulation.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1673472}, pmid = {41341495}, issn = {1664-302X}, abstract = {INTRODUCTION: Food allergy is an increasing health concern worldwide. Microbes, food allergies, and polyphenols are found to be interrelated. However, studies relating polyphenols' effect on food allergy via microbiome modulation are scarce, and there is a lack of common signature microbiome modulation patterns. Thus, this review aims to summarize the effect of polyphenols on food allergy via microbiome modulation.<br><br>METHODS: Research articles were searched from Scopus, PubMed, ScienceDirect, and Web of Science database. The in vivo and in vitro studies were assessed via SYRCLE risk of bias and modified CONSORT checklist, respectively. The population characteristics and experimental details were extracted, and the data were synthesized narratively.<br><br>RESULTS: The included studies were free of selective reporting of results. The allergy of egg (ovalbumin), milk (&#x1d6fd;-lactoglobulin), soybean (&#x1d6fd;-conglycinin), and shrimp allergy contributed to 54%, 23%, 15%, and 8% of the total included studies, respectively. The used compounds were a different source or types of polyphenols such as cocoa, cyanidin-3-O-glucoside (C3G), avenanthramide's (AVA), rosmarinic acid (RA), neohesperidin, and fermented apple juice for egg allergy, luteolin, and green tea polyphenol (GTP) for soybean allergy, and flavonoids (Luteolin, myricetin and hyperoside), ferulic acid, and luteolin for milk allergy. Allergies of milk, egg, wheat, and shrimp occurred with the reduction of Lactobacillus, Alistipes, Odaribactor, Akkermansia, Bacteroides, and Lachnospiraceae_NK4A136_group and an increase of Prevotella, Alloprevotella, Faecalibaculum, Helicobactor, Blautia, Clostridium, and Staphylococcus. The polyphenols modulated these microbes in order to attenuate the food allergies.<br><br>DISCUSSION: The types of polyphenols, food allergies, animal model used, and taxonomic resolution of the microbiome studies lead to variation in the results. Thus, by increasing the studies on effect of polyphenols on individual food allergies, and combining with higher taxonomic resolution techniques such as shotgun metagenomics along with metabolomics would increase reliability of the results of the future studies.}, }
@article {pmid41341171, year = {2025}, author = {Khan, N and Nasir, MM and Mushtaq, A and Kayani, MUR}, title = {SNPraefentia: a toolkit to prioritize microbial genome variants linked to health and disease.}, journal = {Bioinformatics advances}, volume = {5}, number = {1}, pages = {vbaf297}, pmid = {41341171}, issn = {2635-0041}, abstract = {MOTIVATION: Analysis of genomic variation in microbial genomes is crucial for understanding how microbes adapt, interact with their hosts, and influence health and disease. In metagenomic studies, where genetic material from entire microbial communities is sequenced, thousands of single-nucleotide polymorphisms can be detected across species and samples. However, identifying which of these variations has biologically or functionally relevant impacts remains a significant challenge.<br><br>RESULTS: To address this, we present SNPraefentia, a Python-based toolkit for prioritizing microbial SNPs based on their predicted functional relevance. The tool integrates multiple biologically meaningful parameters, including sequencing depth, physicochemical impact of amino acid substitutions, and the structural and functional context of mutations within annotated protein domains. SNPraefentia extracts variation depth and amino acid changes, annotates protein domains using UniProt, and computes individual impact scores. These are then integrated into a composite prioritization score that reflects the potential biological importance of each variant. Overall, SNPraefentia provides researchers with a systematic and reproducible approach to filter and rank microbial variants for downstream functional analysis or experimental validation.<br><br>The toolkit and test data are freely available at https://github.com/muneebdev7/SNPraefentia.}, }
@article {pmid41340567, year = {2025}, author = {Ouradova, A and Ferrero, G and Bratova, M and Daskova, N and Bohdanecka, A and Dohnalova, K and Heczkova, M and Chalupsky, K and Kralova, M and Kuzma, M and Modos, I and Tichanek, F and Najmanova, L and Pardini, B and Pelantová, H and Tarallo, S and Videnska, P and Gojda, J and Naccarati, A and Cahova, M}, title = {A vegan diet signature from a multi-omics study on different European populations is related to favorable metabolic outcomes.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2593050}, doi = {10.1080/19490976.2025.2593050}, pmid = {41340567}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Diet, Vegan ; Male ; Female ; Adult ; Czech Republic ; Cross-Sectional Studies ; *Metabolome ; Middle Aged ; Italy ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Vegans ; Metagenome ; Multiomics ; }, abstract = {Vegan and omnivorous diets differ markedly in composition, but their effects on the gut microbiome, metabolome, and lipidome across populations remain insufficiently characterized. While both diet and country of origin influence these molecular layers, the relative contribution of diet versus country-specific factors has not yet been systematically evaluated within a multi-omics framework.In this cross-sectional, bicentric, observational study, we profiled healthy vegans (n = 100) and omnivores (n = 73) from the Czech Republic and Italy using integrated microbiome, metabolome, and lipidome analyses. Findings were subsequently validated in an independent cohort (n = 142).Significant differences across all omics layers were observed for both country and diet. The predictive models confirmed diet-associated separation, with validation cohort AUCs of 0.99 (lipidome), 0.89 (metabolome), and 0.87 (microbiome). Functional metagenome analysis revealed enrichment of amino acid biosynthesis, inositol degradation, and the pentose phosphate pathway in vegans, while omnivores presented greater potential for amino acid fermentation, fatty acid biosynthesis, and propanoate metabolism. Linear models identified a robust, country-independent "vegan signature" consisting of 27 lipid metabolites, five non-lipid metabolites, and 11 bacterial species. Several lipid features associated with an omnivorous diet were inversely related to the duration of vegan diet adherence. Some of the vegan-associated metabolites and bacteria have been previously linked to favorable cardiometabolic profiles, although causality remains to be established.These findings demonstrate that vegan diets are associated with reproducible, country-independent molecular and microbial signatures. Our results highlight diet-driven shifts in host-microbiota interactions and provide a framework for understanding how dietary patterns relate to host-microbiota interactions.}, }
@article {pmid41340249, year = {2025}, author = {Gluvić, Z and Zafirović, S and Sudar-Milovanović, E and Stanimirović, J and Soskić, S and Jevremović, D and Isenović, ER}, title = {Molecular insights into the gut-thyroid Axis: microbiota-driven biomarkers and diagnostic applications.}, journal = {Expert review of molecular diagnostics}, volume = {}, number = {}, pages = {}, doi = {10.1080/14737159.2025.2599225}, pmid = {41340249}, issn = {1744-8352}, abstract = {INTRODUCTION: New research has shown an intriguing link between the gut bacteria and the thyroid. A gut-thyroid relationship affects energy production, immunological function, and inflammation. As a result, disrupted gut flora harmony is associated with an increased/altered risk of thyroid dysfunction, autoimmune disorders, and metabolic imbalance. In addition to current diagnostic technology, understanding the gut flora-thyroid relationship could assist in the detection of thyroid-related conditions and modify patient treatment.<br><br>AREAS COVERED: This review explores state-of-the-art molecular techniques, e.g. metagenomics profiling and metabolomics, to uncover clinically relevant microbiota-driven biomarkers related to thyroid disorders.<br><br>EXPERT OPINION: Revealing potential microbiota-driven biomarker candidates is pivotal in enhancing our understanding of the mechanisms of thyroid disorders more precisely and identifying diagnostic and prognostic markers with clinical potential. Precisely, the individualization in the approach to patients with thyroid disorder, inevitably considering the harmonization of the gut microbiota-thyroid hormone relationship, is the basis of rational pharmacotherapy.}, }
@article {pmid41340151, year = {2025}, author = {Kropp, DR and Glover, ME and Samanta, R and Unroe, KA and Clinton, SM and Hodes, GE}, title = {Perinatal citalopram exposure alters the gut composition and microbial metabolic profiles of Sprague-Dawley rat dams and female offspring but not male offspring.}, journal = {Biology of sex differences}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13293-025-00794-5}, pmid = {41340151}, issn = {2042-6410}, support = {R01MH105447-01/NH/NIH HHS/United States ; }, abstract = {BACKGROUND: Selective serotonin reuptake inhibitors are widely prescribed during pregnancy. Their main route of administration is through the gut. However, their impact on the maternal and offspring gut microbiome and microbial metabolic pathways remains poorly understood. This study used metagenomic shotgun sequencing to examine the effects of perinatal citalopram exposure in rat dams and their offspring on gut composition and downstream metabolic pathways.<br><br>METHODS: We treated pregnant and nursing rat dams with either citalopram or vehicle (water). Their feces were collected, DNA from these samples was extracted and then sequenced using shotgun metagenomic sequencing. The BioBakery suite of microbiome analysis tools was utilized in tandem with RStudio to analyze the gut composition and microbial metabolic pathways of the rat dams and their offspring.<br><br>RESULTS: Pregnant and nursing dams treated with citalopram exhibited marked shifts in microbial community structure, including phylum-level alterations in Proteobacteria and Defferibacteria. Citalopram treated dams displayed significantly altered beta diversity. Species level alterations due to treatment were composed of five significantly altered microbes, two of which belong to the Proteobacteria phylum. These changes were highly diverse and were not congruent with microbe-level alterations observed in offspring. Alpha diversity of microbial metabolic pathways was compared using the Gini-Simpson index, which was significantly increased in dams suggesting greater metabolic functional diversity with age. Female offspring perinatally exposed to citalopram showed significant changes in gut beta diversity, with seven significant alterations at the microbe level. These microbial shifts were accompanied by twenty-one significantly altered microbial metabolic pathways. In contrast, male offspring showed no significant differences in microbial composition or beta diversity and only minor metabolic changes.<br><br>CONCLUSIONS: These findings demonstrate that maternal citalopram exposure during pregnancy and lactation has lasting, sex-specific impacts on the offspring's gut microbiome and microbial metabolic pathways. The pronounced alterations in female, but not male offspring, suggest that host sex may be a critical determinant in the developmental response to citalopram exposure. This work underscores the value of metagenomic approaches in uncovering complex host-microbiome interactions and highlights the need to consider offspring sex in evaluating the safety and long-term effects of antidepressant use during pregnancy.}, }
@article {pmid41340071, year = {2025}, author = {Peng, J and Liu, X and Wang, J and Meng, N and Cai, R and Peng, Y and Han, Y and Liao, J and Li, C and Rubin-Blum, M and Ma, Q and Dong, X}, title = {Diverse quorum sensing systems regulate microbial communication and biogeochemical processes in deep-sea cold seeps.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-025-02280-x}, pmid = {41340071}, issn = {2049-2618}, support = {1359/23//Israel Science Foundation/ ; 32170121//National Natural Science Foundation of China/ ; 92351304//National Natural Science Foundation of China/ ; 2023J06042//Natural Science Foundation of Fujian Province/ ; 3502Z202373076//Natural Science Foundation Project of Xiamen City/ ; 2022025//Scientific Research Foundation of Third Institute of Oceanography, MNR/ ; }, abstract = {BACKGROUND: Quorum sensing is a fundamental chemical communication mechanism that enables microorganisms to coordinate behavior and adapt to environmental conditions. However, its contribution in deep-sea cold seep ecosystems, where diverse microbial communities and frequent communication occur, remains poorly understood. In this study, we aimed to elucidate the occurrence and potential ecological roles of quorum sensing in cold seeps.<br><br>RESULTS: We analyzed 170 metagenomes and 33 metatranscriptomes from 17 global cold seep sites, identifying 299,355 quorum sensing genes from the cold seep non-redundant gene catalog. These genes represent 34 types across six quorum sensing systems, with distribution patterns influenced by sediment depth and seep type. A total of 32,500 quorum sensing genes were identified in 3576 metagenome-assembled genomes from 12 archaeal and 108 bacterial phyla, revealing a complex network of intraspecies and interspecies communication. Microbial groups involved in key metabolic processes, such as sulfate-reducing bacteria, anaerobic methanotrophic archaea, diazotrophs, and organohalide reducers, were extensively regulated by quorum sensing, influencing biogeochemical cycles in cold seeps. Phylogenetic analysis and protein domain identification highlighted the involvement of key quorum sensing-related proteins (e.g., PDE, RpfC/G, CahR, and LuxR) in modulating microbial behaviors, such as motility and chemotaxis. Heterologous expression further confirmed the activity of representative LuxI-R pairs, and metabolomic profiling suggested the presence of putative quorum sensing inhibitors in cold seep sediments.<br><br>CONCLUSIONS: Overall, these findings highlight the complexity and significance of quorum sensing in microbial interactions, ecological adaptation, and biogeochemical cycling within cold seep ecosystems, advancing our understanding of microbial communication in the deep biosphere. Video Abstract.}, }
@article {pmid41340070, year = {2025}, author = {Jeilu, O and Sumner, JT and Moghadam, AA and Thompson, KN and Huttenhower, C and Catlett, C and Hartmann, EM}, title = {Metagenomic profiling of airborne microbial communities from aircraft filters and face masks.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {249}, pmid = {41340070}, issn = {2049-2618}, mesh = {*Air Microbiology ; *Metagenomics/methods ; Humans ; *Bacteria/genetics/classification/isolation &amp; purification ; *Aircraft ; *Masks/microbiology ; *Microbiota/genetics ; *Air Filters/microbiology ; Metagenome ; }, abstract = {BACKGROUND: Airborne microbial communities, although often challenging to study due to low biomass, play crucial roles in public health and pathogen transmission. Through shotgun metagenomics, this study utilizes non-invasive air sampling of face masks and aircraft cabin filters to investigate microbial diversity in environments with frequent human interactions, including hospitals and airplanes. A comprehensive sampling and analysis workflow was developed, incorporating environmental and enrichment protocols to enhance microbial DNA recovery and diversity profiling.<br><br>RESULTS: Despite limitations in biomass, optimized extraction methods allowed for the successful identification of 407 species, with dominant taxa including Cutibacterium acnes, Staphylococcus epidermidis, Sphingomonas hankookensis, and Methylobacterium radiotolerans. Enrichment processing resulted in greater metagenome-assembled genome (MAG) recovery and higher antimicrobial resistance gene (ARG) identification.<br><br>CONCLUSIONS: The findings highlight the presence of ARGs in high-occupancy public spaces, suggesting the importance of monitoring and the potential for mitigating airborne transmission risks in such environments. This study demonstrates the utility of combining environmental and enrichment sampling to capture comprehensive microbial and ARG profiles in confined spaces, providing a framework for enhanced pathogen monitoring in public health contexts. Video Abstract.}, }
@article {pmid41339959, year = {2025}, author = {McAdams, ZL and Campbell, EJ and Dorfmeyer, RA and Turner, G and Shaffer, S and Ford, T and Lawson, J and Terry, J and Raju, M and Coghill, L and Cresci, L and Lascola, K and Pridgen, T and Blikslager, A and Barrell, E and Banse, H and Paul, L and Gillen, A and Nott, S and VandeCandelaere, M and van Galen, G and Townsend, KS and Martin, LM and Johnson, PJ and Ericsson, AC}, title = {A novel dataset of 2,362 equine fecal microbiomes from veterinary teaching hospitals across three countries reveals effects of geography and disease.}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {124}, pmid = {41339959}, issn = {2524-4671}, abstract = {BACKGROUND: Horses and other equids are reliant on the gut microbiome for health, and studies have reported associations between certain clinical conditions and features of the fecal microbiome. However, research to date on the equine fecal microbiome has often relied on small sample sizes collected from single and relatively localized geographic regions. Previous work also largely employs single timepoint analyses, or horses selected based on limited health criteria.<br><br>RESULTS: To address these limitations and expand our understanding of the core microbiome in health, and the changes associated with adverse outcomes, the Equine Gut Group (EGG) has collected and performed 16S rRNA sequencing on 2,362 fecal samples from 1,190 healthy and affected horses. This resource of 16S rRNA sequencing data with accompanying demographic and clinical metadata represent a diverse equine population in health and disease. We identified features making up the core microbiome of healthy equids and metadata factors influencing the relative abundance of those features. We then identified microbial markers of acute gastrointestinal disease at the community and taxonomic levels.<br><br>CONCLUSIONS: Here we present the EGG database and demonstrate its utility in characterizing the equine microbiome in health and acute gastrointestinal disease. The EGG 16S rRNA database is a valuable resource to study the equine microbiome and its role in equine health.}, }
@article {pmid41339940, year = {2025}, author = {Parwin, N and Dixit, S and Das, S and Sahoo, RK and Subudhi, E}, title = {Metagenomic analysis of microbiome spatial dynamics in urban river confluence affected by city wastewater.}, journal = {Genomics &amp; informatics}, volume = {}, number = {}, pages = {}, doi = {10.1186/s44342-025-00054-3}, pmid = {41339940}, issn = {1598-866X}, abstract = {BACKGROUND: Environmental pollutants have a profound impact on microbial dynamics. This study highlights the influence of anthropogenic activity on the shift in bacterial diversity in the catchment area compared to upstream and downstream at Kathajodi, using a metagenomic approach for the first time in River Kathajodi.<br><br>METHODS: Water samples were collected from upstream, catchment, and downstream locations and transported at 4&#xb0;C to the laboratory for DNA extraction, library preparation, sequencing, and physicochemical analysis employing inductively coupled plasma. The extracted DNA was sequenced via the Illumina HiSeq platform and analyzed through MG-RAST for taxonomic and functional classification using KEGG and COG annotations. Statistical diversity analysis, including rarefaction curves, alpha- and beta-diversity indices, and Venn diagrams, provided insights into microbial composition and community variations across sites.<br><br>RESULTS: A significant abundance of pollution indicator members of phylum Bacteroidetes (29.82%) in the catchment (CM), highly contaminated with metals, fecal, and other organic pollutants, could be attributed to their high metabolic capabilities to degrade them. The pristine upstream (US) exhibited an abundance of Shewanella (25.04%), Pseudomonas (17.35%), and Synechococcus (5.62%). The CM, influenced by high anthropogenic activity, showed higher abundances of Flavobacterium (5.20%), Arcobacter (4.05%), and Bacteroides (3.88%). In contrast, downstream (DS), with fewer anthropogenic activities, displayed higher abundances of Aeromonas (4.40%), Acidovorax (0.52%), and Acidimicrobium (0.32%). The highest bacterial diversity of CM could be due to the influence of the physicochemical properties of city waste effluent. From the Venn diagram, 73 common OTUs at the genera level were observed in all three sites, which indicates that the native microflora of the river water niche remains unaffected irrespective of the temporary changes in the vicinity. The functional profiling through KEGG and COG revealed that CM was enriched in carbohydrate metabolism (12.11%), while DS exhibited higher contributions to amino acid metabolism, along with the highest relative abundance of general function prediction (R) (12.89%), all indicative of stress adaptation and metabolic flexibility under polluted conditions. The clean upstream is home to oxygen-loving helpful bacteria, the catchment supports nutrient-hungry and sewage-linked microbes, while the downstream is dominated by metal-tolerant and possibly harmful bacteria, showing the clear impact of human activities along the river.<br><br>CONCLUSIONS: The marked shift in bacterial diversity between US, CM, and DS regions highlights the ecological consequences of anthropogenic impact. These findings emphasize the need for effective environmental management to safeguard water quality and prevent undesirable health issues.}, }
@article {pmid41339801, year = {2025}, author = {Yang, T and Wang, Y and Zhang, Y and Liu, C and Zeng, Y and Shi, P and Zhou, J and Li, Y and Wei, H}, title = {Haemophilus influenzae dominance in fungal ball microbiome revealed through multi-niche metagenomic sequencing.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-025-04546-8}, pmid = {41339801}, issn = {1471-2180}, support = {7222026//Natural Science Foundation of Beijing Municipality/ ; }, abstract = {OBJECTIVE: This study employed metagenomic sequencing to characterize the sinonasal microbiome in patients with unilateral maxillary sinus fungal ball (MSFB), with specific emphasis on bacterial-fungal interactions and functional pathways implicated in fungal ball pathogenesis.<br><br>METHODS: The study enrolled 30 MSFB patients and 30 healthy controls. Nasal secretion samples were obtained from three anatomical sites in MSFB cases: fungal ball cavity (FC), affected middle nasal meatus (AM), and contralateral unaffected middle nasal meatus (UM). And in the control group, samples were obtained from the healthy middle nasal meatus (HM). Metagenomic sequencing of microbial DNA was performed using the Illumina Novaseq platform. Taxonomic and functional analyses were conducted using Kraken2, Bracken, and HUMAnN2.<br><br>RESULTS: Bacteria dominated the microbiome in the FC group (98.53%), with Haemophilus influenzae identified as a key biomarker (LDA score&#x2009;>&#x2009;5). A negative correlation between H. influenzae and Aspergillus flavus was observed in the FC group (r&#x2009;=&#x2009;-0.46, P&#x2009;=&#x2009;0.013). Functional pathways enriched in the FC group included amino acid biosynthesis (map00290), lipopolysaccharide biosynthesis (map00540), and fatty acid biosynthesis (map00061), supporting H. influenzae survival and immune modulation. FC microbiota showed reduced diversity and distinct composition compared to other groups (PERMANOVA, P&#x2009;<&#x2009;0.001). No significant differences were found in the composition of the microbiota between the bilateral middle nasal meatus groups of MSFB.<br><br>CONCLUSION: This study highlights H. influenzae as a critical bacterial biomarker in MSFB. The inverse relationship between H. influenzae and A. flavus may suggest competitive or immune-mediated interactions. These findings advance understanding of non-invasive fungal sinusitis. Future validation in larger fungal ball cohorts or invasive fungal sinusitis is warranted.}, }
@article {pmid41339745, year = {2025}, author = {Zhang, L and Marfil-Sánchez, A and Kuo, TH and Seelbinder, B and van Dam, L and Depetris-Chauvin, A and Jahn, LJ and Sommer, MOA and Zimmermann, M and Ni, Y and Panagiotou, G}, title = {Gut microbiome-mediated transformation of dietary phytonutrients is associated with health outcomes.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {41339745}, issn = {2058-5276}, support = {Germany's Excellence Strategy (EXC 2051) project ID 390713860//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Germany's Excellence Strategy (EXC 2051) project ID 390713860//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Germany's Excellence Strategy (EXC 2051) project ID 390713860//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; "PerMiCCion" project (Project ID 01KD2101A)//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; "PerMiCCion" project (Project ID 01KD2101A)//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; Excellent Young Scientists Fund (project ID 24HAA01325)//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Food, especially plant-based diet, has complex chemical diversity. However, large-scale phytonutrient-metabolizing activities of gut bacteria are largely unknown. Here we integrated and systematically analysed multiple databases containing information on enzymatic reactions and food health benefits, and 3,068 global public human microbiomes. Transformation of 775 phytonutrients from edible plants was associated with enzymes encoded by diverse gut microbes. In vitro assays validated the biotransformation activity of gut species, for example, Eubacterium ramulus. The biotransformation of phytonutrients demonstrated high interpersonal and geographical variability. Machine learning models based on 2,486 public case-control microbiomes, using the abundances of enzymes associated with modification of phytonutrients present in health-associated foods, discriminated the health status of individuals in multiple disease contexts, suggesting altered biotransformation potential in disease. We validated the association of microbiome-encoded enzymes with the anti-inflammatory activity of common edible plants by combining metagenomics and metatranscriptomics analysis in specific-pathogen-free and germ-free mice. These findings have implications for designing precise, personalized diets to guide an individual towards a healthy state.}, }
@article {pmid41339710, year = {2025}, author = {Pacheco-Valenciana, A and Tausch, A and Veseli, I and Dharamshi, JE and Bergland, F and Delgado, LF and Rodríguez-Gijón, A and Andersson, AF and Garcia, SL}, title = {Microbial model communities exhibit widespread metabolic interdependencies.}, journal = {Communications biology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s42003-025-09306-y}, pmid = {41339710}, issn = {2399-3642}, support = {grant 2022-03077//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; grant 2022-03077//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; grant 2018-05973//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; grant 2022-06725//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; grant 2022-03077//Science for Life Laboratory (SciLifeLab)/ ; }, abstract = {Microorganisms thrive in complex communities shaped by intricate interactions, yet the extent and ecological implications of biosynthetic dependencies in natural communities remain underexplored. Here, we used a dilution approach to cultivate 204 microbial model communities from the Baltic Sea and recovered 527 metagenome-assembled genomes (MAGs) that dereplicated into 72 species-clusters (>95% average nucleotide identity, ANI). Of these species, at least 70% represent previously uncultivated lineages. Combined with 1073 MAGs from Baltic Sea metagenomes, we generated a genomic catalog of 701 species-clusters. Our results show that cultures with more than three species included microorganisms with smaller genome sizes, lower biosynthetic potential for amino acids and B vitamins, and higher prevalence and abundance in the environment. Moreover, the taxa found together in the same model communities had complementary biosynthetic gene repertoires. Our results demonstrate that cultivating bacteria in dilution model communities facilitates access to previously uncultivated but abundant species that likely depend on metabolic partners for survival. Together, our findings highlight the value of community-based cultivation for unraveling ecological strategies. Finally, we confirm that metabolic interdependencies and genome streamlining are widespread features of successful environmental microorganisms.}, }
@article {pmid41339548, year = {2025}, author = {Singleton, CM and Jensen, TBN and Delogu, F and Knudsen, KS and Sørensen, EA and Jørgensen, VR and Karst, SM and Yang, Y and Sereika, M and Petriglieri, F and Knutsson, S and Dall, SM and Kirkegaard, RH and Kristensen, JM and Overgaard, CK and Woodcroft, BJ and Speth, DR and Aroney, STN and ,  and Wagner, M and Dueholm, MKD and Nielsen, PH and Albertsen, M}, title = {The Microflora Danica atlas of Danish environmental microbiomes.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {41339548}, issn = {1476-4687}, abstract = {Over the past 20 years, there have been considerable advances in revealing the microbiomes that underpin processes in natural and human-associated environments. Recent large-scale metagenome surveys have recorded the variety of microbial life in the oceans[1], in the human gut[2] and on Earth[3], with compilations encompassing thousands of public datasets[4,5]. However, despite their broad scope, these studies often lack functional information, and their sample locations are frequently sparsely distributed, limited in resolution or lacking metadata. Here we present Microflora Danica-an atlas of Danish environmental microbiomes encompassing 10,683 shotgun metagenomes and 450 nearly full-length 16S and 18S rRNA datasets, linked to a five-level habitat classification scheme. We show that although human-disturbed habitats have high alpha diversity, species reoccur, revealing hidden homogeneity. This underlines the role of natural systems in maintaining total species (gamma) diversity and emphasizes the need for national baselines for tracking microbial responses to land-use and climate change. Consequently, we focused our dataset exploration on nitrifiers, a functional group closely linked to climate change and of major importance for Denmark's primary land use: agriculture. We identify several lineages encoding nitrifier key genes and reveal the effects of land disturbance on the abundance of well-studied, as well as uncharacterized, nitrifier groups, with potential implications for N2O emissions. Microflora Danica offers an unparalleled resource for addressing fundamental questions in microbial ecology about what drives microbial diversity, distribution and function.}, }
@article {pmid41339392, year = {2025}, author = {Muratore, E and Conti, G and Fabbrini, M and Zama, D and Decembrino, N and Muggeo, P and Mura, R and Perruccio, K and Leardini, D and Barone, M and Zecca, M and Cesaro, S and Brigidi, P and Turroni, S and Masetti, R}, title = {Distinct functional and compositional properties in the gut microbiome of children with acute lymphoblastic leukaemia identified by shotgun metagenomics.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {43082}, pmid = {41339392}, issn = {2045-2322}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; Child ; *Precursor Cell Lymphoblastic Leukemia-Lymphoma/microbiology ; Male ; Female ; Child, Preschool ; RNA, Ribosomal, 16S/genetics ; Adolescent ; Bacteria/genetics/classification ; Case-Control Studies ; }, abstract = {Acute lymphoblastic leukaemia (ALL) represents the most common childhood malignancy, and emerging evidence underscores the impact of the gut microbiome (GM) on its pathogenesis. In this study, we used shotgun metagenomics to investigate the GM of 30 ALL patients at diagnosis-19 with B-ALL and 11 with T-ALL-and compared them to 176 healthy controls (HCs). When considered as a single ALL group versus HCs, clear compositional differences emerged: ALL patients exhibited higher relative abundances of Enterococcus faecium, oral commensals such as Rothia dentocariosa, and multiple opportunistic species, whereas HCs were enriched in short-chain fatty acid producers like Anaerostipes hadrus and Intestinibacter bartlettii. Functionally, the ALL GM relied more on protein and amino acid catabolism, while HCs possessed enhanced pathways for carbohydrate and folate metabolism. These findings broadly align with 16S rRNA-based analyses from previous publications, though some discrepancies highlight differences in technique-driven resolution. In contrast, comparing the two major molecular phenotypes-B-ALL and T-ALL-revealed only minimal taxonomic and functional differences, primarily confined to BAs metabolism pathways. Overall, our results indicate that children with ALL at the time of diagnosis already display a dysbiotic signature, bolstering the notion that a disturbance in GM development during childhood may be linked to the multistep pathogenesis model of ALL.}, }
@article {pmid41339358, year = {2025}, author = {Li, H and Cao, Y and Liu, X and Ke, Z and Chen, L and Siame, BA and Yaron, S and Leung, KY}, title = {Reconstruction of 1,979 prokaryotic metagenome-assembled genomes from 37 global cave environments.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1896}, pmid = {41339358}, issn = {2052-4463}, support = {32373177//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32373177//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2024LKSFG07//Li Ka Shing Foundation (Li Ka Shing Foundation Limited)/ ; 2024LKSFG07//Li Ka Shing Foundation (Li Ka Shing Foundation Limited)/ ; }, mesh = {*Caves/microbiology ; *Metagenome ; *Archaea/genetics/classification ; *Genome, Bacterial ; *Genome, Archaeal ; *Bacteria/genetics/classification ; }, abstract = {Cave microorganisms represent unique extremophiles that have evolved in isolated, nutrient-limited environments and harbor exceptional metabolic capabilities. However, knowledge of cave microbial diversity at genomic level remains limited. Previous studies have focused on individual caves and do not give a global picture. Here, we present the first prokaryotic cave metagenomic catalog from 37 geographical diverse cave environments. We employed an optimized genome reconstruction pipeline to recover 3,837 medium-to-high quality cave metagenome-assembled genomes (MAGs). These MAGs were dereplicated into 1,979 species-level representative clusters that spanned 67 phyla of Bacteria (n = 1,858) and Archaea (n = 121) domains. Classification of representative species showed that 98.7% did not match any existing genome taxonomy classification of named species at ≥ 95% average nucleotide identity (ANI). Most representative genomes harbored putative biosynthetic gene clusters (BGCs) (98.0%) and enzymatic antibiotic resistance genes (ARGs) (95.0%). This comprehensive MAGs catalog provides a foundational resource for exploring cave microbial diversity, secondary metabolism, and the evolutionary origins of antibiotic resistance in subterranean ecosystems.}, }
@article {pmid41339349, year = {2025}, author = {Coe, A and Mullet, JI and Vo, NN and Berube, PM and Anjur-Dietrich, MI and Salcedo, E and Parker, SM and VonEmster, K and Bliem, C and Arellano, AA and Castro, KG and Becker, JW and Chisholm, SW}, title = {A curated protein dataset for taxonomic classification of Prochlorococcus and Synechococcus in metagenomes.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1895}, pmid = {41339349}, issn = {2052-4463}, support = {OCE-2048470//National Science Foundation (NSF)/ ; OCE-1153588//National Science Foundation (NSF)/ ; DBI-0424599//National Science Foundation (NSF)/ ; 984601//Simons Foundation/ ; 337262//Simons Foundation/ ; 329108//Simons Foundation/ ; GBMF495//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; }, mesh = {*Synechococcus/classification/genetics ; *Prochlorococcus/classification/genetics ; *Metagenome ; Phylogeny ; Genome, Bacterial ; Metagenomics ; *Bacterial Proteins/genetics ; }, abstract = {Prochlorococcus and Synechococcus are abundant marine picocyanobacteria that contribute significantly to ocean primary production. Recent genome sequencing efforts, including those presented here, have yielded a large number of high-quality reference genomes, enabling the classification of these picocyanobacteria in marine metagenomic sequence data at high phylogenetic resolution. When combined with environmental data, these classifications can guide cluster/clade/grade assignments and offer insights into niche differentiation within these populations. Here we present ProSynTax, a curated protein sequence dataset and accompanying classification workflow aimed at enhancing the taxonomic resolution of Prochlorococcus and Synechococcus classification. ProSynTax includes proteins from 1,260 genomes of Prochlorococcus and Synechococcus, including single-amplified genomes, high-quality draft genomes, and newly closed genomes. Additionally, ProSynTax incorporates proteins from 41,753 genomes of marine heterotrophic bacteria, archaea, and viruses to assess microbial and viral communities surrounding Prochlorococcus and Synechococcus. This resource enables accurate classification of picocyanobacterial clusters/clades/grades in metagenomic data - even when present at 0.15% of reads for Prochlorococcus or 0.03% of reads for Synechococcus.}, }
@article {pmid41339341, year = {2025}, author = {Bellankimath, AB and Branders, S and Kegel, I and Ali, J and Asadi, F and Johansen, TEB and Imirzalioglu, C and Hain, T and Wagenlehner, F and Ahmad, R}, title = {Metagenomic sequencing enables accurate pathogen and antimicrobial susceptibility profiling in complicated UTIs in approximately four hours.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-025-66865-8}, pmid = {41339341}, issn = {2041-1723}, support = {336420 and 352514//Norges Forskningsr&#xe5;d (Research Council of Norway)/ ; }, abstract = {Urinary tract infections (UTIs) affect 405 million people worldwide. Current diagnostics rely on cultures, which can take 2 to 4 days. This study evaluates eleven culture-independent methods for sample preparation from 78 complicated UTI patients, followed by real-time nanopore sequencing and data analysis. The metagenomic results are highly consistent with culture-based clinical routines (MALDI-TOF/VITEK-2). The optimized method demonstrated an accuracy score of 99% (100/101) for pathogen identification and 90% (589/653) for antimicrobial susceptibility profiling with 95% specificity. The method's robustness is highlighted by its ability to accurately identify pathogens with as few as 32 bacterial cells/µL and a low bacterial-to-host cell ratio limit of 0.5. Additionally, mNGS identified 13 pathogens that routine diagnostics missed, which were subsequently confirmed by Vivalytic or PCR. This method is up to 30% more economical than published studies and commercial kits. DNA yield and flow cytometry can be used for pre-screening to reduce costs, which is crucial for clinical adoption. This research highlights the rapid diagnosis of clinical UTIs using a cost-effective and scalable method that requires around four hours from sample collection to informed decision-making. Furthermore, it aims to improve antimicrobial and diagnostic stewardship by reducing empirical treatment and ensuring more judicious antibiotic use.}, }
@article {pmid41339319, year = {2025}, author = {Harrison, LC and Allnutt, TR and Hanieh, S and Roth-Schulze, AJ and Ngui, KM and Stone, NL and Bandala-Sanchez, E and Backshell, L and Gurruwiwi, G and Gondarra, V and Couper, JJ and Craig, ME and Davis, EA and Huynh, T and Soldatos, G and Wentworth, JM and Vuillermin, P and Penno, MAS and Biggs, BA and , }, title = {Indigenous infants in remote Australia retain an ancestral gut microbiome despite encroaching Westernization.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {9904}, pmid = {41339319}, issn = {2041-1723}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Infant ; Australia ; Female ; Male ; Bacteria/genetics/classification/isolation &amp; purification ; Feces/microbiology ; Infant, Newborn ; Indigenous Peoples ; Metagenome ; }, abstract = {Studies of traditional Indigenous compared to 'Western' gut microbiomes are underrepresented, and lacking in young children, limiting knowledge of early-life microbiomes in different cultural contexts. Here we analyze the gut metagenomes of 50 Indigenous Australian infants (median age <one year) living remotely with variable access to Western foods, compared to age- and sex-matched non-Indigenous infants living in urban Australia. Indigenous infants had greater alpha diversity and significant differences in bacterial beta diversity, with 114 species and 38 genera differing in abundance. Indigenous infants almost exclusively had higher carriage of Megaspaera, Streptococcus, Caecibacter, Parolsenella and Prevotella species, and markedly higher numbers of gut viruses and fungi. Bifidobacteria ssp. were dominant in Indigenous infants. Despite encroaching Westernisation, the gut microbiome of Indigenous infants retains key features of traditional societies worldwide, attesting to the dominant influence of remote environment and traditional lifestyle in maintaining microbiome diversity.}, }
@article {pmid41338553, year = {2025}, author = {,  and , }, title = {[The Chinese guidelines for the diagnosis and treatment of invasive fungal disease in patients with hematological disorders and cancers (the seventh revision)].}, journal = {Zhonghua nei ke za zhi}, volume = {64}, number = {12}, pages = {1155-1168}, doi = {10.3760/cma.j.cn112138-20250808-00468}, pmid = {41338553}, issn = {0578-1426}, mesh = {Humans ; *Invasive Fungal Infections/diagnosis/therapy/drug therapy ; *Hematologic Diseases/complications ; Antifungal Agents/therapeutic use ; *Neoplasms/complications ; Hematologic Neoplasms/complications ; *Mycoses/diagnosis/therapy ; China ; }, abstract = {In 2005, the Chinese Invasive Fungal Infection Working Group published the first guidelines for the diagnosis and treatment of invasive fungal disease (IFD) in patients with hematological disorders and cancers, with the sixth revision released in 2020. Numerous advances in the fields of hematological oncology treatment and the diagnosis and management of IFD have significantly influenced the corresponding strategies. Therefore, the Chinese Invasive Fungal Infection Working Group has reviewed key research advances from 2020 to 2024 and released the seventh revision of the Chinese guidelines. Major revisions include: changes in the epidemiology of IFD; evaluation of novel diagnostic methods (especially PCR and metagenomic next-generation sequencing); updated recommendations on therapeutic drug monitoring and in vitro drug sensitivity test; management of breakthrough IFD; targeted therapy of Pneumocystis jiroveci pneumonia and cryptococcosis; and updated recommendation on the duration of antifungal therapy.}, }
@article {pmid41338426, year = {2025}, author = {Yan, L and Su, Y and Xie, X and Peng, K and Zhang, P and Deng, Y and Gan, Y and Li, Q and Zhang, Y}, title = {Decoding Microbial-Mediated Sulfur Transformation Pathways in Mangrove Wetland: Metagenomic and Hydrogeochemical Insights.}, journal = {Environmental research}, volume = {}, number = {}, pages = {123472}, doi = {10.1016/j.envres.2025.123472}, pmid = {41338426}, issn = {1096-0953}, abstract = {Sulfur (S) cycling is essential to the ecological function of mangrove wetlands, but how microbial processes and gene-level patterns respond to environmental gradients remains poorly understood. Here, we integrated high-resolution hydrogeochemical profiling with metagenomic sequencing to characterize depth-resolved microbial communities and S-cycling genes in the mangrove wetlands of Dongzhai Harbor, Hainan, China. The results revealed pronounced differences in microbial community composition between zones, with Escherichia dominating mangrove sediments (4.22-20.07%) and Salmonella prevailing in mudflat sediments (23.87-60.98%). The abundance of S-cycling genes (e.g., tusA, soeA, aprA, dsrAB, sat) declined markedly with depth. Spatial variation in biogeochemical conditions shaped functional gene distributions: oxidative genes (aprA, soeA) were more abundant in mudflat profiles, whereas sat dominated reductive pathways in mangrove sediments. Environmental gradients structured microbial communities, with salinity, pH, total nitrogen (TN), and total organic carbon (TOC) showing negative correlations, and total sulfur (TS), total phosphorus (TP), SO4[2-] acting as positive drivers. Co-occurrence network analysis indicated tighter microbial associations in surface layers compared to deeper strata. The thiosulfate oxidation pathway was confined to the 5-10 cm interval in mudflat sediments and appeared at both 5-10 cm and 15-20 cm in mangrove sediments, while direct sulfite oxidation occurred in both zones. Moreover, methanogenesis, nitrification, and denitrification were more prominent in mudflat sediments, whereas methane oxidation prevailed in mangrove profiles. These findings advance our understanding of how microbial functional stratification and S metabolic pathways respond to environmental gradients, with implications for biogeochemical coupling in coastal wetland ecosystems.}, }
@article {pmid41338123, year = {2025}, author = {Huang, S and Yang, P and Wang, X and Zhang, K and Li, L and Yao, S and Qian, L and Liu, C and Guo, J and Shi, L and Liu, F and Xie, W and Guo, Y}, title = {Integrated metagenome and metabolome analysis reveals a disease signature of gut microbiota and the key gut microbiota-associated metabolite proline in schizophrenia.}, journal = {Journal of psychiatric research}, volume = {193}, number = {}, pages = {223-235}, doi = {10.1016/j.jpsychires.2025.11.029}, pmid = {41338123}, issn = {1879-1379}, abstract = {Schizophrenia (SCZ) is a multifaceted psychiatric condition with a complex set of etiological factors. Recent studies have revealed that gut microbiota play a significant role in the neurobiology associated with SCZ. Utilizing metagenomic sequencing and analysis techniques, we obtained composition and functional information of the gut microbiota from 68 SCZ patients and 61 healthy control (HC) subjects. We identified 72 inter-group differential species, 49 differential metabolic pathways, and 1987 differential functional genes. A. odontolyticus and F. prausnitzii were the core species enriched in the SCZ group and the HC group, respectively. Arginine and proline metabolism were the most significant differential metabolic pathways, with K00286 being the differential functional gene catalyzing the synthesis of L-proline in this pathway. Notably, a strong disease classification model was developed based on the gut microbiota data, achieving an outstanding AUC of 0.94, outperforming earlier models, the model achieved AUC values of 0.745 and 0.845 in two separate external datasets, respectively. Furthermore, insights into mechanisms were investigated by analyzing the relationships between microbial species and their associated metabolic pathways. Future research is essential to clarify causal connections, detail specific molecular pathways-particularly those involving functional proteins such as K00286-and to explore the communication processes between the gut microbiota and the brain. Our results underscore the potential for microbiota-based biomarkers and therapeutic targets in SCZ, emphasizing the essential role of gut microbiota in this intricate disorder.}, }
@article {pmid41338072, year = {2025}, author = {Jose, S and Lohith Kumar, DH and Malla, MA and Featherston, J and Bux, F and Kumari, S}, title = {Insights into microbial community, nitrogen‑phosphorus metabolism from metagenomic and metabolomic analysis of microalgal-cyanobacterial consortium-based bioinoculants.}, journal = {The Science of the total environment}, volume = {1009}, number = {}, pages = {181092}, doi = {10.1016/j.scitotenv.2025.181092}, pmid = {41338072}, issn = {1879-1026}, abstract = {The intensification of agriculture through chemical fertilizers has led to severe environmental consequences. This study provides a comprehensive investigation on chemical fertilizer, vermiculite and on microalgal-cyanobacterial consortia (bioinoculants) influencing soil microbial community. Chemical fertilizer application significantly altered the microbial community, suppressing the dominant phylum Proteobacteria to 48.3 % abundance from 60.9 % in the control soil. The bioinoculant treatments maintained a high Proteobacteria abundance (58.9 %-59.7 %) and fostered a growth-oriented, anabolic strategy. The 50:50 mix treatment uniquely promoted the fungal phylum Basidiomycota to 18.2 % abundance and showed the highest investment in the Glycolysis/Gluconeogenesis pathway (23.0 %). Chemical fertilizer treatment upregulated genes for rapid nitrogen assimilation (glnA, Log2FC = 0.60) and phosphorus starvation response (phoB, Log2FC = 0.65; pstS, Log2FC = 0.83). The enhanced energy production and conversion (11.83 %), amino acid transport and metabolism (11.20 %), and fatty acid biosynthesis (45.3 %) was observed in bioinoculant treatment. Unlike chemical fertilizer treatment, bioinoculant treatment led to the accumulation of the osmoprotectant trehalose and structural membrane lipids, while the 50:50 mix was uniquely characterized by a higher abundance of xylose. These findings demonstrate that the microalgal-cyanobacterial consortium can enhance nutrient recycling, and potentially boost soil health by reshaping the soil microbiome and metabolic functions, offering a promising strategy for sustainable agriculture.}, }
@article {pmid41335477, year = {2025}, author = {Riskumäki, M and Ruuskanen, MO and Mäenpää, K and Ruokolainen, L and Mäkelä, MJ and Jousilahti, P and Vartiainen, E and Ottman, N and Laatikainen, T and Haahtela, T and Alenius, H and Fyhrquist, N and Sinkko, H}, title = {Shotgun metagenomics reveals distinct skin microbial species in allergen-sensitized individuals.}, journal = {Microbial genomics}, volume = {11}, number = {12}, pages = {}, doi = {10.1099/mgen.0.001527}, pmid = {41335477}, issn = {2057-5858}, mesh = {Humans ; *Metagenomics/methods ; *Allergens/immunology ; *Skin/microbiology/virology ; Finland ; Adolescent ; *Microbiota/genetics ; Male ; Russia ; Female ; *Hypersensitivity/microbiology/immunology ; Malassezia/genetics/isolation &amp; purification ; Immunoglobulin E/immunology ; Bacteria/genetics/classification ; Child ; }, abstract = {The Karelian region, which spans the border between Finland and Russia, presents distinct environmental exposures and lifestyles on either side of the governmental border. In the more urbanized Finnish Karelia, allergic diseases are markedly more prevalent than in the more rural Russian Karelia. Prior studies, based on amplicon sequencing, have demonstrated major differences in skin microbiotas between the two populations. However, compositional differences in microbiota between sensitized and non-sensitized (NS) individuals have not been characterized. Here, in a selected population of 112 allergen-sensitized and NS adolescents, we used shotgun metagenomics to characterize the prokaryotic, eukaryotic and viral species in the skin potentially involved in allergic sensitization via distinct environmental exposures. In the more urban Finnish Karelia, the microbiome species composition was associated with IgE-mediated allergen sensitization status, while in the more rural Russian Karelia, the composition was associated with exposure to furry pets. Finnish participants showing high IgE-mediated sensitization to common allergens (allergen-specific IgE >7.5 kU/L) had less Cutibacterium acnes and Malassezia in their skin and displayed weaker interconnectedness of the microbial co-occurrence network compared with NS participants. Moreover, Malassezia restricta strain-level differences were related to allergen sensitization in both Finnish and Russian participants. In summary, we found distinct skin microbiomes between allergen-sensitized and NS participants and tracked the bacterial and fungal species associated with the degree of allergic sensitization in the more urbanized part of the Karelian region. These findings provide new insights into the factors that shape the human skin microbiome and influence allergic diseases.}, }
@article {pmid41335476, year = {2025}, author = {Docter, J and Mansfeldt, C}, title = {Environmental Census: Modeling Synthetic Biology Ecological Risk with Metagenomic Enzymatic Data and High-Performance Computing.}, journal = {ACS synthetic biology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acssynbio.5c00618}, pmid = {41335476}, issn = {2161-5063}, abstract = {Engineered microorganisms in biotechnology present biosafety and environmental management challenges. As the synthetic biology market develops and deploys new technologies, these engineered organisms may escape into unintended environments. Improved predictive computational tools are necessary to assess the potential establishment risk and environmental location of these escaped engineered microorganisms, assisting their design and management. Here, we present EnCen, a risk assessment Python software package that predicts the environmental range of engineered microorganisms through annotated functional one-hot-encoded similarity between the engineered microorganism and resident microorganisms of a given environment. EnCen utilizes publicly available composite metagenomes as representatives of microbial environments that occur along an agriculture-water cycle and can be customized for any additional target environment. This tool was deployed against case studies reported in the literature and to reassess commercially available bacterial biopesticides, highlighting both the successful recapture of previously reported dynamics and the identification of select commercial products that pose a wider establishment risk in multiple environments. When further utilizing EnCen to investigate the receiving environments comprising the central database, key enzyme classes are mapped as characteristics to select environments, prioritizing certain modifications likely leading to a greater risk (or effectiveness) of establishment. The results demonstrate that EnCen meaningfully summarizes publicly available metagenomic data, prioritizes environments to monitor for adverse effects, and analyzes potential impacts on microbial community composition and functioning. Overall, this study demonstrates a computational approach to managing engineered microorganisms, aiding in the safe deployment and benefit of industrial synthetic biology.}, }
@article {pmid41335362, year = {2025}, author = {Jia, Y and Shi, Y and Wang, J and Liu, H and Wang, H and Huang, Y and Liu, Y and Chen, P and Peng, J}, title = {Astragalin attenuates caerulein-induced acute pancreatitis by targeting the NLRP3 signaling pathway and gut microbiota.}, journal = {Bioresources and bioprocessing}, volume = {12}, number = {1}, pages = {139}, pmid = {41335362}, issn = {2197-4365}, support = {82170661//National Natural Science Foundation of China/ ; 2023DK2002//Key Project of Research and Development Plan of Hunan Province/ ; 2025JJ60669//Hunan Provincial Natural Science Foundation of China/ ; 2024M763719//China Postdoctoral Science Foundation/ ; GZC20242045//Postdoctoral Fellowship Program of CPSF/ ; }, abstract = {BACKGROUND: Acute pancreatitis (AP) has caused great concern worldwide due to its serious threat to human health. Astragalin is a bioactive natural flavonoid compound with several pharmacological activities, but it remains unclear about its effect on AP. The objective of this experiment was to explore the mitigating efficacy of astragalin on caerulein-induced AP model and examine the underlying mechanisms.<br><br>METHODS: Following the assessment of astragalin's direct effects on pancreatic acinar cells using an in vitro AP model, an in vivo mouse model was established to further validate its efficacy and elucidate the underlying mechanisms. Pancreatic histopathology, amylase, and lipase levels of mice were observed to determine the optimal therapeutic dose of astragalin. The network pharmacology and RNA sequencing technology were used to reveal the possible targets and pathways. Subsequent molecular docking and western blot were conducted to validate the association between astragalin and key target molecules, as well as the NLRP3 signaling pathway. Combined with metagenomics and metabolomics analysis, the astragalin effective gut microbiota-metabolite-gene network was constructed. Moreover, fecal microbiota transplantation experiments were performed to clarify the importance of gut microbiota in astragalin-mediated alleviation of AP.<br><br>RESULTS: The results showed that astragalin attenuated caerulein-induced injury in AR42J cells in vitro. Consistent with these findings, in vivo experiments revealed that astragalin treatment significantly improved pancreatic pathological injury, cell apoptosis, and systemic inflammatory response in AP mice, particularly at high doses. The integrated analysis of network pharmacology and transcriptomics revealed that the NLRP3 signaling pathway was a key molecular pathway, which was further validated using western blot. Docking analysis showed that 12 target genes had good docking activity with astragalin. More intriguingly, it was found that astragalin could reverse gut microbiota dysbiosis by restoring microbial diversity, altering bacterial community composition, and modulating key metabolic pathways. Specifically, astragalin-effective correlation networks were constructed with Lachnoclostridium sp. YL32, Roseburia intestinalis, Ruminococcus gnavus, Lachnospiraceae bacterium Choco86, Anaerobutyricum hallii, etc. as the core strains, 22 metabolites, including 5-Methoxytryptophan, D-Serine, L-Tryptophan, L-Methionine, etc. as core metabolites, and NLRP3 pathway-related genes as the main regulatory targets. Furthermore, fecal microbiota transplantation experiments confirmed the involvement of gut microbiota in AP remission.<br><br>CONCLUSION: Collectively, these findings identify astragalin as a promising therapeutic agent for AP, targeting both the NLRP3 signaling cascade and gut microbial homeostasis.}, }
@article {pmid41334926, year = {2025}, author = {Shulman, HB and Pyle, JAM and Classen, AT and Inouye, DW and Simberloff, R and Sorensen, PO and Thomas, W and Rudgers, JA and Kivlin, SN}, title = {Nutrient limitation shapes functional traits of mycorrhizal fungi and phosphorus-cycling bacteria across an elevation gradient.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0052325}, doi = {10.1128/msystems.00523-25}, pmid = {41334926}, issn = {2379-5077}, abstract = {In nutrient-limited high-elevation ecosystems, plants rely on arbuscular mycorrhizal (AM) fungi to provide mineral phosphorus (P) in the form of phosphate (PO4[3-]). AM fungi gather these nutrients from phosphorus-cycling bacteria (PCBs) that can mineralize PO4[3-] from organic matter and solubilize mineral-bound P. How climate, soil factors, and nutrient limitation influence AM fungi and PCB assembly remains unclear. We collected soil from montane meadows across a 1,000-m elevation gradient on three replicate mountainsides and analyzed AM fungal marker genes, P-cycling genes from shotgun metagenomes, and edaphic measurements. High-elevation soils had nearly 50-fold less soil PO4[3-] and 60% more AM fungal hyphae than low-elevation soils. AM fungal turnover was linked to changes in pH, organic carbon, and PO4[3][-]. The composition of 198 P-cycling genes was influenced by the AM fungal community structure. Drivers of individual PCB functional genes, including pH and organic carbon, varied with gene phylogeny. We found a trade-off in P-cycling strategies across elevation: P-rich, low-elevation soils supported root-colonizing AM fungi and organic P-mineralizing bacteria. P-poor, high-elevation soils were dominated by stress-tolerant AM fungi and mineral P-solubilizing bacteria. Our results suggest that AM fungi and PCB community turnover across elevation are both shaped by pH, organic carbon, and P availability. With continued climate warming, the structure and function of mountaintop ecosystems might shift to resemble lower elevations, disrupting long-established and specialized microbial assemblages, with consequences for P-cycling dynamics and the total P available to plant communities.IMPORTANCEPhosphorus (P) limits plant productivity in high-elevation ecosystems, yet the microbial networks that mobilize P, including arbuscular mycorrhizal (AM) fungi and phosphorus-cycling bacteria (PCBs), remain under-characterized in these nutrient-poor soils. We show that across a 10,00-m elevation gradient, AM fungi and P-cycling gene assemblages shift predictably with pH, organic carbon, and phosphate availability. Higher elevations, with less available P, select for stress-tolerant AM fungal taxa and PCB strategies geared toward mineral solubilization, while low-elevation sites favor root colonization by AM fungi and organic P mineralization. These results suggest that nutrient limitation can constrain microbial community assembly in consistent ways across landscapes. High mountain soils are low in P and rely on a network of underground AM fungi and PCB to deliver nutrients to plants. This study shows how those underground relationships reorganize with elevation and how climate change could collapse long-standing microbial strategies by pushing high-elevation ecosystems toward lowland conditions. As soils warm and dry, the microbial scaffolding that supports alpine plant life may become increasingly unstable.}, }
@article {pmid41334911, year = {2025}, author = {Kandathil, AJ and Clipman, SJ and Anantharam, R and Duchen, D and Cox, AL and Larman, HB and Thomas, DL}, title = {Antibody-mediated control of anellovirus infection: evidence from people who inject drugs.}, journal = {Journal of virology}, volume = {}, number = {}, pages = {e0161225}, doi = {10.1128/jvi.01612-25}, pmid = {41334911}, issn = {1098-5514}, abstract = {Infections with viruses belonging to the family Anelloviridae are widespread among humans. Although generally considered a commensal, there is evidence to suggest that these infections may be controlled by host immune responses. However, the mechanism of immune control remains unclear. Previous research has also suggested a possible role of anellovirus capsid spikes in immune evasion. To investigate the role of antibodies in controlling infection, we used AnelloScan to profile plasma collected every 6 months over 2 years from 10 persons who inject drugs (PWID). Participants were selected based on viremia patterns: persistent (n = 6) versus intermittent (n = 4). Long-read metagenomic sequencing revealed a higher median number of alphatorquevirus (TTV) species in participants with persistent viremia compared to those with intermittent viremia (P < 0.0001). AnelloScan detected TTV-specific antibodies among all study participants. No significant differences were observed between the two groups when all antibody-reactive peptides located in the capsid were included. However, among participants with intermittent viremia, antibodies were more frequently reactive to peptides located in the amino acid variable region of the capsid spike domain (P = 0.0429). These findings suggest that among PWID, antibodies targeting the sequence variable region of the spike domain appear to be associated with control of anellovirus infection. Additionally, anelloviruses might be susceptible to pre-existing immunity, and the amino acid variable region of the spike protein may play a role in viral infectivity.IMPORTANCEAnelloviruses are highly diverse and are recognized as the major component of the blood virome in healthy humans. Despite this, little is known about their interactions with their hosts. In this study, we found that anelloviruses can elicit antibody responses. Notably, antibodies that targeted a sequence variable region on spikes present on viral capsids were associated with truncation of plasma viremia. These data suggest a possible mechanism of immune control of anellovirus infections while also indicating a role of the capsid spikes in viral infectivity.}, }
@article {pmid41334589, year = {2025}, author = {Li, J and Xu, Y and Wang, M and Lin, J and Sun, J and Ma, J and Zhang, H}, title = {Dual-source DPP4 drives intestinal fibrosis in Crohn's disease: synergistic therapeutic targeting of host and microbiota pathways.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2593119}, doi = {10.1080/19490976.2025.2593119}, pmid = {41334589}, issn = {1949-0984}, mesh = {Animals ; Humans ; *Dipeptidyl Peptidase 4/metabolism/genetics ; *Crohn Disease/pathology/drug therapy/microbiology/metabolism ; Mice ; Fibrosis ; *Gastrointestinal Microbiome/drug effects ; Disease Models, Animal ; Male ; Myofibroblasts/metabolism ; Dipeptidyl-Peptidase IV Inhibitors/pharmacology ; *Intestines/pathology ; Sitagliptin Phosphate/pharmacology ; Mice, Inbred C57BL ; Female ; Dextran Sulfate ; }, abstract = {Crohn's disease (CD), a chronic inflammatory bowel disorder, often progresses to intestinal fibrosis and stricture, yet no effective anti-fibrotic treatments exist. This study reveals dipeptidyl peptidase 4 (DPP4) as a pivotal driver of fibrosis through bioinformatics analysis, clinical samples, and experimental models. Elevated DPP4 expression was observed in stenotic intestinal tissues of CD patients and dextran sodium sulfate (DSS)-induced fibrotic mice. Mechanistically, both membrane-bound DPP4 and soluble DPP4 (sDPP4) activated human intestinal myofibroblasts (HIMFs) via the PI3K-AKT pathway, stimulating migration, proliferation, and extracellular matrix deposition. Importantly, metagenomic sequencing revealed enrichment of microbial Dpp4 genes in fecal samples from CD patients with stenosis, and in vivo colonization with engineered E. coli overexpressing microbial DPP4 exacerbated fibrotic remodeling, confirming microbiota-derived DPP4 (mDPP4) as a pathogenic driver. Furthermore, pharmacological inhibition of host DPP4 (sitagliptin) or selective blockade of mDPP4 (Dau-d4) attenuated fibrosis in murine models, with combined therapy showing enhanced efficacy. These findings underscore the roles of DPP4, originating from both host and microbiota, and existing in membrane-bound and soluble forms, in promoting CD-associated intestinal fibrosis. This study identifies DPP4 as a novel therapeutic target, proposing dual-source inhibition as a promising strategy to prevent stricture formation in CD patients, thereby addressing a critical unmet clinical need.}, }
@article {pmid41334206, year = {2025}, author = {Yang, L and Liu, Y and Guo, S and Li, T and Nie, Q and Zhang, Y and Zeng, S and Wang, F and Liu, L}, title = {Mechanism of tobacco-sweet potato intercropping in suppressing Ralstonia solanacearum in flue-cured tobacco.}, journal = {Frontiers in plant science}, volume = {16}, number = {}, pages = {1688379}, pmid = {41334206}, issn = {1664-462X}, abstract = {Tobacco bacterial wilt (Ralstonia solanacearum) is a fatal pathogen of tobacco, causing severe losses annually. Intercropping has been proposed as a sustainable strategy to mitigate soil-borne pathogens through rhizosphere interactions. However, the mechanisms by which tobacco-sweet potato intercropping specifically affects the microecological environment and suppresses R. solanacearum remain poorly understood. To investigate the effect of the TSP model on the soil-borne pathogen of bacterial wilt (Ralstonia solanacearum) in tobacco-growing soil, this study compared and analyzed the characteristics and differences in bacterial wilt incidence, Ralstonia solanacearum content, phenolic acid components, metabolome, and metagenome between (T) and (TSP) systems. The results showed that compared to the T treatment, the TSP treatment reduced the incidence of bacterial wilt in flue-cured tobacco and significantly decreased the abundance of R. solanacearum in the soil by 21.4%, while increasing the total phenolic acid content by 21.9%. The total phenolic content in the TSP soil was increased by 21.9% compared to T. Differentially abundant metabolites between TSP and T were primarily enriched in carbohydrate metabolic pathways, such as nucleotide sugar biosynthesis, fructose, and mannose metabolism. The content of substances such as rhamnose, D-allose, and mannitol in T-treated soil was 2.14-6.62 times higher than that in TSP-treated soil, with new tobacco alkaloids being up to 91.09 times higher. Compared to the T treatment, the TSP treatment significantly increased the relative abundances of Acidobacteriota, Chloroflexota, Bradyrhizobium, Pseudolabrys, and Sphingomonas by 64.08%, 18.86%, 23.55%, 21.80%, and 12.98%, respectively. The content of Ralstonia solanacearum in the soil was positively correlated with differential metabolites such as mannitol, rhamnose, and D-allose (r = 0.8), while negatively correlated with phenolic acids such as syringic acid, ferulic acid, caffeic acid, and gallic acid, as well as microorganisms such as Chloroflexota, Gemmatimonadota, Acidobacteriota, and Sphingomonas. In summary, TSP can regulate soil metabolites, phenolic acids, and beneficial microorganisms, forming a synergistic network to suppress the content of Ralstonia solanacearum and reduce the risk of tobacco bacterial wilt. This provides a theoretical basis for regulating soil microecology and enhancing crop disease resistance in intercropping systems.}, }
@article {pmid41333806, year = {2025}, author = {Al Bataineh, MT and Dash, NR and Mysara, M and Saeed, O and Alkhayyal, N and Talaat, IM and Bendardaf, R and Saber-Ayad, M}, title = {Metagenomic analysis of gut microbiota in colorectal adenocarcinoma in the MENA region.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1634631}, pmid = {41333806}, issn = {2235-2988}, mesh = {Humans ; *Colorectal Neoplasms/microbiology ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; *Metagenomics ; Male ; Female ; Middle Aged ; *Adenocarcinoma/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Aged ; DNA, Bacterial/genetics/chemistry ; Middle East ; Feces/microbiology ; Phylogeny ; DNA, Ribosomal/genetics/chemistry ; }, abstract = {BACKGROUND: Growing evidence suggests that gut microbiota plays a role in the development of colorectal cancer (CRC), and a few bacterial strains have been linked to carcinogenesis. Contrary to the Western population, the relationship between pro-cancer microorganisms and CRC among Middle Eastern individuals remains largely unexplored. Ninety-eight samples from Middle Eastern individuals with and without CRC were subjected to microbial profiling based on the 16S rRNA gene.<br><br>RESULTS: The CRC group exhibited a more complex gut microbiota with clusters that were significantly distinct from those of the control group. The taxonomic orders Caulobacterales, Rhizobiales, Sphingomonadales, and Burkholderiales, along with the genera Recibecterium and Sphingobium, were overrepresented in the CRC samples based on differential abundance testing between the CRC and control groups. Utilizing 16S-based functional prediction, we identified a significant enrichment of pathways vital for pentose and glucuronate interconversions, metabolism of terpenoids and polyketides, spliceosome, and dTMP kinase pathways within the CRC group. Moreover, we observed a link between Herbaspirillum huttiense and the pathways regulating the actin cytoskeleton; this intriguing connection may provide insights into the molecular mechanisms underlying cytoskeletal rearrangement and carcinogenesis triggered by H. huttiense.<br><br>CONCLUSIONS: The findings of this study support the connection between gut microbiota and the development of CRC and highlight region-specific microbial signatures that may serve as non-invasive diagnostic biomarkers or predictive tools for early screening in Middle Eastern populations, where CRC is increasingly diagnosed at advanced stages. These insights could inform the development of microbiome-based screening panels and personalized prevention strategies adapted to the MENA region's unique genetic, dietary, and environmental profiles.}, }
@article {pmid41333777, year = {2025}, author = {Zhang, Q and Gong, Q and Sun, X and Zhu, H}, title = {Massive hemoptysis as the sentinel symptom: a case report of pulmonary nocardiosis in an immunocompetent patient.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1677156}, pmid = {41333777}, issn = {2296-858X}, abstract = {Pulmonary nocardiosis is frequently missed or misdiagnosed due to its atypical clinical symptoms and non-specific imaging findings. Moreover, delayed diagnosis and treatment can lead to high mortality rates, underscoring the need to enhance etiological diagnosis. Here, we report a 55-year-old immunocompetent woman who developed pulmonary Nocardia cyriacigeorgica infection with massive hemoptysis as the initial symptom. The patient had no history of chronic respiratory diseases. Metagenomic next-generation sequencing of bronchoalveolar lavage fluid collected via bronchoscopy was performed, which confirmed the diagnosis. After targeted therapy with oral sulfamethoxazole-trimethoprim and linezolid, the patient achieved significant symptomatic and radiological improvement, accompanied by normalization of white blood cell count and neutrophil count. No recurrence was observed during follow-up.}, }
@article {pmid41333773, year = {2025}, author = {Li, Q and Sun, X and Lei, W and Zhu, Y and Du, W and Jiang, X and Su, N}, title = {Psittacosis chlamydia pneumonia complicated with organizing pneumonia: a case report and literature review.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1670456}, pmid = {41333773}, issn = {2296-858X}, abstract = {BACKGROUND: Secondary organizing pneumonia (SOP) may develop following infections. Psittacosis, caused by Chlamydia psittaci (C. psittaci), is a zoonotic disease transmitted from birds to humans. It can present with a wide spectrum of symptoms, ranging from mild flu-like illness to life-threatening severe pneumonia. Cases of C. psittaci infection complicated by organizing pneumonia (OP) are rarely reported, and delayed treatment may pose a life-threatening risk.<br><br>METHODS: We report a case of C. psittaci pneumonia complicated by OP. To identify additional cases and clarify the clinical features of this condition, a literature search was conducted using the PubMed and Embase databases for the period from January 1995 to May 2025. The search included the following keywords: "psittacosis," "Chlamydia psittaci," "chlamydia," "organizing pneumonia," and "bronchiolitis obliterans with organizing pneumonia."<br><br>RESULTS: A 66-year-old male with a history of poultry farming presented with fever, cough, sputum production, and hemoptysis. Empirical antimicrobial therapy with ceftizoxime was ineffective. To identify the etiology of the pulmonary lesions, bronchoscopy was performed, and C. psittaci infection was confirmed by metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF). Although the lesions partially resolved after moxifloxacin therapy, the patient experienced recurrent episodes. Chest CT revealed migratory lesions, which are uncommon in C. psittaci pneumonia. Further pathological examination of the specimen confirmed the diagnosis of OP. The patient's condition improved following corticosteroid therapy. A review of the literature indicated that none of the three previously reported cases were definitively diagnosed at initial admission; all presented primarily with fever and cough. One case progressed to severe pneumonia and resulted in death.<br><br>CONCLUSION: OP caused by C. psittaci pneumonia presents with non-specific symptoms and signs, making early diagnosis challenging. During treatment of C. psittaci pneumonia, if empirical anti-infective therapy shows no response after three days, or if imaging reveals features such as consolidation, migratory lesions, or a reverse halo sign, the possibility of concurrent OP should be considered. Pathological examination is recommended in such cases to avoid missed diagnosis and to ensure timely intervention.}, }
@article {pmid41333054, year = {2025}, author = {Kravchuk, OI and Finoshin, AD and Nikishina, YO and Melnikova, VI and Kublanov, IV and Sutormin, DA and Rusanova, AN and Ri, MT and Isaev, AB and Mikhailov, KV and Ziganshin, RH and Adameyko, KI and Anashkina, AA and Ignatyuk, VM and Gornostaev, NG and Voronezhskaya, EE and Sokolova, AM and Mikhailov, VS and Lyupina, YV}, title = {Evolutionary conservation of dopamine-mediated cellular plasticity in Arctic sponges (Porifera).}, journal = {Frontiers in molecular biosciences}, volume = {12}, number = {}, pages = {1671771}, pmid = {41333054}, issn = {2296-889X}, abstract = {Dopamine is an evolutionarily ancient signaling molecule implicated in stress responses across the tree of life. The role of dopamine is well-documented in the nervous system of animals, yet in the early-branching animal lineage of sponges its utility is poorly understood. Arctic marine sponges inhabiting the tidal zone of the White Sea, with fluctuating seasonal ice cover and solute concentrations, exhibit remarkable physiological plasticity, making them ideal models for studying conserved stress-response mechanisms. We investigated the dopamine signaling in two sponge species, Sycon ciliatum (class Calcarea) and Halisarca dujardini (class Demospongiae), using metagenomics, transcriptomics, high performance liquid chromatography, mass spectrometry, molecular docking, and immunofluorescence. S. ciliatum expresses an aromatic amino acid decarboxylase-like enzyme and efficiently converts L-DOPA to dopamine, whereas H. dujardini lacks this canonical biosynthetic enzyme, but accumulates dopamine, likely via its symbionts. During morphogenetic transitions in H. dujardini, genes involved in dopamine turnover, including tyrosinase, dopamine β-hydroxylase, and G protein-coupled receptors (GPCRs), showed dynamic expression. Molecular docking revealed that GPCR affinity for dopamine is modulated by cellular redox status. Notably, we report the first evidence of post-translational dopaminylation of cytoskeleton proteins in a non-bilaterian animal. Fluctuations in cellular dopamine levels and actin dopaminylation correlated with structural remodeling of the aquiferous system throughout the sponge life cycle. These findings demonstrate that dopamine regulates cellular plasticity through both transcriptional and post-translational mechanisms. The discovery of dopaminylation in sponges expands the evolutionary scope of catecholamine signaling and underscores the ancient role of dopamine in the regulatory interactions of animal cells.}, }
@article {pmid41332906, year = {2025}, author = {Zhao, Z and Lu, L and Yi, Y and Gao, N and Hu, J and Han, G and Ma, X}, title = {Gut microbiota signature in a cohort of Chinese patients with rosacea.}, journal = {Biochemistry and biophysics reports}, volume = {44}, number = {}, pages = {102361}, pmid = {41332906}, issn = {2405-5808}, abstract = {BACKGROUND: Rosacea is a chronic inflammatory skin disease characterized by diverse symptoms and variable clinical progression, which can significantly impair patients' quality of life and mental health. The exact etiology of rosacea remains elusive. It has been hypothesized that specific microorganisms may trigger symptom onset and play crucial roles in the pathogenesis of the disease.<br><br>OBJECTIVE: We performed a case-control study to investigate the gut microbiome of rosacea patients compared to controls matched by age, sex in China.<br><br>METHODS: The study cohort comprised eight patients diagnosed with rosacea and eight age- and sex-matched healthy controls residing in Beijing. Metagenomic sequencing was performed using on a llumina Novaseq 6000 platform. Hospital Anxiety and Depression Scale was used to evaluate the severity of anxiety and depression of rosacea patients. Skindex-16 score was used to assess dermatology-specific health-related quality of life (HrQoL) in patients with rosacea. The clinical evaluation of acne was done using the ECLA score.<br><br>RESULTS: The rosacea patients showed higher HADS and Skindex-16 score (15.375&#x202f;&#xb1;&#x202f;1.302 and 46&#x202f;&#xb1;&#x202f;9.75 respectively) vs healthy controls (3.425&#x202f;&#xb1;&#x202f;1.308 and 0 respectively). A clear distinction was observed between the rosacea group and the control group, characterized by a significant increase in the abundance of Turicibacter_sp._TJ11, Turicibacter_sp._H121,Turicibacter_sp._TA25,Turicibacter_sp._T129,Ruminococcus_sp._AF18-22,Ruminococcus_sp._CAG:379,Ruminococcus_sp._AM2829LB,Ruminococcus_callidus, Ruminococcus_sp._AM36-18,Ruminococcus_sp._AF43-11,Ruminococcus_sp._AM28-41,Streptococcus sp. 23.2,Streptococcus infantarius, Streptococcus vestibularis, Streptococcus salivarius, Streptococcus gordonii, Clostridium_sp._CAG:798, Clostridium_tertium, Alistipes_sp._Z76 and Lachnospiraceae_bacterium_XBB2008in the rosacea group. In contrast, reduced levels were detected in the rosacea group for Clostridium_sp._AF12-41, Clostridium_sp._CAG:299, Clostridium_sp._OM05-5BH,Clostridium_sp._AF24-2LB, Clostridium_sp._AM18-55, Clostridium_sp._CAG:43, Clostridium_sp._OM047,Clostridium_sp._TF1113AC,Clostridium_sp._OF134,Clostridium_disporicum, Butyrivibrio_sp._CB08,Butyrivibrio_sp._INlla14, Roseburia_sp._CAG:50 (p&#x202f;<&#x202f;0.05). Pearson correlation analysis revealed that Gemmiger_sp._An120 was positively correlated with Skindex-16 and negatively correlated with ECLA score (P&#x202f;<&#x202f;0.05). Clostridium_sp._CAG:299 was negatively correlated with HADS scores and positive correlation with ECLA score (P&#x202f;<&#x202f;0.05). KEGG pathway analysis found KO05034, KO04024 and KO00920 pathways exhibited increased activity in the Rosacea group (P&#x202f;<&#x202f;0.05).<br><br>CONCLUSIONS: The gut microbiota in individuals with rosacea displayed changed from that of healthy control. These microbial alterations may contribute to the pathogenesis of rosacea through multiple mechanisms, including impairment of the intestinal barrier function, induction of pro-inflammatory cytokine release, and modulation of neurotransmitter synthesis. By integrating taxonomic shifts with functional alterations, this study provides deeper insights into the gut ecosystem changes associated with systemic inflammation in rosacea.}, }
@article {pmid41332561, year = {2025}, author = {Ahmed, MA and John, J and Campbell, BJ}, title = {Ecological distribution, environmental roles and drivers of Actinobacteriota in two Mid-Atlantic estuaries.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.11.21.689735}, pmid = {41332561}, issn = {2692-8205}, abstract = {Actinobacteriota, a bacterial phylum renowned for members that produce bioactive compounds (e.g., antibiotics), has key roles in terrestrial and aquatic ecosystems. Although soil and marine/freshwater Actinobacteriota are well studied, functions and activities of their estuarine counterparts are poorly understood. We characterized 67 metagenome-assembled genomes (MAGs) belonging to 12 Actinobacteriota families from Chesapeake and Delaware Bay water samples across different seasons, salinities, and size fractions. MAGs from four dominant families, Ilumatobacteraceae, Nanopelagicaceae, Microbacteriaceae, and S36-B12, were examined in depth for their abundance, functional potential, estimated growth rates, and gene expression among samples. Actinobacteriota were most abundant in low- to medium-salinity samples during spring and summer. Their abundance patterns were strongly influenced by combinations of salinity, temperature, and phosphate, nitrate and silicate concentrations. Notably, many exhibited high estimated growth rates under low and medium salinities in summer. Members of the four major families showed a range of metabolic capacities from generalist to specialist, and all encoded biosynthetic gene clusters (BGCs) for secondary metabolites, particularly terpenes and betalactones, that were differentially expressed across conditions. Bay, salinity and size fraction were the primary drivers of gene expression differences. Distinct secondary metabolite genes were expressed between bays, with higher expression generally observed in medium compared to low salinities. These findings underscore the metabolic versatility and environmental responsiveness of Actinobacteriota, highlighting their active role in estuarine microbial communities and their contributions to biogeochemical cycling in dynamic coastal ecosystems.}, }
@article {pmid41332430, year = {2025}, author = {Li, L and Zhou, N and Wang, Z and Wang, T and Wang, Y and Qiao, F and Du, ZY and Zhang, ML}, title = {Intestinal microbiota contributes to the heterogeneity of fat deposition by promoting mitochondrial fatty acid β-oxidation.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2593076}, doi = {10.1080/19490976.2025.2593076}, pmid = {41332430}, issn = {1949-0984}, mesh = {*Gastrointestinal Microbiome/physiology ; Animals ; *Fatty Acids/metabolism ; Carnitine/biosynthesis/metabolism ; Oxidation-Reduction ; *Mitochondria/metabolism ; Zebrafish ; Lipid Metabolism ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Fecal Microbiota Transplantation ; RNA, Ribosomal, 16S/genetics ; Male ; Humans ; Feces/microbiology ; }, abstract = {The gut microbiota plays a crucial role in lipid metabolism in both humans and animals. However, the specific contributions of gut microbiota and their associated metabolites to fat deposition, as well as the underlying mechanisms, remain largely unexplored. In this study, we demonstrated that the intestinal microbiota mediated the heterogeneity of mesenteric fat index (MFI), as evidenced by fecal microbiota transplantation (FMT) experiments. Notably, analysis of the 16S rRNA gene amplicon sequencing of 44 samples revealed a significantly higher abundance of Cetobacterium somerae in the Low MFI group, with a positive correlation to reduced MFI. Serum metabolomics analysis confirmed that L-Carnitine emerged as the most differentially abundant metabolite in the Low MFI group and exhibited a strong positive correlation with C. somerae abundance. Metagenomic analysis showed that microbial genes related to L-Carnitine biosynthesis were significantly enriched in the Low MFI group. Further, C. somerae was isolated and cultured, and its subsequent monocolonization in germ-free zebrafish and tilapia demonstrated its lipid-lowering effects by enhancing mitochondrial fatty acid β-oxidation. Whole genome sequencing demonstrated C. somerae could encode the [EC:1.2.1.3] gene, which promotes the production of 4-trimethylammoniobutanoate, a precursor of L-Carnitine, thereby enhancing L-Carnitine biosynthesis by the host and gut microbiota, leading to the reduced fat deposition in Nile tilapia. In conclusion, C. somerae, a core gut microbe with high abundance in aquatic teleost intestines, plays an important role in host lipid metabolism. This study advances our understanding of how core gut microbes shape host phenotypes and provides novel insights into manipulating core gut colonizers to reduce fat deposition.}, }
@article {pmid41331875, year = {2025}, author = {Kong, L and Mao, Y and Zheng, R and Feng, Y and Chen, B and Wu, X and Zhu, Q and Feng, J and Liu, S}, title = {Overlooked siderophore producers favor ammonium oxidation in global wastewater treatment plants.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-025-02290-9}, pmid = {41331875}, issn = {2049-2618}, support = {523B2095//National Natural Science Foundation of China/ ; Nos. 52270016//National Natural Science Foundation of China/ ; 2022YFC3203003//National Key Research and Development Program of China/ ; }, abstract = {BACKGROUND: Iron is essential for biological nitrogen removal in wastewater treatment plants (WWTPs), as a significant portion of microbial nitrogen-transforming enzymes require iron. However, iron bioavailability is a global challenge for nitrogen removal microbes in WWTPs, where it often exists in insoluble forms due to its complexation with various wastewater constituents.<br><br>RESULTS: Combined laboratory experiment and metagenomic analysis of 52 global WWTPs, we found that siderophore-producing bacteria (SPB) were previously uncharacterized dominant members in activated sludge. SPB enhance the iron uptake of activated sludge microbial communities by facilitating the transport of iron ions from insoluble sources into the cells. Of the 1328 total recovered metagenome-assembled genomes (MAGs) from global WWTPs, 6.2% were identified as SPB, while 79.3% of MAGs could utilize siderophores, indicating widespread sharing of siderophores in WWTPs. Interestingly, nearly all ammonium-oxidizing bacteria (AOB) from WWTPs lacked siderophore-producing capacity, and exogenous siderophore (20&#xa0;&#xb5;M pyochelin) addition boosted ammonium oxidation rates by 28.2%. Moreover, strong indications were found for an association between AOB and the SPB in global WWTPs, suggesting their symbiotic interaction is a common and critical process to maintain ammonium oxidation performance. SPB in WWTPs were predominantly aerobic or facultative anaerobic heterotrophic bacteria, exhibiting low taxonomic diversity but high abundance.<br><br>CONCLUSIONS: This study reveals SPB as previously overlooked but crucial contributors to biological nitrogen removal in global WWTPs, providing foundational insights into iron-based microbial cooperation within engineered systems. Modulating SPB activity based on their metabolic characteristics is a promising strategy to cope with low iron bioavailability issue for biological processes in WWTPs. Video Abstract.}, }
@article {pmid41331807, year = {2025}, author = {Rouzban, T and Goudarzi, R and Motamedi, E and Ghollasi, M and Zeinalabedini, M and Ariaeenejad, S}, title = {Metagenomic laccase-catalyzed crosslinking of wheat proteins for enhanced soybean meal nutritional value: applications in poultry feed and food industry.}, journal = {BMC biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12896-025-01081-2}, pmid = {41331807}, issn = {1472-6750}, support = {0//Agricultural Biotechnology Research Institute of Iran (ABRII)/ ; }, }
@article {pmid41331687, year = {2025}, author = {Abedi, Z and Sheikh Beig Goharrizi, MA and Abbasi, A and Sadat Soleimani Zakeri, N and Jangi, H}, title = {Metagenomic insights into microbial community alterations and co-occurrence networks in infective endocarditis.}, journal = {Genomics &amp; informatics}, volume = {23}, number = {1}, pages = {25}, pmid = {41331687}, issn = {1598-866X}, abstract = {BACKGROUND: Infective endocarditis (IE) is a serious infection of the heart valves, and standard culture methods often miss the bacteria responsible, especially in culture-negative cases. To address this, we used 16S rRNA gene-based next-generation sequencing (NGS) on heart valve tissue. This approach allowed us to map out the bacterial communities present and evaluate their potential role in IE.<br><br>RESULT: We identified six key bacterial genera-Enterococcus, Streptococcus, Coxiella, Staphylococcus, Haemophilus, and Cutibacterium-plus three specific species: Streptococcus troglodytae, Haemophilus parainfluenzae, and Coxiella burnetii. Our co-occurrence analysis showed that these bacteria tend to exist independently within infected valve tissue, with no significant correlations between them.<br><br>CONCLUSION: We detected bacterial taxa, including Cutibacterium and Streptococcus troglodytae. Although S. troglodytae is rarely associated with IE, and Cutibacterium comprises low-abundance bacteria not typically linked to this condition. These findings demonstrate the value of NGS in identifying pathogens that standard culture methods may overlook. As these results are based on computational analyses, further laboratory validation is required. Incorporating NGS into diagnostic protocols may enhance pathogen detection in culture-negative IE and support more targeted treatment and prevention strategies.}, }
@article {pmid41331561, year = {2025}, author = {Tian, J and Wang, X and Zhu, Y and Kong, F and Sun, J}, title = {Diagnosis of esophageal pleural fistula via metagenomic next-generation sequencing of pleural effusion: a case report.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {1689}, pmid = {41331561}, issn = {1471-2334}, }
@article {pmid41331462, year = {2025}, author = {Xu, W and Wang, W and Liu, Q}, title = {Identification of a novel pegivirus in reindeer (Rangifer tarandus valentinae) in Northeastern China.}, journal = {BMC veterinary research}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12917-025-05167-z}, pmid = {41331462}, issn = {1746-6148}, support = {2024YFD1800103//This study was financially supported by the National Key Research and Development Program of China ./ ; }, abstract = {BACKGROUND: Pegiviruses (family Flaviviridae), associated with persistent infections in diverse mammalian and avian hosts, are increasingly recognized for their evolutionary significance. Reindeer (Rangifer tarandus valentinae), semi-domesticated in northeastern China's Greater Khingan Mountains, are critical reservoirs for zoonotic pathogens and face growing human contact due to tourism. This study aims to investigate the viral diversity in reindeer, identify potential viruses of public health or veterinary significance, and highlight the need for viral surveillance at the human-animal interface.<br><br>RESULTS: The metagenomic sequencing analysis identified a novel pegivirus, Rangifer tarandus pegivirus (RPgV), in reindeer serum from Inner Mongolia. The near-complete genome (10,367 nucleotides; GenBank OQ164633) encodes a polyprotein (3,249 amino acids) processed into four structural (Y, E1, E2, X) and six non-structural (NS2-NS5B) proteins. RPgV shares 57.3% nucleotide and 60.6% amino acid identity with its closest relative, equine pegivirus (EPgV), but exceeds species demarcation thresholds for NS3 (p-distance: 0.340) and NS5B (p-distance: 0.408). Phylogenetic analyses placed RPgV within the equine pegivirus clade, while cophylogenetic models revealed strong host specificity and co-divergence over evolutionary timescales. With a 9.5% prevalence (2/21) in sampled reindeer, RPgV represents the first pegivirus detected in Cervidae, underscoring its potential role in wildlife virome dynamics.<br><br>CONCLUSION: This study identified a novel pegivirus, which expands its host range, geographic distribution, and genetic diversity. This discovery highlights the need for enhanced surveillance of understudied viral families in regions where human-wildlife interfaces amplify zoonotic risks.}, }
@article {pmid41331251, year = {2025}, author = {Zhao, Y and Chen, H and Huang, J and Chistoserdova, L and Yu, Z}, title = {The gut methanotroph Methylocystis intestini modulates intestinal peristalsis and fat metabolism via reducing methane levels.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-025-66596-w}, pmid = {41331251}, issn = {2041-1723}, support = {32300051//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Methane, a predominant component of human intestinal gas, has been reported to be associated with a reduction in intestinal transit speed, as well as correlations with elevated body mass index. While the gut methanogenic archaea that produce this gas have been studied, the countervailing role of methane-consuming bacteria (methanotrophs) within the human gut ecosystem remains a critical, under-explored area. The potential for these bacteria to act as a built-in sink for intestinal methane and thereby mitigate its negative physiological effects is unknown. Here, we isolate an unreported methanotroph from human fecal samples, classified as Methylocystis intestini. Using a mouse model, we observe that methane challenge is associated with gastrointestinal motility and fat metabolism. We then demonstrate that the administration of Methylocystis intestini effectively reverses these dysfunctional processes, restoring motility and metabolic parameters. Additional analysis of methane-oxidation genes abundance in 1207 public metagenomic sequences from individuals with varying health statuses, including obesity and constipation, provides consistent correlative support for our experimental conclusions. Expanding this view to a global scale, we conducted a metagenomic survey of 550 human fecal samples from populations across five continents. This broader analysis reveals that methane-oxidizing genes are not a rarity but a common feature of the human gut microbiome, being detectable in over 91% of samples. This ubiquity underscores their fundamental role in human biology. Collectively, our findings establish gut methanotrophs as key mediators of intestinal methane level. Their presence is widespread across global populations, and their functional capacity can balance the effects of methane on host physiology. This work elucidates a crucial component of gut homeostasis and opens a promising avenue for developing microbiome-based therapeutic strategies aimed at managing methane-related gastrointestinal disorders by harnessing the power of these native methane-consuming bacteria.}, }
@article {pmid41333904, year = {2024}, author = {Choi, CH and Lee, M and Lee, SE and Shin, H and Choi, MM and Kim, JW and Yi, H and Chung, YS}, title = {[Monkeypox Virus Genomic Analysis in the Republic of Korea: A Comparison of Metagenomic- and Probe Hybridization Capture Sequencing Methods].}, journal = {Jugan geon-gang gwa jilbyeong}, volume = {17}, number = {20}, pages = {859-873}, pmid = {41333904}, issn = {2586-0860}, abstract = {Monkeypox virus (MPXV) whole-genome from specimens of individuals diagnosed with mpox in the Republic of Korea (ROK) between May 2022 and November 2023 was analyzed comprehensively. An infectious disease originating in Africa, mpox gained global significance after the first case was confirmed in the UK in May 2022, subsequently spreading worldwide. In the ROK, 155 infection cases were recorded, predominantly transmitted through close contact with symptomatic individuals. MPXV, consisting of approximately 197,000 base pairs of double-stranded DNA, encompasses approximately 191 genes consisting of inverted terminal repeats at both ends and a central conserved region. The virus is categorized as Clade I (Central African type) and Clade II (West African type), with Clade I and II reporting fatality rates of 1-10% and less than 1%, respectively. Two sequencing methods, metagenomic and hybridization capture sequencing, were used to perform a thorough whole-genome analysis. Compared to metagenomic sequencing, hybridization capture sequencing demonstrated superior efficiency in generating MPXV read sequences. The proportion of virus reads varied based on specimen type, informing the selection of targets for whole-genome analysis. Genomic phylogenetic analysis revealed that the MPXV in the ROK belonged to lineage C.1, indicating sustained domestic transmission and providing crucial insights for national and international responses to MPXV variants. This information will contribute to understanding infection pathways and improving strategies for disease response and prevention.}, }
@article {pmid41330454, year = {2025}, author = {Zhao, D and Zou, B and Do, QL and Wu, SK and Shen, Y and Yang, Y and Kang, J and Su, KP and Wang, B}, title = {Circadian rhythms and gut microbiota Dysbiosis: emerging gut-brain axis pathways in insomnia pathophysiology and Therapeutics.}, journal = {Brain, behavior, and immunity}, volume = {}, number = {}, pages = {106203}, doi = {10.1016/j.bbi.2025.106203}, pmid = {41330454}, issn = {1090-2139}, abstract = {Insomnia, a widespread sleep disorder, significantly impacts mental and physical health. Emerging research highlights the crucial role of gut microbiota (GM) in modulating circadian rhythms (CR), which regulate sleep-wake cycles. This review explores the interplay between GM dysbiosis, CR disruptions, and insomnia, synthesizing findings from human and animal studies. GM dysbiosis is linked to reduced microbial diversity and altered abundance of key taxa, such as short-chain fatty acid-producing bacteria, which influence clock gene expression and hormonal rhythms. CR disruption exacerbates GM imbalances, forming a feedback loop that impairs sleep regulation through both central and peripheral pathways. We also examine the therapeutic potential of probiotics in restoring GM balance and synchronizing CR. Clinical trials suggest that specific probiotic strains improve sleep quality by modulating microbial metabolites and their downstream effects on the circadian system. However, inconsistencies in outcomes underscore the need for precision interventions. The review concludes by identifying gaps in the current literature, emphasizing the necessity of integrative approaches combining metagenomics and personalized medicine to optimize GM-targeted therapies. These insights pave the way for novel, safer, and more effective strategies to manage insomnia by addressing its biological underpinnings.}, }
@article {pmid41330298, year = {2025}, author = {Huang, Y and Li, R and Dai, Y and Ren, Z and Wu, J}, title = {Migration characteristics of ARGs from pig manure in compost - soil - lettuce.}, journal = {Ecotoxicology and environmental safety}, volume = {308}, number = {}, pages = {119447}, doi = {10.1016/j.ecoenv.2025.119447}, pmid = {41330298}, issn = {1090-2414}, abstract = {This study aims to reveal the contamination patterns, persistence characteristics, and fate dynamics of ARGs during aerobic composting of swine manure with different carbon-nitrogen ratios (C/N = 15:1, 25:1, 35:1) and their subsequent dissemination in soil-plant systems following fertilization. The absolute abundances of 101 ARGs of six categories ranged from 10[5] to 10[14] copies/g during the composting process. The tetracyclines, macrolides and β-lactams ARGs were effectively reduced by the maturation phase. Among them, the β-lactam ARGs had the highest abatement efficiency (73-89 %). Quinolones, aminoglycosides and sulfonamides ARGs had relatively high residues during the maturation phase. Composting treatments with higher C/N (25:1 and 35:1) exhibited superior performance in ARGs reduction. Metagenomic analysis revealed the compost microbial community succession from Firmicutes to Proteobacteria and Actinobacteria. Luteimonas may be potential hosts for high-residual ARGs in compost, while Acinetobacter exhibited strong associations with β-lactam and macrolide ARGs that can be easily reduced. The ARGs in the fertilized soil increased significantly. ARGs such as floR, tetG-01, sul1 and sul2 have the highest abundance in the soil where lettuce is grown. The ARGs reduction is better in C/N 25:1 group, and the ARGs abundance of the soil is lower after fertilization with compost products. The sulfonamide sul1 and sul2 genes have always maintained a high abundance in compost, soil and lettuce. This study provides a theoretical basis for controlling the residue and spread of ARGs by regulating the C/N of compost to drive changes in microbial community.}, }
@article {pmid41330199, year = {2025}, author = {Li, S and Wang, XR and Han, JR and Lian, WH and Ali, M and Liu, YH and Liu, J and Huang, J and He, HH and Govindan, R and Abdalla Abdelshafy Mohamad, O and Fang, BZ and Dong, L and Li, WJ}, title = {Genome-centric culture-enriched metagenomics reveals temperature-driven reassembly and functional stratification in culturable desert soil bacteria.}, journal = {Microbiological research}, volume = {304}, number = {}, pages = {128411}, doi = {10.1016/j.micres.2025.128411}, pmid = {41330199}, issn = {1618-0623}, abstract = {Desert ecosystems cover nearly one-third of Earth's land surface and face rising temperatures and climatic variability. Soil microbiomes underpin biogeochemical cycling and ecosystem resilience in these arid landscapes, yet the genome-resolved temperature responses of their culturable fraction remain poorly understood. Here, we employed genome-centric culture-enriched metagenomics (CE-MGS) to rhizosphere and bulk desert soils from the Gurbantunggut Desert incubated at 15°C, 30°C, and 45°C. From 90 culture-enriched metagenomes, we reconstructed 1184 cultivated metagenome-assembled genomes (cMAGs), including 218 putative novel genomospecies across 73 bacterial genera, substantially expanding the genomic representation of desert bacteria. Temperature influenced both community composition and interactions, with Actinomycetota, Pseudomonadota, and Bacillota dominating at 15°C, 30°C, and 45°C, respectively. Co-occurrence networks showed that lower temperatures and rhizosphere soils supported more interconnected consortia of culturable bacteria and that key hub taxa shifted across thermal regimes, reflecting temperature-driven reorganization of interactions within the culturable microbial community. Functional profiling revealed that temperature selected for specialized taxa, with elevated temperatures favoring redox-efficient pathways and more energy-efficient resource use. While representing only the culturable fraction of desert soil microbiomes, CE-MGS enables genome reconstruction of experimentally tractable microbes, linking identity, function, and thermal adaptation. These results provide a genome-resolved view of temperature responses, extend understanding of desert microbial adaptation beyond previous culture-independent studies, and establish CE-MGS as a practical approach to access ecologically relevant microbes for conservation and biotechnological applications under a warming climate.}, }
@article {pmid41330099, year = {2025}, author = {Barman, P and Paul, A and Sinha, S and Saha, T and Mondal, N and Dutta, S and Chatterjee, S and Ghosh, W and Chakraborty, R}, title = {Microbial-viral synergy in Eisenia fetida gut supports earthworm survival, detoxification, and functional resilience.}, journal = {The Science of the total environment}, volume = {1009}, number = {}, pages = {181101}, doi = {10.1016/j.scitotenv.2025.181101}, pmid = {41330099}, issn = {1879-1026}, abstract = {The ecological success of Eisenia fetida within decomposer food webs is closely linked to the functional diversity of its gut microbiome. This study integrates 16S rRNA gene profiling, whole-metagenome sequencing, and virome analysis to elucidate how microbial and viral communities within the earthworm gut contribute to nutrient biosynthesis, xenobiotic degradation, and environmental adaptation. Earthworms reared on compost feed enriched with Quisqualis indica plant matter showed selective enrichment of bacterial genera such as Ohtaekwangia, Nocardioides, and Steroidobacter, which are associated with hydrocarbon degradation and aromatic compound detoxification. Functional annotation of the gut metagenome revealed complete biosynthetic pathways for riboflavin, lysine, and methionine, and degradation routes for 3-nitropropionic acid (3-NPA) and aromatic pollutants. The gut virome, dominated by Siphoviridae and Myoviridae, carried auxiliary metabolic genes (AMGs) related to redox and xenobiotic metabolism, highlighting viral contributions to microbial adaptability. Reconstruction of metagenome-assembled genomes (MAGs), including a high-quality Flavobacterium MAG encoding both riboflavin biosynthesis and denitrification genes, underscored metabolic specialization within the gut. Collectively, these findings demonstrate that bacterial-viral metabolic synergy underpins E. fetida survival and ecological resilience, suggesting new microbiome-informed strategies for biowaste valorization and soil health restoration through vermicomposting.}, }
@article {pmid41329990, year = {2025}, author = {Choi, HI and Cha, JM}, title = {Non-invasive colorectal cancer screening: emerging tools and clinical evidence.}, journal = {Clinical endoscopy}, volume = {}, number = {}, pages = {}, doi = {10.5946/ce.2025.246}, pmid = {41329990}, issn = {2234-2400}, abstract = {The fecal immunochemical test (FIT) is a widely used non-invasive screening method for colorectal cancer (CRC) in many countries, valued for its simplicity, affordability, and reasonable sensitivity. Typically recommended on an annual or biennial basis, the FIT is effective in reducing CRC incidence and mortality by facilitating early detection. Stool DNA tests, including multitarget DNA tests and DNA methylation assays, demonstrate higher sensitivity than FIT for CRC and advanced adenomas, although they have slightly lower specificity and higher cost. These tests are generally performed at longer intervals, such as every 3 years, and are useful alternatives for individuals who are unwilling or unable to undergo a colonoscopy. Emerging non-invasive CRC screening tools, such as liquid biopsy, microRNA, microbiome tests, and urine-based tests, are being developed to improve patient compliance and test convenience. In particular, liquid biopsy offers a minimally invasive option that may be more acceptable to populations hesitant to undergo stool-based tests. Furthermore, the integration of machine learning with metagenomic sequencing data has shown promise in distinguishing patients with CRC from healthy individuals. As CRC screening evolves, these novel approaches may enable the development of more personalized, accessible, and effective screening strategies, ultimately improving adherence and reducing CRC-related mortality.}, }
@article {pmid41328758, year = {2026}, author = {Plewnia, A and Hoenig, BD and Lötters, S and Heine, C and Erens, J and Böning, P and Bending, GD and Krehenwinkel, H and Williams, MA}, title = {The Emergence of a CRISPR-Cas Revolution in Ecology: Applications, Challenges, and an Ecologist's Overview of the Toolbox.}, journal = {Molecular ecology resources}, volume = {26}, number = {1}, pages = {e70086}, doi = {10.1111/1755-0998.70086}, pmid = {41328758}, issn = {1755-0998}, support = {//University of Warwick/ ; NE/S010270/1//Natural Environment Research Council/ ; }, mesh = {*CRISPR-Cas Systems ; *Ecology/methods ; *Gene Editing/methods ; }, abstract = {CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR-associated nucleases) systems allow researchers to detect, capture, and even alter parts of an organism's genome. However, while the use of CRISPR-Cas has revolutionised many fields in the life sciences, its full potential remains underutilised in ecology and biodiversity research. Here we outline the emerging applications of CRISPR-Cas in ecological contexts, focusing on three main areas: nucleic acid detection, CRISPR-enhanced sequencing, and genome editing. CRISPR-based nucleic acid detection of environmental DNA samples is already reshaping species monitoring, providing highly sensitive and non-invasive tools for both scientists and the public alike, with reduced costs and minimal experience required. Further, CRISPR-enhanced sequencing, including Cas-mediated target enrichment, enables efficient recovery of ecologically relevant loci and supports diverse applications such as amplification-free metagenomics. Finally, while genome editing on wild species remains largely theoretical in ecology, these tools are already being used in controlled settings to study adaptation and resilience in the face of ongoing global stressors. Together, the applications of CRISPR-Cas are paving the way for more affordable, accessible, and impactful applications for species conservation, and promise to improve our ability to tackle the ongoing global biodiversity crisis.}, }
@article {pmid41328492, year = {2025}, author = {Knoll, RL and Podlesny, D and Fortmann, I and Göpel, W and Zemlin, M and Lynch, S and Bork, P and Gehring, S and Härtel, C}, title = {Staphylococcus aureus colonization and bloodstream infection in very preterm infants.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2592423}, doi = {10.1080/19490976.2025.2592423}, pmid = {41328492}, issn = {1949-0984}, mesh = {Humans ; *Staphylococcal Infections/epidemiology/microbiology ; Infant, Newborn ; Feces/microbiology ; *Staphylococcus aureus/isolation &amp; purification/genetics/growth &amp; development/classification ; Female ; Male ; Infant, Premature ; *Bacteremia/microbiology/epidemiology ; Gastrointestinal Microbiome ; Germany/epidemiology ; Infant ; Cohort Studies ; Infant, Very Low Birth Weight ; Metagenomics ; Incidence ; Gestational Age ; }, abstract = {BACKGROUND: Staphylococcus (S.) aureus remains a frequent pathogen for neonatal late-onset bloodstream infections (BSIs). The impact of colonization screening on BSI incidence is less understood.<br><br>METHODS: We assessed the epidemiology of late-onset S. aureus BSI in two independent multicenter cohorts of preterm infants born at&#x2009;<&#x2009;33 weeks' gestation, the German Neonatal Network (GNN, very low birth weight infants) and PRIMAL (infants with a gestational age 28-32 weeks). In the PRIMAL cohort, we determined S. aureus colonization in fecal samples by culture and shotgun metagenomic sequencing (metaG) during the first year of life. In addition, we integrated publicly available metaG data from preterm infant cohorts born at 23-34 weeks' gestation.<br><br>RESULTS: Late-onset S. aureus BSI was noted in 1.5% (336/21491) in preterm infants in the GNN cohort and 0.5% (3/638) in the PRIMAL cohort, respectively. At day 30 of life, 7.6% (42/553) of fecal samples were positive for S. aureus, while available metaG data of corresponding samples revealed S. aureus positivity in 36.6% (159/434). Every 10-fold increase in S. aureus relative abundance (metaG) was associated with a 2.9-fold higher odds of S. aureus detection in blood culture. We also confirmed S. aureus detection in 22% (393/1782) of samples across several published cohorts of preterm infants by metaG, while 95 samples carried at least one Staphylococcus-specific virulence gene (SVG).<br><br>CONCLUSION: Our study demonstrates that metagenomic quantification of pathobionts such as S. aureus in intestinal samples provides a stronger predictor of colonization than culture. Future prevention strategies should focus on promoting S. aureus colonization resistance through microbiome-informed approaches.}, }
@article {pmid41328416, year = {2025}, author = {Ueira-Vieira, C and Santos, ACC and Araújo, TN and Augusto, SC and de Avila, NB and Bonetti, AM and Dos Santos, AR}, title = {A Deep Metagenomic Snapshot as a Proof-of-Concept for Resource Generation: Simultaneous Assembly of Host, Food, and Microbiome Genomes From Stingless Bee Larval Food.}, journal = {Ecology and evolution}, volume = {15}, number = {12}, pages = {e72546}, pmid = {41328416}, issn = {2045-7758}, abstract = {Characterizing the complex web of ecological interactions is a central challenge in molecular ecology. Shotgun metagenomics of environmental samples offers a powerful, high-resolution approach, yet its potential for simultaneously generating multiple genomic resources from different trophic levels remains underexplored. This study serves as a proof-of-concept, using deep sequencing of a single, complex sample-the larval food of the stingless bee Tetragonisca angustula-to demonstrate the method's capacity to recover genomic information across varying template abundances. We successfully assembled three genomes of different completeness levels: a near-complete bacterial genome (Acetilactobacillus jinshanensis, 2,097,977 bp with 0.002% ambiguous bases), a draft mitochondrial genome (T. angustula, 15,498-15,549 bp), and a fragmented chloroplast genome (Lactuca sativa, 130,532 bp with 23.47% ambiguous bases). The assembly quality gradient, observed from complete to fragmented, directly reflects the relative abundance of each DNA template in the environmental sample, demonstrating the method's sensitivity and ecological informativeness. Beyond these genomic resources, the data provided a comprehensive biodiversity profile, revealing DNA from seven major taxonomic groups, including 209 bacterial genera, 123 plant families, and 55 insect taxa. Additionally, genomic comparisons using Average Nucleotide Identity (ANI) and digital DNA-DNA Hybridization (dDDH) analyses suggest that the dominant bacterial strain represents a putative novel species within the genus Acetilactobacillus. This approach simultaneously provided insights into host genetics, food sources, and microbial communities, illustrating the potential of single metagenomic datasets to generate multiple valuable genomic resources for molecular ecology research.}, }
@article {pmid41328415, year = {2025}, author = {Long, D and Zhao, W and Li, X and Sun, Q and Li, J and Lin, X}, title = {Rhizosphere Effect Enhances Belowground Competition of Coastal Invasive Spartina alterniflora With Mangroves.}, journal = {Ecology and evolution}, volume = {15}, number = {12}, pages = {e72565}, pmid = {41328415}, issn = {2045-7758}, abstract = {Spartina alterniflora has severely invaded mangroves in China. In order to explore the possible belowground interspecific interaction along with its invasion, the rhizosphere effect enhancing the competition of S. alterniflora neighboring mangroves was hypothesized. Here, both rhizosphere soil of S. alterniflora and bulk soil were collected from the center of S. alterniflora marsh and border sites where S. alterniflora was adjacent to Kandelia obovata and Aegiceras corniculatum, respectively, in both vigorous growth and senescent periods. Soil nutrient properties, rhizospheric low-molecular-weight organic acids (LMWOAs), soil microbiomes, and microbial functional genes were analyzed. Soil total carbon and total nitrogen contents of S. alterniflora neighboring mangroves were increased, and its LMWOAs were altered when adjacent to mangroves in both vigorous growth and senescent periods. These changes were significantly correlated with variation in the composition of S. alterniflora rhizosphere microbiome. Microbial interkingdom co-occurrence networks were simplified when S. alterniflora neighbored mangroves, while network modularity significantly increased. Metagenomics indicated that genes involved in methanogenesis (ackA, mvhD, etc.) and nitrogen fixation (nifH, nifK, etc.) were significantly enriched in those S. alterniflora neighboring K. obovata, and genes related to phosphate transporter (pstA, pstB, etc.) were significantly enriched in those S. alterniflora neighboring A. corniculatum. These results demonstrated that the rhizosphere effect intensified the belowground interspecific competition of S. alterniflora adjacent to mangroves by altering root exudates, changing the soil microbial composition, and modulating strategies for core nutrient metabolism.}, }
@article {pmid41328248, year = {2025}, author = {Rossi, E and Pato, U and Ayu, DF and Melia, S and Sukma, A and Rahmayuni, R and Salman, AN}, title = {Bacterial biodiversity and metagenomic study of dadih, traditional fermented buffalo milk from Kampar district, Riau, Indonesia.}, journal = {Journal of advanced veterinary and animal research}, volume = {12}, number = {3}, pages = {717-727}, pmid = {41328248}, issn = {2311-7710}, abstract = {OBJECTIVE: This study aimed to investigate the metagenomic and microbial diversity of dadih in Kampar District, Riau, Indonesia.<br><br>MATERIALS AND METHODS: The dadih samples were collected from dadih producers in three villages, namely Limau Manis (LM), Rumbio (RB), and Muaro Jalai (MJ). DNA samples were extracted and sequenced through Oxford Nanopore Technology (ONT), operated by MinKNOW software version 23.04.5. Library preparations were conducted using kits from ONT.<br><br>RESULTS: The next-generation sequencing analysis on three dadih from Kampar identified two bacterial phyla, Bacillota and Pseudomonadota. Furthermore, there was a slight variation in dadih's microbiota composition between LM, RB, and MJ. The Bacillota phylum dominated the dadih microbiota in LM and RB villages, with a relative abundance of 60%-80%. The dadih from MJ was dominated by the phylum Pseudomonadota, which reached 55%. The dominant species found in all three dadih was Lactococcus lactis, with an abundance of 53.80, 80.80, and 40.31% for dadih LM, RB, and MJ, respectively.<br><br>CONCLUSION: Dadih MJ had the highest Simpson's value (~0.8), showing a relatively even abundance of species in the sample. Furthermore, dadih LM had a high Simpson's value (~0.75), indicating similar conditions to dadih MJ. Dadih RB had the lowest Simpson's value (~0.4), confirming that the microbiota in the sample tends to be dominated by certain species with a less even distribution.}, }
@article {pmid41328030, year = {2025}, author = {Hickman, B and Korpela, K}, title = {Impact of data compositionality on the detection of microbiota responses.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2590841}, doi = {10.1080/19490976.2025.2590841}, pmid = {41328030}, issn = {1949-0984}, mesh = {*High-Throughput Nucleotide Sequencing/methods ; *Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota ; Humans ; Computer Simulation ; *Gastrointestinal Microbiome ; Computational Biology/methods ; *Metagenomics/methods ; }, abstract = {Next-generation sequencing (NGS) data usage is widespread, but its compositional nature poses challenges. We evaluated four normalization methods (relative abundance, CLR, TMM, DESeq2) for identifying true signals in compositional microbiota data using simulations. Two experiments were conducted: one with only increases in specific taxa, and a 1:1 increase/decrease in specific taxa. Simulated sequencing produced compositional data, which were normalized using the four methods. The study compared absolute abundance data and the normalized compositional data using variance explained and false discovery rates. All normalization methods showed decreased variance explained and increased false positives and negatives compared to absolute abundance data. CLR, TMM, and DESeq2 did not improve over relative abundance data and sometimes worsened false discovery rates. The study highlights that false positives and negatives are common in compositional NGS datasets, and current normalization methods do not consistently address these issues. Compositionality artefacts should be considered when interpreting NGS results and obtaining absolute abundances of features/taxa is recommended to distinguish biological signals from artefacts.}, }
@article {pmid41328016, year = {2025}, author = {Fresno, C and Oropeza-Valdez, JJ and Alvarado-Luis, PI and Peña-González, P and Tovar, AR and Torres, N and Diener, C and Gibbons, S and Resendis-Antonio, O}, title = {MICOMWeb: a website for microbial community metabolic modeling of the human gut.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2587968}, doi = {10.1080/19490976.2025.2587968}, pmid = {41328016}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome ; Internet ; *Gastrointestinal Tract/microbiology/metabolism ; Models, Biological ; Software ; Computer Simulation ; Computational Biology/methods ; }, abstract = {MICOMWeb is a user-friendly website for modeling microbial community metabolism in the human gut. This website tackles three constraints when generating in silico metagenome-scale metabolic models: i) the prior Python user knowledge for metabolic modeling using flux balance analysis with the MICOM Python package, ii) predefined and user-defined diets to generate ad hoc metabolic models, and iii) the high-throughput computational infrastructure required to obtain the simulated growth and metabolic exchange fluxes, using real abundance from metagenomic shotgun or 16S amplicon sequencing; we present MICOMWeb's features to easily run in silico experiments as a functional hypothesis generator for experimental validation on three previously published databases. MICOMWeb has a constant run-time independent of the number of samples provided and database complexity. In practical terms, this behavior is upper-bounded by the sample with the greatest microbiota diversity, i.e., the sample with the largest metabolic reconstruction model size. The evidence suggests that the bigger the database, the better the MICOMWeb performs compared to MICOM in terms of consumed RAM (from 3.52 up to 7.13 folds) and total execution time (from 10.87 up to 205.05 folds).}, }
@article {pmid41327872, year = {2025}, author = {Zhang, Y and Zhang, Z and Chen, Z and Yang, B and Cai, S and Chen, J and Guo, J and Zhang, W}, title = {2-line Ferrihydrite Enhance Microbial Synthesis of Plant Biostimulants in Composted Biosolid by Regulating Phyla Pseudomonadota and Actinomycetota.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e06502}, doi = {10.1002/advs.202506502}, pmid = {41327872}, issn = {2198-3844}, support = {U24A20193,52270141//The National Natural Science Foundation of China/ ; 2024BCA006//Hubei Province Technological Innovation Plan Project/ ; 122-G1323522145//Fundamental Research Funds for the central Universities, China University of Geosciences/ ; }, abstract = {The discovery of plant biostimulants (PBs) in sewage sludge offers a promising avenue for biosolids valorization. Here, the study investigates how two mineral additives, including 2-line ferrihydrite (a disordered iron oxide) and disordered birnessite (a manganese oxide), modulate microbial activity and molecular pathways to enhance PB production during aerobic sludge composting. Application of 2-line ferrihydrite significantly promotes the synthesis of growth-promoting PBs, including arginine, valine, decanoic acid, and indoleacetic acid (IAA), while disordered birnessite primarily enhances resistance-related PBs, such as decanoic acid, L-pyroglutamate, and trans-aconitic acid. In pot trials, composted biosolids amended with 2-line ferrihydrite significantly improve plant biomass and leaf area compared to mineral-free and birnessite treatments. Metagenomic profiling reveals that PB biosynthesis is dominated by members of the phyla Pseudomonadota and Actinomycetota, with temporal niche partitioning across the thermophilic and maturation stages. 2-line ferrihydrite enhances the abundance of critical biosynthetic genes (e.g., trpA/C/D/E/F), particularly within taxa such as Xanthomonadaceae, Sphingomonadaceae, and Streptosporangiaceae. Additionally, genes involved in IAA and indole biosysnthesis (ALDH, DDC, and tnaA) are enriched, supporting enhanced tryptophan-to-IAA conversion. This study provides a mechanistic link between iron oxide-mediated microbial modulation and PB production in composted biosolids, offering a sustainable approach for upgrading waste into high-value agricultural inputs.}, }
@article {pmid41327491, year = {2025}, author = {Wu, H and Sun, Z and Chen, B and Hu, X and Li, Y}, title = {Enhanced nitrogen load improved soil phosphorus availability by regulating P-cycling microbial genes in a typical subtropical estuary (Min River), Southeast China.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {151}, pmid = {41327491}, issn = {2524-6372}, support = {No. 42371105//the National Natural Science Foundation of China/ ; No. 2023J02012//the Key Program of Natural Science Foundation of Fujian Province/ ; }, abstract = {BACKGROUND: Enhanced nitrogen (N) load was considered a critical factor influencing phosphorus (P) availability and P-cycling in marsh soils. However, information on the links between soil P availability and microbial genes involved in P-cycling processes under N enrichment conditions remains scarce.<br><br>METHODS: A field N load experiment with four treatments (N0, Nlow, Nmedium, and Nhigh) was conducted in Cyperus malaccensis marsh of the Min River estuary, and soil P availability, the relative abundances of P-cycling functional genes and their regulatory roles on P availability were investigated.<br><br>RESULTS: The total phosphorus (TP) contents in soils were significantly positively correlated with N load levels (p&#x2009;<&#x2009;0.05). Compared with the N0 treatment, the TP in the Nlow, Nmedium and Nhigh treatments increased by 8.97%, 17.34% and 15.21%, respectively. With increasing N load levels, the proportions of easily- and moderately-available P in TP contents noticeably increased, suggesting that N additions enhanced soil P availability. Metagenomic sequence analyses showed that N enrichment markedly altered the relative abundances of P-cycling functional genes. Briefly, the abundances of inorganic P solubilization genes (particularly ppa and ppx) increased substantially with increasing N load levels. The total abundances of organic P mineralization genes in the Nlow and Nmedium treatments decreased markedly, while those in the Nhigh treatment increased greatly. The abundances of genes coding for phytase (phy and appA) markedly increased with increasing N load levels, implying that phytase was more sensitive to N enrichment. Furthermore, enhanced N load noticeably reduced the abundances of genes participated in P transportation (particularly ugpABEC) and those involved in P-assimilating process (e.g., phoR, phoB, pstABCS and pit). As affected by enhanced N load, the contents of easily-available P showed strong correlations with the abundances of genes involved in inorganic P solubilization while those of moderately-available P (particularly Sonic-Pi, Sonic-Po and NaOH-Pi) were positively correlated with the abundances of genes involved in P regulation and transportation, indicating strong linkages between P-cycling functional genes and soil P availability.<br><br>CONCLUSIONS: This paper found that, under N enrichment conditions, the increased inorganic P solubilization potential and the weakened microbial P immobilization capacity were beneficial to increasing soil P availability.}, }
@article {pmid41327449, year = {2025}, author = {Zhao, Y and Duanmu, X and Hu, Z and Fan, Y and Mao, R and Zhang, Y and Zhang, X}, title = {Temperature seasonality constrains soil T4-like bacteriophage abundance at large spatial scale.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-025-00824-0}, pmid = {41327449}, issn = {2524-6372}, support = {U21A20188//National Natural Science Foundation of China/ ; jxsq2023102216//Double Thousand Plan of Jiangxi Province/ ; }, abstract = {BACKGROUND: Viruses play key roles in regulating soil microbial dynamics and biogeochemical cycles. T4-like bacteriophages, one of the best-studied viral groups, are abundant in soils, but their biogeographical patterns and ecological drivers remain poorly understood. In this study, we performed the first large-scale assessment of soil T4-like bacteriophages based on metagenomic data using viral hallmark genes, revealing broad spatial structure, identifying dominant environmental factors, and projecting shifts under future climate scenarios.<br><br>RESULTS: We analyzed two viral hallmark genes, gene 20 (g20) and gene 23 (g23), retrieved from global soil metagenomes, and National Center for Biotechnology Information (NCBI) reference sequences, yielding 2,385 and 2,928 full-length sequences clustered into 1,211 and 1,269 operational taxonomic units (OTUs), respectively. Phylogenetic analysis revealed that only a small fraction of soil-derived sequences could be assigned to established viral families, with most remaining unclassified below the class Caudoviricetes. The relative abundances of g20 and g23 were assessed at 116 sites spanning 14 biomes across six continents. Consistent biogeographic patterns were observed for both genes, with higher relative abundance in tropical climates and lower levels in polar and dry regions, indicating strong climatic influence. Temperature seasonality (BIO4) was identified as the primary environmental driver, showing a significant negative correlation with the relative abundance of both genes. Using an extreme gradient boosting (XGBoost) model, we predicted global distribution patterns based on extrapolation, revealing concordant global trends, with lower relative abundances in regions with greater seasonal temperature variation. Future projections of BIO4 and viral gene abundance further supported this significant negative correlation.<br><br>CONCLUSIONS: Our findings reveal that temperature seasonality constrains the abundance of soil T4-like bacteriophages, which serve as sensitive indicators of climate-driven environmental shifts and play important ecological roles within soil microbial communities.}, }
@article {pmid41327428, year = {2025}, author = {Zorea, A and Moraïs, S and Pellow, D and Gershoni-Yahalom, O and Probst, M and Nadler, S and Shamir, R and Rosental, B and Elia, N and Mizrahi, I}, title = {ProFiT-SPEci-FISH: a novel approach for linking plasmids to hosts in complex microbial communities at the single-cell level.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-025-02238-z}, pmid = {41327428}, issn = {2049-2618}, support = {ISF 1947/19//Israel Science Foundation/ ; ISF 1947/19//Israel Science Foundation/ ; 2476/2-1//German-Israeli Project Cooperation (DIP)/ ; ERC 866530//the European Research Council/ ; }, abstract = {BACKGROUND: Plasmids are influential drivers of bacterial evolution, facilitating horizontal gene transfer and shaping microbial communities. Current knowledge on plasmid persistence and mobilization in natural environments is derived from community-level studies, neglecting the single-cell level, where these dynamic processes unfold. Pinpointing specific plasmids within their natural environments is essential to unravel the dynamics between plasmids and their bacterial hosts.<br><br>RESULTS: Here, we overcame the technical hurdle of natural plasmid detectability in single cells by developing SPEci-FISH (Short Probe EffiCIent Fluorescence In Situ Hybridization), a novel molecular method designed to detect and visualize plasmids, regardless of their copy&#xa0;number, directly within bacterial cells, enabling their precise identification at the single-cell level. To complement this method, we created ProFiT (PRObe FInding Tool), a program facilitating the design of sequence-based probes for targeting individual plasmids or plasmid families.<br><br>CONCLUSIONS: We have successfully applied these methods, combined with high-resolution microscopy, to investigate the dispersal and localization of natural plasmids within a clinical isolate, revealing various plasmid spatial patterns within the same bacterial population. Importantly, bridging the technological gap in linking plasmids to hosts in native complex microbial environments, we demonstrated that our method, when combined with fluorescence-activated cell sorting (FACS), can track plasmid-host dynamics in a human fecal sample. This approach identified multiple potential bacterial hosts for a conjugative plasmid that we assembled from this fecal sample's metagenome. Our integrated approach offers a significant advancement toward understanding plasmid ecology in complex microbiomes. Video Abstract.}, }
@article {pmid41327409, year = {2025}, author = {Jin, J and Wang, X and Zhang, X and Mei, J and Zheng, W and Guo, L and Sun, H and Zhang, L and Liu, C and Ye, W and Guo, L}, title = {Grapevine phyllosphere pan-metagenomics reveals pan-microbiome structure, diversity, and functional roles in downy mildew resistance.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-025-02287-4}, pmid = {41327409}, issn = {2049-2618}, support = {ZR2024QC241//Shandong Provincial Natural Science Foundation Youth Project/ ; 2024CXPT031//Key R&amp;D Program of Shandong Province/ ; ZR2023JQ010//Natural Science Foundation for Distinguished Young Scholars of Shandong Province/ ; }, abstract = {BACKGROUND: Grapevines are among the most economically important fruit crops, and the microbiome profoundly influences their health, yield, and quality. However, mechanistic insights into microbiome-orchestrated grapevine biology remain limited.<br><br>RESULTS: Here, we conduct large-scale pan-metagenomic and pan-metatranscriptomic analyses of the phyllosphere microbiome from 107 grapevine accessions spanning 34 Vitis species. We show that the grapevine core microbiome is dominated by phyla Bacillota and Pseudomonadota. Leveraging PacBio sequencing, we assembled 19 high-quality metagenome-assembled genomes (MAGs) from the grapevine pan-microbiome, representing the first MAG reconstruction in plant-associated microbial communities using PacBio reads. These MAGs encode genes associated with antibiotic resistance, secondary metabolism, and carbohydrate-active enzymes (CAZymes), which could potentially influence grapevine biology. During downy mildew (DM) infection, DM-resistant grapevines exhibit significantly higher microbial network complexity than susceptible counterparts. Among the key taxa contributing to this complexity, Bacillota emerged as the dominant phylum, displaying strong abundance correlations with phylum Euglenozoa and Cyanobacteriota, and an isolated Bacillota species from the grapevine leaves, Bacillus cereus, demonstrated potent biocontrol activity against DM infection. Pan-metatranscriptomic analysis further revealed significant upregulation of eukaryotic microbial genes involved in primary and secondary metabolism.<br><br>CONCLUSIONS: This pan-metagenomic study offers unprecedented insights into the complex structure, diversity, and functional roles of the grapevine phyllosphere microbiome and presents valuable genomic and microbial resources for microbiome research and engineering to enhance viticulture productivity and quality. Video Abstract.}, }
@article {pmid41327304, year = {2025}, author = {Zhang, X and Li, Y and Xiong, Z and Zheng, N and Wang, J and Zhao, S}, title = {Biochanin A improves nitrogen utilization efficiency by regulating ruminal microbial community in dairy goats.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-025-02275-8}, pmid = {41327304}, issn = {2049-2618}, support = {32402768//National Natural Science Foundation of China/ ; 2004DA125184G2108//State Key Laboratory of Animal Nutrition and Feeding/ ; CARS-36//Earmarked Fund for CARS/ ; 2022YFD1301000//National Key R&amp;D Program of China/ ; CAAS-ZDRW202304//Agricultural Science and Technology Innovation Program/ ; }, abstract = {BACKGROUND: Rumen microbial nitrogen metabolism is crucial for animal health, productivity, and environmental sustainability in ruminants. Natural products like biochanin A are garnering interest as potential feed additives due to their beneficial effects and safety profiles. Here, we collected total mixed diet, plasma, milk, urine, and feces samples of dairy goats to evaluate the impact of biochanin A on nitrogen metabolism and elucidated regulatory mechanisms of nitrogen metabolism using multi-omics approaches by analyzing plasma metabolites and ruminal microbial communities.<br><br>RESULTS: Supplementation with biochanin A significantly enhanced nitrogen utilization efficiency of dairy goats. Plasma metabolomics revealed that biochanin A altered pathways related to amino acid biosynthesis/metabolism and glycolysis/gluconeogenesis. In the rumen, biochanin A enriched microbial strains from the families Selenomonadaceae and Aminobacteriaceae. Up-regulated proteins predominantly associated with glycolysis were identified by metaproteomics. Integrated metagenomic and metaproteomic analyses demonstrated that biochanin A positively influenced carbohydrate metabolism, amino acid metabolism, and energy metabolism pathways.<br><br>CONCLUSION: Biochanin A enhances nitrogen metabolism by regulating rumen microbial community function, supporting its potential as a natural feed additive to improve nitrogen utilization of ruminants. Video Abstract.}, }
@article {pmid41327286, year = {2025}, author = {Xu, W and Top, J and Viveen, MC and Slyzkyi, A and Hermans, N and van Erp, S and Eiloz, D and Anthony, R and Kremer, K and Schürch, AC}, title = {Limited value of Nanopore adaptive sampling in a long-read metagenomic profiling workflow of clinical sputum samples.}, journal = {BMC medical genomics}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12920-025-02272-8}, pmid = {41327286}, issn = {1755-8794}, support = {LSHM22031//Health~Holland/ ; }, abstract = {BACKGROUND: Oxford Nanopore adaptive sampling (NAS) is a method by which the long-read sequencing flowcell accepts or rejects DNA molecules that are actively being sequenced based on their initial ~ 500 bp sequences, selectively increasing target data output. NAS promises up to 5-10 × enrichment of target sequencing yield without additional sample preparation, but this optimal performance is dependent on ideal sample parameters which may be difficult to achieve under many real-world use-cases. We evaluated the use of NAS for profiling clinical sputum metagenomes.<br><br>METHODS: We sequenced DNA extracted from clinical sputa and spike-in controls of a mock community of bacterial respiratory pathogens, using the current R10.4.1 MinION flowcell chemistry.<br><br>RESULTS: We achieved at best 3.1&#x2009;&#xd7;&#x2009;enrichment of bacterial sequence output with NAS due to the shorter read lengths (~&#x2009;2.5&#xa0;kb) from the PCR amplification necessary to compensate for low DNA extraction yields. More critically, we encountered rapid pore loss during our runs that reduced total sequencing yield by an estimated 80%. We were unable to mitigate the pore loss despite extensive attempts to reduce contaminant carry-over, and we could not determine its cause but ruled out NAS and pore underloading as contributing factors.<br><br>CONCLUSIONS: We conclude that the utility of NAS is often limited by the characteristics of the metagenomic sample studied, and that the factors contributing to pore loss need to be resolved before ONT sequencing can be reliably applied to long-read metagenomics.}, }
@article {pmid41327021, year = {2025}, author = {Chen, B and Shu, W and Le, J and Jin, D}, title = {Application of metagenomic next-generation sequencing technology in hematologic malignancy patients with sepsis following antibiotic use.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {1678}, pmid = {41327021}, issn = {1471-2334}, }
@article {pmid41327018, year = {2025}, author = {Gajjar, K and Patel, S and Chaudhary, M and Agrawal, D and Maniyar, R and Chaudhary, D and Patel, CK and Joshi, C and Joshi, M and Dharajiya, D}, title = {Metagenomic insights reveal the impact of natural farming on soil nutrients, enzyme activities, microbial communities, and yield in turmeric cultivation.}, journal = {BMC plant biology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12870-025-07781-3}, pmid = {41327018}, issn = {1471-2229}, support = {GSBTM/JD(R&amp;D)/661/2022-23/00172688//Gujarat State Biotechnology Mission/ ; GSBTM/JD(R&amp;D)/661/2022-23/00172688//Gujarat State Biotechnology Mission/ ; GSBTM/JD(R&amp;D)/661/2022-23/00172688//Gujarat State Biotechnology Mission/ ; }, }
@article {pmid41326768, year = {2025}, author = {Polizel, GHG and Cánovas, &#xc1; and Diniz, WJS and Ramírez-Zamudio, GD and Cesar, ASM and Fukumasu, H and Fernandes, AC and Furlan, &#xc9; and de Almeida Santana, MH}, title = {Unveiling long-term prenatal nutrition biomarkers in beef cattle via multi-tissue and multi-OMICs analysis.}, journal = {Metabolomics : Official journal of the Metabolomic Society}, volume = {22}, number = {1}, pages = {8}, pmid = {41326768}, issn = {1573-3890}, support = {23/09113-4//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 17/12105-2//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 307593/2021-5//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, mesh = {Animals ; Cattle ; Female ; Pregnancy ; *Biomarkers/metabolism/analysis ; *Metabolomics/methods ; Male ; Liver/metabolism ; Transcriptome ; *Maternal Nutritional Physiological Phenomena ; *Prenatal Nutritional Physiological Phenomena ; Multiomics ; }, abstract = {INTRODUCTION: Maternal nutrition during gestation plays a crucial role in shaping offspring development, metabolism, and long-term health, yet the underlying molecular mechanisms remain poorly understood.<br><br>OBJECTIVES: This study investigated potential biomarkers through multi-OMICs and multi-tissue analyses in offspring of beef cows subjected to different gestational nutrition regimes.<br><br>METHODS: A total of 126 cows were allocated to three groups: NP (control, mineral supplementation only), PP (protein-energy supplementation in the last trimester), and FP (protein-energy supplementation throughout gestation). Post-finishing phase, samples (blood, feces, ruminal fluid, fat, liver, and longissimus muscle/meat) were collected from 63 male offspring. RNA sequencing was performed on muscle and liver, metabolomics on plasma, fat, liver, and meat, and 16S rRNA sequencing on feces and ruminal fluid. Data were analyzed via DIABLO (mixOmics, R).<br><br>RESULTS: The muscle transcriptome showed strong cross-block correlations (|r| > 0.7), highlighting its sensitivity to maternal nutrition. Plasma glycerophospholipids (PC ae C30:0, PC ae C38:1, lysoPC a C28:0) were key biomarkers, particularly for FP. The PP group exhibited liver-associated markers (IL4I1 gene, butyrylcarnitine), reflecting late-gestation effects, while NP had reduced ruminal Clostridia (ASV151, ASV241), suggesting impaired microbial energy metabolism.<br><br>CONCLUSIONS: This integrative multi-OMICs approach provided deeper insights than single-layer analyses, distinguishing nutritional groups and revealing tissue- and OMIC-specific patterns. These findings demonstrate the value of combining transcriptomic, metabolomic, and microbiome data to identify biomarkers linked to maternal nutrition in beef cattle.}, }
@article {pmid41326588, year = {2025}, author = {Yadav, MK and Ranjan, R and Verma, P and Sharma, R}, title = {Discovery and characterization of an enantioselective family VIII esterase from effluent treatment plant sludge metagenome.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-025-29625-8}, pmid = {41326588}, issn = {2045-2322}, support = {BSC0124//Council of Scientific and Industrial Research (CSIR), India/ ; }, }
@article {pmid41326129, year = {2026}, author = {Wu, M and Lu, P and Feng, Y and He, S and Han, G and Hu, S}, title = {Construction and functional characterization of a synthetic consortium for synergistic degradation of dimethachlon.}, journal = {Pesticide biochemistry and physiology}, volume = {216}, number = {Pt 1}, pages = {106807}, doi = {10.1016/j.pestbp.2025.106807}, pmid = {41326129}, issn = {1095-9939}, mesh = {Biodegradation, Environmental ; *Microbial Consortia ; Aniline Compounds/metabolism ; Animals ; Pseudomonas/metabolism/genetics ; *Soil Pollutants/metabolism/toxicity ; Zebrafish ; *Fungicides, Industrial/metabolism/toxicity ; Soil Microbiology ; }, abstract = {The residual dicarboximide fungicide dimethachlon and its primary metabolite 3,5-dichloroaniline entail significant health and ecological risks. Microbial degradation effectively mitigates associated environmental risks. The microbial degradation of organic contaminants is a complex process, typically facilitated by microbial consortia rather than individual species. However, research on the biodegradation of dimethachlon by synergistic microbial consortia is limited. In this study, an enriched bacterial consortium designated as JHJ-2 capable of degrading dimethachlon was obtained. A synthetic consortium was constructed, comprising Bosea sp. S6, which transforms dimethachlon to 3,5-dichloroaniline, and Pseudomonas sp. KH-1, which degrades 3,5-dichloroaniline; both strains were isolated from the enriched consortium JHJ-2 and synergistically degrade dimethachlon. Toxicity assays using the zebrafish showed that dimethachlon is converted into non-toxic products by the synthetic consortium (strains S6 and KH-1). Bioaugmentation with the synthetic consortium led to the complete removal of dimethachlon and its highly toxic metabolite 3,5-dichloroaniline from contaminated soil. In addition, 16 bins were successfully recovered by metagenomic binning, including bin 12 (Bosea sp.) and bin 15 (Pseudomonas sp.), and several potential degradation enzymes were hypothesized in the genomes of bins 12 and 15. Overall, the developed synthetic consortium exhibits significant potential for the enhanced bioremediation and detoxification of dimethachlon-contaminated sites.}, }
@article {pmid41325946, year = {2025}, author = {Yin, Z and Ma, J and Bian, R and Wang, Y and Zhang, K and Ma, Y and Zhang, X and Ye, L}, title = {Xenobiotic degradation promotes enrichment but not dissemination of antibiotic resistance genes in activated sludge.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {133748}, doi = {10.1016/j.biortech.2025.133748}, pmid = {41325946}, issn = {1873-2976}, abstract = {Activated sludge in wastewater treatment bioreactors plays a pivotal role in xenobiotic degradation but is also regarded as a hotspot for the dissemination of antibiotic resistance genes (ARGs). Yet, it remains unclear whether pollutant degradation itself also creates conditions that facilitate ARG spread. To address this, we developed a xenobiotic degradation gene (XDG) database covering 22 degradation pathways. Using this database, we analyzed over 30,000 complete bacterial genomes and identified widespread co-occurrence of ARGs and XDGs, particularly within Pseudomonadota and Campylobacterota. Metagenomic profiling of 119 activated sludge samples further revealed strong positive correlations (Pearson's r > 0.8) between XDG and intrinsic ARGs, especially, modules involved in aromatic ring cleavage showed the highest correlations with ARGs. However, only 30.9 % of ARG-HGT events were found in MAGs carrying XDGs, and genome-level proximity analysis indicated that such microorganisms did not exhibit higher horizontal transfer potential. Cultivation-based experiments revealed that Pseudomonas strains with high degradation capacity carried intrinsic but not mobile ARGs. Together, these results demonstrate that xenobiotic degradation promotes ARG enrichment primarily through shifts in community composition rather than by enhancing gene mobility, highlighting that environmental AMR risk assessments based solely on ARG abundance may be misleading, and should avoid misestimation in future research.}, }
@article {pmid41324463, year = {2025}, author = {Furman, O and Sorek, G and Moraïs, S and Levin, L and Tovar-Herrera, OE and Winkler, S and Mizrahi, I}, title = {Persistent auxiliary microbiome of early novel colonizers in the developing rumen with lasting functional significance.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf252}, pmid = {41324463}, issn = {1751-7370}, abstract = {The early life assembly of the rumen microbiome is a critical process with lasting implications for host development and function. Using high-resolution longitudinal metagenomics in calves tracked from birth to three years (∼800 days) of age, we reconstructed 2873 high-quality metagenome-assembled genomes (MAGs), including 517 novel genomes primarily detected in early life. These novel genomes, spanning 274 genera and largely classified as non-core taxa, reveal a diverse and functionally distinct auxiliary microbiome. Unlike in other ecosystems, this early microbial community persists into adulthood, retaining ecological and functional relevance despite a decline in abundance. Temporal clustering revealed strong associations between auxiliary taxa and dietary transitions, with functional enrichments in environmental sensing, nutrient biosynthesis, and volatile fatty acid metabolism. Metabolic network analyses showed that auxiliary genomes complement non-auxiliary community members in key functions, with potential effects on the host. Our findings suggest that early colonizers act as ecosystem engineers, with the potential to shape the developmental trajectory of the rumen microbiome. This study thus positions the early microbiome not as a transient feature of colonization, but as a structured, functionally coherent auxiliary community that interacts with the mature rumen ecosystem.}, }
@article {pmid41324436, year = {2025}, author = {Gu, H and Liu, Z and Liu, S and Hu, X and Yu, Z and Li, Y and Li, L and Sui, Y and Jin, J and Liu, X and Jia, Z and Sun, L and Adams, JM and van der Heijden, MGA and Liu, J and Wang, G}, title = {Land conversion to cropland homogenizes variation in soil biota, gene assemblages and ecological strategies on local and regional scales.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf264}, pmid = {41324436}, issn = {1751-7370}, abstract = {It is widely considered that conversion of natural landscapes to agriculture results in biotic homogenization. A recent study comparing soil biota of 27 paired natural steppe soil (NS) and agricultural soil (AS) sites across 900km in north-eastern China found that conversion to agriculture had increased spatial gradients in soil functional genes. Using the same shotgun metagenome samples, and bacterial amplicon data, we instead analyzed total observed variation at the between-site and within-site level. We found that from the perspective of community taxonomic composition, archaeal and fungal community variation was decreased in AS compared to NS at both within- and between-site scales. In contrast, the bacterial and metazoal community was homogenized only at the local scale. Total functional KEGG gene assemblage was homogenized in AS at both the local and regional scale, whereas "Y-A-S" strategies in bacteria were homogenized at the local scale but not the between-site scale. Overall, these results show a clear homogenizing effect of agriculture with respect to multiple aspects of soil taxonomic and functional diversity, though varying by scale. Certain abiotic soil properties showed homogenization in AS at within-site and between-site scales may explain this homogenization, and uniformity of plant cover in croplands likely contribute to the effect. These findings confirm and extend global-scale studies showing homogenization of soil biota in agricultural environments, revealing that effects extend to functional genes and the broad taxonomic spectrum of life - with potential loss of soil ecosystem resilience to environmental change resulting from agriculture.}, }
@article {pmid41324077, year = {2025}, author = {Mah, JK and Hogan, JI and Kothadia, S and Keenan, JE and Berger, J and Carugati, M}, title = {Application of plasma cell-free metagenomic next-generation sequencing for the identification of Aspergillus fumigatus donor-derived infections among solid organ transplant recipients.}, journal = {Medical mycology case reports}, volume = {50}, number = {}, pages = {100751}, pmid = {41324077}, issn = {2211-7539}, abstract = {A cluster of Aspergillus fumigatus donor-derived infections (DDI) was rapidly diagnosed using plasma metagenomic next-generation sequencing (mNGS) among solid organ transplant recipients. The heart recipient, experiencing marginal hemodynamics, underwent an endomyocardial biopsy, which was concerning for a fungal infection on histopathology. Plasma mNGS was performed, identifying A. fumigatus two days prior to conventional diagnostics. This timely diagnosis enabled prompt nephrectomies in the kidney recipients, who survived. This report represents the first published use of mNGS in the diagnosis of Aspergillus fumigatus DDI, highlighting the utility of this novel, underutilized assay for early diagnosis of donor-derived infections.}, }
@article {pmid41323881, year = {2025}, author = {Aini, N and Wahyuningsih, SPA and Achhlam, DH and Fatimah,  and Amin, MHF and Do, HDK}, title = {Modulation of Gut Microbiota, Intestinal Physiology, and Digestive Enzyme Levels by Duo-Strain Probiotics in African Catfish (Clarias gariepinus) Challenged With Aeromonas hydrophila.}, journal = {Aquaculture nutrition}, volume = {2025}, number = {}, pages = {6624613}, pmid = {41323881}, issn = {1365-2095}, abstract = {This study aimed to determine the effect of dual-strains probiotic (DSP) consisting of Lactobacillus casei and Bacillus subtilis on bacterial metagenomic profile, gut physiology, and digestive enzyme levels of African catfish (Clarias gariepinus) infected by Aeromonas hydrophila. The ratio between L. casei and B. subtilis was 1:1 each with a density of 10[8] CFU/mL. Catfish (n = 8 fish per tank, three replicates per treatment) were fed diets supplemented with 0%, 5%, 10%, or 15% DSP for 42 days. On the 35th day, selected groups were intraperitoneally challenged with A. hydrophila at a dose of 0.1 mL × 10[8] CFU/mL. The observed parameters included bacterial counts and microbial profile in the gastrointestinal tract (analyzed using next-generation sequencing [NGS]), gut physiology, and digestive enzyme levels (amylase, lipase, and protease). The results showed that DSP supplementation increased both the abundance and diversity of gastrointestinal microbes, elevated digestive enzyme levels, and enhanced the number of goblet cells in the intestinal lining. The dominant microbial phyla observed in the control group were Fusobacteria and Pseudomonadota.}, }
@article {pmid41323829, year = {2025}, author = {Luo, A and Liu, L and Shi, S and Liu, X and Hu, B}, title = {Analysis of Microbial Community Structure and Functional Genes for Volatile Flavor in Stinky Tofu.}, journal = {Food science &amp; nutrition}, volume = {13}, number = {12}, pages = {e71257}, pmid = {41323829}, issn = {2048-7177}, abstract = {The distinctive flavor of stinky tofu arises from intricate microbial metabolic networks during traditional fermentation, yet the genetic mechanisms linking microbial community structure to flavor formation remain incompletely resolved. This study employed metagenomic sequencing (Illumina NovaSeq 6000, Q30 > 92%) to generate 7.32 Gb of high-quality data, integrated with functional annotations from KEGG, eggNOG, and CAZy databases, to systematically dissect core microbial taxa and metabolic genes driving flavor biosynthesis. Dominant genera included Pseudomonas (relative abundance: 74.3%), Acinetobacter (14.4%), and Enterobacter (5%), with Pseudomonas putida (12.5%) and Pseudomonas fluorescens (3.2%) orchestrating carbohydrate metabolism (68.22% KEGG pathways) and amino acid degradation via glycoside hydrolases (GHs, 73% of CAZy-annotated enzymes) and dehydrogenases (e.g., 125 lactate dehydrogenase genes). Key flavor compounds, such as diacetyl (379 α-acetolactate synthase genes) and 3-methylbutanoic acid, were synthesized through synergistic pathways. Additionally, Lactococcus and Kluyvera contributed to ester and short-chain fatty acid production via α-keto acid dehydrogenase complexes (55 genes). A total of 410,231 non-redundant genes were identified, annotated to 4690 microbial species, establishing a multi-layered microbial-gene-metabolite regulatory network. This work elucidates the molecular basis of stinky tofu flavor formation and provides a framework for optimizing traditional fermentation processes through targeted microbial engineering.}, }
@article {pmid41323686, year = {2025}, author = {Shi, X and Fan, C and Hui, M and Tian, Q and Zhang, F and Pan, C}, title = {Multiomics analysis of microbial succession and flavor formation mechanism during the fermentation process of Maotai-flavour Baijiu.}, journal = {Food chemistry: X}, volume = {32}, number = {}, pages = {103236}, pmid = {41323686}, issn = {2590-1575}, abstract = {This study employed metagenomics and metabolomics techniques to investigate the complex relationship between microbial succession and the formation of flavor compounds during the fermentation process of Maotai-flavour Baijiu. Results demonstrated that stacking fermentation, characterized by Weissella, Pichia, and Aspergillus, which secreted amylases and proteases to hydrolyze starch and proteins. Pitting fermentation facilitated the enrichment of anaerobic microbes such as Acetilactobacillus and Pichia, significantly promoting the synthesis of key flavor compounds, including esters, alcohols, and acids, through Glycosyltransferase and Esterification activities. Volatile compound analysis revealed distinct stage-specific profiles, with acids, alcohols, and esters accumulating predominantly in pitting fermentation. These findings elucidate the stage-specific microbial metabolic networks and synergistic mechanisms underlying flavor formation, providing a scientific basis for optimizing traditional Baijiu fermentation processes.}, }
@article {pmid41323679, year = {2025}, author = {He, Y and Qiao, M and Zhang, H and Xiao, D and Guo, X}, title = {Microbial community, metabolic, and flavor differences among high-temperature Daqu with varying Douchi aroma intensities: a comprehensive metagenomic and metabolomic analysis.}, journal = {Food chemistry: X}, volume = {32}, number = {}, pages = {103265}, pmid = {41323679}, issn = {2590-1575}, abstract = {The Douchi aroma is widely regarded as a key quality marker of high-quality high-temperature Daqu, but the compounds related to Douchi aroma formation and the key aroma-producing microorganisms remain unclear, which this study seeks to clarify. Therefore, metagenomic and metabolomic approaches were employed to decode the characteristic compounds and core microbial contributors in high-temperature Daqu samples no (NF), light (LF), and strong (SF) Douchi aroma. Esters were the most abundant volatiles across all groups, while acids increased with aroma intensity. Lentibacillus daqui, enriched in SF, showed strong positive correlations with isocetic, phenylacetic, and nonanoic acids. In contrast, Lichtheimia ramosa and Monascus purpureus were dominant in NF and LF, respectively. Furthermore, functional prediction and KEGG analysis further revealed potential biosynthetic pathways for phenylacetic and acetic acid. These findings clarify the molecular and microbial basis of Douchi aroma formation and provide a scientific reference for targeted quality regulation in Daqu production.}, }
@article {pmid41322275, year = {2025}, author = {Dong, R and Liu, Y and Wang, N and Tan, KKY and Ji, M}, title = {The distribution of antibiotic resistance and virulence factor genes in the sediment of Inexpressible Island, East Antarctica.}, journal = {Marine life science &amp; technology}, volume = {7}, number = {4}, pages = {978-988}, pmid = {41322275}, issn = {2662-1746}, abstract = {UNLABELLED: Inexpressible Island is a small rocky island in Terra Nova Bay, Victoria Land, Antarctica, which is an area with limited human activities. Understanding the distribution of antibiotic-resistance genes (ARGs) and virulence factor genes (VFGs) in this environment can provide key information on their potential risks to humans and their roles for microbial survival. In this study, we investigated the ARGs and VFGs in lake sediments from Inexpressible Island using metagenomic sequencing. We identified 11,502,071 open-reading frames (ORFs), with 1,749 classified as ARGs and 6,838 as VFGs. The dominant ARGs were associated with antibiotic target alteration and efflux pump mechanisms, while the VFGs were related to adherence and immune modulation functions. While associated within microbial genomes, these ARGs and VFGs were mobile genetic elements like viruses and insertion sequences, distinct from ecosystems with strong human influence. We identified 974 metagenome-assembled genomes (MAGs), with 465 being medium-to-high quality. Of these, 325 (69.9%) contained ARGs, primarily affiliated with Actinomycetota and Pseudomonadota. Additionally, 269 MAGs contained VFGs, with 174 MAGs carrying both ARGs and VFGs, highlighting significant microbial antibiotic resistance and pathogenic potential. Our findings highlight the need for ongoing monitoring of ARGs and VFGs in Antarctica, particularly in light of increasing human activity and climate change.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-025-00323-8.}, }
@article {pmid41322254, year = {2025}, author = {Al, MA and Wang, Y and Huang, J and Yu, Y and Juneau, P and He, Z and Yan, Q}, title = {Anammox and denitrifying bacteria and their nitrogen removal potential in lake sediments mediated by environmental changes.}, journal = {Marine life science &amp; technology}, volume = {7}, number = {4}, pages = {670-681}, pmid = {41322254}, issn = {2662-1746}, abstract = {UNLABELLED: Anammox and denitrification are key processes for nitrogen removal in lake sediments. However, how environmental changes mediate the community structure and functional genes of nitrogen removal bacteria in lakes remain unclear. Using metagenome and amplicon sequencing, we investigated the anammox and denitrifying bacteria and their nitrogen removing potentials in lakes experiencing significant spatiotemporal and environmental variations. The community structure of anammox and denitrifying bacteria exhibited stronger lake-wide spatial variations than that of seasonality, while only the denitrification-related functional genes showed substantial variations in both lakes. Anammox genes (e.g., hzsA/B/C and hdh) showed no significant spatial variations. However, the abundances of anammox and denitrifying genes were significantly higher in winter than in summer. The mesotrophic Lake Weishan demonstrated a greater capacity for complete denitrification in winter, while the eutrophic Lake Donghu exhibited a higher potential of anammox in summer. Differences in functional gene abundances between lakes were more pronounced than variations in phylogenetic diversity, indicating clear functional adaptations to local environments. The coupled nitrogen removal potentials also reflected ecological interactions among anammox and denitrifying genes. Importantly, anammox and denitrifying bacterial communities and their functional genes were primarily driven by dissolved organic carbon, total phosphorous and zinc (Zn). The dissimilarities of anammox and denitrifying bacterial communities increased with geographic distance, indicating a clear distance-decay effect. This study highlights the anammox and denitrifying bacteria and their nitrogen removal potentials in lake sediments that are mediated by both spatial and seasonal environmental changes.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-025-00310-z.}, }
@article {pmid41322233, year = {2025}, author = {Chen, X and Yu, X and Deng, J and Yang, J and Chen, P}, title = {Case Report: Blood and cerebrospinal fluid mNGS-assisted diagnosis Toxoplasma gondii infection-associated with hemophagocytic syndrome and systemic lupus erythematosus.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1674391}, pmid = {41322233}, issn = {2296-858X}, abstract = {BACKGROUND: Reactivation of latent Toxoplasma gondii (T. gondii) infection is more prevalent than primary infection in patients with autoimmune diseases. We present a rare case of systemic lupus erythematosus (SLE) and hemophagocytic syndrome (HPS) associated with T. gondii infection.<br><br>CASE PRESENTATION: We describe the case of a young girl with SLE and HPS who presented with fever, dyspnea, and pancytopenia. The patient's T. gondii infection was diagnosed through the detection of double-positive IgM and IgG antibodies. Metagenomic next-generation sequencing (mNGS) analysis of both plasma and cerebrospinal fluid (CSF) samples revealed a high concentration of T. gondii DNA. The patient demonstrated a positive response to a combined treatment regimen consisting of anti-Toxoplasma medications and glucocorticoids.<br><br>CONCLUSIONS: Co-infection with uncommon pathogens is not uncommon in patients with autoimmune diseases. In individuals with immune disorders and positive T. gondii IgM antibodies, mNGS analysis of peripheral blood samples proves valuable in diagnosing disseminated T. gondii infection.}, }
@article {pmid41322208, year = {2025}, author = {Duan, J and Li, X and Hu, Y and Pang, F and Cao, Y and You, Z}, title = {Case Report: Next-generation metagenomic sequencing in the diagnosis of Brucella-associated joint infections-a case series analysis and comprehensive literature review.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1688037}, pmid = {41322208}, issn = {2296-858X}, abstract = {BACKGROUND: The application of next-generation metagenomic sequencing (mNGS) in the diagnosis of human brucellosis, particularly in cases of joint brucellosis infection, remains under-explored, with rarely no case reports available in the literature. We present the first case series focusing on the application of mNGS in the diagnosis of Brucella joint infections. The results indicate that mNGS plays a crucial role in diagnosing Brucella joint infections, serving as a valuable complement, particularly for culture-negative patients.<br><br>CASE PRESENTATION: This study presents a comprehensive analysis of four cases of human joint brucellosis diagnosed using mNGS on the BGI sequencing platform, involving three male and one female patients aged from 42 to 63&#x202f;years, all of whom had documented epidemiological exposure histories. mNGS successfully identified Brucella sequences in all cases, with additional diagnostic findings including a positive Brucella agglutination test in Patient 1, positive joint fluid cultures in Patients 3 and 4, and no positive results in Patient 2. Following surgery and targeted antibiotic therapy, all patients exhibited clinical improvement and favorable follow-up outcomes.<br><br>CONCLUSION: These findings underscore the utility of mNGS as a critical diagnostic tool for joint brucellosis infections and highlight its potential as a complementary approach in cases of culture-negative joint infections. In cases where clinical suspicion of joint infection persists despite the absence of identifiable etiological evidence, the implementation of mNGS is strongly advised to facilitate timely and accurate clinical decision-making.}, }
@article {pmid41321514, year = {2025}, author = {Liu, Z and Jiang, A and Kong, Z and Lv, X and Zhang, J and Wu, J and Zhou, C and Tan, Z}, title = {Multi-omics analysis reveals the mechanism of rosemary extract supplementation in increasing milk production in Sanhe dairy cows via the "rumen-serum-milk" metabolic pathway.}, journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)}, volume = {23}, number = {}, pages = {396-414}, pmid = {41321514}, issn = {2405-6383}, abstract = {Rosemary extract (RE) has shown potential as a plant-derived feed additive, but its effects on Sanhe dairy cows are still unknown. In this study, 30 multiparous Sanhe dairy cows (days in milk 171 ± 17 days) with similar body condition were randomly divided into two groups: the RE group (n = 15) was fed the basal diet plus 20 g RE/d, and the CON group (n = 15) was fed only the basal diet. The experiment lasted for 57 days, including a one-week adaptation period. Compared with the CON group, milk yield (P = 0.022) increased significantly with RE supplementation, while milk fat (P = 0.071) also tended to increase. Milk urea nitrogen (P = 0.003) and serum urea nitrogen (P = 0.013) contents were significantly reduced in the RE group compared with the CON group. In rumen fermentation, the content of butyric acid (P = 0.035) in RE group was significantly increased, while valeric acid (P = 0.080) content had an increasing trend. In addition, RE supplementation improved the antioxidant capacity of Sanhe dairy cows by significantly increasing the serum total antioxidant capacity (P < 0.001), superoxide dismutase activity (P = 0.001), immunoglobulin A content (P < 0.001), and immunoglobulin G content (P = 0.005), while decreasing serum malondialdehyde content (P < 0.001), to improve immunity and also affect the composition of serum free amino acids. Metabolomic results showed that a total of 13 co-differential metabolites were identified in rumen and serum, including ursolic acid, a major component of RE, which was higher in both rumen and serum. The milk metabolome analysis identified glycerides, glycerophospholipids, and sphingolipids as the three lipid types that exhibited higher identification intensity in RE. Rumen metagenomic results showed that RE supplementation affected the composition of rumen microorganisms, and differential microbial Kyoto Encyclopedia of Genes and Genomes (KEGG) functional analyses revealed that the RE group was significantly enriched in the fatty acid biosynthesis pathway and the glycerophospholipid metabolism pathway; two pathways related to lipid synthesis. By associating the genus-level differential microorganisms in the rumen with the "rumen-serum-milk" metabolome and mapping the correlation network, it was found that g_Sharpea, g_Tistlia, and g_Acetobacter, which were more abundant in RE, correlated with more differential metabolites and clustered in the same module. Among the 10 microbial biomarkers screened in the rumen, g_Acetobacter and g_Prevotella were more abundant in the RE, and Mantel's analysis showed that they correlated with rumen fermentation parameters and oxidative and immunological indicators in serum. These results reveal the regulatory mechanism of RE supplementation feeding to enhance milk production and improve milk quality by improving oxidative stress capacity and immunity and reducing nitrogen loss in Sanhe dairy cows, suggesting that RE has the potential as a feed additive for dairy cows.}, }
@article {pmid41321463, year = {2025}, author = {Wang, W and Jiang, X and Wu, W and Zhang, L}, title = {Case Report: Primary segmental volvulus in an infant.}, journal = {Frontiers in pediatrics}, volume = {13}, number = {}, pages = {1707716}, pmid = {41321463}, issn = {2296-2360}, abstract = {Primary segmental volvulus (PSV) is a rare cause of acute abdomen in infants. It is characterized by a form of strangulated intestinal obstruction requiring prompt diagnosis and surgical intervention. This study aimed to report a case of PSV in an infant, which was managed successfully through early recognition, close clinical monitoring, and timely surgical treatment. Although both blood and ascitic fluid cultures were negative postoperatively, metagenomic next-generation sequencing (mNGS) identified the same pathogen in both specimens, enabling targeted antibiotic therapy. This case highlights the importance of including PSV in the differential diagnosis of infants presenting with unexplained abdominal distension and bilious vomiting, particularly when accompanied by anemia. Additionally, the elevated level of the coagulation system biomarker thrombin-antithrombin complex (TAT) may serve as a useful marker for monitoring coagulation status in the perioperative period. The integration of TAT assessment and mNGS-based pathogen identification provides a novel framework for individualized perioperative management in PSV.}, }
@article {pmid41321415, year = {2025}, author = {Horstmann, L and Lipus, D and Bartholomäus, A and Oses, R and Kitte, A and Friedl, T and Wagner, D}, title = {Microbial ecology of subsurface granitic bedrock: a humid-arid site comparison in Chile.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf199}, pmid = {41321415}, issn = {2730-6151}, abstract = {Subsurface microorganisms face extreme challenges such as anoxic, xeric, and oligotrophic conditions. In igneous systems, nutrient limitation is critical, as biomass input relies on surface-derived fluids via tectonic fractures. Despite growing interest in subsurface habitats, little is known about ecosystems beneath arid landscapes, where surface water input is limited by the low annual precipitation. This study compares granitic subsurface environments beneath arid and humid surface ecosystems, highlighting the link between surface climate and subsurface biodiversity. DNA was extracted from granitic subsurface rocks recovered from two endmember sites along a north-south climate gradient in Chile's Coastal Cordillera. Microbial communities inhabiting down to 55 m deep subsurface rocks were characterized using 16S rRNA amplicon and shotgun metagenomic sequencing. We identified an abundant and potentially active subsurface community below both climates dominated by heterotrophic bacteria, including Pseudarthrobacter, Janthinobacterium, and Pseudomonas. However, rare taxa affiliated with common chemolithoautrophs, e.g. Thiobacillus, Sulfuriferula, and Sulfuricurvum, were only observed in the arid subsurface, indicating increased oligotrophic conditions and reliance on inorganic electron donors in the deeper subsurface of the desert. Functional analysis revealed sulphur, hydrogen, and carbon monoxide as potential inorganic electron donors. These findings expand the current understanding of microbial life in the subsurface of granite rocks showing the influence of surface climate on nutrient conditions in the deeper subsurface, providing new insights into the extent and functional capacity of terrestrial subsurface habitats and their role in global biogeochemical processes.}, }
@article {pmid41320762, year = {2025}, author = {Peng, S and Liu, Z and Song, Z and Wang, C and Yu, Z and Zhao, N and Lu, W and Ning, Z and Lyu, A}, title = {Vinegar-processed frankincense extracts alleviate colorectal cancer by butyric acid mediating M1 tumor-associated macrophage pyroptosis.}, journal = {Chinese medicine}, volume = {20}, number = {1}, pages = {208}, pmid = {41320762}, issn = {1749-8546}, support = {CI2021A04201//the Scientific and Technological Innovation Project of China Academy of Chinese Medical Sciences/ ; 82003950//the National Natural Science Foundation Committee of China/ ; YZX-202334//the Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; ZZ14-YQ-035//the Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; }, abstract = {BACKGROUND: Olibanum (RF), a traditional Chinese medicinal resin, shows efficacy in colorectal cancer (CRC) treatment. Its vinegar-processed form (PF) is clinically recognized for enhanced therapeutic effects, with prior mechanistic studies focusing on lipophilic components like boswellic acids. Yet, the regulatory mechanisms of PF's aqueous extracts remain unclear.<br><br>METHODS: The aqueous extracts of RF and PF were characterized and compared through transmission electron microscopy (TEM), nanoparticle analysis, and protein profiling. The accumulation of these fractions in feces was confirmed using DiR dye labeling. A mouse CRC model was employed to evaluate and compare the therapeutic effects of RF and PF. The composition of butyric acid-producing microbiota was analyzed using 16S rRNA gene sequencing and metagenomics. Butyric acid levels were quantified using ultra-high-performance liquid chromatography coupled with triple quadrupole mass spectrometry (UHPLC-TQ-MS). Macrophage phenotypes were assessed via flow cytometry, while mRNA and protein expression levels were determined through RT-qPCR and western blot analysis.<br><br>RESULTS: PF aqueous extracts exhibited distinct morphology, particle size, and protein content and had a superior therapeutic effect in alleviating CRC compared to RF. Further analysis confirmed that both RF and PF accumulated in feces and modulated the butyric acid metabolism of gut microbiota. The increased levels of butyric acid contributed to CRC alleviation by promoting the polarization of M1 tumor-associated macrophages (TAMs) and suppressing the pyroptosis of M1 TAMs.<br><br>CONCLUSION: The study confirmed that vinegar-processed frankincense enhances its therapeutic effect on CRC by modulating M1 tumor-associated macrophages, which may provide efficient treatment of CRC from the perspective of host-gut metabolic interactions.}, }
@article {pmid41320324, year = {2025}, author = {Liu, C and Gong, J and Luo, Z and Lai, P and Guo, S and Liang, D and Chen, G and Xing, M and Yu, J and Xie, Y and Liu, D and Zeng, W and He, Z and Lan, P}, title = {Gut microbe alleviates stress-related cancer metastasis by oleic acid degradation.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2025-335627}, pmid = {41320324}, issn = {1468-3288}, abstract = {BACKGROUND: Chronic stress is a known risk factor for cancer metastasis. However, the underlying mechanisms, particularly those involving the gut microbiota and their metabolites, remain unclear.<br><br>OBJECTIVE: To investigate whether gut microbiota dysbiosis and metabolic alterations mediate the sustained pro-metastatic effects of chronic stress, even after normalisation of stress hormone levels.<br><br>DESIGN: Multiple metastatic models were performed after stress cessation. Shotgun metagenomics and metabolomics were performed to assess changes in microbiota and metabolites. The effects of Bifidobacterium animalis and oleic acid (OA) on metastasis were evaluated in vivo and in vitro. Moreover, we explored how B. animalis degraded OA. Mechanistically, we discovered the interaction between corticosteroids and gut bacteria through guanine metabolism assays. Human samples were collected from patients with colorectal cancer (CRC) with varying perceived stress scores and metastatic status for validation.<br><br>RESULTS: Mice that underwent chronic stress exhibited increased metastasis even after hormone levels recovered. The gut microenvironment was altered, with a significant reduction in B. animalis and an increase in OA. B. animalis administration reduced OA levels and suppressed metastasis, while OA supplementation had the opposite effect. B. animalis expresses oleate hydratase, an enzyme that degrades OA. Stress hormones inhibited B. animalis by altering guanine metabolism in the intestinal epithelium. In patients, high stress was associated with more OA, lower B. animalis levels and increased metastasis.<br><br>CONCLUSIONS: Chronic stress promotes metastasis by altering microbiota and increasing OA. Targeting B. animalis and OA may help prevent stress-related tumour progression.}, }
@article {pmid41319631, year = {2025}, author = {Wang, J and Tian, Y and Zhang, G and Li, Y and Chen, L}, title = {Metagenomic insights into nitrogen and phosphorus metabolisms of bacteria in lakes with distinct nutrient conditions.}, journal = {Journal of environmental management}, volume = {396}, number = {}, pages = {128121}, doi = {10.1016/j.jenvman.2025.128121}, pmid = {41319631}, issn = {1095-8630}, abstract = {Nitrogen (N) and phosphorus (P) cycling are crucial for preserving ecosystem functioning in lakes, yet our comprehension of the dynamics of N/P cycling genes and microorganisms under diverse nutrient levels is still limited. Herein, we conducted a comprehensive investigation into the profiles of N/P cycling genes and bacteria across three lakes with distinct nutrient levels. We found that N and P cycling genes were most abundant in the high-nutrient lake, particularly those involved in ammonification, assimilatory nitrate reduction, P regulation, and P transportation. Bacteria responsible for mediating most N/P cycling processes (excluding nitrogen fixation and P regulation) were predominant in the high-nutrient lake and mainly affiliated with Cyanobacteria, Proteobacteria, Actinobacteriota, and Bacteroidota. Furthermore, a potential biogeochemical hotspot for the co-metabolism of N and P was identified in the high-nutrient lake, consolidated by the most intricate co-occurrence pattern between N and P cycling genes. More importantly, these versatile bacteria capable of N/P metabolisms, primarily influenced by total nitrogen, total phosphorus, Secchi depth, and total dissolved solids, played important roles in maintaining the stability of bacterial communities in lakes. These findings offer significant insights into microbial-mediated N and P biogeochemical cycling in lakes with varying nutrient conditions, improving our understanding of utilizing N/P co-metabolism microbes to regulate ecosystem function and service amid the challenges of global lake eutrophication.}, }
@article {pmid41319542, year = {2025}, author = {Chen, X and Tie, Y and Zhu, M and Wu, Z and Xu, W and Zhang, Z and Ju, F and Zhang, W}, title = {Unraveling microbial synergy in blended Daqu: A multi-omics approach to decoding the unique flavor profile of Jiuliangxiang baijiu.}, journal = {Food chemistry}, volume = {499}, number = {}, pages = {147314}, doi = {10.1016/j.foodchem.2025.147314}, pmid = {41319542}, issn = {1873-7072}, abstract = {This study deciphers the microbial-ecological basis of Jiuliangxiang Baijiu's (JLX) unique flavor through blended Daqu multi-omics. GC-MS comparative analysis of five market-representative Baijiu types identified 25 aroma-active compounds (OAV ≥ 1) in JLX, with ethyl palmitate (OAV = 2) established as a potential characteristic marker. Subsequent investigation of its blended Daqu revealed how microbial consortia govern flavor formation. Physicochemical and microbial analyses demonstrated that Daqu blending elevated enzymatic capacities, including saccharification (+227.5 % vs single Daqu), esterification (+27.4 %), and liquefaction (+15.4 %), while enhancing microbial diversity. Metabolomic profiling identified glycerophospholipid Gpgro (14:0/16:0) as the ethyl palmitate precursor. Metagenomic tracking revealed that the core ester-producing taxa-primarily Bacillus licheniformis (from high-temperature Daqu) and Kroppenstedtia eburnea (from bacterial Daqu)-harbor complementary genetic potential for both esterase and acyltransferase pathways. The results provide a microbial-ecological framework for rational Daqu blending, offering actionable strategies to engineer microbial consortia for flavor-directed liquor innovation.}, }
@article {pmid41319383, year = {2025}, author = {Deng, H and Yang, J and Li, R and Li, K and Lu, H and Lin, B and Xu, X and Liao, J and Ye, C and Deng, J and Wu, B and Sun, L}, title = {ASSR-mediated sludge yield reduction couples deterministic enrichment of Nitrospira with metabolic resource partitioning.}, journal = {Water research}, volume = {290}, number = {}, pages = {125031}, doi = {10.1016/j.watres.2025.125031}, pmid = {41319383}, issn = {1879-2448}, abstract = {The anaerobic side-stream reactor (ASSR) process offers a microbiome-driven strategy for sustainable wastewater treatment, yet the ecological mechanisms governing its sludge yield reduction efficiency remain unresolved. Here, we demonstrate that a pilot-scale anaerobic-anoxic-oxic (AAO) system with integrated anaerobic side-stream reactor (ASSR) (designated AAO-ASSR/SR) reduced sludge production by 43.6 % compared to a conventional AAO system (designated AAO/CK), while maintaining effluent quality. Through integrated multi-omics and ecological modeling, we revealed the core microbiome-driven mechanism for ASSR-mediated sludge yield reduction. This mechanism is characterized by three key features: (1) enhanced microbial stability via cooperative networks, (2) deterministic assembly selecting slow-growing keystone taxa (e.g., Nitrospira, 18.6 % abundance in SR), and (3) metabolic resource partitioning from biomass synthesis to amino acid cross-feeding. Functional metagenomics revealed that Nitrospira (phylum Nitrospirota, comprising >99 % Nitrospira) and Novosphingobium (phylum Proteobacteria) mediated increased amino acid metabolism and reduced ATP biosynthesis in SR, contrasting with Bacteroidota-dominated biomass synthesis in CK through enhanced protein, nucleotide metabolism and ATP biosynthesis. By coupling deterministic microbial assembly with functional repartitioning, this work contributes to establish a design principle for targeted microbiome engineering in low-sludge systems, advancing sustainable wastewater management through ecological optimization of microbial resource allocation.}, }
@article {pmid41318814, year = {2025}, author = {Li, J and Liu, L and Tao, M and Han, Z and Ma, M and Jiang, L and Liu, C and Liu, D and Zhang, P and Zhang, M and Xue, R and Gong, J and Zhang, X and Shen, L and Qi, C}, title = {Impact of concomitant medications on efficacy of CLDN18.2-specific CAR-T cell therapy in advanced gastric cancer.}, journal = {British journal of cancer}, volume = {}, number = {}, pages = {}, pmid = {41318814}, issn = {1532-1827}, abstract = {BACKGROUND: Claudin18.2 (CLDN18.2)-specific CAR-T cell therapy has demonstrated promise in advanced gastric cancer (GC). However, the impact of concomitant medications on the efficacy outcomes remains unclear.<br><br>METHODS: We retrospectively analyzed advanced GC patients receiving CLDN18.2-specific CAR-T cell therapy from a phase I trial. Concomitant medications were defined as any drugs administered within 30 days before and after CAR-T cell infusion, including corticosteroids, antibiotics, tocilizumab, granulocyte colony-stimulating factor (G-CSF), thrombopoietin (TPO), and erythropoietin. Metagenomic sequencing was employed to elucidate the differences in gut microbiome signatures between responders and non-responders.<br><br>RESULTS: Of 72 patients included in the study, 6 (8.3%) received corticosteroids, 49 (68.1%) received tocilizumab, and 22 (30.6%) received antibiotics, 15 (20.8%) received G-CSF, 5 (6.9%) received thrombopoietin, and no patient received erythropoietin. The median progression-free survival (PFS) (2.6 vs. 5.8 months; P&#x2009;<&#x2009;0.001) and overall survival (OS) (3.9 vs. 9.5 months; P&#x2009;<&#x2009;0.001) were significantly shorter for patients who received antibiotics for infection compared to those who did not. No significant differences were observed in objective response rate (ORR), PFS, and OS between patients who received corticosteroids, tocilizumab, antibiotics for prophylaxis, G-CSF, or TPO and those who did not. A higher abundance of Fusobacterium nucleatum, Lactobacillus mucosae, Prevotella pallens, and Streptococcus pseudopneumoniae in gut microbiome was associated with a superior treatment response.<br><br>CONCLUSIONS: The study indicates that the use of antibiotics for infection reduces the efficacy outcomes of CLDN18.2-specific CAR-T cell therapy for advanced GC, while other concomitant medications do not affect the outcomes. Further research is needed to clarify the optimal administration of these medications and the underlying mechanisms of the gut microbiome in impacting CAR-T treatment response.<br><br>TRIAL REGISTRATION: NCT03874897.}, }
@article {pmid41318497, year = {2025}, author = {Wang, Z and Xing, Y and Xu, M and Chen, C and Zhu, Q and Chen, H and Zhang, Y and Chen, W and Feng, J and Zhang, A and Ma, R and Liu, X and Li, S and Yan, Q and Xing, G and Yao, X and Kong, X}, title = {Altered gut mycobiome and cross-kingdom microbial interactions in systemic lupus erythematosus.}, journal = {Journal of translational medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12967-025-07423-0}, pmid = {41318497}, issn = {1479-5876}, support = {LJ212410161043//Basic Research Project of Liaoning Provincial Department of Education for Universities/ ; 2025-BS-0684//Doctoral Start-up Foundation of Liaoning Province/ ; }, }
@article {pmid41317994, year = {2025}, author = {Merrill, LC and Martínez, RL and Palacios, N and Dawson-Hughes, B and Noel, SE and Wang, Y and Tucker, KL and Mangano, KM}, title = {Gut microbes related to the Dietary Approaches to Stop Hypertension score are associated with bone quantity but not with bone quality in a cross-sectional study of older Puerto Rican adults.}, journal = {The American journal of clinical nutrition}, volume = {}, number = {}, pages = {101129}, doi = {10.1016/j.ajcnut.2025.101129}, pmid = {41317994}, issn = {1938-3207}, abstract = {BACKGROUND: BMD explains fractures incompletely; studies relating lifestyle to bone quality are lacking.<br><br>OBJECTIVES: To examine associations of diet quality with bone measures (BMSi, TBS, BMD); evaluate moderation by inflammation; identify gut microbiome features linked to diet quality; and quantify diet-microbiome-bone relationships.<br><br>METHODS: This cross-sectional study included participants from the Boston Puerto Rican Osteoporosis Study. Diet was assessed with a culturally tailored FFQ, and diet quality with the Dietary Approaches to Stop Hypertension (DASH) score.. BMSi was measured using microindentation; BMD by dual-energy X-ray absorptiometry (DXA); TBS derived from DXA. Inflammation was assessed with a biomarker score (BMS) and tested as a moderator of diet-bone associations via interaction terms in linear regression. Gut microbiome composition (shotgun metagenomics) was analyzed with MaAsLin regression to assess diet associations. A machine learning algorithm determined dietary, microbial, and bone-related predictors of bone health; sample sizes varied by outcome: BMSi (n = 86); TBS (n = 204); BMD femoral neck (n = 220), total hip (n = 221), lumbar spine (n = 207).<br><br>RESULTS: DASH score was not associated with BMSi (&#x3b2; = -0.10; 95% CI: -0.46, 0.27; P = 0.60), TBS (&#x3b2; = 0.002; 95% CI: -0.002, 0.005, P = 0.36), BMD at the femoral neck (&#x3b2; = 0.002; 95% CI: -0.002, 0.005; P = 0.30), or lumbar spine (&#x3b2; = 0.002; 95% CI: -0.003, 0.006, P = 0.52 but was at total hip (&#x3b2; = 0.004; 95% CI: 0.003, 0.008; P = 0.03). The association was not moderated by inflammation (&#x3b2; = -0.0001, P = 0.89). Lachnospira eligens was one of 4 taxa positively associated with DASH score, and BMD. No microbial pathways were associated with the DASH score.<br><br>CONCLUSIONS: DASH score was associated with hip BMD, but not with BMSi or TBS. Select diet-related gut microbes, and an inflammation score were associated with BMD. Future studies should examine dietary inflammation in relation to bone quality.}, }
@article {pmid41317922, year = {2025}, author = {Yang, G and Zhen, Z and Zhang, K and Yin, J and Zhong, X and Li, X and Li, Q and Nie, K and Miao, X and Lin, Z and Zhang, D}, title = {Biochar accelerated soil atrazine degradation by promoting dechlorination pathway: A novel mechanism revealed by DNA stable isotope probing (DNA-SIP).}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {133722}, doi = {10.1016/j.biortech.2025.133722}, pmid = {41317922}, issn = {1873-2976}, abstract = {Biochar can accelerate atrazine degradation in soils, with surface modification being a widely accepted method to improve the performance. Nevertheless, the underlying mechanisms remain unclear. This study explored the efficiency of modified biochar in facilitating soil atrazine biodegradation with the aid of DNA stable isotope probing (DNA-SIP) and metabolite profiling. DNA-SIP results confirmed the involvement of ten bacterial genera and six atrazine degradation-related genes in atrazine metabolism in situ. Among them, Candidatus Nitrososphaera, Pedosphaera and Conexibacter were reported to be associated with atrazine degradation for the first time. FeCl3-modified biochar significantly accelerated atrazine degradation (85%) by improving soil physicochemical properties (pH, soil organic matter and humus) and enriching the active atrazine degraders. Notably, atrazine dechlorination pathway was preferentially promoted by modified biochar. The findings suggested that DNA-SIP enabled the discovery of the active atrazine degraders and degradation-related genes in biochar-amended soils, providing novel insights into the mechanisms of biochar-facilitated atrazine removal.}, }
@article {pmid41317625, year = {2025}, author = {Kharaillah, A and Zhong, M and Soriano, JD and Gambardella, N and Sanz-Sáez, I and Yan, D and Bertilsson, S and Björn, E and Bravo, AG and Capo, E}, title = {Low-oxygen freshwaters as ecological niches for mercury methylators.}, journal = {Water research}, volume = {290}, number = {}, pages = {125014}, doi = {10.1016/j.watres.2025.125014}, pmid = {41317625}, issn = {1879-2448}, abstract = {Methylmercury (MeHg) is a hazardous neurotoxin, predominantly formed by microbial transformation of inorganic mercury in oxygen-depleted aquatic and terrestrial ecosystems. The ongoing deoxygenation of aquatic ecosystems due to global warming is likely to expand microbial niches for MeHg production. Although mercury methylators have also been reported to thrive in oxyge-deficients conditions in a few marine and freshwater ecosystems, there is a lack of comprehensive understanding of how they are distributed in freshwater systems. In this study, we retrieved hgcA genes, genomic marker for mercury methylation potential, from 586 metagenomes from the water column of 186 freshwater systems. Overall, hgcA genes were detected in the water column of 30 lakes, with the highest richness and abundance being detected in anoxic (0 mg O2l[-1]) and hypoxic (>0-2 mg O2l[-1]) compared to oxic conditions (>2 mg O2l[-1]). Although Desulfobacterota had the highest hgcA gene richness across most freshwater systems, certain systems were dominated by hgcA genes from Bacteroidales and Kiritimatiellales, implying metabolic and ecological versatility of mercury methylators as a group. Our findings suggest that projected expanding deoxygenation may lead to new niches for mercury methylators in inland waters.}, }
@article {pmid41317490, year = {2025}, author = {Qin, Y and Xie, X and Li, D and Wu, Z and Liu, J and Li, W and Tang, D and Chen, S and Zhang, Y and Liu, N and Zhang, Q and Chen, Y}, title = {NADH-driven bioreductive degradation of azo dyes: Mechanisms of high NADH production, electron transfer, and microbial responses.}, journal = {Journal of hazardous materials}, volume = {502}, number = {}, pages = {140559}, doi = {10.1016/j.jhazmat.2025.140559}, pmid = {41317490}, issn = {1873-3336}, abstract = {Bioreductive co-metabolic degradation of azo dyes represents a promising green technology for addressing the environmental pollution caused by azo dyes. This study investigated the impact of co-metabolized substances on NADH production in microbial systems, focusing on the production of reducing power, electron transfer, and the synergistic effects of microbial communities and associated mechanisms during azo dye degradation. A culture system was developed to maximize NADH production at 3 g/L yeast extract, and it was observed that the system exhibited a significant increase in reducing power, with NADH concentration reaching 909.48 pg/mL (60 h). The electron transfer process in this system primarily depended on factors such as redox mediators, azoreductase, and formic acid. Azo dye reductive degradation and decolorization occurred through an indirect electron transfer pathway. Flavin-based redox mediators (riboflavin and flavin mononucleotide) played a key role in the system, with the application of riboflavin and flavin mononucleotide increasing the system's dye reduction ratio by 14.45 % and 14.40 %, respectively. They were endogenously expressed by the system and facilitated efficient electron transfer by synergizing with specific reductases, particularly when the electron transport chain was inhibited, and alternative pathways ensured the continuation of the reduction reaction. NADH production primarily occurred through glycolysis, the TCA cycle, and fatty acid β-oxidation, with glycolysis contributing the most. Microorganisms such as Enterococcus, Burkholderia, and Escherichia within the microbial community played a crucial role in NADH production while regulating community behavior through a quorum sensing system, thereby enhancing the stability and efficiency of dye degradation. This study investigated the bioreduction of azo dyes in terms of reducing power, offering a theoretical foundation and practical guidance for optimizing the microbial system and enhancing the biodegradation efficiency of azo dyes.}, }
@article {pmid41317467, year = {2025}, author = {Huang, S and Yu, X and Tang, J and Peng, C and Wen, Q and Chen, S and Lei, L and Yang, C and Liu, Y and Xiang, W and Zhang, Q and Lin, H and Zhang, M}, title = {Unveiling the metabolic mechanism of pesticide in food fermentation through metagenomics and metabolomics: A case study of β-cypermethrin in Pixian broad-bean paste.}, journal = {Food chemistry}, volume = {498}, number = {Pt 2}, pages = {147299}, doi = {10.1016/j.foodchem.2025.147299}, pmid = {41317467}, issn = {1873-7072}, abstract = {Fermented foods contain less chemical pollutants, such as pesticide residues, than raw materials. In this study, using Pixian broad-bean paste as a model system, the pesticide degradation during food fermentation was comprehensively elucidated through metagenomic and metabolomics analyses. As a result, β-cypermethrin (β-CY) at 5 mg/kg was almost completely degraded, with a half-life of 6.1 d. β-CY caused flavor changes in fermented products, reducing esters and increasing ketones. Metagenomic analysis revealed that β-CY promoted bacteria phyla Bacteroidota, Pseudomonadota, and enriched the genes of xenobiotic degradation pathways, which is beneficial to its degradation. Microbial-metabolite correlation analysis identified Cyclobacteriaceae, Sulfurovaceae, FEN-1099 and Rhodocyclaceae as key drivers in the synthesis and metabolism of aromatic compounds following β-CY degradation during PBP fermentation. This dual mechanism offers a crucial theoretical foundation for understanding microbial community adaptability and β-CY detoxification in the process.}, }
@article {pmid41316964, year = {2025}, author = {Puchol-Royo, R and Pascual, J and Ortega-Legarreta, A and Otto, P and Tideman, J and de Vries, SJ and Abendroth, C and Tanner, K and Porcar, M and Latorre-Perez, A}, title = {Metagenomic Insights Into the Ecology, Taxonomy and Metabolic Capabilities of 'Candidatus Darwinibacteriales' Ord. Nov. (Formerly MBA03), a Potential Key Player in Anaerobic Digestion.}, journal = {Microbial biotechnology}, volume = {18}, number = {12}, pages = {e70258}, doi = {10.1111/1751-7915.70258}, pmid = {41316964}, issn = {1751-7915}, support = {101000470//European Union's Horizon 2020/ ; }, mesh = {Anaerobiosis ; Phylogeny ; Metagenomics ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Metagenome ; Biofuels ; Sequence Analysis, DNA ; }, abstract = {Biogas, a mix of CO2, CH4 and small proportions of other gases, is a biofuel obtained by anaerobic digestion (AD). Biogas production is often considered a black box process, as the role and dynamics of some of the microorganisms involved remain undisclosed. Previous metataxonomic studies in the frame of the MICRO4BIOGAS project (www.micro4biogas.eu) revealed that MBA03, an uncharacterised and uncultured bacterial taxon belonging to phylum Bacillota, was very prevalent and abundant in industrial full-scale AD plants. Despite the efforts, this taxon has not yet been cultivated, which makes the analysis of its taxonomy, ecology and metabolism even more challenging. In the present work, 30 samples derived from anaerobic digesters were sequenced, allowing the reconstruction of 108 metagenome-assembled genomes (MAGs) potentially belonging to MBA03. According to phylogenetic analyses and genomic similarity indices, MBA03 was classified as a new bacterial order, proposed as 'Candidatus Darwinibacteriales' ord. nov., which includes 'Candidatus Darwinibacter acetoxidans' gen. nov., sp. nov. of 'Candidatus Darwinibacteriaceae' fam. nov., along with 'Candidatus Wallacebacter cryptica' gen. nov., sp. nov. of the 'Candidatus Wallacebacteriaceae' fam. nov. Ecotaxonomic studies determined that AD processes are the main ecological niche of 'Candidatus Darwinibacteriales'. Moreover, metabolic predictions identified Darwinibacteraceae members as putative syntrophic acetate-oxidising bacteria (SAOB), as they encode for the reversed Wood-Ljungdahl (W-L) pathway coupled to the glycine cleavage system. This suggests that Darwinibacteraceae members could work in collaboration with hydrogenotrophic methanogenic archaea to produce methane in industrial biogas plants. Overall, our findings present 'Candidatus Darwinibacteriales' as a potential key player in anaerobic digestion and pave the way towards the complete characterisation of this newly described bacterial taxon, which has not yet been cultured.}, }
@article {pmid41316759, year = {2025}, author = {Li, RX and Qiu, CS and Li, F and Xu, F and Liu, NN and Chen, X and Qi, L and Wang, CC and Wang, D and Wang, SP}, title = {[Effects of Thermal-alkaline and Thermal Hydrolysis Treatments on Antibiotic Resistance Genes in Sludge].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {46}, number = {11}, pages = {6940-6947}, doi = {10.13227/j.hjkx.202410028}, pmid = {41316759}, issn = {0250-3301}, mesh = {*Sewage/microbiology/chemistry ; Hydrolysis ; *Waste Disposal, Fluid/methods ; *Drug Resistance, Microbial/genetics ; Hot Temperature ; Wastewater/microbiology ; Genes, Bacterial ; }, abstract = {Sewage sludge from urban wastewater treatment plants is an important source of antibiotic resistance gene (ARGs) dissemination into various environmental media. In this study, two treatment methods were employed to treat sewage sludge: thermal-alkaline lysis (60-100℃, pH 10-12) and thermal hydrolysis (140-200℃, 60-120 min). Through metagenomic sequencing and quantitative polymerase chain reaction technology (qPCR), the effects of different treatment conditions on the physicochemical properties of sludge and the removal of ARGs were systematically investigated. In addition, the correlation between ARGs, intI1, and the physicochemical properties of sludge was analyzed in detail. The results indicated that both thermal-alkaline lysis and thermal hydrolysis treatments could break sludge cells, with thermal hydrolysis showing a more significant effect. Moreover, both treatment methods could effectively reduce the abundance of ARGs in sludge under certain conditions. Under thermal hydrolysis conditions at 200℃ for 120 mins, the absolute abundance of ARGs in sludge reached its lowest level of 4.08×10[6] copies·g[-1], and the absolute abundance of intI1 also achieved its minimum value of 1.83×10[6] copies·g[-1] under these conditions. Correlation analysis revealed a significant positive correlation (P < 0.05) between soluble polysaccharides and intI1 under thermal-alkaline lysis conditions. However, under thermal hydrolysis conditions, multiple ARGs and intI1 exhibited significant negative correlations (P < 0.05) with physicochemical indicators such as soluble chemical oxygen demand (SCOD), soluble proteins, and soluble polysaccharides. The removal of ARGs by these different treatment methods was mainly influenced by the treatment conditions and the degree of microbial cell disruption in the sludge.}, }
@article {pmid41316756, year = {2025}, author = {Huang, W and Zhu, C and Yang, YJ and Zhang, HZ and Hu, SG and Wu, K and Cui, KP and Chen, YH}, title = {[Distribution Characteristics and Driving Mechanism of Antibiotic Resistance Genes in a Water Source in Hefei, China].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {46}, number = {11}, pages = {6906-6916}, doi = {10.13227/j.hjkx.202409265}, pmid = {41316756}, issn = {0250-3301}, mesh = {China ; *Drug Resistance, Microbial/genetics ; *Water Microbiology ; Soil Microbiology ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Water Supply ; Bacteria/genetics ; *Drug Resistance, Bacterial/genetics ; Drinking Water/microbiology ; }, abstract = {One of the important water sources in Hefei serves as a crucial water supplier, playing a vital role in water provisioning. Its water quality is related to both drinking water safety and ecological water safety. To elucidate the distribution characteristics and influencing factors of antibiotic resistance genes (ARGs) within the water source, water, sediment, and soil samples were collected in July 2021 and December 2021. Metagenomic sequencing was employed to identify and characterize ARGs, mobile genetic elements (MGEs), and bacterial communities in the samples. The correlations between ARGs and physical-chemical properties, antibiotics, MGEs, and bacterial communities were also analyzed. Lastly, the factors were categorized into physical-chemical and biological factors, and their degrees of influence on ARGs were analyzed. The results showed that a total of 544 subtypes of ARGs were detected in the water source, which were classified into 26 major categories. Multidrug, bacitracin, β-lactam, and polymyxin resistance genes were the dominant types of ARGs in all three media, with the subtype bacA exhibiting the highest abundance across all. The numbers of certain classifications of ARGs tended to be higher in soil compared to those in sediment and water, and the abundance of ARGs in the soil was also significantly higher than that in the sediment. PCoA analysis showed significant differences in the structural composition of ARGs among the three media. Correlation analyses showed that TP, pH, LINs, and FQs in the water and SAs in the sediment were significantly correlated with ARGs. Additionally, strong correlations were observed between MGEs and bacterial communities and ARGs in the three media. The VPA results indicated that biological factors played a pivotal role in influencing ARGs in water, whereas physical-chemical factors exerted a stronger influence in soil. However, the synergistic effect of both physical-chemical and biological factors on ARGs in all three media was not negligible.}, }
@article {pmid41316726, year = {2025}, author = {Nishijima, S and Fullam, A and Schmidt, TSB and Kuhn, M and Bork, P}, title = {VIRE: a metagenome-derived, planetary-scale virome resource with environmental context.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkaf1225}, pmid = {41316726}, issn = {1362-4962}, support = {12/RC/2273-P2//Uehara Memorial Foundation/ ; //EMBL/ ; }, abstract = {Viruses are the most abundant biological entities on Earth, yet their global diversity remains largely unexplored. Here, we present VIRE, a comprehensive resource comprising over 1.7 million high- and medium-quality viral genomes recovered from >100 000 publicly available metagenomes derived from samples that cover diverse ecosystems, including host-associated, aquatic, terrestrial, and anthropogenic environments. Using a unified and scalable pipeline, we systematically assembled viral genomes and provided detailed information on genome completeness, taxonomic classification, predicted lifestyle, and host assignment based on CRISPR spacer matches. VIRE contains >89 million predicted viral open reading frames, as well as detailed functional annotations derived from multiple databases. Importantly, VIRE is seamlessly integrated with related microbiome resources such as SPIRE (https://spire.embl.de) and Metalog (https://metalog.embl.de), enabling users to jointly explore viral genomes, metagenome-assembled genomes, and associated environmental or clinical metadata. Accessible at https://vire.embl.de, VIRE provides an open-access, scalable platform for investigating viral diversity, evolution, and ecology on a planetary scale.}, }
@article {pmid41316344, year = {2025}, author = {Ren, Y and Liang, J and Xie, J and Hu, W and Lai, M and Li, X and Zhang, J and Zheng, Y and Wu, Q and Zhou, H and Yin, J}, title = {Sodium oligomannate modulates the gut-brain axis to alleviate post-stroke cognitive impairment by restoring butyrate metabolism.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-025-02257-w}, pmid = {41316344}, issn = {2049-2618}, support = {82171317//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Post-stroke cognitive impairment (PSCI) affects up to half of stroke survivors, severely impacting their quality of life. Despite its prevalence, the pathogenesis of PSCI remains poorly understood, and no specific pharmacological treatments are currently available.<br><br>RESULTS: In PSCI patients, fecal butyrate levels were significantly reduced and correlated with cognitive scores. A machine learning model incorporating butyrate levels, butyrate-producing bacteria, and clinical factors (education, smoking, body mass index [BMI], hemoglobin) demonstrates strong predictive performance (area under the curve [AUC]: 0.793 internal, 0.795 external validation). In a transient middle cerebral artery occlusion (tMCAO) mouse model, both sexes displayed sustained gut microbiota dysbiosis featuring decreased butyrate-producing bacteria and fecal butyrate concentrations, concomitant with hippocampal neuronal loss and microglial activation.&#xa0;Sodium oligomannate (GV-971) treatment ameliorated cognitive impairment in a sex-independent manner and restored butyrate-producing gut bacteria. Metagenomic analysis revealed that GV-971 enhanced butyrate production by promoting D-glucuronate degradation and upregulating butyrate synthesis pathway abundance. The elevated butyrate promoted acetylation of histone H3 at lysines 9 and 14 (Ac-H3K9/K14) in colonic and hippocampal neurons, stimulating neurogenesis, while concurrently reducing gut-derived lipopolysaccharide (LPS) and microglial inflammation. Antibiotic treatment and fecal microbiota transplantation established the essential role of butyrate-producing microbiota in mediating GV-971's effects.&#xa0;In vitro, butyrate supplementation significantly inhibited HDAC3 enzymatic activity in HT22 cells and alleviated LPS-induced inflammatory responses in BV2 microglia.<br><br>CONCLUSIONS: Intestinal butyrate levels are significantly associated with PSCI. GV-971 mitigates post-stroke cognitive decline by modulating the gut microbiota to increase butyrate production, highlighting its potential as a therapeutic agent for PSCI.}, }
@article {pmid41316248, year = {2025}, author = {Wang, L and Wang, L and Liu, M and Yuan, Q and Cheng, L and Chen, H and Mao, S and Li, S and Yan, Q and Xing, G and Zheng, N}, title = {Characterization of the gut virome in patients with nonalcoholic fatty liver disease.}, journal = {Journal of translational medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12967-025-07443-w}, pmid = {41316248}, issn = {1479-5876}, }
@article {pmid41316012, year = {2025}, author = {Ye, X and Li, JA and Wang, S and Luan, S and Zheng, J and Lv, S and Zheng, G and Jiang, W and Huang, X and Xu, J and Zhu, L and Niu, B}, title = {Submandibular infection in a healthy child caused by Legionella maceachernii.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-025-12203-8}, pmid = {41316012}, issn = {1471-2334}, }
@article {pmid41315949, year = {2025}, author = {Chen, Y and Hu, Y and Liang, H and Xia, J and Tang, L and Zhang, S}, title = {Embolism of coronary, cerebral, and limb arteries resulting from infective endocarditis of a prosthetic aortic valve: a clinical case report.}, journal = {BMC cardiovascular disorders}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12872-025-05287-2}, pmid = {41315949}, issn = {1471-2261}, abstract = {BACKGROUND: Infective endocarditis (IE) involving prosthetic valves is a critical cardiac condition that can lead to complications such as structural heart damage, heart failure, and arterial embolism, with a high associated mortality rate. This report describes an uncommon instance of infective endocarditis of a prosthetic aortic valve leading to multiorgan embolism.<br><br>CASE PRESENTATION: A 52-year-old male with a history of Bentall surgery and prosthetic aortic valve replacement presented with chest pain and dyspnea. Coronary angiography demonstrated blockage of the distal left anterior descending artery, which was addressed with balloon angioplasty. A transesophageal echocardiogram (TEE) detected vegetation on the prosthetic valve, and metagenomic next-generation sequencing of blood confirmed infection with Cardiobacterium hominis. During treatment, he experienced acute ischaemia in the right lower limb necessitating thrombectomy, and MRI disclosed numerous tiny infarct foci in the brain. Following a period of six weeks of antibiotic treatment, the patient was discharged in a better condition. However, the valve dysfunction persisted and regular follow-up was required in order to determine whether to perform a further operation.<br><br>CONCLUSION: This case underscores the risk of multi-organ embolic consequences in prosthetic valve infective endocarditis, highlighting the necessity for prompt identification, antimicrobial treatment, and surgical intervention where warranted.}, }
@article {pmid41315849, year = {2025}, author = {Zhang, R and Wang, M and Liu, X and Yang, F and Xu, X and Zi, L and Liang, Z and Liu, X and Gao, H and Chen, X and Zhou, G}, title = {The bacterial spectrum of spinal infections based on blood culture, tissue culture, and molecular methods: a systematic review and meta-analysis.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-025-28576-4}, pmid = {41315849}, issn = {2045-2322}, support = {CB23059C065A//Yunnan Fundamental Research Projects/ ; }, abstract = {Spinal infections (SI) are on the rise due to an aging population and the prevalence of more invasive procedures. This study aims to systematically review the microbiological spectrum of SI to enhance diagnostic accuracy and inform effective antibiotic treatment strategies. The last search was conducted on May 9th, 2024, from databases including EMBASE, PubMed, and Web of Science. The outcome variable is infection rate, and the detection method used should be blood culture, tissue culture, or molecular biology method. Two researchers independently extracted research data and evaluated its quality using the JBI Critical Appraisal Tools. Out of 14,639 identified records, 156 studies (encompassing 13,539 patients) were included. Staphylococcus aureus was identified as the most prevalent pathogen, with pooled infection rates of 17.6% (95%CI: 12.8-22.9%; I[2]=93%) in blood culture, 16.8% (95%CI: 14.0-19.8%; I[2]=96%) in tissue culture, and 12.0% (95%CI: 9.3-15.0%; I[2]=35%) in molecular methods. The bacterial spectrum also featured Staphylococcus epidermidis, Escherichia coli, and Mycobacterium tuberculosis (MTB). Molecular methods, particularly metagenomic next-generation sequencing (mNGS), demonstrated markedly superior sensitivity for MTB detection, with a pooled rate of 9.7% (95%CI: 4.6-16.3%; I[2]=90%) compared to 1.3% (95%CI: 0.6-2.1%; I[2]=86%) by tissue culture. The odds ratio for MTB detection with mNGS versus conventional culture was 4.24 (95%CI: 1.68-10.73). This review confirms that a core group of pathogens, including Staphylococcus aureus, Staphylococcus epidermidis, MTB, and Escherichia coli. Our findings underscore that tissue culture is fundamental for common pyogenic bacteria, while metagenomic next-generation sequencing is indispensable for detecting fastidious organisms like MTB. Trial registration: The protocol was registered with PROSPERO (No. CRD42023427429). Registered on May 28, 2023.}, }
@article {pmid41315738, year = {2025}, author = {Medvedeva, S and Guyet, U and Pelletier, E and Ruscheweyh, HJ and Sunagawa, S and Ogata, H and Aylward, FO and Gaïa, M and Yutin, N and Koonin, EV and Krupovic, M and Delmont, TO}, title = {Widespread and intron-rich mirusviruses are predicted to reproduce in nuclei of unicellular eukaryotes.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {41315738}, issn = {2058-5276}, support = {ANR-23-CE02-0025//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-23-CE02-0025//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-23-CE02-0025//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-23-CE02-0025//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-23-CE02-0022//Agence Nationale de la Recherche (French National Research Agency)/ ; }, abstract = {Mirusviruses infect unicellular eukaryotes and are related to tailed bacteriophages and herpesviruses. Here we expand the known diversity of mirusviruses by screening diverse metagenomic assemblies and characterizing 1,202 non-redundant environmental genomes. Mirusviricota comprises a highly diversified phylum of large and giant eukaryotic viruses that rivals the evolutionary scope and functional complexity of nucleocytoviruses. Critically, major Mirusviricota lineages lack essential genes encoding components of the replication and transcription machineries and, concomitantly, encompass numerous spliceosomal introns that are enriched in virion morphogenesis genes. These features point to multiple transitions from cytoplasmic to nuclear reproduction during mirusvirus evolution. Many mirusvirus introns encode diverse homing endonucleases, suggestive of a previously undescribed mechanism promoting the horizontal mobility of spliceosomal introns. Available metatranscriptomes reveal long-range trans-splicing in a virion morphogenesis gene. Collectively, our data strongly suggest that nuclei of unicellular eukaryotes across marine and freshwater ecosystems worldwide are a major niche for replication of intron-rich mirusviruses.}, }
@article {pmid41315665, year = {2025}, author = {Goraj, W and Kagan, K and Kuźniar, A and Banach, A and Jurczyk, S and Podlewski, J and Wolińska, A}, title = {Spatial and functional differentiation of microbial biofilms in a traditional cheese ripening environment.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-025-30318-5}, pmid = {41315665}, issn = {2045-2322}, abstract = {Biofilms in historic buildings represent stable microbial ecosystems shaped by long-term environmental filtering. We investigated bacterial and fungal communities forming biofilms on walls and ceilings in a 19th-century cheese ripening cellar in Poland, characterized by low temperature, high humidity, and minimal light - conditions resembling natural subterranean habitats. Using high-throughput 16 S rRNA and ITS sequencing, we revealed distinct taxonomic and predicted functional profiles associated with surface type (wall vs. ceiling) and material (brick vs. stone). The wall biofilms exhibited greater taxonomic and functional diversity, with enrichment in heterotrophic, fermentative, and polymer-degrading taxa and pathways, whereas ceiling biofilms showed predicted enrichment in aerobic, stress-tolerant, and potentially methanogenic lineages. The co-occurrence network analysis revealed more complex and tightly connected associations in wall biofilms, dominated by Actinobacteriota (21-97%) and Ascomycota (60-97%), suggesting stable ecological organization despite the limited sample size. Environmental factors, such as pH, redox potential, and electrolytical conductivity, explained a substantial proportion of the variance in the microbial diversity and predicted functional traits. Overall, this study highlights traditional ripening cellars as semi-natural built ecosystems that sustain specialized, spatially structured microbiomes. The results provide new insights into microbial adaptation, functional potential, and ecological resilience in heritage food environments.}, }
@article {pmid41315430, year = {2025}, author = {Lynch, KF and Triplett, EW and Hyöty, H and Ahrens, AP and Laiho, JE and Petrosino, JF and Lloyd, RE and Agardh, D}, title = {Microbial associations and viruses on the risk of celiac disease (MAVRiC): a longitudinal post-hoc case-cohort study.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {42704}, pmid = {41315430}, issn = {2045-2322}, support = {R01 DK124581-01/NH/NIH HHS/United States ; 2022-00537//Swedish research Council, Sweden/ ; }, mesh = {Humans ; *Celiac Disease/virology/epidemiology/microbiology/immunology/etiology ; Female ; Male ; Longitudinal Studies ; Child, Preschool ; *Gastrointestinal Microbiome ; Autoantibodies/immunology ; Risk Factors ; Transglutaminases/immunology ; Child ; Autoimmunity ; Cohort Studies ; Glutens ; }, abstract = {Celiac disease etiopathogenesis requires genetic predisposition and exposure to gluten, yet these factors alone are not sufficient. Larger longitudinal studies are needed to determine the role of time-varying infections and gut microorganisms. The aim was to design a celiac disease case-cohort longitudinal study using The Environmental Determinants of Diabetes in the Young (TEDDY) study. By age 3-years, persistent tissue transglutaminase autoantibodies (tTGA), i.e., celiac disease autoimmunity (CDA), was confirmed in 704 of the 6132 genetically at-risk TEDDY children. Celiac disease onset (CD-onset) was defined as the age CDA developed when followed by a biopsy-proven diagnosis. A competing risk analysis on CD-onset and CDA children with no diagnosis (CDA-only) revealed female-sex, HLA and non-HLA genes and higher gluten-consumption correlate with an increased risk of both outcomes. However, reports of virus-related respiratory infections from August to October correlate consistently with an increased risk of CD-onset and not CDA-only. A sub-cohort of 561 children (9% sampling fraction) has been randomly selected to represent the TEDDY cohort. All incident CD-onset cases (N = 306) were included. The case-cohort will be utilized to analyze virus antibodies and bacteriome from longitudinal plasma and stool samples (the Microbial Associations and Viruses on the Risk of Celiac disease study, MAVRiC).}, }
@article {pmid41060580, year = {2025}, author = {Vega-Carranza, AS and Escamilla-Montes, R and Luna-González, A and Diarte-Plata, G and Fierro-Coronado, JA and García-Gutiérrez, C and Ceseña, CE}, title = {Investigating the effects of synbiotics, postbiotics and bacilli in the modulation of gut microbiota and the survival of Litopenaeus vannamei challenged with Vibrio parahaemolyticus.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {56}, number = {4}, pages = {2845-2854}, pmid = {41060580}, issn = {1678-4405}, abstract = {The effect of feed and water additives was evaluated on the gut microbiota and survival of white shrimp challenged with V. parahaemolyticus. Bacillus licheniformis BCR 4 − 3 and vibrio cultures were spray dried. Inulin, probiotics, and postbiotics of bacilli (SPB) and postbiotics of vibrios (PVp) were added to commercial feed. Viable bacilli cells were added to water. An experiment with four treatments in triplicate was performed to determine the effect of diet on survival and the intestinal microbiota by sequencing the V3 region of the bacterial 16S ribosomal gene. Metagenomic analysis was performed on the Shaman, MicrobiomeAnalyst, and Ivikodak platforms. The growth was not affected by the additives but survival of animals in treatments was significantly higher as compared to control group. The phyla and genera that predominated in the white shrimp intestine were Proteobacteria, Bacteroidetes, Firmicutes, Vibrio, Agarivorans, Tropicibacter, and Roseovarius. The Vibrio genus increased in treatments with bacilli in feed and water and decreased in PVp in feed. The control and treatments shared 219 Operational Taxonomic Units. No changes were observed in the bacterial diversity (richness and relative abundance of species). In the bacterial community of the shrimp intestine (species replacement) changes were observed. Bacterial functional profile (Lipid, amino acid, and energy metabolism and digestive and immune systems) was modulated in treatments. Synbiotics, postbiotics, and bacilli in water enhance survival rates and modulated the gut microbiota of L. vannamei.}, }
@article {pmid41315421, year = {2025}, author = {Thystrup, C and Gobena, T and Salvador, EM and Fayemi, OE and Kumburu, H and Buys, EM and Gichure, J and Moiane, BT and Belina, D and Hugho, EA and Faife, S and Ogunbiyi, TS and Akanni, G and Ayolabi, CI and Mmbaga, B and Thomas, KM and Pires, SM and Njage, PMK and Hald, T}, title = {Using metagenomics and whole-genome sequencing to characterize enteric pathogens across various sources in Africa.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-025-66400-9}, pmid = {41315421}, issn = {2041-1723}, support = {OPP1195617//Bill and Melinda Gates Foundation (Bill &amp; Melinda Gates Foundation)/ ; }, abstract = {Foodborne diseases (FBDs) remain a major public health concern in low- and middle-income countries (LMICs), with the African region carrying the heaviest burden globally. Surveillance efforts in these settings often overlook rural and resource-limited communities, limiting our understanding of pathogens transmission dynamics in these settings. In this study, we use whole-genome sequencing (WGS) and metagenomic approaches to characterize enteric pathogens from human, animal, and environmental sources across four African LMICs between 2019 and 2023. We analyze 446 bacterial isolates of Salmonella, Shigella, Escherichia coli, and Campylobacter, of which 380 high-quality genomes were subjected to phylogenetic and genotypic analyses. Additionally, 139 of 168 metagenomic samples pass quality control and were assessed for pathogen abundance and diversity. Our results reveal a geographically stable distribution of foodborne pathogens over time, suggesting persistent ecological or infrastructural factors influencing their maintenance. Genomic comparisons also identify closely related isolates across distinct sources and regions, pointing to potential transmission routes. These findings highlight the value of incorporating targeted environmental and food-chain sampling into surveillance strategies and demonstrate that metagenomic sequencing can serve as a practical and informative addition to WGS-based surveillance in resource-limited settings.}, }
@article {pmid41315331, year = {2025}, author = {Jiang, Y and Liu, J and Zhang, Y and Zhou, L and Kao, E and Hou, S and Niu, Q and Liu, Y and Xu, ZZ and Ding, T and Su, YX and Liu, Y and Zhang, G and Wang, X and Teng, F and Huang, S}, title = {High-resolution microbiome analysis of host-rich samples using 2bRAD-M without host depletion.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {223}, pmid = {41315331}, issn = {2055-5008}, support = {10212276//Health and Medical Research Fund/ ; 10212276//Health and Medical Research Fund/ ; 10212276//Health and Medical Research Fund/ ; 10212276//Health and Medical Research Fund/ ; 10212276//Health and Medical Research Fund/ ; ZR2024MH23//Natural Science Foundation of Shandong Province/ ; tsqn201909126//Taishan Scholar Award For Young Expert/ ; }, mesh = {Humans ; *Microbiota/genetics ; Saliva/microbiology ; *Metagenomics/methods ; *Bacteria/classification/genetics/isolation &amp; purification ; Mouth Neoplasms/microbiology ; Dental Caries/microbiology ; *Host Microbial Interactions ; *Sequence Analysis, DNA/methods ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/methods ; Child ; Child, Preschool ; }, abstract = {Characterizing human microbiota in host-dominated samples is crucial for understanding host-microbe interactions, yet is challenged by the high host DNA context (HoC). Current depletion strategies are limited by DNA loss and require immediate processing. In this paper, we introduce 2bRAD-M, a reduced metagenomic sequencing method that enables efficient host-microbe analysis without prior host depletion. Validated on mock samples with >90% human DNA, 2bRAD-M achieved over 93% in AUPR and L2 similarity. In both saliva and oral cancer samples, 2bRAD-M closely matched WMS profiles; in the former, it captured diurnal and host-specific patterns with only 5-10% of the sequencing effort. In an early childhood caries (ECC) study, 2bRAD-M identified key bacterial indicators and distinguished ECC from healthy subjects (AUC = 0.92). By providing high-resolution microbial profiles without host depletion, 2bRAD-M offers a practical and efficient solution for HoC-challenged microbiome research.}, }
@article {pmid41315266, year = {2025}, author = {He, X and Gu, L and Wang, D and Baer, M and Schaaf, G and Apostolakis, A and Meijide, A and Chen, X and Hochholdinger, F and Yu, P}, title = {Rhizosheath inhabiting Massilia are linked to heterosis in roots of maize.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {10777}, pmid = {41315266}, issn = {2041-1723}, support = {444755415//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, mesh = {*Zea mays/microbiology/genetics/growth &amp; development/metabolism ; *Hybrid Vigor/genetics ; *Plant Roots/microbiology/genetics ; Soil Microbiology ; Biomass ; Microbiota/genetics ; Flavonoids/metabolism ; Metabolomics ; Rhizosphere ; }, abstract = {Heterosis, or hybrid vigor, describes the superior performance of F1 hybrids compared to parental inbreds. While soil microbiomes are proposed to influence heterosis, it remains unclear how heterotic plants shape their microbiomes and how interactions relate to stress responses. Here, we investigate the role of rhizosheath formation-the soil tightly adhering to roots-in maize heterosis under nitrogen deprivation. Across sterilization, inoculation, and transplantation experiments, hybrids develop larger rhizosheaths than inbreds, and rhizosheath size associates with biomass heterosis. Rhizosheath-enriched genus Massilia correlates with lateral root density, rhizosheath size, and growth. Untargeted metabolomics and flavone-deficient mutants reveal links between Massilia and flavonoid pathways, while growth promotion by Massilia can also occur independently of host flavones. Metagenomic analysis shows that larger rhizosheaths recruit microbial functions related to nutrient cycling and stress adaptation. These findings identify rhizosheath formation as an integrative trait associated with heterosis and a promising target for breeding resilient crops.}, }
@article {pmid41315190, year = {2025}, author = {Worp, N and Nieuwenhuijse, DF and Izquierdo-Lara, RW and Schapendonk, CME and Brinch, C and Jensen, EEB and Munk, P and Hendriksen, RS and ,  and Aarestrup, F and Oude Munnink, BB and Koopmans, MPG and de Graaf, M}, title = {Unveiling the global urban virome through wastewater metagenomics.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {10707}, pmid = {41315190}, issn = {2041-1723}, support = {874735//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Societal Challenges | H2020 Health (H2020 Societal Challenges - Health, Demographic Change and Well-being)/ ; }, mesh = {*Wastewater/virology ; *Metagenomics/methods ; *Virome/genetics ; Humans ; *Viruses/genetics/classification/isolation &amp; purification ; Cities ; Animals ; Metagenome ; }, abstract = {Understanding global viral dynamics is critical for public health. Traditional surveillance focuses on individual pathogens and symptomatic cases, which may miss asymptomatic infections or newly emerging viruses, delaying detection and response. Wastewater-based epidemiology has been used to track pathogens through targeted molecular assays, but its reliance on predefined targets limits detection of the full viral spectrum. Here, we analyse longitudinal wastewater samples from 62 cities across six continents (2017-2019) using metagenomics and capture-based sequencing with probes targeting viruses associated with gastrointestinal disease. We detect over 2500 viral species spanning 122 families, many with human, animal, or plant health relevance. The bacteriophage family Microviridae and plant virus family Virgaviridae dominate the metagenomic dataset, while Astroviridae and Picornaviridae prevail in the capture-based sequence dataset. Virus distributions are broadly similar across continents at the family and genus levels, yet distinct city-level fingerprints reveal geographical and temporal variation, enabling spatiotemporal surveillance of viruses such as astroviruses and enteroviruses. Global wastewater-based epidemiology enables early detection of emerging viruses, including Echovirus 30 in Europe and Tomato brown rugose fruit virus. These findings highlight the potential of wastewater sequencing for the early detection of emerging viruses and population-wide virome monitoring across diverse hosts.}, }
@article {pmid41314968, year = {2025}, author = {Li, YX and Wang, RY}, title = {Autoimmune glial fibrillary acidic protein astrocytopathy following human herpesvirus-7 infection: a case report.}, journal = {Brain injury}, volume = {}, number = {}, pages = {1-4}, doi = {10.1080/02699052.2025.2596225}, pmid = {41314968}, issn = {1362-301X}, abstract = {OBJECTIVE: Human herpesvirus-7 encephalitis (HHV7E) is exceedingly rare in immunocompetent adults, and the subsequent development of autoimmune glial fibrillary acidic protein astrocytopathy (GFAP-A) following HHV7E is even rarer. We present the inaugural Chinese case of GFAP-A triggered by HHV7E, confirmed via metagenomic next-generation sequencing (mNGS).<br><br>RESULTS: A 37-year-old male initially presented with fever and significant memory impairment. Brain magnetic resonance imaging (MRI) revealed T2/fluid-attenuated inversion recovery (FLAIR) hyperintensity in the right temporal lobe. The diagnosis of HHV7E was confirmed by the detection of HHV7 in the cerebrospinal fluid (CSF) via mNGS. His symptoms improved significantly following acyclovir treatment. However, five weeks post-discharge, he experienced acute neurological deterioration, with symptoms including bifrontal headaches, vomiting, memory impairment, and visual hallucinations. Repeat brain MRI revealed new bilateral punctate and patchy T2/FLAIR hyperintensities in the periventricular white matter. Contrast-enhanced MRI demonstrated bilateral linear radial perivascular enhancements. A cell-based assay detected GFAP antibodies in CSF at a titer of 1:100, establishing a diagnosis of postinfectious GFAP-A. The patient responded well to combined intravenous steroid and immunoglobulin therapy.<br><br>CONCLUSIONS: This case highlights the importance of considering autoimmune encephalitis in patients with new or recurrent neurological symptoms after HHV7E recovery. Systematic mNGS and neuronal antibody testing are essential for timely diagnosis, and early aggressive immunotherapy may improve outcomes in post-HHV7E GFAP-A.}, }
@article {pmid41314430, year = {2025}, author = {Gabbay, U and Carmi, D}, title = {The Paradox of Rapid and Synchronized Propagation of Seasonal Influenza 'A' Outbreaks in Contrast with COVID-19: a Testable Hypothesis.}, journal = {Virus research}, volume = {}, number = {}, pages = {199670}, doi = {10.1016/j.virusres.2025.199670}, pmid = {41314430}, issn = {1872-7492}, abstract = {Seasonal influenza A virus (SIAV) apparently exhibits a paradoxical pattern: despite a lower basic reproduction number (R0) than SARS-CoV-2, it propagates across the Northern Hemisphere with remarkable speed and synchronicity. We propose a testable hypothesis, developed in two conceptual steps to explain this phenomenon. First, we discuss what may explain the rapid, near-synchronous propagation of SIAV seasonal outbreak. We suggest that it may result from parallel seeding from multiple sources, rather than emerging from a singular origin, as observed with COVID-19. Second, we examined potential mechanisms for parallel seeding. The hypothesis is testable through genomic and metagenomic methods. Sequencing viruses from humans and migratory birds across regions may be evaluated to reveal identical viral lineages. The hypothesis may highlight the potential role of ecological reservoirs in global influenza propagation dynamics. If validated, this framework would advance understanding of influenza seasonality and may guide integrated surveillance strategies linking avian ecology with human epidemiology.}, }
@article {pmid41314145, year = {2025}, author = {Li, X and Lin, X and Dong, Z and Zhou, R and Niu, Q}, title = {Biomass ratio regulates methane conversion and carbon fixation in a methanotrophs-microalgae symbiotic system: Efficiency optimization and mechanisms driven by co-metabolism.}, journal = {Water research}, volume = {290}, number = {}, pages = {125016}, doi = {10.1016/j.watres.2025.125016}, pmid = {41314145}, issn = {1879-2448}, abstract = {The methanotrophs-microalgae symbiotic system for greenhouse gas treatment is a novel biological carbon fixation technology. However, practical applications are limited by low conversion efficiency, which arises from metabolic heterogeneity in growth rates and carbon-nitrogen resource utilization within the system. To improve metabolic stability of such symbiotic systems, this study systematically assessed CH4 metabolic fluxes by regulating the methanotrophs-microalgae biomass ratio, and further revealed synergistic mechanisms that enhance system stability. Experimental results indicated that at a methanotrophs to microalgae ratio of 1:5, the CH4 consumption rate peaked at 1.1 L CH4/d/g biomass. The extended Derjaguin-Landau-Verwey-Overbeek (XDLVO) theory and the laser confocal revealed that the co-aggregation force of methanotrophs and microalgae was significantly enhanced at the optimal ratio. This enhancement was crucial for regulating the spatial mutualistic growth and metabolic interactions within the methanotrophs-microalgae symbiotic community. Structural equation modeling (SEM) indicated that poly-β-hydroxybutyrate (PHB) exerts a significant negative effect on methane consumption (-0.68***). Metagenomics results indicated that at the optimal methanotrophs-microalgae ratio, the relative abundance of genes associated with the methane oxidation center metabolic pathway increased by 1.38 times. This significantly enriched Type I methanotrophs (1.89 times) and Type II methanotrophs (1.51 times), while the relative abundance of genes involved in the PHB production pathway decreased by 16 %. This change accelerated the conversion and assimilation of methane carbon, ultimately improving the carbon fixation efficiency by 16 %. This study provided theoretical foundations and technical support for advancing the engineering application of methanotrophs and microalgae symbionts to achieve efficient, stable methane conversion and simultaneous carbon sequestration.}, }
@article {pmid41314069, year = {2025}, author = {Kumari, SP and Hooda, S and Diwan, P and Gupta, RK}, title = {Seasonal variations and functional insights into the urban air microbiome across public transit environments at railway stations in Delhi, India.}, journal = {The Science of the total environment}, volume = {1009}, number = {}, pages = {181062}, doi = {10.1016/j.scitotenv.2025.181062}, pmid = {41314069}, issn = {1879-1026}, abstract = {Airborne microbial communities play an underappreciated yet critical role in shaping urban environmental health, particularly in densely crowded public transit systems. This study aimed to explore the taxonomic and functional landscape of airborne bacteria, highlighting the seasonal disparities across summer and autumn seasons, in the public transit air (railway stations) of Delhi, a populated megacity characterized by extreme pollution levels and one of the world's busiest railway networks. Metagenomic analyses revealed distinct seasonal signatures in microbial community composition and diversity. Alpha diversity was higher during autumn, though not statistically significant, while beta diversity differed significantly between seasons. LEfSe analysis identified season-specific indicator taxa, including Moraxella, Barrientosiimonas, Methylobacterium, for autumn and Stutzerimonas, Caulobacter, Pseudomonas for summer, representing a mix of opportunistic pathogens and environmentally significant taxa. Correlation networks highlighted distinct seasonal clustering patterns. Resistome and virulome profiling revealed the presence of different resistance gene classes and virulence factor categories in abundance. Correlation networks uncovered significant associations between specific genes and bacterial genera, suggesting ecological partitioning in gene carriage. Temperature and air quality index explained a part of the variance observed in the taxonomic and functional dynamics. Metagenome-assembled genomes captured seasonally distinct taxa, and biosynthetic gene cluster screening identified 317 gene clusters, including terpene, RiPP-like, and hserlactone clusters. The findings underscore the ecological complexity and public health relevance of airborne bacteria and raise concerns about their potential role in microbial transmission and long-term respiratory health risks. These insights are crucial for public health surveillance, urban air quality management, and guiding future investigations into the microbial safety of urban environments.}, }
@article {pmid41313993, year = {2025}, author = {Zheng, Y and Crowther, TW and Qin, Y and Lei, J and Xu, M and Xu, Y and Chu, H and Wu, Q and Shi, Y}, title = {Liquor fermentation industry reshapes soil microbiomes and drives CO2 emissions via microbial dispersal.}, journal = {Journal of environmental management}, volume = {396}, number = {}, pages = {128135}, doi = {10.1016/j.jenvman.2025.128135}, pmid = {41313993}, issn = {1095-8630}, abstract = {The rapid expansion of industrial fermentation has raised concerns about its environmental impacts, particularly regarding microbial dispersal from production facilities into adjacent terrestrial ecosystems; however, the ecological and functional consequences of microbial introductions originating from fermentation facilities remain poorly elucidated. We studied eight Chinese liquor fermentation facilities spanning 26°-47°N and 83°-124°E, covering the major geographical range of the industry. Using large-scale soil metagenomics, in situ CO2 flux measurements, and microcosm experiments, we demonstrate that industrial fermentation significantly alters local soil microbial communities and enhances carbon decomposition potential. The results showed that soil carbon decomposition genes increased 13.6 % around fermentation facilities. Biologically, the fermentation process at the facilities introduced microorganisms into soil, such as Actinobacteria, whose abundance increased by 2.8 %. These microorganisms directly increased the abundance of carbon decomposition genes in the soil, while Actinobacteria also enhance soil carbon decomposition capacity by reducing microbial α diversity. Abiotically, the soil total carbon increased by 3-89 % around facilities, thereby enriching carbon decomposition genes. These soil microbial activities changed by fermentation facilities lead to an increase in soil CO2 emissions. Our study provides the first evidence that industrial fermentation facilities inadvertently modify soil microbial community and function. These findings establish a critical link between fermented food production systems and terrestrial carbon emissions, with important implications for sustainable fermentation practices and climate-smart industrial planning.}, }
@article {pmid41313912, year = {2025}, author = {Li, Y and Tang, C and Qin, X and Qin, W and Fu, Y and Shi, D and Lan, W and Tang, Y and Wu, R and Yu, F}, title = {Rhizosphere nutrient dynamics and physiological responses of Oryza sativa L. under polyethylene terephthalate microplastic stress.}, journal = {Plant physiology and biochemistry : PPB}, volume = {229}, number = {Pt E}, pages = {110797}, doi = {10.1016/j.plaphy.2025.110797}, pmid = {41313912}, issn = {1873-2690}, abstract = {Polyethylene terephthalate microplastics (PET-MPs), as emerging environmental contaminants, pose growing threats to agricultural ecosystems. This study investigated the impacts of PET-MPs on key physiological traits of Oryza sativa L. and the abundance of functional genes involved in carbon (C), nitrogen (N), and phosphorus (P) cycling within rhizosphere soils. Results demonstrated that PET-MPs were absorbed by rice roots and translocated to aerial tissues, significantly inhibiting chlorophyll biosynthesis (p < 0.05). Exposure to PET-MPs induced oxidative stress, with the 2.5 g kg[-1] treatment elevating root malondialdehyde levels by 175.3 %, and reducing plant height and biomass by 15.8 % and 44.6 %, respectively. Metagenomic analysis revealed a marked increase in the denitrification gene narI, while genes associated with C fixation (korB, korA), methanogenesis (mch), organic N metabolism (glnA), and P transport (ugpC) were significantly suppressed, indicating disruptions to soil nutrient cycling. Actinomycetota and Pseudomonadota were identified as predominant microbial hosts of these functional genes. Pearson correlation analysis showed significant positive associations (p < 0.05) between plant growth parameters and the abundance of korA, korB, IDH1, mch, glnA, and ugpC. These findings advance our understanding of the ecological risks posed by PET-MPs in terrestrial environments and underscore their potential to compromise soil fertility and sustainable rice production.}, }
@article {pmid41313659, year = {2025}, author = {Sun, W and Pan, J and Gao, X}, title = {Research on the influence mechanism of low-temperature storage on nitrifying bacteria.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {92}, number = {10}, pages = {1426-1440}, pmid = {41313659}, issn = {0273-1223}, support = {2022JH1/10800006//Science and Technology Program of Guizhou Province/ ; }, mesh = {*Nitrification ; *Bacteria/metabolism/genetics ; Sewage/microbiology ; *Cold Temperature ; Nitrites/metabolism ; Ammonia/metabolism ; Waste Disposal, Fluid/methods ; Oxidation-Reduction ; }, abstract = {To develop a more cost-effective nitrogen removal strategy, this study investigated the impact of low-temperature storage methods on nitrifying bacterial activity. Sludge was stored under laboratory-scale static batch conditions in three media: (1) distilled water, (2) nutrient solution, and (3) nutrient solution supplemented with hydroxylamine (NH2OH). Ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) activity, sludge properties, and microbial characteristics were examined. Results revealed that all storage methods inhibited both AOB and NOB activity. Notably, nutrient solution storage demonstrated the most significant effect: it suppressed NOB activity by 86.6% and reduced its relative abundance by 20%, while maintaining high extracellular polymeric substance content (43.5 mg/g VSS) and AOB relative abundance (0.18%). This method substantially shortened the required storage duration (from 8 months to 60 days) and better preserved AOB activity and sludge stability. Metagenomic analysis indicated strong inhibition of the NOB functional gene nitrite oxidoreductase across all methods, while nutrient solution storage specifically elevated the abundance of the AMO gene. Although NH2OH supplementation exhibited inhibitory effects on microorganisms, the concurrent addition of nutrient solution effectively mitigated this impact. Consequently, sludge properties and functional microbiota abundance showed no significant difference between the NH2OH-supplemented nutrient solution method and distilled water storage.}, }
@article {pmid41313651, year = {2025}, author = {Zhang, Q and Jiang, X and Xi, Y and Ma, X and Zhang, W}, title = {Complete genome sequences of two Cressdnaviricota viruses identified in respiratory tract samples from forest musk deer in China.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0063225}, doi = {10.1128/mra.00632-25}, pmid = {41313651}, issn = {2576-098X}, abstract = {We identified two circular single-stranded DNA viruses from forest musk deer in China through metagenomic analysis. Phylogenetic results suggest they represent unclassified Cressdnaviricota lineages. This study highlights the diversity of the deer's respiratory virome and underscores the importance of wildlife virus surveillance for conservation and public health.}, }
@article {pmid41313537, year = {2025}, author = {Vishwakarma, RK and Gautam, P and Sahu, M and Nath, G and Yadav, BS}, title = {Gut Microbiome in Obesity: A Narrative Review of Mechanisms, Interventions, and Future Directions.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {41313537}, issn = {1867-1314}, abstract = {Obesity has reached pandemic levels worldwide and is increasingly recognized as a multifactorial condition beyond excess caloric intake and sedentary lifestyle. Accumulating evidence emphasizes that the gut microbiota (GM), primarily composed of Firmicutes and Bacteroidetes, plays a crucial role in regulating energy balance, immune response, and host metabolism. Gut dysbiosis, characterized by reduced microbial diversity and altered phylum-level composition and shifts toward commonly observed higher Firmicutes-to-Bacteroidetes ratios (although this finding is inconsistent across studies), contributes to enhanced energy harvest, systemic inflammation, and metabolic dysfunction. Key mechanisms involve GM production of short-chain fatty acids (SCFAs) and modulation of hormonal signals, including leptin, ghrelin, insulin, GLP-1, and PYY, alongside interactions via the gut-brain axis. These pathways link microbial composition to appetite regulation, fat storage, and energy balance. Emerging microbiome-targeted therapies, such as probiotics, prebiotics, dietary modulation (e.g., fiber-rich diets), fecal microbiota transplantation, and bacteriophage therapy, show promise in restoring GM balance, promoting weight loss, and improving metabolic health, though results vary and require further validation. Despite advances in metagenomics and metabolomics, gaps persist in establishing causality and long-term efficacy. The integration of GM data with host genetics, diet, and environmental factors through systems biology has the potential to facilitate personalized management of obesity. This review synthesizes the GM's role in obesity pathogenesis and hormonal regulation, highlighting therapeutic potential and research directions for microbiota-based prevention and treatment.}, }
@article {pmid41313246, year = {2025}, author = {Rigonato, J and Lozano, JC and Vergé, V and Jaillon, O and Bouget, FY}, title = {Latitudinal Diversity in Circadian and Light-Sensing Genes in an Ecologically Vital Group of Marine Picoeukaryote Algae.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf263}, pmid = {41313246}, issn = {1751-7370}, abstract = {Organismal life cycles are influenced by Earth's rotation and orbit, generating daily and seasonal light cycles that vary with latitude, especially in temperate and polar zones. Photoperiodism relies on organisms' ability to measure time via the circadian clock and detect light through specific photoreceptors. Molecular basis of photoperiodism is well-characterized in plants, but photoperiod adaptation in phytoplankton remain largely unexplored. Here, we investigated circadian clock components, photoreceptors, and associated effectors in eukaryote picoalga species from Ostreococcus, Bathycoccus, and Micromonas. We showed that the investigated species shared a conserved set of homologous circadian clock-related genes that appeared in the early evolution of Mamielalles order. Furthermore, gene duplication events account for the specific occurrences and uneven gene copy numbers among these genera. Through metagenomic and metatranscriptomic analyses, we assessed the gene expression profiles of candidate photoperiod-related genes across the global ocean. Our findings reveal an unexpected diversity in photoreceptors, particularly within Micromonas, and highlight the CCT domain family, a key group of transcription factors governing circadian rhythms (TOC1 family) and photoperiodism (CONSTANS family) in plants. TOC1, a central component of the circadian clock in Ostreococcus tauri, is either absent or truncated in tropical species. Functional assays further indicate that the TOC1/CCA1 oscillator is non-functional in the tropical strain of Ostreococcus sp. RCC809. These results imply that certain circadian mechanisms may be dispensable at low latitudes, underscoring the diversity of photoperiod adaptations in marine phytoplankton. These results provide valuable insights into the molecular evolution of cosmopolitan plankton groups, particularly their mechanisms of local adaptation.}, }
@article {pmid41313177, year = {2025}, author = {Hoque, MN and Rahman, MS}, title = {Bacteriome and resistome dysbiosis in subclinical mastitis and antibiotic-treated milk of dairy cows.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0107025}, doi = {10.1128/mra.01070-25}, pmid = {41313177}, issn = {2576-098X}, abstract = {Shotgun metagenomics revealed distinct bacteriome profiles in subclinical mastitis, antibiotic-treated, and healthy cow milk, with enriched resistance repertoires in diseased and treated samples. Findings highlighted the need for better diagnostics, precision antimicrobial use, and antibiotic alternatives to ensure milk safety and address antimicrobial resistance in dairy farming.}, }
@article {pmid41313018, year = {2025}, author = {Wang, K and Wang, H and Zhao, Z and Shen, X and Zhao, J and Zhang, H}, title = {Bifidobacterium animalis subsp. lactis Probio-M8 enhances chondroitin efficacy for knee osteoarthritis in postmenopausal women via the gut-joint axis.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0086225}, doi = {10.1128/msystems.00862-25}, pmid = {41313018}, issn = {2379-5077}, abstract = {UNLABELLED: Knee osteoarthritis (KOA) is a chronic joint disease marked by cartilage degradation and inflammation. Probiotics exhibit anti-inflammatory properties and may influence the gut-joint axis. Thus, a 4-month human trial was conducted to assess the adjunctive effects of Bifidobacterium animalis subsp. lactis Probio-M8 on KOA in postmenopausal women. Sixty-five KOA patients were randomly allocated to the probiotic group (n = 37; Probio-M8 and chondroitin sulfate) or placebo group (n = 28; placebo and chondroitin sulfate). Following a 3-month intervention, participants from both groups entered a 1-month observation without probiotic supplementation. Our findings revealed that Probio-M8 co-administration significantly reduced Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) scores at months 1, 3, and 4 compared to the placebo group (P < 0.001). The probiotic group showed a significant decrease in serum IFN-γ and increases in IL-4 and IL-10 (P < 0.05). Fecal metagenome analysis showed significant changes in the gut microbiota of the probiotic group, with increases in potentially beneficial species, including Agathobaculum butyriciproducens, Bacteroides stercoris, B. animalis, Roseburia hominis, and Ruminococcus bromii, while Dorea formicigenerans decreased (P < 0.05). Changes in B. animalis were strongly associated with WOMAC scores. The gut metabolic potential analysis showed elevated levels of N-oleoylethanolamine and decreased levels of cholesterol and hypoxanthine in probiotic receivers (P < 0.05). Metabolite analysis revealed post-interventional alternations in fecal prostaglandin E2, stearic acid, cholic acid, chenodeoxycholic acid, xanthine, testosterone, and serum bile acids (P < 0.05). Collectively, Probio-M8 enhances the effectiveness of chondroitin sulfate in KOA management through modulating the gut-joint axis, potentially via regulating multiple inflammatory pathways.<br><br>IMPORTANCE: The pathogenesis of knee osteoarthritis (KOA) and its phenotypic expression have been associated with the human gut microbiota. Our study demonstrated that the co-administration of Probio-M8 with chondroitin sulfate significantly alleviates KOA symptoms. This probiotic intervention enhances therapeutic efficacy through modulation of the gut microbiota and associated metabolic pathways, reducing inflammation and improving clinical outcomes. Our results underscore the potential of probiotic-driven therapies as an adjunctive treatment strategy and underscore the importance of the gut-joint axis in KOA management.}, }
@article {pmid41313013, year = {2025}, author = {Babb, PL and Akhund-Zade, J and Spacek, D and Brick, K and Christians, FC and Portnoy, V and Tsai, M-S and Jarman, KH and Bercovici, S and Vilfan, ID and Blauwkamp, TA}, title = {In-matrix library preparation for metagenomic sequencing of microbial cell-free DNA.}, journal = {Journal of clinical microbiology}, volume = {}, number = {}, pages = {e0094425}, doi = {10.1128/jcm.00944-25}, pmid = {41313013}, issn = {1098-660X}, abstract = {Metagenomic sequencing of microbial cell-free DNA (mcfDNA) enables comprehensive identification and quantification of diverse pathogens from blood and other biofluids. This approach enables minimally invasive diagnosis of deep-seated infectious disease, provides culture-free identification of antimicrobial resistance, and powers the discovery of novel microbial biomarkers for disease. However, widespread implementation of this approach is limited by lengthy and complex workflows, high host background cfDNA leading to high sequencing costs, and prevalent environmental DNA contamination risks. Addressing these barriers is critical for scalable deployment in both centralized and decentralized settings. To overcome these limitations, we developed Karius Helion-4 Chemistry (Helion-4), an in-matrix (DNA extraction-free) sample-to-DNA sequencing library workflow, to serve as a platform for mcfDNA sequencing applications in infectious disease, microbiome analyses, and disease biomarker discovery. We compared Helion-4 to two widely used metagenomic extraction-based sequencing workflows, as well as to the prior Karius chemistry platform (Digital Culture-3), using 36 clinical plasma specimens. Helion-4 enables end-to-end sequencing library construction for up to 96 samples in 5.25-6.1 h, including setup and final quality control evaluation, with 2.25 h of hands-on time when using automated liquid handling robots. Compared to the other methods, Helion-4 recovered 58-fold to 817-fold more endogenous mcfDNA per volume of plasma, while simultaneously demonstrating 1.8-fold to 6-fold lower exogenous background DNA contamination, likely due to the absence of DNA extraction. The fraction of mcfDNA reads among total reads was enriched by 60-fold to 164-fold for Helion-4 compared to current state-of-the-art methods, significantly lowering sequencing costs required for applications built on the Helion-4 platform vs other platforms. Collectively, these advances enable routine processing of small specimen volumes and provide a simple, efficient, and scalable approach for mcfDNA sequencing applications.IMPORTANCEMetagenomic sequencing of microbial cell-free DNA (mcfDNA) enables the identification and quantification of diverse pathogens from blood and other biofluids, providing minimally invasive and rapid diagnosis of deep-seated infectious disease. However, widespread implementation of this approach is limited by complex workflows, high sequencing costs, and prevalent contamination risks. Karius Helion-4 Chemistry, the first in-matrix (DNA extraction-free) sample-to-DNA sequencing library workflow, overcomes these limitations. Compared to the other methods, Helion-4 is faster, cleaner, and more sensitive. Helion-4 recovered up to 817-fold more endogenous mcfDNA per volume of plasma, while simultaneously demonstrating up to sixfold lower exogenous background DNA contamination. The fraction of mcfDNA reads among total reads was enriched by up to 164-fold for Helion-4, lowering sequencing costs. These advances by Helion-4 technology enable a simple, efficient, and scalable approach for mcfDNA sequencing applications and bring us closer to widespread, high-resolution, and real-time microbial profiling across diverse healthcare settings.}, }
@article {pmid41312992, year = {2025}, author = {D'Amico González, G and Rodríguez, MM and Penzotti, P and Brunetti, F and Ghiglione, B and Moe, LA and Centrón, D and Gutkind, G and Gao, L and Haider, S and Powers, RA and Klinke, S and Power, P}, title = {Proposal of metagenomic-origin LRA-5 as a precursor of active β-lactamases through Tyr69Gln and Val166Glu amino acid substitutions: a functional and structural analysis.}, journal = {Antimicrobial agents and chemotherapy}, volume = {}, number = {}, pages = {e0067525}, doi = {10.1128/aac.00675-25}, pmid = {41312992}, issn = {1098-6596}, abstract = {Wild-type LRA-5, recovered from Alaskan soil samples, shares no more than 33% amino acid sequence identity with enzymes from pathogens like PER β-lactamases. Recombinant E. coli expressing wild-type LRA-5 and its engineered variants LRA-5[Y69Q] and LRA-5[V166E] showed MIC values equivalent to control strains. However, LRA-5[Y69Q/V166E] displayed MICs above the resistant breakpoint for some β-lactams. Kinetic parameters correlated with the MICs, showing that the catalytic efficiency of LRA-5[Y69Q/V166E] was comparable to those from class A β-lactamases, such as CTX-M-15, PER-2, and KPC-2. LRA-5[Y69Q/V166E] exhibited kcat/Km values up to 11,000-fold higher compared to wild-type LRA-5, which is associated with the presence of Glu166. The X-ray crystallographic structure of wild-type LRA-5 (1.80 Å; PDB 8EO5) shows that the lack of both Glu166 and a deacylation water molecule contributes to a biologically insignificant activity. Interactions observed between LRA-5 and ceftazidime (2.35 Å; PDB 8EO6) show structural conservation with other β-lactamases. In contrast, the crystallographic structure of LRA-5[Y69Q/V166E] (2.15 Å; PDB 8EO7) bears a deacylation water molecule that is associated with the increase in catalytic activity compared to the wild-type variant. Circular dichroism results confirm that amino acid substitutions in LRA-5 do not affect the overall content of the secondary/tertiary structures. Evidence suggests that alternative evolutionary paths could have occurred for β-lactamases like LRA-5, produced by environmental microorganisms: (i) proteins having similar structural features than active β-lactamases may accumulate a small number of mutations (e.g., Y69Q/V166E) to yield active enzymes and (ii) the β-lactamase fold may have lost key residues in the absence of antibiotics.}, }
@article {pmid41312680, year = {2025}, author = {Koike, Y and Morisaki, H and Motooka, D and Matsumoto, M and Takenaka, M and Murota, H}, title = {Postauricular Skin Mycobiome Profiles in Atopic Dermatitis Treated With Dupilumab or Cyclosporine A: A Descriptive Case Series.}, journal = {The Journal of dermatology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1346-8138.70083}, pmid = {41312680}, issn = {1346-8138}, support = {//Leading Medical Research Core Unit, Life Science Innovation, Nagasaki University Graduate School of Biomedical Sciences/ ; 25K11567//Japan Society for the Promotion of Science/ ; JP256f0137009//Japan Agency for Medical Research and Development/ ; }, abstract = {Atopic dermatitis (AD) essentially exhibits dysbiosis of skin fungal microbiome, mycobiome, characterized by depletion of Malassezia. The effects of recent systemic therapies for AD on skin mycobiome were not understood enough. We examined changes of skin mycobiome before and after systemic treatments with anti-IL-4Rα antibody (dupilumab: DUP) and calcineurin inhibitor (cyclosporine, CyA). Swab samples from postauricular areas in 19 AD patients treated with dupilumab (n = 13) and cyclosporine (n = 6) were collected before and 4-8 weeks after starting each treatment. Fungal DNA was amplified from the samples and sequenced with ITS1 metagenomic analysis, and taxonomic classification was performed. Fungi belonging to total 89 genera were detected. The share of the fungus was most occupied by Malassezia (81.3%), followed by Aspergillus (3.7%), and Trametes (1.1%) before DUP and CyA treatment, and occupied by Malassezia (87.3%), followed by Aspergillus (1.9%), and Candida (1.7%) after treatment. Three AD patients whose ratio of Malassezia in the skin mycobiome was under 50%, showed an exploratory increase of Malassezia after treatments (before 17.3%, after 67%). Analysis of the Malassezia species revealed an increase in M. restricta (before 70.5%, after 79.5%) and a decrease in M. globosa (before 23.9%, after 16.1%). No consistent patterns distinguishing DUP and CyA were observed. Systemic treatment with DUP and CyA was associated with shifts toward higher Malassezia abundance and modulation between M. restricta and M. globosa. These findings are exploratory and require validation in larger controlled studies.}, }
@article {pmid41312645, year = {2025}, author = {Fiamenghi, MB and Camargo, AP and Chasapi, IN and Baltoumas, FA and Roux, S and Egorov, AA and Aplakidou, E and Ndela, EO and Vasquez, YM and Chen, IA and Palaniappan, K and Reddy, TBK and Mukherjee, S and Ivanova, NN and Schulz, F and Woyke, T and Eloe-Fadrosh, EA and Pavlopoulos, GA and Kyrpides, NC}, title = {Meta-virus resource (MetaVR): expanding the frontiers of viral diversity with 24 million uncultivated virus genomes.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkaf1283}, pmid = {41312645}, issn = {1362-4962}, support = {DE-AC02-05CH11231//US DOE/ ; FWP 70880//BER's Genomic Sciences Program/ ; 1U01DE034196-01/GF/NIH HHS/United States ; //Hellenic Foundation for Research and Innovation/ ; //Royal Physiographic Society of Lund/ ; 45379//Natural Sciences, Medicine and Technology/ ; }, abstract = {Viruses are ubiquitous in all environments and impact host metabolism, evolution, and ecology, although our knowledge of their biodiversity is still extremely limited. Viral diversity from genomic and metagenomic datasets has led to an explosion of uncultivated virus genomes (UViGs) and the development of specialized databases to catalog this viral diversity, though many lack comprehensive integration. Here, we introduce meta-virus resource (MetaVR), the successor of the IMG/VR database, designed to overcome previous limitations such as large-scale querying and programmatic access. Drawing on the increase of publicly available genomes and metagenomes, MetaVR significantly expands viral diversity, now comprising 24,435,662 UViGs, a 57.6% increase from its predecessor, organized into over 12 million viral operational taxonomic units. Key enhancements include the integration of curated eukaryotic host information, the integration of protein clusters and predicted structures for comparative studies, and an API for programmatic data access. Furthermore, MetaVR features an updated taxonomic framework based on ICTV release 39, assignment to Baltimore classes, and enhanced host assignment through novel computational tools like iPHoP. These advancements position MetaVR as a unique resource for exploring viral diversity, evolution, and host interactions across diverse environments. MetaVR can be freely accessed at https://www.meta-virome.org/.}, }
@article {pmid41312456, year = {2025}, author = {Huang, W and Ran, X and Zhang, Z and Yang, L and Yin, J and Lv, S and Liu, G and Pei, Y}, title = {Multiple brain abscesses caused by Nocardia asiatica co-infection with Torque teno virus in an "immunocompetent" patient: a rare case report and literature review.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1661345}, pmid = {41312456}, issn = {2296-858X}, abstract = {Brain abscess is a suppurative infection of brain tissue caused by one or more pathogens under specific susceptible conditions and is associated with a high clinical fatality rate. Beyond surgical intervention, the identification of pathogens is key to clinical antimicrobial therapy, yet this remains a challenge. Nocardia is a ubiquitous bacterium that typically manifests as an opportunistic infection, primarily affecting immunocompromised individuals. Pulmonary involvement, characterized by suppurative inflammation, commonly occurs following inhalation, with subsequent hematogenous dissemination potentially leading to widespread infection. To our knowledge, central nervous system (CNS) infection by Nocardia asiatica (N. asiatica) resulting in brain abscess has hitherto rarely been reported. We present a rare case of multiple brain abscesses caused by N. asiatica co-infection with Torque teno virus (TTV) in an immunocompetent patient with suspected multiple organ involvement. The patient was admitted to our hospital, presenting with a headache, and imaging revealed brain abscess-like lesions. A robot-assisted stereotactic puncture and drainage were used for abscess removal. N. asiatica and TTV were identified by metagenomic next-generation sequencing (mNGS) of the brain abscess aspirate, with N. asiatica subsequently confirmed by mass spectrometry of the cultured organism. A disseminated Nocardia infection was suspected based on the patient's skin trauma history, pulmonary inflammatory changes, and imaging findings (liver cysts, subcutaneous nodules). However, etiological confirmation was not obtained prior to his death. While this is not the first reported instance of Nocardia and TTV co-infection in brain abscesses, our case is notable for its occurrence in an immunocompetent patient. This report highlights the significance and value of TTV in the context of brain abscesses and warrants a re-evaluation of Nocardia and TTV co-infection. Given that the diagnosis of intracranial infection depends on the detection of pathogens, we advocate for the routine and early implementation of mNGS testing in patients with brain abscesses. Moreover, systemic nutritional support and immunomodulatory therapies should be considered in the early stage of treatment for complex cases. Earlier diagnosis and treatment in this case might have altered the patient's outcome.}, }
@article {pmid41312302, year = {2025}, author = {Steindler, L and Maldonado, M and Pita, L and Riesgo, A and Erpenbeck, D and Hentschel, U and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and ,  and ,  and ,  and ,  and , }, title = {The chromosomal genome sequence of the stone sponge Petrosia ficiformis (Poiret, 1789) and its associated microbial metagenome sequences.}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {450}, pmid = {41312302}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual Petrosia ficiformis (stone sponge; Porifera; Demospongiae; Haplosclerida; Petrosiidae). The genome sequence is 191.3 megabases in span. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 18.89 kilobases in length. Gene annotation of the host organism assembly identified 18,339 protein coding genes. The metagenome of the specimen was also assembled, and 112 binned bacterial genomes were identified, including 57 high-quality MAGs. Besides MAGs characteristic of HMA sponge symbionts (i.e., Chloroflexota, Acidobacteriota), the P. ficiformis specific symbiont Candidatus Synechococcus feldmanni (formerly Aphanocapsa feldmanni (Cyanobacteriota) was recovered, as well as notably MAGs of several candidate phyla (Candidatus Latescibacteria, Poribacteria, Tectomicrobia, Dadabacteria, Kapabacteria and Binatia).}, }
@article {pmid41312195, year = {2025}, author = {Chen, J and Gong, G and Huang, S and Chen, Y and Yang, S and Shen, Q and Wang, X and Wu, P and Liu, Y and Ji, L and Zhang, W}, title = {Gut Virome of Tibetan Pigs Reveals the Diversity, Composition, and Distribution of Potential Novel Viruses/Variants.}, journal = {Transboundary and emerging diseases}, volume = {2025}, number = {}, pages = {5191656}, pmid = {41312195}, issn = {1865-1682}, mesh = {Animals ; Swine ; Tibet/epidemiology ; *Virome ; Phylogeny ; *Swine Diseases/virology/epidemiology ; Feces/virology ; *Viruses/classification/genetics/isolation &amp; purification ; Metagenomics ; Genetic Variation ; *Gastrointestinal Microbiome ; }, abstract = {As a local breed adapted to the extreme environment of the Tibetan Plateau, Tibetan pigs have not yet been systematically characterized in terms of their gut viral communities. In this study, we applied viral metagenomics to sequence fecal samples from 191 Tibetan pigs (including both healthy and diarrheal individuals) across four farms in Nyingchi, Tibet, aiming to reveal the diversity, composition, and distribution of gut viral communities in Tibetan pigs living at high altitudes. A total of nearly 120 million high-quality viral sequence reads were obtained, which were annotated into 16 viral families. The viral community was predominantly dominated by Microviridae, but its composition varied across different farms and health statuses. Phylogenetic analysis identified numerous virus sequences associated with pigs, including RNA viruses (such as Astroviridae (n = 7), Caliciviridae (n = 6), Picornaviridae (n = 15), etc.) and DNA viruses (such as Circoviridae (n = 3), Genomoviridae (n = 4), Smacoviridae (n = 41), Parvoviridae (n = 11), etc.). Notably, the study found multiple viral sequences exhibiting genetic differences from known strains, suggesting the potential presence of novel viruses or variants. For instance, a papain-like protease (PLP) insertion sequence, identified to have high sequence identity with Torovirus (ToV), was found in six Enterovirus G (EV-G) strains, indicating a cross-family genetic recombination event. This study systematically outlines the viral metagenomic profile of gut viral communities in Tibetan pigs at high altitudes, revealing their unique viral diversity and complex community structure. The results suggest that the gut viral community of Tibetan pigs consists of host-associated viruses, bacteriophages, and potentially viruses originating from the environment or diet, with its composition influenced by farming conditions and host health status. These findings provide an important data foundation for understanding the interactions between viruses, hosts, and the environment in unique ecological settings and offer new insights into the health management and virology research of Tibetan pigs.}, }
@article {pmid41312164, year = {2025}, author = {Onohuean, H and Nnolum-Orji, NF and Naik Bukke, SP and Abass, KS and Alagbonsi, AI and Choonara, YE}, title = {Non-alcoholic fatty pancreas disease (NAFPD) as a pre-neoplastic niche: Metabolic and inflammatory Gateways to pancreatic ductal adenocarcinoma.}, journal = {Journal of clinical &amp; translational endocrinology}, volume = {42}, number = {}, pages = {100424}, pmid = {41312164}, issn = {2214-6237}, abstract = {Non-alcoholic fatty pancreas disease (NAFPD), marked by ectopic triglyceride accumulation in the exocrine pancreas, is increasingly observed yet its recognition as a cancer-predisposing condition remains limited. We synthesize evidence supporting NAFPD as an early and modifiable niche for pancreatic ductal adenocarcinoma (PDAC), using a PRISMA-ScR-guided framework. The findings were synthesized into three domains: epidemiological risk, metabolic-inflammatory signaling, and immune-stromal remodeling. Mechanisms include palmitate-induced ER stress, ROS-driven NLRP3-IL-1β and STAT5 signaling, and KRAS^G12D-mediated lipotoxicity. Lipid-laden stellate cells promote fibrosis, immunosuppression, and epithelial-mesenchymal transition. NAFPD may represent an early, modifiable PDAC niche, warranting further imaging-omic studies and targeted prevention trials.}, }
@article {pmid41311850, year = {2025}, author = {Aditya, C and Bukke, SPN and Anitha, K and Meeraraje, P and Goruntla, N and Yadesa, TM and Onohuean, H}, title = {A comprehensive review on diabetic foot ulcer addressing vascular insufficiency, impaired immune response, and delayed wound healing mechanisms.}, journal = {Frontiers in pharmacology}, volume = {16}, number = {}, pages = {1622055}, pmid = {41311850}, issn = {1663-9812}, abstract = {Diabetic foot ulcers (DFUs) continue to represent one of the most significant and costly complications related to diabetes mellitus, posing serious challenges to healthcare systems and resulting in considerable morbidity rates. This narrative review explores the complex pathophysiology of DFUs, focusing on the interplay between peripheral neuropathy, vascular insufficiency, and a weakened immune response, all of which contribute to delayed wound healing. Neuropathy leads to a loss of protective sensation, causing unnoticed repetitive injuries, while both microvascular and macrovascular complications reduce tissue perfusion and hinder angiogenesis. Additionally, immune dysfunction and exaggerated inflammatory responses raise the occurrence of infection and negatively affect the healing process. The clinical manifestation, progression, and key risk factors of DFUs were discussed in this review, emphasizing the importance of early detection, careful foot care, and routine screening in individuals who are at risk. Numerous therapeutic approaches are reviewed, including wound debridement, sophisticated wound dressings, offloading techniques, glycemic control, and adjuvant therapies such as growth factor administration, hyperbaric oxygen therapy, and negative pressure wound therapy. For optimal results, a multidisciplinary team combining of vascular surgeons, podiatrists, endocrinologists, and wound care specialists was included. The analysis also points out that promising advancements in bioengineered skin substitutes, intelligent dressings, and regenerative medicine hold promise for the treatment of DFU in the future. Self-monitoring, appropriate footwear, and patient education are all important components of prevention, which remains a fundamental strategy. In the clinical management of DFUs, this narrative review incorporates the most recent research and highlights the value of proactive, customized, and multidisciplinary approaches.}, }
@article {pmid41311501, year = {2025}, author = {Wu, Q and Hu, S and Wang, Y and Wu, Y and Zhao, Y and Niu, L and Zhou, X and Shen, L and Liu, Y and Chen, Y and Gan, M and Zhu, L}, title = {Age-related gut microbiota succession in Neijiang pigs: insights for precision feeding and productivity.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1698169}, pmid = {41311501}, issn = {1664-302X}, abstract = {OBJECTIVE: To characterize age-related gut microbiota succession in Neijiang pigs and translate these dynamics into actionable insights for precision feeding and productivity improvement.<br><br>METHODS: Growth data from 0 to 180&#x202f;days (n&#x202f;=&#x202f;16, 780 weight records) were fitted with three non-linear models to determine the optimal growth curve and partition physiological stages. Fresh feces were collected at 25, 70, 110, and 150&#x202f;days (n&#x202f;=&#x202f;6/stage). 16S rRNA V3-V4 amplicon sequencing was used to profile microbiota composition and diversity; PICRUSt2 was employed to predict metagenome functions against the KEGG database.<br><br>RESULTS: The Gompertz model best described growth (R [2]&#x202f;=&#x202f;0.996) with an inflection point at 84.2&#x202f;days (25.9&#x202f;kg). Microbial alpha-diversity (Shannon, Chao1) increased with age and plateaued after 110&#x202f;days. Firmicutes and Bacteroidota dominated (>90% relative abundance), whereas Spirochaetota and Euryarchaeota expanded significantly in finishing pigs. LEfSe identified 45 stage-specific biomarkers: Prevotella_9, Collinsella and Blautia characterized suckling-weaning stages; Faecalibacterium and Clostridium_sensu_stricto_1 peaked at 70&#x202f;days; Lactobacillus was dominant at 110&#x202f;days; Treponema, Streptococcus and Bacteroides defined the 150-day microbiome. Functional prediction revealed a metabolic shift from basal biosynthesis and DNA repair in early life toward enhanced ABC transporters, bacterial motility proteins, oxidative phosphorylation and methane metabolism in finishing pigs.<br><br>CONCLUSION: Our data provide a temporal blueprint of gut microbiota maturation that mirrors host nutrient requirements across growth phases. These microbial indicators and functional signatures can guide stage-specific dietary formulations and microbiota-targeted interventions to improve feed efficiency, reduce environmental emissions and enhance the productivity of indigenous pig breeds.}, }
@article {pmid41311499, year = {2025}, author = {Wang, J and Su, W and Chen, Q and Zhou, J and Wang, X and Jiang, R and Li, J and Xing, P}, title = {Microbiome-metabolome dysbiosis of bronchoalveolar lavage fluid of lung cancer patients.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1669172}, pmid = {41311499}, issn = {1664-302X}, abstract = {BACKGROUND: Recent studies indicate that microorganisms significantly influence lung cancer pathogenesis. This research explores the variations in microbiota and metabolites in the lower respiratory tract between lung cancer patients and individuals with benign pulmonary lesions to identify potential diagnostic biomarkers.<br><br>METHODS: Two hundred eight patients undergoing bronchoscopy at Tianjin Cancer Institute &amp; Hospital and Tianjin Chest Hospital from October 2022 to October 2023 were screened. Ninety-five bronchoalveolar lavage fluid (BALF) was collected for metagenomic sequencing and untargeted metabolomic analysis. Comparisons of microbial diversity, taxonomic composition, and metabolite profiles were conducted between groups with lung cancer and benign lung conditions.<br><br>RESULTS: The cohort comprised 70 patients with lung cancer and 25 with benign lung lesions. Patients with lung cancer showed significantly reduced &#x3b2;-diversity (p =&#x202f;0.005). Predominant microbes in lung cancer cases included Streptococcus, Haemophilus influenzae, and Veillonella parvula. A microbial-based diagnostic model differentiated lung cancer from benign lesions with an AUC of 0.931 (95%CI: 0.916-0.946). Metabolites increased in lung cancer were Citric acid, N-Acetylneuraminic acid, Oxoglutaric acid, and Neopterin, whereas L-Tryptophan, Uridine, 3-Hydroxybutyric acid decreased. The KEGG pathways suggest a significant link between microbial presence and both tumorigenesis and progression.<br><br>CONCLUSION: Specific microbial patterns in the lower respiratory tract of lung cancer patients could assist in the auxiliary diagnosis of the disease. The notably altered microorganisms and metabolites in the BALF from lung cancer patients, as opposed to those with benign conditions, correlate with cancer initiation and advancement.}, }
@article {pmid41311484, year = {2025}, author = {Xu, J and Yao, Y and Pan, L and Zhang, N and Li, D and Chen, X}, title = {Pea-cucumber crop rotation suppresses Fusarium pathogens by reshaping soil microbial communities and enhancing nutrient availability.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1697343}, pmid = {41311484}, issn = {1664-302X}, abstract = {INTRODUCTION: Pea-cucumber rotation combined with straw return as green manure is an environmentally friendly management strategy to suppress cucumber (Cucumis sativus L.) Fusarium wilt (FW) and alleviate continuous cropping obstacles.<br><br>METHODS: We evaluated the variations in soil microbial compositions and nutrient levels between long-term cucumber monocropping and pea-cucumber rotation patterns via metagenomic sequencing and determination of soil properties.<br><br>RESULTS: The study found that the bacterial communities exhibited marked diversity, whereas the &#x3b1;-diversity of fungal communities was significantly reduced. Based on the relative abundance of differential fungi and bacteria at the genus level, the genus Bacillus showed the highest abundance, with a two-fold increase, whereas Fusarium species exhibited a 4.9-fold reduction following the pea-cucumber rotation. Additionally, the contents of available nitrogen, potassium, and phosphorus in the soil increased by more than 1.3-fold after the rotation. Correlation analysis revealed that the genus Bacillus and available potassium were significantly and negatively correlated with Fusarium pathogens. Notably, the isolated B. pumilus and B. safensis strains significantly suppressed the growth of cucumber FW pathogens.<br><br>DISCUSSION: These findings provide valuable insights for optimizing the combination of soil Bacillus populations and nutrient availability to maintain soil ecosystem health and improve cucumber growth and yield.}, }
@article {pmid41311478, year = {2025}, author = {Zhong, Y and Li, R and E, J and Chi, H and Cao, N and Bai, Z and Du, X and Wang, L}, title = {Effects of maize straw and corncob return on the soil quality and on the soil microbial structures and functions.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1675172}, pmid = {41311478}, issn = {1664-302X}, abstract = {Straw return is an effective agricultural strategy for incorporating organic carbon into soil organic matter pools through microbial decomposition. This process modifies soil physicochemical properties, thereby altering microbial habitats and resource availability, which can influence the structure and function of soil microbial communities. However, the changes of soil physicochemical properties and microbial communities under different straw incorporation forms remain poorly understood. And how these straw return materials alter soil physicochemical properties and microbial communities within a single cycle. In this study, we conducted straw returning experiments in a maize-producing region of Jilin Province, China, comparing the impact of two distinct maize-derived residues (crushed maize straw and crushed corncob) on soil quality and microbial communities. Our results demonstrated that corncob return more effectively improved key soil physicochemical properties compared to maize straw return. While neither residue significantly alters microbial alpha diversity, both induced shifts in beta diversity. We identified distinct correlations between dominant microbial taxa and key soil physicochemical parameters. Furthermore, KEGG and GO analyses revealed that both of the residues altered microbial functional hierarchies, with corncob return inducing more pronounced changes than maize straw return. These findings provide a mechanistic basis for optimizing straw management strategies to enhance microbial-mediated soil fertility.}, }
@article {pmid41311042, year = {2025}, author = {Choi, JH and Oh, S and Yi, MH and Kang, D and Choi, DY and Chavarria, X and Shatta, A and Cho, YH and Choe, S and Lee, SH and Kim, JY}, title = {Detection of intestinal parasites in leopard cat fecal samples using shotgun metagenomics.}, journal = {Parasites, hosts and diseases}, volume = {63}, number = {4}, pages = {349-353}, doi = {10.3347/PHD.25032}, pmid = {41311042}, issn = {2982-6799}, support = {RS-2024-00456300//National Research Foundation of Korea/ ; //Ministry of Science and ICT/ ; //Korea Health Industry Development Institute/ ; RS-2024-00406488//Ministry of Health and Welfare/ ; RS-2023-KH139971//Ministry of Health and Welfare/ ; }, mesh = {Animals ; *Feces/parasitology ; *Metagenomics/methods ; *Intestinal Diseases, Parasitic/veterinary/parasitology/diagnosis ; RNA, Ribosomal, 18S/genetics ; *Panthera/parasitology ; *Parasites/isolation &amp; purification/genetics/classification ; *Felidae/parasitology ; Cats ; }, abstract = {The leopard cat (Prionailurus bengalensis) is a wild felid species that serves as a reservoir of zoonotic parasites. In this study, we investigated intestinal parasite taxa by reanalyzing previously published shotgun metagenomic sequencing data from fecal samples of wild leopard cats using a custom 18S rRNA gene reference database constructed from the NCBI nucleotide database. Among 11 metagenomic samples, 5 parasite species were identified: Toxoplasma gondii, Clonorchis sinensis, Strongyloides planiceps, Cylicospirura petrowi, and Pharyngostomum cordatum. These findings demonstrate that shotgun metagenomic analysis of fecal samples can be a useful tool for monitoring zoonotic parasite infections in this species and for investigating parasite life cycles. However, this approach is limited by its dependence on existing reference databases and requires experimental validation of the findings.}, }
@article {pmid41310806, year = {2025}, author = {Utkina, I and Fan, Y and Willing, BP and Parkinson, J}, title = {Metabolic modeling of microbial communities in the chicken ceca reveals a landscape of competition and co-operation.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {248}, pmid = {41310806}, issn = {2049-2618}, support = {RGPIN-2019-06852//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Animals ; *Chickens/microbiology ; *Cecum/microbiology ; *Gastrointestinal Microbiome ; Metagenomics/methods ; Metagenome ; *Bacteroides/metabolism/genetics/classification ; *Bacteria/classification/metabolism/genetics ; Fatty Acids, Volatile/metabolism ; Escherichia coli/metabolism/genetics ; }, abstract = {BACKGROUND: Members of the Bacteroidales, particularly Bacteroides species, with their ability to degrade dietary fibers and liberate otherwise unavailable substrates, exert a substantial influence on the microbiome of the lower intestine. However, our understanding of how this influence translates to the metabolic interactions that support community structure remains limited. In this study, we apply constraint-based modeling to investigate metabolic interactions in chicken cecal communities categorized by the presence or absence of Bacteroides.<br><br>RESULTS: From metagenomic datasets previously generated from 33 chicken ceca, we constructed 237 metagenome-assembled genomes. Metabolic modeling of communities built from these genomes generated profiles of short-chain fatty acids largely consistent with experimental assays and confirmed the role of B. fragilis as a metabolic hub, central to the production of metabolites consumed by other taxa. In its absence, communities undergo significant functional reconfiguration, with metabolic roles typically fulfilled by B. fragilis assumed by multiple taxa. Beyond B. fragilis, we found Escherichia coli and Lactobacillus crispatus also mediate influential metabolic roles, which vary in the presence or absence of B. fragilis. Notably, the microbiome's compensatory adaptations in the absence of B. fragilis produced metabolic alterations resembling those previously associated with inflammatory bowel disease in humans, including energy deficiency, increased lactate production, and altered amino acid metabolism.<br><br>CONCLUSIONS: This work demonstrates the potential of using the chicken cecal microbiome as a model system for investigating the complex metabolic interactions and key contributions that drive community dynamics in the gut. Our model-based predictions offer insights into how keystone taxa like B. fragilis may shape the metabolic landscape and functional organization of microbial communities. The observed metabolic adaptations in the absence of B. fragilis share metabolic similarities with profiles seen in dysbiotic states in humans and underscore the translational relevance of these insights for understanding gut health across different host systems. Video Abstract.}, }
@article {pmid41310797, year = {2025}, author = {Du, H and Lin, B and Zhu, Y and Hao, X and Tang, M and Wu, W and Wang, D and Yang, Y and Liang, Y and Tang, W and Xu, H and Li, J and Gao, F and Du, X}, title = {Exploring the mechanisms of protective effect of high-energy X-ray FLASH radiotherapy on intestine through multi omics analysis.}, journal = {Radiation oncology (London, England)}, volume = {20}, number = {1}, pages = {179}, pmid = {41310797}, issn = {1748-717X}, support = {2025ZNSFSC0555//Sichuan Science and Technology Program/ ; U2330122//Projects of National Natural Science Foundation/ ; 2023ZYDF073//Minyang Science and Technology Program/ ; miancaijian2022-186//Mianyang Municipal Finance Bureau/ ; }, mesh = {Animals ; Mice ; Female ; Mice, Inbred C57BL ; *Colonic Neoplasms/radiotherapy/pathology ; *Intestines/radiation effects ; X-Rays ; Metabolomics/methods ; Gastrointestinal Microbiome/radiation effects ; Multiomics ; }, abstract = {BACKGROUND: The aim of this study is to investigate the potential mechanisms underlying the protective effects of high-energy X-ray FLASH radiotherapy (FLASH-RT) on intestine through multi-omics analysis.<br><br>METHODS: This study utilized syngeneic colon carcinoma mouse models of CT26 and MC38 to evaluate the therapeutic efficacy of FLASH-RT versus conventional dose rate radiotherapy (CONV-RT) by monitoring survival, tumor size, and body weight. Furthermore, healthy C57BL/6 female mice received whole-abdominal irradiation with either FLASH-RT, CONV-RT, or sham irradiation to compare differences in normal tissue protection. 72&#xa0;h post-irradiation, intestinal contents from mice were collected for metagenomic analysis, and intestinal tissue was harvested for non-targeted metabolic and single-cell sequencing analyses.<br><br>RESULTS: In CT26 and MC38 models, both CONV-RT and FLASH-RT have demonstrated similar anti-tumor efficacy. Compared with CONV-RT, whole-abdominal FLASH-RT significantly alleviated acute intestinal injury in mice, as evidenced by better preservation of crypt numbers and villus architecture in the FLASH group. Metagenomic analysis revealed that the relative abundance of the gut-protective bacterium Ligilactobacillus ruminis was significantly higher in the FLASH group than in the CONVgroup. Non-targeted metabolomic profiling identified 34 differential metabolites, of which 29 were upregulated and 5 were downregulated in the FLASH group. Notably, the abundance of 2-hydroxyglutarate, a metabolite associated with the butyrate metabolism pathway, was significantly elevated in the FLASH group compared with the CONV group (p&#x2009;<&#x2009;0.05). Single-cell sequencing data revealed notable differences in cell distribution and proportions between the groups, with a higher proportion of fibroblasts, proliferative cells, macrophages, and CD4&#x2009;+&#x2009;T cells in the FLASH group compared to the CONV and control groups. Immunofluorescence analysis revealed a significantly greater number of Lgr5&#x207a; intestinal stem cells in the FLASH group compared to the CONV group. Conversely, immunohistochemical analysis demonstrated stronger p50/p65 staining intensity in the CONV group relative to the FLASH group.<br><br>CONCLUSIONS: This study confirms that FLASH-RT, compared to CONV-RT, maintains equivalent antitumor efficacy while mitigating damage to normal intestinal tissues. Moreover, it preliminarily reveals that the protective mechanism of FLASH-RT is multifaceted, involving remodeling of the microbiota-metabolite axis, attenuation of inflammatory responses, and enhanced preservation of stem cells.}, }
@article {pmid41310780, year = {2025}, author = {Liu, Y and Brinkhoff, T and Simon, M}, title = {Ecogenomics and functional biogeography of the Roseobacter group in the global oceans based on 653 MAGs and SAGs.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {247}, pmid = {41310780}, issn = {2049-2618}, support = {TRR51//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Roseobacter/genetics/classification/isolation &amp; purification ; Phylogeny ; Oceans and Seas ; RNA, Ribosomal, 16S/genetics ; *Seawater/microbiology ; Phylogeography ; DNA, Bacterial/genetics ; Metagenomics/methods ; Sequence Analysis, DNA ; Genome, Bacterial ; }, abstract = {BACKGROUND: The Roseobacter group is a major component of prokaryotic communities in the global oceans. Information on this group is based predominantly on isolates and their genomic features and on the 16S rRNA gene. Assessments of prokaryotic communities in the pelagic of the global oceans indicated an unveiled diversity of this group but studies of the diversity and global biogeography of the entire group are still missing. Hence, we aimed at a comprehensive assessment of the Roseobacter group in the global oceans on the basis of MAGs and SAGs.<br><br>RESULTS: The obtained 610 MAGs and 43 SAGs of high quality were subjected to in-depth analyses of their phylogeny, genomic and functional features. The recruitment locations range from the tropics to polar regions, include all major ocean basins. The phylogenetic analysis delineated the known RCA cluster and five pelagic clusters, two of which were completely novel: TCR (Temperate and Cold Roseobacter), AAPR (Arctic-Atlantic-Pacific Roseobacter, novel), AAR (Arctic-Atlantic Roseobacter, novel), COR (Central Oceanic Roseobacter), LUX (Cand. Luxescamonaceae) cluster. These clusters account for&#x2009;~&#x2009;70% of all Roseobacter MAGs and SAGs in the epipelagic. The TCR, AAPR, AAR, and LUX clusters are among the most deeply branching lineages of the Roseobacter group. These clusters and several sublineages of the RCA and COR clusters exhibit distinct features of genome streamlining, i.e. genome sizes of&#x2009;<&#x2009;2.9 Mbp and G&#x2009;+&#x2009;C contents of&#x2009;<&#x2009;40%. The clusters exhibit differences in their functional features and also compared to other lineages of the Roseobacter group. Proteorhodopsin is encoded in most species of the AAPR, AAR, TCR, and RCA clusters and in a few species of the COR cluster, whereas in most species of the latter, the LUX cluster and in a few species of the RCA cluster aerobic anoxygenic photosynthesis is encoded. Biogeographic assessments showed that the AAPR, AAR, TCR and RCA clusters constitute the Roseobacter group in the temperate to polar regions to great extent whereas the COR and LUX clusters in the tropics and subtropics.<br><br>CONCLUSIONS: Our comprehensive analyses shed new light on the diversification, genomic features, environmental adaptation, and global biogeography of a major lineage of pelagic bacteria. Video Abstract.}, }
@article {pmid41310694, year = {2025}, author = {Liu, P and Deng, Z and Wang, Y and Wu, F and Peng, J and Huang, P and Wang, Y and Lao, J}, title = {Application of Probe-Capture metagenomics in rabies diagnosis.}, journal = {Virology journal}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12985-025-03029-6}, pmid = {41310694}, issn = {1743-422X}, support = {82460480//National Natural Science Foundation of China/ ; 20223638//Qinzhou Scientific Research and Technology Development Program/ ; 2024GXNSFAA010067//Guangxi Natural Science Foundation/ ; }, abstract = {BACKGROUND: Rabies, a lethal viral encephalitis caused by Rabies virus (RabV), is transmitted via bites, scratches, or mucosal contact with infected animals, as well as through inhalation of aerosolized particles, ingestion of contaminated raw animal products, or transplantation of infected organs. It's near-universal fatality, diverse transmission routes, and marked clinical variability significantly impede timely diagnosis, highlighting the demand for a rapid and precise diagnostic approach.<br><br>METHODS: Single-center retrospective case series.<br><br>RESULTS: This series reported three rabies cases admitted to the First People's Hospital of Qinzhou: one without identifiable exposure and two with confirmed exposure histories. Clinical presentations were highly variable and diagnostically misleading. Application of Probe-Capture Metagenomics (pc-mNGS) to cerebrospinal fluid and blood samples enabled direct identification of RabV and concurrent detection of coexisting pathogens.<br><br>CONCLUSION: pc-mNGS demonstrates potential as a rapid, economical diagnostic tool capable of detecting RabV in specimens with low viral loads-such as blood and cerebrospinal fluid-from both exposed and unexposed individuals. Simultaneous identification of additional pathogens further supports its diagnostic utility.}, }
@article {pmid41310465, year = {2025}, author = {Bae, J and Han, JW and Song, JY and Nam, SH and Sung, JS and Ko, HC and Kim, SH and Lee, YJ}, title = {Targeted elimination of latent endophytes improves cryopreservation success in in vitro grapevine (Vitis vinifera) cultures.}, journal = {BMC plant biology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12870-025-07821-y}, pmid = {41310465}, issn = {1471-2229}, support = {PJ017462//the National Institute of Agricultural Sciences, RDA, ROK/ ; PJ017462//the National Institute of Agricultural Sciences, RDA, ROK/ ; PJ017462//the National Institute of Agricultural Sciences, RDA, ROK/ ; PJ017462//the National Institute of Agricultural Sciences, RDA, ROK/ ; PJ017462//the National Institute of Agricultural Sciences, RDA, ROK/ ; PJ017462//the National Institute of Agricultural Sciences, RDA, ROK/ ; PJ017462//the National Institute of Agricultural Sciences, RDA, ROK/ ; }, abstract = {BACKGROUND: Latent endophytic bacteria are common in grapevine in vitro cultures and, while not always causing visible culture decline, can negatively affect downstream applications such as cryopreservation by reducing post-thaw recovery. While antibiotic treatments are widely used for microbial control, their efficacy varies with bacterial species, plant genotype, and application conditions. Few studies have directly linked targeted elimination of identified endophytes with improved post-cryopreservation recovery.<br><br>RESULTS: In this study, we identified Leifsonia poae in 'Ruby Seedless' and Curtobacterium oceanosedimentum in 'Merlot' using 16&#xa0;S rRNA sequencing. Species-specific antibiotic susceptibility testing revealed rifampicin (minimum bactericidal concentration, MBC&#x2009;=&#x2009;31&#xa0;&#xb5;g mL&#x207b;&#xb9;) as effective against L. poae, and cefotaxime (MBC&#x2009;=&#x2009;1000&#xa0;&#xb5;g mL&#x207b;&#xb9;) as effective against C. oceanosedimentum. In vitro application of these antibiotics eliminated the respective endophytes without significant phytotoxic effects at optimal concentrations. Amplicon-based 16&#xa0;S metagenomic profiling confirmed complete removal of the target bacteria and revealed substantial shifts in community composition, with reduced abundance of dominant taxa but maintenance of overall endophytic diversity. Cryopreservation experiments in 'Ruby Seedless' showed that removal of endophytes increased post-thaw survival from 31.8 to 70.9% and eliminated variability in regrowth across replicates.<br><br>CONCLUSIONS: This study demonstrates that targeted antibiotic elimination of dominant endophytes can restructure the in vitro microbial community and substantially improve cryopreservation outcomes in grapevine. The approach offers a reproducible sanitation strategy for clonal crops vulnerable to endophyte-related culture failures and can be readily adapted for germplasm conservation programs.}, }
@article {pmid41310455, year = {2025}, author = {Feng, Y and Yang, F and Klopatek, SC and Oltjen, JW and Yang, X}, title = {The fecal resistome of beef cattle from conventional grain-fed and grass-fed systems in the Western United States.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-025-04562-8}, pmid = {41310455}, issn = {1471-2180}, support = {20-1078-000-SG//Antimicrobial Use and Stewardship (AUS) Branch of the California Department of Food and Agriculture/ ; 20-1078-000-SG//Antimicrobial Use and Stewardship (AUS) Branch of the California Department of Food and Agriculture/ ; 20-1078-000-SG//Antimicrobial Use and Stewardship (AUS) Branch of the California Department of Food and Agriculture/ ; 20-1078-000-SG//Antimicrobial Use and Stewardship (AUS) Branch of the California Department of Food and Agriculture/ ; 20-1078-000-SG//Antimicrobial Use and Stewardship (AUS) Branch of the California Department of Food and Agriculture/ ; }, abstract = {Bacteria in the gastrointestinal tract of cattle may develop antimicrobial resistance (AMR) due to the use of antibiotics in live animals and can be excreted in feces, posing a risk of contamination. However, it remains unclear whether different beef production systems influence the levels of AMR in cattle feces. The objective of this study was to characterize and compare the fecal resistome of cattle raised in grass and grain-feeding systems in the Western United States. Fecal samples were collected from individual cattle at 14 months of age and two days before their respective harvest date. Groups included: (1) Conventional grain-fed (CON, n = 10), (2) Grass-fed for 20 months (20GF, n = 10), (3) Grass-fed and then grain-finished for 45 days (GR45, n = 10), (4) Grass-fed for 25 months (25GF, n = 10). According to metagenomic analysis, grass-feeding systems, particularly the one with extended grass-feeding, are associated with a less diverse resistome. The 25GF group had smaller (P < 0.05) Chao1 value than the other groups at the harvest time. Antimicrobial resistance genes (ARGs) richness and evenness were higher in CON and GR45 than in 20GF and 25GF (P < 0.05). Additionally, the resistome of GR45 and CON differed from 25GF (P = 0.018). In grass-feeding systems where antibiotics were not administered, animals' feces exhibited greater (P < 0.05) diversity in transferable biocide and metal resistant genes (BMRGs) compared with the grass-fed but grain-finished system. Greater ARG diversity in grain-finished feeding systems may enhance the spread of antimicrobial-resistant bacteria (ARB) during production, posing additional risks to food safety. Similarly, higher BMRG diversity observed in grass-fed systems may promote ARB spreading through co-selection mechanisms, which could also contribute to potential food safety concerns.}, }
@article {pmid41310063, year = {2025}, author = {Plomp, N and Gacesa, R and Slager, J and Samsom, JN and Faber, KN and Jonkers, IH and Withoff, S and Wijmenga, C and Weersma, RK and Harmsen, HJM}, title = {Synergy between culturomics and metagenomics of health status-associated gut bacteria originating from non-IBD and IBD populations.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-025-29138-4}, pmid = {41310063}, issn = {2045-2322}, support = {LSHM18057-SGF//Samenwerkende Gezondheidsfondsen/ ; NWO Gravitation project 024.003.001//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; 016.136.308//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; MLDS D16-14//Maag Lever Darm Stichting/ ; 101095470//HORIZON EUROPE Framework Programme/ ; }, abstract = {The bacteria in the human intestinal tract are important for health and associate with diseases, such as inflammatory bowel disease (IBD). Although metagenomic studies can identify certain bacteria or even specific strains and associate their presence or specific phenotypes with health or diseases, actual isolates for experimental validation of metagenomic associations are often lacking. Therefore, this study sets out to culture health- and IBD-associated bacteria from 32 fecal samples from 2 cohorts, for which extensive metadata is available. The cultivation of those samples resulted in 4,347 isolates, of which 1,362 isolates were obtained from IBD patients. Irrespective of health or IBD, Actinomycetota, Bacillota and Bacteroidota were the most represented phyla and members of 5 other phyla were less frequently isolated (Campylobacterota, Fusobacteriota, Pseudomonadota, Thermodesulfobacteriota and Verrucomicrobiota). Comparison of the genus richness between the culturomics approach and available metagenomic sequencing data of the corresponding participants revealed that both methods largely capture the same genera. Although not all genera could be identified in both methods, our results show that combining both methods has a synergetic effect, providing a higher identification rate. Furthermore, genetic analysis of 2 isolates of Bifidobacterium adolescentis strains shows that these isolates closely resembled the metagenome-assembled genome that was identified within the same participant. This showcases that it is possible to isolate specific strains that are important in the experimental validation of specific associations within a species. The culture collection that is presented in this study contains bacterial isolates that are strongly associated with health or IBD. Our results show that we are able to generate a valuable culture collection that opens a promising avenue for functional validation experiments of associations that are identified with metagenomic data.}, }
@article {pmid41309890, year = {2025}, author = {Kuzmichenko, P and Fedorov, D and Galeeva, J and Postoeva, A and Krieger, E and Kudryavtsev, A and Pavlenko, A and Vvedensky, A and Starikova, E and Govorun, V and Ilina, E}, title = {Comparing alignment and de-novo approaches for gut microbiota metagenomic data analysis reveals differences in taxonomic resolution and novel functional insights.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {42423}, pmid = {41309890}, issn = {2045-2322}, support = {100217/WT_/Wellcome Trust/United Kingdom ; 075-15-2025-530//Ministry of Science and Higher Education of the Russian Federation/ ; }, mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Metagenomics/methods ; Feces/microbiology ; Metagenome ; Male ; *Bacteria/genetics/classification ; Female ; Adult ; }, abstract = {Microbiome annotation based on metagenomic data is primarily conducted using two global approaches: alignment-based approach (AL) and de novo approach (DN). This study aimed to evaluate the limitations of each approach, explore correlations between their results, and assess the equivalence of findings derived from different methodologies when analyzing the same dataset. Shotgun metagenomic sequencing data from 346 fecal samples, collected longitudinally within individuals in Arkhangelsk, Northwestern Russia, were analyzed. Each of the 173 participants provided two samples, one during 2015-2017 and another in 2022. The alterations in the microbiota associated with BMI served as a critical variable for facilitating the comparisons between the AL and DN. Exploratory analyses, including PERMANOVA, alpha diversity and beta diversity, revealed no significant differences between the two approaches. However, differential abundance analysis based on the AL yielded more statistically significant results, with the DN producing only a subset of these findings. An analysis of the metagenome-assembled genomes (MAGs) of bacteria that were differentially abundant revealed that one group of MAGs of Alistipes onderdonkii encodes the enzyme 2,5-diketo-D-gluconate reductase A. Using AL and DN together offers complementary functional insights, as the methods produce partially overlapping results. The novel enzyme finding suggests a potential role in metabolic pathways and underscores the value of integrative metagenomic analysis.}, }
@article {pmid41309644, year = {2025}, author = {Qiu, D and Wang, Y and Xu, N and Chen, B and Zhu, Y and Zhang, Z and Zhang, Q and Lu, T and Dong, H and Shou, J and Qian, H}, title = {Global variation in plant-beneficial bacteria in soil under pesticide stress.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {10685}, pmid = {41309644}, issn = {2041-1723}, support = {42377107//National Natural Science Foundation of China (National Science Foundation of China)/ ; 22376187//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42307158//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Soil Microbiology ; *Pesticides/toxicity ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; Soil/chemistry ; *Soil Pollutants/toxicity ; Agriculture ; Metagenomics ; Crops, Agricultural/microbiology/growth &amp; development ; }, abstract = {The presence of plant-beneficial bacteria (PBB) in soil significantly affects crop production. Excessive agrochemical use in intensive agriculture causes substantial soil residue accumulation, compromising soil health, crop quality, and human health. Understanding changes in beneficial bacteria under pesticide pollution is crucial for guiding sustainable agricultural practices and promoting soil health. We analyze metagenomic data from 1919 soil samples to identify 364 PBBs. We find higher PBB diversity in agricultural soils than in non-agricultural soils; however, pesticide pollution negatively affects the abundance of PBB, particularly those with plant growth-promoting traits. Pesticides not only reduce PBB diversity as individual factors, but they also exert synergistic negative effects with other anthropogenic factors, as determined by Hedges'd effect size and 95% confidence intervals, further accelerating the decline in PBB diversity. Increased pesticide risk also leads to a loss of functional gene diversity in PBB about carbon and nitrogen cycling within essential nutrient cycles, and a reduction in specific amino acid and vitamin synthesis. Artificial application of specific amino acids and vitamins could be an effective strategy to restore PBB in high-pesticide-risk soils. This study provides guidance for regulating pesticide use to mitigate their negative effects on soil PBB and suggests potential remedial measures.}, }
@article {pmid41309591, year = {2025}, author = {Zhou, N and Li, Q and Liang, Z and Yu, K and Zhang, C and Wang, H and Li, P and He, Z and Wang, S}, title = {Microbially-mediated halogenation and dehalogenation cycling of organohalides in the ocean.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {10670}, pmid = {41309591}, issn = {2041-1723}, mesh = {*Halogenation ; Oceans and Seas ; *Seawater/microbiology ; Metagenome ; *Bacteria/genetics/metabolism/classification ; Phylogeny ; Archaea/genetics/metabolism/classification ; Molecular Docking Simulation ; *Hydrocarbons, Halogenated/metabolism ; }, abstract = {Microbially mediated organohalide cycling in the ocean has profound implications for global biogeochemical cycles and climate, but the geographic distribution and diversity of the halogenation-dehalogenation cycling microorganisms remain unknown. Here, we constructed an organohalide-cycling gene database (HaloCycDB) to explore the global atlas of halogenation-dehalogenation cycling microorganisms and genes from 1473 marine metagenomes. Strikingly, 6204 out of 15,252 metagenome-assembled genomes (MAGs) carry organohalide-cycling genes, of which 84.30% are dehalogenating populations. Microorganisms of Pseudomonadota with even spatial distribution dominate both halogenation and dehalogenation potentials in the ocean, in contrast to lineages of Asgardarchaeota and Thermoproteota solely mediating dehalogenation in the Northern hemisphere. Notably, 80.91% of reductive dehalogenase (RDase) genes and 91.35% of RDase-containing prokaryotes represent uncharacterized lineages, substantially expanding known dehalogenation diversity. Further integration of microbial cultivation, protein structure prediction, and molecular docking revealed four unique "microorganism-RDase-organohalide" patterns for marine dehalogenation and its coupling with carbon/sulfur cycles, being distinctively different from their terrestrial patterns. These results advance our understanding of microbial organohalide cycling by providing insights into the halogenation-dehalogenation microbiomes in the ocean.}, }
@article {pmid41309379, year = {2025}, author = {Kim, H and Jeon, HJ and Jeong, HM and Bang, WY and Lee, HB and Lee, KS and Moon, JS and Kwon, H and Lee, J and Yang, J and Jung, YH}, title = {Modulation of the Gut Microbiome and Metabolomes by Fermentation Using a Probiotic Complex in a Dysbiosis-Associated Fecal Model.}, journal = {Journal of microbiology and biotechnology}, volume = {35}, number = {}, pages = {e2506014}, doi = {10.4014/jmb.2506.06014}, pmid = {41309379}, issn = {1738-8872}, mesh = {*Probiotics/pharmacology ; *Dysbiosis/microbiology/therapy ; *Gastrointestinal Microbiome/drug effects ; Humans ; Fermentation ; *Feces/microbiology ; *Metabolome ; Inflammatory Bowel Diseases/microbiology ; Bifidobacterium/metabolism ; Lactobacillus/metabolism ; Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Streptococcus/metabolism ; }, abstract = {Inflammatory bowel disease (IBD), affecting up to 0.5% of the global population, is frequently associated with gut microbiota dysbiosis and metabolic imbalances, which contribute to chronic constipation and abdominal discomfort. This study investigated the modulatory effects of an eight-strain probiotic complex comprising Lactobacillus, Bifidobacterium, and Streptococcus species on the gut microbiome and metabolome using an in vitro fecal fermentation model derived from a single IBD patient with dysbiosis. Metagenomic analysis demonstrated that increased abundance of beneficial bacteria, such as Lacticaseibacillus rhamnosus, while suppressing opportunistic pathogens, such as Escherichia coli and Enterococcus faecium. Metabolomic profiling further revealed significant alterations in metabolite levels that may help alleviate gut dysbiosis-related symptoms. These included increases in 3-hydroxybutyric acid, ascorbic acid, cadaverine, L-hydroxyproline, and N-acetylornithine and decreases in lysine and 3-aminoalanine. Given the single-donor design and the use of technical replicates, findings are presented as preliminary and descriptive rather than confirmatory. Collectively, these findings support the potential of probiotic fermentation to modulate microbial composition and metabolic output in a dysbiosis-associated context.}, }
@article {pmid41309042, year = {2025}, author = {Lin, QB and Xiao, S and Sheng, YZ and Shen, YX and He, Y and Liu, HY and Ye, YW and Chen, SD}, title = {Case report: Pulmonary extranodal mucosa-associated lymphoid tissue lymphoma with eosinophilia diagnosed via exclusion using metagenomic next-generation sequencing.}, journal = {The Journal of international medical research}, volume = {53}, number = {11}, pages = {3000605251399037}, doi = {10.1177/03000605251399037}, pmid = {41309042}, issn = {1473-2300}, mesh = {Humans ; Male ; *Lymphoma, B-Cell, Marginal Zone/diagnosis/genetics/complications/pathology ; *High-Throughput Nucleotide Sequencing ; *Lung Neoplasms/diagnosis/genetics/pathology/complications ; Adult ; *Eosinophilia/diagnosis/genetics/complications/pathology ; *Metagenomics/methods ; Tomography, X-Ray Computed ; Bronchoscopy ; Bronchoalveolar Lavage Fluid ; }, abstract = {Pulmonary extranodal mucosa-associated lymphoid tissue lymphoma (MALToma) is a slow-growing lymphoma often misdiagnosed or undiagnosed due to its nonspecific clinical symptoms. A man in his late 30s initially presented with cough, sputum production, and chest pain, which improved after antibiotic treatment. A definitive diagnosis of pulmonary MALToma was established via bronchoscopic biopsy. Following the exclusion of alternative diagnoses through metagenomic next-generation sequencing of bronchoalveolar lavage fluid, the marked eosinophilia and diverse chest computed tomography findings highlight the need for clinical awareness of this disease.}, }
@article {pmid41308933, year = {2025}, author = {Yue, J and Han, X and Yu, J}, title = {Multi-omics insights into ultra-rapid formation of aerobic granular sludge in 9 % salinity wastewater by filling of halotolerant loose mycelial pellets.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {133705}, doi = {10.1016/j.biortech.2025.133705}, pmid = {41308933}, issn = {1873-2976}, abstract = {Salt-tolerant aerobic granular sludge (SAGS) had great potential in ultra-hypersaline wastewater treatment while slow and unstable formation hindered its application. Mycelial pellets (MPs) inoculation strategy could accelerate SAGS formation but collapse or peeling commonly occurred due to dense hyphal structures hindering microbial colonization in the connection layer between the shell and core. Besides, no MPs were reported to maintain structure under ultra-hypersaline environment. Herein, a novel strategy using newly-isolated ultra-high salt tolerant fungi Penicillium steckii NCSL-JXA6 with a loose MPs structure was applied for AGS start-up in 9 % salinity wastewater. Granulation completed on Day 1 and maintained stable for 97 days (D10 &amp; D50 > 200 μm, SVI30/SVI5 = 1), which was the fastest under similar salinity. SEM and stained cross-sectional slides showed the loose MPs structure allowed early inner microbial colonization and dense connection layer and core formed before hyphae collapsed, enabling stable transition within 27 days without fragmentation or peeling. Extracellular polymeric substances (EPS) and acyl-homoserine lactone signals (AHLs) (mainly PN, C8-HSL, C12-HSL) increased during transition period, supporting rapid microbial colonization. High TOC and TN removal (∼93 % and ∼ 82 %, respectively) was obtained within only 5 days. Metaproteomic analysis identified Penicillium as module hub of community. Integrative metagenomics and metaproteomics revealed upregulated colonization-related pathways and further confirmed that Penicillium steckii NCSL-JXA6 probably facilitated microbial colonization through metabolic complementarity, adhesion sites, and a loose hyphal structure easily enabling bacterial sensing, motility, adhesion, and biofilm construction. This study proposed a novel loose MPs inoculation theory and achieved the fastest SAGS formation in ultra-hypersaline wastewater.}, }
@article {pmid41308930, year = {2025}, author = {Wang, S and Dai, B and Wang, Z and Yang, S and Xia, S and Rittmann, BE}, title = {S[0] powder as biofilm carrier and electron donor enhances autotrophic nitrogen removal in sulfur-driven partial denitrification coupled with anammox.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {133707}, doi = {10.1016/j.biortech.2025.133707}, pmid = {41308930}, issn = {1873-2976}, abstract = {Sulfur-driven partial denitrification coupled with anammox (SPD/A) has been proposed as an innovative strategy for nitrogen removal from wastewater. This study proposes a novel strategy that integrates 20-μm S[0] powders with anammox granules to establish S[0]-driven partial denitrification coupled with anammox (i.e., S[0]PD/A) for the simultaneous removal of NH4[+] and NO3[-] from wastewater. When the influent concentrations of NH4[+] and NO3[-] were maintained at 31 and 52 mg-N/L, respectively, the efficiency of total-nitrogen removal reached 92 %, with anammox, S[0]-driven denitrification, and sulfammox accounting for 71 %, 27.4 %, and 1.6 %, respectively. Microbial community analysis revealed that anammox bacteria and sulfur-oxidizing bacteria were dominant functional genera involved in the S[0]PD/A. Anammox bacteria were enriched in anammox granules, and sulfur-oxidizing bacteria were enriched in microgranules of S[0] powders and Candidatus Brocadia. These findings highlight distinct microbial niche differentiation, elucidate nitrogen-sulfur metabolic interactions, and offer insights into an autotrophic process for total-nitrogen removal.}, }
@article {pmid41308739, year = {2025}, author = {Zhang, Y and Liu, J and Zhang, X and Cheng, S and Liu, S and Huang, A and Yu, Y and Liu, J and Chen, H and Shang, D and Yin, P and Ma, S}, title = {Rhein alleviates acute pancreatitis by inhibiting TMAO-mediated inflammatory signaling pathways and reducing acinar cell injury.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2025.11.056}, pmid = {41308739}, issn = {2090-1224}, abstract = {INTRODUCTION: Acute pancreatitis (AP) represents a significant global health challenge. Despite recent advances in medical treatment, the development of novel therapeutic strategies remains crucial.<br><br>OBJECTIVES: Rhein, a natural compound of the Chinese herb Rheum, shows promise in the treatment of AP. However, the exact mechanism underlying its therapeutic effect is still not fully understood.<br><br>METHODS: To investigate the association between the rhein-related gut microbiota and AP, we conducted antibiotic-mediated microbiota depletion experiments, fecal microbiota transplantation (FMT), and in vitro bacterial culture experiments. Concurrently, we performed 16S rRNA gene sequencing, metagenomic sequencing, and liquid chromatography&#x2012;mass spectrometry (LC&#x2012;MS) analyses on mouse fecal samples to characterize alterations in the microbiota and metabolome. Transcriptomic studies were also performed to elucidate the mechanisms underlying acinar cell inflammation.<br><br>RESULTS: Rhein alleviated AP by modulating the gut microbiota, as demonstrated by changes in the gut microbiota composition and improvements in AP after FMT in rhein-treated mice compared with those in cerulein-induced AP mice. Specifically, rhein is concentrated mainly in the stomach and intestines, where it exerts anti-inflammatory effects on acinar cells by antagonizing the TLR4/NF-&#x3ba;B/NLRP3 signaling pathway activated by trimethylamine-N-oxide (TMAO). This mechanism is associated with lipid peroxidation and necrosis mediated by oxidative stress. Clinically, disease severity in patients with AP is positively correlated with serum TMAO concentration.<br><br>CONCLUSION: Rhein alleviates AP by modulating the intestinal microbiota to reduce TMAO production, thereby suppressing TMAO-induced activation of the TLR4/NF-&#x3ba;B/NLRP3 signaling pathway and inhibiting acinar cell inflammation.}, }
@article {pmid41308447, year = {2025}, author = {Yang, Z and Chen, B and Zhang, Q and Hu, X and Sun, L and Lu, T and Zhu, L and Ma, Y and Zhong, H and Ni, Y and Qian, H}, title = {Potential of traditional Chinese medicine as an antibiotic alternative for mitigating antibiotic resistance: A case study of Tetrastigma hemsleyanum.}, journal = {Journal of hazardous materials}, volume = {500}, number = {}, pages = {140613}, doi = {10.1016/j.jhazmat.2025.140613}, pmid = {41308447}, issn = {1873-3336}, abstract = {The overuse of antibiotics in livestock production has accelerated the spread of antibiotic resistance genes (ARGs), posing a serious global public health threat. Identification of safe and effective alternatives to antibiotics has therefore become a research priority. Tetrastigma hemsleyanum (TH), a traditional Chinese medicine, modulates the intestinal microbiota; however, the mechanisms underlying its antibiotic-like effects are not fully understood. In this study, we investigated the anti-inflammatory effects of TH in a lipopolysaccharide-induced mouse model of intestinal inflammation. Metagenomic sequencing was used to evaluate its effects on intestinal microbiota composition and ARG abundance. TH effectively alleviated intestinal inflammation, significantly increased the abundance of beneficial microbes such as Lactobacillus, and suppressed the proliferation of major ARG-carrying pathogens, including Proteus and Shigella. Functional analysis revealed that TH treatment markedly enhanced the Wnt and TGF-β signaling pathways, which are associated with intestinal barrier repair and immune response regulation, respectively. Furthermore, TH supplementation restored ARG diversity, reduced the abundance of high-risk ARGs, and suppressed the spread of multidrug resistance genes, underscoring its potential for mitigating antibiotic resistance risks. These findings highlight the potential of TH as an alternative antibiotic and may be used as a feed additive to reduce antibiotic usage while enhancing animal health.}, }
@article {pmid41308344, year = {2025}, author = {Mao, YL and Hu, Y and Wu, ZP and Sun, YP and Hou, J and Cui, HL}, title = {Natronorubrum marinum sp. nov., Natronorubrum amylolyticum sp. nov., Natronorubrum halobium sp. nov., and Natronorubrum salinum sp. nov., halophilic archaea from a coastal saline-alkali land and two saline lakes.}, journal = {Systematic and applied microbiology}, volume = {49}, number = {1}, pages = {126680}, doi = {10.1016/j.syapm.2025.126680}, pmid = {41308344}, issn = {1618-0984}, abstract = {Four novel halophilic archaeal strains, DTA7[T], DTA28[T], FCH18a[T], and WLHS9[T], were isolated from a coastal saline-alkali land and two saline lakes in China. The metagenomic analyses revealed that the coastal saline-alkali land from Dongtai tidal flat the highest relative abundance of archaea compared to the saline sediment samples of Feicui Salt Lake and Wulanhushao Salt Lake. These four strains showed high sequence similarities to current species within the genus Natronorubrum judged by 16S rRNA gene and rpoB' gene sequence similarities, and formed tight clusters with current Natronorubrum species based on the phylogenies of these two house-keeping genes. Phylogenomic analysis confirmed the phylogenies based on 16S rRNA gene and rpoB' genes. Comparative genomic analysis revealed that the average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), and average amino acid identity (AAI) values among these four strains and existing species of the genus Natronorubrum were 76.8-92.7 %, 22.8-52.7 %, and 73.4-94.7 %, respectively. These overall genome-related indexes were significantly below the thresholds for species delineation. These four strains showed optimal growth at 1.7-3.1 M NaCl, 37 °C, and pH 7.0-9.5. Strain WLHS9[T] was found to be a neutrophilic halophile, while the others exhibited alkaliphilic halophilic characteristics. The major phospholipids detected in these four strains included phosphatidic acid (PA), phosphatidylglycerol (PG), and phosphatidylglycerol phosphate methyl ester (PGP-Me). The glycolipid of strain WLHS9[T] was identical to that of the current neutrophilic species of Natronorubrum. Based on phylogenetic analysis, phenotypic characteristics, polar lipid profiles, and phylogenomic data, strains DTA7[T], DTA28[T], FCH18a[T], and WLHS9[T] represent four novel species within the genus, namely, Natronorubrum marinum sp. nov., Natronorubrum amylolyticum sp. nov., Natronorubrum halobium sp. nov., and Natronorubrum salinum sp. nov., respectively.}, }
@article {pmid41307726, year = {2025}, author = {Ferreira, CM and de Affonseca, DB and Barbosa, FAS and Campos, AB and Menezes, R and Brait, L and Viana, PAB and Trindade-Silva, AE and Loiola, M and Azevedo, AR and Coutinho, FH and Assis, APA and Bruce, T and Ramos, PIP and Ara, A and Brouns, R and Andrade, RFS and Guimarães, PR and Meirelles, PM}, title = {Rare Phyla, Such as CPR and DPANN, Shape Ecosystem-Level Microbial Community Structure Dissimilarities.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02595-0}, pmid = {41307726}, issn = {1432-184X}, support = {88887-468244-2019-00//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 114693/2022-6//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; RYC2022-037094-I//Ministerio de Ciencia e Innovaci&#xf3;n/ ; Serra-1709-17818//Instituto Serrapilheira/ ; }, abstract = {Rare microbial lineages, such as members of the candidate phyla radiation (CPR) bacteria and Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN) archaea, are increasingly recognized as key components of microbial communities in natural systems. Yet, their global distribution, biogeographic patterns, and broader role in shaping microbial community structure across diverse ecosystems remain poorly characterized. Here, we analyzed 2860 metagenomes spanning nine ecosystems using a curated reference database and a bias-aware taxonomic filtering approach to quantify the richness, relative abundance, and structural influence of low-abundance microbial taxa on community structure across a wide range of ecosystems. Our findings reveal that rare taxa, primarily CPR and DPANN, disproportionately shape microbial community dissimilarities across global ecosystems. We observed that the richness of these two groups, that drives community structure variation, increases with latitude, peaking in temperate regions, thereby contrasting classical latitudinal diversity patterns and suggesting unique biogeographic drivers. CPR and DPANN were predominantly enriched in free-living environments, particularly groundwater and soil, then in host-associated habitats, consistent with niche specialization shaped by environmental filtering and dispersal constraints. These findings challenge abundance-centric assumptions in microbial ecology and highlight the need to integrate low-abundance taxa into macroecological frameworks. Fully resolving their ecological functions, however, will require targeted experimental and multi-omics investigations.}, }
@article {pmid41307551, year = {2025}, author = {Tamura, T and Ohsugi, Y and Katagiri, S and Kusano, A and Handa, T and Lin, P and Liu, A and Toyoshima, K and Takagi, S and Shiwaku, H and Sugihara, G and Takahashi, H}, title = {Oral Microbiota Associated With Cognitive Impairment in Schizophrenia: Composition and PICRUSt2-Predicted Functional Pathways.}, journal = {Schizophrenia bulletin}, volume = {}, number = {}, pages = {}, doi = {10.1093/schbul/sbaf212}, pmid = {41307551}, issn = {1745-1701}, support = {24K18736//KAKENHI JP/ ; 24K12944//KAKENHI JP/ ; 24K02619//KAKENHI JP/ ; //Ministry of Education, Culture, Sports, Science and Technology of Japan/ ; //Enomoto Mental Health Association/ ; }, abstract = {BACKGROUND AND HYPOTHESIS: Cognitive impairment is a core disabling feature of schizophrenia (SZ). Changes in gut microbiota have been linked to cognitive dysfunction in SZ; however, changes in the oral microbiota in relation to immune dysregulation have only been recently reported, and their relevance to cognition remains unclear. The objective of this study was to explore the relationship between oral microbiota alterations and cognitive impairment in patients with SZ and to evaluate potential mediating mechanisms, including neuroinflammation and microbial functions.<br><br>STUDY DESIGN: In this cross-sectional study, we recruited 68 patients with SZ and 32 healthy controls (HC). Cognitive function was assessed using the Wechsler Adult Intelligence Scale-Fourth Edition. Oral microbiota composition was characterized by 16S rRNA gene sequencing, and microbial functions were predicted using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2 (PICRUSt2) based on the 16S profiles. Neuroinflammation was assessed using peripheral kynurenine (KYN) pathway activity as a proxy.<br><br>STUDY RESULTS: The patients with SZ exhibited significantly lower oral microbiota alpha diversity (driven by reduced evenness) and showed greater cognitive impairment and differences in the KYN pathway markers (neuroinflammation proxies) compared to HC. They also showed shifts in specific bacterial genera and the PICRUSt2-predicted functional pathways. Importantly, the oral microbiota alterations were significantly associated with cognitive impairment. Exploratory mediation analysis suggested that several pathways, including glycan biosynthesis and metabolism, may play a role in this association. In contrast, KYN pathway markers showed no significant association.<br><br>CONCLUSIONS: Our findings show an association between the oral microbiota alpha diversity and cognitive impairment in SZ, with the PICRUSt2-predicted functional pathways potentially implicated.}, }
@article {pmid41307322, year = {2025}, author = {Baima, G and Dabdoub, S and Thumbigere-Math, V and Ribaldone, DG and Caviglia, GP and Tenori, L and Fantato, L and Vignoli, A and Romandini, M and Ferrocino, I and Aimetti, M}, title = {Multi-Omics Signatures of Periodontitis and Periodontal Therapy on the Oral and Gut Microbiome.}, journal = {Journal of periodontal research}, volume = {}, number = {}, pages = {}, doi = {10.1111/jre.70055}, pmid = {41307322}, issn = {1600-0765}, support = {CUP B83C22004800006//Next Generation EU/ ; DM 1557 11.10.2022//Next Generation EU/ ; Prot. P2022YEX5R//Next Generation EU Program and the Italian Ministry of University and Research/ ; }, abstract = {AIM: To characterize the impact of periodontitis and of Steps I-II of periodontal therapy on microbiome composition, function, and metabolic output across the oral and gut environments.<br><br>METHODS: A multi-omics analysis was performed on saliva and stool samples collected from 50 systemically healthy individuals with and without Stage III-IV periodontitis. For participants with periodontitis, samples were analyzed both at baseline and 3&#x2009;months after Steps I-II of periodontal therapy. High-throughput whole metagenome sequencing was used to profile microbial taxa and functional genes, NMR-based metabolomics profiled host-microbial metabolites. Single-omic differential abundance analysis between healthy samples and periodontitis samples was performed with MaAsLin2, while analysis between pre- and post-treatment was conducted with timeOmics. Variable selection and subsequent supervised multivariate analysis to determine group-separating markers utilized multi-level sparse Partial Least Squares Discriminant Analysis (sPLS-DA) through mixOmics. KEGG pathway enrichment was analyzed using clusterProfiler, whereas multi-omic data integration was performed with multi-block Partial Least Squares regression analysis.<br><br>RESULTS: Periodontitis was associated with significant compositional and functional changes in both saliva and stool, with increased abundance of pathobionts and loss of health-associated taxa in both niches. A subset of species was shared across oral and gut habitats, with detectable differences across clinical groups. As functional potential, periodontitis enriched microbial pro-inflammatory pathways (lipopolysaccharide biosynthesis, bacterial motility) and depleted beneficial short-chain fatty acid (SCFA)- and vitamin-producing functions. Metabolomic profiles revealed reduced SCFAs and amino acids in periodontitis, with elevated pro-inflammatory metabolites (succinate, trimethylamine) in both saliva and stool. Following therapy, microbial communities and their metabolic output partially reverted toward health-associated profiles, particularly in saliva. Stool samples showed subtler but consistent shifts, including a decrease in some typically oral species and decreased succinate and methylamine and restoration of amino acid and SCFA-related metabolites.<br><br>CONCLUSIONS: Periodontitis is associated with coordinated microbial and metabolic signatures across the oral and gut environments. Non-surgical periodontal therapy promotes partial ecological restoration in both niches, supporting the view of oral health as a modifiable target for influencing systemic microbial homeostasis.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov identification number: NCT04826926.}, }
@article {pmid41306993, year = {2025}, author = {Cai, X and Yi, H and Chen, K and Dai, J and Yi, J and Tu, B and Wang, Y and Li, J and Zhuang, J}, title = {Meta-Analysis of the Application Value of Metagenomic Next-Generation Sequencing Technology in the Diagnosis of Infectious Diseases of the Spine.}, journal = {JOR spine}, volume = {8}, number = {4}, pages = {e70134}, pmid = {41306993}, issn = {2572-1143}, abstract = {OBJECTIVE: To evaluate the diagnostic efficacy of metagenomic next-generation sequencing (mNGS) in infectious diseases of the spine (IDS).<br><br>METHODS: Systematic literature on the application of mNGS in the diagnosis of IDS was retrieved by two independent researchers from databases including Pubmed, China National Knowledge Infrastructure (CNKI), Wanfang, and VIP from the inception to 30 November 2024. Meta-analysis was conducted using Meta-Disc 1.4 and Stata 18.0 software.<br><br>RESULTS: The initial search identified 314 articles. After applying predefined inclusion and exclusion criteria, 15 studies were included, encompassing 1236 patients, of which 835 had confirmed IDS. Meta-analysis revealed that the pooled sensitivity and specificity of mNGS for IDS diagnosis were 0.95 (95% CI: 0.88-0.98) and 0.60 (95% CI: 0.48-0.71), respectively. The positive likelihood ratio was 2.3 (95% CI: 1.7-3.2), and the negative likelihood ratio was 0.09 (95% CI: 0.04-0.22). The pooled diagnostic odds ratio was 26 (95% CI: 9-75), with an area under the summary receiver operating characteristic curve of 0.85 (95% CI: 0.82-0.88).<br><br>CONCLUSION: The primary diagnostic value of mNGS lies in its ability to serve as a rapid screening tool for disease exclusion. However, for diagnosing IDS, it is essential to integrate other clinical indicators for a comprehensive assessment to confirm the diagnosis.}, }
@article {pmid41306730, year = {2025}, author = {Nielsen, AB and Kvist-Hansen, A and Todberg, T and Zachariae, C and Pedersen, O and Skov, L}, title = {Dysbiosis of the Saliva Microbiota in Patients with Psoriasis: A Case-Control Study.}, journal = {Journal of inflammation research}, volume = {18}, number = {}, pages = {16315-16330}, pmid = {41306730}, issn = {1178-7031}, abstract = {PURPOSE: Accumulating evidence supports the association between altered salivary microbiota and inflammatory diseases. The existing literature on the salivary microbiota in patients with psoriasis is limited. However, differences in the prevalence of Candida species and abundance of several bacterial taxa in saliva have been found between patients and controls. This study aimed to investigate the differences in the composition and functional potential of salivary microbiota in patients with psoriasis compared to their cohabiting partners and healthy controls.<br><br>PATIENTS AND METHODS: Samples from 115 of 123 individuals qualified for statistical analysis: patients with psoriasis who did not receive systemic anti-psoriatic treatment (n=47); cohabiting partners (n=21); and age-, sex-, and BMI-matched healthy controls (n=47). One saliva sample was collected from each participant and analysed by shotgun metagenomic sequencing.<br><br>RESULTS: A difference in the &#x3b1;-diversity of bacterial species was observed exclusively between patients and controls, with a lower diversity in patients (p=0.041). Variation in bacterial composition (&#x3b2;-diversity) was influenced by smoking (p=0.001) and diet (p=0.025) but not by group status. Using a linear regression model adjusted for smoking and diet, we identified four bacterial classes and five species that were significantly different between the patient, partner, and control groups. One Kyoto Encyclopedia of Genes and Genomes module differed significantly between patients with psoriasis and their partners. No differences in Candida species or abundance were found among the three groups.<br><br>CONCLUSION: Comparison of salivary microbiota at the levels of bacterial diversity, composition, and predicted function indicated that psoriasis cases are characterised by dysbiosis.}, }
@article {pmid41306593, year = {2025}, author = {Xu, H and Xu, Y and Gu, J and Wang, X and Liao, B and Zhou, P and Wu, S and Tao, R and Fu, Y}, title = {Clinical characteristics of Treponema denticola-associated lung abscess diagnosed by metagenomic next-generation sequencing: a case series analysis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1688498}, pmid = {41306593}, issn = {2235-2988}, mesh = {Humans ; Male ; Middle Aged ; *Treponema denticola/genetics/isolation &amp; purification ; *High-Throughput Nucleotide Sequencing ; *Lung Abscess/microbiology/diagnosis/drug therapy ; Retrospective Studies ; Female ; Aged ; Metagenomics/methods ; Anti-Bacterial Agents/therapeutic use ; *Treponemal Infections/diagnosis/microbiology/drug therapy ; Adult ; }, abstract = {INTRODUCTION: Treponema denticola is an oral anaerobic bacterium commonly associated with periodontitis, but its role in lower respiratory tract infections (e.g., lung abscess) has long been overlooked. For bacteria that grow anaerobically, traditional culture methods exhibit low detection rates, which directly lead to the mis-diagnosis of anaerobic infection. With the ultilization of metagenomic next-generation sequencing (mNGS) in clinical practice, we studied the clinical features and treatment strategies of T. denticola-associated lung abscess.<br><br>METHODS: A retrospective analysis was conducted on patients confirmed with T. denticola lung abscess by mNGS from October 2023 to October 2024. Routine aerobic bacterial culture and stains were used. Histopathological analysis and Warthin-Starry silver staining was completed on samples from lung tissue. A literature review was performed using PubMed and CNKI (up to June 2025).<br><br>RESULTS: Seven patients were diagnosed with T. denticola lung abscess under mNGS. The cohort predominantly comprised elderly males (mean age 62.3 years), all of whom had underlying oral diseases. Clinical manifestations featured chronic cough (mean symptom duration 3.6 months) and frequent hemoptysis (85.7%), with notably mild systemic inflammation (only one febrile case). Characteristic CT findings included mass-like lesions with necrosis (100%) and cavitation (71.4%), without air-fluid levels. Conventional cultures were overwhelmingly negative, whereas mNGS detected T. denticola in all seven cases. Among the seven patients, one showed clinical improvement after two months of amoxicillin-clavulanate therapy, and another responded well to seven months of doxycycline treatment. The remaining five patients initially treated with levofloxacin or moxifloxacin demonstrated poor responses, with three cases ultimately requiring surgical resection of the lesions.<br><br>DISCUSSION: T. denticola lung abscess is most commonly seen in individuals with poor oral hygiene. It presents as an indolent, chronic course and a high incidence of hemoptysis. Typical CT findings include a mass-like lesion with cavitation but no air-fluid level. Traditional microbiological detection often yield false negative results, making mNGS a critical diagnostic tool. First-line therapy should include &#x3b2;-lactams or tetracyclines, and surgery is warranted for refractory cases or massive hemoptysis.}, }
@article {pmid41306589, year = {2025}, author = {Yu, HL and Liu, R and Wang, HT and Hou, QY and Qin, Y and Yang, X and Gao, ZQ and Yang, LH and Zhao, Q and Ma, H}, title = {Metagenomic analysis of gut microbiota composition and function in wild mice (Rattus flavipectus) infected with Enterocytozoon bieneusi.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1708266}, pmid = {41306589}, issn = {2235-2988}, mesh = {Animals ; *Enterocytozoon ; *Gastrointestinal Microbiome/genetics ; Metagenomics ; *Microsporidiosis/microbiology/veterinary ; Feces/microbiology ; Mice ; China ; Animals, Wild/microbiology ; Virome ; Bacteria/classification/genetics/isolation &amp; purification ; *Murinae/microbiology ; }, abstract = {BACKGROUND: Enterocytozoon bieneusi (E. bieneusi) is a pathogenic microsporidian that infects a variety of hosts, including wild mice, potentially influencing their gut microbiota. This study aims to explore how E. bieneusi infection influences the gut microbiota composition and function in wild mice.<br><br>METHODS: Fecal samples were collected from 20 wild mice (Rattus flavipectus) in September 2023 in Yunnan Province, China. The PCR results showed that 10 were infected with E. bieneusi and 10 were uninfected, with no samples testing positive for Cryptosporidium spp., Blastocystis, Giardia, Cyclospora or Balantioides coli. DNA was extracted and subjected to metagenomic sequencing using Illumina HiSeq. Gut microbiota composition was assessed using MetaPhlAn4 for species-level annotation. The contigs were used to construct a gene catalog and perform functional annotation. Additionally, viral sequences were identified by analyzing the contigs with software, such as CheckV and Vibrant.<br><br>RESULTS: The gut microbiota diversity showed no significant difference between mice infected with E. bieneusi and the control group, with the dominant phyla being Firmicutes and Bacteroidetes. Virome analysis identified 18,192 high-quality viral sequences, with the E. bieneusi group exhibiting higher viral species diversity. Furthermore, significant differences were observed in 178 viral operational taxonomic units (vOTUs) between the two groups, with 161 vOTUs enriched in the E. bieneusi group. Functional analysis demonstrated significant enrichment of several metabolic pathways in the gut microbiota of wild mice infected with E. bieneusi, particularly in the metabolism of terpenoids and polyketides, digestive system, biosynthesis of other secondary metabolites and metabolism of cofactors and vitamins. Notably, unique virus-bacteria correlations were observed in the E. bieneusi group.<br><br>CONCLUSIONS: E. bieneusi infection significantly alters the gut virome in wild mice, affecting microbial composition and interactions. The infection appears to drive adaptive changes in microbial functions, especially in metabolic processes, suggesting a host response to infection-related stress.}, }
@article {pmid41306406, year = {2025}, author = {Hongbin, W and Jing, X and Xianwei, W and Hui, G and Xutao, F}, title = {Successful Treatment of Escherichia coli-Related Spondylitis With an Extended Meropenem Infusion Time for a 72-Year-Old Woman: A Case Report.}, journal = {Clinical case reports}, volume = {13}, number = {12}, pages = {e71531}, pmid = {41306406}, issn = {2050-0904}, abstract = {Escherichia coli (E. coli) causes spinal infections relatively rarely and is often closely associated with parenteral infections. E. coli spondylitis can cause fever and local pain and, in severe cases, can lead to bone destruction, abscess formation, and even the risk of high paraplegia. Therefore, timely and precise diagnosis and effective treatment are crucial. We report successful conservative management of E. coli spondylitis in a 72-year-old female using metagenomic sequencing-guided prolonged meropenem infusion. Extending the infusion time of meropenem achieved clinical resolution without surgery, demonstrating this strategy's efficacy for carbapenem-sensitive spinal infections.}, }
@article {pmid41306274, year = {2025}, author = {Xue, N and Xia, M and Hu, B and Gong, X and Wang, Z and Zhao, X}, title = {Factors influencing the spatial distributions of river microbial communities at the watershed scale: a case study involving the Wuding River Basin.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1667966}, pmid = {41306274}, issn = {1664-302X}, abstract = {Microbial communities regulate water quality and biogeochemical cycling in rivers, but their responses to geomorphological factors remain unclear. Water samples were collected in August 2024 (summer wet season) from the Wuding River, and metagenomic sequencing was used to investigate microbial community changes and the influences of geomorphological factors. Environment (nutrients, etc.,) exhibited significant spatial heterogeneity with temperature (p < 0.01), total organic carbon (TOC, p < 0.001), dissolved organic carbon (DOC, p < 0.001), chemical oxygen demand (COD, p < 0.05), total phosphorus (TP, p < 0.001) and suspended solids (SS, p < 0.001), which were significantly higher downstream than upstream. Pseudomonadota, Cyanobacteriota, and Actinomycetota were the most important microbial phyla, and Cyanobacteriota (p = 0.016) was significantly more abundant upstream than downstream. The linear discriminant analysis effect size (LEfSe) revealed 8 and 10 biomarkers upstream and downstream, respectively. Upstream microbial communities were adapted to oligotrophic and high-light environments, whereas heterotrophic, carbon-metabolizing communities occurred downstream. Significantly higher ACE (p < 0.05), Chao1 (p < 0.05), Shannon (p < 0.001), and Pielou's evenness (p < 0.001) indices were observed downstream than upstream. The relative abundance of genes associated with carbon cycling (the methane metabolism pathway, TCA cycle, and rTCA cycle) was greater downstream than upstream, as was the relative abundance of nitrogen functional genes. Elevation affected the upstream microbial communities, whereas temperature, TP, TOC, and nitrate nitrogen (NO3-N) affected the downstream communities. The results improve our understanding of how geomorphology drives the environmental factors and then governs the microbial community and their carbon and nitrogen cycling pathways.}, }
@article {pmid41306264, year = {2025}, author = {Shi, Y and Wang, X and Mao, X and Mi, L and Liu, W and Wang, N}, title = {Severe mitral valve papillary muscle rupture of isolated Whipple's endocarditis: a case report and review of the literature.}, journal = {Frontiers in cardiovascular medicine}, volume = {12}, number = {}, pages = {1669997}, pmid = {41306264}, issn = {2297-055X}, abstract = {BACKGROUND: Tropheryma whipplei endocarditis (TWE) is rarely reported. Diagnosis is particularly challenging when it occurs as isolated TWE without classical manifestations of Whipple's disease.<br><br>CASE PRESENTATION: A 35-year-old Asian female with systemic lupus erythematosus presented with acute heart failure secondary to mitral valve papillary muscle rupture as her sole symptom, requiring emergent veno-arterial extracorporeal membrane oxygenation support and urgent valve replacement. Intraoperative absence of vegetations and negative conventional microbiological examination preliminarily ruled out infective endocarditis. However, on postoperative day (POD) 3, her condition rapidly deteriorated into septic shock. Follow-up chest CT revealed bilateral asymmetric pulmonary infiltrates inconsistent with cardiogenic pulmonary edema alone. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid detected T. whipplei, providing a crucial diagnostic breakthrough. Subsequent periodic acid-Schiff staining of the resected valve confirmed the definitive diagnosis of isolated TWE. Targeted meropenem therapy for 5 days resulted in significant improvement in both pneumonia and septic shock, permitting ECMO discontinuation. The patient was successfully extubated by POD 12 and discharged on POD 22 with oral co-trimoxazole and doxycycline in a stable condition.<br><br>CONCLUSION: We present the first case of isolated TWE in a young Asian female, notable for its atypical clinical presentation, fulminant progression, and profound diagnostic challenges. Clinicians should maintain a high vigilance for blood culture-negative endocarditis. Timely diagnosis and appropriate treatment are crucial for improving prognosis. mNGS analysis of samples from suspected disseminated sites may yield crucial diagnostic breakthrough.}, }
@article {pmid41305954, year = {2025}, author = {Osei Sekyere, J}, title = {Next-Generation Sequencing in Infectious-Disease Diagnostics: Economic, Regulatory, and Clinical Pathways to Adoption.}, journal = {MicrobiologyOpen}, volume = {14}, number = {6}, pages = {e70104}, doi = {10.1002/mbo3.70104}, pmid = {41305954}, issn = {2045-8827}, support = {//The author received no specific funding for this study./ ; }, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/economics/methods ; *Communicable Diseases/diagnosis ; *Molecular Diagnostic Techniques/economics/methods ; Whole Genome Sequencing/economics/methods ; Polymerase Chain Reaction/economics/methods ; }, abstract = {Next-generation sequencing (NGS) has emerged as a transformative tool for infectious disease diagnosis, offering broad pathogen detection, antimicrobial resistance profiling, and syndromic panel testing. However, widespread clinical adoption remains hindered by insurance reimbursement challenges, high costs, and regulatory barriers. Unlike polymerase chain reaction (PCR), which enjoys well-established Current Procedural Terminology (CPT) codes and reimbursement pathways, many NGS-based tests lack standardized billing mechanisms, discouraging laboratories from integrating NGS into routine diagnostics. This article explores the economic, clinical, and technological considerations of targeted amplicon sequencing (tNGS) versus PCR and whole-genome sequencing (WGS), demonstrating how optimized multiplexing strategies, emerging NGS platforms, and regulatory advancements can enhance feasibility. It is argued that insurance policies must evolve to recognize NGS's superior clinical utility in detecting polymicrobial infections, emerging pathogens, and antimicrobial resistance determinants, ultimately improving patient outcomes and reducing healthcare costs. Current reagent-only costs now average US $65 per microbial genome, US $600 per 30× human genome, and US $130-600 per metagenomic sample when multiplexed; these figures continue to fall with higher multiplexing. To accelerate equitable adoption, we recommend near-term payer coverage pilots for clearly defined clinical indications, dedicated CPT pathways for infectious-disease sequencing (including metagenomic assays), and pragmatic validation frameworks that acknowledge genotype-phenotype limits while leveraging multiplexing and centralized reference workflows.}, }
@article {pmid41305578, year = {2025}, author = {Rehner, J and Gund, M and Becker, SL and Hannig, M and Rupf, S and Schattenberg, JM and Keller, A and The Imagine Consortium,  and Molano, LG and Keller, V}, title = {Joint Bacterial Traces in the Gut and Oral Cavity of Obesity Patients Provide Evidence for Saliva as a Rich Microbial Biomarker Source.}, journal = {Nutrients}, volume = {17}, number = {22}, pages = {}, doi = {10.3390/nu17223527}, pmid = {41305578}, issn = {2072-6643}, support = {469073465//DFG/ ; }, mesh = {Humans ; *Saliva/microbiology ; *Obesity/microbiology ; *Gastrointestinal Microbiome ; Feces/microbiology ; *Mouth/microbiology ; Male ; Female ; Biomarkers/analysis ; Middle Aged ; Adult ; Dental Plaque/microbiology ; *Bacteria/isolation &amp; purification/classification/genetics ; Metagenome ; }, abstract = {Background: The human microbiome holds promise for identifying biomarkers and therapeutic targets. In obesity, interactions between oral and gut communities are increasingly implicated and end in organ injury. Methods: From the IMAGINE study, we analyzed 418 shotgun metagenomes from three specimen types (dental plaque (n = 143; 65 non-obese, 78 obese), saliva (n = 166; 75 non-obese, 91 obese), and stool (n = 109; 57 non-obese, 52 obese)) to compare site-specific microbial shifts between obese (BMI > 30 kg/m[2]) and non-obese individuals. Differential abundance was assessed with ANCOM-BC; effect sizes were summarized as Cohen's d. Results: Across all samples, we detected 240 bacterial species in plaque, 229 in saliva, and 231 in stool, with 46 species present across all three sites. Absolute effect sizes were significantly larger in plaque (mean |d| = 0.26) and saliva (0.25) than in stool (0.21; p = 9 × 10[-3]). Several taxa showed an opposite directionality between oral and gut sites, including Streptococcus salivarius and Bifidobacterium longum, indicating site-specific associations. Notably, Actinomyces sp. and Streptococcus sp. exhibited promising effect sizes as diagnostic markers. Conclusions: The oral and gut microbiomes capture complementary obesity-related signals, with stronger shifts observed in oral sites. We suggest that integrating oral and gut profiling could enhance diagnostic and therapeutic strategies in obesity.}, }
@article {pmid41305529, year = {2025}, author = {Dong, Y and Fan, S and Zhu, L and Sharshov, K and Wang, W}, title = {Viromic Insights into Gut RNA Virus Diversity Among Three Corvid Species.}, journal = {Viruses}, volume = {17}, number = {11}, pages = {}, doi = {10.3390/v17111508}, pmid = {41305529}, issn = {1999-4915}, support = {grant No. 2022-HZ-812//the program of science and technology international cooperation project of Qinghai province/ ; grant No. 32111530018//the National Natural Science Foundation of China and Russian Foundation for Basic Research Cooperative Exchange Project/ ; }, mesh = {Animals ; *RNA Viruses/genetics/classification/isolation &amp; purification ; Phylogeny ; Metagenomics ; *Crows/virology ; *Gastrointestinal Microbiome ; *Virome ; *Birds/virology ; Genome, Viral ; Tibet ; Genetic Variation ; }, abstract = {As viromics advances, the diversity and ecological significance of RNA viruses in global ecosystems are gaining growing recognition. Nevertheless, studies on RNA viruses in wildlife, especially non-model avian species, are still relatively scarce. This study employed viral metagenomics to systematically characterize the gut RNA viromes of three widely distributed corvid species on the Qinghai-Tibet Plateau: the Red-billed chough (Pyrrhocorax pyrrhocorax), Daurian jackdaw (Coloeus dauuricus), and Rook (Corvus frugilegus). These three corvid species are closely associated with human-inhabited areas on the Qinghai-Tibet Plateau and display distinctive scavenging behaviors that may lower their exposure to environmental pathogens while concurrently elevating their risk of viral infection, rendering them key targets for viral surveillance and research into zoonotic disease transmission. The analysis annotated viral communities into 4 phyla and 8 classes, with Pisuviricota and Kitrinoviricota emerging as the predominant phyla in all samples. Alpha diversity analysis indicated no significant differences among groups, while beta diversity showed significant compositional differences. KEGG annotation revealed that enriched functional pathways were mainly concentrated in "Global and overview maps", "Drug resistance: antimicrobial", and "Biosynthesis of other secondary metabolites". Furthermore, 4 antibiotic resistance genes and 13 putative virulence factor genes were identified. Phylogenetic analysis further indicated that several identified viruses have the potential for cross-species transmission, underscoring the pivotal role of wild birds in viral ecosystems and disease spread. This study uncovered multi-faceted features of the gut RNA viromes in the three crow species, spanning structural, functional, and evolutionary dimensions. These results offer novel perspectives on the viromes of wild corvids and their potential contributions to viral emergence and dissemination in the Qinghai-Tibet Plateau ecosystem.}, }
@article {pmid41305512, year = {2025}, author = {Storms, S and Lim, A and Savard, C and Olivera, YR and Kayastha, S and Wang, L}, title = {Identification of Hunnivirus in Bovine and Caprine Samples in North America.}, journal = {Viruses}, volume = {17}, number = {11}, pages = {}, doi = {10.3390/v17111491}, pmid = {41305512}, issn = {1999-4915}, support = {1U18FD006673//Food and Drug Administration Veterinary Laboratory Investigation and Response Network/ ; }, mesh = {Animals ; Cattle ; Goats/virology ; Phylogeny ; Feces/virology ; Genome, Viral ; *Cattle Diseases/virology ; North America/epidemiology ; *Goat Diseases/virology ; High-Throughput Nucleotide Sequencing ; *Diarrhea/veterinary/virology ; Sheep ; Metagenomics ; }, abstract = {Diarrhea in young ruminants is a global issue and causes significant economic losses worldwide. In addition to common pathogens like rotavirus, coronavirus, and astrovirus, new viruses can be identified through unbiased next-generation sequencing (NGS) techniques. Here, we report the initial identification of a hunnivirus from a one-month-old goat with diarrhea using shotgun metagenomic NGS. A complete hunnivirus genome was recovered. Phylogenetic tree analysis revealed that this goat hunnivirus was more closely related to cattle hunnivirus than to small ruminant hunnivirus strains, suggesting a prior cross-species transmission event. The genome was used to design primers/probes for the conserved 3D[pol] RdRP gene for real-time RT-PCR to screen banked ruminant fecal samples. Screening of 144 ruminant fecal samples showed that 9 of 38 goat, 22 of 96 cattle, and 0 of 8 sheep samples were positive for hunnivirus. Sequencing of the 3D[po] region was performed on selected positive samples and revealed two lineages of hunnivirus circulating in North America. Our study highlights the importance of further investigation and monitoring of fecal samples using unbiased metagenomic tools to identify potential pathogens or co-infections in ruminants.}, }
@article {pmid41305373, year = {2025}, author = {Pham, TTN and Dao, TK and Nguyen, TVH and Phung, TBT and Nguyen, HD and Nguyen, TQ and Le, TTH and Do, TH}, title = {Diversity and Functional Predictions of Gut Microbiota in Vietnamese Children Aged 6-24 Months with Persistent Diarrhea of Unknown Etiology.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {11}, pages = {}, doi = {10.3390/pathogens14111136}, pmid = {41305373}, issn = {2076-0817}, support = {&#x110;T&#x110;LCN.63/22//Ministry of Science and Technology/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Infant ; *Diarrhea/microbiology ; Male ; Female ; Feces/microbiology ; Child, Preschool ; RNA, Ribosomal, 16S/genetics ; Prospective Studies ; *Bacteria/classification/genetics/isolation &amp; purification ; Vietnam ; Biodiversity ; DNA, Bacterial/genetics ; Metagenomics/methods ; Southeast Asian People ; }, abstract = {Persistent diarrhea remains a significant cause of morbidity in young children, yet the role of gut microbiota has not been fully clarified. This prospective study evaluated the diversity and predicted functions of the gut microbiota in 30 children aged 6-24 months with persistent diarrhea of unknown etiology (patient group, PG) and 30 healthy controls (healthy group, HG). Nearly full-length 16S rRNA genes from fecal bacterial metagenomic DNA were sequenced and taxonomically annotated. Subsequently, all downstream analyses, including diversity assessment, differential abundance and functional prediction analyses, and data visualization, were performed using R software (version 4.5.0, 2025). The PG showed lower Shannon and higher Simpson indices than the HG (p < 0.05), reflecting reduced microbial diversity. At the phylum level, Firmicutes predominated in the PG, whereas Actinobacteriota, Bacteroidota, and Verrucomicrobiota were more abundant in the HG (|log2FC| > 1 and FDR < 0.05). At the genus and species levels, the PG exhibited a marked depletion of essential commensals such as Bifidobacterium longum, Faecalibacterium, Lactobacillus, and Eubacterium, alongside an enrichment of opportunistic taxa including Klebsiella, Enterococcus lactis, and Streptococcus spp. (FDR < 0.05). Functional predictions using PICRUSt2 indicated an enrichment of carbohydrate metabolism and reductions in amino acid metabolism, B-vitamin pathways, and the biosynthesis of endogenous antibiotics (FDR < 0.05). These findings suggest that the PG harbors a dysbiotic gut microbiota characterized by reduced diversity, depletion of key commensal taxa, expansion of opportunistic bacteria, and potentially adverse shifts in metabolic functions.}, }
@article {pmid41304932, year = {2025}, author = {Hasan, GM and Mohammad, T and Shamsi, A and Sohal, SS and Hassan, MI}, title = {Applications of Genome Sequencing in Infectious Diseases: From Pathogen Identification to Precision Medicine.}, journal = {Pharmaceuticals (Basel, Switzerland)}, volume = {18}, number = {11}, pages = {}, doi = {10.3390/ph18111687}, pmid = {41304932}, issn = {1424-8247}, support = {PSAU/2025/RV/7//Prince Sattam Bin Abdulaziz University/ ; }, abstract = {Background: Genome sequencing is transforming infectious-disease diagnostics, surveillance, and precision therapy by enabling rapid, high-resolution pathogen identification, transmission tracking, and genomic-informed antimicrobial stewardship. Methods: We review contemporary sequencing platforms (short- and long-read), targeted and metagenomic approaches, and operational workflows that connect laboratory outputs to clinical and public health decision-making. We highlight strengths and limitations of genomic AMR prediction, the role of plasmids and mobile elements in resistance and virulence, and practical steps for clinical translation, including validation, reporting standards, and integration with electronic health records. Results: Comparative and population genomics reveal virulence determinants and host-pathogen interactions that correlate with clinical outcomes, improving risk stratification for high-risk infections. Integrating sequencing with epidemiological and clinical metadata enhances surveillance, uncovers cryptic transmission pathways, and supports infection control policies. Despite these advances, clinical implementation faces technical and interpretative barriers, as well as challenges related to turnaround time, data quality, bioinformatic complexity, cost, and ethical considerations. These issues must be addressed to realize routine, point-of-care sequencing. Conclusions: Emerging solutions, including portable sequencing devices, standardized pipelines, and machine-learning models, promise faster, more actionable results and tighter integration with electronic health records. The widespread adoption of sequencing in clinical workflows has the potential to shift infectious disease management toward precision medicine, thereby improving diagnostics, treatment selection, and public health responses.}, }
@article {pmid41304632, year = {2025}, author = {Wang, B and Meng, F and Cheng, T and Niu, J and Rao, D and Han, Z and Zhang, W and Zhang, Z}, title = {Comprehensive Responses of Physiology and Rhizosphere Microbiome to Saline-Alkaline Stress in Soybean Seedlings with Different Tolerances.}, journal = {Plants (Basel, Switzerland)}, volume = {14}, number = {22}, pages = {}, doi = {10.3390/plants14223480}, pmid = {41304632}, issn = {2223-7747}, support = {2023YFD2300100//National Key Research and Development Program of China/ ; CARS-04-PS15//China Agriculture Research System/ ; JLARS-2025030101//Jilin Agriculture Research System/ ; }, abstract = {Soil salinization severely threatens global crop production. Understanding the relationship between crop saline-alkaline tolerance physiology and the rhizosphere microbiome, and leveraging beneficial microorganisms to enhance crop stress resistance, holds importance for sustainable agricultural development. This study investigated the physiological and rhizosphere microbial responses of two soybean cultivars with different saline-alkaline tolerance to stress. Under saline-alkaline conditions, the tolerant cultivar exhibited superior physiological performance, including higher chlorophyll content, photosynthetic efficiency, and elevated activities of antioxidant enzymes (SOD, POD, and CAT), alongside reduced oxidative damage (MDA) and greater biomass accumulation. Combined metagenomic and physiological analyses revealed significant correlations of Bradyrhizobium and Solirubrobacter with key physiological indicators, including dry weight, PIABS, φpo, and MDA. The tolerant cultivar selectively enriched distinct marker microbes, such as Bradyrhizobium sp. and Bradyrhizobium liaoningense, in its rhizosphere. We conclude that the tolerant cultivar exhibits strong intrinsic physiological resistance. This resistance is further enhanced by a beneficially assembled rhizosphere microbiome, while the host plant's physiology remains the dominant factor.}, }
@article {pmid41304493, year = {2025}, author = {Sun, H and Li, J and Zhuang, L and Zhang, Y and Zhou, Z and Sun, J and Wang, D and Ren, Y and Xu, X and He, J and Xue, Y}, title = {Ultrasonic Cavitation Transforms Organic Matter to Achieve Reduction of Excess Sludge and Recycling of Carbon Sources.}, journal = {Toxics}, volume = {13}, number = {11}, pages = {}, doi = {10.3390/toxics13110941}, pmid = {41304493}, issn = {2305-6304}, support = {BK20240983//Natural Science Foundation of Jiangsu Province/ ; 52500021//National Natural Science Foundation of China/ ; SJCX24_1645//Postgraduate Research &amp; Practice Innovation Program of Jiangsu Province/ ; }, abstract = {Reducing the generation of excess sludge and achieving resource recovery are crucial for enhancing the economic efficiency and environmental sustainability of wastewater treatment plants (WWTPs). This study utilizes ultrasonic cavitation technology to transform organic matter into excess sludge to achieve sludge reduction and carbon source recovery. To this end, we systematically investigated the effects of various ultrasonic cavitation conditions on sludge reduction, organic matter conversion, and denitrification efficiency. The results showed that the optimal sludge reduction effect occurs at an original mixed liquid suspended solids (MLSS) of 10 g/L, under neutral and non-aerated conditions, reaching 15.07%. Ultrasonic cavitation treatment significantly enhanced the conversion efficiency of organic matter in the sludge, greatly increasing the concentration of organic matter in the supernatant, with soluble chemical oxygen demand (SCOD) maintained around 900 mg/L, thereby significantly improving the denitrification process. Furthermore, through magnetic-nanoparticle mediated isolation (MMI) and metagenomic sequencing analysis, the dominant denitrifying bacteria and their functional genes that utilize organic matter in the supernatant of ultrasonically treated sludge as a carbon source were identified. Finally, long-term pilot-scale operations further validated the practical application potential of ultrasonic cavitation technology for excess sludge reduction and resource utilization.}, }
@article {pmid41304327, year = {2025}, author = {Li, X and Ma, X and Wu, L and Mo, Z and Chen, Z and Zhang, R and Xing, M}, title = {Metagenomic Analysis of Gut Microbiota Structure and Function in Adults with Subclinical Hypothyroidism: A Cross-Sectional Study in China.}, journal = {Microorganisms}, volume = {13}, number = {11}, pages = {}, doi = {10.3390/microorganisms13112643}, pmid = {41304327}, issn = {2076-2607}, support = {2025JK158//Zhejiang Science and Technology Plan for Disease Prevention and Control/ ; 2025JK151//Zhejiang Science and Technology Plan for Disease Prevention and Control/ ; 2025KY758//Zhejiang Provincial Project for Medical Research and Health Sciences/ ; 2024KY910//Zhejiang Provincial Project for Medical Research and Health Sciences/ ; 25TJYX05//Research Project of Zhejiang Provincial Bureau of Statistics/ ; 2025ZL254//Zhejiang Province Traditional Chinese Medicine Science and Technology Plan Project/ ; 2023-B-04//Zhejiang CDC Science and Technology Talent Incubation Project/ ; }, abstract = {Subclinical hypothyroidism (SCH) is a condition characterized by thyroid hormone dysregulation, often associated with subtle clinical symptoms and metabolic disturbances. Emerging evidence suggests that the gut microbiota plays a crucial role in modulating thyroid function, but the microbiota-thyroid axis in SCH remains poorly understood. This study systematically investigates the gut microbiota composition, functional characteristics, and their correlation with thyroid hormone profiles in SCH patients. Using metagenomic sequencing and thyroid function assessments, we identified significant alterations in the gut microbiota of SCH patients, including a depletion of beneficial microbes such as Blautia and Bifidobacterium, and an enrichment of opportunistic pathogens like Bacteroides and Escherichia. Notably, Blautia depletion was negatively correlated with TSH levels, while Bacteroides abundance positively correlated with TSH levels, further highlighting the role of gut microbiota in thyroid dysfunction. Moreover, functional gene analysis revealed significant alterations in microbial metabolic pathways, with key pathways demonstrating correlations with thyroid hormone levels (free triiodothyronine (FT3) and triiodothyronine (T3)). Our findings suggest that gut microbial dysbiosis is closely associated with SCH. The study provides novel insights into the gut-thyroid axis and its role in SCH, offering new targets for early diagnosis, risk stratification, and intervention strategies in thyroid diseases.}, }
@article {pmid41304325, year = {2025}, author = {Garzon, A and Portillo-Gonzalez, R and Habing, G and Weimer, BC and Schlesener, C and Silva-Del-Rio, N and Karle, BM and Miramontes, C and Pereira, RV}, title = {Co-Occurrence Patterns of Bacterial Communities and Resistance Genes: A Comprehensive Multi-Pen Fecal Microbiome and Resistome Study in Dairy Farms.}, journal = {Microorganisms}, volume = {13}, number = {11}, pages = {}, doi = {10.3390/microorganisms13112641}, pmid = {41304325}, issn = {2076-2607}, support = {2018-68003-27466//USDA National Institute of Food and Agriculture/ ; }, abstract = {Antimicrobial resistance (AMR) poses a critical public health threat, with rising multidrug resistance cases compromising treatment effectiveness. Knowledge about the resistome in dairy production systems remains limited, particularly regarding lactating cows. This study investigated the microbiome and resistome across the hospital, fresh, and mid-lactation pens on 18 conventional dairy farms in California and Ohio using shotgun metagenomic sequencing of pooled fecal samples. Pooled fecal pat samples were collected as part of a larger field study using a quasi-experimental design that assigned farms to the training intervention group (six per state) or the control group (three per state). For the training intervention group, farm worker(s), identified as having the task of diagnosing and treating adult cows on the farm, participated in a training program on antimicrobial stewardship practices. Pooled fecal samples (n = 7) were collected at enrollment and 3 months after the intervention was completed on each participating farm (n = 18). A total of 10,221 bacterial species and 345 AMR genes conferring resistance to 22 antimicrobial classes were identified. The hospital pen exhibited a higher AMR gene diversity compared to fresh and mid-lactation pens (p < 0.05). Several AMR genes showed bimodal distribution, suggesting complex transmission mechanisms. Network analysis revealed distinct gene correlation profiles across pens, with the hospital pen showing fewer gene interactions. Our findings suggest that farm-level antimicrobial drug use may not be the sole or primary driver of resistome composition in pooled fecal samples from dairy cattle, highlighting the need to investigate other factors influencing AMR dynamics in livestock systems.}, }
@article {pmid41304316, year = {2025}, author = {Hu, P and Carr, AN and Parlov, M and Swift, D and Tiesman, JP and Ramji, N and Schoch, JJ and Teufel, AG}, title = {Metagenomics Investigation on Baby Diaper Area Microbiome and Its Association with Skin pH and Dermatitis in the Diapered Area.}, journal = {Microorganisms}, volume = {13}, number = {11}, pages = {}, doi = {10.3390/microorganisms13112632}, pmid = {41304316}, issn = {2076-2607}, abstract = {Dermatitis in the diapered area (DDA) is the most common skin condition in infants and can cause significant pain and discomfort, leading to disturbed sleep, changes in temperament, and heightened concern and anxiety for caregivers. This study investigates the relationship between skin pH, microbiome composition, and DDA severity in 158 infants from China, the US, and Germany, focusing on the buttocks, perianal, and thigh regions. Significant variations in DNA biomass and microbiota profiles were noted. Escherichia coli and Veillonella atypica were linked to higher rash scores and elevated skin pH, while Bifidobacterium longum showed a negative correlation with buttocks pH and rash severity but not with perianal rash. Correlation patterns emerged for other species, like Enterococcus faecalis, between perianal and buttocks rashes. Functional analysis identified key categories, including lipid and fatty acid metabolism, cofactor, amino acid, and carbohydrate metabolism, homeostasis and osmolarity stress, and microbial virulence and oxidative stress response, which are vital for skin health, DDA, and pH regulation in infants. These findings underscore the importance of maintaining a mildly acidic skin pH and minimizing fecal and urine residues for optimal infant skin health, suggesting that microbiota significantly influence DDA development, and provide insights for future preventive strategies and therapeutic interventions.}, }
@article {pmid41304309, year = {2025}, author = {Paoli, JE and Thongthum, T and Bassett, M and Beardsley, J and Tagliamonte, MS and Cash, MN and Spertus Newman, J and Smith, LM and Anderson, BD and Salemi, M and Subramaniam, K and von Fricken, ME and Braun de Torrez, E and Mathis, V and Mavian, CN}, title = {Virome and Microbiome of Florida Bats Illuminate Viral Co-Infections, Dietary Viral Signals, and Gut Microbiome Shifts.}, journal = {Microorganisms}, volume = {13}, number = {11}, pages = {}, doi = {10.3390/microorganisms13112625}, pmid = {41304309}, issn = {2076-2607}, support = {Department of Pathology EPIG RAS 2021-2022//University of Florida/ ; Florida Informatics Institute SEED 2022-2023//University of Florida/ ; Biodiversity Institute SEED 2022-2023//University of Florida/ ; }, abstract = {Florida's bat virome remains poorly characterized despite the state's high bat species diversity and conservation importance. We characterized viral metagenomes from rectal tissues, anal swabs, and feces of Myotis austroriparius and Tadarida brasiliensis sampled across north Florida. We recovered a near-complete Hubei virga-like virus 2 (HVLV2) genome from T. brasiliensis feces, a finding consistent with an arthropod-derived dietary signal rather than active bat infection. An Alphacoronavirus (AlphaCoV) was detected in two M. austroriparius specimens, including one with a putative co-infection involving an Astrovirus (AstV), the first detection of AstV in Florida bats to date. Parallel profiling of the M. austroriparius gut microbiome highlighted compositional differences in the co-infected individual relative to AlphaCoV-only and virus-negative bats, suggestive of potential associations between viral detection and gut microbial shifts. Our study expands the known viral diversity in Florida bat populations, and demonstrates how metagenomics can simultaneously illuminate host diet, viral exposure, and gut microbial ecology. This approach provides a scalable framework for monitoring how diet, microbiome composition, and environmental pressures shape the bat virome, and inform conservation and zoonotic risk assessments.}, }
@article {pmid41304302, year = {2025}, author = {Xiao, H and Jing, Y and Ma, K and Wang, Y and Xu, C and Yu, X}, title = {Spring Rest-Grazing Time Influenced Soil Phosphorus Fractions by Altering the Abundance of Genes Involved in Phosphorus Cycling in a Subalpine Meadow.}, journal = {Microorganisms}, volume = {13}, number = {11}, pages = {}, doi = {10.3390/microorganisms13112618}, pmid = {41304302}, issn = {2076-2607}, support = {GAU-KYQD-2021-01//Scientific Research Start-up Funds for Openly-recruited Doctors, China/ ; GSAU-DKZY-2025-004//China Agricultural University Collaborative Research Support Fund, China/ ; 32460356, 32301509//National Natural Science Foundation of China/ ; }, abstract = {Soil phosphorus (P) availability is a critical factor limiting plant growth and ecosystem productivity that can be strongly influenced by land use factors, such as grazing by livestock. Seasonal grazing management can benefit grassland productivity and soil nutrient cycling in alpine meadows, but its effects on soil P availability and the microbial processes driving P transformation remain poorly understood. To address this, a long-term field experiment was conducted with five different spring rest-grazing periods, where soil P fractions were examined and metagenomic sequencing was employed to assess the functional profiles of microbial genes involved in P cycling. Early spring rest-grazing led to higher concentrations of labile P fractions (Resin-P and NaHCO3-Pi), indicating improved soil P availability. Moreover, rest-grazing in early spring significantly reduced HCl-Pi concentration while increased the concentration of conc. HCl-Po. Metagenomic analysis revealed that early spring rest-grazing may have contributed to a higher relative abundance of the organic P mineralization gene phnA but decreasing the relative abundance of inorganic P solubilization genes ppa, and P-uptake and transport gene pstB. The dominant microbial genera involved in P cycling were Rhodopseudomonas and Mesorhizobium. Soil temperature and water infiltration rate, both affected by early rest-grazing, were identified as the main environmental variables correlated with P-cycling functional gene composition. These influenced taxa with functional genes involving organic P mineralization, inorganic P solubilization, and P-uptake and transport, which may associate with enhancing soil labile P. This study provides insights into potential microbial processes under grazing management in grassland ecosystems.}, }
@article {pmid41304301, year = {2025}, author = {Martinez, A and St-Pierre, B}, title = {Metagenomic Identification and Characterization of Novel Vitamin B12 Synthesizers from the Rumen of Beef Cattle Fed High-Lipid Inclusion Diets.}, journal = {Microorganisms}, volume = {13}, number = {11}, pages = {}, doi = {10.3390/microorganisms13112617}, pmid = {41304301}, issn = {2076-2607}, support = {SD00H866-26//South Dakota State University Agricultural Experiment Station Hatch funds (USDA National In-stitute of Food and Agriculture)/ ; }, abstract = {Beef production in intensive systems requires optimal nutrition to maximize growth and profitability. While triglycerides contain twice the energy per unit weight compared to polysaccharides, they are not nearly as commonly used as a supplemental source of energy compared to starch, largely in part due to their negative effects on rumen physiology when their inclusion levels are too high. To gain further insights into the response of rumen microbial communities to elevated dietary lipid levels, we took advantage of rumen samples collected as part of a previously published study that tested high inclusion (4% and 8%) of tallow or linseed oil in beef cattle as part of a 5 × 5 Latin square design, with corn used as a base dietary ingredient. Using a 16S rRNA gene-based profiling approach, two uncharacterized candidate rumen bacterial Operational Taxonomic Units (OTUs), referred to as Bt-995 and Bt-1367, were found to be in higher abundance in rumen samples collected from steers when they were fed diets with higher inclusion of linseed oil. Using a metagenomics approach to assemble contigs corresponding to genomic regions of these OTUs, various predicted metabolic functions were found to be shared. Consistent with the dietary treatments of the original animal study, functions associated with starch utilization and triglyceride metabolism were identified. Unexpectedly, however, contig sets from both OTUs also encoded genes predicted to be involved in vitamin B12 biosynthesis, as well as ethanolamine utilization, a function that is dependent on vitamin B12 as a co-factor. Together, these results indicate that vitamin B12-related functions may provide an advantage to rumen bacteria under conditions of high dietary triglyceride inclusion.}, }
@article {pmid41304286, year = {2025}, author = {Wu, Y and Liu, C and Qiu, Q and Zhao, X}, title = {Xylo-Oligosaccharide Production from Wheat Straw Xylan Catalyzed by a Thermotolerant Xylanase from Rumen Metagenome and Assessment of Their Probiotic Properties.}, journal = {Microorganisms}, volume = {13}, number = {11}, pages = {}, doi = {10.3390/microorganisms13112602}, pmid = {41304286}, issn = {2076-2607}, support = {20224ACB205007, 20242BAB20309, 20252BAC240121//Natural Science Foundation of Jiangxi Province/ ; 20252ZDF030003//Central Leading Local Science and Technology Development Special Project/ ; 2024H-100160//Ji'an Municipal Science and Technology Plan Project/ ; }, abstract = {A novel xylanase gene (RuXyn854) was identified from the rumen metagenome and was heterologously expressed in Escherichia coli to produce xylo-oligosaccharides (XOSs) as a prebiotic in this study. RuXyn854, a member of glycosyl hydrolase family 10, demonstrated peak enzymatic activity at pH 7.0 and 50 °C. RuXyn854 retains more than 50% of its activity after treatment at 100 °C for 10 min, highlighting the enzyme's excellent heat resistance. RuXyn854 showed a preferential hydrolyzation of xylan, especially rice straw xylan. RuXyn854 activity was significantly increased in the presence of 15 mM Mn[2+], 0.25% Tween-20, and 0.25% Triton X-100 (125%, 20%, and 26%, respectively). The reaction temperature (30, 40, and 50 °C), dosage (0.20, 0.27, and 0.34 U), and time (90, 120, and 150 min) of RuXyn854 affected the XOS yield and composition, with a higher yield at 0.27 U, 50 °C, and 120-150 min. Xylobiose, xylotriose, and xylotetraose were characterized as the predominant XOS products resulting from the enzymatic hydrolysis of wheat straw xylan by RuXyn854, with xylose present at a mere 0.49% of the total yield. The prebiotic potential of XOSs was assessed through in vitro fermentation with established probiotic strains of Bifidobacterium bifidum and Lactobacillus brevis. The results showed that, regardless of incubation time, XOSs stimulated the growth and xylanolytic enzyme secretion of the two probiotics compared to the controls. These results demonstrate that the feature of RuXyn854 to withstand temperatures up to 100 °C is impressive, and its ability to hydrolyze wheat xylan into XOSs promotes the growth of probiotics.}, }
@article {pmid41304279, year = {2025}, author = {Zhou, M and Li, Q and Han, Y and Wang, Q and Yang, H and Li, H and Hu, C}, title = {Sulfur Cycling and Life Strategies in Successional Biocrusts Link to Biomass Carbon in Dryland Ecosystems.}, journal = {Microorganisms}, volume = {13}, number = {11}, pages = {}, doi = {10.3390/microorganisms13112594}, pmid = {41304279}, issn = {2076-2607}, support = {32370125//National Natural Science Foundation of China/ ; 41877419//National Natural Science Foundation of China/ ; 41877339//National Natural Science Foundation of China/ ; XDA17010502//Strategic Priority Research Program at the Chinese Academy of Science/ ; }, abstract = {Examining the changing patterns and underlying mechanisms of soil biomass carbon stocks constitutes a fundamental aspect of soil biology. Despite the potential influence of the sulfur cycle and the life strategies of organisms on community biomass, these factors have rarely been studied in tandem. Biocrusts are model systems for studying soil ecosystems. In this study, metagenomic analysis of biocrusts related to different life strategies from five batches over four consecutive years demonstrated that, in free-living communities, microbial biomass carbon (MBC) synthesis, via assimilatory sulfate reduction (ASR), is primarily coupled with the 3-hydroxypropionate/4-hydroxybutyrate and Calvin-Benson-Bassham cycles. These pathways are affected by the oxidation-reduction potential (Eh), pH, electrical conductivity, and nutrient levels. The decomposition of organic carbon (OC) via dissimilatory sulfate reduction (DSR) was accompanied by the production of dimethyl sulfide (DMS), which was influenced by the C/S ratio and moisture, whereas the synthesis of MBC by symbiotic communities was found to be affected by Eh and pH, and decomposition was affected by the C/S ratio. The MBC stock was influenced by all strategies, with resource strategies having the greatest impacts during the growing season, and the contribution of chemotrophic energy was most significant in free-living communities. In conclusion, the MBC in biocrusts is associated with both ASR and DSR and is facilitated by the A-, S-, and P-strategies under the regulation of the stoichiometric C/S ratio. The exploration of microbial life strategies and sulfur cycling in biocrusts within arid ecosystems in this study offers a new perspective on the patterns of change in soil biomass carbon stocks.}, }
@article {pmid41304278, year = {2025}, author = {Qiao, T and Zhu, Z}, title = {Multi-Kingdom Gut Microbiome Interaction Characteristics Predict Immune Checkpoint Inhibitor Efficacy Across Pan-Cancer Cohorts.}, journal = {Microorganisms}, volume = {13}, number = {11}, pages = {}, doi = {10.3390/microorganisms13112595}, pmid = {41304278}, issn = {2076-2607}, support = {2025A04J5264//Guangzhou Basic and Applied Basic Research Project/ ; 2023A1515010744//Guangdong Basic and Applied Basic Research Foundation/ ; }, abstract = {An increasing number of studies have confirmed that the gut microbiota, especially bacteria, is closely related to the efficacy of immune checkpoint inhibitor (ICI) therapy. However, the effectiveness of multi-kingdom microbiota and their interactions in predicting the therapeutic effect of ICI therapy remains uncertain. We integrated extensive gut metagenomic databases, including 1712 samples of 10 cohorts from 7 countries worldwide, to conduct rigorous differential analysis and co-occurrence network analysis targeting multi-kingdom microbiota (bacteria, fungi, archaea, and virus). We ultimately identified two subtypes (C1 and C2) by employing a weighted similarity network fusion (WSNF) method. Subtype C2 exhibited higher microbial diversity, better treatment response, and improved prognosis compared to subtype C1. Notably, subtype C2 was associated with higher abundance of beneficial genera such as Bacteroides and Kluyveromyces, while subtype C1 contained potentially detrimental taxa like Malassezia. A multi-kingdom model incorporating 32 genera demonstrated superior predictive accuracy for ICI therapy efficacy compared to single-kingdom models. Co-occurrence network analysis revealed a more robust and interconnected microbiome in subtype C2, suggesting a stable gut environment correlates with effective ICI therapy efficacy. This study highlights the potential of a multi-kingdom signature in predicting the efficacy of ICI therapy, offering a novel perspective for personalized therapy in oncology.}, }
@article {pmid41304274, year = {2025}, author = {Li, J and Hou, L and Liu, Y and Sun, Y and Li, Y and He, B and Tu, C and Zhou, X}, title = {Metagenomic Sequencing Reveals the Viral Diversity of Bactrian Camels in China.}, journal = {Microorganisms}, volume = {13}, number = {11}, pages = {}, doi = {10.3390/microorganisms13112589}, pmid = {41304274}, issn = {2076-2607}, support = {32130104//National Natural Science Foundation of China/ ; 32460902//National Natural Science Foundation of China/ ; 2021GKLRLX10//Ningxia Hui Autonomous Region Science and Technology Innovation Leading Talents Cultivation Project/ ; Ning Ren She Han [2024] No. 106//Ningxia Hui Autonomous Region Young Top-notch Talents Cultivation Project/ ; }, abstract = {The Bactrian camel is a key economic livestock species in China and around the world. It yields meat and milk (high-quality functional foods), and the milk reports health benefits. Dromedary camels, as intermediate hosts of MERS-CoV, have garnered significant public health attention. In contrast, viral surveillance in Bactrian camels from the same genus as dromedaries has received limited attention, with only sporadic or regionally confined reports available. Systematic investigations into the virome of viral species, viral diversity, and novel viruses in Bactrian camels are lacking. In this study, swabs were collected from 701 Bactrian camels in China. Through metagenomics, 3262 viral contigs were classified into 16 viral phyla, 29 viral families, and an unclassified group. The different landforms were found to influence viral diversity and composition in Bactrian camels, with mountainous area exerting the greatest impact. The viral composition significantly differed between captive and free-ranging camels. The study identified at least 12 viruses with zoonotic potential, and phylogenetic analysis indicated cross-species transmission in some of them. Additionally, picornavirus, circular Rep-encoding single-stranded (CRESS) DNA virus, and polyomavirus from Bactrian camels may represent novel species or genotypes. To summarize, in this study, we described the baseline virome profile of Chinese Bactrian camels, investigated the ecological factors influencing the viral distribution of Bactrian camels, identified key potential viral risks, and provided a scientific basis for the prevention, control, and early warning of critical viral diseases in Bactrian camels from China.}, }
@article {pmid41304268, year = {2025}, author = {Bednarska, NG and Reitlo, LS and Beisvag, V and Stensvold, D and Haberg, AK}, title = {Microbial Signatures Mapping of High and Normal Blood Glucose Participants in the Generation 100 Study.}, journal = {Microorganisms}, volume = {13}, number = {11}, pages = {}, doi = {10.3390/microorganisms13112582}, pmid = {41304268}, issn = {2076-2607}, abstract = {Intestinal dysbiosis has been linked to metabolic disorders, including insulin resistance and type 2 diabetes mellitus (T2DM). T2DM typically follows a prediabetic stage, during which insulin resistance develops. During the early stages of T2DM, its development can be corrected, thus potentially preventing or delaying the onset of the disease. This secondary, exploratory, cross-sectional comparison study aimed to contrast the gut microbiome of individuals with elevated fasting blood glucose to that of individuals with glucose levels within the normal range. This study involved 65 older adults (ages 76-83 years) enrolled from the randomized controlled trial entitled the "Generation 100 Study", all of whom consented to provide their gut microbiome samples. We employed a high-throughput sequencing of the bacterial 16S rRNA gene to obtain metagenomic microbial profiles for all participants. These profiles were then correlated with clinical measures. Overall, microbial alpha diversity was significantly reduced in the high glucose group. We have also observed distinct patterns of microbial beta diversity between high and normal glucose groups. At the phylum level, we found that Synergistes, Elusimicobia, Euryarchaeota, Verrucomicrobia, and Proteobacteria were all significantly decreased in participants with high blood glucose. Additionally, P. copri (ASV 909561) was significantly elevated (10-fold increase) in the high glucose groups, suggesting that it may serve as an early T2DM marker. In contrast to prior reports on the Fusobacterium genus, we found that it was significantly increased in the normal glucose group, with a significant 151-fold increase compared to the high glucose group. Directly linking gut microbiota profiles with clinical indicators such as fasting blood glucose and T2DM diagnosis allows the identification of specific microbial features associated with glucose dysregulation, providing preliminary population-level evidence to guide future translational research. Our results indicate significant changes in the microbiome that may provide valuable insights for early intervention in pre-diabetic states.}, }
@article {pmid41304199, year = {2025}, author = {Zhang, J and Jiang, F and Li, X and Song, P and Zhang, T}, title = {Metagenome-Based Functional Differentiation of Gut Microbiota and Ecological Adaptation Among Geographically Distinct Populations of Przewalski's Gazelle (Procapra przewalskii).}, journal = {Microorganisms}, volume = {13}, number = {11}, pages = {}, doi = {10.3390/microorganisms13112513}, pmid = {41304199}, issn = {2076-2607}, support = {QHEG-2024-04//the 2023 award fund of Qinghai Provincial Key Laboratory of Animal Ecological Genomics/ ; 2024-ZZ-14//Independent Project of State Key Laboratory of Plateau Ecology and Agriculture, Qinghai Univer-sity/ ; 2024T170992//the China Postdoctoral Science Foundation/ ; }, abstract = {Przewalski's gazelle (Procapra przewalskii) is an endangered ungulate endemic to the Qinghai-Tibet Plateau, with a small population size and exposure to multiple ecological pressures. Its gut microbiota may play a crucial role in host environmental adaptation. To investigate the functional divergence of gut microbial communities, we performed high-throughput metagenomic sequencing on 105 wild fecal samples collected from 10 geographic regions around Qinghai Lake. The results revealed significant regional differentiation in key functional modules related to metabolism, antibiotic resistance mechanisms, and virulence-associated pathways. All populations showed enrichment in core metabolic pathways such as carbohydrate and amino acid metabolism, with carbohydrate-active enzymes dominated by glycoside hydrolases (GHs) and glycosyltransferases (GTs), exhibiting overall functional conservation. Although populations shared many antibiotic- and virulence-related reference genetic markers, the marker composition associated with distinct resistance mechanisms and pathogenic processes exhibited clear population-specific patterns, suggesting differential microbial responses to local environmental pressures. Correlation network analysis further identified core taxa (e.g., Arthrobacter and Oscillospiraceae/Bacteroidales lineages) as key genera linking community structure with core metabolic, resistance-related, and virulence-associated marker functions. Overall, the gut microbiota of Przewalski's gazelle exhibits a complex spatially structured functional differentiation, reflecting host-microbiome co-adaptation under region-specific ecological pressures. These findings provide critical methodological and theoretical support for microecological health assessment and regionally informed conservation management of this endangered species.}, }
@article {pmid41304195, year = {2025}, author = {Wen, L and Luo, H and Li, C and Cheng, K and Shi, L and Liu, L and Wang, K and Tang, H}, title = {Substituting Chemical by Organic Fertilizer Improves Soil Quality, Regulates the Soil Microbiota and Increases Yields in Camellia oleifera.}, journal = {Microorganisms}, volume = {13}, number = {11}, pages = {}, doi = {10.3390/microorganisms13112509}, pmid = {41304195}, issn = {2076-2607}, support = {U21A20187//National Natural Science Foundation of China/ ; 2022tfs201//Director Fund of Hunan Soil and Fertilizer Institute/ ; XDA0440404//Strategic Priority Research Program of Chinese Academy of Sciences/ ; }, abstract = {The partial substitution of chemical fertilizer with organic fertilizer has been regarded as an effective strategy for enhancing crop yield and soil quality. Nevertheless, its effects on soil properties and microbes remain contentious. In this study, we examined the effects of four different fertilization strategies (including without fertilizer (CK), 100% chemical fertilizer (NPK), 30% organic fertilizer + 70% chemical fertilizer (LOM) and 60% organic fertilizer + 40% chemical fertilizer (HOM)) on soil nutrients and microbial communities through metagenomic sequencing in a Camellia oleifera field experiment. Compared to CK and NPK, HOM significantly increased SOC, TN, TP, AK and AN contents. The substitution of organic fertilizer notably increased Camellia oleifera yield, with the highest increase of 93.35% observed in HOM relative to NPK. Soil bacterial and fungal communities responded inconsistently to fertilization patterns. Bacteria predominated as the main soil microorganisms, and higher rates of organic fertilizer substitution facilitated a shift from bacterial to fungal communities. Organic fertilizer substitution significantly increased soil bacteria diversity and fungal richness, particularly in the HOM. Soil bacterial community structure was more sensitive to fertilization regimes than soil fungi. High rates of organic fertilizer substitution substantially suppressed oligotrophic and increased copiotrophic bacterial communities. Mucoromycota emerged as the dominant fungal group, with a considerable increment in HOM soils. SOC and TN were the main factors affecting Camellia oleifera yield and shaping soil bacteria and fungal diversity and composition. This study provided crucial insights into the ecological implications of organic fertilizer application and the potential of managing soil microorganisms for sustainable Camellia oleifera productivity.}, }
@article {pmid41304167, year = {2025}, author = {Vitezić, BM and Franović, B and Renko, I and Kuiš, D and Begić, G and Blašković, M and Gabrić, D and Nikolić, M and Vranić, T&#x160; and Veljanovska, D and Cvijanović Peloza, O}, title = {Microbiome Profiling of Biofilms Formed on d-PTFE Membranes Used in Guided Bone Regeneration.}, journal = {Microorganisms}, volume = {13}, number = {11}, pages = {}, doi = {10.3390/microorganisms13112478}, pmid = {41304167}, issn = {2076-2607}, support = {2170-137-08-24-19//UNIRI-biomed/ ; IP-2020-02-7875//the Croatian Science Foundation/ ; }, abstract = {In guided bone regeneration (GBR) procedures, d-PTFE membranes are often used as a barrier to promote alveolar ridge regeneration. The aim of this randomized clinical trial was to examine the microbial diversity and structure of biofilms on two types of d-PTFE membranes, Permamem[®] and Cytoplast™, over four-week oral cavity exposure periods. Bacterial biofilm analysis was performed using 16S rRNA next-generation sequencing (NGS) on 36 samples (20 Permamem[®] and 16 Cytoplast™). The results showed significant differences in the microbial profiles: Cytoplast™ membranes showed reduced microbial diversity and an enhanced proportion of pathobionts like Selenomonas, Segatella, Fusobacterium and Parvimonas, which are associated with periodontal and peri-implant diseases and alveolar bone loss. Permamem[®] membranes promoted colonization by bacteria associated with healthy oral conditions, such as the genera Streptococcus, Kingella and Corynebacterium. Overall, our results showed that Cytoplast™ membranes generate a specific type of biofilm, leading to reduction in health-related bacterial species and facilitating growth conditions for dysbiosis shift. Further research and patient follow-ups are essential to thoroughly evaluate the clinical implications of different d-PTFE membranes used in guided bone regeneration.}, }
@article {pmid41304165, year = {2025}, author = {Tong, F and Feng, X and Yuan, H and Chen, Y and Chen, P}, title = {Oyster Aquaculture Impacts on Environment and Microbial Taxa in Dapeng Cove.}, journal = {Microorganisms}, volume = {13}, number = {11}, pages = {}, doi = {10.3390/microorganisms13112480}, pmid = {41304165}, issn = {2076-2607}, support = {SML2023SP237//Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai)/ ; 2023TD06//Central Public-interest Scientific Institution Basal, Research Fund, CAFS/ ; 2024YFD2401405; 2024YFB4206600//National Key Research and Development Program of China/ ; }, abstract = {Environmental physicochemical factors and microorganisms play critical roles in the health of oysters. However, the impact of high-density oyster farming-a highly efficient filter-feeding bivalve system-on environmental conditions and microbial community structure and function remains poorly understood. This study conducted four-season monitoring of the water and sediment parameters in a semi-enclosed bay commercial oyster aquaculture (OA) system and a control area (CT), coupled with 16S rRNA amplicon sequencing of the environmental microbiota. Oyster aquaculture caused negligible disruption to water column parameters but significantly increased the concentrations of total organic carbon (TOC, annual mean OA vs. CT:1.15% vs. 0.56%), sulfides (annual mean OA vs. CT:67.72 vs. 24.99 mg·kg[-1]), and heavy metals (Cd, Pb, Cu, Zn, and Cr) in the sediment. α-diversity (Shannon and Chao indices) exhibited minimal overall perturbation, with significant inter-regional differences observed only in winter for both water and sediment. The bacterial community structure of the water column was significantly altered only in winter, whereas sediment communities showed structural shifts in spring, summer, and autumn. Water microbiota were primarily influenced by turbidity, dissolved oxygen, salinity, the Si/N ratio, and silicates. Sediment microbiota were correlated with Pb, Cu, Zn, TOC, Cr, and sediment particle size. Water bacterial functions displayed only four significantly divergent biogeochemical processes annually (sulfur compound respiration; OA vs. CT). In contrast, sediment bacteria exhibited 29 significantly disrupted functions annually, with the greatest seasonal divergence in winter (11/67 functions). Spring, summer, and autumn sediment functions showed distinct patterns. Understanding these environmental-microbial interactions is essential for sustainable oyster aquaculture and ecological optimization.}, }
@article {pmid41304105, year = {2025}, author = {Zhong, Y and Wu, C and Yao, Z and Li, X and Chi, H and Wu, T and Du, X}, title = {Metagenomic Analysis of Distribution Characteristics and Driving Mechanisms of Antibiotic Resistance Genes, Virulence Factors, and Microbial Communities in Rice Seedling Cultivation Soils.}, journal = {Microorganisms}, volume = {13}, number = {11}, pages = {}, doi = {10.3390/microorganisms13112419}, pmid = {41304105}, issn = {2076-2607}, abstract = {The extensive utilization of antibiotics in both healthcare and agricultural sectors has precipitated an exponential surge in antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARBs) within environmental matrices, thereby posing formidable threats to ecosystem stability and human health. Given soil's pivotal role as a primary reservoir for ARGs and the inherent potential for these genes to translocate into agricultural produce, this study endeavors to evaluate the distribution patterns of ARGs and virulence factors (VFs) in soils designated for rice seedling cultivation. This study employed metagenomic sequencing to analyze antibiotic resistance genes (ARGs), virulence factors (VFs), and microbial communities in four rice seedling cultivation soils. The results revealed significant variations in microbial alpha diversity, community structure, ARGs, and VFs across soils, with multidrug resistance, glycopeptide resistance, and tetracycline resistance genes predominating. The inclusion of organic matter increased the complexity of the microbial network by increasing the levels of ARGs and VFs. Neutral community model analysis revealed that stochastic processes predominantly governed the assembly of microbial taxa, ARGs, and VFs, though ARGs were subject to stronger deterministic pressures. These communities were shaped by the pH, nitrogen, organic carbon content, electrical conductivity, and salinity of the soil. The core Actinobacteria genera acted as key vectors for ARGs and VFs dissemination. Our findings elucidate the complex interactions between microbes, ARGs, and VFs in cultivation soils and highlight that organic matter amendment, while enhancing fertility, can also increase the potential spread of microbial risk genes, underscoring the need for monitoring and managing ARGs and VFs in agricultural soils to mitigate public health risks.}, }
@article {pmid41302874, year = {2025}, author = {Berlanga, M and Miñana-Galbis, D and Guerrero, R}, title = {Disentangling Gut Bacterial Community Patterns in Cryptocercus punctulatus and Comparing Their Metagenomes with Other Xylophagous Dyctioptera Insects.}, journal = {Insects}, volume = {16}, number = {11}, pages = {}, doi = {10.3390/insects16111128}, pmid = {41302874}, issn = {2075-4450}, support = {project PID2021-123735OB-C22.//MCIN/ ; }, abstract = {Gut microbiota enable wood-feeding insects to digest recalcitrant diets. Two DNA-based analyses were performed. Amplicon sequencing of gut microbiota samples from Cryptocercus punctulatus showed inter-individual heterogeneity with visually distinct ordination patterns; however, no statistically significant differences were detected. Shotgun metagenomics was used to compare the taxonomic and functional profiles of C. punctulatus gut microbiota with those of other xylophagous Dictyoptera. Despite taxonomic differences, C. punctulatus microbiota revealed functional convergence with termites (Mastotermes darwiniensis and Nasutitermes sp.). Carbohydrate metabolism was performed by different bacterial phyla across all insects. All insect species possessed metabolic potential for cellulose, hemicellulose, pectin, and starch digestion, but lignin degradation capabilities were not detected. Termites showed higher abundance of chitin and xylan degradation pathways and nitrogen fixation genes, though nitrogen fixation was also present in Cryptocercus cockroaches. Genes for oxidative stress tolerance were present across all species but were most abundant in cockroaches, particularly, Cryptocercus. All insects harbored antibiotic resistance genes, with highest levels found in cockroaches. These findings indicate that metabolic requirements for wood digestion shape gut microbial community assembly across xylophagous insects, with distinct microbial taxa contributing to cellulose and hemicellulose breakdown. Moreover, the widespread presence of antibiotic resistance genes raises concerns about the potential transmission of antibiotic resistance within insect-associated microbiomes.}, }
@article {pmid41301629, year = {2025}, author = {Wang, Y and Li, L and Liang, Y and Xu, K and Ye, Y and He, M}, title = {Phage Therapy for Acinetobacter baumannii Infections: A Review on Advances in Classification, Applications, and Translational Roadblocks.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {14}, number = {11}, pages = {}, doi = {10.3390/antibiotics14111134}, pmid = {41301629}, issn = {2079-6382}, support = {82302568//National Natural Science Foundation of China/ ; 2308085QH283//Anhui Provincial National Science Foundation/ ; 2022xkjT012//Basic and Clinical Collaboration Enhancement Program Foundation of Anhui Medical University/ ; }, abstract = {The global spread of carbapenem-resistant Acinetobacter baumannii (CRAB) poses a severe public health threat, driving growing interest in phage-based precision antibacterial strategies. This systematic review synthesizes recent advances in the field of A. baumannii phage. Modern taxonomy, based on whole-genome phylogeny, has reclassified the majority of A. baumannii phages into the class Caudoviricetes, revealing distinct evolutionary clades that correlate with host tropism and biological properties, superseding the traditional morphological families (Myoviridae, Siphoviridae, Podoviridae). To overcome limitations of natural phage therapy, such as narrow host range, cocktail therapies (ex vivo resistance mutation rates < 5%) and phage-antibiotic synergism (enabling antibiotic efficacy at 1/4 minimum inhibitory concentration) have significantly enhanced antibacterial efficacy. Preclinical models demonstrate that phage therapy efficiently clears pathogens in pneumonia models and promotes the healing of burn wounds and diabetic ulcers via immunomodulatory mechanisms. Technical optimizations include nebulized inhalation delivery achieving 42% alveolar deposition, and thermosensitive hydrogels enabling sustained release over 72 h. Genetic engineering approaches, such as host range expansion through tail fiber recombination and CRISPR/Cas-mediated elimination of lysogeny, show promise. However, the genetic stability of engineered phages requires further validation. Current challenges remain, including limited host spectrum, the absence of clinical translation standards, and lagging regulatory frameworks. Future efforts must integrate metagenomic mining and synthetic biology strategies to establish a precision medicine framework encompassing resistance monitoring and personalized phage formulation, offering innovative solutions against CRAB infections.}, }
@article {pmid41301609, year = {2025}, author = {Abi Younes, JN and McLeod, L and Otto, SJG and Chai, Z and Lacoste, S and McCarthy, EL and Links, MG and Herman, EK and Stothard, P and Gow, SP and Campbell, JR and Waldner, CL}, title = {Evaluating the Diagnostic Performance of Long-Read Metagenomic Sequencing Compared to Culture and Antimicrobial Susceptibility Testing for Detection of Bovine Respiratory Bacteria and Indicators of Antimicrobial Resistance.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {14}, number = {11}, pages = {}, doi = {10.3390/antibiotics14111114}, pmid = {41301609}, issn = {2079-6382}, support = {Not applicable//Genome Prairie/ ; Not applicable//Genome Canada/ ; Not applicable//Genome Alberta/ ; Not applicable//Saskatchewan Agriculture Development Fund/ ; }, abstract = {Background/Objectives: Long-read metagenomic sequencing can detect bacteria and antimicrobial resistance genes (ARGs) from bovine respiratory samples, providing an alternative to culture and antimicrobial susceptibility testing (C/S). This study applied Bayesian latent class models (BLCMs) to estimate the sensitivity (Se) and specificity (Sp) of long-read metagenomic sequencing compared to C/S for detecting Mannheimia haemolytica, Pasteurella multocida, and Histophilus somni, as well as associated macrolide and tetracycline resistance potential. Methods: Deep nasopharyngeal swabs were collected from fall-placed feedlot calves at arrival, 13, and 36 days on feed across two years and two metaphylaxis protocols. Samples underwent C/S and long-read metagenomic sequencing. BLCMs were used to estimate Se and Sp for the detection of bacteria and potential for antimicrobial resistance (AMR). Results: Se and Sp for detecting respiratory bacteria by metagenomics were not significantly different than culture, with four exceptions. For the 2020 samples, Se for M. haemolytica was lower than culture, and Sp for H. somni was lower, while in both 2020 and 2021 samples, Se for P. multocida was higher for metagenomics than culture. The estimated Se and Sp of metagenomics for the detection of msrE-mphE, EstT, and tet(H) within bacterial reads were either not significantly different or were lower than AST, with Sp > 95% with one exception. Conclusions: This study provided BLCM-based estimates of clinical Se and Sp of metagenomics and C/S without assuming a gold standard in a large pen research setting. These findings demonstrate the potential of long-read metagenomics to support bovine respiratory disease diagnostics, AMR surveillance, and antimicrobial stewardship in feedlot cattle.}, }
@article {pmid41301606, year = {2025}, author = {Aguilar-Rangel, EJ and Paredes-Cárcamo, F and Andrade, MD and Contreras-Sánchez, D and Rain-Medina, V and Campanini-Salinas, J and Medina, DA}, title = {Hospital Wastewater as a Reservoir of Contaminants of Emerging Concern: A Study Report from South America, Chile.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {14}, number = {11}, pages = {}, doi = {10.3390/antibiotics14111111}, pmid = {41301606}, issn = {2079-6382}, support = {Proyectos Colaborativos 2024 #3557//San Sebasti&#xe1;n University/ ; Fondecyt Iniciaci&#xf3;n #11230295//Agencia Nacional de Investigaci&#xf3;n y Desarrollo de Chile/ ; }, abstract = {Background/Objectives: Hospital wastewater is a complex effluent containing a wide range of biological and chemical contaminants, including pharmaceuticals, pathogens, and antimicrobial resistance determinants. These discharges pose a growing threat to aquatic ecosystems and public health, particularly in regions where wastewater treatment is insufficient. This study aimed to characterize the chemical and microbiological composition of untreated effluent from a tertiary care hospital in southern Chile, focusing on contaminants of emerging concern. Methods: Wastewater samples were collected at the hospital outlet before any treatment. The presence of two commonly used pharmaceutical compounds, paracetamol and amoxicillin, was quantified using high-performance liquid chromatography (HPLC). Bacterial isolation was performed using selective media, and antibiotic susceptibility testing was conducted via the disk diffusion method following CLSI guidelines. In addition, metagenomic DNA was extracted and sequenced to assess microbial community composition and functional gene content, focusing on the identification of resistance genes and potential pathogens. Results: A total of 42 bacterial isolates were recovered, including genera with known pathogenic potential such as Aeromonas, Klebsiella, and Enterococcus. Antibiotic susceptibility tests revealed a high prevalence of multidrug-resistant strains. Metagenomic analysis identified the dominance of Bacillota and Bacteroidota, together with 56 antimicrobial-resistance gene (ARG) families and 38 virulence-factor families. Functional gene analysis indicated the presence of efflux-pump systems, β-lactamases, and mobile genetic elements, suggesting that untreated hospital effluents serve as potential sources of resistance and virulence determinants entering the environment. Paracetamol was detected in all samples, with an average concentration of 277.4 ± 10.7 µg/L; amoxicillin was not detected, likely due to its instability and rapid degradation in the wastewater matrix. Conclusions: These findings highlight the complex microbiological and chemical burden of untreated hospital wastewater and reinforce the need for continuous monitoring and improved treatment strategies to mitigate environmental dissemination of antibiotic resistance.}, }
@article {pmid41301593, year = {2025}, author = {Abi Younes, JN and McLeod, L and Lacoste, SR and Chai, Z and Herman, EK and McCarthy, EL and Campbell, JR and Gow, SP and Stothard, P and Links, MG and Otto, SJG and Waldner, CL}, title = {Respiratory Bacteria and Antimicrobial Resistance Genes Detected by Long-Read Metagenomic Sequencing Following Feedlot Arrival, Subsequent Treatment Risk and Phenotypic Resistance in Feedlot Calves.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {14}, number = {11}, pages = {}, doi = {10.3390/antibiotics14111098}, pmid = {41301593}, issn = {2079-6382}, support = {NA//Genome Canada/ ; NA//Genome Prairie/ ; NA//Genome Alberta/ ; NA//Saskatchewan Agriculture Development Fund/ ; }, abstract = {Background/Objectives: Long-read metagenomic sequencing can assign antimicrobial resistance genes (ARGs) to speciated bacterial reads. This study evaluated whether metagenomic data from respiratory bacteria derived from feedlot calves sampled in the early feeding period were associated with subsequent bovine respiratory disease (BRD) treatment and phenotypic antimicrobial resistance (AMR) at treatment. Methods: Deep nasopharyngeal swabs (DNPSs) obtained at arrival processing (1 day on feed; DOF), 13 DOF, and the time of BRD treatment were cultured and subjected to antimicrobial susceptibility testing (AST) and long-read metagenomic sequencing. Analyses focused on macrolide (mphE-msrE, EstT) and tetracycline (tet(H)) ARGs within reads assigned to Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, or Bibersteinia trehalosi. Generalized estimating equations assessed associations between metagenomic results from 1 and 13 DOF and subsequent BRD treatment risk and AST outcomes at treatment, at both the individual animal (calf) and pen levels. Results: Calf-level detection of H. somni at 13 DOF was associated with a greater BRD treatment risk between 14 and 45 DOF. An increased pen prevalence of either M. haemolytica or P. multocida at 13 DOF was associated with a greater BRD treatment risk from 14 to 45 DOF. At 13 DOF, detections of mphE-msrE, EstT, or tet(H) in target bacteria were associated with corresponding phenotypic AMR at BRD treatment. Similarly, a higher pen-level prevalence of mphE-msrE or EstT at 13 DOF was also associated with increased macrolide resistance at BRD treatment. Conclusions: The results from long-read metagenomic sequencing of DNPSs collected at 13 DOF were associated with both BRD risk and AMR at treatment. These findings align with prior culture-based results and support the potential utility of pen-level metagenomic testing for AMR surveillance and informing antimicrobial selection in feedlots.}, }
@article {pmid41301447, year = {2025}, author = {Rehman, Y and Kim, Y and Tong, M and Blaby, IK and Blaby-Haas, CE and Beatty, JT}, title = {Mining Thermophile Photosynthesis Genes: A Synthetic Operon Expressing Chloroflexota Species Reaction Center Genes in Rhodobacter sphaeroides.}, journal = {Biomolecules}, volume = {15}, number = {11}, pages = {}, doi = {10.3390/biom15111529}, pmid = {41301447}, issn = {2218-273X}, support = {DE-AC02-05CH11231//United States Department of Energy/ ; DE-AC02-05CH11231//United States Department of Energy/ ; RGPIN 2018-03898//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN 2025-04928//Natural Sciences and Engineering Research Council of Canada/ ; 3-1/PDFP/HEC/2022(B-3)/2339/02//Higher Education Commission/ ; }, mesh = {*Rhodobacter sphaeroides/genetics/metabolism ; *Operon ; *Photosynthesis/genetics ; *Photosynthetic Reaction Center Complex Proteins/genetics/metabolism ; *Chloroflexi/genetics ; Bacterial Proteins/genetics/metabolism ; }, abstract = {Photosynthesis is the foundation of the vast majority of life systems, and is therefore the most important bioenergetic process on earth. The greatest diversity of photosynthetic systems is found in microorganisms. However, our understanding of the biophysical and biochemical processes that transduce light into chemical energy is derived from a relatively small subset of proteins from microbes that are amenable to cultivation, in contrast to the huge number of predicted proteins that catalyze the initial photochemical reactions deposited in databases, such as from metagenomics. We describe the use of a Rhodobacter sphaeroides laboratory strain for the expression of heterologous photosynthesis genes to demonstrate the feasibility of mining this resource, focusing on hot spring Chloroflexota gene sequences. Using a synthetic operon of genes, we produced a photochemically active complex of reaction center proteins in our biological system. We also present bioinformatic analyses of anoxygenic type II reaction center sequences from metagenomic samples collected from hot (42-90 °C) springs available through the JGI IMG database, to generate a resource of diverse sequences that are potentially adapted to photosynthesis at such temperatures. These data provide a view into the natural diversity of anoxygenic photosynthesis, through a lens focused on high-temperature environments. The approach we took to express such genes can be applied for potential biotechnology purposes as well as for studies of fundamental catalytic properties of these heretofore inaccessible protein complexes.}, }
@article {pmid41301445, year = {2025}, author = {Zhang, J and Xu, G and Yi, Z and Tang, X}, title = {Efficient Mining and Characterization of Two Novel Keratinases from Metagenomic Database.}, journal = {Biomolecules}, volume = {15}, number = {11}, pages = {}, doi = {10.3390/biom15111527}, pmid = {41301445}, issn = {2218-273X}, support = {2024YFC2815900//National Key R\&amp;D Program of China/ ; SOA: 2017002//Scientific Research Foundation of Third Institute of Oceanography/ ; 23CZB005HJ08//Xiamen Southern Oceanographic Center/ ; 2021J02015//Fujian Provincial Natural Science Foundation of China/ ; }, mesh = {*Peptide Hydrolases/genetics/metabolism/chemistry ; Phylogeny ; Keratins/metabolism ; Animals ; Enzyme Stability ; *Metagenomics ; Data Mining ; *Metagenome ; Feathers ; Kinetics ; Substrate Specificity ; Amino Acid Sequence ; Databases, Genetic ; }, abstract = {Keratin is a fibrous structural protein found in various natural materials such as hair, feathers, and nails. Its high stability and cross-linked structure make it resistant to degradation by common proteases, leading to the accumulation of keratinous waste in various industries. In this study, we developed and validated an effective bioinformatics-driven strategy for mining novel keratinase genes from the Esmatlas (ESM Metagenomic Atlas) macrogenomic database. Two candidate genes, ker820 and ker907, were identified through sequence alignment, structural modeling, and phylogenetic analysis, and were subsequently heterologously expressed in Escherichia coli Rosetta (DE3) with the assistance of a solubility-enhancing chaperone system. Both enzymes belong to the Peptidase S8 family. Enzymatic characterization revealed that GST-tagged ker820 and ker907 exhibited strong keratinolytic activity, with optimal conditions at pH 9.0 and temperatures of 60 °C and 50 °C, respectively. Both enzymes showed significant degradation of feather and cat-hair keratin. Kinetic analysis showed favorable catalytic parameters, including Km values of 9.81 mg/mL (ker820) and 5.25 mg/mL (ker907), and Vmax values of 120.99 U/mg (ker820) and 89.52 U/mg (ker907). Stability tests indicated that GST-ker820 retained 70% activity at 60 °C for 120 min, while both enzymes remained stable at 4 °C for up to 10 days. These results demonstrate the high catalytic capacity, thermal stability, and substrate specificity of the enzymes, supporting their classification as active keratinases. This study introduces a promising strategy for efficiently discovering novel functional enzymes using an integrated computational and experimental approach. Beyond keratinases, this methodology could be extended to screen for enzymes with potential applications in environmental remediation.}, }
@article {pmid41301179, year = {2025}, author = {Liu, D and Kuo, J and Lin, CH}, title = {Computational Investigation of Smooth Muscle Cell Plasticity in Atherosclerosis and Vascular Calcification: Insights from Differential Gene Expression Analysis of Microarray Data.}, journal = {Bioengineering (Basel, Switzerland)}, volume = {12}, number = {11}, pages = {}, doi = {10.3390/bioengineering12111223}, pmid = {41301179}, issn = {2306-5354}, abstract = {The dedifferentiation of smooth muscle cells (SMCs) is the main cause of atherosclerosis and vascular calcification. This study integrated the gene expression data of multiple microarrays to identify relevant marker molecules. A total of 72 Gene Expression Omnibus (GEO) samples (GSM) were collected from 10 gene expression data series (GSE) and divided into five groups: non-SMC, SMC, atherosclerotic SMC (SMC-ath), calcified SMC (SMC-calc), and treated SMC (SMC-t). The SMC-t group included synthetic SMCs that had undergone treatment to inhibit proliferation, migration, or inflammation. The gene expression data were merged, normalized, and batch effects were removed before differential gene expression (DGE) analysis was performed via linear models for microarray data (limma) and statistical analysis of metagenomic profiles (STAMPs). The genes with expressions that significantly differed were subsequently subjected to protein-protein interaction (PPI) and functional prediction analyses. In addition, the random forest method was used for classification. Twelve proteins that may be marker molecules for SMC differentiation and dedifferentiation were identified, namely, Proprotein convertase subtilisin/kexin type 1 (PCSK1), Transforming growth factor beta-induced (TGFBI), Complement C1s (C1S), Phosphomannomutase 1 (PMM1), Claudin 7 (CLDN7), Calcium binding and coiled-coil domain 2 (CALCOCO2), SAC3 domain-containing protein 1 (SAC3D1), Natriuretic peptide B (NPPB), Monoamine oxidase A (MAOA), Regulator of the Cell Cycle (RGCC), Alpha-crystallin B Chain (CRYAB), and Alcohol dehydrogenase 1B (ADH1B). Finally, their possible roles in SMCs are discussed. This study highlights the feasibility of bioinformatics analysis for studying SMC dedifferentiation.}, }
@article {pmid41301089, year = {2025}, author = {Ostos, I and Ruiz, I and Cruz, D and Flórez-Pardo, LM}, title = {Methane Concentration Prediction in Anaerobic Codigestion Using Multiple Linear Regression with Integrated Microbial and Operational Data.}, journal = {Bioengineering (Basel, Switzerland)}, volume = {12}, number = {11}, pages = {}, doi = {10.3390/bioengineering12111133}, pmid = {41301089}, issn = {2306-5354}, support = {No. DGI-01-2025//Direcci&#xf3;n General de Investigaciones of Universidad Santiago de Cali/ ; }, abstract = {Anaerobic codigestion of organic residues is a proven strategy for enhancing methane recovery. However, the complexity of microbial interactions and variability in operational conditions make it difficult to estimate methane concentration in real time, particularly in rural contexts. This study developed a multiple linear regression model to predict methane concentration using operational data and microbial community profiles derived from 16S rRNA gene sequencing. The system involved the codigestion of cassava by-product and pig manure in a two-phase anaerobic reactor. Predictor variables were selected through a hybrid approach combining statistical correlation with microbial functional relevance. The final model, trained on 70% of the dataset, demonstrated satisfactory generalization capability on the other 30 test set, achieving a coefficient of determination (R[2]) of 0.92 and a mean relative error (MRE) of 6.50%. Requiring only a limited set of inputs and minimal computational resources, the model offers a practical and accessible solution for estimating methane levels in decentralized systems. The integration of microbial community data represents a meaningful innovation, improving prediction by capturing biological variation not reflected in operational parameters alone. This approach can support local decision making and contribute to Sustainable Development Goal 7 by promoting reliable and affordable technologies for clean energy generation in rural and resource-constrained settings.}, }
@article {pmid41300910, year = {2025}, author = {Jin, X and Shen, H and Zhou, P and Yang, J and Yang, S and Ni, H and Yu, Y and Zhang, Z}, title = {Research Progress on Sepsis Diagnosis and Monitoring Based on Omics Technologies: A Review.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {15}, number = {22}, pages = {}, doi = {10.3390/diagnostics15222887}, pmid = {41300910}, issn = {2075-4418}, support = {2023YFC3603104//China National Key Research and Development Program/ ; Nos. 82472243 and 82272180//National Natural Science Foundation of China/ ; LHDMD24H150001//Huadong Medicine Joint Funds of the Zhejiang Provincial Natural Science Foundation of China/ ; 2024C03240//the Key Research &amp; Development Project of Zhejiang Province/ ; No. GZY-ZJ-KJ-24082//a collaborative scientific project co-established by the Science and Technology Department of the National Administration of Traditional Chinese Medicine and the Zhejiang Provincial Administration of Traditional Chinese Medicine/ ; No. 2024KY1099//the General Health Science and Technology Program of Zhejiang Province/ ; No. ZJDXLQCXZCJBGS2024016//the Project of Zhejiang University Longquan Innovation Center/ ; 320.6750.2024-23-07//Wu Jieping Medical Foundation Special Research Grant/ ; }, abstract = {Sepsis poses a significant global health burden, with millions of cases and high mortality rates annually, largely due to challenges in early diagnosis and monitoring. Traditional methods, reliant on nonspecific clinical manifestations and limited biomarkers like C-reactive protein and procalcitonin, often fail to distinguish infection from non-infectious inflammation or capture disease heterogeneity. This review synthesizes recent progress in omics technologies-genomics, transcriptomics, proteomics, and metabolomics-for advancing sepsis management. Genomics, via metagenomic next-generation sequencing, enables rapid pathogen identification and genetic variant analysis for susceptibility and prognosis. Transcriptomics reveals molecular subtypes and immune dynamics through RNA sequencing and single-cell approaches. Proteomics and metabolomics uncover protein and metabolite profiles linked to immune imbalance, organ damage, and metabolic disorders. Multi-omics integration, enhanced by artificial intelligence and machine learning, facilitates biomarker discovery, patient stratification, and predictive modeling, bridging laboratory findings to bedside applications like rapid diagnostic tools and clinical decision support systems. Despite advancements, challenges including data heterogeneity, high costs, and ethical concerns persist. Future directions emphasize single-cell and spatial omics, AI-driven personalization, and ethical frameworks to transform sepsis care from reactive to proactive, ultimately improving outcomes.}, }
@article {pmid41300336, year = {2025}, author = {Liu, Y and Xie, J and He, Y and Shi, Q and Gong, Q and Zhao, W and Qin, C and Zhou, C}, title = {Metabolome and Metagenome Signatures Underlying the Differential Resistance of Percocypris pingi, Crucian Carp, and Yellow Catfish to Ichthyophthirius multifiliis Infection.}, journal = {Biology}, volume = {14}, number = {11}, pages = {}, doi = {10.3390/biology14111546}, pmid = {41300336}, issn = {2079-7737}, support = {2023M732476//China Postdoctoral Science Foundation/ ; NJTCSC24-3//Open Project of Sichuan Provincial Key Laboratory of Fish Resources Conservation and Utilization in the Upper Reaches of the Yangtze River/ ; 2023YFH0046//Sichuan Science and Technology Program/ ; }, abstract = {Ichthyophthirius multifiliis poses a significant threat to global aquaculture, yet some fish species exhibit remarkable resistance. This study employed a combined LC-MS-based metabolomics and 16S rRNA gene sequencing approach to investigate the intrinsic mechanisms underlying the differential susceptibility of Percocypris pingi, crucian carp, and yellow catfish. Our results revealed distinct skin molecular and microbial profiles in P. pingi associated with its enhanced resilience. Metabolomic analysis identified a significant upregulation of key antioxidants (L-Glutathione reduced, L-Glutathione oxidized, L-Cysteine-glutathione gisulfide, Uric acid, Histamine, N-Acetylhistamine, and scorbic acid) in P. pingi, most notably L-Glutathione reduced, which was 31- and 59-fold higher than in yellow catfish and crucian carp, respectively. Functional enrichment further highlighted the critical role of enhanced antioxidant capacity (centered on glutathione metabolism) and immune/inflammatory responses in the resistance to I. multifiliis of P. pingi. Concurrently, skin microbiome analysis showed that P. pingi hosted a microbial community distinct from the other two species, with significantly higher α-diversity. Notably, P. pingi skin was significantly depleted of the parasitic bacteria Candidatus_Megaira and Candidatus_Midichloria, which were highly abundant in the susceptible species. Furthermore, predicted metagenomic functions indicated that P. pingi's microbiota was enriched in fundamental metabolic pathways, whereas the microbiota of crucian carp and yellow catfish was skewed towards disease- and immune-related pathways. In conclusion, our findings demonstrate that the superior resistance of P. pingi to I. multifiliis is likely conferred by a synergistic effect of a robust skin antioxidant capacity (primarily driven by glutathione) and a protective skin microbiome that excludes specific parasites. This study provides novel insights into the multi-faceted mechanisms of disease resistance in fish.}, }
@article {pmid41300008, year = {2025}, author = {Rajah Kumar, M and Amankwaa, AO and Razali, NS and Mohamad, NE and Khalid, M and Abdullah, JO and Masarudin, MJ and Osman, MA and Abd Rahman, NMAN and Alitheen, NB}, title = {Preliminary Evaluation of the Gut Microbiota Modulatory Potential of Malaysian Kefir Water in Ageing Mice.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {22}, pages = {}, doi = {10.3390/foods14223851}, pmid = {41300008}, issn = {2304-8158}, support = {FRGS-777 MRSA/1/2018/SKK10/UPM/02/1//Fundamental Research Grant Scheme (FRGS) by the Malaysian Ministry of Higher Education (MoHE)/ ; }, abstract = {Ageing is often accompanied by gut microbiota alterations that contribute to dysbiosis-a recognised hallmark of ageing and a risk factor for neurodegenerative diseases. Probiotic interventions offer a promising approach to restore microbial homeostasis. This preliminary study explored the potential modulatory effects of Malaysian kefir water, a Lactobacillus-enriched fermented beverage with previously reported antioxidant and neuroprotective properties in D-galactose-induced ageing mice. Kefir water was administered as both a pre-treatment and co-treatment, and gut microbiota changes were assessed using 16S rRNA metagenomic sequencing of faecal samples. Alpha and beta diversity analyses showed a stable microbial diversity across treatments. However, preliminary descriptive trends suggested that kefir water may influence specific bacterial populations. Increases were observed in Muribaculaceae and Lactobacillaceae, along with apparent decreases in Lachnospiraceae and Prevotellaceae. Both kefir treatments tended to increase the abundance of Ligilactobacillus, with the co-treatment group appearing to restore the Firmicutes/Bacteroidota ratio toward control levels, while the pre-treatment group showed a tendency to further reduce this ratio. Collectively, these findings provide preliminary indications that kefir water may hold potential as a dietary approach to modulate gut microbial changes associated with ageing. However, confirmation through studies with larger sample sizes and broader analytical coverage is necessary to substantiate these initial observations.}, }
@article {pmid41299763, year = {2025}, author = {Manrique-de-la-Cuba, MF and López-Rodríguez, M and Abades, S and Trefault, N}, title = {Cold adaptation and horizontal gene transfer shape Antarctic sponge microbiomes.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-025-02262-z}, pmid = {41299763}, issn = {2049-2618}, support = {Fondecyt 1230758//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; DG_02-22//Instituto Antartico Chileno/ ; }, abstract = {BACKGROUND: Marine sponges exhibit wide distribution in tropical, temperate, and polar environments. They host diverse microbiomes important to their survival and ecological roles. Antarctic sponges, thriving in extreme cold environments, harbor unique microbial communities. However, functional differences distinguishing Antarctic sponge microbiomes have been poorly investigated. In this study, we investigated how the functional composition of the microbiomes of Antarctic sponges differs from that of their counterparts in other environments, with a particular focus on functions related to cold adaptation. We also assessed the role of horizontal gene transfer (HGT) in driving these functional adaptations.<br><br>RESULTS: Antarctic sponge microbiomes displayed a unique functional signature characterized by significantly higher proportions of genes related to cold adaptation, such as cold shock proteins, chaperones, heat shock proteins, and osmoprotectants, compared to their tropical and temperate counterparts, and antioxidants compared to the surrounding seawater. HGT was prevalent in Antarctic sponge symbionts, particularly in the dominant Gammaproteobacteria, Alphaproteobacteria, and Bacteroidia, contributing equally to metabolic functions and cold adaptation, with an important fraction of the latter exhibiting long-distance horizontal gene transfer (HGT). Conjugation, primarily mediated by integrative and conjugative elements (ICE), is a proposed crucial mechanism driving horizontal gene transfer (HGT) in Antarctic sponge symbionts. The cold shock protein C (CspC), linked to cold adaptation, was restricted to Proteobacteria and identified as a potential horizontally acquired gene exclusive to sponge symbionts compared to free-living bacteria in the Antarctic marine ecosystem.<br><br>CONCLUSIONS: Antarctic sponge microbiomes exhibit higher proportions of functional adaptations for cold environments facilitated by horizontal gene transfer (HGT). These findings highlight the evolutionary importance of HGT mechanisms in shaping microbial symbioses in extreme environments. Further exploration of HGT dynamics and the role of specific symbionts in cold adaptation could reveal novel insights into microbial evolution and host-symbiont interactions in polar ecosystems. Video Abstract.}, }
@article {pmid41299634, year = {2025}, author = {Meawad, M and Singh, D and Deng, A and Sonthalia, R and Cai, E and Dumeaux, V}, title = {Functional archetypes in the human gut microbiome reveal metabolic diversity, stability, and influence disease-associated signatures.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {241}, pmid = {41299634}, issn = {2049-2618}, support = {Vector Scholarship in Artificial Intelligence//Vector Institute/ ; Globalink Summer Internship Award//MITACS/ ; 391682//Natural Sciences and Engineering Research Council of Canada/ ; 43481//Canadian Foundation for Innovation J. Evans Leaders Fund/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Metagenomics/methods ; Adult ; Metagenome ; Female ; Male ; }, abstract = {BACKGROUND: Understanding the functional diversity of the gut microbiome is critical for elucidating its roles in human health and disease. While traditional approaches focus on taxonomic composition, functional configurations of the microbiome remain understudied. This study introduces a deep-learning framework combined with archetypal analysis to identify and characterize functional archetypes in the adult human gut microbiome. This approach aims to provide insights into interindividual variability, function-driven microbiome stability, and the potential confounding role of functional diversity in disease-associated microbial signatures.<br><br>RESULTS: Analyzing 9838 whole-genome metagenomic samples from healthy adults across 29 countries, we identified three distinct functional archetypes that define the boundaries of the gut microbiome's functional space. Each archetype is characterized by unique metabolic potentials: Archetype 1 is enriched in sugar metabolism, branched-chain amino acid biosynthesis, and cell wall synthesis; Archetype 2 is dominated by fatty acid metabolism and TCA cycle pathways; and Archetype 3 is defined by amino acid and nitrogen metabolism. While most gut microbiome communities are a blend of these archetypes, some align closely with a single archetype, potentially reflecting adaptation to host factors such as distinct dietary patterns. Proximity to these archetypes correlates with microbiome stability, with Archetype 2 representing the most resilient state, likely due to its metabolic flexibility and diversity. Functional archetypes emerged as a potential confounder in disease-associated microbial signatures, including in type-2 diabetes, colorectal cancer, and inflammatory bowel disease (IBD). In IBD, archetype-specific shifts were observed: Archetype 1-dominant samples exhibited increased carbohydrate metabolism, while Archetype 3-dominant samples showed enrichment in inflammatory pathways. These findings highlight the potential for archetype-specific functional changes to inform microbiome-targeted interventions.<br><br>CONCLUSIONS: The identified functional archetypes provide a robust framework for addressing interindividual variability and potential confounding in gut microbiome-based disease studies. By incorporating archetypes as potential confounders or stratification factors, researchers can reduce variability, uncover novel pathways, and improve the precision of microbiome-targeted interventions. The deep-learning framework can be applied to other host-associated microbial ecosystems, providing new insights into microbial functional dynamics and their implications for the host's health.}, }
@article {pmid41299624, year = {2025}, author = {Zhang, XA and Zhang, MQ and Liu, YW and Lin, L and Zhang, JT and George, T and Jalloh, MB and Sevalie, S and Kargbo, KB and Jiang, BG and Mi, ZQ and Wang, SC and Si, GQ and Zhang, L and Fang, LQ and Chen, WW and Dong, G and Huang, WJ and Liu, W}, title = {Virome characterization of wild small mammals provides new insight into zoonotic pathogens in West Africa.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {242}, pmid = {41299624}, issn = {2049-2618}, support = {81825019//National Science Fund for Distinguished Young Scholars/ ; }, mesh = {Animals ; *Virome/genetics ; *Zoonoses/virology/transmission ; Metagenomics/methods ; Chiroptera/virology ; *RNA Viruses/genetics/classification/isolation &amp; purification ; Phylogeny ; Africa, Western ; Humans ; Shrews/virology ; Genome, Viral ; *Animals, Wild/virology ; Disease Reservoirs/virology ; *Mammals/virology ; Rodentia/virology ; *Viral Zoonoses/virology/transmission ; }, abstract = {BACKGROUND: A significant number of infectious diseases affecting humans have been associated with zoonotic viruses. Wild small mammals, such as bats, rodents, and shrews, serve as natural reservoirs for a multitude of zoonotic viruses, particularly in Africa, where zoonosis is prevalent. Nevertheless, our knowledge of the virome composition within these hosts remains limited, impeding a more profound understanding of spillover events into human populations.<br><br>RESULTS: We employed a viral metagenomics approach to characterize the virome in 846 wild small mammals sampled from Sierra Leone. Based on the complete RNA-dependent RNA polymerase genome, a total of 39 RNA viruses infecting mammals were identified, comprising 13 known viruses and 26 novel viruses. Notably, the Paramyxoviridae family exhibited the highest diversity of viral species across all three orders of wild mammal. The animal species Hipposideros jonesi and Lophuromys chrysopus were found to harbor the highest viral richness. Among these viral species, 15 were identified as cross-species transmitted viruses shared among different animal species, 3 were classified as zoonotic (Encephalomyocarditis virus, Rocahepevirus sp., and Lassa virus), while 3 others posed a potential risk for spillover (melian virus, Rodent hepacivirus, Hunnivirus A). Cross-species transmission analysis revealed that rodents played central roles in virus sharing, while cross-order viral transmission was less likely to occur in bats. Among 26 newly identified viruses, four viruses (Bat ledantevirus 2, Rattus rattus jeilongvirus, Miniopterus inflatus ribovirus, and Rat mamastrovirus) were predicted to have high zoonotic potential. Among them, Bat ledantevirus 2 exhibited the highest zoonotic potential and phylogenetic relatedness to the known human-infecting virus (Le Dantec virus). Further seroepidemiological analysis in patients, using single-round infectious virus particles as antigens, revealed the presence of neutralizing antibodies against Bat ledantevirus 2, a novel virus belonging to the Rhabdoviridae family.<br><br>CONCLUSIONS: These findings highlight the critical need for enhanced surveillance at the human-animal interface in order to identify viruses with cross-species transmission potential prior to their spillover into human population. Video Abstract.}, }
@article {pmid41299512, year = {2025}, author = {Kansou, E and Aubry, A and Brochot, E and Priam, A and Cabry-Goubet, R and Bosquet, D and Demey, B}, title = {Human papillomavirus seminal carriage alters virome diversity and male fertility: a case-control study.}, journal = {Reproductive biology and endocrinology : RB&amp;E}, volume = {23}, number = {1}, pages = {154}, pmid = {41299512}, issn = {1477-7827}, mesh = {Humans ; Male ; Case-Control Studies ; *Virome/genetics ; Adult ; *Semen/virology ; Retrospective Studies ; *Papillomavirus Infections/virology/complications ; *Infertility, Male/virology ; *Papillomaviridae/genetics/isolation &amp; purification ; *Fertility/physiology ; Spermatozoa/virology ; Human Papillomavirus Viruses ; }, abstract = {BACKGROUND: A link between idiopathic male infertility and viral infections exhibiting seminal carriage has emerged recently. In this respect, human papillomavirus (HPV) appears to be the most prevalent sexually transmitted agent worldwide. The viruses present in the genital environment comprise the genital virome. HPV infection reportedly disrupts homeostasis of the virome in women but this topic has not previously been studied in men.<br><br>METHODS: This was a retrospective study of males attending the fertility clinic at Amiens University Medical Center (Amiens, France). Men with a multiple-type HPV infection in the sperm (n&#x2009;=&#x2009;15) were considered to be cases, and men with no detectable HPV in the sperm were considered to be controls (n&#x2009;=&#x2009;13). The molecular virome in cases and controls was described via metagenomic next-generation sequencing. The cases and controls were compared with regard to genomic, clinical and sperm-related characteristics.<br><br>RESULTS: The seminal virome analysis revealed the predominance of Papillomaviridae in cases (63.4%). Other virus families found in both groups (albeit with lower proportions of reads in cases than in controls) were Herpesviridae (6.9% vs. 40.5%, respectively), Polyomaviridae (11.3% vs. 17.8%, respectively), and other viral sequences (18.4% vs. 40%, respectively). There was no difference in viral diversity between the two groups (p&#x2009;=&#x2009;0.0692). Viral diversity was correlated with the semen sample volume, progressive sperm motility, total motility, and sperm vitality in cases but not in controls. Univariate and multivariate comparative analyses did not reveal significant differences in sperm parameters between cases and controls.<br><br>CONCLUSIONS: The male seminal virome mainly comprises viruses from the Papillomaviridae, Herpesviridae and Polyomaviridae families. The correlation between viral diversity and sperm parameters in HPV-positive patients suggests that HPV-specific interactions within the seminal virome are responsible for variations in sperm parameters. Hence, alterations in the seminal virome (due mostly to HPV infection) might impact sperm parameters and thus male fertility.}, }
@article {pmid41299356, year = {2025}, author = {Shen, A and Xu, X and Xu, L and Nie, X and Ai, J and Chen, W}, title = {Clinical utility of metagenomic next-generation sequencing (mNGS) and a novel PCR-based point-of-care testing (POCT) for pathogen detection in pulmonary infections: a retrospective study.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-025-11814-5}, pmid = {41299356}, issn = {1471-2334}, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) and multiple point-of-care testing (POCT) techniques have demonstrated significant potential in pathogen detection. However, neither technology fully meets all clinical diagnostic needs for pulmonary infections. This study aimed to evaluate the complementary detection performance and clinical applicability of POCT and mNGS in pulmonary infections, using conventional culture as a reference.<br><br>METHODS: This study enrolled forty-five patients with suspected lower respiratory tract infections for concurrent evaluation using POCT and mNGS. The detection performance of traditional culture methods, POCT, and mNGS was subsequently analyzed and compared.<br><br>RESULTS: Both molecular methods showed high positive detection rates, surpassing that of the culture method. When conventional culture was used as the gold standard, the sensitivity and positive predictive value (PPV) within the detection range of the PM Easy Lab Respiratory Panel (RP) were 97.1% and 80.5%, respectively, whereas for mNGS, these values were 90.2% and 92.5%, respectively. A comparison of the PM Easy Lab RP and mNGS results revealed that the PM Easy Lab was faster (100&#xa0;min vs. 24&#xa0;h) and more sensitive (88 vs. 63 pathogens) within its detection range, whereas mNGS offered a broader spectrum of pathogen detection. The overall consistency between PM Easy Lab RP and mNGS was 88.9%. Klebsiella pneumoniae and Acinetobacter baumannii were identified as the most prevalent bacterial infections by all three detection methods. Moreover, both PM Easy Lab RP and mNGS demonstrated enhanced capability over culture in detecting mixed infections (57.8%, 84.4% vs. 15.6%, all P&#x2009;<&#x2009;0.01), uncovering a substantial number of viral and bacterial-viral co-infections that are undetectable by conventional culture methods. The most common combination of mixed infections in the PM Easy Lab RP was mixed bacterial infections (76.9%, 20/26), whereas in mNGS, it was bacterial-fungal-viral mixed infections (36.8%, 14/38).<br><br>CONCLUSIONS: The findings indicate that PM Easy Lab RP and mNGS offer distinct yet complementary value. PM Easy Lab has potential advantages in speed, sensitivity, and efficiency in detecting pathogens within its panel, and it could be considered for rapid, frontline testing, while mNGS provides a broad-spectrum detection capability, making it more suitable for comprehensive investigation of complex cases, though careful clinical interpretation is required to distinguish pathogenic from colonizing or contaminating organisms. Understanding their respective strengths can guide the development of optimized, hierarchical diagnostic pathways.}, }
@article {pmid41299229, year = {2025}, author = {Thurimella, K and Mohamed, AMT and Li, C and Vatanen, T and Graham, DB and Owens, RM and La Rosa, SL and Plichta, DR and Bacallado, S and Xavier, RJ}, title = {Protein language models uncover carbohydrate-active enzyme function in metagenomics.}, journal = {BMC bioinformatics}, volume = {26}, number = {1}, pages = {285}, pmid = {41299229}, issn = {1471-2105}, mesh = {*Metagenomics/methods ; Humans ; *Enzymes/metabolism/chemistry/genetics ; Carbohydrate Metabolism ; Molecular Sequence Annotation ; }, abstract = {BACKGROUND: The functional annotation of uncharacterized microbial enzymes from metagenomic data remains a significant challenge, limiting our understanding of microbial metabolic dynamics. Traditional annotation methods often rely on sequence homology, which can fail to identify remote homologs or enzymes with structural rather than sequence conservation. To address this gap, we developed CAZyLingua, the first annotation tool to use protein language models (pLMs) for the accurate classification of carbohydrate-active enzyme (CAZyme) families and subfamilies.<br><br>RESULTS: CAZyLingua demonstrated high performance, maintaining precision and recall comparable to state-of-the-art hidden Markov model-based methods while outperforming purely sequence-based approaches. When applied to a metagenomic gene catalog from mother/infant pairs, CAZyLingua identified over 27,000 putative CAZymes missed by other tools, including horizontally-transferred enzymes implicated in infant microbiome development. In datasets from patients with Crohn's disease and IgG4-related disease, CAZyLinuga uncovered disease-associated CAZymes, highlighting an expansion of carbohydrate esterases (CEs) in IgG4-related disease. A CE17 enzyme predicted to be overabundant in Crohn's disease was functionally validated, confirming its catalytic activity on acetylated manno-oligosaccharides.<br><br>CONCLUSIONS: CAZyLingua is a powerful tool that effectively augments existing functional annotation pipelines for CAZymes. By leveraging the deep contextual information captured by pLMs, our method can uncover novel CAZyme diversity and reveal enzymatic functions relevant to health and disease, contributing to a further understanding of biological processes related to host health and nutrition.}, }
@article {pmid41299176, year = {2025}, author = {Wirbel, J and Hickey, AS and Chang, D and Enright, NJ and Dvorak, M and Chanin, RB and Schmidtke, DT and Bhatt, AS}, title = {Long-read metagenomics reveals phage dynamics in the human gut microbiome.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {41299176}, issn = {1476-4687}, abstract = {Gut bacteriophages profoundly impact microbial ecology and health[1-3]; yet, they are understudied. Using deep long-read bulk metagenomic sequencing, we tracked prophage integration dynamics in stool samples from six healthy individuals, spanning a 2-year timescale. Although most prophages remained stably integrated into their hosts, approximately 5% of phages were dynamically gained or lost from persistent bacterial hosts. Within a sample, we found that bacterial hosts with and without a given prophage coexisted simultaneously. Furthermore, phage induction, when detected, occurred predominantly at low levels (1-3× coverage compared to the host region), in line with theoretical expectations[4]. We identified multiple instances of integration of the same phage into bacteria of different taxonomic families, challenging the dogma that phages are specific to a host of a given species or strain[5]. Finally, we describe a new class of 'IScream phages', which co-opt bacterial IS30 transposases to mediate their mobilization, representing a previously unrecognized form of phage domestication of selfish bacterial elements. Taken together, these findings illuminate fundamental aspects of phage-bacterial dynamics in the human gut microbiome and expand our understanding of the evolutionary mechanisms that drive horizontal gene transfer and microbial genome plasticity.}, }
@article {pmid41299116, year = {2025}, author = {Akhtar, S and Malik, A}, title = {Integrated physicochemical and metagenomic analysis of the Ganges River water.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {41299116}, issn = {1614-7499}, abstract = {The perennial River Ganges, one of India's most vital freshwater resources, is increasingly threatened by growing human activities. The present study provides an integrated assessment of water quality, heavy metal pollution, antibiotic resistance, and microbial community dynamics along a culturally important section of the river. Physicochemical parameters showed seasonal variations, with higher pH, TDS, nitrate, and sulfate levels, indicating significant human activities. ICP-AES analysis of heavy metals revealed high levels of Cr and Cd, with a contamination degree of 38.25, indicating a very high pollution level. Antibiotic susceptibility testing of 84 bacterial isolates demonstrated 64.28% multidrug resistance, mainly against β-lactam antibiotics. Although the Water Quality Index was 43.43 (classified as good), microbial and metal contamination indicated hidden ecological risks. 16S rRNA gene-based metagenomic profiling showed dominance of pollution-tolerant bacterial groups, especially Pseudomonadota, Bacillota, and Fusobacteriota. Genera like Brevundimonas, Methylobacterium, Pseudomonas, and Acinetobacter were most common, indicating microbial shifts due to ongoing human activities. Functional predictions (KEGG) suggested enrichment in pathways for xenobiotic degradation, energy production, and environmental information processing. These findings highlight the importance of comprehensive monitoring that combines chemical, microbiological, and genomic tools to better assess the river pollution and efforts to reduce public health risks.}, }
@article {pmid41298564, year = {2025}, author = {Qu, T and Koch, L and Mukherjee, R and Tu, Y and Seidel, AL and Püttmann, LD and Winkel, A and Yang, I and Grischke, J and Liu, D and Wolkers, WF and Kittler, S and Chichkov, B and Stiesch, M and Szafrański, SP}, title = {Laser-assisted microbial culturomics.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {10614}, pmid = {41298564}, issn = {2041-1723}, support = {German Cluster of Excellence Ex62/2 Rebirth//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SFB/TRR 298 SIIRI - Project-ID 426335750//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC 2155 - project number 390874280//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Laser-Tissue-Perfude, 101054009//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; }, mesh = {Biofilms/growth &amp; development ; Humans ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Bacteria/genetics/isolation &amp; purification/classification/growth &amp; development ; *Lasers ; Dental Plaque/microbiology ; Bioprinting/methods ; Metagenomics/methods ; }, abstract = {Even though metagenomics have revolutionized the characterization of the human microbiome, detailed mechanistic studies are impracticable, as there is a dearth of robust culture collections. We now describe the development and use of a laser-assisted culturomics platform, incorporating the elements of a bioprinter, the culture conditions, the methods to characterize the microorganisms and a biobank. With laser-assisted bioprinting, the microorganisms can be rapidly and precisely transferred from clinical biofilms to highly organized arrays of microbial colonies, which are suitable for co-culturing and molecular analyses. The presented technique has propagated 99 of 100 microbial species and recovered 79% of abundant species from dental plaque in accordance with full 16S rRNA gene profiling of 691,199 sequences. Microscopy, spectroscopy and enzyme assays have been used to guide isolations. Processing of oral biofilms from four individuals has yielded 249 representative isolates, from 14 classes and 124 species in total. Functional profiling with bioprinting has indicated commensals which could potentially contribute to disease development. Isolates from peri-implantitis cover 85.4% of the transcriptionally active clinical biofilms at genus level. Taken together, this work provides the basis for generating on-demand culture collections and biofilms for research and clinical use.}, }
@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 Investigaci&#xf3;n (Spanish Agencia Estatal de Investigaci&#xf3;n)/ ; }, 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 &amp; development ; *Rivers/microbiology ; *Bacteria/genetics/classification/metabolism/isolation &amp; 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.}, }
@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.}, }
@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 &amp; 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.}, }
@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.<br><br>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.<br><br>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.<br><br>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 &#x3b2;-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.<br><br>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.<br><br>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.<br><br>METHODS: APC[min/+] (CRC model, n&#xa0;=&#xa0;8) and wild-type controls (n&#xa0;=&#xa0;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.<br><br>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.<br><br>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-W&#xfc;rttemberg (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.<br><br>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&#xa0;57357 (August 2021-October 2022). Whole&#xa0;genome sequencing was used to assess sequence types, resistance genes, virulence factors, plasmid content, and transmission dynamics.<br><br>RESULTS: Carbapenem resistance was primarily mediated by blaNDM-5, carried on species-specific plasmids: IncFIA/IncFII in E.&#xa0;coli and IncFIB/IncHIB megaplasmids in K.&#xa0;pneumoniae, frequently co-harboring additional aminoglycoside, sulfonamide, and fluoroquinolone resistance genes. The most common sequence types were ST361, ST167, and ST405 in E.&#xa0;coli, and ST11, ST383, and ST147 in K.&#xa0;pneumoniae. Clonal clustering was observed in 62.5% of K.&#xa0;pneumoniae but only 17% of E.&#xa0;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.&#xa0;pneumoniae isolates, but no hypermucoviscous phenotype was observed.<br><br>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.&#xa0;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&amp;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.<br><br>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.<br><br>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.<br><br>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.<br><br>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.<br><br>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.<br><br>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.<br><br>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.}, }
@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 &amp; 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.}, }
@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 &amp; 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.<br><br>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.<br><br>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/&#x3bc;l, interquartile range (IQR) [3.320-6.348]) compared with the non-PJI group (0.028 ng/&#x3bc;l, IQR [0.009-0.273]) (p < 0.001). The Youden index identified a cfDNA concentration &#x2265; 1.59 ng/&#x3bc;l 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).<br><br>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.}, }
@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.<br><br>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.<br><br>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 &#x2265;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.<br><br>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%.<br><br>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.}, }
@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.<br><br>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&#x2009;=&#x2009;0.284&#xa0;m/s, NO3[-]-N&#x2009;=&#x2009;0.031&#xa0;mg/L) and high (V&#x2009;=&#x2009;0.461&#xa0;m/s, NO3[-]-N&#x2009;=&#x2009;0.055&#xa0;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&#x2009;<&#x2009;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.<br><br>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 &amp; 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.}, }
@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.}, }
@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.}, }
@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.}, }
@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 &amp; 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.}, }
@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 &amp; 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 &amp; 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.}, }
@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.}, }
@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.}, }
@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 Cient&#xed;fico e Tecnol&#xf3;gico (D.G. Br&#xed;cio master scholarship, Process number 161678/2021-1)/ ; //Bank of the Amazon (BASA S.A., Brazil; Contract No. 2022-230)/ ; //Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel 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.<br><br>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&#x2009;&#x2264;&#x2009;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.<br><br>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. &#xa9; 2025 The Author(s). Journal of the Science of Food and Agriculture published by John Wiley &amp; 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.<br><br>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.<br><br>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.<br><br>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.<br><br>METHODS: Adults (&#x2265;&#x2009;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[&#xae;] 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).<br><br>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.<br><br>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.}, }
@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.<br><br>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.<br><br>RESULTS: mNGS demonstrated a significantly higher positive rate than CMT (72.63% vs. 55.31%, P&#x2009;<&#x2009;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&#x2009;<&#x2009;0.001). The specificity of mNGS was 73.08%, relatively lower than that of CMT (88.46%, P&#x2009;<&#x2009;0.05). Specific to ICH and ICO, mNGS showed significantly higher sensitivity than CMT (ICH: 94.94% vs. 81.01%, P&#x2009;<&#x2009;0.01; ICO:85.42% vs. 60.42%, P&#x2009;<&#x2009;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&#x2009;<&#x2009;0.05).<br><br>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.}, }
@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.<br><br>METHODS: A six-week, randomised, double-blind, placebo-controlled trial was conducted in UK children aged 8-13&#x2009;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.<br><br>RESULTS: Fifty-three participants (mean age&#x2009;=&#x2009;10.2&#x2009;years, SD&#x2009;=&#x2009;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&#x2009;=&#x2009;2.03, SE&#x2009;=&#x2009;0.33 vs. 2.86, SE&#x2009;=&#x2009;0.34), p&#x2009;=&#x2009;0.088. Actigraphy revealed the kefir group spent fewer minutes awake during the down period at week six (M&#x2009;=&#x2009;70.10, SE&#x2009;=&#x2009;0.09) than the placebo group (M&#x2009;=&#x2009;89.72, SE&#x2009;=&#x2009;0.07), p&#x2009;=&#x2009;0.04. However, the kefir group self-reported more sleep problems post-intervention (M&#x2009;=&#x2009;39.81, SE&#x2009;=&#x2009;0.75 vs. 37.40, SE&#x2009;=&#x2009;0.65), p&#x2009;=&#x2009;0.02. For Go/NoGo RT variance, a non-significant interaction (p&#x2009;=&#x2009;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.<br><br>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.<br><br>ETHICS: Ethical approval for the study was granted by St Mary's University Ethics Committee.<br><br>TRIAL REGISTRATION: The trial protocol has been prospectively registered with ClinicalTrials.gov: NCT05155696. Registered on 13 December 2021.}, }
@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 &amp; 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.}, }
@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 &amp; 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.}, }
@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.}, }
@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 &amp; 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.<br><br>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.<br><br>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).<br><br>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.}, }
@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.<br><br>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.<br><br>DESIGN: A cross-sectional, two-group comparative study.<br><br>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.<br><br>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.<br><br>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.<br><br>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.<br><br>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%).<br><br>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 &amp; purification ; *Microbiota ; Archaea/genetics/isolation &amp; 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.<br><br>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.<br><br>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&#xa0;=&#xa0;0.038 at the family, P&#xa0;=&#xa0;0.019 at the genus and P&#xa0;=&#xa0;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&#xa0;<&#xa0;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&#xa0;=&#xa0;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.<br><br>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.}, }
@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.}, }
@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.<br><br>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.<br><br>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.<br><br>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.<br><br>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.<br><br>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.<br><br>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.<br><br>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.<br><br>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.<br><br>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.<br><br>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.<br><br>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.<br><br>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.}, }
@article {pmid41279103, year = {2025}, author = {Seki, K and Nguyen, MTA and Penev, PI and Banfield, JF and Isaacs, FJ and Jewett, MC}, title = {Engineered orthogonal translation systems from metagenomic libraries expand the genetic code.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.10.30.685624}, pmid = {41279103}, issn = {2692-8205}, abstract = {Genetic code expansion with non-canonical amino acids (ncAAs) opens new opportunities for the function and design of proteins by broadening their chemical repertoire. Unfortunately, ncAA incorporation is limited both by a small collection of orthogonal aminoacyl-tRNA synthetases (aaRSs) and tRNAs and by low-throughput methods to discover them. Here, we report the discovery, characterization, and engineering of a UGA suppressing orthogonal translation system mined from metagenomic data. We developed an integrated computational and experimental pipeline to profile the orthogonality of >200 tRNAs, test >1,250 combinations of aaRS:tRNA pairs, and identify the AP1 TrpRS:tRNA [Trp] UCA as an orthogonal pair that natively encodes tryptophan at the UGA codon. We demonstrate that the AP1 TrpRS:tRNA [Trp] UCA is highly active in cell-free and cellular contexts. We then use Ochre , a genomically recoded Escherichia coli strain that lacks UAG and UGA codons, to engineer an AP1 TrpRS variant capable of 5-hydroxytryptophan incorporation at an open UGA codon. We anticipate that our strategy of integrating metagenomic bioprospecting with cell-free screening and cell-based engineering will accelerate the discovery and optimization of orthogonal translation systems for genetic code expansion.}, }
@article {pmid41278862, year = {2025}, author = {Liu, J and Coker, MO and Osazuwa-Peters, N and Peter, O and Idemudia, NL and Schlecht, NF and Obuekwe, O and Eki-Udoko, FE and Bromberg, Y}, title = {Whole Metagenome Sequencing: not Deep Enough for Complete Microbial Function Recovery.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.11.04.685665}, pmid = {41278862}, issn = {2692-8205}, abstract = {BACKGROUND: Whole metagenome shotgun sequencing (WMS) is widely used to profile microbial function. However, technical variability in sequencing and analysis often obscures true biological patterns. Large-scale studies are particularly susceptible to batch effects, such as differences in sequencing depth and platform and annotation strategies, as well as sample-to-flow-cell assignments. However, the relative effects of these factors on functional inference in such studies have yet to be systematically evaluated.We analyzed oral-rinse WMS data from a study cohort including 671 Nigerian youths aged 9-18, sequenced on two Illumina platforms. Microbial molecular functionality encoded in these data were annotated using the mi-faser/Fusion pipeline, to capture the broad functional repertoire, and HUMAnN 3/EC numbers pipeline to characterize curated enzymatic activities. We then quantified how technical factors and batch effects shaped the recovery of microbial functionality.<br><br>RESULTS: Three findings of our work were most salient. First, we observed that the choice of annotation strategy traded off between breadth and specificity of functional coverage. Second, we found that low-prevalence functions were disproportionately lost at shallow sequencing depths, indicating that in e.g. case-control studies with few representatives of the minor class, sequencing depth could critically impact study resolution. Finally, using our newly developed model relating sequencing depth to functional recovery, we demonstrated that increasing sequencing depth does not directly or proportionally improve functional recall. That is, at as little as 10% of this study's sequencing depth, 30% of the estimated complete microbiome functional repertoire was detectable. However, even at the full depth used in this study, we were only able to recover an estimated 60% of that complete functional repertoire.<br><br>CONCLUSIONS: Together, these findings and our depth-to-function mapping framework provide practical guidelines for the design and interpretation of WMS studies. Coordinating sequencing depth planning with annotation strategy, experimental design, and rigorous batch control is thus essential for robust detection of microbial functions and for ensuring reproducible microbiome insights.}, }
@article {pmid41278782, year = {2025}, author = {Duan, J and Marques, AD and Hogenauer, M and Hwang, Y and Zhang, Y and Timperman, A and Higgins, S and Wilson, NG and Fitts, EA and Lim, HK and Bittinger, K and Moustafa, AM and Collman, RG and Bushman, FD}, title = {Optimizing methods for virome analysis based on studies of a synthetic viral community.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.10.23.683462}, pmid = {41278782}, issn = {2692-8205}, abstract = {Studies of whole viral populations--the "virome"--are yielding exciting new insights into biological systems, but methods are still being optimized. Here we describe generation and use of a synthetic viral community to assess several technical challenges important in virome analysis. Our mock community was comprised of phages lambda, T4, M13, MS2, and phi6, together with adeno-associated virus (AAV), murine hepatitis virus (MHV), and vaccinia virus (VV). We spiked the mock community into different human sample types, including stool, saliva, oropharyngeal (OP) wash, and bronchoalveolar lavage (BAL), then passed the samples through different virus enrichment protocols and analyzed by Illumina sequencing. Compared to direct metagenomic sequencing, VLP enrichment protocols greatly increased viral read yields from virus-rich samples such as from stool and saliva. Three VLP enrichment work flows were compared, and each was found to have strengths and weaknesses. Four methods for DNA amplification were compared, with three showing over-amplification of small circular ssDNA viruses, most notably GenomiPhi. Studies of viral particle stability in the presence of nuclease showed that most viral genomes were stable when protected in viral particles, but phage MS2 RNA was unexpectedly labile under some of the conditions tested. Comparison of Illumina 1000-cycle sequencing versus 300-cycle sequencing showed that longer reads supported generation of longer viral genome assemblies. Bacteriophage DNA can be modified by at least 12 different chemistries, raising the question of whether these modifications might block recovery in virome analytical protocols. We tested bacteriophage T4 DNA modified with glucosyl-hydroxymethylcytosine (ghmC) and hydroxymethylcytosine (hmC), and found that both were readily detected, though the recovery of ghmC-modified DNA was reduced. These studies together with published data help provide guidance for virome researchers optimizing analytical protocols.}, }
@article {pmid41278757, year = {2025}, author = {Luo, RS and Kille, B and Vaughan, EE and Clark, JR and Maresso, AW and Nute, MG and Treangen, TJ}, title = {Strainify: Strain-Level Microbiome Profiling for Low-Coverage Short-Read Metagenomic Datasets.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.10.10.681738}, pmid = {41278757}, issn = {2692-8205}, abstract = {MOTIVATION: Strain-level microbiome profiling has revealed key insights into microbial community composition and strain dynamics. However, accurate strain-level analysis remains challenging due to limited linkage information, ambiguous read mapping, and complicating factors such as genome similarity, sequencing depth, and community complexity. These challenges are especially pronounced for short-read metagenomic data when estimating the relative abundances of multiple strains, a task critical for genotype-phenotype association studies.<br><br>RESULTS: To address this gap, we present Strainify, which enables accurate strain-level abundance estimation from short-read metagenomes with as little as 1% genome coverage. Specifically, Strainify combines (1) identification of informative variants via core genome alignment, (2) filtering of confounding variants via a window-based test, and (3) maximum likelihood estimation of strain abundances. A Shannon entropy-weighted version of the model further improves robustness in noisy, low-coverage settings by downweighting sites with low information content. Across simulated communities of varying complexity, Strainify consistently outperformed existing approaches. On mock community sequencing data, Strainify's estimates aligned more closely with reference abundances. When applied to a longitudinal gut microbiome dataset, Strainify successfully recapitulated the reported temporal dynamics of Bacteroides ovatus strain groups, demonstrating its ability to recover biologically meaningful patterns from real-world metagenomes. Together, these results establish Strainify as a robust and versatile solution for accurate strain-level abundance estimation in short-read, low-coverage microbiome studies.<br><br>AVAILABILITY: The Strainify code and results are available at: https://github.com/treangenlab/Strainify.}, }
@article {pmid41278729, year = {2025}, author = {Lu, R and Lee, N and Drake, AK and Fulton, RP and Abutaleb, NS and Seleem, M and Oakland, DN and Garin-Laflam, MP and Pop, M and Luo, XM}, title = {Discovery of Novel Probiotic Species to Improve Infant Health.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.10.27.684727}, pmid = {41278729}, issn = {2692-8205}, abstract = {UNLABELLED: Selecting an appropriate infant formula can be challenging for parents given the wide range of available options, which may lead to suboptimal choices or frequent switching. Our recent studies in mice demonstrated that the maternal microbiota-particularly Limosilactobacillus reuteri present in breast milk-plays a critical role in shaping neonatal immunity by promoting the production of immunoglobulin A (IgA), a key antibody for defense against enteric pathogens. To extend these findings to humans, we analyzed fecal samples from healthy breastfed infants using shotgun metagenomic sequencing combined with whole-bacterial-cell ELISA to assess associations between specific taxa and pathogen-reactive IgA. We found that members of the Oscillibacter species (including Oscillibacter sp. KLE1728, KLE1745, PC13, PEA192, and O. valericigenes) and Morganella (e.g., M. morganii, Morganella sp. EGD-HP17, and Morganella sp. HMSC11D09) were strongly correlated with IgA responses against Salmonella and Shigella . In contrast, IgA reactive to enterohemorrhagic Escherichia coli (EHEC) was associated with other genera, including Staphylococcus . Notably, Lactobacillus species (L. bombi, L. kefiri, L. equi , and L. rhamnosus) were consistently linked to elevated IgA responses against Salmonella, Shigella , and EHEC. Moreover, levels of anti- Salmonella and anti- Shigella IgA were positively correlated with the use of infant formula containing prebiotic fibers or human milk oligosaccharides (5-HMO). Collectively, these findings highlight novel commensal taxa with potential as probiotic candidates to guide the development of next-generation infant formulas aimed at enhancing mucosal immunity and supporting infant health.<br><br>IMPORTANCE: Early-life nutrition shapes immune maturation, yet the microbial factors driving mucosal antibody responses remain poorly defined. Through integrated metagenomic and IgA profiling, this study identifies commensal taxa, particularly Lactobacillus, Oscillibacter , and Morganella , associated with pathogen-specific IgA in infants. These taxa may enhance mucosal defense against enteric pathogens, revealing key microbial contributors to early immune development. The findings provide a foundation for designing next-generation infant formulas that leverage targeted probiotics or prebiotics to promote protective IgA responses and gut health.}, }
@article {pmid41278541, year = {2025}, author = {Khannous-Lleiffe, O and Fuentes-Palacios, D and Májer, D and Gabaldón, T}, title = {MeTAline: enabling reproducible and scalable metagenomic analyses.}, journal = {NAR genomics and bioinformatics}, volume = {7}, number = {4}, pages = {lqaf158}, pmid = {41278541}, issn = {2631-9268}, mesh = {*Metagenomics/methods ; *Software ; Metagenome ; Microbiota/genetics ; Reproducibility of Results ; Computational Biology/methods ; }, abstract = {The taxonomic and functional characterization of microbial communities inhabiting a given niche can elucidate associations between the microbiota and relevant variables, including health and disease. As compared to metabarcoding, shotgun metagenomic sequencing, which analyzes all DNA present in a sample, offers superior taxonomic resolution and additionally enables the inference of functional capabilities encoded within the microbial community of interest. However, this approach requires the use of diverse computational tools and substantial computational resources. Here, we present MeTAline, a bioinformatics pipeline for the analysis of shotgun metagenomics data. Implemented in Snakemake, MeTAline provides an efficient and reproducible workflow encompassing read trimming and filtering, host read removal, taxonomic classification via both k-mer and gene marker-based methodologies, and extensive functional annotation. Containerization in Docker and Singularity ensures ease of installation, portability, and reproducibility. Finally, the pipeline's architecture supports high parallelization, rendering it suitable for both local and high-performance computing environments. MeTAline is freely available at https://github.com/Gabaldonlab/meTAline under an open-source GNU GPL v3.0 license.}, }
@article {pmid41278535, year = {2025}, author = {Berg, M and Reiter, T and Emerson, J and Brown, CT and Roux, S}, title = {Comparison of short-read and long-read metagenome assemblies in a natural soil community highlights systematic bias in recovery of high-diversity populations.}, journal = {NAR genomics and bioinformatics}, volume = {7}, number = {4}, pages = {lqaf163}, pmid = {41278535}, issn = {2631-9268}, mesh = {*Soil Microbiology ; *Metagenome ; *Metagenomics/methods ; Sequence Analysis, DNA/methods ; Genetic Variation ; High-Throughput Nucleotide Sequencing ; }, abstract = {Comparisons of long-read and short-read (meta)genome assemblies typically show that short-read sequence assemblies are less error-prone, but struggle to assemble complicated genome regions (e.g. repeats) compared to long-read sequence assemblies. Accurate metagenome assembly is especially challenging in diverse environments, such as soil, and long-read sequencing has been shown to improve assembly. Here, we use metagenomic data with paired long-read and short-read sequences to identify specific factors that impact genome assembly and assess their relative importance in a natural soil community. Our analysis suggests that low coverage and high sequence diversity are the two main factors leading to misassemblies in short-read data, and many of these "missed" regions tend to be variable parts of the genome, such as integrated viruses or defense system islands. Taken together, our results demonstrate that short-read metagenomes can possibly underestimate the diversity of these genome regions and that long-read sequencing can complement short-read metagenomes by improving assembly contiguity and the recovery of variable regions.}, }
@article {pmid41278475, year = {2025}, author = {An, W and Zhang, Y and Liu, Y and Yang, T and Bai, S and Zhou, P and Si, J and Zhao, Y and He, Y and Pan, Y and Jiang, Y}, title = {Impact of metagenomic sequencing on clinical outcomes in patients with suspected central nervous system infections: a retrospective case-control study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1677092}, pmid = {41278475}, issn = {2235-2988}, mesh = {Humans ; Retrospective Studies ; Male ; *Central Nervous System Infections/diagnosis/microbiology/cerebrospinal fluid/mortality ; Female ; Middle Aged ; *Metagenomics/methods ; Case-Control Studies ; Aged ; Adult ; Treatment Outcome ; Hospital Mortality ; }, abstract = {OBJECTIVES: Although the value of metagenomic sequencing (mNGS) in diagnosing pathogens in central nervous system infections (CNSi) has been confirmed, its impact on the clinical outcomes of patients remains to be elucidated. This study intended to investigate the clinical impact of cerebrospinal fluid (CSF) mNGS on the outcomes of patients with suspected CNSi.<br><br>METHODS: Between January 2022 and July 2024, patients who met both the inclusion and exclusion criteria were enrolled in the study and assigned to either the mNGS group (CSF tested by both mNGS and conventional microbiological tests [CMTs]) or the CMT group (CMTs alone). Following this, propensity score matching (PSM) was applied to balance baseline differences. The primary endpoint, time to clinical improvement, was then compared between the two groups and analyzed in stratified subgroups. Secondary endpoints included the rates of clinical improvement at 14 and 30 days, hospital stay, in-hospital mortality, and the proportion of GCS score <15.<br><br>RESULTS: A retrospective analysis of 338 patients was conducted, with 169 cases in each group. In the mNGS group, a comparison of diagnostic performance between the two testing methods demonstrated that mNGS yielded a significantly higher positivity rate in patients with CNSi compared to CMTs (67.5% vs. 18.3%, p < 0.001), identifying 111 pathogens in total, which was substantially more than the 24 detected by CMTs. Subsequent comparison of clinical outcomes between the groups showed that the duration until clinical improvement was significantly reduced in the mNGS group when compared to the CMT group (median: 14 days vs. 17 days; p=0.032). Moreover, a significantly higher percentage of patients in the mNGS group experienced clinical improvement within 14 days compared to those in the CMT group(42.6% vs. 31.4%; p=0.032). Subgroup analysis further revealed that the mNGS group's superiority in clinical improvement over the CMT group was only evident in patients with CNSi, especially when complicated by pneumonia.<br><br>CONCLUSION: The combination of mNGS with CMT significantly improves the clinical outcome of CNSi patients, offering greater clinical utility than traditional methods alone.}, }
@article {pmid41278474, year = {2025}, author = {Huang, R and Zhang, Y and Dong, C and Chen, J and Zou, H and Liu, Y and Guo, M and Gao, H and Ke, Q and Wu, W}, title = {Clinical application of metagenomic next-generation sequencing in the diagnosis of severe pneumonia pathogens.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1661213}, pmid = {41278474}, issn = {2235-2988}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; Male ; Retrospective Studies ; Female ; *Metagenomics/methods ; Middle Aged ; Aged ; Bronchoalveolar Lavage Fluid/microbiology/virology ; Sensitivity and Specificity ; *Pneumonia/diagnosis/microbiology ; *Bacteria/genetics/isolation &amp; purification/classification ; Intensive Care Units ; Adult ; Fungi/genetics/isolation &amp; purification/classification ; *Pneumonia, Bacterial/diagnosis/microbiology ; Aged, 80 and over ; }, abstract = {BACKGROUND: Severe pneumonia is a significant cause of mortality among ICU patients. Metagenomic next-generation sequencing (mNGS) is an advanced, comprehensive, unbiased diagnostic tool for pathogen identification in infectious diseases. This study aimed to evaluate the clinical efficacy of mNGS for diagnosing severe pneumonia.<br><br>METHODS: This study retrospectively analyzed 323 patients with suspected severe pneumonia admitted to the intensive care unit (ICU) of Wuhan University Renmin Hospital between January 2022 and December 2023. Bronchoalveolar lavage fluid (BALF) samples were collected from all 323 patients, and blood samples were obtained from 80 patients. Both mNGS and conventional microbial testing (CMT) were performed on the collected BALF and blood samples to analyze the pathogen spectrum. The diagnostic performance of mNGS and CMT was systematically evaluated and compared.<br><br>RESULTS: The overall positivity rate of mNGS was significantly greater than that of CMT (93.5% vs. 55.7%, p < 0.001). mNGS demonstrated significantly greater sensitivity than did CMT (94.74% vs. 57.24%, p < 0.001) but lower specificity (26.32% vs. 68.42%, p < 0.01). mNGS identified 36 bacterial species, 14 fungal species, 7 viral species, and 1 Chlamydia species, whereas CMT detected 21 bacterial species and 9 fungal species. According to the pathogen spectrum, Klebsiella pneumoniae, Acinetobacter baumannii, and Candida albicans were the predominant pathogens associated with severe pneumonia. The detection rate of mixed infections was significantly higher with mNGS than with CMT (62.8% vs. 18.3%, p < 0.001).<br><br>CONCLUSIONS: Compared with CMT methods, mNGS has significant advantages in pathogen detection for severe pneumonia. Owing to its broad detection range and high sensitivity, mNGS serves as a valuable complementary approach to traditional culture-based methods.}, }
@article {pmid41278471, year = {2025}, author = {Wang, Y and Guo, P and Chen, Y and Zhu, H and Yu, X and Deng, J}, title = {Comparison and evaluation of metagenomic next-generation sequencing (mNGS) and real-time PCR for the detection of Mycobacterium tuberculosis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1694179}, pmid = {41278471}, issn = {2235-2988}, mesh = {Humans ; *Mycobacterium tuberculosis/genetics/isolation &amp; purification ; *Real-Time Polymerase Chain Reaction/methods ; *High-Throughput Nucleotide Sequencing/methods ; Sensitivity and Specificity ; *Metagenomics/methods ; Male ; Female ; Adult ; *Tuberculosis/diagnosis/microbiology ; Middle Aged ; Sputum/microbiology ; Aged ; *Molecular Diagnostic Techniques/methods ; Bronchoalveolar Lavage Fluid/microbiology ; Young Adult ; Adolescent ; }, abstract = {OBJECTIVE: This study aimed to evaluate and compare the performance of metagenomic next-generation sequencing (mNGS) and real-time polymerase chain reaction (RT-PCR) for the detection of Mycobacterium tuberculosis (MTB) in patients with suspected tuberculosis (TB).<br><br>METHODS: Samples from patients undergoing routine clinical testing for MTB using both mNGS and RT-PCR were included. The diagnostic agreement between the two methods was assessed. Discordant results were further validated using the Xpert MTB/RIF assay on cryopreserved aliquots.<br><br>RESULTS: A total of 556 samples from suspected TB patients were analyzed. The majority were lower respiratory tract specimens, including bronchoalveolar lavage fluid (BALF; 94.06%), sputum (3.24%), and extrapulmonary samples (2.70%). Compared with Xpert MTB/RIF and clinical diagnosis as composite reference standard, both mNGS and RT-PCR showed high sensitivity (92.31% and 90.38%, respectively) and perfect specificity (100%). There was a high level of agreement between mNGS and RT-PCR, with a positive agreement of 82.69%, negative agreement of 98.25%, overall agreement of 98.38%, and a kappa value of 0.896 (P < 0.001). Concordance was higher in samples with lower RT-PCR cycle threshold (Ct) values: 100% at Ct &#x2264; 15, 100% at 15<Ct &#x2264; 20, 76.47% at 20<Ct &#x2264; 25. Among concordant positive samples (n=43), mNGS SMRNs showed a strong negative correlation with RT-PCR Ct values (r = -0.668, P < 0.001). Analysis of nine discordant cases identified five mNGS-positive/RT-PCR-negative samples with low SMRNs (median: 7 vs. 1788 in concordant positives), four of which were confirmed by Xpert MTB/RIF to have extremely low bacterial loads. The remaining four mNGS-negative/RT-PCR-positive samples exhibited higher Ct values (median: 22.97 vs. 17.06 in concordant positives), and three of these were also verified by Xpert MTB/RIF to contain extremely low bacterial concentrations.<br><br>CONCLUSION: Both RT-PCR and mNGS demonstrate high overall agreement for MTB detection, with concordance strongly influenced by microbial burden. These findings support the complementary use of these methods in the diagnosis of TB.}, }
@article {pmid41278154, year = {2025}, author = {Zheng, L and Duan, SL and Wang, K}, title = {Research progress concerning the involvement of the intestinal microbiota in the occurrence and development of inflammatory bowel disease.}, journal = {World journal of gastroenterology}, volume = {31}, number = {42}, pages = {113170}, pmid = {41278154}, issn = {2219-2840}, mesh = {Humans ; *Gastrointestinal Microbiome/immunology/genetics ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; Intestinal Mucosa/microbiology/immunology/pathology ; *Crohn Disease/microbiology/therapy/immunology ; *Colitis, Ulcerative/microbiology/therapy/immunology ; Genetic Predisposition to Disease ; Dysbiosis/microbiology/immunology/therapy ; *Inflammatory Bowel Diseases/microbiology/therapy ; Metagenomics ; Animals ; Metabolomics ; Immunity, Mucosal ; }, abstract = {Inflammatory bowel disease (IBD), a chronic disorder characterized by intestinal inflammation and mucosal damage, includes mainly Crohn's disease and ulcerative colitis. However, the cause of its onset remains unclear. The pathogenesis of IBD is closely related to host genetic susceptibility, disorders of the intestinal flora, damage to the intestinal mucosal barrier, and abnormal intestinal mucosal immunity. On the basis of the progress in research on the structure of the intestinal microbiota involved in IBD, the influence of genetics on the intestinal barrier and intestinal microbiota; the metagenomics, metatranscriptomics, and metabolomics of the intestinal microbiota involved in IBD; and treatments such as probiotics and fecal microbiota transplantation are important for the future treatment of IBD and the development of drugs for effective treatment.}, }
@article {pmid41278038, year = {2025}, author = {Li, B and Liao, Y and Li, J}, title = {Legionella-induced suppurative cervical lymphadenitis in a child diagnosed by metagenomic next-generation sequencing: a case report.}, journal = {Frontiers in pediatrics}, volume = {13}, number = {}, pages = {1655298}, pmid = {41278038}, issn = {2296-2360}, abstract = {Legionella pneumophila, primarily associated with respiratory infections, rarely causes extrapulmonary disease. Conventional diagnostic methods for Legionella are often limited. Here we report a case of suppurative cervical lymphadenitis caused by L. pneumophila. And we highlight the critical role of mNGS in enabling rapid and accurate pathogen identification, guiding effective targeted therapy for rare and challenging infections.}, }
@article {pmid41278006, year = {2025}, author = {Minch, B and Moniruzzaman, M}, title = {BEREN: a bioinformatic tool for recovering giant viruses, polinton-like viruses, and virophages in metagenomic data.}, journal = {Bioinformatics advances}, volume = {5}, number = {1}, pages = {vbaf284}, pmid = {41278006}, issn = {2635-0041}, abstract = {MOTIVATION: Viruses in the kingdom Bamfordvirae, specifically giant viruses (NCLDVs) in the phylum Nucleocytoviricota and smaller members in the Preplasmiviricota phylum, are widespread and important groups of viruses that infect eukaryotes. While viruses in this kingdom, such as giant viruses, polinton-like viruses, and virophages, have gained large interest from researchers in recent years, there is still a lack of streamlined tools for the recovery of their genomes from metagenomic datasets.<br><br>RESULTS: Here, we present, BEREN, a comprehensive bioinformatic tool to unlock the diversity of these viruses in metagenomes through five modules for NCLDV genome, contig, and marker gene recovery, metabolic protein annotation, and Preplasmiviricota genome identification and annotation. BEREN's performance was benchmarked against other mainstream virus recovery tools using a mock metagenome, demonstrating superior recovery rates of NCLDV contigs and Preplasmiviricota genomes. Overall, BEREN offers a user-friendly, transparent bioinformatic solution for studying the ecological and functional roles of these eukaryotic viruses, facilitating broader access to their metagenomic analysis.<br><br>BEREN is available at https://gitlab.com/benminch1/BEREN, and results from testing BEREN on a real-world metagenome are available in the Supplementary Files.}, }
@article {pmid41277975, year = {2025}, author = {Wang, B and Li, W and Xue, N and Xi, R and Wang, Y and Fang, L and Wang, Q and Liang, X and Xiao, Y and Yang, X and Wu, X}, title = {Co-application of biochar and compost enhanced soil carbon sequestration in urban green space.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1707894}, pmid = {41277975}, issn = {1664-302X}, abstract = {The mechanism of biochar and compost as soil amendments in urban green spaces remains unclear. Using Euonymus kiautschovicus as a model system, this study established eight treatment gradients, 0 (CK), single biochar applications: 4% (BC4), 8% (BC8), 12% (BC12), 7.5% compost (COM), and their combinations BCC4 (BC4 + 7.5% COM), BCC8 (BC8 + 7.5% COM), BCC12 (BC12 + 7.5% COM). Through metagenomic sequencing and metagenome-assembled genomes (MAGs) analysis, we investigated soil microbiome structure, carbon sequestration functional genes, and their interactions in response to amendments. The combined application of medium-low dose biochar (4-8%) with compost significantly optimized the physicochemical properties and microbial functions in soils. Compared to single amendments, hybrid treatments synergistically enhanced soil moisture content. Specifically, BCC8 increased by 27% compared to the CK, organic carbon levels reached 12.8 g/kg with BCC12, and available nutrients showed 45% higher available phosphorus with BCC4. Metagenomic analysis revealed that hybrid treatments reshaped microbial community structure, with BCC8 significantly enriching Acidobacteria (8.72%) and Nitrospira (1.42%), driving an increased abundance of carbon fixation genes. Among key carbon fixation pathways, the reductive tricarboxylic acid cycle (rTCA) exhibited the highest gene abundance (mean 15.03), dominated by MAG176. The Calvin-Benson-Bassham (CBB) cycle displayed broad adaptability, with MAG59 identified as a core carbon-fixing strain. This study has significant implications for the application of biochar-compost combinations in carbon management of urban green spaces.}, }
@article {pmid41277970, year = {2025}, author = {Chapagain, C and Khezri, A and Ali, J and Smistad, M and Sølverød, LS and Ahmad, R}, title = {Optimizing sample preparation for culture-free nanopore sequencing to enable rapid pathogen and antimicrobial resistance profiling in bovine mastitis.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1680165}, pmid = {41277970}, issn = {1664-302X}, abstract = {Long-read metagenomic sequencing allows for the rapid, culture-independent, and accurate identification of causative pathogens and antimicrobial resistance (AMR) profiles, supporting precise antibiotic use and reducing the spread of resistance. However, its application to mastitis milk is challenging due to the complex milk matrix, low bacterial count, and high somatic cell content. This study primarily aimed to further optimize our previously developed culture-free nanopore sequencing protocol for milk samples from mastitis cases. Additional optimizations included combining centrifugation, gradient centrifugation, and fat fraction treatment with Tween 20 and citric acid. Subsequently, four DNA extraction kits (Blood and Tissue, Molysis Complete5, HostZero, and SPINeasy Host depletion) were evaluated for their ability to remove host DNA and enrich bacterial DNA for long-read sequencing with Oxford Nanopore technologies. qPCR was used to quantify bacterial and bovine DNA, allowing comparison of host depletion efficiency among the kits. Our results show that simple centrifugation effectively concentrates bacterial cells, removing the need for chemical treatments. The HostZero kit consistently produced higher DNA yields, improved DNA integrity, and more effective host DNA depletion. Using nanopore sequencing, both Gram-positive and Gram-negative mastitis pathogens, along with their AMR genes, were successfully detected. Overall, this study underscores the importance of an effective DNA extraction method for the direct sequencing of mastitis milk samples. Additionally, our findings support the potential of direct metagenomic sequencing as a rapid, culture-free approach for identifying mastitis pathogens and their resistance profiles.}, }
@article {pmid41277885, year = {2025}, author = {Solís, VE and Bangratz, M and Brugo Carivali, MF and Comte, A and Luciani, CE and Lacombe, S and Fontana, ML and Filloux, D and Pachecoy, MI and Fernandez, E and Dirchwolf, PM and Ayala, JOA and Julian, C and Kruger, RD and Hébrard, E and Fernandez, FD and Perotto, MC and Roumagnac, P and Gutiérrez, SA and Poulicard, N and Celli, MG}, title = {Near-complete genome sequences of a rice necrosis mosaic virus isolate infecting rice in Argentina.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0059825}, doi = {10.1128/mra.00598-25}, pmid = {41277885}, issn = {2576-098X}, abstract = {While rice necrosis mosaic virus (RNMV) has only been described in Asia, we identified this virus on a rice plant from Argentina using a viral metagenomic approach. We further confirmed this result by RT-PCR and small-RNA Illumina sequencing to obtain the near-complete genome and to confirm actual infection by RNMV.}, }
@article {pmid41277537, year = {2025}, author = {Liu, C and Wang, X and Zhang, Z and Wang, W and Wang, T and Zhao, Y and Wang, M and Chen, WH}, title = {GMrepo v3: a curated human gut microbiome database with expanded disease coverage and enhanced cross-dataset biomarker analysis.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkaf1190}, pmid = {41277537}, issn = {1362-4962}, support = {2024YFA0918500//National Key Research and Development Program of China/ ; 5001170159//Hubei Province/ ; 202505AF350080//Yunnan Expert Workstation/ ; }, abstract = {GMrepo (Gut Microbiome Data Repository) is a curated and consistently annotated database of human gut metagenomes, designed to improve data reusability and enable cross-project and cross-disease comparisons. In this latest release, GMrepo v3 has been expanded to 890 projects and 118 965 runs/samples, including 87 048 16S rRNA and 31 917 metagenomic datasets. The number of annotated diseases has increased from 133 to 302, allowing more comprehensive disease-related microbiome analyses. We systematically identified microbial markers between phenotype pairs (e.g. healthy versus diseased) at the project level and compared them across datasets to detect reproducible signatures. As of this release, GMrepo v3 includes 1299 marker taxa (726 species and 573 genera) associated with 167 phenotype pairs, derived from 275 carefully curated projects. To assess marker stability, we developed the Marker Consistency Index (MCI), which summarizes the prevalence and directional consistency of markers across studies. Among 400 markers showing altered abundances in ≥10 projects, 143 were consistently enriched in healthy controls (MCI > 75%), while 85 were enriched in diseases (MCI < 25%). A marker-centric interface enables users to explore marker behavior across diseases. The GMrepo v3 database is freely accessible at https://gmrepo.humangut.info.}, }
@article {pmid41276871, year = {2025}, author = {Torres-Beltrán, M and Hernández-Guzman, M and Barcelos, C and Chong-Robles, J and Sidón-Ceseña, K and García-Maldonado, JQ and Aguirre-Macedo, ML and Lago-Lestón, A}, title = {Alternative carbon and energy metabolisms linked to hydrocarbon degradation are widely distributed across the different microbial communities from deep-sea sediments of the Gulf of Mexico.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-025-00823-1}, pmid = {41276871}, issn = {2524-6372}, support = {201441/WT_/Wellcome Trust/United Kingdom ; Postdoctoral fellowship//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; Master fellowship//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; Doctoral fellowship//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; }, abstract = {In marine sediments, microorganisms' roles in recycling organic and inorganic molecules, including hydrocarbons, are critical for ecosystem function. Genomic studies in the Gulf of Mexico (GoM) reveal that microbial community composition and function are shaped by environmental gradients, with hydrocarbon degradation relying on consortia dynamics rather than single species, highlighting their collective ecological importance. Our study evaluated the prokaryotic microbial community in deep-sea GoM sediments, under a depth gradient, in Coatzacoalcos and Perdido regions, two areas influenced by crude-oil efflux and petroleum extraction. Findings indicated depth was the primary driver of microbial community structure, with distinct compositional shifts between shallow (< 1000 m) and deep (> 1200 m) sediments, showcasing microbial adaptation to deep-sea nutrient-limited conditions. Furthermore, functional gene analysis revealed depth-specific metabolic partitioning, with Deltaproteobacteria dominating amino acid and energy metabolism in shallow sediments, while Alphaproteobacteria and Thaumarchaeota prevailed in deeper zones. This underlines the importance of microbial community shifts in composition and structure in ensuring environmental resilience. In addition, relatively low-abundance but critical hydrocarbon degradation genes were detected, primarily in shallow/transition zones, indicating niche-specific potential for bioremediation despite their apparent limited representation. This research contributes to advancing our understanding of alternative carbon and energy metabolisms linked to hydrocarbon degradation that are widely distributed across different microbial communities inhabiting deep-sea marine sediments.}, }
@article {pmid41275986, year = {2025}, author = {Raj, DS and Gao, B and Sohn, MB and Brydges, C and Srivastava, A and Rabb, H and Cheung, AK and Fiehn, O and Kendrick, C and Gassman, JJ and Tariq, A and Isakova, T and Fried, LF and Wolf, M and Raphael, KL and Middleton, JP and Abdalla, Y and , }, title = {Prebiotic Administration to CKD Patients Modifies Their Microbiome and Metabolism.}, journal = {Journal of renal nutrition : the official journal of the Council on Renal Nutrition of the National Kidney Foundation}, volume = {}, number = {}, pages = {}, doi = {10.1053/j.jrn.2025.10.015}, pmid = {41275986}, issn = {1532-8503}, abstract = {BACKGROUND AND HYPOTHESIS: Prebiotics are believed to improve gut microbial dysbiosis and dysmetabolism in chronic kidney disease (CKD) patients. However, impact of prebiotics on gut microbial metagenome and dynamic changes in metabolome has not been clearly defined.<br><br>METHODS: We conducted a non-randomized, open-label, three-phase pilot trial, to investigate the effect of daily oral oligofructose-enriched inulin (p-inulin) on stool functional metagenome and changes in plasma, urine and stool metabolites in 13 CKD patients. The study comprised a pre-treatment phase (8 weeks), p-inulin treatment phase (12 weeks), and post-treatment phase (8 weeks).<br><br>RESULTS: During treatment phase, there was a significant increase in the abundance of Bifidobacterium adolescentis, Bifidobacterium longum, and Lachnospiraceae species. Microbial pathways related to carbohydrate degradation and amino acid biosynthesis were enriched during the treatment phase, but urea biosynthetic pathway was attenuated. In the plasma metabolic biosynthetic pathways for valine, leucine and isoleucine were activated during the treatment phase. Microbial genes related to lipid metabolism were enriched during post-treatment. Abundance of several polar and non-polar lipids were altered in plasma and stool samples during treatment and post-treatment phases. Pathway analysis for lipids indicated suppression of triglyceride biosynthesis in plasma and enhanced triglyceride degradation in stool during the treatment phase. Secondary bile acid levels in plasma, urine and stool were significantly reduced during p-inulin consumption. Urine levels of indoxyl sulfate and p-cresol sulfate were reduced during treatment phase.<br><br>CONCLUSION: P-inulin administration to CKD patients resulted a distinct shift in toxin-generating proteolysis to amino acid biosynthesis and favorable changes in lipid metabolism.}, }
@article {pmid41275762, year = {2025}, author = {Stevenson, EM and Buckling, A and Cole, M and Hayes, A and Lindeque, PK and Murray, AK}, title = {Sewers to Seas: exploring pathogens and antimicrobial resistance on microplastics from hospital wastewater to marine environments.}, journal = {Environment international}, volume = {206}, number = {}, pages = {109944}, doi = {10.1016/j.envint.2025.109944}, pmid = {41275762}, issn = {1873-6750}, abstract = {Microplastic particles are extremely prevalent environmental pollutants which support microbial biofilms known as the 'plastisphere'. Antimicrobial resistant (AMR) and pathogenic bacteria have been detected in these communities, but it is currently unknown whether microplastics pose a unique risk in terms of AMR or pathogen enrichment. In addition, previous work has been largely lab-based, so it is difficult to understand the role of different substrates in supporting AMR pathogens within the environment, and how this varies as a function of levels of pollution from wastewater. This study investigated in situ bacterial colonisation dynamics on microplastics alongside natural, inert and free-living controls. Samples were incubated along a transect predicted to decrease in anthropogenic pollution, and taxonomy, AMR gene and pathogen presence were assessed using whole metagenome sequencing. Several AMR gene (e.g. aminoglycosides, oxazolidinones and tetracyclines) and pathogen classes (e.g. Flavobacteriia, Chlamydiia and Sphingobacteriia) of concern were detected, and increased in relative abundance in biofilms moving downstream, with polystyrene and HDPE nurdle communities posing a particular risk by supporting AMR bacteria. This work contributes to our understanding of how microplastics may support AMR development, persistence and dispersal in natural systems. In addition, these findings highlight the importance of considering the combined impacts of co-contaminants in wastewater settings, especially following spills into surface water.}, }
@article {pmid41275684, year = {2025}, author = {Liu, Q and Chen, J and Xu, R and Huang, C and Ren, N and Gao, S and Li, W and Xin, X and Lv, S and Yang, S and Ben, W and Wang, AJ}, title = {Bacterial, viral and environmental interactions shape antibiotic resistance genes in China's anaerobic-anoxic-oxic wastewater treatment systems.}, journal = {Water research}, volume = {289}, number = {Pt B}, pages = {124911}, doi = {10.1016/j.watres.2025.124911}, pmid = {41275684}, issn = {1879-2448}, abstract = {The dissemination of antibiotic resistance genes (ARGs) threatens global public health. Urban wastewater treatment plants (WWTPs), serving as critical reservoirs and dissemination hubs for ARGs, are driven by complex bacteria-virus interactions and environmental factors in activated sludge. This study employed metagenomics and 16S rRNA gene sequencing of activated sludge from 28 A[2]O WWTPs across China to decipher the national distribution of ARGs and their associations with bacterium-phage systems and environmental factors. Research outcomes: fluoroquinolone resistance genes (adeF) and sulfonamide resistance genes (sul1, sul2) dominated ARG abundance (mean 41.7 %, 11.51 %), with significant regional differentiation (PERMANOVA, R[2] = 0.153, p = 0.043). The involvement of bacteria and viruses was significantly associated with ARG dissemination. Among these, Proteobacteria and Actinobacteria were identified as pivotal putative bacterial vectors. Additionally, Myoviridae was predicted to be the predominant viral host for ARGs, while Siphoviridae and Demerecviridae were preferentially associated with specific ARG types. Correlation analysis indicated that ions, such as cobalt, zinc and cadmium, were positively correlated with specific ARG subtypes, whereas arsenic was consistently negatively correlated with most ARG subtypes. Additionally, the oxidation-reduction potential was significantly linked to ARG abundance. This study reveals complex ARG association patterns from the perspective of bacteria-virus interactions and environmental factors, providing insights and a valuable reference for future phage-based control strategies and regional antibiotic resistance pollution policies.}, }
@article {pmid41275679, year = {2025}, author = {Matu, A and Valverde, A and Cason, E and Gomez-Arias, A and Maleke, M and Castillo, J}, title = {Microbial consortia in mine water bioremediation: principles, design and practical applications.}, journal = {Water research}, volume = {289}, number = {Pt B}, pages = {124956}, doi = {10.1016/j.watres.2025.124956}, pmid = {41275679}, issn = {1879-2448}, abstract = {The impact of mining activities on water sources is a global concern, especially in water-scarce countries such as Southern Africa, Mediterranean region, western Asia, and South America. Bioremediation emerges as a feasible and attractive alternative to address this environmental issue. However, while biological sulfate reduction and the emerging use of using microbially induced carbonate precipitation (MICP) for remediating polluted mine water have gained attention, strategies for designing effective microbial consortia have seen little advancement. The performance of microbial consortia in these treatments can be quite variable. Most improvement strategies have focused mainly on bioreactor design and selecting suitable carbon sources, addressing technical aspects while neglecting the central players in this process: the microbes themselves. Enhancing consortium effectiveness requires revisiting foundational concepts such as monoculture, co-culture, division of labor, and bottom-up versus top-down approaches. While these concepts offer significant theoretical potential to improve consortium performance, they have seldom been applied in practice for mine water bioremediation. In this literature review, we revisit these principles and explore the integration of novel tools such as metagenomics and bioinformatics. These approaches can deepen our understanding of indigenous microbial diversity, uncover dynamic interactions among microbial species, and identify keystone species as potential candidates for bioremediation. By leveraging their genomic potential, it becomes possible to design consortia that are more efficient and better suited to support the recovery of contaminated water sources.}, }
@article {pmid41275070, year = {2025}, author = {Gao, H and Wang, Y and Zhao, Y and Jiao, X and Guo, Z and Zheng, L and Li, Y and Su, Y and Wang, Z and Bai, J and Yao, J and Bushman, FD and Luo, S and Song, X and Liang, G}, title = {Human gut prophage landscape identifies a prophage-mediated fucosylation mechanism alleviating colitis.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-025-66733-5}, pmid = {41275070}, issn = {2041-1723}, support = {32200036//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82341116//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92474105//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32270945//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Functions of the human gut virome are little understood, particularly for the hyperabundant prophages integrated in prokaryotic genomes. Here we identified 254,273 prophage sequences in 47.7% of 289,232 human gut metagenomic genomes, significantly expanding the known taxonomic and functional diversity of prophages in the human gut microbiome. Analysis of 8503 gut metagenomic samples showed the ratios of lysogens (cells harboring prophages) to non-lysogens varied widely associated with age, health condition, and geography, with the latter linked to industrialization. Notably, the alterations of the prophage-encoded genes exhibited disease-specific patterns. For inflammatory bowel diseases, the prophage-encoded futC gene, encoding α-1,2-fucosyltransferase, was less prevalent in affected patients. This enzyme was experimentally validated to direct 2-fucosyllactose (2'-FL) biosynthesis in vitro. Here we show that 2'-FL could diminish colitis in mice induced by treatment with dextran sodium sulfate. Mechanistically, 2'-FL promoted maintenance of mucosal barrier integrity, leading to intestinal IgA secretion and intraepithelial CD4[+]CD8αα[+] T cell development mediated by the gut microbiome. Together, our findings thus link lysogeny to human age, geography, and disease, and demonstrate an immunomodulatory mechanism of prophage-encoded genes in alleviating colitis.}, }
@article {pmid41274992, year = {2025}, author = {Becsei, &#xc1; and Stéger, J and Visontai, D and Munk, P and Aarestrup, FM and Csabai, I and Papp, K}, title = {A case study using sewage metagenomic data for assessment of text-to-SQL capabilities in large language models.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-025-28341-7}, pmid = {41274992}, issn = {2045-2322}, support = {No. 874735 (VEO)//European Union's Horizon 2020 research and innovation programme/ ; U24AI183840//National Institute Of Allergy And Infectious Diseases of the National Institutes of Health/ ; RRF-2.3.1-21-2022-00004//National Research, Development, and Innovation Office of Hungary within the framework of the MILAB Artificial Intelligence National Laboratory/ ; }, abstract = {Relational databases offer an efficient solution for storing and retrieving complex data sets, yet the requirement for SQL programming expertise presents a significant challenge for many life science users. We explore whether a cutting-edge large language model can effectively translate plain English queries into SQL scripts (Text-to-SQL), thereby simplifying database interaction and eliminating the typical usage barriers. A complex database comprising 19 interconnected tables of metagenomic analyses from 239 sewage samples across five European cities was available. A large language model was provided with details of the database's structure and background information on its contents. We evaluated the functionalities of this "SewageGPT" tool and assessed the accuracy of its responses to complex questions and visualisation of results. Providing a detailed description of the database enabled SewageGPT to accurately respond to complex inquiries, accelerating the database querying process. Knowledge of the database content proved beneficial, as it minimized the risk of ambiguities in queries; however, ambiguities can lead to incorrect responses. Therefore, human oversight remains crucial, particularly for questions that lack detail or involve ambiguities. The integration of state-of-the-art large language models with direct database connectivity substantially enhances the efficiency of query generation, statistical analysis and visualization of the results.}, }
@article {pmid41274878, year = {2025}, author = {Ferretti, P and Allert, M and Johnson, KE and Rossi, M and Heisel, T and Gonia, S and Knights, D and Fields, DA and Albert, FW and Demerath, EW and Gale, CA and Blekhman, R}, title = {Assembly of the infant gut microbiome and resistome are linked to bacterial strains in mother's milk.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-025-66497-y}, pmid = {41274878}, issn = {2041-1723}, support = {R01HD109830//U.S. Department of Health &amp; Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; R21HD099473//U.S. Department of Health &amp; Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; F32HD105364//U.S. Department of Health &amp; Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; R01HD080444//U.S. Department of Health &amp; Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; }, abstract = {The establishment of the gut microbiome in early life is critical for healthy infant development. Although human milk is recommended as sole nutrition for the infant, little is known about how variation in the milk microbiome shapes the microbial communities in the infant gut. Here, we quantified the similarity between the maternal milk and the infant gut microbiomes using 507 metagenomic samples collected from 195 mother-infant pairs at one, three, and six months postpartum. Microbial taxonomic overlap between milk and the infant gut was driven by Bifidobacterium longum, and infant microbiomes dominated by B. longum showed greater temporal stability than those dominated by other species. We identified numerous instances of strain sharing between milk and the infant gut, involving both commensal (e.g. B. longum) and pathobiont species (e.g. K. pneumoniae). Shared strains also included typically oral species such as S. salivarius and V. parvula, suggesting possible transmission from the infant's oral cavity to the mother's milk. At one month, the infant gut microbiome was enriched in biosynthetic pathways, suggesting that early colonisers might be more metabolically independent than those present at six months. Lastly, we observed significant overlap in antimicrobial resistance gene carriage within mother-infant pairs. Together, our results suggest that the human milk microbiome has an important role in the assembly, composition, and stability of the infant gut microbiome.}, }
@article {pmid41274873, year = {2025}, author = {Peng, H and Andreu-Sanchez, S and Ruiz-Moreno, AJ and Fernández-Pato, A and Wu, J and Gacesa, R and Zhernakova, A and Wang, D and Fu, J}, title = {Longitudinal gut microbiota tracking reveals the dynamics of horizontal gene transfer.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-025-66612-z}, pmid = {41274873}, issn = {2041-1723}, abstract = {Horizontal gene transfer (HGT) is a major driver of bacterial evolution, but its role in shaping the human gut microbiome over time remains poorly understood. Here, we present a longitudinal metagenomic analysis of 676 fecal samples from 338 individuals in the Lifelines-DEEP study collected ~4 years apart, using a newly developed workflow to detect recent HGT events from metagenome-assembled genomes. We identified 5,644 high-confidence HGT events occurring within the past ~10,000 years across 116 gut bacterial species. We find that species pairs with an HGT relationship were significantly more likely to maintain stable co-abundance relationships over the 4-year period, suggesting that gene exchange contributes to community stability. Notably, HGT and strain replacement act together to disseminate mobile genes in the population. Furthermore, our observation that an individual's mobile gene pool remains highly personalized and stable over time indicates that host lifestyles drive specific gene transfer. For example, proton pump inhibitor usage is linked to increased transfer of multidrug transporter genes. Our findings demonstrate, at the individual gut microbiome level, that HGT is both an integral and stabilizing force in the human gut ecosystem and an important mechanism for disseminating adaptive functions, underscoring HGT potential for tracking host lifestyle.}, }
@article {pmid41274479, year = {2025}, author = {Xu, X and Hong, X and Zeng, W and Yan, R and Li, F and Meng, C and Shi, X and Luo, J and Wang, G}, title = {Stereoselective synthesis of (S)-3-Hydroxy-3-phenylpropionate with a novel carbonyl reductase identified from a soda lake metagenome.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {149193}, doi = {10.1016/j.ijbiomac.2025.149193}, pmid = {41274479}, issn = {1879-0003}, abstract = {This study aimed to discover novel carbonyl reductases from a soda lake metagenome for the efficient synthesis of the chiral drug intermediate (S)-ethyl 3-hydroxy-3-phenylpropionate ((S)-EHPP). A carbonyl reductase (denoted as SLCR1) was identified and found to share less than 30 % sequence identity with known functionally characterized NAD(P)-dependent oxidoreductases, suggesting its novelty. The recombinant enzyme demonstrated optimal activity at 50 °C and pH 7.0, along with excellent stability at 45 °C and within a pH range of 6.0-7.5. Semi-rational design was applied to enhance the catalytic efficiency of SLCR1 toward ethyl benzoylacetate (EBA). After three rounds of mutagenesis and screening, a triple mutant (I212F/I176L/R216L) was obtained, which exhibited a ~ 29-fold improvement in catalytic efficiency compared to the wild-type. Molecular docking indicated that the triple mutant achieves superior catalytic efficiency and binding affinity at the expense of reduced structural stability. In whole-cell biocatalysis co-expressing the mutant enzyme and Bacillus subtilis glucose dehydrogenase (GDH), 150 mM EBA was fully consumed within 1 h, affording (S)-EHPP with 95 % conversion yield and > 99 % enantiomeric excess (e.e.). To the best of our knowledge, this biocatalytic system sets a new benchmark by enabling unprecedented single-batch substrate loading (150 mM) coupled with a remarkably short completion time of 1 h. This study demonstrates an efficient one-step synthesis of (S)-EHPP through the discovery of a novel carbonyl reductase, engineered enhancement, and optimized biocatalysis, providing a promising basis for the industrial production of chiral intermediates.}, }
@article {pmid41274194, year = {2025}, author = {Jin, L and Xinting, L and Shuaiyang, Z and Qiaoyun, R and Obaid, MK and Peiwen, D and Guiquan, G and Guangyuan, L and Hong, Y}, title = {Comparative metagenomic profiling of microbial pathogen diversity in Haemaphysalis longicornis and Hyalomma dromedarii ticks.}, journal = {Veterinary parasitology}, volume = {341}, number = {}, pages = {110656}, doi = {10.1016/j.vetpar.2025.110656}, pmid = {41274194}, issn = {1873-2550}, abstract = {Ticks are globally important vectors of human and animal pathogens. This study characterized microbial communities in Haemaphysalis longicornis (from humid Zhangjiachuan County) and Hyalomma dromedarii (from arid Minqin County, Gansu Province, China) using metagenomic sequencing. We identified diverse bacteria and viruses including known pathogens (Anaplasma phagocytophilum, Totivirus spp., Escherichia spp.) and potentially novel agents (Totivirus-like and Trachysalambria curvirostris-associated sequences). These results highlight the role of these tick species in pathogen transmission across different environments and emphasize the need for region-specific surveillance. Our findings contribute to the understanding of tick-borne disease risks and inform strategies for targeted control.}, }
@article {pmid41273975, year = {2025}, author = {Yuan, C and Zhao, X and Qing, C and Li, P}, title = {Phylogenetic diversity and divergent arsenite oxidation of photoarsenotrophs in geothermal springs.}, journal = {Journal of hazardous materials}, volume = {500}, number = {}, pages = {140531}, doi = {10.1016/j.jhazmat.2025.140531}, pmid = {41273975}, issn = {1873-3336}, abstract = {A unique metabolic process coupling anoxygenic photosynthesis with arsenite oxidation plays a critical role in arsenic (As) biogeochemical cycling within terrestrial thermal springs. While previous studies have identified restricted ranges of photoarsenotrophic bacteria, their phylogenetic diversity and physiological characteristics remain poorly understood. In this study, we obtain 12 putative metagenome-assembled genomes (MAGs) of photoarsenotrophs from global geothermal springs using metagenomics. These MAGs belong to five thermophilic taxa: Chloroflexales, Burkholderiales, Rhizobiales, Steroidobacterales, Rhodobacterales, significantly expanding the photoarsenotrophic bacteria diversity beyond the previously recognized Gammaproteobacteria. We identified the first Betaproteobacteria lineage supported by integrated physiological characterization, phylogenomics and genomic analysis, which belonging to Calidifontimicrobium sediminis of the order Burkholderiales. Comparative genomic analysis revealed their divergent arsenite oxidase systems: strains G02091 and YIM 73032 employ the arx gene cluster (ARX system), whereas strain SYSU G00088 have evolved the aio gene cluster (AIO system). Our finding extends the known phylogenetic range of photoarsenotrophy, and reveals metabolic versatility of among these bacteria, offering insights into their ecological roles in As cycling, as well as a potential biological resource for its remediation in environments.}, }
@article {pmid41273973, year = {2025}, author = {Peng, L and Yang, F and Zhang, J and Shang, J and Xu, W and Sheng, S and Li, Q and Zou, Y and Yue, Z}, title = {Ecological drivers and functional roles of phage communities in the Yangtze River's freshwater ecosystems.}, journal = {Journal of hazardous materials}, volume = {500}, number = {}, pages = {140564}, doi = {10.1016/j.jhazmat.2025.140564}, pmid = {41273973}, issn = {1873-3336}, abstract = {The Yangtze River, China's largest and most significant freshwater system, is facing increasing pollution pressures due to rapid urbanization. While bacterial-mediated antibiotic resistance has been extensively studied, the functional roles and ecological risks of phage communities remain poorly understood. Here, we conducted a comprehensive virome analysis across four habitats (free-living setting, particle-associated setting, sediment, and bank soil) using 204 samples from the Yangtze River. We identified 18,865 viral operational taxonomic units (vOTUs) and observed significant correlations between viral communities and metagenome-assembled genomes (MAGs) across all habitats. Notably, the virus-to-host ratio (VHR) decreased significantly with increased elevation. Functional annotation revealed 1367 viruses contigs carrying genes associated with six functional categories, each showing distinct habitat-specific patterns. Carbohydrate-degrading enzymes (CAZy) were abundant in free-living setting water. Among phage-borne ARGs, vancomycin resistance was predominated, especially in sediment and bulk soil, while mercury resistance were most prevalent in sediments. Chitinase genes constituted the most abundant group among phage-encoded genes for plastic degradation. We identified 84 high-confidence virus-host pairs, predominantly infecting Proteobacteria. Random forest modeling identified elevation as the dominant driver of viral community abundance across habitats. Higher elevations were correlated with increased pH and reduced NH4[+]-N concentrations, suggesting nutrient limitation may weaken virus-host interactions. This study provides the first systematic assessment of viral diversity and functional potential in the Yangtze River, offering novel insights into phage ecology in freshwater.}, }
@article {pmid41273932, year = {2025}, author = {Tang, J and Kang, Z and Cui, S and Xu, H and Ren, H and Li, P and Han, J and Zou, Y}, title = {Exploration of molecular diagnosis for HHV-6 encephalitis in immunocompetent individuals: A study combining mNGS and PCR.}, journal = {Diagnostic microbiology and infectious disease}, volume = {114}, number = {3}, pages = {117196}, doi = {10.1016/j.diagmicrobio.2025.117196}, pmid = {41273932}, issn = {1879-0070}, abstract = {PURPOSE: To evaluate clinical features, diagnosis, treatment, and prognosis of HHV-6 encephalitis in immunocompetent adults, a rare and challenging condition.<br><br>METHODS: In this retrospective, single-centre study, we enrolled six immunocompetent adults (mean age 60.67 &#xb1; 15.57 years) diagnosed with HHV-6 encephalitis at Hengshui People's Hospital between January 2022 and December 2024. Clinical data, laboratory variables, cerebrospinal fluid (CSF) parameters, brain magnetic resonance imaging (MRI) findings, and electroencephalography (EEG) recordings were systematically collected. CSF samples underwent metagenomic next-generation sequencing (mNGS) for unbiased pathogen detection. All HHV-6-positive findings were subsequently confirmed by quantitative real-time polymerase chain reaction (PCR).<br><br>RESULTS: HHV-6 encephalitis presented with fever, unconsciousness, convulsions, headache, and cognitive dysfunction. CSF analysis showed mild intracranial pressure elevation(median 186.67 mmH2O, IQR 157.50-217.50mmH2O), lymphocytic pleocytosis(58.6 &#xb1; 31.70 %), and normal or mildly elevated protein(0.234&#xb1;0.99 g/L) and glucose(median 4.03 mmol/L, IQR 3.42-4.50 mmol/L) levels. MRI revealed high-FLAIR signals in the right temporal lobe in three patients and chronic foci in the frontal lobe and basal ganglia in three others. EEG abnormalities were noted in two patients. mNGS revealed an average of 578&#xb1;512.09 unique HHV-6 reads, with HHV-6A identified in five patients and HHV-6B in one. All findings were confirmed by quantitative PCR. Prompt ganciclovir therapy led to complete recovery without sequelae in all six cases.<br><br>CONCLUSIONS: mNGS enables rapid detection of the rare but treatable HHV-6 meningitis in immunocompetent adults that conventional tests miss, prompting early antiviral therapy and better outcomes.}, }
@article {pmid41273911, year = {2025}, author = {Zhang, Z and Wang, R and An, Z and Liu, Y and Zhao, J and Zhang, T and Ye, X and Liu, P and Jia, H}, title = {Polystyrene and its dissolved organic matter accelerate antibiotic resistance gene dissemination in anaerobic digestion by posing resistance pressure on functional microorganisms.}, journal = {Water research}, volume = {289}, number = {Pt B}, pages = {124997}, doi = {10.1016/j.watres.2025.124997}, pmid = {41273911}, issn = {1879-2448}, abstract = {Microplastics (MPs) in sludge can release dissolved organic matter (MP-DOM) and affects the dissemination of co-existing antibiotic resistance genes (ARGs). However, the contributions and mechanisms of MPs themselves and released MP-DOM on ARGs dissemination during anaerobic digestion (AD) remain unclear. This study investigated the dissemination potential of ARGs under MP and MP-DOM treatment by combining metagenomic sequencing with partial least squares structural equation modeling (PLS-SEM). Results showed that both treatments increased the abundances of ARGs, virulence factor genes and mobile genetic elements, with 1.25-1.79 fold enhancement relative to control, highlighting ARGs dissemination in AD. Notably, MP-DOM exhibited a stronger enhancement than MPs. The enhancement was mainly ascribed to the resistance pressure on functional microbial communities becoming ARGs hosts by increasing membrane permeability and type IV secretion system activation through reactive oxygen species generation, as evidenced by the 108.2 % and 120.5 % increases in VirD4 expression under MPs and MP-DOM, respectively. Different from the induced selection pressure of MPs on ARGs dissemination, MP-DOM mainly exerted a strongly biological effect by stimulating stress-adaptive carbohydrate metabolism (glycolysis and pentose phosphate) within hydrolytic microorganisms (Clostridium and Defluviicoccus) in the microbially-driven AD environment. This study identifies a dominant factor yet previously overlooked driver of MP-DOM that amplifies ARGs dissemination in sludge AD, providing new insights into the risks of plastic-derived contaminants.}, }
@article {pmid41273495, year = {2025}, author = {Liu, Z and Shao, X and Jin, Y and Shan, X and Zhang, H and Liang, Q and Lu, W and Zhou, G and Lan, H and Zhang, Y}, title = {GO/iron series enhance performance of anaerobic system for treatment of sulfate-containing organic wastewater.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {41}, number = {12}, pages = {472}, pmid = {41273495}, issn = {1573-0972}, support = {2024TSGC0781//Shandong Province Science and Technology Small and Medium sized Enterprise Inno vation Ability Enhancement Project/ ; 2024ZDYF010019//Key R&amp;D Program of Rizhao City/ ; ZR2021MB085//Shandong Provincial Natural Science Foundation/ ; }, mesh = {*Wastewater/chemistry/microbiology ; Anaerobiosis ; *Sulfates/metabolism/chemistry ; *Graphite/chemistry ; Methane/metabolism ; Biological Oxygen Demand Analysis ; *Iron/chemistry ; Bioreactors/microbiology ; Ferric Compounds/chemistry ; Biofuels ; Bacteria/metabolism/genetics/classification ; *Water Purification/methods ; }, abstract = {This study combined with the analysis of co-metabolic microbial communities and investigated the enhancing effects of graphene oxide (GO)/iron series (GO/Fe[0], GO/Fe3O4 and GO/Fe2O3) on anaerobic treatment of sulfate-laden organic wastewater at varying chemical oxygen demand to sulfate ion (COD/SO4[2-]) ratios (COD/SO4[2-]=2.5, COD/SO4[2-]=1.25 and COD/SO4[2-]=0.8). Our results indicate that all GO/iron series significantly improved CODCr and SO4[2-] removal efficiencies and methane production and the enhancement effect was more pronounced at lower COD/SO4[2-] ratios. At COD/SO4[2-]=0.8, compared to the blank control system, the CODCr and SO4[2-] removal efficiencies and the biogas production rate of the GO/Fe3O4 and GO/Fe2O3 system were enhanced by 14.1%, 18.3%, and 24.7%; 5.8%, 9.6%, and 23.3% respectively. Notably, with GO/Fe[0] exhibiting the most significant improvement, the CODCr removal efficiency, SO4[2-] removal efficiency and biogas production were improved by 34.4%, 41.1% and 42.5%, respectively, relative to the blank control. This mechanism is primarily attributed to the corrosion of Fe[0] under anaerobic conditions, which releases electrons and H2 (supplying electron donors for hydrogenotrophic methanogens) and produces elevated levels of soluble Fe[2+] which precipitates sulfide (reducing H2S toxicity). Furthermore, they optimized the system's pH (GO/Fe[0]:7.30-7.69; GO/Fe3O4: 7.30-7.57; GO/Fe2O3: 7.17-7.54; blank: 6.99-7.18), and oxidation-reduction potential (ORP) (GO/Fe[0]: -350~-370 mV; GO/Fe3O4 and GO/Fe2O3: -303~-325 mV; blank: -303~-325 mV) and enhanced the physicochemical properties of the activated sludge. Metagenomic sequencing revealed that the addition of GO/iron series maintained the stability of the microbial community structure, thereby conferring stronger shock resistance to the system. This research provides a scientific basis for exploring the application of anaerobic systems in treating sulfate-containing organic wastewater.}, }
@article {pmid41272806, year = {2025}, author = {Zhang, CJ and Hou, J and Zhou, J and Zou, D and Zhang, H and Ma, Q and Li, M}, title = {Methane cycling microorganisms drive seasonal variation of methane emission in mangrove ecosystems.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {149}, pmid = {41272806}, issn = {2524-6372}, abstract = {Coastal mangroves are one of the significant hotspots of natural methane (CH4) emissions, yet the seasonal dynamics of these emissions and the underlying microbial drivers remain poorly understood. A clearer understanding of these processes is critical for predicting and mitigating methane emissions from these crucial ecosystems. In this study, we conducted a seasonal investigation (from March 2021 to January 2022) in mangrove sediments of the Futian Natural Reserve. We measured in situ methane fluxes and analyzed the microbial community structure via 16S rRNA gene sequencing, metagenomics and metatranscriptomics. Our results revealed significant seasonal variations in methane emissions, with the highest rates occurring in summer. Based on relative abundance of 16S rRNA gene amplicons and methyl-coenzyme M reductase (mcrA) and particulate methane monooxygenase (pmoA) gene sequences obtained from metagenomes, we identified three dominant methanogenic lineages (hydrogenotrophic Methanomicrobiales, acetoclastic Methanosaeta and H2-dependent methylotrophic Methanomassiliicoccales), two anaerobic methanotrophic archaea (ANME-1 and ANME-2b) and one group of aerobic methanotrophic bacteria (Methylococcaceae). Metatranscriptomic data further illuminated that the transcripts of methanogenic mcrA genes were significantly higher in summer and autumn, while the transcriptional activity of anaerobic (ANME-mcrA) and aerobic (pmoA) methanotrophs were most pronounced in autumn. Correlation analyses established a significantly negative relationship between methane emissions and salinity levels. This study highlights that salinity is a key environmental factor mediating methane emissions in mangroves, likely through suppressing methanogenic activity. Our findings thus reveal that seasonal microbial interactions regulate mangrove methane flux, providing critical insights for modeling global methane budgets and guiding climate-smart mangrove management.}, }
@article {pmid41272756, year = {2025}, author = {Dubovitskiy, N and Kurskaya, O and Solomatina, M and Loginova, A and Derko, A and Khozyainova, A and Denisov, E and Shemyakin, E and Shestopalov, A and Sharshov, K}, title = {Metagenomic identification, isolation, and complete genome characterization of two novel picornaviruses in wild duck from Northeastern Siberia.}, journal = {Virology journal}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12985-025-03017-w}, pmid = {41272756}, issn = {1743-422X}, support = {225020408196-1//State funded budget projects/ ; 225020408196-1//State funded budget projects/ ; 225020408196-1//State funded budget projects/ ; 225020408196-1//State funded budget projects/ ; 23-64-00005//Russian Science Foundation/ ; 23-64-00005//Russian Science Foundation/ ; 23-64-00005//Russian Science Foundation/ ; }, abstract = {Duck hepatitis A virus (DHAV, Avihepatovirus ahepati species) is a well-known pathogen of domestic ducks, causing fatal disease in ducklings and posing a significant burden to duck poultry farms. Avihepatovirus ahepati is the sole species within the genus Avihepatovirus and is classified into three distinct genotypes: DHAV-1, DHAV-2, and DHAV-3. In our study, we detected and isolated two strains belonging to the Picornaviridae family from Anas crecca in Northeastern Asia. One of the isolates is related to the DHAV-1 group; however, its polyprotein gene sequence shares only 77.83% nucleotide identity and 89.68% amino acid identity with the most closely related DHAV-1 sequence available, suggesting it represents a highly divergent lineage. The second isolated duck picornavirus shows 60.16% nucleotide identity to the polyprotein gene sequence of the previously described duck picornavirus strain detected during an outbreak in domestic ducks in China. The identification of these two novel picornaviruses in wild ducks, along with their efficient replication in duck embryos and primary cell cultures, emphasizes the need for comprehensive studies of their prevalence in wild ducks and their biological traits to assess potential risks for wildlife and poultry farming. The obtained complete genome sequences and viral isolates enhance our understanding of the diversity, evolution, and ecology of avian picornaviruses.}, }
@article {pmid41272260, year = {2025}, author = {Akyazı, H and Güldür, F&#xc7; and Beyzi, E}, title = {Anode surface modification with reduced graphene oxide (rGO) and molybdenum (Mo) enhances microbial diversity and chemical oxygen demand (COD) removal in microbial fuel cells.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {41272260}, issn = {1614-7499}, support = {FCD-2023-8721//Gazi &#xdc;niversitesi/ ; }, abstract = {This study aimed to investigate the effects of anode surface modifications on microbial community composition and chemical oxygen demand (COD) removal efficiency in microbial fuel cells (MFCs). Four different anode electrodes were fabricated: bare nickel foam (NF), reduced graphene oxide-coated nickel foam (rGO/NF), and rGO/NF modified with 30 wt% and 50 wt% molybdenum (Mo). These electrodes were tested in a single-chamber, membraneless, air-cathode MFC. Surface morphology was characterized using scanning electron microscopy (SEM), and microbial diversity was assessed through 16S rRNA metagenomic sequencing. Distinct microbial profiles were observed across the electrode types. The NF anode supported high abundances of Mesoterricola sediminis (22.2%), Klebsiella pneumoniae (10.1%), and other facultative species. The rGO/NF electrode promoted colonization by Cutibacterium acnes (8.1%) and Paracidovorax avenae (5.4%). On the 30Mo/rGO/NF electrode, notable species included Escherichia coli (8.4%) and Salmonella enterica (6.0%). The 50Mo/rGO/NF anode exhibited the highest microbial diversity, with species such as Streptomyces sp. RerS4 (6.9%) and Micromonospora endophytica (6.5%) being predominant. The highest COD removal efficiency (88.58%) was achieved using the 50Mo/rGO/NF anode. These findings demonstrate that molybdenum-modified rGO coatings enhance both microbial colonization and electrochemical performance, offering a promising strategy for improving MFC efficiency in wastewater treatment applications.}, }
@article {pmid41271719, year = {2025}, author = {Martiny, HM and Munk, P and Fuschi, A and Becsei, &#xc1; and Pyrounakis, N and Brinch, C and ,  and Larsson, DGJ and Koopmans, M and Remondini, D and Csabai, I and Aarestrup, FM}, title = {Geographics and bacterial networks differently shape the acquired and latent global sewage resistomes.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {10278}, pmid = {41271719}, issn = {2041-1723}, support = {NNF16OC0021856: Global Surveillance of Antimicrobial Resistance//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; 874735//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Excellent Science (H2020 Priority Excellent Science)/ ; }, mesh = {*Sewage/microbiology ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; Metagenomics ; *Drug Resistance, Bacterial/genetics ; Genes, Bacterial/genetics ; North America ; Geography ; Cities ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Antimicrobial resistance genes (ARGs) have rapidly emerged and spread globally, but the pathways driving their spread remain poorly understood. We analyzed 1240 sewage samples from 351 cities across 111 countries, comparing ARGs known to be mobilized with those identified through functional metagenomics (FG). FG ARGs showed stronger associations with bacterial taxa than the acquired ARGs. Network analyses further confirmed this and showed potential for source attribution of both known and novel ARGs. The FG resistome was more evenly dispersed globally, whereas the acquired resistome followed distinct geographical patterns. City-wise distance-decay analyses revealed that the FG ARGs showed significant decay within countries but not across regions or globally. In contrast, acquired ARGs showed decay at both national and regional scales. At the variant level, both ARG groups had significant national and regional distance-decay effects, but only FG ARGs at a global scale. Additionally, we observed stronger distance effects in Sub-Saharan Africa and East Asia compared to North America. Our findings suggest that differential selection and niche competition, rather than dispersal, shape the global resistome patterns. A limited number of bacterial taxa may act as reservoirs of latent FG ARGs, highlighting the need of targeted surveillance to mitigate future resistance threats.}, }
@article {pmid41271709, year = {2025}, author = {Bay, SK and Ni, G and Lappan, R and Leung, PM and Wong, WW and Ry Holland, SI and Athukorala, N and Knudsen, KS and Fan, Z and Kerou, M and Jain, S and Schmidt, O and Eate, V and Clarke, DA and Jirapanjawat, T and Tveit, A and Featonby, T and White, S and White, N and McGeoch, MA and Singleton, CM and Cook, PLM and Chown, SL and Greening, C}, title = {Microbial aerotrophy enables continuous primary production in diverse cave ecosystems.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {10295}, pmid = {41271709}, issn = {2041-1723}, mesh = {*Caves/microbiology ; *Ecosystem ; Carbon Dioxide/metabolism ; Metagenome ; Geologic Sediments/microbiology ; Microbiota/genetics ; Hydrogen/metabolism ; Metagenomics ; *Bacteria/genetics/metabolism/classification ; Biodiversity ; Carbon Monoxide/metabolism ; Biofilms ; Gammaproteobacteria/genetics/metabolism ; }, abstract = {Aerated caves receive minimal light energy, yet host diverse microbial communities and the strategies allowing them to meet energy and carbon needs remain unclear. We determined the processes and mediators of primary production in aerated limestone and basalt caves through paired metagenomic and biogeochemical profiling. Four caves were sampled, including sediments and biofilms, yielding 94 metagenomes. Based on 1458 metagenome-assembled genomes, over half of microbial cells encode enzymes to use atmospheric trace gases as energy and carbon sources. The most abundant microbes are chemosynthetic primary producers, notably the gammaproteobacterial methanotrophic order Ca. Methylocavales and two uncultivated actinobacterial genera predicted to grow on atmospheric hydrogen, carbon dioxide, and carbon monoxide. Biogeochemical and isotopic measurements confirmed that these gases are rapidly consumed at rates likely sustaining a substantial fraction of the community and potentially driving primary production. Conventional chemolithoautotrophs, using ammonium and sulfide, are also enriched and active. Altogether, these results indicate that caves are unique in microbial biodiversity and the biogeochemical processes sustaining them. Consumption of atmospheric trace gases likely has a dual role in caves, providing energy for microbial survival and potentially supporting chemosynthetic growth, thereby introducing organic carbon. This process, defined as 'aerotrophy', operates alongside organic and inorganic inputs.}, }
@article {pmid41271554, year = {2025}, author = {Wang, J and Chen, Y and Chen, T and Cai, H and Chen, Q and Sun, W and Ni, J}, title = {Genomic blueprint enables early intervention in cyanobacterial risk management.}, journal = {Science bulletin}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.scib.2025.11.005}, pmid = {41271554}, issn = {2095-9281}, abstract = {While existing early-warning systems struggle to achieve cross-species cyanobacterial risk prediction with the required synchronicity and accuracy in aquatic ecosystems, our study pioneers a genome architecture-driven monitoring paradigm through decoding 317 cyanobacterial metagenome-assembled genomes from the world's largest phosphorus-limiting water transfer system, the Middle Route of the South-to-North Water Diversion Canal (MR-SNWDC). We found an evolutionary blueprint where genome minimization (<3 Mbp) confers ecological dominance under phosphorus scarcity. These streamlined genomes showed predominance and remarkable seasonal dynamics and demonstrated metabolic specialization in phosphorus turnover, light harvesting, and carbon fixation compared to larger genomes. Importantly, we identified a 3 Mbp genomic threshold distinguishing low-risk cyanobacterial consortia from their toxin-producing counterparts. This genome-proxy system enables preemptive risk mitigation by predicting toxic transitions through genome size tracking, fundamentally advancing algal management from reactive monitoring to proactive regulation in water transfer networks.}, }
@article {pmid41271358, year = {2025}, author = {Li, Z and Chen, Y and Zheng, J and Su, J and Lu, Y and Xia, Y and Luo, H}, title = {From fungi to lactic acid bacteria: Dominant microorganisms govern stage-specific esters biosynthesis in pit microecology of strong-flavor baijiu.}, journal = {Food research international (Ottawa, Ont.)}, volume = {222}, number = {Pt 2}, pages = {117797}, doi = {10.1016/j.foodres.2025.117797}, pmid = {41271358}, issn = {1873-7145}, mesh = {*Esters/metabolism ; Fermentation ; *Lactobacillales/metabolism ; *Fungi/metabolism/genetics ; *Wine/microbiology/analysis ; *Flavoring Agents/metabolism ; Butyrates/metabolism ; Food Microbiology ; Taste ; }, abstract = {Esters are vital flavor compounds in strong-flavor baijiu (SFB). However, their biosynthetic mechanisms during pit fermentation are not fully understood. This study employed integrated metagenomic and metabolomic analyses to investigate stage-specific microecological dynamics governing ester biosynthesis and identified three distinct fermentation stages. Stage P1 (days 0-15) featured initial ester accumulation driven by fungal dominance (e.g., Saccharomyces, Aspergillus, and Rhizopus) and high α-diversity. Elevated esterase (EST) genes mainly involved to the ethyl acetate and ethyl butyrate synthesis. Stage P2 (15-35 d) exhibited minimal changes in esters content (except ethyl lactate increase linked to 42 EST genes). During this stage, acidogenic microorganisms, primarily Acetilactobacillus (> 64 % relative abundance), Lactobacillus, and Clostridium, proliferated and co-aggregated with methanogens, including Methanosarcina and Methanobacterium. In Stage P3 (35-117 d), Lactobacillus-Acetilactobacillus consortium (> 74 %) exhibited rapid ester accumulation alongside acids and alcohols increases, with high EST abundance for ethyl caproate and ethyl butyrate synthesis. Dominant microorganisms govern the ester synthesis, with catalytic dominance shifting from fungal (Aspergillus, Saccharomyces, etc.) to lactic acid bacteria (Lactobacillus, Acetilactobacillus, etc.) systems across stages. Five physicochemical properties exerted the stage-dependent control: pH and reducing sugars shaped the microbial structure in P1 (R[2] = 0.40, 0.46); temperature and ethanol drove community simplification in P2 (R[2] = 0.35, 0.64); Acidity and ethanol regulated functional dominance in P3 (R[2] = 0.85, 0.64). PLS-SEM confirmed direct inhibition/promotion effects on α/β-diversity. This microecology-guided framework provided references for manipulation of ester profiles via phase-specific environmental control, offering a scientific basis for improving the quality of SFB flavor.}, }
@article {pmid41270974, year = {2025}, author = {Wang, L and Zhao, Z and Zhao, Y and Dong, S and Feng, S and Cao, L and Song, K}, title = {Comparative Diagnostic Accuracy of Metagenomic Next-Generation Sequencing and Targeted Next-Generation Sequencing for Periprosthetic Joint Infection: A Systematic Review and Meta-Analysis.}, journal = {The Journal of infection}, volume = {}, number = {}, pages = {106661}, doi = {10.1016/j.jinf.2025.106661}, pmid = {41270974}, issn = {1532-2742}, abstract = {OBJECTIVES: The aim of this meta-analysis was to assess the diagnostic performance of metagenomic next-generation sequencing and targeted next-generation sequencing for periprosthetic joint infection (PJI).<br><br>BACKGROUND: Next-generation sequencing (NGS) is increasingly used for diagnosing periprosthetic joint infection (PJI), but its clinical utility remains poorly defined. Discrepancies between metagenomic NGS (mNGS) and targeted NGS (tNGS) results pose a significant clinical challenge for PJI diagnosis. To address this, we conducted a systematic review and meta-analysis comparing the diagnostic accuracy of mNGS and tNGS for PJI.<br><br>METHODS: This study adhered to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. We comprehensively searched PubMed, EMBASE, Cochrane Library, Web of Science, and Scopus from inception through June 1, 2025. Two reviewers independently extracted data and assessed study quality using the Quality Assessment of Diagnostic Accuracy Studies 2 (QUADAS-2) tool. Pooled sensitivity, specificity, diagnostic odds ratio (DOR), and the area under the hierarchical summary receiver operating characteristic curve (AUC) were calculated.<br><br>RESULTS: Following screening and eligibility assessment, 23 studies were included in the analysis. The pooled sensitivity and specificity for diagnosing PJI were 0.89 (95% CI: 0.84-0.93) and 0.92 (95% CI: 0.89-0.95) for mNGS, and 0.84 (95% CI: 0.74-0.91) and 0.97 (95% CI: 0.88-0.99) for tNGS. The DORs were 58.56 (95% CI: 38.41-89.26) for mNGS and 106.67 (95% CI: 40.93-278.00) for tNGS. The areas under the summary receiver-operating characteristic curves (AUCs) were 0.935 (95% CI: 0.90-0.95) for mNGS and 0.911 (95% CI: 0.85-0.95) for tNGS. Comparisons of DOR and AUC between mNGS and tNGS revealed no statistically significant differences (P > 0.05).<br><br>CONCLUSIONS: This meta-analysis indicates that mNGS demonstrates higher sensitivity and a numerically greater AUC than tNGS for diagnosing PJI, with acceptable specificity, although the difference in AUC was not statistically significant. Conversely, tNGS exhibits higher specificity and DOR, alongside acceptable sensitivity, making it valuable for confirming PJI. Overall, the diagnostic accuracy of both next-generation sequencing (NGS) methods is comparable, with each possessing distinct advantages and limitations.}, }
@article {pmid41270973, year = {2025}, author = {Zhu, TY and Guo, JY and Zhang, D and Weng, L and Yang, QW and Peng, JM and Du, B}, title = {A Comparative Study of DNA- and RNA-Metagenomic Next-Generation Sequencing for Pathogen Detection in Lower Respiratory Tract Infections.}, journal = {The Journal of infection}, volume = {}, number = {}, pages = {106659}, doi = {10.1016/j.jinf.2025.106659}, pmid = {41270973}, issn = {1532-2742}, abstract = {OBJECTIVES: To compare the clinical utility of DNA- and RNA-metagenomic next-generation sequencing (mNGS) for pathogen detection in lower respiratory tract infections (LRTIs), and evaluate strategies to optimize RNA-mNGS performance.<br><br>METHODS: We retrospectively analyzed 82 patients with suspected LRTI undergoing simultaneous DNA-mNGS and RNA-mNGS testing. The concordance of two methods in detecting microorganisms was assessed. Performance in detecting causative pathogens was compared using multi-label classification metrics. Impacts of RNA-mNGS workflow adjustments were evaluated using mock samples.<br><br>RESULTS: In a total of 196 microbial detections, DNA-mNGS and RNA-mNGS showed poor overall agreement (Cohen's &#x3ba;=0.166, p<0.01). In identifying causative pathogens, RNA-mNGS demonstrated significantly higher precision (1.00 vs. 0.50, p<0.05) and F1 scores (0.80 vs. 0.67, p<0.05) compared to DNA-mNGS. DNA-mNGS possessed higher sensitivity for bacteria, fungi, and atypical pathogens, while RNA-mNGS excelled in detecting RNA viruses. Improved RNA-mNGS sensitivity and significant DNA-RNA read correlations were observed in causative pathogens at high abundance. Neither homogenization nor increased sequencing depth improved RNA-mNGS testing.<br><br>CONCLUSIONS: DNA-mNGS and RNA-mNGS exhibited low overall consistency. However, RNA-mNGS showed superior precision in identifying causative pathogens in LRTI and additional capacity for RNA virus detections, while DNA-mNGS possessed essential sensitivity for low abundance pathogens.}, }
@article {pmid41270957, year = {2025}, author = {Xu, Y and Zhao, J and Huang, N and Wang, Z and Liu, L and Wang, Y and Qu, Q and Li, Q and Yang, Q and Wang, G and Liu, G and Wang, Q and Wu, W}, title = {Metagenomic characterization of the resistome, bacteriome and mobilome in raw milk from intensive farming systems.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2025.11.017}, pmid = {41270957}, issn = {2090-1224}, abstract = {INTRODUCTION: Intensive farming, as the dominant paradigm in global dairy production, exacerbates antimicrobial resistance (AMR) risks via concentrated animal operations and routine antimicrobial prophylaxis. Nevertheless, the spatiotemporal dissemination patterns of antibiotic resistance genes (ARGs) in regional intensive dairy systems remain insufficiently elucidated.<br><br>OBJECTIVES: Elucidating the spatiotemporal dissemination patterns of ARGs in regional intensive dairy systems by characterizing ARGs across diverse sample matrices.<br><br>METHODS: This investigation employed an integrated approach, combining metagenomic sequencing with comprehensive experimental validation, including bacterial isolation, antimicrobial susceptibility testing, PCR based detection of ARGs, biofilm formation assays, and conjugation experiments to characterize the antibiotic resistome across 539 samples (encompassing raw milk, forage, water, and breast swabs) collected from 42 intensive farms in Shandong, China.<br><br>RESULTS: DY exhibited the most pronounced microbial diversity (16,347 species) and the highest ARG abundance (547 subtypes), which were predominantly &#x3b2;-lactamase genes (56.3&#x202f;%). Multidrug-resistant determinants were pervasive across all sample types. Klebsiella pneumoniae (K. pneumoniae) was identified as a high-risk vector, showing 96.43&#x202f;% resistance to &#x3b2;-lactam antibiotics and a 25&#x202f;% rate of multidrug resistance (MDR). Crucially, conjugation experiments confirmed the horizontal transfer of the blaSHV gene to Escherichia coli (E. coli), demonstrating its potential for cross-species transmission. Furthermore, a significant correlation (P&#x202f;<&#x202f;0.05) was found between biofilm formation and enhanced &#x3b2;-lactam resistance, implicating biofilms in the maintenance of resistance.<br><br>CONCLUSION: This pioneering regional ARG atlas delineates K. pneumoniae's epidemiological significance in Shandong's intensive dairy continuum. Our findings advocate for precision intervention strategies and establish the utility of metagenomics for operational surveillance.}, }
@article {pmid41270896, year = {2025}, author = {Diakité, MT and Sun, S and Somboro, AM and Diakité, B and Koné, A and Kassogué, Y and Fofana, D and Balam, S and Traoré, CB and Maiga, A and Kamaté, B and Ba, D and Diarra, M and Boré, S and Maiga, AI and Dai, Q and Nannini, DR and Holl, J and Murphy, R and Hou, L and Fodor, A and Maiga, M}, title = {Characterization of the gut microbiota in patients with stage III colorectal cancer: A case-control study.}, journal = {Gene}, volume = {}, number = {}, pages = {149913}, doi = {10.1016/j.gene.2025.149913}, pmid = {41270896}, issn = {1879-0038}, abstract = {AIM: To conduct a case-control study (pilot study) in Africa (Mali) in comparing the gut microbiota of patients with stage III colorectal cancer (CRC) using next-generation sequencing.<br><br>METHODS: Shotgun sequencing was performed to characterize participants' fecal microbiota using Illumina's HiSeq platform. This case-control study involved newly diagnosed CRC patients (n&#x202f;=&#x202f;23) prior to any treatment initiation, and unrelated healthy controls (n&#x202f;=&#x202f;24) to elucidate their microbial diversity and relative abundance.<br><br>RESULTS: The findings revealed that the gut microbiota in CRC and in healthy were significantly distinctive according to the PERMANOVA test (R[2]&#x202f;=&#x202f;0.132, P = 0.001), and the alpha-diversity was significantly lower in CRC. Beta-diversity, based on principal coordinate analysis, showed a distinct taxonomy between the CRC and the healthy. Levels of Pseudomonadota, Escherichia, Citrobacter freundii, Klebsiella sp. LTGPAF-6F, Escherichia albertii, Escherichia coli, Caudovirales, Apicomplexa, and Verrucomicrobiota populations were significantly elevated in CRC. The major metabolic pathways with higher relative abundance levels found in CRC compared to healthy were related to HEMESYN2-PWY: heme biosynthesis II (anaerobic), PWY-5154:L-arginine biosynthesis III (via N-acetyl-L-citrulline), FUC-RHAMCAT-PWY: superpathway of fucose and rhamnose degradation, ECASYN-PWY: enterobacterial common antigen biosynthesis, ENTBACSYN-PWY: enterobactin biosynthesis, and AEROBACTINSYN-PWY:aerobactin biosynthesis.<br><br>CONCLUSION: Distinct gut microbiome profiles between healthy and CRC were observed. In particular, the findings showed a significant reduction in microbial diversity in stage III CRC. This study provides initial metagenomic data on Malian patients with CRC. It will be used to create a larger cohort to better understand the relationship between CRC and the gut microbiota in the Malian CRC population.}, }
@article {pmid41270740, year = {2025}, author = {Yi, X and Cai, H and Liu, H and Xu, S and Meng, R and Rao, J and Wu, M and Yang, L and Shi, Y and Zhang, J and Zhu, T and Yang, Y and Wen, P and Qin, Y and Song, W and Li, JT and Shu, W and Dai, J and Sun, J and Lin, L and Guan, WJ and Brightling, CE and Zheng, XY and Wang, Z}, title = {Environmental exposure augments the abundance and transferability of antibiotic resistance genes in the respiratory tract.}, journal = {Cell reports}, volume = {}, number = {}, pages = {116517}, doi = {10.1016/j.celrep.2025.116517}, pmid = {41270740}, issn = {2211-1247}, abstract = {Exposure to environmental pollutants has been linked to increased antibiotic resistance, a critical global health challenge. The respiratory microbiome constitutes a key reservoir of antibiotic resistance genes (ARGs). Here, we constructed a respiratory ARG catalog from sputum metagenomes of 1,128 individuals. We demonstrate that exposures, particularly to cigarette smoke and biofuels, are associated with increased abundance and enhanced mobility of respiratory ARGs. These resistome alterations correlate inversely with lung function, with elevated mobile ARG abundance detectable even in individuals with mild airflow limitation within normal spirometry. Specific ARGs, including opmD and tet(K), interact with smoking in relation to lung function impairment. Murine experiments recapitulate these findings, showing exposure-induced increases in homologous ARGs that confer heightened phenotypic resistance in cultured respiratory bacteria. Our results elucidate a pathway through which environmental pollutants augment the respiratory resistome, suggesting the need for actions to mitigate the antimicrobial resistance burden by addressing environmental pollution.}, }
@article {pmid41270667, year = {2025}, author = {Kodamatani, H and Yamamoto, M and Takaki, Y and Hamasuna, S and Ichitani, K and Kanzaki, R and Tomiyasu, T}, title = {Three-year dynamics of methylmercury production in Hg[2+]-spiked paddy soils: Mercury speciation, microbial communities, and rice contamination.}, journal = {Chemosphere}, volume = {393}, number = {}, pages = {144767}, doi = {10.1016/j.chemosphere.2025.144767}, pmid = {41270667}, issn = {1879-1298}, abstract = {We investigated three-year changes in soil mercury (Hg) pools, methylmercury (MeHg) production, rice contamination, and microbial communities after a single Hg[2+] addition to two soils (Soil I and Soil II). In Soil I, total Hg (T-Hg) concentration of brown rice grain was 0.150 ± 0.023 mg/kg (n = 143) in 2015 and increased to 0.233 ± 0.080 (n = 135) and 0.240 ± 0.118 mg/kg (n = 225) in 2016 and 2017. In Soil II, T-Hg declined from 0.530 ± 0.101 (n = 130) in 2015 to 0.124 ± 0.059 (n = 213) and 0.168 ± 0.059 mg/kg (n = 200) in 2016 and 2017. Variations in T-Hg concentrations in rice grains cultivated in the two soils showed a relationship with soil MeHg concentrations within the same soil, but not between different soils. Sequential extraction, which partitioned soil Hg into seven fractions, indicated that Soil II contained a higher proportion of water-extractable Hg. This finding suggests that the mobility of Hg may have influenced the level of Hg contamination in rice grains. The proportion of Hg sulfide peaked approximately one month after the addition of Hg[2+] in both soils, then decreased over time. In contrast, the fractions of organic-bound and elemental Hg tended to increase over time. In soil II, where DNA extraction was successful, microbial communities showed no clear differences at the phylum level between the Hg-added and non-added samples, but distinct shifts were observed at lower taxonomic levels. Metagenomics showed that the MeHg/T-Hg ratio correlated positively with hgcAB gene abundance (r = 0.85, P < 0.05), while merA/merB showed no clear relationship.}, }
@article {pmid41270588, year = {2025}, author = {Pramanick, A and Saikh, SR and Mushtaque, MA and Karri, D and Gandhi, N and Das, SK}, title = {Long-range transported bacteria perturbing airborne bacterial diversity and pathogenicity over Eastern Himalayas, India.}, journal = {The Science of the total environment}, volume = {1008}, number = {}, pages = {180981}, doi = {10.1016/j.scitotenv.2025.180981}, pmid = {41270588}, issn = {1879-1026}, abstract = {Long-range transported bacteria have a significant impact on hill-top airborne bacterial diversity and pathogenicity. Present study investigates airborne bacterial community structure over a hill-top region of the Eastern Himalayas, based on two years (2022--23) of investigations on culture-independent metagenomic analysis. Winter-time hill-top microbial loading is found to be a minimum of about 21,401.5 ± 2791.0 × 10[5] m[-3], representing background Himalayan airborne bacterial concentration, and a maximum of 6.7 ± 1.2 × 10[5] m[-3] on dusty summer days. 80 % of the total Himalayan bacterial population is due to long-range transport via horizontal and vertical movement of atmosphere, causing about 60 % perturbation in Himalayan bacterial diversity. Space-borne observations with 3-days back-trajectories analysis reveal a thick dust layer between 2 and 3 km over Eastern Himalayas, coming from the Thar Desert. Long-range transported dust-attached bacteria cause a 40 % enhancement in unique bacterial loading, while 6 % unique genera are noticed in upwelling of foothill pollution, and 8 % unique bacterial genera are found in downwelling from free troposphere to the hill-top atmosphere. Desert dust-attached long-range transported bacteria contain one-third skin-infecting pathogens, while upwelling pollutants carry mainly respiratory-infecting bacteria (45 %), and downwelling transport is dominated by gastrointestinal tract-infecting bacteria (50 %). Interestingly, local Himalayan bacteria (20 %) are consistently loaded with pathogens, predominantly causing respiratory (36 %) and skin (31 %) infections throughout the study period. Present results highlight the profound impact of atmospheric transport processes on regional bacterial diversity and public health in hill-top region, highlighting Himalayan atmosphere as a dynamic and global conveyor of life, including pathogens across long distances.}, }
@article {pmid41270407, year = {2025}, author = {Zhang, T and Zhang, P and Zhang, J and Hu, Z and Zhang, J and Wah, TY and He, Y}, title = {Interfacial electron transfer between artificial carbon nanowires clusters and Cyt c: Enabling electron transport for methanogenesis.}, journal = {Water research}, volume = {289}, number = {Pt B}, pages = {124994}, doi = {10.1016/j.watres.2025.124994}, pmid = {41270407}, issn = {1879-2448}, abstract = {Intercellular electron transfer via microbial nanowires and Cytochrome c (Cyt c) is a key mechanism for syntrophic metabolism in anaerobic digestion, yet this functionality is encoded in only a limited number of microbial genomes. To address this limitation, we developed artificial carbon nanowire clusters (ACNCs) derived from plastic/sludge precursors, featuring densely arranged nanowires (Φ 20-60 nm), which form a conductive network supporting microbial colonization and electron transport. Calculations of pseudocapacitance and double-layer capacitance derived from cyclic voltammetry (CV), along with electrochemical impedance spectroscopy (EIS) characterization, revealed enhanced interfacial electron transfer between Cyt c and ACNC compared to biochar (BC) and, carbon nanotubes (CNT). Mott-Schottky analysis revealed superior energy level alignment between ACNC and Cyt c in comparison to BC/CNT, resulting in an enhanced current response in the ACNCCyt c complex, which is critical for efficient electron transfer. Circular dichroism and EPR spectroscopy revealed that ACNC induced an increase in β-sheet content in Cyt c, optimizing its electron transfer orientation. In microbial communities, ACNC supplementation enriched electroactive populations. Metagenomic analysis showed a 1.67-fold increase in Methanothrix abundance and a 1.16-fold upregulation of multiheme cytochromes (MtrC/Ech/Rnf), leading to a 123 % elevation in methanation rates compared to BC.}, }
@article {pmid41269405, year = {2025}, author = {Liu, S and Chen, Q and Gu, Y and Lei, H and Li, B and Qin, Q}, title = {Microorganisms, Microbial Metabolites and Precision Nutrition: Targeting the Gut-Skin Axis for Immune Microenvironment Remodeling in Atopic Dermatitis.}, journal = {Clinical reviews in allergy &amp; immunology}, volume = {68}, number = {1}, pages = {102}, pmid = {41269405}, issn = {1559-0267}, support = {CG24016//Project of Industrialization of Major Achievements in Heilongjiang Province: "Development and Industrialization Demonstration of Key Technologies for Processing Functional Probiotics"/ ; CG24016//Project of Industrialization of Major Achievements in Heilongjiang Province: "Development and Industrialization Demonstration of Key Technologies for Processing Functional Probiotics"/ ; CG24016//Project of Industrialization of Major Achievements in Heilongjiang Province: "Development and Industrialization Demonstration of Key Technologies for Processing Functional Probiotics"/ ; }, mesh = {Humans ; *Dermatitis, Atopic/immunology/metabolism/microbiology/therapy/etiology ; *Skin/immunology/metabolism/microbiology ; *Gastrointestinal Microbiome/immunology ; Precision Medicine ; Animals ; Dysbiosis ; Disease Susceptibility ; Probiotics ; Cellular Microenvironment/immunology ; }, abstract = {Atopic dermatitis (AD), characterized by skin barrier dysfunction and microbiota dysbiosis, is closely linked to immune microenvironment imbalance. Growing evidence highlights the crucial role of microorganisms and their metabolites in immune regulation. Understanding their molecular mechanisms in AD, combined with precision nutrition-driven personalized network analysis, will accelerate innovative intervention strategies. This review summarizes these regulatory mechanisms and current research progress, outlining applications, challenges, and limitations for key targets, such as the TSLP-ILC2-IL-13 axis, IL-31-TRP channels, and SCFA-GPR43 signaling. The precision nutrition-driven approach will leverage multi-omics data, including metagenomics, metabolomics, and host transcriptomics, with integration techniques such as network analysis and machine learning to explore the spatio-temporal regulation of the immune microenvironment. Beyond immunomodulation, dietary factors significantly impact AD progression. We propose "precision nutrition" strategies to mitigate AD risk and burden, including microbiota-targeted dietary patterns, personalized probiotics, and delivery systems for "precise skin nutrition." Synergizing traditional interventions with localized innovations and interdisciplinary tools is expected to enable precise, spatio-temporal immune regulation. This enhances understanding of microorganism-metabolite, precision nutrition, and immune microenvironment connections, advancing AD intervention and treatment.}, }
@article {pmid41269281, year = {2025}, author = {Yazhini, A and Morice, &#xc9; and Jochheim, A and Lieser, B and Söding, J}, title = {Evaluation of metagenome binning: advances and challenges.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {6}, pages = {}, doi = {10.1093/bib/bbaf617}, pmid = {41269281}, issn = {1477-4054}, support = {101111457//Marie Sk&#x142;odowska-Curie Actions/ ; //Horizon Europe programme of the European Union and from the Max Planck Society/ ; }, mesh = {*Metagenome ; *Metagenomics/methods ; *Deep Learning ; Computational Biology/methods ; Humans ; Algorithms ; }, abstract = {Several recent deep learning methods for metagenome binning claim improvements in the recovery of high-quality metagenome-assembled genomes. These methods differ in their approaches to learn the contig embeddings and to cluster them. Rapid advances in binning require rigorous benchmarking to evaluate the effectiveness of new methods. We have benchmarked newly developed state-of-the-art deep learning binners on CAMI2 and real metagenomic datasets. The results show that SemiBin2 and COMEBin give the best binning performance, although not always the best embedding accuracy. Interestingly, post-binning reassembly consistently improves the quality of low-coverage bins. We find that binning coassembled contigs with multi-sample coverage is effective for low-coverage dataset, while binning sample-wise assembled contigs with multi-sample coverage (multi-sample) is effective for high-coverage samples. In multi-sample binning, splitting the embedding space by sample before clustering showed enhanced performance compared with the standard approach of splitting final clusters by sample. Deep-learning binners using contrastive models emerged as the top-performing tools overall, with MetaBAT2 and GenomeFace demonstrating superior speed. To facilitate future development, we provide workflows for standardized benchmarking of metagenome binners.}, }
@article {pmid41268511, year = {2025}, author = {Almeida, NEC and Kalil, AC and Gomez, CA}, title = {Prostatic Abscess due to Ureaplasma parvum in a Heart Transplant Recipient: Diagnostic Challenges and Clinical Utility of Metagenomics Next-Generation Sequencing (NGS).}, journal = {Case reports in infectious diseases}, volume = {2025}, number = {}, pages = {7511507}, pmid = {41268511}, issn = {2090-6625}, abstract = {Ureaplasma spp. are small and fastidious bacteria that may cause urogenital infections in healthy adults and, in rare cases, invasive disease. These bacteria have been increasingly recognized in immunocompromised patients and have been associated with hyperammonemia syndrome, particularly in lung transplant recipients. In this context, we present a unique clinical case of Ureaplasma parvum prostate abscess, a condition rarely observed in heart transplant recipients, diagnosed using next-generation sequencing (NGS).}, }
@article {pmid41268311, year = {2025}, author = {Han, JA and Lee, J and An, HJ and Yi, ES and Kim, Y and Koo, BK and Lee, H and Kim, EY and Lee, HS}, title = {Exploring the Panax ginseng Meyer soil metagenome to uncover antagonistic bacteria against ginseng root rot disease.}, journal = {Journal of ginseng research}, volume = {49}, number = {6}, pages = {767-775}, pmid = {41268311}, issn = {1226-8453}, abstract = {BACKGROUND: Ginseng, renowned for its health benefits, is often cultivated with pesticides, which contradicts its health-enhancing properties. To address this, we identified Bacillus velezensis ARRI17 through a 5-year monitoring of ginseng yield on a national scale and comparative metagenome analysis. ARRI17 is a biocontrol agent that enhances ginseng growth and disease resistance under authentic field conditions.<br><br>METHODS: We identified ARRI17 through metagenomic analysis of soil samples collected from ginseng fields classified as high-yield (3.54&#xa0;&#xb1;&#xa0;0.46&#xa0;kg per 1.62&#xa0;m[2]) or low-yield (0.9&#xa0;&#xb1;&#xa0;0.21&#xa0;kg per 1.62&#xa0;m[2]), based on comparisons to the national 5-year average yield of 2.13&#xa0;&#xb1;&#xa0;0.35&#xa0;kg per 1.62&#xa0;m[2]. The biocontrol efficacy of ARRI17 was validated under laboratory conditions and field trials. Additionally, we analyzed the genomic and physiological characteristics of ARRI17 to clarify its antifungal mechanisms and adaptability to diverse environments.<br><br>RESULTS: ARRI17 exhibited strong inhibitory activity against multiple ginseng fungal pathogens, including Ilyonectria mors-panacis, in both controlled and field conditions. The application of ARRI17 improved ginseng growth parameters and reduced disease incidence in infested soil. Genomic analysis revealed that ARRI17 produces antimicrobial compounds, such as Iturin A, confirmed by HPLC. Furthermore, ARRI17 naturally thrived in rice straw compost, a traditional biofertilizer used in ginseng cultivation, suggesting its long-term presence and compatibility with standard ginseng farming practices.<br><br>CONCLUSION: Bacillus velezensis ARRI17 is an effective biocontrol agent that promotes ginseng growth and enhances disease resistance. Its natural compatibility with traditional farming practices, especially its presence with rice straw compost, positions ARRI17 as a promising and sustainable alternative.}, }
@article {pmid41268301, year = {2025}, author = {Zhang, D and Zhou, M and Qiu, Y and Xu, H and Liu, H and Liu, Y and Xie, L}, title = {Cross-generational mechanisms of maternal gut microbiota in modulating offspring autism spectrum disorder risk: from the gut-brain axis to translational challenges in precision interventions.}, journal = {Frontiers in aging neuroscience}, volume = {17}, number = {}, pages = {1642240}, pmid = {41268301}, issn = {1663-4365}, abstract = {Autism Spectrum Disorder (ASD) manifests as a group of neurodevelopmental disorders with high clinical and genetic heterogeneity, characterized by core features including social communication deficits, repetitive behaviors, and restricted interests. Current research primarily focuses on genetic variations, immune dysregulation, synaptic dysfunction, and gene-environment interactions. Nowadays, accumulating evidence indicates that maternal gut microbiota dysbiosis, induced by high-fat diets, antibiotic overuse, and urbanization, significantly correlates with abnormal fetal neurodevelopment and increased ASD risk. This review systematically delineates three transplacental mechanisms whereby maternal dysbiosis regulates fetal neurodevelopment: Metabolite-mediated pathways, Immune pathway activation, and Epigenetic reprogramming. Meanwhile, the key translational challenges are highlighted. At last, metagenomics-metabolomics-fetal neuroimaging, Development of microbiota metabolite-treated brain organoids, and Artificial Intelligence-driven (AI-driven) probiotic screening were proposed as research directions in future.}, }
@article {pmid41268226, year = {2025}, author = {Liu, Y and Zhang, Y and Li, Y and Yang, J}, title = {Liver abscess caused by Bacteroides thetaiotaomicron complicated by purulent pericarditis: a case report.}, journal = {American journal of translational research}, volume = {17}, number = {10}, pages = {8164-8170}, pmid = {41268226}, issn = {1943-8141}, abstract = {BACKGROUND: Liver abscess complicated by purulent pericarditis is a rare clinical condition. To date, no cases of liver abscess caused by Bacteroides thetaiotaomicron with concomitant purulent pericarditis have been reported. We present a rare case of this dual pathology to improve clinicians' understanding of liver abscess-related complications and uncommon pathogens.<br><br>CASE PRESENTATION: A 33-year-old female was admitted with hypothermia, chest tightness, and vomiting. Upon admission, laboratory tests showed elevated inflammatory markers. Ultrasound imaging revealed both pericardial effusion and a hepatic abscess, leading to a diagnosis of liver abscess complicated by purulent pericarditis. Metagenomic next-generation sequencing (mNGS) of pericardial fluid identified Bacteroides thetaiotaomicron. The patient received anti-infective therapy with meropenem and ornidazole, combined with pericardial effusion drainage. During the later stage of treatment, the patient developed thoracic empyema, necessitating thoracic drainage. Following treatment, the inflammatory markers significantly improved, the liver abscess reduced in size, and the pericardial effusion nearly resolved. At the 8-week follow-up after discharge, clinical and imaging findings were normal.<br><br>CONCLUSION: This case highlights the importance of recognizing atypical manifestations in immunocompromised patients and emphasizes the critical role of early comprehensive examination, prompt and effective anti-infective therapy, and puncture drainage for improving patient outcome. Pathogen identification methods such as mNGS can guide more precise treatment strategies, thereby shortening hospitalization and reducing complications.}, }
@article {pmid41268133, year = {2025}, author = {Li, J and Popovich, PG and Kigerl, KA and McTigue, DM and Schwab, J and Barnes, S and Yarar-Fisher, C}, title = {Multiomic Analysis of the Gut Microbiome and Serum Metabolome in Response to a Low-Carbohydrate, High-Protein Diet in Individuals With Spinal Cord Injury.}, journal = {Topics in spinal cord injury rehabilitation}, volume = {31}, number = {4}, pages = {111-129}, pmid = {41268133}, issn = {1945-5763}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Spinal Cord Injuries/diet therapy/microbiology/blood/metabolism ; Male ; Female ; *Metabolome ; Adult ; Middle Aged ; *Diet, High-Protein Low-Carbohydrate ; *Diet, High-Protein ; }, abstract = {BACKGROUND: Dietary interventions play a significant role in preventing and managing cardiometabolic diseases partly through their impact on the gut microbiome and circulating metabolites.<br><br>OBJECTIVES: To assess the impact of an 8-week low-carbohydrate, high-protein (LC/HP) diet on gut microbiome composition, function, and serum metabolome in individuals with spinal cord injury (SCI).<br><br>METHODS: Twenty-four adults with chronic SCI were randomized into an LC/HP diet or a control group for 8 weeks. Stool and fasting serum samples were collected at baseline and week 8. The gut microbiome composition and metabolic potential were determined using metagenomic sequencing, while serum metabolome was assessed through untargeted liquid chromatography-tandem mass spectrometry. Statistical analyses focused on diet and time interaction effects, using R (version 4.1.0).<br><br>RESULTS: A trend for increased alpha diversity (Gini-Simpson, P = .09) in the diet group indicated a more evenly distributed microbial community. Compared to the control group, several microbiome species (e.g., Fusicatenibacter saccharivorans, Eubacterium siraeum) that are implicated with better intestinal health and reduced inflammation increased, while other species (e.g., Hungatella hathewayi, Clostridium symbiosum) that are associated with colorectal cancer risk decreased in the diet group. Microbial metabolic pathways related to amino acid and purine nucleotides were altered. Increased tryptophan betaine and decreased 8-hydroxy-deoxyguanosine were observed in the serum in the diet group (P interaction < .05), indicating compliance and reduced oxidative stress, respectively.<br><br>CONCLUSION: Adopting an LC/HP diet resulted in favorable gut microbiome and metabolome adaptations that may reduce the risk for cardiometabolic disease and colorectal cancer in individuals with SCI.}, }
@article {pmid41267936, year = {2025}, author = {Ogbuji, NG and Agogbua, JU}, title = {Genomics in plant pathogen identification and control.}, journal = {Frontiers in plant science}, volume = {16}, number = {}, pages = {1661432}, pmid = {41267936}, issn = {1664-462X}, abstract = {Recent advances in genomics have revolutionized plant pathogen detection and control by enabling faster and more accurate identification compared to traditional culture-based methods. Genomic tools like metagenomics and next generation sequencing (NGS) facilitate the detection of microorganisms (bacteria, fungi, viruses, and nematodes) directly from environmental samples. Genomics also provides information on plant-pathogen interactions, especially the detection of Resistance (R) genes and their role in plant defense against pathogens, aiding in the development of genetic markers for breeding disease-resistance crop species. Gene editing systems such as clustered regularly interspaced short palindromic repeats (CRISPR) associated protein 9 (CRISPR-Cas9), transcription activator-like effector nucleases (TALENs), and Zinc Finger nucleases (ZFNs) allow for precise genetic modification, either by incorporating a beneficial R genes or disabling susceptibility (S) genes of the host plant. RNA interference (RNAi) is another genomic tool used to suppress important pathogenic genes and inhibit disease development. Although the use of genomics in plant pathology is hampered by limitations such as high costs, complexity of data analysis and interpretation, and limited access to sequencing platforms, especially in developing countries, recent innovations and multi-disciplinary collaborations are tackling these issues. In general, genomics offers powerful tools that can be employed in the development of sustainable and effective plant disease management strategies, which will help to enhance crop protection and contribute to global food security.}, }
@article {pmid41267688, year = {2025}, author = {Song, K and Ren, L and Guo, X and Ren, G and Sun, Y and Tian, X and Hu, C and Pan, M and Yu, Q and Luo, Z and Hao, Y and Lei, P and Yu, H and Yang, S and Chen, Q and Li, Y and Wang, S and He, Y and Hui, Z and Zheng, W and Jiang, J and Wang, L}, title = {Microbiota-responsive oral nano-amifostine enables colorectal-specific radioprotection and tumor immunity via gut microenvironment reprogramming.}, journal = {Advanced composites and hybrid materials}, volume = {8}, number = {6}, pages = {432}, pmid = {41267688}, issn = {2522-0136}, abstract = {UNLABELLED: Radiotherapy for abdominal malignancies is limited by intestinal toxicity and secondary colorectal cancers. Here, we develop an oral, microbiota-responsive nano-amifostine (CS/PEC-AMF NPs) system that achieves site-specific radioprotection in the colorectum without compromising antitumor efficacy. By conjugating amifostine to pectin and encapsulating it with chitosan, the nanoparticles enable pH- and microbiota-triggered release in the large bowel, safeguarding drug bioactivity during gastrointestinal transit. In murine models, CS/PEC-AMF NPs attenuate both acute and chronic radiation-induced bowel injury, restore epithelial integrity, preserve stem cell populations, and promote tight junction repair. Integrated metagenomic and metabolomic analyses reveal that the system normalizes gut microbiota diversity and composition, increases short-chain fatty acid production, and facilitates macrophage polarization towards the anti-inflammatory M2 phenotype. Notably, the formulation synergistically enhances tumor suppression and extends survival in orthotopic colorectal tumor models undergoing radiotherapy and reduces the incidence of secondary colorectal tumors post-irradiation. Mechanistically, transcriptomic analysis demonstrates the suppression of proinflammatory pathways and the promotion of DNA repair programs. This study provides a paradigm for leveraging functional nanomaterials to orchestrate precise, tissue-specific radioprotection and immune modulation, addressing a key challenge in abdominal cancer therapy.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42114-025-01492-x.}, }
@article {pmid41267624, year = {2025}, author = {Li, H and Fu, J and Fan, X and He, Z and Wang, Y and Yang, S and Wu, J and Wu, L and Zhou, J}, title = {Eutrophication Reshapes Microbial Communities and Life-History Strategies in the Riverine Ecosystems.}, journal = {Environmental microbiology reports}, volume = {17}, number = {6}, pages = {e70234}, doi = {10.1111/1758-2229.70234}, pmid = {41267624}, issn = {1758-2229}, support = {32100081//Youth Program of National Natural Science Foundation of China/ ; 2024QT03//Central Public-Interest Scientific Institution Basal Research Fund, Chinese Academy of Fishery Sciences/ ; 91428207//Key Program of National Natural Science Foundation of China/ ; //National Key Basic Research Program of China (2012CB417300)/ ; }, mesh = {*Eutrophication ; *Rivers/microbiology/chemistry ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; Metagenomics ; Phylogeny ; }, abstract = {Rivers are increasingly affected by human activities, leading to widespread eutrophication. However, the responses of riverine microbiomes to eutrophication remain poorly understood. In this study, we compared microbiomes between eutrophic urban rivers (UR) and relatively undisturbed natural rivers (NR) to elucidate how eutrophication influences community structures, assembly processes, functions and life-history strategies. Amplicon and metagenomic sequencing revealed that eutrophication substantially enhanced microbial abundance and diversity in riverine ecosystems, with UR harbouring a higher proportion of fast-growing, nitrogen-transforming and antibiotic-resistant taxa. Neutral and null model analyses further revealed that, while stochastic processes predominantly shaped communities in NR, deterministic environmental selection exerted stronger control under eutrophic conditions in UR. Correspondingly, microbial communities in UR exhibited higher 16S rRNA gene copy numbers (median 4.69 vs. 4.28), stronger codon usage bias (0.0209 vs. 0.0204), greater predicted growth rates (0.2664 vs. 0.1567 h[-1]), larger genomes (5.91 vs. 5.19 Mb), higher guanine-cytosine content (57.68% vs. 56.41%) and enriched transposase genes (4.37% vs. 2.98%), collectively indicating a community-wide shift from K-selected to r-selected life-history strategies under eutrophication. Overall, this work elucidates how human activities reshape riverine microbial communities and life-history strategies, providing a basis for predicting the ecological outcomes of nutrient over-enrichment in fluvial environments.}, }
@article {pmid41267035, year = {2025}, author = {Li, X and Tian, C and Zhuang, D and Shi, X and Tian, L and Bai, L and Gao, H and Zhou, H and Zhao, F and Dai, M and Zhu, L and Yu, J and Wu, Q and Liu, X and Zhang, T and Sang, J and Li, T and Luo, Y and Tang, Z and Sahu, SK and Xu, X and Wang, J and Liu, H and Xiao, L and Kristiansen, K and Zhang, Z}, title = {A unified catalog of 14,062 microbial species reference genomes provides new insight into the gut microbiota in high-altitude mammals.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {236}, pmid = {41267035}, issn = {2049-2618}, support = {no. 2019QZKK0503//the Second Tibetan Plateau Scientific Expedition and Research (STEP) program/ ; no. U2002206//the Chinese National Natural Science Foundation/ ; no. 202001BB050001//the Major Science and Technology Project in Yunnan Province of China/ ; no. KC-22221159//Yunnan University graduate Research innovation project/ ; No. XZ202401YD0012//Tibet Autonomous Region Science and Technology Program Project/ ; No. 202407AA110009//the Central Guidance on Local Science and Technology Development Fund of Yunnan Province/ ; }, mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; *Mammals/microbiology ; Phylogeny ; *Bacteria/classification/genetics/isolation &amp; purification ; *Genome, Bacterial ; Altitude ; Tibet ; Symbiosis ; }, abstract = {BACKGROUND: The gut microbiota is essential for host health and survival. The understanding of the diversity, stability, and functional traits of mammalian gut microbiota, as well as the evolutionary patterns of the host-gut microbiota holobiont in non-human mammals remains limited. Here, we conducted a comprehensive analysis of the gut microbiota in non-human mammals.<br><br>RESULT: We used 1,412 samples from large herbivores living in the Qinghai-Tibetan Plateau (QTP), recovered 14,062 high-confidence species-level genome bins (SGBs), of which more than 88% represent potentially novel species. We found that recurring lineage-specific bacterial gain-loss events along the host phylogeny might drive the shaping of the gut microbiota in these QTP mammals. Functional characteristics of host-specific SGBs showed host-specific functional enrichment, but few cases of convergence in at least two hosts. Our analyses further revealed that both co-phylogeny and host-swap events are frequent between mammalian hosts and their individual gut symbionts at QTP ecosystem. The genome-wide evolutionary analyses of 60 genera, comprising 376 core microbial species occurring within at least two animal hosts, discovered that co-phylogeny or host-swap signals might be impacted by phylogenetic inertia, but not by selective constraints.<br><br>CONCLUSIONS: Our results showed that animals living in harsh environments are promising sources for the discovery of novel biological functions of gut residing microbes. The results of this study provide insight into the diversity and functionality of the gut microbiota in large herbivores living at QTP as well as the diverse evolutionary patterns of host-gut microbiota interaction over evolutionary times. Video Abstract.}, }
@article {pmid41266796, year = {2025}, author = {Weng, Y and Guccione, C and McDonald, D and Oles, R and Devkota, S and Kopylova, E and Sepich-Poore, GD and Salido, RA and Din, MO and Song, SJ and Curtius, K and Chu, H and Bartko, A and Hasty, J and Knight, R}, title = {Calculating fast differential genome coverages among metagenomic sources using micov.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {1624}, pmid = {41266796}, issn = {2399-3642}, mesh = {*Metagenomics/methods ; *Genome, Bacterial ; *Metagenome ; *Microbiota/genetics ; Humans ; }, abstract = {Breadth of coverage, the proportion of a reference genome covered by at least one sequencing read, is critical for interpreting metagenomic data, informing analyses from genome assembly to taxonomic profiling. However, existing tools typically summarize coverage breadth at the whole-genome or aggregate-sample level, missing informative variation along genomes and between sample groups. Here we introduce MIcrobiome COVerage (micov), a tool that computes and compares per-sample breadth of coverage across many genomes and samples. micov offers two key advances: (1) rapid cumulative coverage breadth calculations specific to each sample type, and (2) detection of differential coverage breadth along genomes. Applying micov to three metagenomic datasets, we show that it identifies a genomic region in Prevotella copri that explains variation in community composition independent of host country of origin, uncovers dietary association with a partially annotated region in an uncharacterized Lachnospiraceae genome, enabling hypothesis generation for genes of unknown function, and improves sensitivity in low-biomass settings by detecting a single genomic copy of enteropathogenic Escherichia coli (EPEC) in wastewater and distinguishing Mediterraneibacter gnavus across specimen types.}, }
@article {pmid41266391, year = {2025}, author = {Pairoh, S and Mhuantong, W and Boonyapakron, K and Yuvaniyama, J and Kanokratana, P and Bunterngsook, B and Lekakarn, H and Arunrattanamook, N and Laothanachareon, T and Champreda, V}, title = {Machine learning-guided discovery of thermophilic carbonic anhydrases from environmental metagenomes.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {40969}, pmid = {41266391}, issn = {2045-2322}, support = {B13F670055//Program Management Unit for Human Resources &amp; Institutional Development, Research and Innovation (PMU-B)/ ; }, mesh = {*Carbonic Anhydrases/genetics/chemistry/metabolism ; *Machine Learning ; *Metagenome ; Metagenomics/methods ; Hot Springs/microbiology ; }, abstract = {Thermophilic carbonic anhydrases (CAs) are promising biocatalysts for carbon capture utilization and storage (CCUS) due to their stability and efficiency at elevated temperatures. This study presents a machine learning (ML)-guided approach to discover thermostable γ-class CA (γ-CA) from metagenomic datasets derived from Fang Hot Spring, Northern Thailand. To develop classification models, two sets of protein descriptors-dipeptide composition (DPC) and physicochemical/biochemical properties (AAindex)-were used to train classification models. Fourteen ML algorithms were systematically evaluated for each feature set. AdaBoost achieved the best performance for the DPC-based model, while LightGBM performed best with AAindex-based features. External validation with known CA sequences confirmed the ability of the models to discriminate thermophilic from non-thermophilic proteins. Applying the optimized models, we screened 1,534 predicted CAs and identified three high-confidence candidates (TtCA, CrCA, and ToCA). These were heterologously expressed in E. coli, purified, and biochemically validated. All candidates exhibited carbonic anhydrase activity, trimeric oligomeric structures, and high melting temperatures (Tm ranging from 97.0 °C to 109.1 °C). Although their hydration activity was modest compared to α-class CAs, their thermal robustness highlights their potential for industrial CO2 capture. This study demonstrates an approach in which ML integrated with metagenomics enables efficient discovery and validation of robust enzymes from extreme environments, providing a scalable strategy for CCUS applications.}, }
@article {pmid41266356, year = {2025}, author = {Deng, Y and Zhao, H and Zhang, L and Yang, S and Zou, D and Ma, M and Hou, C}, title = {Symbiotic Enterococcus faecalis potentiates viral pathogenesis via fructose-1,6-bisphosphate-mediated insect gut epithelial damage.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {215}, pmid = {41266356}, issn = {2055-5008}, support = {32300418//National Natural Science Foundation of China/ ; 32300418//National Natural Science Foundation of China/ ; 2024RC1069//The Science and Technology of Innovation Program of Hunan Province/ ; CAAS-BRC-CB-2025-01//Agricultural Science and Technology Innovation Program/ ; GLKY-2022-16//Guangxi Forestry Science and Technology Promotion and Demonstration Project/ ; }, mesh = {Animals ; *Enterococcus faecalis/physiology/genetics ; Bees/virology/microbiology ; *Symbiosis ; Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Larva/virology/microbiology ; Apoptosis ; }, abstract = {Chinese sacbrood virus (CSBV) is highly lethal to Asian honey bee (Apis cerana) larvae. While gut symbionts are known to regulate viral infection, their role in CSBV pathogenesis remains poorly understood. Through 16S rRNA gene sequence analysis of the field-collected honey bees, we found that the larvae had a substantially higher relative abundance of Enterococcus than pupae or adults. Metagenome sequencing analysis of field-collected larvae demonstrated that CSBV infection significantly induced more than 45-fold enhancement in the abundance of Enterococcus faecalis, an opportunistic pathogen implicated in the development of purulent cystic lesions. In microbiota-free (MF) bees, colonization with E. faecalis markedly suppressed phospholipid metabolism and elevated levels of 4-guanidinobutyric acid and fructose-1,6-bisphosphate (FBP). These metabolic changes were associated with cytotoxicity and apoptosis, which worsened goblet cell damage and thereby facilitated CSBV infection, as indicated by metabolomics and pathological section analysis. Crucially, exogenous FBP administration directly enhanced cytotoxicity and apoptosis of gut in CSBV-infected MF bees, mirroring the CSBV susceptibility was mediated by E. faecalis. Our study unveiled a symbiotic bacteria's involvement in promoting RNA virus infection through metabolic reprogramming and epithelial barrier dysfunction, providing new insights into host-microbe-virus interactions in pollinators.}, }
@article {pmid41266326, year = {2025}, author = {Stanislawski, MA and Litkowski, E and Arehart, CH and Luo, K and Gilmore, N and Lange, LA and Lange, EM and Barnes, K and Avery, CL and Meyer, KA and Holguin, F and North, KE and Burk, RD and Kaplan, RC}, title = {Relationships among host genetics, gut microbiota, and asthma in US Hispanic/Latino adults.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {10223}, pmid = {41266326}, issn = {2041-1723}, support = {1OT3HL14715//U.S. Department of Health &amp; Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; K01HL157658//U.S. Department of Health &amp; Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; R01HL157069//U.S. Department of Health &amp; Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; HHSN268200625235C//U.S. Department of Health &amp; Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; R01HL136266//U.S. Department of Health &amp; Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; R01AI152504//U.S. Department of Health &amp; Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; R01MD011389//U.S. Department of Health &amp; Human Services | NIH | National Institute on Minority Health and Health Disparities (NIMHD)/ ; }, mesh = {Adult ; Female ; Humans ; Male ; Middle Aged ; *Asthma/genetics/microbiology/epidemiology/ethnology ; Body Mass Index ; Cross-Sectional Studies ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; *Hispanic or Latino/genetics ; Obesity/microbiology/genetics/complications ; Risk Factors ; United States/epidemiology ; }, abstract = {Asthma is a heterogeneous condition that is often comorbid with obesity and influenced by diverse risk factors. Elucidating the association of gut microbial characteristics with asthma could improve our understanding of the pathophysiology. Here, we investigate relationships of host genetics and stool microbiota characteristics with asthma among US Hispanic/Latino adults, while considering the influence of obesity status, using host whole genome sequencing and stool shotgun metagenomic microbiota data from participants of the Hispanic Community Health Study/Study of Latinos. We evaluate cross-sectional associations of microbiota characteristics with asthma and analyse whether they are modified by obesity status (body mass index≥30 kg/m[2]). We assess differences in alpha diversity, beta diversity, and taxonomic abundance with asthma, independent of obesity, and interactions between asthma and obesity using covariate-adjusted regression-based methods. We generate an asthma polygenic risk score (PRS) and compare the classification accuracy of genetic and microbial factors for asthma status. We report that asthma is associated with differences in overall taxonomic composition (beta diversity; p = 0.001), which is not dependent on obesity status (p = 0.31). Asthma is not associated with alpha diversity metrics (p > 0.17), though obesity is associated with lower alpha diversity (p < 0.01). We identify multiple taxa that are associated with asthma, including decreased abundance of Lactobacillus and Enterococcus species, and some taxonomic associations vary by obesity status. Compared to models including baseline risk factors and an asthma PRS, microbial information improves classification accuracy of asthma (p = 0.04). Our results support that there are microbiota characteristics associated with asthma in Hispanic/Latino adults independent of obesity.}, }
@article {pmid41265635, year = {2025}, author = {Wang, S and Huang, Y and Wang, N and Zhou, H and Ren, X and Li, K and Xia, Y and Xu, J and Huang, L and Cai, H}, title = {Epstein-Barr virus in suspected intracranial infection: a multicenter, retrospective study.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {}, number = {}, pages = {108235}, doi = {10.1016/j.ijid.2025.108235}, pmid = {41265635}, issn = {1878-3511}, abstract = {OBJECTIVES: The clinical relevance of Epstein-Barr virus (EBV) detection in cerebrospinal fluid (CSF) using metagenomic next-generation sequencing (mNGS) in patients with suspected intracranial infections has not been fully clarified. This study aimed to assess the clinical features, imaging characteristics, and outcomes in EBV-positive patients.<br><br>METHODS: We retrospectively enrolled patients with suspected intracranial infection who underwent commercial mNGS of CSF samples between December 2019 and October 2023 across 13 hospitals in four cities. Clinical data were collected, and multivariable logistic regression was performed to assess the association between EBV positivity and unfavorable outcomes.<br><br>RESULTS: Among 507 patients, 51 (10.1%) were EBV-positive in CSF. EBV-positive cases showed higher CSF mononuclear cell proportions (83.8% vs. 32.8%, p<0.001), lower chloride levels (123.0 vs. 126.1 mmol/L, p=0.019), and more frequent herpesvirus co-detection (21.6% vs. 8.6%, p=0.007). Imaging abnormalities did not differ significantly. After adjustment, multivariable logistic regression showed that EBV was not an independent risk factor for clinical outcomes (OR 1.005, 95% CI 0.516 - 1.972, p&#x202f;=&#x202f;0.988).<br><br>CONCLUSIONS: EBV was detected in 10.1% of patients in CSF samples from patients with suspected intracranial infections. EBV positivity correlated with a lymphocytic CSF profile and co-detection of other herpesviruses but was not independently associated with unfavorable outcomes.}, }
@article {pmid41265331, year = {2025}, author = {Zeng, Y and Gao, H and Huang, H and Xiong, W and Bin, L and Liao, B and Chen, W and Chen, X and Wen, S and Li, P and Huang, S and Tang, B}, title = {Performance, metabolism, and resistance of an SMX-stressed continuous-flow AGS-MBR system: Microscopic mechanism of macroscopic instability phenomena.}, journal = {Water research}, volume = {289}, number = {Pt B}, pages = {124968}, doi = {10.1016/j.watres.2025.124968}, pmid = {41265331}, issn = {1879-2448}, abstract = {To clarify how long-term sulfamethoxazole (SMX) pressure converts macro-scale performance loss into micro-level mechanistic change, a continuous-flow aerobic granular sludge membrane bioreactor (AGS-MBR) was operated for 140 days at SMX concentrations ranging from 0 to 5 mg L[-1]. At 0.2-1 mg L[-1], the system remained resilient: TN and TP removal stabilized at 90 % and 72.8 %, respectively, and the volume-mean granule diameter remained 282 µm. Metagenomics revealed significant up-regulation of the glycogen-metabolising gene glk and the polyphosphate gene ppk, which fuelled an energy-compensation pathway that supplied ATP and precursors for TB-EPS synthesis and reinforced granule scaffolding. When influent SMX rose to 5 mg L[-1] this compensation collapsed: EPS dropped 45 %, Dv shrank 38 %, granules disintegrated, TN removal fell to 70 % and TP to 44.8 %. The community shifted to a filamentous bacteria dominated state with Thiothrix >25 % relative abundance. Concurrently, the non-pathogen Rubrivivax became a shared host for antibiotic resistance genes (sul1, sul2) and multiple transposases; mobile genetic elements mediated the co-transfer of resistance and virulence genes and eroded functional redundancy. LC-MS further showed that the major transformation products P4 and P6 exhibited 2.3 folds higher chronic toxicity than the parent compound and imposed additional chemical stress on the already impaired granule microbiota. SMX dose dictated a cascade in which metabolic compensation was followed by selection of filamentous hosts prone to gene mobility and finally by chemical toxicity, progressively dismantling granule structure, nutrient removal services and ecological safety. These results elucidate the dose-dependent macro-to-micro cascade under SMX stress and provide insights for mitigating ecological risks in antibiotic laden wastewater.}, }
@article {pmid41264852, year = {2025}, author = {Kosmopoulos, JC and Anantharaman, K}, title = {Viral Dark Matter: Illuminating Protein Function, Ecology, and Biotechnological Promises.}, journal = {Biochemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.biochem.5c00349}, pmid = {41264852}, issn = {1520-4995}, abstract = {Viruses are the most abundant biological entities on Earth and play central roles in shaping microbiomes and influencing ecosystem functions. Yet, most viral genes remain uncharacterized, comprising what is commonly referred to as "viral dark matter." Metagenomic studies across diverse environments consistently show that 40-90% of viral genes lack known homologues or annotated functions. This persistent knowledge gap limits our ability to interpret viral sequence data, understand virus-host interactions, and assess the ecological or applied significance of viral genes. Among the most intriguing components of viral dark matter are auxiliary viral genes (AVGs), including auxiliary metabolic genes (AMGs), regulatory genes (AReGs), and host-physiology-modifying genes (APGs), which may alter host function during infection and contribute to microbial metabolism, stress tolerance, or resistance. In this Review, we explore recent advances in the discovery and functional characterization of viral dark matter. We highlight representative examples of novel viral proteins across diverse ecosystems, including human microbiomes, soil, oceans, and extreme environments, and discuss what is known and still unknown about their roles. We then examine the bioinformatic and experimental challenges that hinder functional characterization and present emerging strategies to overcome these barriers. Finally, we highlight both the fundamental and applied benefits that multidisciplinary efforts to characterize viral proteins can bring. By integrating computational predictions with experimental validation and fostering collaboration across disciplines, we emphasize that illuminating viral dark matter is both feasible and essential for advancing microbial ecology and unlocking new tools for biotechnology.}, }
@article {pmid41264233, year = {2025}, author = {Yun, Y and Duan, C and He, X and Tang, R and Lan, Y and Lu, M and Liu, T and Fan, X and Fan, Z and Ran, J}, title = {Gut microbiome plasticity explains the altitudinal distribution pattern and adaptability in a small mammal species (Apodemus draco).}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0238825}, doi = {10.1128/spectrum.02388-25}, pmid = {41264233}, issn = {2165-0497}, abstract = {Altitudinal distribution patterns of species, a central focus of ecology, predominantly focus on environmental factors and only rarely on the host's intrinsic adaptive capacity. Particularly, the role of gut microbiota has not yet been studied. Here, we used the wild South China Field Mouse (Apodemus draco), a widely distributed small mammal species, as the study subject to investigate the altitudinal distribution pattern of the species and assess how gut microbiota contributes to the formation of this pattern. A total of 219 wild samples were captured in the middle section of the Qionglai Mountains, China, and 121 adult individuals were selected for metagenomic sequencing (e.g., gut microbial diversity, network topology, composition, and functional profiles). Vegetation cover of each sampling quadrat was assessed using Normalized Difference Vegetation Index. Our results indicate that A. draco exhibited a hump-shaped altitudinal distribution, but the peak abundance of A. draco corresponds to lower vegetation cover of habitats. Gut microbial diversity, complexity, robustness, energy harvesting ability, and carbohydrate utilization capacity all peaked at the mid-altitude zone, matching the host's spatial distribution pattern. Furthermore, the gut microbiome in high-altitude A. draco populations facilitates host acclimatization in extreme high-altitude niches by enhancing energy harvesting, hypoxia tolerance, and pathogen resistance.IMPORTANCEWe propose for the first time that the gut microbiome serves as a pivotal factor in structuring the altitudinal distribution pattern of species and further reveal a gut microbiota-mediated adaptive strategy underlying mammalian high-altitude adaptation. These results demonstrate that the gut microbiome fundamentally facilitates host adaptation to ecological niches. The study provides a novel insight into the factors of species' spatial distribution from a gut microbiota perspective.}, }
@article {pmid41263111, year = {2025}, author = {Feng, X and Li, Y and Zheng, J and Chen, X and Yang, S and Chen, Y and Li, SC}, title = {MicrobialScope: an integrated genomic resource with rich annotations across bacteria, archaea, fungi, and viruses.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkaf1234}, pmid = {41263111}, issn = {1362-4962}, support = {C2004-23Y//Young Collaborative Research/ ; JCYJ20220818101201004//Shenzhen Science and Technology Program/ ; 32300527//National Natural Science Foundation of China/ ; 32470695//National Natural Science Foundation of China/ ; 2022A1515110784//Guangdong Basic and Applied Basic Research Foundation/ ; 2023B0303040004//Key-Area Research and Development Program of Guangdong Province/ ; TC2024JC43//Basic Research Programs of Taicang, 2024/ ; //Shenzhen-Hong Kong Institute of Brain Science/ ; //SIAT-HKUST Joint Laboratory of Brain Science/ ; }, abstract = {Microorganisms, including bacteria, archaea, fungi, and viruses, are the most taxonomically diverse and ecologically dominant life forms on Earth, playing critical roles in ecosystems, human health, and industrial applications. While existing microbial databases such as BV-BRC and IMG archive both monoisolate and metagenome-assembled genomes (MAGs) across domains, challenges remain in standardized, multi-level annotations and interactive tools for all microbial groups. Here, we present MicrobialScope (https://microbial.deepomics.org/), a comprehensive microbial genomic platform that integrates large-scale genome collections, multilevel annotations, and interactive visualizations. MicrobialScope harbors 2 411 503 bacterial, 24 472 archaeal, 20 203 fungal, and 188 267 viral genomes derived from both monoisolate assemblies and MAGs. Integrating 15 state-of-the-art bioinformatics tools and 10 specialized databases, MicrobialScope provides extensive annotations encompassing basic genomic features, genomic element prediction (e.g., genes, tRNAs, tmRNAs, CRISPR-Cas and anti-CRISPR elements, secondary metabolite biosynthetic clusters, signal peptides, and transmembrane proteins), and functional and structural annotations. This includes 1 072 114 935 proteins with diverse annotations, 24 640 186 tRNAs and tmRNAs, 140 888 CRISPR-Cas systems, 173 256 anti-CRISPR elements, 105 121 secondary metabolite biosynthetic clusters, 13 235 096 signal peptides, and 50 811 729 transmembrane proteins. In addition, MicrobialScope offers unrestricted access to all data resources, interactive visualization tools, and built-in online analytical modules for intuitive exploration and comparative analysis. With its extensive genome collection, comprehensive annotations, and user-friendly interface, MicrobialScope serves as a scalable platform to advance genome research across diverse microbial domains.}, }
@article {pmid41263098, year = {2025}, author = {Yan, Y and Patel, RSKR and Shanmugam, NRS and Akresi, J and Yin, Y}, title = {dbCAN-HGM: CAZyme gene clusters in gut microbiomes of diverse human populations.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkaf1185}, pmid = {41263098}, issn = {1362-4962}, support = {R01GM140370/NH/NIH HHS/United States ; R03OD039979/NH/NIH HHS/United States ; 58-8042-3-076//United States Department of Agriculture/ ; //Nebraska Tobacco Settlement Biomedical Research Enhancement Funds/ ; }, abstract = {CAZymes (Carbohydrate Active EnZymes) play key metabolic functions in human gut microbiomes (HGM). Genes of glycan degrading CAZymes often form physically linked CAZyme Gene Clusters (CGCs) in gut bacterial genomes. Here we developed dbCAN-HGM (https://pro.unl.edu/dbCAN_HGM), a comprehensive data repository for human gut bacterial CGCs and CAZymes. dbCAN-HGM has the following unique features: (i) 121 883 CGCs are identified in 6031 high-quality species-level representative metagenome assembled genomes (MAGs), from a wide range of human populations, especially the under-studied African population; (ii) Each CGC page includes metagenomic read mapping results from different diets (vegan, vegetarian, omnivore, flexitarian) and disease statuses (ulcerative colitis [UC and Crohns disease), with interactive coverage plot and Jbrowse alignment tracks; (iii) CGCs are clustered with 1358 polysaccharide utilization loci into CGC families (CGC-Fs) to infer glycan substrates; (iv) Metadata and visualization are available for CGC-Fs by substrate, taxonomy, host geographic distribution, and top abundant CAZyme families; (v) CGCs are fully annotated with CAZymes, transporters, signal transduction proteins, transcriptional factors, sulfatases, peptidases, Pfam families, and protein 3D structure comparison results for unannotated proteins; and (vi) User-friendly and highly interactive web interface is provided for easy browsing and downloading of HGM genomes, CGCs, CGC-Fs by glycan substrates and continents.}, }
@article {pmid41262935, year = {2025}, author = {Zhang, B and Meng, D and Wang, X and Hu, J and Fan, J and Li, X and Yang, Z and He, W and Zhou, D and Cheng, Y and Li, J and Zou, J and Liu, Z}, title = {Additive of cow dung weakened the influences of microbial interactions on nitrogen dynamic during composting of rice husks.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1641502}, pmid = {41262935}, issn = {1664-302X}, abstract = {Rice husk (RH) and cow dung (CD) are two of the most abundant agricultural solid waste. Converting these residues into peat-free substrates through co-composting supports sustainable agricultural development. A 40-day rice husk composting experiment was conducted to assess the effects of cow dung addition on microbial networks and carbon-nitrogen dynamics using 16S rRNA and metagenomic analyses. Furthermore, Furthermore, we prepared seedling substrates from composts of RH alone and RH combined with CD (RHCD), and evaluated their plant growth-promoting effects. The addition of cow dung (CD) to rice husk (RH) composting increased the average temperature from 52.8 °C to 60.1 °C and acted as a pH buffer, maintaining values around 7.4. CD significantly (p < 0.05) enhanced microbial network complexity, as indicated by larger network size and higher average degree, but disrupted the linear correlations between network properties and carbon or nitrate nitrogen contents (p > 0.05). This decoupling suggests that CD weakened the linkage between microbial interactions and carbon or nitrogen biotransformation processes. CD also significantly suppressed (p < 0.05) denitrification-related genes (norB, nir and nar) after the thermophilic phase, implying reduced nitrogen loss during compost maturation. We further found that larger network size or higher average degree reduced the abundance of key genes involved in assimilatory nitrite reduction (e.g., nirBD), while increasing those related to denitrification (e.g., nirK and nirS). Moreover, seedling substrates derived from RH (95.06%) and RHCD (93.21%) composts achieved higher germination rates of Solanaceae crops than the commercial peat-based substrate (81.48%). Germination rate and seedling biomass were positively correlated with dissolved organic carbon (r = 0.820, p = 0.045) and ammonium nitrogen (r = 0.858, p = 0.029), respectively. These findings advance the understanding of microbial interaction regulating carbon and nitrogen cycling during RH composting, and support the sustainable production of peat-free seedling substrates from agricultural waste.}, }
@article {pmid41262931, year = {2025}, author = {Trunfio, M and Scutari, R and Fox, V and Vuaran, E and Dastgheyb, RM and Fini, V and Granaglia, A and Balbo, F and Tortarolo, D and Bonora, S and Perno, CF and Di Perri, G and Alteri, C and Calcagno, A}, title = {The cerebrospinal fluid virome in people with HIV: links to neuroinflammation and cognition.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1704392}, pmid = {41262931}, issn = {1664-302X}, abstract = {INTRODUCTION: Despite durable viral suppression, neuroinflammation and neurocognitive complications remain common yet poorly understood in people with HIV (PWH). HIV alters human viromes, and virome perturbations have been linked to neurocognitive issues in people without HIV. Recently characterized, the brain and cerebrospinal fluid (CSF) viromes represent a new avenue to understand brain and mental health in PWH.<br><br>METHODS: This cross-sectional study analyzed 85 CSF samples (74 from PWH on suppressive antiretroviral therapy, and 11 from controls without HIV, CWH) through shotgun metagenomics for DNA and RNA viruses. Taxonomic composition (reads and contigs), diversity, and relative abundance (RA) of prokaryotic (PV), human eukaryotic (hEV), and non-human eukaryotic viruses (nhEV) were evaluated in relation to HIV status, markers of neuroinflammation/neurodegeneration, cognitive functions, and depressive symptoms. Sensitivity analyses and post-hoc cluster analysis on the RA of hEV, non-human viruses (NHV) and blood-brain barrier permeability were performed. Multivariable models assessed the relationship between cognition and clusters.<br><br>RESULTS: Of 46 read-positive CSF samples, 93.5% contained PV sequences, 47.8% hEV, and 45.6% nhEV. PWH displayed lower &#x3b1; diversity, although p > 0.05. At &#x3b2; diversity analysis, HIV status explained 3.4% of the variation in viral composition (p = 0.016). Contigs assembly yielded 13 samples positive for 8 hEV, 2 nhEV, and 6 PV. Higher RA of PV was correlated with higher CSF S100&#x3b2; (rho 0.36, p = 0.002) and &#x3b2;-Amyloid 1-42 fragment (&#x3b2;A-42, rho 0.27, p = 0.026), whereas higher RA of nhEV with poorer cognitive performance (rho 0.26, p = 0.022). Conversely, higher RA of hEV correlated with better cognition (rho -0.38, p = 0.003) and lower &#x3b2;A-42 (rho -0.30, p = 0.012). Sensitivity analyses restricted to only CSF samples with detectable reads confirmed these findings. Three CSF clusters were identified and showed differences in astrocytosis, &#x3b2;A-42, tau protein, and cognitive functions. Participants with hEV-enriched CSF showed better cognitive performance compared to those with virus-devoid and NHV-enriched CSF (all p < 0.05).<br><br>CONCLUSION: This study provides the first comprehensive description of the CSF virome in PWH, revealing associations with neuroinflammation and cognition. These findings highlight the potential involvement of the CSF virome in brain health and inform about its composition, origin, and potential clinical implications in people with and without HIV.}, }
@article {pmid41262456, year = {2025}, author = {Ma, Y and Li, Z and Liu, P and Wei, Y and Jiang, K and Yue, Y and Zhang, A and Wang, W and Li, L and Zhang, P and Gu, X and Liu, Q and Lu, L}, title = {Metagenomics research on the gut microbiota of the Marmota himalayana of the Sanjiangyuan National Nature Reserve in Qinghai Province, China.}, journal = {Biosafety and health}, volume = {7}, number = {5}, pages = {281-294}, pmid = {41262456}, issn = {2590-0536}, abstract = {With the improvement of transportation and the rise of tourism on the Qinghai-Xizang Plateau, the scope of human activities has continuously expanded, increasing opportunities for contact with wildlife, also exacerbating the outbreak rate of zoonotic emerging infectious diseases. Currently, research on the gut microbiota of wildlife, especially Marmota himalayana (M. himalayana), which are reservoir hosts for plague, is scarce. In this study, we investigated the composition, function, and regional variations of the gut microbiota in M. himalayana based on the metagenomic sequencing of 45 fecal samples from the Sanjiangyuan National Nature Reserve in Qinghai Province. The results indicated that at the phylum level, the dominant bacterial phyla in the gut microbiota of the M. himalayana were Firmicutes, Bacteroidota, and Proteobacteria, collectively accounting for 74.16 % of the community. At the genus level, the top three most abundant genera were Alistipes (11.86 % ± 1.56 %), Bacteroides (6.68 % ± 0.95 %), and Clostridium (4.92 % ± 1.04 %). Kyoto encyclopedia of genes and genomes (KEGG) database annotation results showed that the most enriched functional categories of the marmot gut microbiota were metabolism, genetic information processing (GIP), and environmental information processing (EIP). These active functions played a crucial role in food digestion, nutrient absorption, metabolic balance maintenance, and pathogen defense, aiding the marmot in better adapting to the extreme environment of the Qinghai-Xizang Plateau. The study provided critical insights into host-microbe interactions, highlighting the role of microbiota in the survival and conservation of endangered species in unique habitats.}, }
@article {pmid41262425, year = {2025}, author = {Morelle-Hungría, E}, title = {Molecular genetics as evidence of environmental harm in ecocriminological analysis.}, journal = {Open research Europe}, volume = {5}, number = {}, pages = {244}, doi = {10.12688/openreseurope.21126.2}, pmid = {41262425}, issn = {2732-5121}, abstract = {This research focuses on the potential of molecular genetics as a tool that can complement the assessment and evaluation of environmental damage from the perspective of green criminology or ecocriminology. This would have an impact on the effectiveness and efficiency of the mechanisms established for assessing the damage caused to ecosystems. We are facing a planetary crisis with the risk of ecosystem collapse, so it is proposed to overcome the limitations that we can identify in traditional criminal law by adopting an ecocentric approach reinforced with innovative mechanisms provided by science. This requires, among other things, recognising the intrinsic value of nature and committing to ecological justice. Molecular genetics methods, such as environmental DNA, metagenomics and population genetics, allow us to visualise the biological and ecological transformations induced by pollutants, even when these are invisible to the naked eye. These techniques provide objective and quantifiable data on biodiversity loss, changes in community composition and even possible genotoxic effects. Therefore, these molecular tests can complement preventive and restorative measures in environmental crimes. By fostering dialogue between science, law, and ethics, this study advocates for an integrated paradigm of environmental damage analysis in which molecular genetics enhances our ability to detect, understand, and legally address ecological damage. The convergence of green criminology, molecular genetics, and ecological justice reorients institutional responses toward restoring ecosystem integrity and defending the rights of nature.}, }
@article {pmid41261745, year = {2025}, author = {Liu, B and Zhu, L and Zhou, S and Li, A and Xu, P and Han, Y and Shu, Y and Chen, L and Yang, J and Wu, Z}, title = {ZOVER 2.0: a virome-based platform for zoonotic and vector-borne viruses.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkaf1243}, pmid = {41261745}, issn = {1362-4962}, support = {2022FY100905//Science &amp; Technology Fundamental Resources Investigation Program/ ; 2021-I2M-1-038//CAMS Innovation Fund for Medical Sciences/ ; 2024-I2M-ZD-007//CAMS Innovation Fund for Medical Sciences/ ; 32370176//National Natural Science Foundation of China/ ; 2023-PT310-04//Chinese Academy of Medical Sciences/ ; GZNL2024A01019//Major Project of Guangzhou National Laboratory/ ; }, abstract = {Emerging zoonotic and vector-borne viruses pose a continuous threat to global public health, highlighting the need for effective virome surveillance that targets key wildlife reservoirs and vectors. Addressing this challenge requires a systematic understanding of both viral and host diversity, especially across broad spatiotemporal scales. Building on the previous genome-centric release, the upgraded ZOVER 2.0 (https://www.mgc.ac.cn/ZOVER/) expands its scope by incorporating 5883 curated metagenomic next-generation sequencing libraries from 72 independent projects, spanning 12 years and covering 362 distinct wildlife species of bats, rodents, mosquitoes, and ticks. To ensure consistent and sensitive virome profiling across heterogeneous datasets, ZOVER 2.0 employs a standardized analysis pipeline based on reads for taxonomic annotation and viral abundance estimation. After normalization, sequencing reads were collectively assigned to 110 recognized viral families, substantially expanding the known virome diversity within these four wildlife groups. Furthermore, a series of interactive modules enables users to visualize virome composition and perform comparative analyses across different host taxa, geographic regions, and temporal scales. By integrating current genomic and metagenomic knowledge, ZOVER 2.0 provides a robust platform for virus discovery, ecological interpretation, and surveillance of potential interspecies transmission, thereby contributing to One Health-oriented monitoring of emerging infectious diseases.}, }
@article {pmid41261182, year = {2025}, author = {Prusty, G and Prasad, BR and Polaki, S and Mereddy, S}, title = {Integrative multi-omics characterization of the gut microbiome in Pila globosa: functional insights into nutrient cycling and detoxification potential.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {41}, number = {12}, pages = {464}, pmid = {41261182}, issn = {1573-0972}, mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Metagenomics/methods ; Proteomics/methods ; *Snails/microbiology ; Phylogeny ; Metagenome ; Multiomics ; }, abstract = {Pila globosa, a freshwater snail endemic to Indian aquatic ecosystems, plays a pivotal role in nutrient cycling and organic matter turnover. In this study, we present the first integrative multi-omics characterization of its gut microbiome using shotgun metagenomics, metaproteomics, and genome-resolved analyses. The gut microbiota was taxonomically diverse yet compositionally stable, dominated by Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria, with core genera including Pseudomonas, Clostridium, Bacillus, and Streptomyces. Alpha diversity metrics (Shannon = 4.22 ± 0.15; Simpson = 0.90 ± 0.01) and low Bray-Curtis dissimilarity (0.12-0.15) indicated a conserved core microbiome across replicates. Functional profiling through HUMAnN2 and metaproteomic validation revealed enrichment of pathways related to carbohydrate metabolism, short-chain fatty acid (SCFA) synthesis, amino-acid biosynthesis, and oxidative phosphorylation, reflecting the community's contribution to host nutrition and metabolic balance. Genes and proteins associated with xenobiotic degradation (benzoate, toluene metabolism) and oxidative stress response (superoxide dismutase, catalase, glutathione S-transferase) were abundant, suggesting microbial support for redox regulation and detoxification. Twelve high-quality metagenome-assembled genomes (MAGs) reconstructed from dominant taxa encoded traits for secondary metabolite production, metal resistance, and stress tolerance, underscoring their ecological versatility. Together, these results establish a foundational reference for understanding the functional potential of the P. globosa gut microbiome and its possible role in nutrient transformation and pollutant processing in freshwater systems. The study provides baseline data for future comparative and ecotoxicological investigations of gastropod holobionts.}, }
@article {pmid41261035, year = {2025}, author = {Rahman, T and Samia, NSN and Moon, SB and Islam, MS and Mahmud, ZH and Kabir, MS and Karim, MM and Rahman, M and Jubair, M}, title = {2024 Bangladesh Floodwaters Harbour Regional Hotspots of Pathogens and Antimicrobial Resistance.}, journal = {Environmental microbiology reports}, volume = {17}, number = {6}, pages = {e70240}, doi = {10.1111/1758-2229.70240}, pmid = {41261035}, issn = {1758-2229}, support = {//International Centre for Diarrhoeal Disease Research, Bangladesh/ ; //Government of Bangladesh/ ; //Global Affairs Canada/ ; }, mesh = {Bangladesh ; *Floods ; *Bacteria/genetics/drug effects/isolation &amp; purification/classification ; Anti-Bacterial Agents/pharmacology ; Metagenomics ; *Drug Resistance, Bacterial/genetics ; Virulence Factors/genetics ; Drug Resistance, Multiple, Bacterial/genetics ; *Water Microbiology ; }, abstract = {Seasonal flooding in Bangladesh poses severe public health risks through waterborne disease, yet a comprehensive, genomic-level understanding of the associated microbial hazards is lacking. This study presents a comprehensive shotgun metagenomic analysis of floodwaters from four districts of Bangladesh (Cumilla, Feni, Lakshmipur, and Noakhali) during the devastating 2024 floods, profiling the distribution of pathogenic bacteria, antimicrobial resistance genes, and virulence factors. A total of 12 samples were collected during peak flooding periods and processed using Illumina sequencing. Taxonomic profiling and resistome analysis were performed using MetaPhlAn4, ABRicate, and MEGAHIT, referencing the NCBI and CZ ID databases. Across all regions, 301 operational taxonomic units were identified. Feni exhibited the highest diversity of pathogenic species, including multidrug-resistant Klebsiella pneumoniae, toxigenic Pseudomonas aeruginosa, and mobilizable resistance plasmids (e.g., IncP1, Col440I). Noakhali samples revealed co-detection of zoonotic and emerging pathogens such as Aliarcobacter spp. and Streptococcus suis, along with key resistance genes like blaOXA and ermB. Microbial community clustering revealed strong spatial heterogeneity. This study provides genomic evidence that floodwaters harbour emerging pathogens and AMR. It strongly advocates for incorporating metagenomic tools into Bangladesh's national flood response and AMR monitoring frameworks.}, }
@article {pmid41260473, year = {2025}, author = {Dyukova, K and Paloyan, A and Khoyetsyan, L and Mkhitaryan, A and Antranikian, G and Hambardzumyan, A}, title = {Characterization of thermostable β-glucosidase immobilized on linen fabric.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2025-27014}, pmid = {41260473}, issn = {1525-3198}, abstract = {In this study, a thermostable β-glucosidase derived from a hot spring metagenome was successfully immobilized on linen fabric to create an eco-friendly and reusable biocatalyst for lactose hydrolysis. The enzyme is derived from a metagenome of the high-temperature Pisciarelli hot springs, an extreme environment known to yield robust biocatalysts with industrial relevance. Two immobilization strategies were employed: direct covalent binding (Lf-β-glucosidase) and binding via a spacer arm (LfEG-β-glucosidase). The latter exhibited superior enzymatic performance, retaining 76.6% of its initial activity and demonstrating enhanced thermal and operational stability. Both free and immobilized forms of enzyme showed similar pH and temperature optima, with the immobilized form exhibiting significantly improved long-term thermostability and storage stability-retaining full activity after 1 yr at 4°C. The LfEG-β-glucosidase biocatalyst was effectively applied in the enzymatic treatment of cheese whey, retaining 90% activity after 15 reuse cycles, yielding more than 6.4 g of glucose. These findings highlight the promising use of biodegradable, low-cost linen fabric as a carrier for thermostable enzymes in food biotechnology. The high efficiency and reusability of the developed biocatalyst offer a compelling solution for lactose hydrolysis and valorization of dairy industry by-products, particularly whey, within a circular and environmentally conscious production model.}, }
@article {pmid41260470, year = {2025}, author = {Dilireba, E and Lu, Q and Chang, L and Luo, F}, title = {Antibiotic resistance profile and molecular mechanism of enterococci in traditional fermented yogurts.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2025-27212}, pmid = {41260470}, issn = {1525-3198}, abstract = {Enterococci are present in traditional fermented foods, but their potential role as reservoirs of antibiotic resistance and virulence genes has raised concerns about food safety. To evaluate the prevalence of antibiotic-resistant enterococci in traditional fermented yogurt, microbial sequencing and culture methods were used to analyze the microbiota and Enterococcus composition in a total of 75 yogurts from Xinjiang Uygur Autonomous Region (Xinjiang, China). Enterococcus faecium and Enterococcus durans were the predominant enterococcal species and belonged to 20 and 5 biotypes, respectively, according to randomly amplified polymorphic DNA PCR analysis. Antibiotic resistance testing revealed that 98.92% of Enterococcus strains were resistant to at least one kind of antibiotic, of which E. faecium showed high resistance to gentamicin (96.92%), erythromycin (55.38%), and ciprofloxacin (49.23%), whereas E. durans was most resistant to tetracycline (58.82%) and chloramphenicol (55.82%), followed by gentamicin (47.06%). Multidrug-resistant strains were more abundant in E. faecium (37.3%). Furthermore, vancomycin resistance was observed in E. faecium strains, highlighting the risk of resistance spread. Molecular analysis revealed vancomycin and tetracycline resistance phenotypes were consistent with genotypes, but not for penicillin, gentamicin and erythromycin. Moreover, mobile genetic elements were detected, such as 5'ococs/3'ococs and IntI3, which facilitate gene transfer. Metagenomic sequencing further revealed the high abundance of antibiotic resistance genes, such as mlaF, macB, and ImrD. Additionally, the microbial co-occurrence network analysis revealed significant positive correlations between E. faecium and Acetobacter in the Zhaosu region. This study highlights that traditional fermented yogurt may serve as a reservoir for multidrug-resistant enterococci, posing a potential risk to public health.}, }
@article {pmid41161417, year = {2025}, author = {Mussert, CMA and Miesbach, W and Chowdary, P and Lillicrap, D and Mahlangu, J and Peyvandi, F and Pipe, SW and Srivastava, A and Voorberg, J and Pierce, GF and Kaczmarek, R and Batty, P and Cutica, I and Nathwani, A and Leebeek, FWG}, title = {A comprehensive care pathway of gene therapy for hemophilia based on current guideline documents and summary of product characteristics: communication from the ISTH SSC working group on gene therapy.}, journal = {Journal of thrombosis and haemostasis : JTH}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jtha.2025.09.041}, pmid = {41161417}, issn = {1538-7836}, abstract = {BACKGROUND: Gene therapy for hemophilia has recently been implemented as standard clinical care, requiring organizational and multistakeholder preparedness and clear guidelines. In addition to pharmaceutical summaries of product characteristics (SMPCs), various (inter)national guidance documents have been published. However, no guidance document or SMPC covers the entire gene therapy care pathway.<br><br>OBJECTIVES: This study provides a complete and comprehensive overview of current guidance documents and SMPCs to develop a comprehensive care pathway for hemophilia gene therapy delivery.<br><br>METHODS: Published gene therapy guidance documents and collected SMPCs were complemented by a selective search in online databases, including PubMed and scientific societies' websites. Reference lists were checked for additional relevant articles.<br><br>RESULTS: Four SMPCs and 11 (inter)national guidance documents and recommendations were collected. The documents were focused on either the intervention or the care pathway, and none were comprehensive covering all aspects of hemophilia gene therapy delivery. Considerable differences were found between the 2 approved gene therapy products and between the SMPCs issued by the 2 regulatory authorities, the Food and Drug Administration and the European Medicines Agency. (Inter)national guidance documents provided additional information and recommendations not covered in SMPCs.<br><br>CONCLUSION: Based on SMPCs and (inter)national guidance documents and recommendations a care pathway has been developed and visualized in a Metro Map. This provides a clear and comprehensive overview of all activities, contact moments, and responsibilities within the longitudinal gene therapy treatment process. This comprehensive care pathway may help navigate gene therapy implementation, providing guidance to clinicians, patients, and caregivers.}, }
@article {pmid41260397, year = {2025}, author = {Abbasi, E}, title = {Metagenomic Surveillance of Emerging Viruses in Mosquito Populations from High-Risk Regions of Iran.}, journal = {Journal of virological methods}, volume = {}, number = {}, pages = {115301}, doi = {10.1016/j.jviromet.2025.115301}, pmid = {41260397}, issn = {1879-0984}, abstract = {BACKGROUND: Mosquito-borne arboviruses pose a growing threat to public health, particularly in ecologically vulnerable and climatically dynamic regions. This study aimed to investigate the diversity of emerging arboviruses in mosquito populations from high-risk provinces in southern and southeastern Iran using a metagenomic surveillance approach.<br><br>METHODS: Adult mosquitoes were collected from 36 sites across Hormozgan, Sistan and Baluchestan, and Khuzestan provinces. Specimens were pooled by species and location, followed by RNA extraction and high-throughput sequencing. Bioinformatics analysis was performed to identify viral taxa and assess phylogenetic relationships.<br><br>RESULTS: A total of 4275 mosquitoes representing six species were analyzed. Virome analysis revealed 43 viral taxa, including medically important arboviruses such as dengue virus serotype 2 (DENV-2), chikungunya virus (CHIKV), and West Nile virus (WNV). Multiple novel viral sequences were also detected, including putative members of Phenuiviridae and Orthomyxoviridae. Viral diversity was highest in Hormozgan province and positively correlated with ambient temperature.<br><br>CONCLUSION: This study provides the first comprehensive metagenomic insight into mosquito viromes in Iran, revealing both endemic and potentially novel arboviruses. These findings underscore the need for integrated genomic surveillance and regional vector-borne disease preparedness.}, }
@article {pmid41260377, year = {2025}, author = {Chen, Z and Zhu, S and Gao, S and Wu, H and Tian, S and Wen, X}, title = {Fe3O4-Enhanced continuous production of medium-chain fatty acids from Sludge: Metagenomic Perspective on microbial synergy.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {133673}, doi = {10.1016/j.biortech.2025.133673}, pmid = {41260377}, issn = {1873-2976}, abstract = {Fe3O4 exhibits promising potential in enhancing chain elongation (CE) for medium-chain fatty acids (MCFAs) production from sludge, yet its application in continuous flow processes remains underexplored. In this study, MCFAs were continuously produced from sludge via a Fe3O4-enhanced CE process. Optimal performance was achieved with 20 g/L Fe3O4, 5.8 g COD/L/d ethanol loading rate (ELR), and 3-day hydraulic retention time (HRT), yielding 11.4 ± 0.8 g COD/L MCFAs and a production rate of 3.7 ± 0.1 g COD/L/d. n-Caproate and n-caprylate accounted for 40.9 % and 54.4 % of total MCFAs, respectively. Fe3O4 addition halved CE start-up time and increased MCFA production fourfold. Metagenomic analysis identified Clostridium kluyveri, Petrimonas sp., Alcaligenes faecalis, Proteiniphilum acetatigenes, and Anaerosalibacter sp. as biomarkers enhancing the fatty acid biosynthesis (FAB) cycle. These taxa could increase malonyl-ACP availability, improve reductive reaction efficiency, and promote acetyl-CoA generation, facilitating a streamlined microbial community with Pseudomonas caeni. This investigation offers strategic insights and data support for the high-value utilization of excess sludge.}, }
@article {pmid41260374, year = {2025}, author = {Zhang, Q and Lin, L and Hu, T and Liu, Q and Wang, Y and Mo, H and Jin, W and Zhang, W and Chen, J and Zeng, H and Wang, X and Chen, S and Zhang, Y}, title = {Nitrogen removal driven by zonal supply of thiosulfate and pyrite in an up-flow blanket filter (UBF) reactor.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {133677}, doi = {10.1016/j.biortech.2025.133677}, pmid = {41260374}, issn = {1873-2976}, abstract = {Despite its effectiveness in nitrogen removal, the anammox process faces challenges in practical applications due to NO3[-]-N accumulation, which can lead to effluent breaches of discharge standards. This study developed a single-stage up-flow blanket filter (UBF) reactor featuring three axially stratified functional zones with multi-point supplementation of thiosulfate and pyrite. During stable operation, the high-intensity anammox layer (L1) contributed to 82.3 % of total nitrogen (TN) removal and generated alkalinity to support subsequent sulfur autotrophic denitrification (SAD). The SAD-coupled anammox layer (L2) effectively removed accumulated NO3[-]-N, reducing TN from 42.8 mg/L to 25.2 mg/L. The advanced nitrogen removal layer (L3) further polished the effluent to a TN concentration of 4.3 ± 2.8 mg/L and a pH of 7.1 ± 0.1, achieving advanced nitrogen removal and pH self-regulation. Anammox bacteria exhibited an inhibition-recovery response to thiosulfate addition, while pyrite served a triple role as a filter medium, metabolic accelerator, and electron donor. Metagenomic analysis revealed that thiosulfate supplementation selectively enrichedThiobacillusandPFJX01in each functional zone, with denitrification gene abundance increasing along the reactor's height. Notably, functional and associated microorganisms showed layer-specific gene expression and co-metabolism patterns. Even within the same genus, differential gene regulation in response to local microenvironments drove functional divergence at the genetic level. In summary, this work innovatively establishes spatially segregated functional layers within a single UBF reactor, offering a novel low-carbon strategy for advanced nitrogen removal and facilitating the resource utilization of tailings.}, }
@article {pmid41260114, year = {2025}, author = {Ahmad, W and Ray, R and Khan, AL}, title = {Can silicate types regulate plant defense and rhizospheric microbiome diversity differently during heat stress conditions?.}, journal = {The Science of the total environment}, volume = {1007}, number = {}, pages = {180812}, doi = {10.1016/j.scitotenv.2025.180812}, pmid = {41260114}, issn = {1879-1026}, abstract = {Silicates (Si) improve plant growth; however, how different types of silicate sources influence plant growth and rhizosphere microbiome remains underexplored. We compare two Si types (pure and bioavailable silicic acid (Si) and mineral magnesium silicate (MgSi)) applied to the soybean (Glycine max L.) rhizosphere to determine whether two silicate types (Si-types) differently impact plant growth, defense responses, and microbiome diversity and function during heat stress. Under heat stress, Si-type treatments improved biomass (86 % with Si and 82 % with MgSi), reduced H2O2 (26 % phyllosphere; 33 % rhizosphere), and enhanced β-glucosidase activity (2.6-fold rhizosphere) compared to heat-only treatment and increased Proteobacteria relative abundance from ∼65 % (heat-only) to ∼74 % in Si-type-treated rhizospheric soil. Si-types showed downregulation of heat shock transcription factors, suggesting regulatory defense effects during heat stress. Metagenome-assembled genomes (MAGs) analysis revealed significant bacterial shifts across the Si-treatments, with Proteobacteria and Bacteroidetes being the dominant phyla in the rhizospheric soil. Under heat stress, the core microbiome comprised 14 rhizosphere genera (including Pelomonas, Achromobacter, Paracoccus, Nocardioides), whereas Pelomonas was the sole core root genus, and Pelomonas puraquae core species in both compartments. MAGs analysis revealed Si-based shifts in microbial metabolic pathways and enrichment of auxin biosynthesis in Si-treated roots during heat stress. Because MgSi supplies both Mg and Si, effects observed with MgSi are interpreted as combined Si + Mg effects. In conclusion, both Si-types caused shifts in microbiome diversity and function, and impacted plant growth and defense responses under heat stress, providing a foundation for improving thermotolerance in plants.}, }
@article {pmid41260011, year = {2025}, author = {Wang, J and Zhao, S and Shi, X and Sun, B and Tian, Z and Zhang, H and Zhao, Y and Cui, Z and Zhang, J}, title = {Dynamic succession patterns, nitrogen cycling potential, and multi-scale assembly mechanisms of cross-habitat bacterial communities in lakes driven by seasonal frozen conditions.}, journal = {Marine pollution bulletin}, volume = {223}, number = {}, pages = {119004}, doi = {10.1016/j.marpolbul.2025.119004}, pmid = {41260011}, issn = {1879-3363}, abstract = {Microorganisms are key bioindicators of aquatic environment, yet their dynamics under seasonal ice cover-affecting 50 % of global lakes-remain poorly understood. This study comprehensively employed metagenomics and bioinformatics to analyze the diversity characteristics, species composition, nitrogen cycling potential, and community assembly mechanisms of bacterial communities during frozen and non-frozen periods. Results showed that bacterial species richness and diversity in water were significantly higher during the frozen period compared to the non-frozen period, with both metrics consistently higher in water than in sediment. In winter, ice formation significantly reshaped the bacterial community structure in water, while exerting no notable disturbance on the sediment bacterial community composition. Freezing exerts contrasting regulatory effects on the primary nitrogen cycling functions of bacterial communities in the water column versus the sediments. In the water column, the potential of ammonia assimilation is significantly suppressed during freezing, whereas mineralization and assimilatory nitrate reduction to ammonium persist. In contrast, within the sediments, ice cover generally enhances the activity of major nitrogen transformation pathways, including ammonia assimilation, mineralization, and nitrification. Notably, sediment nitrogen fixation potential is nearly four times higher in non-frozen periods compared to frozen periods. Stochastic processes dominate bacterial community assembly, while the freezing process shifts the dominant role from drift to dispersal limitation. However, in deterministic processes, heterogeneous selection serves as a key regulatory factor. The study revealed the adaptive strategies of bacterial communities to freezing in shallow lakes of cold-arid regions, providing a theoretical basis for ecological risk prediction in frozen lakes and ecological management of shallow lakes in cold-arid regions.}, }
@article {pmid41259923, year = {2025}, author = {Wang, YC and He, LY and Wu, DL and Gao, FZ and Liu, YS and Ying, GG}, title = {Long-term manure applications promote persistent antibiotic resistance in soil.}, journal = {Journal of hazardous materials}, volume = {500}, number = {}, pages = {140476}, doi = {10.1016/j.jhazmat.2025.140476}, pmid = {41259923}, issn = {1873-3336}, abstract = {Manure application has the potential to influence soil microbial composition and the antibiotic resistome; however, its long-term effects remain largely unknown. This study investigated the prolonged impacts of manure applications (pig and chicken manure/compost) on soil antibiotic resistance over a two-year period. Compared with the control (51.9-85.1 ng/g), manure-amended soils contained markedly higher antibiotic concentrations (356-26100 ng/g), remaining 4-300 times higher after 730 days, especially in pig compost treatments. The abundances of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in amended soils (4.48 × 10[8]-2.74 × 10 [12] copies/g) consistently exceeded those in controls (1.24 × 10[7]-6.10 × 10[7] copies/g). Notably, 62.5 % of ARGs were located on plasmid-associated contigs, and high-risk genes such as floR and aph(3')-III persisted throughout incubation. Elevated MGE levels after 730 days indicated sustained horizontal gene transfer (HGT) potential under antibiotic selection pressure. Overall, these results reveal the long-lasting enrichment of ARGs and highlight the need for improved manure management and long-term.}, }
@article {pmid41259914, year = {2025}, author = {Yang, W and Wang, X}, title = {Transmission mechanisms and risk tracing of antibiotic resistance genes in rivers driven by wastewater inputs.}, journal = {Journal of hazardous materials}, volume = {500}, number = {}, pages = {140523}, doi = {10.1016/j.jhazmat.2025.140523}, pmid = {41259914}, issn = {1873-3336}, abstract = {Aquatic environments are critical for ARG dissemination, yet contributions from different wastewater sources, dominant HGT mechanisms, and residual risks in natural waters remain unclear. Based on 863 metagenomic samples across China, we systematically analyzed wastewater inputs, HGT mechanisms, and risks of riverine ARGs. Wastewater treatment plants were the primary source, contributing about 50 % of riverine ARGs. Conjugation dominated ARG transfer, primarily via F-type type IV secretion systems. High-transmission plasmids were widespread. Although phage-mediated transduction represented only 3 % of HGT, it facilitated cross-environmental spread of clinically significant blaGES-18. Metagenome-assembled genomes revealed 78 % of resistant bacteria belonged to Pseudomonadota; 42 % co-harbored virulence factors. Phylogenetic analysis showed high inter-generic mobility of sul1/sul2, explaining their environmental persistence. Overall risk in rivers decreased by 44 % - 93 % compared to wastewaters. However, Acinetobacter carrying blaOXA and Cellvibrio sp002483145 carrying blaKHM-1 were phylogenetically close to Acinetobacter baumannii and Pseudomonas aeruginosa, indicating potential pathways toward key pathogens. Our study identifies wastewater as the main source of riverine ARGs, reveals conjugation as the primary transmission mechanism with transduction playing a secondary role, and demonstrates that high-risk ARGs can still spread to pathogenic bacteria in rivers. These findings are crucial for developing effective strategies to mitigate ARG risks.}, }
@article {pmid41259660, year = {2025}, author = {Wahl, NA and Koutsovoulos, G and Bettisworth, B and Stamatakis, A}, title = {Raxtax: A k-mer-based non-Bayesian Taxonomic Classifier.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btaf620}, pmid = {41259660}, issn = {1367-4811}, abstract = {MOTIVATION: Taxonomic classification in biodiversity studies is the process of assigning the anonymous sequences of a marker gene (barcode) or whole genomes (metagenomics) to a specific lineage using a reference database that contains named sequences in a known taxonomy. This classification is important for assessing the diversity of biological systems. Taxonomic classification faces two main challenges: first, accuracy is critical as errors can propagate to downstream analysis results; and second, the classification time requirements can limit study size and study design, in particular when considering the constantly growing reference databases. To address these two challenges, we introduce raxtax, an efficient, novel taxonomic classification tool for barcodes that uses common k-mers between all pairs of query and reference sequences. We also introduce two novel uncertainty scores which take into account the fundamental biases of reference databases.<br><br>RESULTS: We validate raxtax on three widely used empirical reference databases and show that it is 2.7-100 times faster than competing state-of-the-art tools on the largest database while being equally accurate. In particular, raxtax exhibits increasing speedups with growing query and reference sequence numbers compared to existing tools (for 100,000 and 1,000,000 query and reference sequences overall, it is 1.3 and 2.9 times faster, respectively), and therefore alleviates the taxonomic classification scalability challenge.<br><br>raxtax is available at https://github.com/noahares/raxtax under a CC-NC-BY-SA license. The scripts and summary metrics used in our analyses are available at https://github.com/noahares/raxtax_paper_scripts. The source code, sequence data and summarized results of the analyses are available at https://doi.org/10.5281/zenodo.15057027.}, }
@article {pmid41259558, year = {2025}, author = {Issilbayeva, A and Jarmukhanov, Z and Kozhakhmetov, S and Bakytgul, Y and Chulenbayeva, L and Muniz-Terrera, G and Furukawa, M and Nikawa, H and Supiyev, A and Kushugulova, A and Zhumadilova, A}, title = {Oral microbiome patterns of dental caries in Kazakhstani adolescents.}, journal = {Journal of applied oral science : revista FOB}, volume = {33}, number = {}, pages = {e20250476}, doi = {10.1590/1678-7757-2025-0476}, pmid = {41259558}, issn = {1678-7765}, mesh = {Humans ; *Dental Caries/microbiology ; Adolescent ; Male ; *Microbiota/genetics ; Female ; Child ; RNA, Ribosomal, 16S/genetics ; *Mouth/microbiology ; DMF Index ; Reference Values ; }, abstract = {OBJECTIVE: The oral microbiome is one of the most complex microbial ecosystems in the host. This study aimed to investigate and characterize the oral microbiome composition in Kazakhstani adolescents associated with dental caries.<br><br>METHODOLOGY: The study included 312 adolescents, with 241 individuals presenting with caries and 71 caries-free, aged 12-15 years. Dental caries assessment was performed using DMFT (Decayed, missed, filled teeth) index. Oral samples were collected, and 16S rRNA (16S ribosomal ribonucleic acid) gene sequencing targeting the V3-V4 hypervariable regions on an Illumina MiSeq platform was performed to profile the microbial communities. Functional metagenomic predictions were generated using PICRUSt2 v2.5.0, using the KEGG database for bacterial pathway abundance estimation. Data analysis was conducted using Python 3.9.16 and R 4.2.2.<br><br>RESULTS: The alpha diversity was insignificant, while beta diversity analysis demonstrated clear distinctions by Bray-Curtis (F=2.5, p=0.003) and weighted UniFrac distances (F=4.4, p=0.002). The Neisseria and Prevotella genera, and Gammaproteobacteria class showed significant associations with dental caries (MaAsLin2 p&#x2264;0.05, LDA&#x2265;2), stronger predictive power (AUC=0.65, F1=0.83), and higher predicted functional activity through glutathione metabolism, RNA degradation, and unsaturated fatty acid metabolism pathways.<br><br>CONCLUSIONS: This study identified specific oral microbiome patterns associated with dental caries in Kazakhstani adolescents, revealing interactions between key bacterial taxa and metabolic pathways.}, }
@article {pmid41258718, year = {2025}, author = {Markkanen, M and Pezzutto, D and Virta, M and Karkman, A}, title = {Sulfonamide resistance gene sul4 is hosted by common wastewater sludge bacteria and found in various newly described contexts and hosts.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0085725}, doi = {10.1128/spectrum.00857-25}, pmid = {41258718}, issn = {2165-0497}, abstract = {UNLABELLED: The introduction of the first broad-spectrum antibiotics, sulfonamide drugs, fundamentally revolutionized medicine in the 1930s. Shortly after, and ever since, sulfonamide resistance genes (sul genes) have been widely detected. Still, the most recent variant of these genes, sul4, was first described only in 2017, and its host range and transmission mechanisms are still largely unknown. Here, we applied PacBio long-read metagenomic sequencing and bacterial methylation signals to investigate the genetic contexts and bacterial carriage of the sul4 gene in wastewater. Furthermore, we extended our description of sul4 carriers to previously published data sets. Our results indicate that sul4 is prominently found in sludge and hosted by various bacteria, such as the species from the phyla Myxococcota and Chloroflexota and genera Trichlorobacter and Desulfobacillus, which are commonly found in activated sludge. Additionally, according to our results, sul4 has already spread into multiple strains of opportunistic human pathogens, such as Aeromonas and Moraxella, in addition to the previously described Salmonella. The sequence region flanking sul4 included a truncated folK gene and an ISCR28 element and exhibited a high degree of conservation across the investigated sequences. Furthermore, the module was associated with various integron integrase genes. Also, other mobility-related elements that could further increase the likelihood of sul4 mobilization were detected. Altogether, our results describing the sul4 hosts of bacteria from distant lineages indicate the efficient mobility of sul4 by genetic elements that traverse both clinical and environmental bacteria. Finally, we suggest that wastewater may provide favorable conditions for such horizontal gene transfer events.<br><br>IMPORTANCE: Antibiotic resistance is an ancient phenomenon and a common trait of many environmental bacteria. However, human activities in the post-antibiotic era, coupled with the bacteria's ability to exchange genetic material across different lineages, have drastically increased the spread of resistance traits among bacteria from various niches. The primary concern is the resistance genes encoded by infections causing pathogens, already causing over 1 million deaths annually and indirectly contributing to nearly 4 million more. Therefore, understanding the bacteria that harbor ARGs and the genetic mechanisms driving their mobilization is crucial for understanding the dynamics and emerging trends of resistance. Here, we focus on revealing these crucial aspects of the newly discovered sulfonamide resistance gene, sul4. Given the limitations of the metagenomic approach in linking the functional genes to their host genomes, the significance of our research lies in our workflow, which allows this linkage through the identification of shared methylation profiles.}, }
@article {pmid41258716, year = {2025}, author = {Marsh, CC and Nel Van Zyl, K and Babalola, OO and Böhmer, R and Cowan, DA and Moganedi, KLM and Moroenyane, I and Naidoo, J and Nieves Delgado, A and Posma, JM and Segal, LN and Setati, ME}, title = {From description to implementation: key takeaways from the 3rd African Microbiome Symposium.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0068325}, doi = {10.1128/msphere.00683-25}, pmid = {41258716}, issn = {2379-5042}, abstract = {The 3rd African Microbiome Symposium was held in Cape Town, South Africa, from 20 to 22 November 2024. The symposium featured a diverse range of local and international microbiome research and provided a platform for 79 researchers, students, and industry members to engage in discussions on the microbiome within an African context and focusing on translational research. This meeting review shares highlights, findings, and recommendations derived from the event. Insights from two panel discussions revealed key barriers to microbiome research in Africa, including limited funding, infrastructure gaps, and a shortage of trained local scientists. Recommendations centered on increased investment, institutional training, adherence to ethical guidelines, and the fostering of equitable global partnerships.}, }
@article {pmid41258552, year = {2025}, author = {Singh, G and Tyagi, I and Tyagi, K and Kumar, V and Donthu, RK}, title = {Multi-marker metagenomic assessment of eukaryotic communities in Najafgarh Drain reveals public health and ecological risks.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {12}, pages = {1354}, pmid = {41258552}, issn = {1573-2959}, support = {core funding//Zoological Survey of India/ ; }, mesh = {*Environmental Monitoring/methods ; Public Health ; *Eukaryota/classification/genetics ; RNA, Ribosomal, 18S/genetics ; Metagenomics ; *Metagenome ; Biodiversity ; }, abstract = {A multi-marker sequencing approach was applied to characterize the eukaryotic microbial community of the Najafgarh Drain. It will provide the first comprehensive view of eukaryotic diversity in this system, highlighting both its ecological significance and pathogenic potential. We combined 18S rRNA, internal transcribed spacer (ITS), and whole-metagenome shotgun (WMS) sequencing; 18S rRNA captured broad protist diversity but offered limited fungal resolution, which was complemented by ITS, while WMS provided higher, often species level resolution across kingdoms. To improve WMS classification, a dual-database strategy was employed, sequences were first classified using a eukaryote-filtered NCBI clustered nr database, unclassified sequences were subsequently analyzed with a combined database comprising of SILVA, MIDORI2, PlantITS, and COInr. This approach consistently increased the number of identified genera and species compared with using a single database. Using the multi-marker and dual database approach, multiple phyla were detected, including Chlorophyta (55.72%), Ciliophora (21.46%), Ascomycota (6.44%), Mucoromycota (1.35%), and Nematoda (0.80%). Beneficial taxa such as Chlorella, members of Ciliophora, and Penicillium, known for organic-matter degradation, nutrient cycling, and heavy-metal remediation, were observed. Additionally, human pathogens such as Pneumocystis jirovecii, Rhizopus arrhizus and Trichuris trichiura along with plant pathogenic fungi such as Fusarium, Sporisorium, and Rhizopus were also observed. These findings underscore the need to incorporate eukaryotic pathogen surveillance into water quality monitoring and environmental policy frameworks. Such measures would contribute to more resilient water management practices and support broader public health protection goals.}, }
@article {pmid41258495, year = {2025}, author = {Gutiérrez-Sarmiento, W and Fosado-Mendoza, M and Lozano-Flores, C and Varela-Echavarría, A}, title = {The Body Wall Microbiome of the Terrestrial Slug Deroceras laeve Reveals Potential Endosymbionts and Shares Core Organisms with Other Mollusks.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02652-8}, pmid = {41258495}, issn = {1432-184X}, support = {CBF2023-2024-834//SECIHTI/ ; IN211322//DGAPA-UNAM PAPIIT/ ; }, abstract = {The marsh slug Deroceras laeve is an invasive mollusk found in gardens, field crops, and wetlands. It lacks a protective shell, suggesting that microbial communities are associated with its adaptability to the environment. Here, we used a whole shotgun metagenomic approach to analyse the complex microbiome of D. laeve and compared it to that of other mollusks. This demonstrated the presence in D. laeve of bacteriophages such as Erwinia phage, Certrevirus, and Machinavirus, which target plant pathogen bacteria. In the Archaea domain the halophilics Halovivax and Halobaculum predominated, but also present were the methanogens Methanobacterium, Methanobrevibacter, Methanocaldococcus, Methanococcus, and Methanosarcina, involved in phosphate solubilization and methanogenesis during decomposition of organic matter. The Bacteria domain was dominated by γ-Pseudomonadota such as Buttiauxella, Citrobacter, Enterobacter, Klebsiella, Kluyvera, Leclercia, and Pseudomonas which are producers of enzymes that degrade biomass and complex carbohydrates. Regarding the fungal community, filamentous or yeast ascomycetes predominated such as Debaryomyces, Puccina, and Pyricularia known as plant pathogens or associated with decaying organic matter. Consistent with these findings, functional analysis revealed enrichment in genes involved in fermentation and carbohydrate metabolism. Remarkably, regardless of species, ecosystem, and tissue type, we found that the core microbiome of the mollusks in this study is mainly structured by the Phyla Uroviricota, Euryarchaeaota, Pseudomonadota, and Ascomycota, with diversity at the genus level. This suggests ancient symbiotic interactions of these mollusks with specific types of microbes which may have been critical for adaptability to their environment.}, }
@article {pmid41258468, year = {2025}, author = {Bui, HT and Bui, ATP and Ngo, HT and Ngo, XT and Nguyen, HT and Nguyen, AH and Tran, VC and Pham, TD and Nguyen, ATV}, title = {Vaginal-spray Bacillus spore probiotics as a potential treatment and reducing recurrence of bacterial vaginosis: randomized, double-blind, and controlled pilot study.}, journal = {Communications medicine}, volume = {}, number = {}, pages = {}, doi = {10.1038/s43856-025-01236-4}, pmid = {41258468}, issn = {2730-664X}, abstract = {BACKGROUND: Bacterial vaginosis (BV) is a common vaginal disorder characterized by reduced beneficial species and overgrowth of pathogens. Probiotics, especially direct vaginal sprays, offer a promising alternative to antibiotics by restoring healthy vaginal microbiota, relieving symptoms, and preventing recurrence.<br><br>METHODS: We conducted a clinical trial (ClinicalTrials.gov: NCT06165354; 8/12/2023) to evaluate the effectiveness of the vaginal-spray probiotic LiveSpo X-Secret, containing Bacillus subtilis, B. clausii, and B. coagulans spores (&#x2265;1 billion CFU/mL). A total of 120 women were randomized equally into Control and X-Secret groups at Bac Ninh CDC. Outcomes were assessed at day 7 (end of standard treatment) for symptom resolution and day 28 (21 days post-treatment) for recurrence. Both Per-Protocol and Intention-to-Treat analyses were performed to assess efficacy and account for attrition.<br><br>RESULTS: Here we show that no adverse events occur in either group. Compared to the Control, the X-Secret group exhibits a faster reduction in BV symptoms (odor, discharge, pH >4.5, and itching) by days 7 and 28, with odds ratios at day 28 of 3.61, 4.87, 2.95, and 3.34, respectively. Vaginal swab analysis reveals a 3.7-225.3-fold greater reduction in Gardnerella vaginalis. By day 28, metagenomic profiling indicates increases in beneficial species Lactobacillus crispatus (3.71-fold) and Streptococcus salivarius (from non-detectable to 2.1%), along with reductions in harmful species G. vaginalis (14.29-fold) and Sneathia sanguinegens (806-fold).<br><br>CONCLUSIONS: The vaginal-spray Bacillus spore probiotic (LiveSpo X-Secret) provides a safe, convenient, and effective approach for BV treatment and reducing recurrence, supporting its potential as an adjunctive therapy for maintaining vaginal health.<br><br>CLINICAL TRIAL NUMBER: ClinicalTrials.gov NCT06165354, first posted 8/12/2023.}, }
@article {pmid41258374, year = {2025}, author = {Aydin, E and Karaynir, A and Ozkan, RG and Bozdogan, B}, title = {Metagenomic analysis of bacteriome and phageome of wastewater from a ceramic factory in Türkiye.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, pmid = {41258374}, issn = {1618-1905}, abstract = {Bacteriophages are major determinants of bacterial community dynamics. Industrial wastewaters constitute distinctive microbe-phage ecosystems shaped by heavy-metal and chemical stressors, yet they remain sparsely characterized by metagenomics. Most existing studies focus on municipal or hospital wastewaters, while phage and bacteriome communities in industrial effluents such as ceramic wastewater are largely unexplored. This study aimed to comprehensively characterize bacterial and phage communities in influent and effluent samples from a ceramic factory using metagenomic approaches. Phage DNA was sequenced on an Illumina NextSeq and processed with a standard bioinformatics pipeline for taxonomic and functional annotation. Of 657 million raw reads, 66% mapped to phage sequences. Caudovirales predominated, with Autographiviridae comprising 59% of classified viral reads. Functional annotation indicated that 64% of assigned genes encoded structural or replication functions. For the bacteriome, 16 S rRNA (V3-V4) amplicons were sequenced on an Illumina NovaSeq 6000 and classified with Kraken2. Proteobacteria dominated both sample types, but community structure shifted along the treatment line: the influent was enriched in environmental-water genera-Flavobacterium (25%), Aeromonas (16%), and Acinetobacter (11%) -whereas the effluent was dominated by Flavobacterium (37%), Hydrogenophaga (25%), and Rhodoferax (14%). Genus-level richness contracted from 228 (influent) to 67 (effluent), and the number of reads entering taxonomic classification declined sharply (1,482,914 vs. 55,847), consistent with selective removal and physicochemical filtering during treatment. Collectively, these results demonstrate that ceramic wastewater harbors a distinct microbe-phage ecosystem molded by chemical and particulate stress. By illuminating an understudied industrial niche, this work provides actionable insights for wastewater treatment, environmental bioremediation, and microbial risk assessment.}, }
@article {pmid41258115, year = {2025}, author = {Yepes-García, J and Novoa-Montenegro, N and Otero-Jiménez, V and Uribe-Vélez, D and Barreto-Hernández, E and Falquet, L}, title = {Genome-Resolved Metagenomics of Rice Straw Degradation Experiments in Colombian Fields.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1823}, pmid = {41258115}, issn = {2052-4463}, mesh = {*Oryza ; Colombia ; Metagenomics ; *Metagenome ; *Soil Microbiology ; Bacillus/genetics ; Agriculture ; Fermentation ; }, abstract = {Extensive rice harvesting yields more than 800 million tons of rice straw (RS) per year globally, generating a byproduct that is often difficult for farmers to manage efficiently without burning it. In the quest for enhanced RS degradation systems, we recovered 146 Metagenome-Assembled Genomes (MAGs) from experiments aiming at decomposing RS. Such assays included the application of a Bacillus strain, a Trichoderma-based commercial product, organic and inorganic compounds in different combinations during a solid-state fermentation in Colombian rice fields. The set of MAGs comprises 30 MAGs from bulk soil and 116 MAGs from RS surface, for which taxonomic classification indicates that 67% of them may constitute novel taxa. Furthermore, functional analysis through different approaches suggests the presence of both mid-quality and high-quality MAGs with potential to biotransform RS within this dataset. Finally, these MAGs represent a valuable resource for exploring uncharacterized microbial diversity in Colombian agricultural ecosystems.}, }
@article {pmid41258100, year = {2025}, author = {Wang, C and Zheng, R and Sun, C}, title = {Deep-sea viral diversity and their role in host metabolism of complex organic matter.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {10134}, pmid = {41258100}, issn = {2041-1723}, mesh = {*Seawater/virology/microbiology ; *Viruses/genetics/classification/metabolism ; Virome/genetics ; Metagenomics ; Geologic Sediments/virology/microbiology ; *Host Microbial Interactions ; Genome, Viral ; Oceans and Seas ; Ecosystem ; RNA Viruses/genetics/classification ; Microbiota ; Biodiversity ; Carbon Cycle ; Transcriptome ; }, abstract = {Viruses exert a pervasive influence on biogeochemical cycles in deep-sea ecosystems. Cold seeps and seamounts, globally distributed across the oceans and harboring diverse microbial communities, remain largely unexplored regarding their viral inhabitants and functions. By integrating metagenomic, DNA viromic, RNA viromic, and metatranscriptomic data, coupled with characterization of purified viral communities, we uncover the diversity of DNA and RNA viral communities and virus-host interactions, which vary significantly across distinct deep-sea sediment sites. These sites represent a declining cold seep, a site distant from the declining cold seep (sediment site), a nascent cold seep site, and a seamount. The viral community in the nascent cold seep displays unique characteristics, with an increased proportion of RNA viruses and temperate viruses. Viral genomic and metatranscriptomic analyses reveal viral functional genes are actively expressed, potentially enhancing host metabolism of complex organic matter. Here, our findings underscore the diversity, ecological roles, and host interactions of viral communities in different cold seeps and seamounts, suggesting the importance of viruses in deep-sea carbon cycling and microbial community structure.}, }
@article {pmid41258067, year = {2025}, author = {Zhang, Q and Sun, Y and Liu, W and Zhao, Q and Yuan, K and Chen, D}, title = {Clinical characteristics of Torquetenovirus infected immunocompromised patients explored by metagenomic next-generation sequencing.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {40857}, pmid = {41258067}, issn = {2045-2322}, support = {Grant No. MTP2022D027//Medical Talent Program for High-hroughput Sequencing Technology in Infectious Diseases, China/ ; }, mesh = {Humans ; *Immunocompromised Host ; *Torque teno virus/genetics ; *High-Throughput Nucleotide Sequencing/methods ; Female ; Male ; Middle Aged ; *DNA Virus Infections/virology/immunology/diagnosis ; *Metagenomics/methods ; Adult ; Aged ; }, abstract = {Since the recent application of metagenomic next-generation sequencing (mNGS) techniques to clinics, Torquetenoviruses (TTV) have received much attention due to their high positive rates. However, there is an insufficient understanding in clinical settings of the pathogen, especially in immunocompromised patients. This study explores the clinical characteristics of TTV infection in immunocompromised patients using mNGS. We enrolled a total of 120 TTV-infected patients in the study, including 81 immunocompromised and 39 immunocompetent individuals. The prevalence, diagnosis, treatment, and co-pathogens were compared between the two groups. The microbial diversity and presence of co-pathogens in patients infected with Torquetenovirus (TTV) were elucidated through comprehensive analysis. T-tests compared the normally distributed continuous data. The immunocompromised patients exhibited significantly elevated TTV loads, and a notable proportion of these patients also presented with hematopoietic disorders. Importantly, our investigation revealed that current treatments showed no efficacy against TTV infection.Furthermore, the presence of copathogens such as Staphylococcus, Bacillus, Mycobacterium, and Acinetobacter was observed in TTV-infected individuals. Immunocompromised patients exhibited a significantly higher abundance of Staphylococcus and Shewanella compared to immunocompetent patients (p < 0.05). Cautious use of antiviral therapy is recommended for patients with TTV mono-infection. However, greater attention should be given to co-pathogens, such as Staphylococcus spp. and Shewanella spp. This cohort study provides valuable insights into the clinical significance of TTV infection, particularly in immunocompromised patients. We found that TTV is frequently detected in this population, often with higher viral loads and an increased burden of co-pathogens. These findings suggest that TTV may serve primarily as a marker of immune dysfunction rather than as a sole pathogen. Incorporating TTV monitoring into mNGS-based diagnostics could help identify high-risk patients, support early intervention, and guide tailored management strategies in immunocompromised settings.}, }
@article {pmid41257635, year = {2025}, author = {Liu, J and Wu, J and Zheng, Z and Xue, J and Zhang, W}, title = {Clinical spectrum of Talaromyces marneffei infections in HIV-negative patients: an 18-case series including a rare presentation with gastrointestinal onset, adrenal mass, and hemophagocytic lymphohistiocytosis.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {1616}, pmid = {41257635}, issn = {1471-2334}, support = {2024J0112//Nature Science Foundation of Fujian Province of China/ ; }, mesh = {Humans ; Male ; Female ; *Talaromyces/isolation &amp; purification/genetics ; Middle Aged ; *Lymphohistiocytosis, Hemophagocytic/microbiology ; *Mycoses/diagnosis/microbiology/pathology/complications ; Retrospective Studies ; Aged ; Adult ; Coinfection ; *Gastrointestinal Diseases/microbiology ; HIV Seronegativity ; }, abstract = {BACKGROUND: The diverse manifestations of Talaromyces marneffei (TM) infection in HIV-negative patients complicate and often delay diagnosis. This study reviews 18 cases to better characterize the clinical spectrum of this disease, with the goal of improving recognition of its varied presentations.<br><br>METHODS: Retrospective analysis of 18 patients assessing underlying diseases, manifestations, co-infections, diagnostics, treatment, and outcomes. Diagnosis required TM positivity via culture, histopathology, or metagenomic next-generation sequencing(mNGS).<br><br>RESULTS: This cohort (14 males and 4 females; mean age 57.94&#x2009;&#xb1;&#x2009;11.12 years) exhibited diverse comorbidities, including renal transplantation (27.8%), tuberculosis (22.2%), cancer (16.7%), bronchiectasis (16.7%), and anti-interferon-&#x3b3; autoantibody (AIGA) syndrome (11.1%). Common manifestations included respiratory symptoms (72.2%), fever (55.6%), and anemia (50.0%). Immunodeficiency was frequent, with an abnormal CD4/CD8 ratio in in 10/15 patients (66.7%). Notably, 94.4% of cases were initially misdiagnosed-often as tuberculosis (35.3%) or bacterial pneumonia (23.5%)-leading to a mean diagnostic delay of 8.97&#x2009;&#xb1;&#x2009;7.02 weeks. mNGS provided diagnosis in 77.8% of cases. Overall mortality was 22.2%, with two relapses linked to AIGA syndrome. We report the first documented TM triad in a patient with systemic lupus erythematosus (SLE) and Epstein-Barr virus (EBV) coinfection: concurrent gastrointestinal onset (manifesting as ileocolonic ulcers), adrenal mass, and hemophagocytic lymphohistiocytosis (HLH).<br><br>CONCLUSIONS: TM infection in HIV-negative hosts demonstrates broad clinical heterogeneity, often masked by comorbidities and leading to delayed diagnosis. mNGS is critical for early identification. The unprecedented triad of gastrointestinal onset, adrenal mass, and HLH underscores TM's capacity for atypical dissemination. AIGA may predict relapse.<br><br>CLINICAL TRIAL NUMBER: Not applicable.}, }
@article {pmid41257101, year = {2025}, author = {He, X and Wang, M and Sun, T and Tang, J and Zeng, Y}, title = {Metagenomic Next-Generation Sequencing Diagnosis of Streptococcus agalactiae Meningitis in a Diabetic Patient.}, journal = {Cureus}, volume = {17}, number = {10}, pages = {e94759}, pmid = {41257101}, issn = {2168-8184}, abstract = {Streptococcus agalactiae meningitis is primarily observed among neonates and is uncommon in adults. We present a rare case of Streptococcus agalactiae meningitis in an adult. The patient was a 74-year-old male with a history of gastric perforation surgery, chemotherapy for neck lymphoma, and hypertension. He presented to the emergency department with an 11-day history of neck pain, one day of limited mouth opening and dysphagia, and eight hours of altered consciousness. On examination, he exhibited impaired consciousness (Glasgow Coma Scale score: 8) and cervical rigidity. He was intubated and received oxygen therapy. Laboratory findings revealed elevated infection markers and turbid cerebrospinal fluid (CSF). Metagenomic next-generation sequencing (mNGS) of the CSF detected Streptococcus agalactiae. Enhanced MRI of the head and neck showed a small subdural effusion, spinal cord edema at C5-C6, thickening and enhancement of the anterior and posterior longitudinal ligaments and meninges at the skull base, suggestive of Streptococcus agalactiae infection. After 10 days of anti-infective treatment with ceftriaxone, the patient's condition improved, and he was transferred to a local hospital for continued management.}, }
@article {pmid41256608, year = {2025}, author = {Wang, Y and Chang, HW and Cheng, J and Webber, DM and Lynn, HM and Hibberd, MC and Kao, C and Mostafa, I and Ahmed, T and Barratt, MJ and Gordon, JI}, title = {Using gnotobiotic mice to decipher effects of gut microbiome repair in undernourished children on tuft and goblet cell function.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.10.02.680046}, pmid = {41256608}, issn = {2692-8205}, abstract = {UNLABELLED: Studies have implicated perturbations in the postnatal development of the gut microbiome as a contributing factor to childhood undernutrition. Compared to a standard ready-to-use supplementary food, a microbiome-directed complementary food (MDCF-2) designed to repair these perturbations produced superior improvements in ponderal and linear growth in clinical trials of Bangladeshi children with moderate acute malnutrition. Here, 'reverse translation' experiments are performed where intact fecal microbiomes collected from trial participants prior to and at the end of treatment are introduced into female gnotobiotic mice just after delivery of their pups. Pups received diets designed to resemble those consumed by children in the trials to recreate "unrepaired" and "repaired" gut ecosystems. Analyses of the abundances of bacterial strains (metagenome-assembled genomes), their expressed genes and metabolic products, combined with assessments of ponderal growth and intestinal epithelial lineage transcriptomes (single-nucleus RNA-Seq with follow-up immunocytochemistry) disclosed effects of MDCF-2 associated microbiome repair that cannot be determined, in part because 'no treatment' control arms cannot be ethically incorporated into these trials. Specifically, microbiome repair in these mice produced significant increases in ponderal growth, changes microbial gene expression consistent with a less virulent gut ecosystem and changes in expression of (i) components of gut epithelial cell junctions in the enterocytic and goblet cell lineages, (ii) pathways for synthesis and secretion of eicosanoid immune effectors in chemosensory tuft cells, and (iii) goblet cell pathways involved in glycosylation and secretion of mucin. Experiments of the type described can help formulate and test hypotheses about how microbiome repair affects host biology.<br><br>SIGNIFICANCE STATEMENT: Undernutrition is a global health problem. Recent clinical trials of a gut microbiome-directed complementary food (MDCF-2) designed to repair the perturbed gut microbiomes of undernourished Bangladesh children produced superior growth outcomes versus a standard nutritional supplement. Given ethical considerations and tissue sampling constraints associated with these types of studies, we colonized gnotobiotic mice postnatally with microbiome samples obtained from trial participants before and after treatment to model "unrepaired" and "repaired" gut ecosystems. Using a multi-omics approach, we uncover heretofore unappreciated changes in expressed chemosensory tuft cell, mucus-producing goblet cell and absorptive enterocytic functions and interactions accompanying microbiome repair. Extending microbiome clinical trials back to preclinical models ('reverse translation') provides mechanistic insights that can inform design/interpretation of future interventions.}, }
@article {pmid41256588, year = {2025}, author = {Chakrawarti, A and Cromarty, RT and Basting, CM and Anderson, J and Schroeder, TA and Escandon, K and Shields-Cutler, R and Langat, R and Swanson, E and Soon-Shiong, P and Safrit, JT and Sender, LS and Reddy, S and Miller, JS and Rhein, J and Schacker, TW and Klatt, NR}, title = {Pre-treatment Microbiome Diversity and Function is associated with Expansion of Cytotoxic and Regulatory Immune Populations after N-803 treatment in People with HIV.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.10.01.679827}, pmid = {41256588}, issn = {2692-8205}, abstract = {BACKGROUND: N-803, an IL-15 superagonist, is currently being studied in clinical trials as a treatment to reverse HIV latency. However, its effects on the gut microbiome are not well understood.<br><br>METHODS: In this longitudinal metagenomic study, we analyzed fecal microbiomes from ART-suppressed people with HIV at four different timepoints before, during, and after N-803 treatment.<br><br>RESULTS: Overall taxonomic and functional diversity did not change significantly, yet beneficial microbial taxa and pathways were enriched after N-803. Specifically, the relative abundance of Faecalibacterium prausnitzii increased significantly after N-803, whereas histidine degradation pathways, often associated with pro-inflammatory mucosal state, decreased. A higher baseline microbial diversity correlated with stronger CD8 [+] and natural killer (NK) cells activation and reduced frequency of rectal HIV RNA [+] cells. MaAsLin2 analyses further associated short-chain fatty acid (SCFA)-producing taxa and pathways with increased immune activation markers.<br><br>CONCLUSIONS: These results indicate that gut microbiome diversity prior to immunotherapy influences host response and suggest that microbiome-based strategies could improve efforts to cure HIV.}, }
@article {pmid41256293, year = {2025}, author = {Agrawal, H and Agarwal, N and Gupta, N}, title = {Impact of gut microbiome on outcomes following endoscopic interventions in gastrointestinal disease.}, journal = {World journal of gastrointestinal endoscopy}, volume = {17}, number = {11}, pages = {110207}, pmid = {41256293}, issn = {1948-5190}, abstract = {BACKGROUND: Endoscopic interventions play a vital role in diagnosing and managing gastrointestinal diseases, but complications such as bleeding, infection, and delayed healing can adversely affect patient outcomes. The influence of the gut microbiome on these outcomes is increasingly being recognized.<br><br>AIM: To evaluate the role of the gut microbiome in influencing clinical outcomes after endoscopic interventions, focusing on microbial diversity, specific taxa, metabolic functions, and emerging predictive models.<br><br>METHODS: A systematic literature search was conducted in PubMed, EMBASE, and Cochrane databases up to May 2025, selecting human studies that analyzed gut microbiome composition or function in relation to endoscopic interventions and clinical outcomes. Microbiome analysis techniques included 16S rRNA gene sequencing, metagenomics, and metabolomics.<br><br>RESULTS: Forty-two studies met the inclusion criteria. Our review identifies key beneficial microbes, such as Faecalibacterium prausnitzii and Bacteroides spp., which support mucosal healing. In contrast, dysbiosis (e.g., an increased abundance of Proteo bacteria) is associated with poorer healing and higher complication rates. Notably, microbiome-informed predictive models have shown strong potential for forecasting post-procedural complications, offering a pathway to personalized treatment strategies. Probiotics have also emerged as a promising intervention, helping to restore microbial balance and reduce complications such as infection and delayed healing.<br><br>CONCLUSION: The gut microbiome plays a significant role in recovery after endoscopy. Integrating microbiome analysis into clinical decision-making could improve outcomes through personalized predictions and targeted therapies. Future research should focus on standardizing microbiome assessment protocols and validating predictive models to optimize patient care.}, }
@article {pmid41255950, year = {2025}, author = {Li, S and Peng, X and Tang, Z and Li, W and Song, X}, title = {Talaromyces marneffei Infection in Non-Endemic Areas: Two Case Reports, Diagnostic Insights, and Literature Review.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {5895-5903}, pmid = {41255950}, issn = {1178-6973}, abstract = {PURPOSE: Talaromycosis is an invasive fungal infection caused by the pathogenic fungus Talaromyces marneffei (T. marneffei), prevalent in Southeast Asia and Southern China. This disease is rare in non-endemic areas and primarily affects the respiratory system with atypical manifestations. Therefore, the condition is often misdiagnosed as other respiratory infections. This article presents two cases of talaromycosis in non-endemic areas, aiming to provide diagnostic and therapeutic references for this rare fungal infection.<br><br>CASE PRESENTATION: Two cases of talaromycosis in non-endemic areas were retrospectively analyzed. The first case involved a human immunodeficiency virus (HIV)-infected patient with tracheobronchial talaromycosis. Bronchoscopy revealed multiple nodular neoplasms in the trachea and bilateral main bronchi. Histopathological examination of the biopsy tissue showed histiocyte aggregation and intracellular pathogens. T. marneffei was identified by microbial culture of bronchoalveolar lavage fluid (BALF). The second case was an HIV-negative patient with pulmonary talaromycosis. Bronchoscopy revealed mucosal congestion and edema, and T. marneffei was detected by metagenomics next-generation sequencing (mNGS) of BALF.<br><br>CONCLUSION: Talaromycosis warrants more clinical attention in both HIV-negative individuals and non-endemic areas. In addition, clinicians should improve diagnostic recognition of this disease for timely management. Bronchoscopy combined with mNGS can facilitate early diagnosis of talaromycosis, particularly in culture-negative cases where conventional methods fail. This strategy directly addresses a major diagnostic challenge and improves patient prognosis.}, }
@article {pmid41255826, year = {2025}, author = {Jin, J and Chao, X and Zhu, Z and Zhang, B and Fu, Y and Xu, J and Ma, S and Chen, T and Wang, Y and Ding, J}, title = {Metagenomic Analysis of Tick-Borne Viruses Associated With Hyalomma asiaticum From Different Hosts in the Surrounding Areas of Urumqi, China.}, journal = {Transboundary and emerging diseases}, volume = {2025}, number = {}, pages = {9985595}, pmid = {41255826}, issn = {1865-1682}, mesh = {Animals ; China/epidemiology ; Metagenomics ; *Ixodidae/virology ; Phylogeny ; Horses ; Sheep ; Tick-Borne Diseases/veterinary/epidemiology/virology ; *RNA Viruses/isolation &amp; purification/genetics/classification ; }, abstract = {Tick-borne viruses (TBVs) represent a serious risk to global public and animal health. Despite the remarkable species diversity of ticks documented in Urumqi and its adjacent regions of China, scientific investigations into TBVs in this ecologically significant area have been strikingly scarce. In this study, we conducted metagenomic sequencing on 752 Hyalomma asiaticum (H. asiaticum), including questing ticks from Wujiaqu and blood-feeding ticks collected from sheep and horses in the Changji area. A total of 11 different RNA viruses were detected, belonging to six viral families and some unclassified families, with double-stranded RNA viruses being the most prevalent (49.1%), including Totiviridae and Sedoreoviridae. Single-stranded RNA viruses accounted for 11.9% of the virome, encompassing Chuviridae, Flaviviridae, Rhabdoviridae, and Phenuiviridae. Notably, 39.0% of the viral sequences remained unclassified, highlighting a substantial reservoir of uncharacterized viral diversity. Genomic and phylogenetic characterizations were performed on six highly abundant viruses, including Bole tick virus 1, Mivirus boleense, Bole tick virus 4, Lonestar tick totivirus, Hubei toti-like virus 24, and a novel strain of Hulunbuir Totiv tick virus 1. However, their zoonotic potential requires further investigation. By integrating cytochrome c oxidase subunit Ⅰ (COI) gene-based tick species identification with viral metagenomics, this study provided a comprehensive assessment of tick species and TBVs diversity in Urumqi and its surrounding areas, China. These results provide new insights into both the genetic diversity of tick-borne RNA viruses and their phylogenetic connections, while also expanding knowledge about the geographical distribution patterns of these pathogens.}, }
@article {pmid41255529, year = {2025}, author = {Horiachok, M and Potapova, K and Ivanykovych, T and Yerokhovych, V and Ilkiv, Y and Sokolova, L}, title = {Integrating gut microbiota into multidisciplinary perspectives on diabetic neuropathy.}, journal = {Frontiers in endocrinology}, volume = {16}, number = {}, pages = {1710868}, pmid = {41255529}, issn = {1664-2392}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Diabetic Neuropathies/microbiology/therapy/metabolism ; *Dysbiosis/microbiology ; Animals ; Probiotics/therapeutic use ; }, abstract = {Diabetic neuropathy (DN) is one of the most common and debilitating complications of diabetes mellitus, yet its precise pathogenesis remains incomplete. Emerging evidence highlights the gut microbiome as a key factor linking metabolic dysfunction, immune activation, and neuronal damage. Even minor dysbiosis may interfere with microbial metabolite balance and disrupt intestinal integrity, leading to local and, consequently, systemic inflammation, which in turn drives altered pain response via the gut-brain-immune axis. Recent clinical and preclinical data show that reduced short-chain fatty acid availability, altered bile acid and tryptophan metabolism, let alone expansion of pro-inflammatory species collaboratively contribute to DN onset and progression. Moreover, advances in metagenomics and metabolomics reveal reproducible microbiome-derived biomarkers that could predict neuropathy risk and pain phenotypes independent of glycemic control, supporting the microbiome as both a mechanistic driver and a measurable potential diagnostic tool. In the context of management, microbiota-affected interventions, such as probiotics, synbiotics, omega-3 supplementation, and fecal microbiota transplantation, show early promise in alleviating symptoms and improving nerve function. This mini-review synthesizes current evidence on the microbiome's role in DN, emphasizing its dual potential as a biomarker for early diagnosis and a therapeutic target for precision microbiome-based interventions.}, }
@article {pmid41255157, year = {2025}, author = {Chen, J and Wu, C and Yang, R and Chen, Z and Yang, X and Xu, Y and Cheng, X and Sui, H and Zhang, S and Zhu, X and Wu, M and Huang, Y and Chen, X and Liu, H and Yang, J and Tan, X and Chen, F and Cheng, C and Shao, D and Han, X and Shi, B and Yang, C and Leong, KW and Huang, H}, title = {LPS-Binding Hydrogel for TLR4-Mediated Microbiota-Immune Modulation.}, journal = {Advanced materials (Deerfield Beach, Fla.)}, volume = {}, number = {}, pages = {e14484}, doi = {10.1002/adma.202514484}, pmid = {41255157}, issn = {1521-4095}, support = {82301148//National Natural Science Foundation of China/ ; 82470955//National Natural Science Foundation of China/ ; 2024T170605//China Postdoctoral Science Foundation/ ; RD-02-202511//Research and Develop Program, West China Hospital of Stomatology Sichuan University/ ; 2025ZNSFSC0758//Sichuan Province Science and Technology Support Program/ ; RCDWJS2024-7//West China School of Stomatology, Sichuan University/ ; 24QNMP060//Health Commission of Sichuan Province/ ; TB2022005//Sichuan Provincial Postdoctoral Science Foundation/ ; }, abstract = {Lipopolysaccharide (LPS), a conserved component of Gram-negative bacteria, is a potent immune activator that disrupts tissue repair when released during microbial dysbiosis. LPS-scavenging strategies are often limited by the poor accessibility of lipid A, the bioactive core of LPS, which is shielded by variable oligosaccharide structures and embedded in bacterial membranes. To address this, a synergistic LPS-binding hydrogel (OCMC-PMBP) is developed, combining polymyxin B (PMB) for lipid A-targeted bacterial lysis and polyethyleneimine (PEI) for electrostatic LPS capture. This system is applied to oronasal-perforating wounds, a complex and infection-prone condition associated with cleft palate repair. Clinical microbiome analysis and murine models reveal that LPS-TLR4 signaling contributes to immune dysregulation and impaired healing. OCMC-PMBP treatment reduces LPS levels, restores microbiota balance, suppresses inflammation, and accelerates epithelial regeneration and collagen remodeling. Integrated 16S rRNA sequencing, metagenomics, and single-cell transcriptomics show that the hydrogel reprograms immune cell phenotypes and modulates macrophage interactions with neutrophils, epithelial cells, and fibroblasts across healing phases. This study introduces a biomaterials design combining antimicrobial and immunomodulatory functions to resolve dysbiosis-induced inflammation and enhance regenerative healing in complex mucosal wounds.}, }
@article {pmid41254499, year = {2025}, author = {Bring Horvath, ER and Winter, JM}, title = {SeqForge: a scalable platform for alignment-based searches, motif detection, and sequence curation across meta/genomic datasets.}, journal = {BMC bioinformatics}, volume = {26}, number = {1}, pages = {280}, pmid = {41254499}, issn = {1471-2105}, support = {1R01AI155694/NH/NIH HHS/United States ; }, mesh = {*Software ; *Sequence Alignment/methods ; Databases, Genetic ; *Genomics/methods ; Amino Acid Motifs ; Metagenomics/methods ; }, abstract = {BACKGROUND: The rapid increase in publicly available microbial and metagenomic data has created a growing demand for tools that can efficiently perform custom large-scale comparative searches and functional annotation. While BLAST + remains the standard for sequence similarity searches, population-level studies often require custom scripting and manual curation of results, which can present barriers for many researchers.<br><br>RESULTS: We developed SeqForge, a scalable, modular command-line toolkit that streamlines alignment-based searches and motif mining across large genomic datasets. SeqForge automates BLAST&#x2009;+&#x2009;database creation and querying, integrates amino acid motif discovery, enables sequence and contig extraction, and curates results into structured, easily parsed formats. The platform supports diverse input formats, parallelized execution for high-performance computing environments, and built-in visualization tools. Benchmarking demonstrates that SeqForge achieves near-linear runtime scaling for computationally intensive modules while maintaining modest memory usage.<br><br>CONCLUSIONS: SeqForge lowers the computational barrier for large-scale meta/genomic exploration, enabling researchers to perform population-scale BLAST searches, motif detection, and sequence curation without custom scripting. The toolkit is freely available and platform-independent, making it suitable for both personal workstations and high-performance computing environments.}, }
@article {pmid41254331, year = {2025}, author = {Bersch-Ferreira, &#xc2;C and Fonseca, DC and Tramujas, L and Schiavon, CA and Nakagawa Santos, RH and V Machado, RH and Biasi Cavalcanti, A and Marcadenti, A}, title = {Gut Microbiota Composition and Arterial Hypertension Improvement Post-Roux-en-Y Gastric Bypass: GATEWAY Trial Sub-Analysis After 5 Years.}, journal = {Obesity surgery}, volume = {}, number = {}, pages = {}, pmid = {41254331}, issn = {1708-0428}, abstract = {INTRODUCTION: The aim of this study was to explore the relationship between gut microbiota composition and hypertension remission in individuals with obesity and hypertension who underwent Roux-en-Y gastric bypass (RYGB) surgery five years prior.<br><br>METHODS: This is a sub-analysis of the GATEWAY trial using cross-sectional data from participants five years post-surgery. Three groups were included: patients who underwent RYGB and achieved hypertension remission (Group 1, n&#x2009;=&#x2009;12), patients who underwent RYGB but did not achieve remission (Group 2, n&#x2009;=&#x2009;12), and a control group of individuals with obesity and hypertension who did not undergo surgery (Group 3, n&#x2009;=&#x2009;15). Gut microbiota composition was evaluated using metagenomic sequencing of fecal samples, with taxonomic classification at the phylum, class, and order levels.<br><br>RESULTS: No statistically significant differences were found in overall microbiota composition between the groups. However, microbial richness was higher in both surgical groups compared to the control group, suggesting a potential link between bariatric surgery and increased gut microbial diversity.<br><br>CONCLUSION: While gut microbiota composition did not significantly differ between individuals with and without hypertension remission, the observed increase in microbial richness among those undergoing bariatric surgery underscores the complex interplay between obesity treatment, gut microbiota, and blood pressure regulation. Further research is needed to elucidate these long-term relationships.}, }
@article {pmid41253025, year = {2025}, author = {Tian, R and Chen, N and Liu, Z and Yan, YG and Wang, YW and Zhao, P and Bo Zhao, C and Zhang, L and Zhang, Q and Tang, YP}, title = {Lactobacillus johnsonii alleviates rhubarb-induced diarrhoea by regulating the gut microbiota and TLR4/NF-κB signalling pathway.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {149}, number = {}, pages = {157550}, doi = {10.1016/j.phymed.2025.157550}, pmid = {41253025}, issn = {1618-095X}, abstract = {BACKGROUND: Rhubarb (RH) is a commonly used traditional Chinese medicine (TCM) for treating digestive system diseases. However, long-term or excessive use of RH can cause gastrointestinal adverse reactions, such as diarrhoea. RH steaming with wine (PRH) can affect gut microbiota (GM) and alleviate diarrhoea caused by rhubarb. Nevertheless, the causal relationship between differential strains and wine steaming in alleviating RH-induced diarrhoea remains unclear.<br><br>PURPOSE: This study aimed to further elucidate the mechanism of wine steaming in alleviating the RH-induced diarrhoea through establishing a causal relationship.<br><br>METHODS: The components of RH and PRH were detected using ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) technology. Differential strains were screened using metagenomic sequencing technology. To evaluate the alleviating effect of Lactobacillus johnsonii (L. john) on RH-induced diarrhoea, the faecal water rate, intestinal propulsion rate, intestinal transit time, and six-hour defecation volume were measured. Histopathological observations of the duodenum, jejunum, and ileum were conducted using the hematoxylin-eosin (HE) staining method. Meanwhile, the levels of inflammatory factors and immunoglobulins (IgG and IgA) in the ileum were detected by enzyme-linked immunosorbent assay (ELISA). The counts of CD4[+], CD8[+], and T regulatory cells (Treg) in peripheral blood were measured using flow cytometry. The protein expression of toll-like receptor 4 (TLR4), nuclear factor kappa-B (NF-&#x3ba;B), zonula occludens-1 (ZO-1), and occludin in the ileum tissue was detected using immunohistochemistry and Western blotting. Faecal samples were analysed using 16S rRNA sequencing technology, and the levels of short-chain fatty acids (SCFAs) were detected using gas chromatography-mass spectrometry (GC-MS). Endogenous metabolites were analysed using UPLC-MS.<br><br>RESULTS: Thirty-seven chemical ingredients in RH and PRH were identified, mainly containing anthraquinones, phenolic acids, and flavonoids. The relative peak areas of anthraquinone components decreased in PRH. Screened from RH and PRH, the differential strain L. john alleviated diarrhoea induced by RH, decreased faecal water rate and intestinal propulsion rate, and improved the degree of pathological damage in the small intestine. L. john can downregulate the levels of inflammatory factors (IL-6, TNF-&#x3b1;, IL-17, and IFN-&#x3b3;), inhibit the expression of TLR4/NF-&#x3ba;B, upregulate the expression of ZO-1 and Occludin, increase the contents of IgG and IgA, CD4[+]/CD8[+] ratio, and Treg cell percentage. The supplementation of L. john can regulate the composition of GM, with decreased Streptococcus and increased norank_f_Muribaculaceae, and elevate the levels of SCFAs, including acetic acid, propionic acid, and butyric acid mediated by GM. Metabolic analysis showed that L. john alleviated the disorder in the glycerophospholipid metabolic pathway.<br><br>CONCLUSION: L. john can alleviate diarrhoea and intestinal pathological damage caused by RH by improving GM dysbiosis and SCFAs level abnormalities, restoring cellular immune function and intestinal barrier function, and regulating abnormal expression of TLR4/NF-&#x3ba;B and release of inflammatory factors. The findings have revealed the causal relationship between GM and the alleviation of RH-induced diarrhoea by steaming with wine and contributed to the understanding of the mechanism of wine steaming in alleviating the RH-induced diarrhoea.}, }
@article {pmid41252983, year = {2025}, author = {Cao, S and Zhu, J and Gan, X and Fu, Q and Hu, H and Huang, Q}, title = {Synergic impact mechanisms of cover crop residue on Cd and As availability and native organic carbon mineralization in Cd and As co-contaminated paddy soil.}, journal = {Journal of hazardous materials}, volume = {500}, number = {}, pages = {140491}, doi = {10.1016/j.jhazmat.2025.140491}, pmid = {41252983}, issn = {1873-3336}, abstract = {The synergic impacts of cover crop residue on heavy metal and metalloid availability and soil organic carbon (SOC) mineralization in contaminated paddy soil and the underlying microbial mechanism remain unclear. This study investigated the availability of cadmium (Cd) and arsenic (As) and mineralization of native SOC in paddy soil treated with 0, 0.4 %, 0.8 % and 1.2 % of δ[13]C-labeled cover crop residue (Astragalus sinicus L.) via 90-day incubation experiments, the related functional genes and functional microbial communities were analyzed using metagenomic binning assembly. Cover crop residue with addition rate from 0.4 % to 1.2 % significantly decreased available Cd by 56 %-85 % but increased available As by 39 %-66 % compared to the control treatment. Cover crop residue resulted in a positive priming effect on native SOC mineralization but benefited SOC sequestration. Cover crop residue increased the abundance of genes encoding iron reductase (mtrABC, pilA, omcB), sulfate reductase (sir, fpr), As(V) reductase (ArsC), organic carbon hydrolases, methanogenesis, and methylotrophy. Genomes associated with Chloroflexota and Bacteroidota encoded all these key pathways, and their abundance increased with cover crop residue application. Cover crop residue decreased soil Eh, dissolved crystalline iron oxides, enriched specific microorganisms, including Chloroflexota and Bacteroidota, and then synergistically promoted the decrease in Cd availability and the increase in As availability and native SOC mineralization in the examined paddy soil. These findings provided practical and feasible guidance for achieving both safe production and carbon sequestration in contaminated paddy fields, highlighting the requirement to cautious utilization of cover crop residue in As-contaminated paddy fileds.}, }
@article {pmid41252855, year = {2025}, author = {Oh, S and Wijaya, J}, title = {Predictive surveillance and diagnosis of COVID-19: An integrative machine learning and wastewater multi-omics approach.}, journal = {Water research}, volume = {289}, number = {Pt B}, pages = {124981}, doi = {10.1016/j.watres.2025.124981}, pmid = {41252855}, issn = {1879-2448}, abstract = {COVID-19 has had major global impacts, highlighting the importance of robust predictive surveillance and diagnostic systems to ensure effective public health responses. Traditional surveillance methods based on passive case counting and diagnostic testing of individual patients often suffer from delays and resource constraints, preventing timely responses. This study proposed an integrative framework integrating machine learning (ML)-derived predictive surveillance with wastewater-based diagnosis, aiming to predict temporal trends in Korea and identify disease-causing agents. The ML model utilized crowdsourced COVID-19-related keywords, climatic, and environmental data, optimized via model selection and feature selection. The integrated data-driven model predicted COVID-19 cases over three years more accurately than those using single source data (i.e., baseline model). The explainable AI technique (i.e., helping to inform how the model made those predictive decisions) identified six keywords (reducing phlegm, throat pain, long COVID-19, sore throat, COVID-19 self-kit, and COVID-19 kit) as robust predictors of disease trends. In a proof-of-concept experiment, wastewater-based genotyping of disease-causing agents and affected human communities in sewershed areas was conducted. Metatranscriptomics of municipal wastewater was conducted to identify COVID-19 viral variants, evolutionarily related to those clinically isolated strains, distinguishable from conventional diagnostic testing of individual patients. Wastewater-derived metagenomics was also performed to assess genomic variation in the affected human populations. The integrative framework proposed in this study offers a rapid, cost-effective approach for the surveillance and diagnosis of COVID-19 and other infectious diseases, thus strengthening or complementing existing health systems.}, }
@article {pmid41206954, year = {2025}, author = {Mao, Y and Jiang, Z and Wang, T and Hu, Y and Zhan, X}, title = {TCVS: tree-guided compositional variable selection analysis of microbiome data.}, journal = {Bioinformatics (Oxford, England)}, volume = {41}, number = {11}, pages = {}, doi = {10.1093/bioinformatics/btaf617}, pmid = {41206954}, issn = {1367-4811}, support = {12371287//National Natural Science Foundation of China/ ; 2022YFA1305400//National Key R&amp;D Program of China/ ; }, mesh = {Humans ; *Microbiota ; *Software ; *Gastrointestinal Microbiome ; Algorithms ; *Computational Biology/methods ; *Metagenomics/methods ; Phylogeny ; }, abstract = {MOTIVATION: Studies of microbial communities, represented by the relative abundances of taxa at various taxonomic levels, have underscored the significance of microbiota in numerous aspects of human health and disease. A pivotal challenge in microbiome research lies in pinpointing microbial taxa associated with disease outcomes, which could play crucial roles in prevention, detection, and treatment of various health conditions. Alongside these relative abundance data, taxonomic information sometimes offers a unique lens to explore the impact of shared evolutionary histories on patterns of microbial abundance.<br><br>RESULTS: In pursuit of this goal, we utilize the tree structure to more flexibly identify taxa associated with disease outcomes. To enhance the accuracy of our selection process, we introduce auxiliary knockoff copies of microbiome features designated as noise. This approach allows for the assessment of false positives in the selection process and aids in refining it towards more precise outcomes. Extensive numerical simulations demonstrate that our methodology outperforms several existing methods in terms of selection accuracy. Furthermore, we demonstrate the practicality of our approach by applying it to a widely used gut microbiome dataset, identifying microbial taxa linked to body mass index.<br><br>TCVS R code is available at https://github.com/Yicong1225/TCVS.}, }
@article {pmid41189540, year = {2026}, author = {Inoue, J and Hirai, J and Ikeba, K and Yu, Z and Ahmed, SI and Lin, Z and Lin, Y and Wong, MK and Shinzato, C and Itoh, S and Ito, SI and Saito, H and Hyodo, S}, title = {eDNAmap: A Metabarcoding Web Tool for Comparing Marine Biodiversity, With Special Reference to Teleost Fish.}, journal = {Molecular ecology resources}, volume = {26}, number = {1}, pages = {e70066}, doi = {10.1111/1755-0998.70066}, pmid = {41189540}, issn = {1755-0998}, support = {21H04922//Japan Society for the Promotion of Science/ ; //The University of Tokyo - FSI Project &#x201b;Ocean DNA'/ ; }, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Fishes/genetics/classification ; *Biodiversity ; Internet ; *DNA, Environmental/genetics ; *Computational Biology/methods ; *Aquatic Organisms/classification/genetics ; *Metagenomics/methods ; *Software ; }, abstract = {Marine environmental DNA (eDNA) metabarcoding data are beginning to accumulate, even for remote and poorly studied areas, such as marine environments. These data enable us to identify distributions of target organisms and then to compare biological compositions between different marine areas. However, there is no platform to effectively utilise and accumulate these data. In this study, we developed eDNAmap, a web-based platform designed to analyse and store marine eDNA metabarcoding data. By uploading species or sequence composition data with location information, eDNAmap users can automatically (1) plot sampling locations on a map, (2) generate a heatmap to evaluate potential batch effects arising from methodological differences and (3) perform nonmetric multidimensional scaling and cluster analyses using similarity indices. Furthermore, users can specify scientific names to display species distributions and upload species lists to assess species compositions of the target sea area. As an example, fish sequence composition data obtained from 55 stations around the Watase line-believed to exist along a geographic canyon known as the Tokara Gap-were used to verify its existence using eDNAmap. The platform includes a database primarily consisting of teleost fish data from the Northwestern Pacific, which users can analyse similarly to their own uploads. Although originally designed for fish, eDNAmap is flexible enough to handle data from other marine organisms. Analysing multiple taxa enables the detection of concordant biogeographic patterns across different groups, which can strengthen ecological interpretations and lay the groundwork for identifying environmental drivers shaping community structures. eDNAmap is available at https://github.com/jun-inoue/eDNAmap.}, }
@article {pmid41168956, year = {2026}, author = {Ruiz, E and Lamy, T and Mouillot, D and Durand, JD}, title = {Benchmarking the Taxonomic Resolution of Fish eDNA Metabarcodes Against COI Barcodes.}, journal = {Molecular ecology resources}, volume = {26}, number = {1}, pages = {e70069}, doi = {10.1111/1755-0998.70069}, pmid = {41168956}, issn = {1755-0998}, mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; *Fishes/genetics/classification ; *Electron Transport Complex IV/genetics ; Benchmarking ; *Metagenomics/methods ; *DNA, Environmental/genetics ; Cluster Analysis ; Biodiversity ; Computational Biology/methods ; }, abstract = {Even though environmental DNA metabarcoding is revolutionizing biomonitoring, many critical steps remain unstandardized, leading to arbitrary choices, particularly regarding the selection of metabarcode, clustering method and similarity threshold, among others. Additionally, these studies were hindered by biases resulting from the presence of mislabeled sequences in international databases such as GenBank and the lack of explicit definitions for taxonomic resolution. To address these issues, we developed a robust framework to compare the performance of 22 metabarcodes derived from the same mitogenomes (all available for Actinopterygians in NCBI) against a standardized taxonomic baseline based on COI Barcode Index Numbers (BINs). This framework allows for the separate quantification of over-splitting (splitting the same taxon/BIN) and over-merging (merging different taxon/BIN). Comparison of OTUs obtained with multiple de novo clustering methods to BINs confirmed the metabarcode ranking based on error sums. Although each metabarcode exhibited varying sensitivities to over-merging or over-splitting errors, the clustering threshold emerged as the most important factor influencing biodiversity estimates whatever the clustering method. This led us to propose optimal thresholds for each metabarcode to delineate taxonomic levels (metabarcode gaps). Additionally, we found that taxonomic resolution varied significantly among genes, orders and community diversity, but independently of metabarcode length. Overall, the choice of metabarcode and clustering threshold should aim to minimize over-merging or over-splitting while ensuring accurate lower taxonomic delineations. A set of documented R functions makes this evaluation of taxonomic resolution easily applicable to any other taxonomic group for which a representative set of full genes or mitogenomes is available.}, }
@article {pmid41257040, year = {2023}, author = {Gündoğdu, A and Charyyeva, A and Nalbantoğlu, &#xd6;U}, title = {Metagenomic Profiling of Human Protozoan Parasites in Wastewater and Hospital Effluents.}, journal = {Journal of clinical practice and research}, volume = {45}, number = {5}, pages = {435-446}, pmid = {41257040}, issn = {2980-2156}, abstract = {OBJECTIVE: Advancements in metagenomic techniques have provided new tools for profiling human parasites in environmental matrices such as wastewater. This study aimed to profile protozoan parasites in wastewater from a major city, rural area, and hospital in Kayseri, Türkiye, using metagenomic techniques.<br><br>MATERIALS AND METHODS: Shotgun metagenome sequencing was conducted on ten water samples collected from five sampling sites over a two-week period. The sequences were aligned to 80 human parasite genomes to evaluate the presence and relative abundance of each parasite species. A comparative bioinformatic analysis was performed on the metagenomes from each sampling point.<br><br>RESULTS: The diversity of parasites in the city wastewater exceeded that of the rural and hospital sampling points. Blastocystis spp. subtypes and Giardia intestinalis were dominant in rural wastewater, while Plasmodium falciparum, Plasmodium ovale, Toxoplasma gondii, and Acanthamoeba species showed significant abundance in hospital effluent (p<0.01). Moreover, protozoan parasites not previously reported in a clinical setting were identified in the water samples.<br><br>CONCLUSION: This is the first study in T&#xfc;rkiye investigating the presence of human parasites in wastewater using metagenomics. The study highlights the risk posed by human parasites in treated wastewater to population using natural resources. Implementing a specialized wastewater treatment targeting parasites could mitigate the potential spread of these pathogens in the environment. The study revealed certain sequences associated with species not previously identified in clinical instances. This finding may result from genomic resemblances with other eukaryotic organisms that were not systematically excluded, or alternatively, the displacement of protozoa linked to the increasing influx of refugees.}, }
@article {pmid41252801, year = {2025}, author = {Gacem, A and Soltane, R and Wanale, SG and Mohammed, SA and Almulla, N and Eltayeb, LB and Alreshidi, MA and Alasiri, A and Albakri, GS and Raghuvanshi, U and Abdulmonem, WA and Qasim, MT and Gupta, R and Islam, S and Yadav, KK}, title = {Advances in molecular methodologies and nanotechnology-enabled drug delivery in biomedicine: An overview of current progress.}, journal = {Computational biology and chemistry}, volume = {120}, number = {Pt 1}, pages = {108765}, doi = {10.1016/j.compbiolchem.2025.108765}, pmid = {41252801}, issn = {1476-928X}, abstract = {Recent advances in molecular techniques and nanosystems have significantly transformed biomedical research, particularly in pathogen detection and drug delivery. Traditional culture-based methods are being increasingly replaced by rapid and precise molecular approaches, offering greater accuracy in identifying pathogens and uncovering the genetic mechanisms underlying antimicrobial resistance (AMR). This review highlights key molecular tools, including matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS), whole-genome sequencing, DNA microarrays, metagenomics, and polymerase chain reaction (PCR) and others with a critical evaluation of their strengths, limitations, and applications in global surveillance. Alongside, the integration of nanostructured systems has opened new avenues for designing advanced drug-delivery platforms with improved bioavailability, targeted action, and reduced toxicity. Together, these innovations emphasize the potential of molecular and nanoscale technologies to address pressing challenges in diagnostics, therapeutics, and the management of infectious diseases.}, }
@article {pmid41252568, year = {2025}, author = {Severino, A and Marchitto, SA and Bisegna, P and Porcari, S and Rondinella, D and Schepis, T and Barbaro, F and Pecere, S and Maida, M and Spada, C and Gasbarrini, A and Cammarota, G and Facciorusso, A and Ianiro, G}, title = {Measuring gut microbiome as a colorectal cancer screening tool: potential and challenges.}, journal = {Expert review of gastroenterology &amp; hepatology}, volume = {}, number = {}, pages = {}, doi = {10.1080/17474124.2025.2592078}, pmid = {41252568}, issn = {1747-4132}, abstract = {INTRODUCTION: Colorectal cancer (CRC) represents a global public health challenge, ranking as the third most prevalent cancer globally. Population-based screening programs for average-risk populations have proven effective in reducing incidence and mortality of CRC through early detection of cancer. The fecal immunochemical test (FIT), the standard diagnostic method in many nations, still falls short in diagnostic effectiveness, resulting in undetected adenomas and, more significantly, unnecessary colonoscopies.<br><br>AREAS COVERED: One of the primary research focuses in the field of CRC is the discovery of new, noninvasive biomarkers. Recent studies, including metagenomic meta-analyses, have discovered common microbial signatures able to reproducibly discriminate between patients with CRC and healthy controls. Based on this evidence, international guidelines have recently recommended the use of microbiome-based biomarkers for CRC screening in clinical settings, although such studies have yet to be conducted.<br><br>EXPERT OPINION: This field of research needs considerable multidisciplinary efforts, including large and geographically different meta-cohorts, and the application of state-of-the-art computational approaches, to identify reproducible signatures able to predict early lesions. Such diagnostic tool would revolutionize CRC screening. More widely, it would provide a mind-set shift in the clinical and scientific community promoting the exploitation of diagnostic and therapeutic microbiome tools in clinical practice.}, }
@article {pmid41252442, year = {2025}, author = {Zentgraf, J and Schmitz, JE and Rahmann, S}, title = {Cleanifier: Contamination removal from microbial sequences using spaced seeds of a human pangenome index.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btaf632}, pmid = {41252442}, issn = {1367-4811}, abstract = {MOTIVATION: The first step when working with DNA data of human-derived microbiomes is to remove human contamination for two reasons. First, many countries have strict privacy and data protection guidelines for human sequence data, so microbiome data containing partly human data cannot be easily further processed or published. Second, human contamination may cause problems in downstream analysis, such as metagenomic binning or genome assembly. For large-scale metagenomics projects, fast and accurate removal of human contamination is therefore critical.<br><br>RESULTS: We introduce Cleanifier, a fast and memory frugal alignment-free tool for detecting and removing human contamination based on gapped k-mers, or spaced seeds. Cleanifier uses a pangenome index of known human gapped k-mers, and the creation and use of alternative references is also possible. Reads are classified and filtered according to their gapped k-mer content. Cleanifier supports two filtering modes: one that queries all gapped k-mers and one that queries only a sample of them. A comparison of Cleanifier with other state-of-the-art tools shows that the sampling mode makes Cleanifier the fastest method with comparable accuracy. When using a probabilistic Cuckoo filter to store the complete k-mer set, Cleanifier has similar memory requirements to methods that use a sampled minimizer index. At the same time, Cleanifier is more flexible, because it can use different sampling methods on the same index.<br><br>Cleanifier is available via gitlab (https://gitlab.com/rahmannlab/cleanifier), PyPi (https://pypi.org/project/cleanifier/) and Bioconda (https://anaconda.org/bioconda/cleanifier). The pre-computed human pangenome index is available at Zenodo (https://doi.org/10.5281/zenodo.15639519).<br><br>SUPPLEMENTARY INFORMATION: Available online.}, }
@article {pmid41252249, year = {2025}, author = {Febinia, CA and Luqman, H and Kusuma, P and Priliani, L and Lewis, J and Wihandani, DM and Pinatih, GN and Sudoyo, H and Almeida, A and Malik, SG and Jacobs, GS}, title = {From sporulation to village differentiation: The shaping of the social microbiome over rural-to-urban lifestyle transition in Indonesia.}, journal = {Cell reports}, volume = {44}, number = {11}, pages = {116573}, doi = {10.1016/j.celrep.2025.116573}, pmid = {41252249}, issn = {2211-1247}, abstract = {Despite established roles in human health and profound global diversity, microbiome datasets remain biased toward Western urban cohorts, with especial under-representation of Southeast Asia. Here, we present a gut microbiome dataset from 116 Indonesians spanning transitional hunter-gatherer, rural agricultural, and urban lifestyles. We identify 1,304 species and 3,258 subspecies by assembling 11,070 metagenome-assembled genomes, revealing substantial species- (15%) and subspecies- (50%) level novelty. Novel taxa are rare, often village specific, and depleted for sporulation genes, revealing a link between bacterial physiology, transmission, prevalence, and discovery. We identify rural-to-urban clines across multiple levels of biological organization, from species abundance to microbiome composition and diversity. Furthermore, between-community, but not within-community, diet variation is strongly predictive of microbiome composition, suggesting that microbiome divergence is driven by community-level differences. Our work highlights the interplay of host lifestyle, population structure, and bacterial physiology in shaping microbiome diversity and biogeography, at the key scale of human communities.}, }
@article {pmid41251845, year = {2025}, author = {Saggu, SK and Kumar, M and Kumar, S}, title = {Metagenomics and its impact on environmental and therapeutic microbiology.}, journal = {Archives of microbiology}, volume = {208}, number = {1}, pages = {24}, pmid = {41251845}, issn = {1432-072X}, mesh = {*Metagenomics/methods ; *Environmental Microbiology ; *Bacteria/genetics/classification/isolation &amp; purification ; Humans ; High-Throughput Nucleotide Sequencing ; }, abstract = {Metagenomics has significantly advanced our understanding of microbial life by enabling the direct analysis of environmental DNA, thereby deciphering the vast microbial dark matter comprising unknown and uncultivable microbial diversity that remains inaccessible through conventional culture-dependent methods. The culture-independent approach provides a comprehensive view of microbial composition, function, and evolution, facilitating discoveries across environmental and clinical domains. Recent developments in high-throughput sequencing, hybrid long-read assemblies, and AI/ML-based genome binning have enhanced our understanding to reconstruct complete genomes, predict metabolic pathways, and engineer microbial consortia. This review summarizes the impact of metagenomics on environmental and therapeutic microbiology, emphasizing its contributions in the field of bioremediation, greenhouse gas mitigation, sustainable agriculture, industrial enzyme discovery, and novel drug development. It further explores metagenomics-driven innovations in pathogen detection, antimicrobial resistance surveillance, and multi-omics integration. Furthermore, it discusses methodological developments, computational challenges, and translational limitations, offering future perspectives for harnessing metagenomic insights in sustainable biotechnology and precision medicine.}, }
@article {pmid41251544, year = {2025}, author = {Pang, X and Zhang, B and Zhang, Q and Jiang, J}, title = {Freeze-Thaw Cycling Accelerates Microbial Reduction and Immobilization of Vanadium(V) in Groundwater.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c11332}, pmid = {41251544}, issn = {1520-5851}, abstract = {As global warming intensifies, freeze-thaw cycling has become more pronounced, significantly impacting microbial metabolic processes. In this study, microbial vanadium(V) [V(V)] reduction under freeze-thaw conditions was investigated. Temperature fluctuations between -4 and +4 °C accelerated V(V) reduction, together with the faster decrease in organic matter and total nitrogen in the sediment, compared to constant-temperature incubations at either -4 or +4 °C. V(V) was bioreduced to vanadium(IV) precipitates, increasing the acid-soluble, reducible, and oxidizable fractions of vanadium in the sediment. Freeze-thaw cycling enhanced microbial carbon and nitrogen utilization, as well as the richness and diversity of the microbial community. Metagenomics, real-time quantitative polymerase chain reaction quantification, and electron-transfer measurements revealed the underlying mechanisms. During thawing, microorganisms such as Flavobacterium sp., Stutzerimonas sp., and Giebergeria sp. reduced V(V) via denitrification genes (narG, nirS, and nosZ). Under freezing conditions, enriched Pseudomonas sp. and Acinetobacter sp. achieved V(V) reduction through the electron-transfer gene (mtrC), with increased cytochrome c concentration. Key cold-adaptation genes, including cspA, HSP, SOD, katG, and SCD, were prevalent in these microorganisms, supporting antifreeze activities. This study offers insights into microbial V(V) reduction under freeze-thaw cycling scenarios and is helpful in developing pertinent remediation strategies.}, }
@article {pmid41251358, year = {2025}, author = {Wilson, A and Jauregui, R and Bueno, R and Begg, D and Hannah, M and Sheeba, E and Bestbier, M and Green, D and O'Keefe, J and McCulley, M}, title = {Genome sequence of Babesia gibsoni detected in a domestic dog in New Zealand.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0108325}, doi = {10.1128/mra.01083-25}, pmid = {41251358}, issn = {2576-098X}, abstract = {We report the draft genome sequence of Babesia gibsoni detected in a domestic dog in New Zealand. A high-quality near-complete genome, comprised of an apicoplast, mitochondrion, and four chromosomes, was produced through long-read metagenomic sequencing.}, }
@article {pmid41251138, year = {2025}, author = {Shukla, M and Wattam, AR and Aleman, A and Bhattacharya, R and Bowers, N and Brettin, T and Capria, A and Chia, N and Cucinell, C and Davis, JJ and Dempsey, DM and Dickerman, A and Dietrich, EM and Gokdemir, O and Hendrickson, RC and Kenyon, RW and Klahn, B and Kuscuoglu, M and Lefkowitz, EJ and Ma, H and Machi, D and Macken, C and Mann, CM and Mao, C and Nguyen, M and Olsen, GJ and Olson, RD and Overbeek, R and Owens, SM and Parrello, B and Poretsky, R and Pusch, GD and Ramanathan, A and Sheriff, JT and Singh, I and Stewart, L and VanOeffelen, M and Vonstein, V and Warren, AS and Wilke, A and Zmasek, CM and Zuniga, A and Stevens, RL}, title = {BV-BRC: a unified bacterial and viral bioinformatics resource with expanded functionality and AI integration.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkaf1254}, pmid = {41251138}, issn = {1362-4962}, support = {//National Institute of Allergy and Infectious Diseases/ ; /NH/NIH HHS/United States ; U24AI183849/HH/HHS/United States ; }, abstract = {The Bacterial and Viral Bioinformatics Resource Center (BV-BRC; https://www.bv-brc.org) is a comprehensive resource supporting research on bacterial and viral pathogens. It currently hosts over 14 million publicly available genomes and 33 high-throughput bioinformatic analysis services with numerous visual analytic tools allowing researchers to analyze their private data, generate comparisons with public data, and share data and results with colleagues. In recent years, the BV-BRC has added several new analysis services to support rapid comparative genomics and epidemiological analysis, viral genome assembly and annotation, viral subspecies classification, wastewater analysis, and molecular docking. In addition, several existing services have been updated to incorporate state-of-the-art tools, including assembly, annotation, taxonomic classification, metagenomic read mapping, and RNA-seq analysis. A new tool, called BV-BRC Copilot, provides an AI-powered natural-language interface that combines large language models with retrieval-augmented generation to guide users through data exploration, analysis workflows, and knowledge integration. With expanded outbreak tracking pages, training and educator engagement, and continued development of novel AI-driven analytics, BV-BRC continues to provide a unified resource to meet the evolving needs of the global research community.}, }
@article {pmid41250695, year = {2025}, author = {Pathi, B and Sahoo, JP and Mahapatra, A and Panigrahy, R and Padhi, S and Lenka, PR and Mohanty, I and Ramadass, B and Panigrahi, K and Dixit, S and Das, MK}, title = {Genome Sequencing to Prevent Hospital-Acquired Infections Caused by Carbapenem-Resistant Acinetobacter baumannii Due to Importation and Intra-facility Transmission in a Regional Hospital Network: Study Protocol for Implementation Research.}, journal = {Cureus}, volume = {17}, number = {10}, pages = {e94812}, pmid = {41250695}, issn = {2168-8184}, abstract = {BACKGROUND AND OBJECTIVES: Carbapenem-resistant Acinetobacter baumannii (CRAb) is among India's leading bacteria responsible for hospital-acquired infections (HAIs). The CRAb causing intra-facility and inter-facility (or importation) HAI transmissions may differ phylogenetically. For control and prevention of CRAb-associated HAIs within and across facilities, information about the phylogenetic lineage characterization and contextual risk factors is critical. To our knowledge, there is no preliminary state-level data available from Odisha state in India regarding the dynamics of CRAb transmission (intra- and inter-facility), phylogenetic lineages, risk factors, and geospatial epidemiology. This study shall document the dynamics of CRAb-associated HAIs, the phylogenetic lineages responsible for intra-facility and inter-facility transmissions, and the risk factors. We shall leverage the CRAb phylogenetic data and risk factors identified through an integrated laboratory-clinical-epidemiological-genomic surveillance for tackling the intra-facility and inter-facility transmissions and outbreaks using implementation research approaches with adoption of contextualized hospital infection control and prevention measures and antibiotic stewardship efforts in a hospital network in Odisha state, India.<br><br>METHODS: This study adopts an integrated prospective facility-based surveillance with a quasi-experimental design using the plan-do-study-act (PDSA) implementation research cycles with mixed-methods data collection approaches. The study will be conducted over three years at six tertiary care medical institutions in Odisha. Prospective surveillance over 24 months at these hospitals will monitor the CRAb isolates to identify HAI outbreaks and intra- and inter-facility transmissions. The metagenomic and genome-wide sequencing (GWS) shall document CRAb phylogenetic lineages for outbreaks and intra- and inter-facility transmissions. Geospatial mapping shall document the spatial characterization of CRAb transmission for the index cases. Formative research shall identify potential risk factors at various levels for HAIs, outbreaks, intra- and inter-facility CRAb transmissions, hospital infection prevention, surveillance, and antibiotic stewardship efforts, using the Consolidated Framework for Implementation Research (CFIR). Based on this information, contextualized strategies and interventions to strengthen hospital infection prevention, surveillance, and antibiotic stewardship efforts shall be implemented at these facilities using incremental PDSA cycles. Data from these PDSA cycles shall be compared to document the impact on CRAb outbreaks and process indicators. The practices' and interventions' feasibility, acceptability, and sustainability shall be documented.<br><br>RESULTS: We do not have any observations, as we have not started the study yet.<br><br>CONCLUSION: The study shall generate evidence on genoepidemiology, transmission dynamics of HAIs due to CRAb in Odisha, India, and the associated risk factors. The lessons from context-specific implementation strategies (covering infection surveillance, prevention strategies, and antibiotic stewardship domains) to tackle CRAb-associated HAIs outbreaks and the feasibility, acceptability, and sustainability shall inform the policy and practices. The geographic signatures of horizontal CRAb-associated HAIs will generate a new knowledge base to design future intervention measures.}, }
@article {pmid41250675, year = {2025}, author = {Gao, Y and Bai, J and Zhou, F and He, Y and Wang, Y and Huang, X}, title = {ICCTax: a hierarchical taxonomic classifier for metagenomic sequences on a large language model.}, journal = {Bioinformatics advances}, volume = {5}, number = {1}, pages = {vbaf257}, pmid = {41250675}, issn = {2635-0041}, abstract = {MOTIVATION: Metagenomic data increasingly reflect the coexistence of species from Archaea, Bacteria, Eukaryotes, and Viruses in complex environments. Taxonomic classification across the four superkingdoms is essential for understanding microbial communities, exploring genomic evolutionary relationships, and identifying novel species. This task is inherently imbalanced, uneven, and hierarchical. Genomic sequences provide crucial information for taxonomy classification, but many existing methods relying on sequence similarity to reference genomes often leave sequences misclassified due to incomplete or absent reference databases. Large language models offer a novel approach to extract intrinsic characteristics from sequences.<br><br>RESULTS: We present ICCTax, a classifier integrating the large language model HyenaDNA with complementary-view-based hierarchical metric learning and hierarchical-level compactness loss to identify taxonomic genomic sequences. ICCTax accurately classifies sequences to 155 genera and 43 phyla across the four superkingdoms, including unseen taxa. Across three datasets built with different strategies, ICCTax outperforms baseline methods, particularly on Out-of-Distribution data. On Simulated Marine Metagenomic Communities datasets from three oceanic sites, DairyDB-16S rRNA, Tara Oceans, and wastewater metagenomic datasets, it demonstrates strong performance, showcasing real-world applicability. ICCTax can further support identification of novel species and functional genes across diverse environments, enhancing understanding of microbial ecology.<br><br>Code is available at https://github.com/Ying-Lab/ICCTax.}, }
@article {pmid41250628, year = {2025}, author = {Yathindra, MR and Badugu, R and Singh, SK and Paluri, S and Poudala, H and Swathi, NL}, title = {The role of the urinary microbiome in diabetes-associated UTIs: current understanding and future directions.}, journal = {Journal of basic and clinical physiology and pharmacology}, volume = {}, number = {}, pages = {}, pmid = {41250628}, issn = {2191-0286}, abstract = {This review explores the interplay between type 2 diabetes mellitus (T2DM) and urinary microbiome dysbiosis, focusing on its role in urinary tract infections (UTIs). Once considered sterile, the urinary tract hosts a diverse microbiota that supports mucosal immunity and pathogen resistance. In T2DM, chronic hyperglycemia and glycosuria disrupt microbial balance, impair immune responses, and increase UTI susceptibility. Glycosuria promotes pathogenic colonization, biofilm formation, and microbial shifts, with studies reporting a threefold rise in Escherichia coli and a 56 % reduction in Lactobacillus spp. in diabetic women with recurrent UTIs. Diabetic urine shows reduced diversity, higher abundance of Klebsiella, Pseudomonas, and Enterococcus, and elevated IL-8. Microbiota-targeted interventions, including probiotics (Lactobacillus crispatus, Lactobacillus rhamnosus GR-1), prebiotics (astaxanthin), and phytotherapeutics (cranberry), demonstrate potential via lactic acid, hydrogen peroxide production, competitive exclusion, and NF-κB modulation. A 12-month RCT showed significant UTI recurrence reduction with probiotics. Advances in 16 S rRNA sequencing and metagenomics reveal microbial signatures associated with diabetic UTIs, though methodological heterogeneity limits comparability. A review of 1,200 publications (2000-2024) highlights the need for longitudinal studies and precision microbiota therapeutics to translate findings into clinical practice.}, }
@article {pmid41250240, year = {2025}, author = {Gwak, HJ and Rho, M}, title = {DeepCOI: a large language model-driven framework for fast and accurate taxonomic assignment in animal metabarcoding.}, journal = {Genome biology}, volume = {26}, number = {1}, pages = {393}, pmid = {41250240}, issn = {1474-760X}, support = {RS-2020-II201373//the Korea government (MSIT)/ ; 20220517//Ministry of Oceans and Fisheries, Korea/ ; 2023R1A6C101A009//Korea Basic Science Institute/ ; }, mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; Electron Transport Complex IV/genetics ; *Software ; Biodiversity ; Large Language Models ; }, abstract = {Metabarcoding remains challenging due to incomplete taxonomic annotations and computationally intensive processes. We present DeepCOI, a large language model-based classifier pre-trained on seven million cytochrome c oxidase I gene sequences. DeepCOI enables fast and accurate taxonomic assignment across eight major phyla, achieving an AU-ROC of 0.958 and AU-PR of 0.897-outperforming existing methods while significantly reducing inference time. Additionally, DeepCOI demonstrates interpretability by identifying taxonomically informative sequence positions. By integrating large-scale datasets and self-supervised learning, DeepCOI enhances both the accuracy and efficiency of metabarcoding processes, providing a scalable solution for biodiversity assessment and environmental monitoring.}, }
@article {pmid41250148, year = {2025}, author = {Lam, AY and Lau, CH and Tam, WY and Chan, CT and Lok, TM and Suen, LK and Lee, LK and Yeung, EY and Lam, TK and Cheung, WK and Chui, MW and Soong, HS and Chow, FW and Lam, SC and So, SN and Yuen, SK and Siu, GK}, title = {Targeted probe capture metagenomics-enabled surveillance of multidrug-resistant organisms and antimicrobial resistance genes in post-handwashing areas of public washrooms.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {143}, pmid = {41250148}, issn = {2524-6372}, support = {2023-00-51 CRG230402//Tung Wah College/ ; 1-ZVZL//The Hong Kong Polytechnic University/ ; }, abstract = {BACKGROUND: Public washrooms (toilets) are potential hubs for pathogen transmission, yet the risk of microbial re-contamination via post-handwashing surfaces remains understudied. We characterized the prevalence and distribution of multidrug-resistant organisms (MDROs) and antimicrobial resistance genes (ARGs) in post-handwashing areas by sampling four high-contact sites, including faucets, paper dispensers, hand dryers, and exit door handles, in public washrooms across healthcare, commercial, and recreational facilities.<br><br>RESULTS: From the 232 post-handwashing surface samples collected, we isolated 17 MDROs (7.33% prevalence) from cultures, including extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales (ESBL-E, n&#x2009;=&#x2009;10), carbapenem-resistant Pseudomonas aeruginosa (CRPA, n&#x2009;=&#x2009;5), and methicillin-resistant Staphylococcus aureus (MRSA, n&#x2009;=&#x2009;2). Additionally, we novelly employed targeted probe capture metagenomics (TCM), which utilizes oligonucleotide probes to enrich and detect low-abundance microbial species and ARG sequences. TCM revealed the detection of human pathogenic taxa in 65.2% of samples, including P. aeruginosa (78.4%), Acinetobacter baumannii (77.9%), and S. aureus (71.1%). Clinically critical ARGs, such as blaCTX-M (2.0%), blaNDM (2.9%), blaSHV (3.4%), and mecA (62.3%), were detected in 63.7% of samples, indicating a potential transmission within the post-handwashing area.<br><br>CONCLUSIONS: Our findings highlight the role of post-handwashing areas as underrecognized reservoirs for MDROs, particularly MRSA. Furthermore, this study demonstrates the utility of TCM in public health surveillance by enabling a sensitive detection of rare but high-risk microbial species and drug resistance determinants in low-biomass environmental samples. This study offers a comprehensive and nuanced view of the microbial and resistome landscape of washroom environments, offering a revolutionary approach for future environmental surveillance.}, }
@article {pmid41250124, year = {2025}, author = {Huang, SW and Lin, CR and Chang, YH and Ni, YH and Chen, HL and Liu, HH}, title = {Cross-country multi-modal evidence links Aspergillus to biliary atresia.}, journal = {Gut pathogens}, volume = {17}, number = {1}, pages = {94}, pmid = {41250124}, issn = {1757-4749}, abstract = {BACKGROUND: Biliary atresia (BA) is the leading cause of pediatric liver transplantation. It is characterized by progressive extrahepatic bile duct obstruction in young infants. Inspired by the success of antifungal treatment in a newborn with BA-related obstructive cholangitis, we explored a potential link between BA and fungi, particularly Aspergillus. Fecal DNA was analyzed using 18S ribosomal sequencing and validated with a published fecal metagenomic dataset. Epidemiological data from the UK, Taiwan, and Japan were also examined.<br><br>RESULTS: Gut Aspergillus was exclusively detected in BA cases, suggesting it may be a potential trigger. Independent fecal metagenomic data from China and epidemiological correlations further supported this hypothesis. In the UK, BA presentations strongly correlated (r = 0.98, 95% CI [0.36, 1.0], p = 0.02) with Aspergillosis, but not with Candidiasis, during the COVID-19 lockdown. In Taiwan, a decade of data showed BA incidence was significantly associated (r = 0.78, 95% CI [0.29, 0.94], p = 0.01) with yearly Aspergillus-positive isolates among cancer-adjusted hospital admissions. In Japan, BA cases over 25 years correlated significantly (r = 0.85, 95% CI [0.37, 0.97], p = 0.01) with visceral Aspergillus burdens in autopsied cases, but not with other fungal infections.<br><br>CONCLUSIONS: The resolution of obstructive cholangitis in the antifungal-treated index case, together with multi-modal, cross-country evidence, highlights a potential link between gut Aspergillus and BA. Although limited by small sample size, retrospective design, and lack of mechanistic validation, the study may still be interpreted as hypothesis-generating and underscores the need for prospective studies to validate and extend these observations.}, }
@article {pmid41249836, year = {2025}, author = {Huang, Y and Sun, Y and Ronda, C and Mavros, CF and Li, J and Jacobse, J and Huang, LH and Resnick, SJ and Giddins, M and Freedberg, DE and Chavez, A and Goettel, JA and Wang, HH}, title = {Fecal exfoliome sequencing captures immune dynamics of the healthy and inflamed gut.}, journal = {Nature biotechnology}, volume = {}, number = {}, pages = {}, pmid = {41249836}, issn = {1546-1696}, support = {MCB-2025515//National Science Foundation (NSF)/ ; 1R01DK118044//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; 1R21AI146817//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; 1R01CA272898//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; 5U19AI067773//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R03DK123489//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; 1R21HG011855//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; 1R21HG011855//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; N00014-18-1-2237//United States Department of Defense | United States Navy | Office of Naval Research (ONR)/ ; N00014-17-1-2353//United States Department of Defense | United States Navy | ONR | Office of Naval Research Global (ONR Global)/ ; HR00111920009//United States Department of Defense | Defense Advanced Research Projects Agency (DARPA)/ ; S-168-4X5-001//United States Department of Defense | United States Air Force | AFMC | Air Force Research Laboratory (AFRL)/ ; 1016691//Burroughs Wellcome Fund (BWF)/ ; Career Awards for Medical Scientists//Burroughs Wellcome Fund (BWF)/ ; Career Awards for Medical Scientists//Burroughs Wellcome Fund (BWF)/ ; 1061046//Crohn's and Colitis Foundation (Crohn's &amp; Colitis Foundation)/ ; 1513935//Crohn's and Colitis Foundation (Crohn's &amp; Colitis Foundation)/ ; IRIS Award//Columbia University/ ; }, abstract = {Metagenomic sequencing and metabolomics of fecal matter have revealed the impact of the gut microbiome on health and disease. In addition to microbiota, feces also contain shed or exfoliated host epithelial, secretory and immune cells, but RNA profiling of these cells is challenging owing to degradation and cross-contamination. Here we introduce exfoliome sequencing (Foli-seq) to profile fecal exfoliated eukaryotic messenger RNAs (feRNAs) originating from the upper and lower gastrointestinal regions and show that this 'fecal exfoliome' harbors stable RNAs that reflect intestinal and immune function. By selectively amplifying targeted transcripts, Foli-seq demonstrates robust, accurate, sensitive and quantitative measurement of feRNAs. In murine colitis models, feRNA reveals temporal processes of epithelial damage, immune response and intestinal recovery specific to different types of gut inflammation. Simultaneous exfoliome and microbiome profiling uncovers a dense host-microbe interaction network. Moreover, we demonstrate stratification of patients with inflammatory bowel disease into subgroups that correlate with disease severity. Fecal Foli-seq is a noninvasive strategy to longitudinally study the gut and profile its health.}, }
@article {pmid41249624, year = {2025}, author = {Kocher, A and Krause, J and Spyrou, MA}, title = {Insights into infectious diseases through ancient pathogen genomics.}, journal = {Nature reviews. Microbiology}, volume = {}, number = {}, pages = {}, pmid = {41249624}, issn = {1740-1534}, abstract = {Major advances in metagenomic and biomolecular techniques have opened avenues for the recovery and sequencing of rare and highly fragmented DNA molecules from ancient biological samples, including those of pathogens that may persist in the remains of infected hosts long after their death. Initially consisting of relatively rare findings for a few disease-causing agents of historical importance, the field of ancient pathogen genomics is rapidly progressing towards genome-level analyses of larger sample sets encompassing a wider range of bacterial, viral and eukaryotic taxa. These advances have provided important insights into past pathogen distribution and genomic make-up, and the unprecedented opportunity to track their evolution 'in action' over large timescales. In this Review, we explore the major contributions of ancient DNA research to the understanding of pathogen evolution and its association with past epidemics, as well as human sociocultural and migration history, including numerous important studies that have been published in recent years. Moreover, we discuss existing limitations and future prospects of ancient pathogen genomics and the relevance of the field to current public health challenges.}, }
@article {pmid41249313, year = {2025}, author = {Kok, PJR and Wisse, BB and Kapuściak, M and Lampo, M}, title = {Amphibian supercooling capacity is not limited to sub-zero thermal environments.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {40311}, pmid = {41249313}, issn = {2045-2322}, support = {2020/39/D/NZ8/02399//Narodowe Centrum Nauki/ ; }, mesh = {Animals ; Freezing ; *Amphibians/physiology ; Skin/microbiology ; Cold Temperature ; Acclimatization ; Microbiota ; }, abstract = {Freeze-tolerant amphibians initiate controlled freezing using ice nucleators and survive internal ice formation by accumulating cryoprotectants. In contrast, freeze-avoidant (supercooling) species rely on the inhibition of ice nucleators to prevent freezing altogether. All confirmed supercooling species are native to the Northern Hemisphere and regularly endure negative temperatures. The occurrence, ecological role, and underlying mechanisms of supercooling in amphibians remain poorly understood. Here, we demonstrate for the first time that amphibian supercooling capacity may be present even if not expressed (i.e., latent) and not limited to freezing thermal environments. Exploratory metagenomic data allow us to evaluate whether skin-associated bacteria could contribute to freeze avoidance. In addition, using field experiments, we assess cold and dehydration tolerance limits in two syntopic amphibian species from a high tepui summit (Roraima-tepui in Venezuela) and explore the potential role of cryoprotective dehydration in facilitating supercooling. Despite being syntopic, these species showed striking differences in thermal and dehydration tolerance. Physiological freeze avoidance in tropical montane amphibians is shown to be associated with low critical thermal minima, high dehydration tolerance and possibly antifreeze-producing skin microbiota, although the latter needs further investigation. These traits may determine species persistence under shifting climatic regimes, particularly in thermally variable montane systems.}, }
@article {pmid41249299, year = {2025}, author = {Wu, Y and Meng, X and Han, X and Bu, Z and Li, Y and Zhan, H and Zhang, S}, title = {Integrated metagenomic and metabolomic analysis reveals microbial metabolite interactions involved in the quality formation of Codonopsis Radix.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {40278}, pmid = {41249299}, issn = {2045-2322}, mesh = {*Codonopsis/metabolism/microbiology/growth &amp; development/chemistry ; *Metabolomics/methods ; *Metagenomics/methods ; Soil Microbiology ; *Drugs, Chinese Herbal/metabolism ; Plants, Medicinal/metabolism/microbiology ; }, abstract = {Due to the impact of various environmental factors, in conjunction with the ecological adaptability and biochemical diversity of Chinese medicinal materials, Codonopsis Radix from Shanxi Province has developed into two distinct commercial specifications, namely Tai Codonopsis Radix (TCP) and Lu Codonopsis Radix (LCP). The present study examined the relationships between TCP and LCP from Shanxi Province regarding their environment, secondary metabolites, and Traditional Chinese Medicinal plant authenticity using metagenomic, metabolomic, and comprehensive quality assessment methods. The findings revealed that the two types of CPs met the quality standards. With respect to the growing environment, TCP and LCP grow in the same longitudinal extent, with a maximum longitudinal span of only 53'. Both regions presented similar natural environments conducive to the growth of CP. Additionally, the Lobetyolin content in TCP was greater than that in LCP. The soil microbial abundance in the TCP group was considerably significantly greater than that in the LCP group, and a new genus, Ascobolus, was found in TCP. Additionally, comparison of the metallic element data of the two groups soils revealed that the contents of Ti, Mg, Cr (P < 0.01) in the TCP group were significantly greater than those in the LCP group. Through correlation analysis, the ternary network of microbial-metal-metabolite interactions was constructed. The rhizosphere fungus Ascobolus was found to enhance the bioavailability of Zn via mineralization processes, thereby underscoring the significance of rhizosphere microecology in promoting plant growth. This study offers novel insights and approaches for the cultivation and processing of Codonopsis Radix.}, }
@article {pmid41249223, year = {2025}, author = {Li, CM and Cheng, TH and Chen, YJ and Liang, YR and Huang, CL}, title = {Crab shell meal promotes root-knot nematode control through shifts in soil microbial communities and enhanced nitrification.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {40115}, pmid = {41249223}, issn = {2045-2322}, support = {108AS-8.5.2-PI-P2//Ministry of Agriculture, Taiwan/ ; Higher Education Sprout Project//Ministry of Education, Taiwan/ ; }, mesh = {Animals ; *Soil Microbiology ; *Cucumis sativus/parasitology/growth &amp; development ; *Microbiota/drug effects ; *Nitrification/drug effects ; Plant Roots/parasitology ; *Tylenchoidea ; Soil/chemistry ; *Plant Diseases/parasitology/prevention &amp; control ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; *Brachyura/chemistry ; }, abstract = {With growing environmental awareness, eco-friendly agricultural practices are gaining increased attention. Among these, crab shell meal (CSM) is recognized for its potential to suppress root-knot nematodes (Meloidogyne spp.), largely through the enrichment of chitinolytic bacteria, particularly members of the phylum Actinobacteriota. However, the broader effects of CSM on the soil microbiome remain poorly understood. This study employed 16S amplicon metagenomics to investigate the impact of CSM application on the soil bacterial community associated with root-knot nematode-infected cucumber (Cucumis sativus L.) in a pot experiment. Plant growth parameters and soil chemical properties were also assessed. CSM application at concentrations ranging from 0% to 4% significantly altered the soil microbiome, increasing in the relative abundances of Firmicutes and Actinobacteriota in a dose-dependent manner. These microbial shifts were associated with enhanced cucumber growth and reduced nematode infection severity. Functional predictions indicated that CSM-enriched microbial communities exhibited higher potential for chitin hydrolysis and nitrification, processes that likely contributed to nematode suppression and plant growth promotion. By contrast, the introduction of Streptomyces as a biocontrol agent was less effective, as this strain struggled to establish within the potting system. Overall, the application of CSM successfully enhanced the abundance of chitinolytic bacteria and soil nitrification, providing a dual benefit of nematode control and improved plant growth.}, }
@article {pmid41229281, year = {2026}, author = {Richardson, RT and Avalos, G and Garland, CJ and Trott, R and Hager, O and Hepner, MJ and Raines, C and Goodell, K}, title = {Sensitive Environmental DNA Methods for Low-Risk Surveillance of At-Risk Bumble Bees.}, journal = {Molecular ecology resources}, volume = {26}, number = {1}, pages = {e70073}, doi = {10.1111/1755-0998.70073}, pmid = {41229281}, issn = {1755-0998}, support = {RC22-B5-7373//Environmental Security Technology Certification Program/ ; //Maryland Department of Natural Resources/ ; //University of Maryland/ ; }, mesh = {Animals ; Bees/genetics/classification/physiology ; *DNA, Environmental/genetics/isolation &amp; purification ; *DNA Barcoding, Taxonomic/methods ; *Metagenomics/methods ; }, abstract = {Terrestrial environmental DNA (eDNA) techniques have been proposed as a means of sensitive, non-lethal pollinator monitoring. To date, however, no studies have provided evidence that eDNA methods can achieve detection sensitivity on par with traditional pollinator surveys. Using a large-scale dataset of eDNA and corresponding net surveys, we show that eDNA methods enable sensitive, species-level characterisation of whole bumble bee communities, including rare and critically endangered species such as the rusty patched bumble bee (RPBB; Bombus affinis). All species present in netting surveys were detected within eDNA surveys, apart from two rare species in the socially parasitic subgenus Psithyrus (cuckoo bumble bees). Further, for rare non-parasitic species, eDNA methods exhibited similar sensitivity relative to traditional netting. Compared with flower eDNA samples, sequenced leaf surface eDNA samples resulted in significantly lower rates of Bombus detection, and these detections were likely attributable to high rates of background eDNA on environmental surfaces, perhaps due to airborne eDNA or eDNA movement during rainfall events. Lastly, we found that eDNA-based frequency of detection across replicate surveys was strongly associated with net-based measures of abundance across site visits. We conclude that the COI-based metabarcoding method we present is cost-effective and highly scalable for quantitative characterisation of at-risk bumble bee communities, providing a new approach for improving our understanding of species habitat associations.}, }
@article {pmid41249177, year = {2025}, author = {Zhang, D and Hu, Q and Zhou, Y and Yu, H and Cong, W and Cheng, M and Wang, J and Liu, X and Zou, K and Long, S and Zhao, C and Jiang, J and Zhang, Y}, title = {Multi-omic profiling reveals distinct gut microbial and metabolic landscapes in golden snub-nosed monkeys under contrasting conservation strategies.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {209}, pmid = {41249177}, issn = {2055-5008}, support = {2020BCA081//Key Research and Development Project of Hubei Province/ ; 2013BAD03B02//National Key Technology R&amp;D Program of China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology/chemistry ; Metagenomics/methods ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Conservation of Natural Resources/methods ; Metabolomics/methods ; Metabolome ; *Colobinae/microbiology ; Endangered Species ; Multiomics ; }, abstract = {Gut microbiota are crucial for the fitness of endangered wildlife, yet how different conservation strategies affect these microbial ecosystems and their metabolic activities remains insufficiently understood. This study employed integrated metagenomic and metabolomic analyses to compare the gut microbial communities and fecal metabolomes of endangered golden snub-nosed monkeys (Rhinopithecus roxellana) under three distinct conservation scenarios: natural wild, food provisioning, and captivity. We established a comprehensive species-specific gut microbial gene catalog and observed significant microbial and metabolic divergence associated with each conservation strategy. Monkeys in managed settings (captive and provisioned) exhibited larger gut microbial gene catalogs than wild individuals. While alpha diversity was highest in the provisioned group, both captive and provisioned groups showed notably altered microbial community structures and co-occurrence networks compared to the wild baseline. Captivity was linked to the most pronounced shifts, including a microbiome assembly more strongly governed by deterministic processes, reduced network stability, and an enrichment of habitat specialists, alongside an increased abundance of antibiotic resistance genes (ARGs) and virulence factors (VFs), and distinct alterations in microbiota-metabolite co-variation patterns, particularly concerning amino acid metabolism. These findings highlight that food provisioning, when managed to emulate natural conditions, is associated with a less disruptive microbial and metabolic profile than intensive captivity, offering crucial insights for developing microbiome-informed conservation practices to enhance the health and long-term viability of this endangered primate.}, }
@article {pmid41249156, year = {2025}, author = {Liu, L and Wang, Z and Zhang, W and Lin, W}, title = {Recovery of 1,773 microbial genomes and 2,060 viral genomes from the Mars-analog Qaidam Basin desert.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1795}, pmid = {41249156}, issn = {2052-4463}, support = {T2225011//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Genome, Viral ; Desert Climate ; *Soil Microbiology ; *Mars ; *Genome, Microbial ; Metagenome ; Metagenomics ; Tibet ; }, abstract = {The Qaidam Basin on the northern Tibetan Plateau represents a terrestrial Mars-analog desert characterized by hyperaridity, low temperatures, intense ultraviolet radiation, and high-salinity soils. To unveil the largely unexplored genomic diversity of microbes and viruses in this extreme environment, we collected 58 soil samples from various landforms and depths for metagenomic sequencing and analysis. We reconstructed 1,773 microbial metagenome-assembled genomes (mMAGs) and 2,060 viral MAGs (vMAGs), the vast majority (>94%) of which represent novel taxa. Among these, 327 mMAGs (completeness ≥ 90% and contamination ≤ 5%) and 325 vMAGs (completeness ≥ 90%) were classified as high-quality genomes. Taxonomic classification revealed that the bacterial, archaeal, and viral phyla with the largest numbers of genomes were Actinomycetota (n = 565), Halobacteriota (n = 111), and Uroviricota (n = 836), respectively. This metagenomic and genomic dataset provides valuable reference data for advancing our understanding of the diversity and function of microbial and viral communities across global desert ecosystems. Furthermore, these data offer astrobiological insights for research on life in Mars-analog extreme environments.}, }
@article {pmid41248761, year = {2025}, author = {Wang, X and Liu, L and Fan, W and Liu, R and Yuan, H and Li, X}, title = {Enhanced anaerobic digestion performance of food waste by Fe-Mn MOF-derived carbon composite: Methane production, microbial response, and intrinsic mechanisms.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {133667}, doi = {10.1016/j.biortech.2025.133667}, pmid = {41248761}, issn = {1873-2976}, abstract = {This study investigated the effects of Fe-Mn MOF-derived carbon composite (Fe-Mn MDC) on anaerobic digestion (AD) performance of food waste (FW) and elucidated the underlying mechanisms. The methane yield increased to 457.44 ± 14.21 mL/g VS under 0.05 g/g TS Fe-Mn MDC addition, representing a 36.47 % increase compared to the control group. Metagenomics analysis indicated that Fe-Mn MDC altered the microbial community structure, enriched the abundance and mutualism of exoelectrogenic bacteria (Geobacter) and electroactive methanogenic microorganisms (Methanothrix) involved in direct interspecies electron transfer. The metabolic activity of hydrogenotrophic methanogens was enhanced under Fe-Mn MDC addition, and the content of dehydrogenase and coenzyme F420 was also stimulated, thereby accelerating substrate consumption and methane production. The physicochemical characterization results of Fe-Mn MDC demonstrated that it could act as an electron shuttle and facilitate proton transfer. Besides, AD system exhibited not only an increase in e-pili and c-type genes abundance, but also an enhanced representation of gene modules linked to the biosynthesis of V/A-type ATPases (M00159) and F-type (M00157), which further indicated that Fe-Mn MDC enhanced the proton-coupled electron transfer in AD system. These results provided potential applications in FW management and new insights into the mechanism of renewable energy recovery from AD.}, }
@article {pmid41248707, year = {2025}, author = {Mizuno, S and Horiba, K and Nakahashi, T and Atsumi, Y and Takahara, T and Hashino, M and Ito, Y and Kamimura, K}, title = {A 1-year-old boy presenting with roseola accompanied by bilateral eyelid oedema and acute infectious mononucleosis syndrome caused by human herpesuvirus-6B: a case report.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {}, number = {}, pages = {108213}, doi = {10.1016/j.ijid.2025.108213}, pmid = {41248707}, issn = {1878-3511}, abstract = {Bilateral eyelid oedema, also known as Hoagland sign, is a specific physical sign of infectious mononucleosis (IM) syndrome caused by Epstein-Barr virus (EBV) infection in older children and adolescents. IM syndrome, which is mainly caused by EBV or cytomegalovirus infection, has milder symptoms in young children than in older children and adolescents. The human herpesvirus 6B (HHV-6B) causes roseola infantum (sixth disease) and various complications in children younger than 2 years; however, bilateral eyelid oedema and IM syndrome are rarely reported. We report the case of a 1-year-old boy with bilateral upper eyelid oedema and severe IM syndrome, including pancytopenia with an increased atypical lymphocyte count, purpura due to thrombocytopenia, and elevated liver enzyme and ferritin levels. Metagenomic next-generation sequencing indicated active HHV-6B infection. The patient improved within 1 week without any specific treatment. Our experience with this case suggests that the presentations observed should be considered rare complications of HHV-6B infection.}, }
@article {pmid41248576, year = {2025}, author = {Zhou, Y and Chang, L and Sun, H and Li, W and Ao, T and Lin, J}, title = {Evaluation of reclaimed treated wastewater on soil quality, microbial community and function in urban greening irrigation.}, journal = {Journal of environmental management}, volume = {395}, number = {}, pages = {127958}, doi = {10.1016/j.jenvman.2025.127958}, pmid = {41248576}, issn = {1095-8630}, abstract = {Reclaimed treated wastewater (TWW) offers a sustainable irrigation alternative for urban greening amid freshwater scarcity. However, its impact on soil quality and microbial ecology in urban landscapes remains underexplored. This study assessed the effects of three TWW types and one TWW-purified water mixture on soil properties, heavy metal accumulation, enzyme activity and microbial community dynamics in Common Nandina (Nandina domestica Thunb.) systems over three- and five-month in Nanjing, China, using a metagenomic approach. The results showed that TWW irrigation significantly increased soil nitrogen, phosphorus content and pH (P < 0.05), with stronger effects observed at three-month (P < 0.05). Soil heavy metal content varied, with Cr and As exhibiting potential accumulation. Enzyme activity (N-acetyl-glucosaminidase and phosphatase) was positively influenced by TWW irrigation at three-month. Metagenomic analysis revealed significant shifts in microbial community composition, particularly fungi, with Mucoromycota increasing and Ascomycota decreasing under TWW. The Normalized Stochasticity Ratio indicated increased stochasticity in microbial assembly under TWW irrigation (P < 0.05). Functionally, TWW increased abundance of functional genes related to amino acid metabolism and peroxisomes (P < 0.05), but decreased degradation genes for aromatic compounds. TWW also increased the abundance of antibiotic resistance genes (ARGs), particularly those related to triclosan and glycopeptide, and plant pathogenic genera like Aspergillus and Fusarium. The findings suggest that while TWW irrigation improves certain soil properties and microbial functions in the short term, it may pose ecological risks from heavy metal and microbial contamination, offering key insights for sustainable urban irrigation strategies.}, }
@article {pmid41247052, year = {2025}, author = {Huang, X and Zeng, J and Yang, F and Liu, Y and Chen, J and Wang, H and Li, S and Li, C and Zhang, S}, title = {Microbial succession in human tissues postmortem: insights from 2bRAD-M sequencing.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0266624}, doi = {10.1128/spectrum.02666-24}, pmid = {41247052}, issn = {2165-0497}, abstract = {Microbial communities play a crucial role in decomposition, yet their patterns in human tissues remain underexplored. Most previous research has often focused on animal models such as mice and swine, with limited studies on human samples, primarily targeting specific environments like the gut and skin. Consequently, gaps persist in understanding postmortem microbial dynamics within internal human organs. The 2bRAD-M sequencing technology offers a powerful approach for human thanatomicrobiome research, overcoming key limitations of 16S rRNA and metagenomic sequencing methods. In this study, we used 2bRAD-M to profile microbial succession across seven human tissues-heart, liver, spleen, lung, kidney, calf muscle, and gut-at various postmortem intervals (PMIs). Significant variations in microbial community composition were observed across organs and decomposition stages, with Proteobacteria dominating early and Firmicutes later. A comparison of frozen and unfrozen cadavers (PMI 1-7 days) revealed divergent microbial shifts in the liver and spleen, while other tissues exhibited limited variation. These findings highlight complex, organ-specific microbial trajectories and suggest that microbial signatures could serve as biomarkers for PMI estimation. This research deepens our understanding of the microbial succession within internal human organs postmortem and contributes to elucidating the identity and role of microorganisms in human decomposition.IMPORTANCEHumans host a diverse array of microbial communities that play a crucial role in the decomposition process after death. Understanding these postmortem microbial dynamics is essential, as they offer valuable insights into the progression of decomposition with significant implications for forensic science. The role of microorganisms in corpse decomposition has gained increasing attention in both forensic and ecological research, but studies in this area remain in their early stages, requiring further in-depth exploration. This work pioneers the use of 2bRAD-M sequencing to investigate microbial changes across various human organs over increasing postmortem intervals. By enhancing knowledge of postmortem microbiota dynamics, the study contributes to refining and improving the accuracy of forensic methodologies.}, }
@article {pmid41247049, year = {2025}, author = {Ma, J and Yu, L and Zhao, K and Qiao, Q and Zhu, X and Wu, T and Rong, H and Ning, S and Guo, J and Ding, Y and Chi, Y and Cui, L and Ge, Y}, title = {A novel targeted hybrid capture-NGS assay for sensitive detection of multiplex respiratory pathogens.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0290825}, doi = {10.1128/spectrum.02908-25}, pmid = {41247049}, issn = {2165-0497}, abstract = {UNLABELLED: Emerging respiratory infectious diseases represented by COVID-19, along with traditional respiratory infections, pose a serious threat to human health. High-throughput sequencing (NGS), with its high sensitivity and ultra-high throughput, is particularly suitable for the detection of respiratory pathogens (RP) that are extremely diverse in types and frequently involved in mixed infections. In this study, by integrating a Micro-Targets Hybrid Capture (MT-Capture) system, we developed previously with NGS, we developed a novel assay (termed RP-MT-Capture NGS) for the detection of multiple respiratory pathogens (more than 300 species/types). By optimizing probe design and hybridization capture procedures, RP-MT-Capture NGS achieved high detection sensitivity for different types of pathogens. For influenza viruses, this assay could acquire full-length sequences of hemagglutinin (HA) and neuraminidase (NA) genes for samples with CT values < 32, offering a robust tool for viral mutation surveillance and recombination analysis. The results of clinical sample detection showed that RP-MT-Capture NGS exhibited superior accuracy and sensitivity compared to TaqMan array and metagenomic NGS (mNGS) technologies for respiratory pathogen detection. Compared with traditional probe hybridization-based targeted NGS (tNGS), RP-MT-Capture NGS significantly shortens the wet lab experiment time to within 6 h. In summary, the RP-MT-Capture NGS assay developed in this study offers a novel tool for detecting multiple respiratory pathogens, with substantial clinical and public health relevance.<br><br>IMPORTANCE: Emerging and traditional respiratory infections pose threats to human health. These diseases are caused by a variety of pathogens, which often lead to co-infections and, thus, make detection difficult. This study combines a novel probe hybridization capture system with high-throughput sequencing to develop a new detection tool (RP-MT-Capture NGS), which can identify over 300 types of respiratory pathogens. For influenza viruses, it can reveal complete details of key viral genes, facilitating the tracking of viral mutations. Compared with existing detection methods, this new tool is more accurate, more sensitive, and has a higher throughput. It provides great value for clinical practice and public health in respiratory pathogen detection.}, }
@article {pmid41246284, year = {2025}, author = {Yang, C and Lv, M and Li, Y and He, Y and Zhang, S and Zhang, G and Lan, J and Guo, Z and Cheng, Y and Yang, Y and Sun, J and Ma, L and Zhang, L}, title = {The interactions between psychological stress, gut microbiota, and fecal metabolites: A longitudinal multi-omics study in Chinese adolescents.}, journal = {Current research in microbial sciences}, volume = {9}, number = {}, pages = {100498}, doi = {10.1016/j.crmicr.2025.100498}, pmid = {41246284}, issn = {2666-5174}, abstract = {OBJECTIVES: This study investigated the bidirectional associations between psychological stress, gut microbiota, and fecal metabolites in a cohort of Chinese adolescents using a multi-omics approach.<br><br>METHODS: Baseline fecal samples from 124 adolescents were subjected to 16S rRNA gene amplicon sequencing, with 51 participants providing samples for metagenomic sequencing and untargeted metabolomics at baseline and follow-up. Psychological stress was assessed via the Adolescent Self-Rating Life Events Checklist.<br><br>RESULTS: After covariates adjustment, baseline total stress was associated with depleted alpha- and beta-diversity and abundances of the genera Lachnospiraceae NK4A136 group and unclassified Muribaculaceae.In longitudinal analyses, with the same covariates, baseline total stress was associated with six follow-up microbial species (Pfdr < 0.1; Actinomyces spp. HMSC035G02, Actinomyces sp. ICM58, Actinomyces sp. oral taxon 172, Schaalia odontolytica, Blautia sp. AF17-9LB, and Blautia sp. AM47-4) and 83 metabolites, predominantly lipids. These metabolites were primarily enriched in Kyoto Encyclopedia of Genes and Genomes pathways of lipid metabolism. Schaalia odontolytica, Actinomyces sp. ICM58, and Actinomyces spp. HMSC035G02 mediated associations between the total stress score and five lipids, with Schaalia odontolytica demonstrating the strongest effect (26.3 % mediated). Seven baseline metabolites but no microbial species were predictive of follow-up total stress. These metabolites exhibited an area under the curve of 0.72 for differentiating adolescents with high versus low stress, with 5-oxo-eicosatetraenoic acid being the strongest predictor.<br><br>CONCLUSIONS: This study suggests that psychological stress is associated with specific gut microbes and lipid metabolites change, and in turn, specific metabolites contribute to psychological stress change. These findings provide insights into bidirectional interactions between psychological stress and gut microbiota in adolescents.}, }
@article {pmid41246108, year = {2025}, author = {Benghanem, S and Pérot, P and Rodriguez, C and Fourgeaud, J and Bouguerra, M and Mathon, B and Seilhean, DD and Bielle, F and Plu, I and Jamet, A and Weiss, N and Marois, C and Rohaut, B and Eloit, M and Demeret, S}, title = {Diagnostic Yield of Next-Generation Sequencing in CSF or Brain Biopsy for Severe Encephalitis Requiring Intensive Care.}, journal = {Neurology. Clinical practice}, volume = {15}, number = {6}, pages = {e200558}, doi = {10.1212/CPJ.0000000000200558}, pmid = {41246108}, issn = {2163-0402}, abstract = {OBJECTIVES: The aim of this study was to evaluate the contribution of metagenomic next-generation sequencing (mNGS) in critically ill patients with encephalitis of unknown etiology.<br><br>METHODS: This retrospective study (2016-2023) was conducted in a tertiary care referral neuro-ICU at La Piti&#xe9;-Salp&#xea;tri&#xe8;re Hospital (Paris, France). The inclusion criteria were encephalitis with unknown etiology and mNGS performed on CSF, brain biopsy, and/or autopsy. We assessed the yield of mNGS and whether specific treatments were initiated. Neurologic outcome at 1 year was assessed using the Glasgow Outcome Scale-Extended (GOSE-1: death; GOSE-8: upper good recovery).<br><br>RESULTS: A total of 49 patients were included, of whom 44.9% were immunosuppressed. At 1 year, 38.8% had a GOSE score 4-8 and 47.7% died. mNGS was performed on the CSF of 40 of 49 patients (81.6%) and on brain biopsy of 19 of 49 patients (38.8%), including 12 patients who underwent both CSF and biopsy testing. Among the 40 mNGS analyses performed on the CSF, 7 (17.5%) yielded positive results but only 1 (2.5%) was likely causative. Conversely, 7 of 19 mNGS analyses (36.8%) on biopsies were positive and causative. Regarding the yield of mNGS in the entire cohort, 15 of 49 patients (30.6%) had a positive result but only 7 of 49 (14.3%) were causative (dengue virus, measles virus, rubella virus, Nocardia spp, HHV6, astrovirus, and orthobunyavirus), all from brain biopsies of immunocompromised patients. Conversely, 8 of 49 mNGS analyses (16.3%) were noncausative (polyomavirus, HHV8, HHV7, EBV, 2 pegiviruses, and 2 rhinoviruses). Specific treatments were initiated in 4 of 7 patients (57%). Among the 34 patients with a negative mNGS result, 5 (14.7%) were diagnosed with infectious encephalitis using conventional methods.<br><br>CONCLUSION: In critically ill patients with encephalitis of unknown etiology, mNGS performed on brain biopsy could reduce diagnostic uncertainty.}, }
@article {pmid41245671, year = {2025}, author = {Orbea, M and Fortini, M and Amerson-Brown, MH and Palazzi, DL and Dunn, JJ}, title = {Mycetohabitans rhizoxinica bacteremia in the setting of invasive fungal disease in an immunocompromised patient.}, journal = {ASM case reports}, volume = {1}, number = {4}, pages = {}, doi = {10.1128/asmcr.00014-24}, pmid = {41245671}, issn = {2996-2684}, abstract = {BACKGROUND: Mycetohabitans [Burkholderia] rhizoxinica is an endosymbiotic bacteria of Rhizopus microsporus that normally causes rice seedling blight. In our case report, we present one of the first known cases of concomitant bacteremia with M. rhizoxinica and invasive mold infection due to Rhizopus spp. in an immunocompromised child.<br><br>CASE SUMMARY: A 3 year old male recently diagnosed with B-cell acute lymphoblastic leukemia developed febrile neutropenia. His workup was significant for invasive fungal sinusitis due to Exserohilum spp. based on histopathology and culture, a right middle lobe infiltrate, and a blood culture positive for gram-negative coccobacilli, later identified as M. rhizoxinica. Additionally, metagenomics next-generation sequencing was positive for R. microsporus as was broad-range fungal PCR testing of a lung biopsy sample. His surgical treatments included sinus debridement and a near total right pneumonectomy, and his antimicrobial treatment included 10 days of cefepime for his bacteremia, 4 weeks of liposomal amphotericin B, 4 weeks of micafungin following his pneumonectomy, and approximately 12 months of posaconazole.<br><br>CONCLUSION: This case highlights the association of M. rhizoxinica with Rhizopus spp., wherein the isolation of M. rhizoxinica led to a high index of suspicion of Rhizopus infection in an immunocompromised patient who developed bacteremia with a slow-growing, oxidase positive, gram-negative bacteria not able to be identified by traditional identification methods.}, }
@article {pmid41245635, year = {2025}, author = {Wongwattanarat, S and Schorn, A and Klose, L and Carré, C and Malvis Romero, A and Liese, A and Pérez-García, P and Streit, WR}, title = {A combined chemo-enzymatic treatment for the oxidation of epoxy-based carbon fiber-reinforced polymers (CFRPs).}, journal = {Frontiers in bioengineering and biotechnology}, volume = {13}, number = {}, pages = {1670548}, doi = {10.3389/fbioe.2025.1670548}, pmid = {41245635}, issn = {2296-4185}, abstract = {Carbon fiber-reinforced polymers (CFRPs), particularly epoxy-based composites, have become essential in the aerospace, automotive, and wind energy industries due to their robust mechanical properties, and lightweight nature. However, there is a lack of recycling technologies that are environmentally sustainable while also ensuring the recovery of carbon fibers in their original state. Although certain bacterial and fungal strains can colonize epoxy polymers, enzymes capable of efficiently degrading these materials have not yet been reported. Consequently, there is an urgent need for an effective, sustainable, and biologically inspired solution for CFRP recycling. Here, a chemo-enzymatic two-step oxidation process was developed. A chemical pre-treatment with propionic acid and hydrogen peroxide was used to recover imbedded carbon fibers. Additionally, three novel bacterial laccases isolated from a European spruce bark beetle gut metagenome (Ips typographus) demonstrated the ability to oxidize three epoxy resin scaffolds derived from TGMDA-based epoxy resin system, a high-performance material commonly used in aerospace applications. The sequential combination of both oxidative steps enabled the retrieval of clean carbon fibers and showed the potential of the laccase to partially further modify the pre-treated cured epoxy. This bio-inspired approach marks an initial step toward developing a bio-based recycling method for epoxy CFRPs.}, }
@article {pmid41245257, year = {2025}, author = {Devarajalu, P and Attri, SV and Kumar, J and Dutta, S and Kabeerdoss, J}, title = {Correction: Characterization of gut microbiota signatures in Indian preterm infants with necrotizing enterocolitis: a shotgun metagenomic approach.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1706582}, doi = {10.3389/fcimb.2025.1706582}, pmid = {41245257}, issn = {2235-2988}, abstract = {[This corrects the article DOI: 10.3389/fcimb.2025.1649384.].}, }
@article {pmid41244979, year = {2025}, author = {Ladines-Lim, JB and Yang, WT and Tebas, P and O'Donnell, J and Koenig, H and Kreider, E and Dyer, K and Anwar, M and Rodriguez, E and Patel, S and Rodino, K and Glaser, L and Richterman, A}, title = {Delayed diagnosis of disseminated Mycobacterium intracellulare subsp. chimaera infective endocarditis via cell-free metagenomic next-generation sequencing: a case report.}, journal = {ASM case reports}, volume = {1}, number = {5}, pages = {}, doi = {10.1128/asmcr.00003-25}, pmid = {41244979}, issn = {2996-2684}, abstract = {BACKGROUND: Mycobacterium intracellulare subsp. chimaera infective endocarditis associated with contaminated heater-cooler units has been well documented, leading to the discontinuation of these devices in most hospitals by 2018. The rarity of this infection and its nonspecific symptoms often result in delayed diagnosis.<br><br>CASE SUMMARY: We describe a 56-year-old female diagnosed with M. intracellulare subsp. chimaera infective endocarditis with disseminated intracranial abscess 7 years after aortic and mitral valve replacement. Diagnosis was achieved using cell-free microbial DNA next-generation sequencing (cfmNGS). She underwent left temporal craniotomy for abscess drainage and aortic and mitral valve replacement. Diagnosis was confirmed via mycobacterial culture from blood, brain tissue, and explanted valve tissue. Treatment included rifabutin, ethambutol, azithromycin, and amikacin, alongside a prednisone taper prescribed for a previously diagnosed undifferentiated inflammatory process. Amikacin was discontinued 6 weeks after valve surgery because of unilateral hearing loss. She remained clinically stable 5 months after valve surgery.<br><br>CONCLUSION: This case highlights that M. intracellulare subsp. chimaera infections may continue to emerge years after heater-cool unit discontinuation, suggesting that the time window for case incidence may still be active. cfmNGS may serve as a valuable diagnostic tool for disseminated M. intracellulare subsp. chimaera. Finally, we discuss pharmacotherapeutic factors, including the need for multiple agents over long durations, in this case with specific considerations given to the dissemination of infection into the central nervous system and potential drug-drug interactions, including steroids.}, }
@article {pmid41244776, year = {2025}, author = {Tan, J and Liu, L and Wang, L and Qu, Y and Sun, Z and Wang, Q and Liu, Y}, title = {Case Report: First pulmonary infection caused by Mycobacterium colombiense in a non-immunosuppressed host with bronchiectasis: diagnosis facilitated by synergistic mNGS and culture.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1671968}, doi = {10.3389/fmed.2025.1671968}, pmid = {41244776}, issn = {2296-858X}, abstract = {Mycobacterium colombiense, a rare slow-growing mycobacterium within the Mycobacterium avium complex (MAC), causes disseminated disease almost exclusively in immunocompromised hosts, with no prior reports of localized pulmonary infection in non-immunosuppressed individuals. A 47-year-old non-immunosuppressed male with bronchiectasis presented with progressive cough, night sweats, and fatigue. Computed tomography (CT) revealed bronchiectasis with nodules in the right middle and lower lobes. Empirical β-lactam therapy failed, and conventional bronchoalveolar lavage fluid (BALF) tests (smears, cultures, PCR) yielded no pathogens at 48 h. Although metagenomic next-generation sequencing (mNGS) of BALF detected a low number of M. colombiense sequences (eight reads), definitive confirmation was achieved through extended culture, which is considered the gold standard for the diagnosis of nontuberculous mycobacteria. This culture revealed acid-fast bacilli within 12 days (160 CFU), confirming the presence of viable M. colombiense. Subsequent mNGS of the isolated colonies further confirmed the species identity with high sequence reads (25,787 reads). Guideline-based triple therapy (guided by drug susceptibility testing and guidelines) with clarithromycin, rifampicin, and ethambutol achieved significant radiographic resolution at 24 weeks. This case demonstrates that M. colombiense pulmonary infection is diagnostically elusive and mimics non-specific respiratory syndromes. It defines the clinical features of this pathogen in non-immunosuppressed hosts and highlights the need for heightened surveillance for nontuberculous mycobacteria (NTM) in bronchiectasis patients, given the likelihood of underdiagnosis.}, }
@article {pmid41244772, year = {2025}, author = {Li, Q and Song, XC and Li, K and Wang, J}, title = {Gut-lung immunometabolic crosstalk in sepsis: from microbiota to respiratory failure.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1685044}, doi = {10.3389/fmed.2025.1685044}, pmid = {41244772}, issn = {2296-858X}, abstract = {Sepsis is a systemic immune-metabolic disorder syndrome caused by infection, in which gut microbiota dysbiosis plays a central role in the occurrence and development of multi-organ dysfunction. This paper systematically elaborates on the bidirectional regulatory mechanism of the "gut-lung axis" in sepsis. Gut microbiota dysregulation damages the gut barrier function, reduces the production of short-chain fatty acids (SCFAs), and increases endotoxin translocation. Subsequently, it activates alveolar macrophage polarization, promotes the formation of neutrophil extracellular traps (NETs), and leads to an imbalance in the Treg/Th17 cell ratio, ultimately exacerbating the pathological process of acute lung injury (ALI) or acute respiratory distress syndrome (ARDS). Conversely, the pulmonary inflammatory response can also aggravate gut barrier damage through circulating inflammatory mediators, forming a vicious cycle. Mechanistically, HIF-1α, mTOR, and Sirtuins do not act in isolation. Instead, they jointly regulate the metabolic fate of immune cells through spatiotemporally dynamic interactions. During the evolution of sepsis, these signals exhibit opposite regulatory polarities during the hyper-inflammatory phase and the immunosuppressive phase, and mitochondrial dysfunction and oxidative stress further amplify the inflammatory cascade reaction. Preclinical research evidence shows that microbiota-based intervention measures (including probiotic preparations, fecal microbiota transplantation, and SCFA supplementation) and vagus nerve electrical stimulation can effectively alleviate sepsis-related lung injury and improve prognosis, but there is significant individual heterogeneity in their therapeutic effects. Future research should not be restricted to descriptive associations. Instead, it is essential to conduct in-depth analyses of the specific logic of the aforementioned signaling networks in terms of cell types, subcellular compartments, and disease course timings, and clarify their context-dependent controversies to promote the transformation of mechanistic understanding into precision treatment. Meanwhile, research efforts should focus on constructing a multi-omics dynamic biomarker system integrating metagenomics, metabolomics, and immunophenotyping analysis and designing clinical trials through precise patient stratification to facilitate the clinical translation of individualized treatment strategies based on gut-lung axis regulation.}, }
@article {pmid41244681, year = {2025}, author = {Ru, J and Jiang, Z and Li, J and Li, X and Su, Z and Li, T and Xu, M}, title = {Screening of microbial consortium with high efficiency of lignin-degrading and its synergistic metabolic mechanism.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1709019}, doi = {10.3389/fmicb.2025.1709019}, pmid = {41244681}, issn = {1664-302X}, abstract = {INTRODUCTION: Lignin is difficult to degrade, which makes its high-value utilization a challenge. So finding an efficient method to degrade lignin is very important. At present, microbial degradation is considered to be one of the most effective and environmentally friendly degradation methods that is widely accepted.<br><br>METHODS: This study enriched three lignin-degrading microbial consortia R0, R1 and R2 using alkali lignin as the sole carbon source under 15&#x202f;&#xb0;C conditions. Using the methods of 16S rRNA sequencing, metagenomics, and metabolomics, the degradation mechanism of these three microbial consortia were systematically analyzed.<br><br>RESULTS: The microbial consortium R0, which has the best degradation efficiency, can degrade more than 80% within 6&#x202f;days, with dominant genera being Achromobacter and Pseudomonas. The dominant genera in other two microbial consortia R1 and R2 are Pseudomonas and Achromobacter in R1, Pseudomonas and Sphingobacterium in R2. Protocatechuic acid is a central intermediate in the degradation of lignin, its degradation pathway was fully annotated in microbial consortia R0 and R1. Microbial consortium R0 has the most abundant of AA (Auxiliary Activities) family genes annotated as carbohydrate annotation enzymes. The dominant genera in the microbial consortium R0 based on AA family gene abundance were Pseudomonas and Achromobacter.<br><br>DISCUSSION: Our results indicated that Pseudomonas is the dominant genus in lignin degradation, the metabolic potential of other abundant genera suggests a possible complementary role in the lignin degradation process. In the lignin degradation system with Pseudomonas as the dominant genera, the degradation of protocatechuic acid is the core of the degradation process. This study could enrich the mechanism of efficient and stable lignin degradation by microbial consortium, and could provide theoretical guidance for the development of lignin biodegradation technology in industry.}, }
@article {pmid41244617, year = {2025}, author = {Ma, ZS}, title = {Microbial Biomarkers of Breast Tumor and Mastitis: Deciphering the Delicate Balance between Potentially "Evil" and "Benign" Alliances in Mammary Microbiomes.}, journal = {Breast care (Basel, Switzerland)}, volume = {}, number = {}, pages = {}, doi = {10.1159/000548037}, pmid = {41244617}, issn = {1661-3791}, abstract = {INTRODUCTION: Breast cancer and mastitis significantly impact women's health and their infants' wellbeing. The advent of metagenomic sequencing technology has opened new avenues to explore the relationships between mammary microbiomes and these diseases. Despite recent extensive studies, detailed understanding of the mammary microbiome-disease relationships remains incomplete.<br><br>METHODS AND RESULTS: Here, we apply the Specificity and Specificity Diversity framework (Ma 2024, BMC Biology) to identify unique/enriched species (US/ES) associated with mastitis, breast cancer, or their healthy controls. The US/ES lists contain potential biomarkers and offer fresh insights into the intricacies of mastitis etiology and the relationship between breast tissue microbiomes and breast cancer.<br><br>CONCLUSIONS: (i) The dynamic balance between coexisting alliances of beneficial microbes and harmful microbes (including opportunistic pathogens) holds key to understanding mastitis etiology. (ii) Intra-tumor microbes may serve multiple roles - as oncogenic microbes, neutral bystanders, or tumor suppressors, and their dynamic balance can influence breast cancer onset and progression. (iii) Significant challenges remain in developing effective probiotics, prebiotics and infant formulas due to complex entanglements between beneficial and harmful microbes. This complexity suggests that broad-spectrum or one-size-fits-all probiotic approaches may prove inadequate, pointing instead to the need for personalized prebiotic/probiotic/infant-formula solutions to restore and maintain healthy mammary microbiomes.}, }
@article {pmid41244590, year = {2025}, author = {An, Z and Cha, JH and Lee, KH and Lee, I}, title = {Metagenome-assembled genomes enhance bacterial read decontamination and variant calling in oral samples.}, journal = {iScience}, volume = {28}, number = {11}, pages = {113772}, doi = {10.1016/j.isci.2025.113772}, pmid = {41244590}, issn = {2589-0042}, abstract = {Whole genome sequencing (WGS) offers advantages over DNA chip-based genotyping, typically using blood-derived DNA. However, saliva and buccal samples-popular in direct-to-consumer tests-suffer reduced accuracy because of oral bacterial contamination. Decontamination strategies using decoy bacterial genomes yielded limited improvements, likely because they cover only a subset of oral bacteria with available isolate genomes. To overcome this, we developed a decontamination pipeline leveraging metagenome-assembled genomes (MAGs). Concordance analysis of variant calling between blood and matched oral samples confirmed the superiority of MAG-augmented decontamination over conventional methods relying mainly on isolate genomes. Although the underlying mechanism remains unclear, it particularly improves variant calls in GC-rich regions, recovering many likely pathogenic variants. Additionally, we demonstrate that certain bacterial genomic regions mimic human regions with clinically relevant variants, potentially confounding genotyping. These results highlight the need for MAG-based bacterial read decontamination to achieve accurate personal genotyping from non-invasive, self-collected oral samples.}, }
@article {pmid41244294, year = {2025}, author = {Fuller, R and Petersen, BE and Hussein, S and Salib, C and Duffield, A and Gaglia, R and Gabrilove, JL and Hernández, C and Ramirez, JD and Jacobs, SE and Paniz-Mondolfi, A}, title = {Expedited diagnosis of disseminated Mycobacterium kansasii infection using targeted (amplicon-based) next-generation sequencing in an immunocompromised patient.}, journal = {ASM case reports}, volume = {1}, number = {6}, pages = {}, doi = {10.1128/asmcr.00110-24}, pmid = {41244294}, issn = {2996-2684}, abstract = {BACKGROUND: Mycobacterium kansasii is typically associated with pulmonary disease and is an uncommon cause of disseminated infection and thus can be challenging to diagnose and treat.<br><br>CASE SUMMARY: We present a 59-year-old female with a history of renal cell carcinoma (RCC) and T-cell large granular lymphocytic leukemia (T-LGLL) who developed disseminated Mycobacterium kansasii infection. Targeted next-generation sequencing (tNGS) facilitated the rapid detection of M. kansasii from formalin-fixed, paraffin-embedded (FFPE) tissue, aiding in clinical decision-making prior to culture confirmation.<br><br>CONCLUSION: The case highlights the diagnostic challenges posed by overlapping clinical features and chronic granulomatous inflammation in immunocompromised patients, as well as the utility of amplicon-based sequencing in expediting diagnostic turnaround and guiding therapeutic interventions.}, }
@article {pmid41244270, year = {2025}, author = {Rabinowitz, PM and Walia, R and Pottinger, P and Lieberman, JA}, title = {Tropheryma whipplei native valve endocarditis diagnosed by sequencing of microbial cell-free DNA in plasma.}, journal = {ASM case reports}, volume = {1}, number = {6}, pages = {}, doi = {10.1128/asmcr.00070-25}, pmid = {41244270}, issn = {2996-2684}, abstract = {BACKGROUND: Endocarditis is an important manifestation of extra-intestinal Whipple's disease. The etiologic agent, the bacterium Tropheryma whipplei, cannot be cultivated in clinical laboratories, making the diagnosis of this culture-negative infection challenging. Molecular methods have emerged as useful adjuncts for the diagnosis of culture-negative endocarditis.<br><br>CASE SUMMARY: A 67-year-old male was seen in an infectious disease clinic for evaluation of a possible infectious etiology of chronic musculoskeletal pain with exercise intolerance. He had a history of an embolic stroke 2 years earlier, echocardiographic evidence of aortic valve thickening, and multiple negative blood cultures. Following an evaluation that included serology and extended incubation blood culture, plasma was sent for metagenomic sequencing of microbial cell-free DNA, which was positive for Tropheryma whipplei.<br><br>CONCLUSION: The patient's musculoskeletal complaints and his exercise intolerance resolved after treatment with ceftriaxone and trimethoprim-sulfamethoxazole. To our knowledge, this is the first report of T. whipplei native valve endocarditis diagnosed by metagenomic sequencing.}, }
@article {pmid41244037, year = {2025}, author = {Leys, SP and Hentschel, U and Easson, CG and Stimson, D and Lopez, JV and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and ,  and ,  and ,  and ,  and , }, title = {The chromosomal genome sequence of the fragile freshwater sponge, Eunapius fragilis (Leidy, 1851) and its associated microbial metagenome sequences.}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {268}, doi = {10.12688/wellcomeopenres.24165.1}, pmid = {41244037}, issn = {2398-502X}, abstract = {We present a genome assembly from a specimen of Eunapius fragilis (fragile freshwater sponge; Porifera; Demospongiae; Spongillida; Spongillidae). The genome sequence has a total length of 218.91 megabases. Most of the assembly (99.98%) is scaffolded into 23 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 28.5 kilobases in length. Gene annotation of this assembly on Ensembl identified 26,614 protein-coding genes. Additionally, eight high-quality bacterial metagenomes belonging to the Bacteroidota and Pseudomonadota phyla were assembled.}, }
@article {pmid41243980, year = {2025}, author = {Aguilar, C and Fontove-Herrera, F and Pashkov, A and García-Estrada, DA and Contreras-Peruyero, H and Guerrero-Flores, S and Ramírez-Sánchez, O and Sélem-Mojica, N}, title = {MicroAgroBiome: a toolkit for exploring specialized metabolism and ecological interactions in rhizosphere microbiomes of cultivated crops.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkaf1083}, pmid = {41243980}, issn = {1362-4962}, support = {320237//Secretar&#xed;a de Ciencia, Innovaci&#xf3;n, Tecnolog&#xed;a e Innovaci&#xf3;n (SECIHTI)/ ; //Secretar&#xed;a de Ciencia, Innovaci&#xf3;n, Tecnolog&#xed;a e Innovaci&#xf3;n (SECIHTI) Postdoctoral Fellowship 2025/ ; IN114323//Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; }, abstract = {The microbiome is crucial to agroecosystems, as it influences plant nutrition, resilience, and overall health. Recent advances in metagenomics have expanded our understanding of plant-microbe interactions, yet curated, high-resolution data capturing the global diversity of crop-associated microbiomes remain scarce. To fill this gap, we developed MicroAgroBiome, a publicly accessible platform that offers standardized taxonomic and functional data, mainly from the rhizosphere microbiomes of agriculturally important crops. The platform integrates 554 metagenomes from 28 crops and soil sample health, advancing microbiome-informed agricultural strategies. It also underscores Latin America's growing leadership in agricultural microbiome research. MicroAgroBiome is available at https://agrobiom.matmor.unam.mx.}, }
@article {pmid41243635, year = {2025}, author = {Wu, S and Wei, Z and He, Z and Li, M and Zeng, W}, title = {Clinical characteristics of tracheobronchial mucormycosis: a retrospective analysis of twenty cases.}, journal = {Annals of medicine}, volume = {57}, number = {1}, pages = {2584286}, doi = {10.1080/07853890.2025.2584286}, pmid = {41243635}, issn = {1365-2060}, mesh = {Humans ; *Mucormycosis/diagnosis/drug therapy ; Middle Aged ; Male ; Female ; Retrospective Studies ; Aged ; *Antifungal Agents/therapeutic use/administration &amp; dosage ; Adult ; Amphotericin B/therapeutic use/administration &amp; dosage ; Bronchoscopy ; Tomography, X-Ray Computed ; *Bronchial Diseases/diagnosis/microbiology/drug therapy ; Immunocompromised Host ; Treatment Outcome ; }, abstract = {BACKGROUND: Tracheobronchial mucormycosis (TM) is a rare and potentially fatal disease commonly occurred in immunocompromised individuals, with death risk from massive hemoptysis or asphyxia.To enhance clinical understanding, we retrospectively analyzed the clinical features, therapeutic regimen, and outcomes of TM patients.<br><br>METHODS: We conducted a comprehensive analysis of hospitalized patients diagnosed with TM between January 1, 2010, and April 30, 2025, systematically collecting and evaluating data on clinical manifestations, treatment strategies, and clinical outcomes.<br><br>RESULTS: Twenty patients were included in this study, with a median age of 56&#x2009;years. Most patients had diabetes mellitus, followed by those with hematological malignancies. Common symptoms included cough, expectoration, hemoptysis, and fever. Chest CT revealed pulmonary infiltrates, bronchial stenosis or occlusion, obstructive pneumonia, and pleural effusion, while bronchoscopy revealed neoplasms, purulent secretions, and bronchial obstruction or stenosis.Metagenomic next-generation sequencing demonstrated a higher positive diagnostic rate and shorter time to diagnosis compared to histopathology and culture. Three patients received intravenous amphotericin B (AmB) monotherapy, eight patients were treated with a combination of intravenous and intratracheal AmB, one patient was treated with intravenous triazole drug alone, two patients received a regimen consisting of intravenous triazole drugs combined with intratracheal AmB, and five patients underwent triple therapy involving both intravenous triazole drugs and concurrent intravenous and intratracheal AmB administration. Additionally, one patient underwent bronchoscopic intervention, and two patients underwent lobectomy. Fourteen patients demonstrated clinical improvement, whereas six died. Massive hemoptysis was the leading cause of mortality.<br><br>CONCLUSIONS: TM is a highly lethal disease that is often underdiagnosed. Bronchoscopy plays an essential role in both diagnosis and management. Systemic antifungal therapy, combined with intratracheal administration of AmB, has shown favorable therapeutic outcomes.}, }
@article {pmid41243436, year = {2025}, author = {Cen, Q and Cui, Y and Jin, J and Feng, J and Xin, Y and Zhang, Z and Li, J and Wang, J and Zhang, A}, title = {Unraveling multiple sclerosis: a hidden interaction between intestinal microbiota and host lipid metabolism.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2576657}, doi = {10.1080/19490976.2025.2576657}, pmid = {41243436}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Multiple Sclerosis/metabolism/microbiology/therapy ; *Lipid Metabolism ; Animals ; }, abstract = {Dysregulation of the structure of the gut microbiota is closely linked to the risk of onset and progression of multiple sclerosis. The intricate interaction between the gut microbiota and lipid metabolism likely serves as a crucial pathway mediating this relationship: the gut microbiota directly or indirectly modifies lipid metabolism (including cholesterol, sphingolipids, phospholipids, and fatty acids) by controlling the production of specific metabolites (such as short-chain fatty acids, tryptophan metabolites, bile acids, trimethylamine-N-oxide, and lipopolysaccharides), thereby impacting core pathological processes in multiple sclerosis. Therefore, elucidating the specific roles and mechanisms of the gut microbiota in modulating lipid metabolism in multiple sclerosis will accelerate the development of precision therapeutic strategies. In this review, we conduct an in-depth exploration of the interaction between the gut microbiota and lipid metabolism in the context of multiple sclerosis and provide a comprehensive summary of existing strategies targeting the gut microbiota and lipid metabolism for treating multiple sclerosis (including microbiota-based therapies, pharmacotherapy, and lifestyle modifications). Finally, we outline the present challenges in this field and offer an in-depth prospect for future directions.}, }
@article {pmid41243097, year = {2025}, author = {Hang, WJ and Yin, R and Kang, XW and He, L and Cao, X and Chen, J}, title = {Berberine ameliorates high-fat diet-induced metabolic disorders through promoting gut Akkermansia and modulating bile acid metabolism.}, journal = {Chinese medicine}, volume = {20}, number = {1}, pages = {190}, pmid = {41243097}, issn = {1749-8546}, support = {82100402//National Natural Science Foundation of China/ ; 82370837//National Natural Science Foundation of China/ ; 2022CFB201//Bureau of Science and Technology of Hubei Province/ ; 2022YFE0209900//National Key Research and Development Program of China/ ; WZ21A02//Wuhan Municipal Health Commission's Scientific Research/ ; }, abstract = {BACKGROUND: Coptidis Rhizoma, the rhizome of Coptis chinensis Franch., has long been employed in the treatment of diabetes. Its active component, berberine, has been utilized in clinical practice; however, the underlying mechanisms of its protective effects remain to be fully elucidated.<br><br>METHODS: Metabolomics and lipidomics analyzed plasma metabolite and lipid changes in mice fed a high-fat diet and treated with 25&#xa0;mg/kg/day berberine for three months. Metagenomics and microbiota transplantation identified gut microbiota responding to berberine. Co-administration of berberine and Akkermansia was studied for metabolic effects, analyzing plasma and fecal metabolomics.<br><br>RESULTS: Berberine reduced triglycerides and cholesterol, showing metabolic protective effects. Metagenomics identified Akkermansia as key to berberine's benefits, validated by microbiota transplantation. Berberine enhanced Akkermansia growth, preserving intestinal mucus and tight junctions. It promotes the conversion of cholesterol to bile acids by inhibiting adenosine 5 '-monophosphate -activated protein kinase (AMPK), which promotes the expression of cholesterol 7-alpha hydroxylase (CYP7A1). Co-administration of berberine and Akkermansia amplified these effects. Potential metabolites, including linoleic acid and N-acetylputrescine, contributed to the observed benefits.<br><br>CONCLUSION: Berberine, through Akkermansia, maintains intestinal integrity and reduces cholesterol, highlighting its potential as a therapeutic agent for metabolic disorders. Combining berberine with Akkermansia enhances its efficacy against hyperlipidemia.}, }
@article {pmid41243094, year = {2025}, author = {Andreani-Gerard, CM and Jiménez, NE and Palma, R and Muller, C and Hamon-Giraud, P and Le Cunff, Y and Cambiazo, V and González, M and Siegel, A and Frioux, C and Maass, A}, title = {Modeling the emergent metabolic potential of soil microbiomes in Atacama landscapes.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {142}, pmid = {41243094}, issn = {2524-6372}, support = {Associated Team "SymBioDiversity"//Institut national de recherche en informatique et en automatique (INRIA)/ ; Associated Team "SymBioDiversity"//Institut national de recherche en informatique et en automatique (INRIA)/ ; Associated Team "SymBioDiversity"//Institut national de recherche en informatique et en automatique (INRIA)/ ; Associated Team "SymBioDiversity"//Institut national de recherche en informatique et en automatique (INRIA)/ ; Associated Team "SymBioDiversity"//Institut national de recherche en informatique et en automatique (INRIA)/ ; FB210005//Centro de Modelamiento Matem&#xe1;tico, Facultad de Ciencias F&#xed;sicas y Matem&#xe1;ticas/ ; FB210005//Centro de Modelamiento Matem&#xe1;tico, Facultad de Ciencias F&#xed;sicas y Matem&#xe1;ticas/ ; FB210005//Centro de Modelamiento Matem&#xe1;tico, Facultad de Ciencias F&#xed;sicas y Matem&#xe1;ticas/ ; FB210005//Centro de Modelamiento Matem&#xe1;tico, Facultad de Ciencias F&#xed;sicas y Matem&#xe1;ticas/ ; ANID-MILENIO-ICN2021_044//Millennium Institute Center for Genome Regulation/ ; ANID-MILENIO-ICN2021_044//Millennium Institute Center for Genome Regulation/ ; ANID-MILENIO-ICN2021_044//Millennium Institute Center for Genome Regulation/ ; ANID-MILENIO-ICN2021_044//Millennium Institute Center for Genome Regulation/ ; Exploraci&#xf3;n 13220002//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; Exploraci&#xf3;n 13220002//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; Exploraci&#xf3;n 13220002//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; Exploraci&#xf3;n 13220002//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; ANR-22-PEAE-0011//Agence Nationale de la Recherche/ ; ANR-22-PEAE-0011//Agence Nationale de la Recherche/ ; }, abstract = {BACKGROUND: Soil microbiomes harbor complex communities from which diverse ecological roles unfold, shaped by syntrophic interactions. Unraveling the mechanisms and consequences of such interactions and the underlying biochemical transformations remains challenging due to niche multidimensionality. The Atacama Desert is an extreme environment that includes unique combinations of stressful abiotic factors affecting microbial life. In particular, the Talabre Lejía transect is a natural laboratory for understanding microbiome composition, functioning, and adaptation.<br><br>RESULTS: We propose a computational framework for the simulation of the metabolic potential of microbiomes,&#xa0;as a proxy of how communities are prepared to respond to the environment. Through the coupling of taxonomic and functional profiling, community-wide and genome-resolved metabolic modeling, and regression analyses, we identify key metabolites and&#xa0;species from six contrasting soil samples across the Talabre Lej&#xed;a transect. We highlight the functional redundancy of whole metagenomes, which act as a gene reservoir, from which site-specific adaptations emerge at the species level. We also link the physicochemistry from the puna and the lagoon samples to metabolic machineries that are likely crucial for&#xa0;sustaining microbial life in these unique environmental conditions. We further provide an abstraction of community composition and structure for each site that allowed us to describe microbiomes as resilient or&#xa0;sensitive to environmental shifts, through putative cooperation events.<br><br>CONCLUSION: Our results show that the study of multi-scale metabolic potential, together with targeted modeling, contributes to elucidating the role of metabolism in the adaptation of microbial communities. Our framework was designed to handle non-model microorganisms, making it suitable for any (meta)genomic dataset that includes high-quality environmental data for enough samples.}, }
@article {pmid41243090, year = {2025}, author = {Liu, Z and Xiao, L and Tang, X and He, Y and Nan, X and Wang, H and Guo, Y and Xiong, B}, title = {Salvianolic acid C inhibits methane emissions in dairy cows by targeting MCR and reshaping the rumen microbial community.}, journal = {Journal of animal science and biotechnology}, volume = {16}, number = {1}, pages = {151}, pmid = {41243090}, issn = {1674-9782}, support = {2022YFD1301100//Integrated Demonstration of Scalable and Efficient Healthy Breeding for Cattle and Sheep/ ; 2024-YWF-ZYSQ-10//State Key Laboratory for Diagnosis and Treatment of Infectious Diseases/ ; }, abstract = {BACKGROUND: Methane (CH4) emissions from ruminants significantly contribute to greenhouse gas effects and energy loss in livestock production. Methyl-coenzyme M reductase (MCR) is the key enzyme in methanogenesis, making it a promising target for CH4 mitigation. This study aimed to identify and validate plant-derived inhibitors by using molecular docking to screen compounds with strong binding affinity to the F430 active site of MCR and assessing their efficacy in reducing CH4 emissions.<br><br>RESULTS: Molecular docking analysis identified salvianolic acid C (SAC) as a potent inhibitor of MCR, showing a strong binding affinity to the F430 active site (binding energy:&#x2009;-8.2&#xa0;kcal/mol). Enzymatic inhibition assays confirmed its inhibitory effect, with a half-maximal inhibitory concentration (IC50) of 692.3&#xa0;&#xb5;mol/L. In vitro rumen fermentation experiments demonstrated that SAC supplementation (1.5&#xa0;mg/g DM) significantly reduced CH4 production (P&#x2009;<&#x2009;0.01) without negatively affecting major fermentation parameters. Microbial community analysis using 16S rRNA sequencing and metagenomics revealed that SAC selectively altered the rumen microbiota, increasing the relative abundance of Bacteroidota while significantly reducing Methanobrevibacter (P&#x2009;=&#x2009;0.04). Moreover, metagenomic analysis showed the downregulation of key methanogenesis-related genes (mcrA&#xa0;and rnfC), suggesting a dual mechanism involving direct enzymatic inhibition and microbial community modulation.<br><br>CONCLUSIONS: These findings indicate that SAC effectively reduces CH4 production by inhibiting MCR activity and reshaping the rumen microbial community. As a plant-derived compound with strong inhibitory effects on methanogenesis, SAC presents a promising and sustainable alternative to synthetic CH4 inhibitors, offering potential applications for mitigating CH4 emissions in livestock production.}, }
@article {pmid41242690, year = {2025}, author = {Li, X and Pan, L and Li, Z and Li, Y and Yang, L and Ye, X and Wubuli, A and Ye, Q and Yang, F and Yi, H and Maitusong, R and Liang, Y and Cai, Y and Chen, Z}, title = {Etiology and Clinical Characteristics of Pathogen Co-detection in Pediatric Mycoplasma pneumoniae Pneumonia: A Multicenter Retrospective Study.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {}, number = {}, pages = {108230}, doi = {10.1016/j.ijid.2025.108230}, pmid = {41242690}, issn = {1878-3511}, abstract = {OBJECTIVES: Co-detection are frequent in pediatric Mycoplasma pneumoniae pneumonia (MPP), yet their full pathogen spectrum and clinical impact remain incompletely characterized. This study aimed to characterize co-detection etiology and clinical impacts of MPP in hospitalized children.<br><br>METHODS: A multicenter retrospective cohort study was conducted among hospitalized children under 14 years with MPP, diagnosed by metagenomic or targeted next-generation sequencing of bronchoalveolar lavage fluid, from June 2023 to July 2024. Multivariate logistic regression models were used to assess differences in clinical characteristics among various Mycoplasma pneumoniae (MP) co-detection patterns.<br><br>RESULTS: Among 570 MPP cases, co-detection occurred in 338 (59.3%) cases: viral-only (29.3%), bacterial-only (30.2%), and viral-bacterial (40.5%). The main bacteria were Streptococcus pneumoniae and Haemophilus influenzae, while human adenovirus and Epstein-Barr virus were the most common viruses. Co-detection rates inversely correlated with age, decreasing from 91.1% in infants to 48.1% in adolescents. Younger age (36-72mo vs 72-168mo, OR: 1.57), non-summer seasons (Spring, OR: 2.44; Autumn, OR: 1.93; Winter, OR: 2.77), and elevated white blood cell count (OR: 1.18) were associated with higher risk of co-detection, whereas higher fibrinogen and pleural effusion reduced risk (all P < 0.01).<br><br>CONCLUSIONS: The high prevalence of co-detection in pediatric MPP, notably viral-bacterial, exhibits distinct age and seasonal patterns essential for informing targeted control strategies. Study limitations include its retrospective design and potential heterogeneity from multicenter differences in NGS methodologies.}, }
@article {pmid41242396, year = {2025}, author = {Sharma, R and Walia, A and Lakhanpal, D}, title = {Human metapneumovirus: an underdiagnosed public health threat.}, journal = {Infectious diseases now}, volume = {}, number = {}, pages = {105189}, doi = {10.1016/j.idnow.2025.105189}, pmid = {41242396}, issn = {2666-9919}, abstract = {Human metapneumovirus (hMPV), a negative-sense RNA virus in the Pneumoviridae family, has emerged as a major yet under-recognized cause of acute respiratory infections worldwide. Since its identification in 2001, hMPV has shown steady genetic evolution into genotypes A and B, with newer sublineages such as A2.2.1, A2.2.2, and B2 currently detected across continents. A recent global rise in hMPV detections, detailed in reports from China, Europe, and the USA, likely reflects both expanded testing and the re-establishment of seasonal circulation following the COVID-19 pandemic. Co-infections with respiratory viruses, including RSV and influenza, contribute to severe clinical outcomes and hospital burden. Multiplex RT-PCR remains the most sensitive and widely used diagnostic method for detection of hMPV, outperforming conventional PCR approaches, while metagenomic sequencing and CRISPR-based assays are primarily research tools. Diagnostic sensitivity also varies with sample source, and access to advanced technologies remains globally uneven. Despite its growing clinical impact, no approved antiviral is available. Promising candidates, including monoclonal antibodies against the fusion protein, siRNA therapies, and mRNA-based vaccines, are in the early stages of development. This review encompasses recent evidence on hMPV epidemiology, molecular evolution, diagnostic approaches, and therapeutic and vaccine development, underscoring a need for sustained surveillance, equitable diagnostic capacity, and proactive vaccine research more effectively addressing a largely overlooked respiratory pathogen.}, }
@article {pmid41242241, year = {2025}, author = {Yang, L and Chen, J and Chen, Z and Gao, Y and Su, Y and Zeng, S and He, Q and Qiu, Q}, title = {Integrated metagenomic and metabolomic analyses reveal that nitrogen fertilizer reduction combined with biochar application improves the soil microenvironment of Phoebe bournei seedlings.}, journal = {Journal of environmental management}, volume = {395}, number = {}, pages = {127954}, doi = {10.1016/j.jenvman.2025.127954}, pmid = {41242241}, issn = {1095-8630}, abstract = {Biochar has emerged as a globally recognized soil amendment, yet its synergistic effects with nitrogen fertilization on rhizosphere ecosystems remain underexplored. This study employed non-targeted metabolomics and metagenomic analyses to investigate the soil microenvironment of Phoebe bournei seedlings under four treatments: control (CK), optimum nitrogen application (F1), 20 % nitrogen fertilizer reduction with biochar application (F2B1), and 40 % nitrogen fertilizer reduction with biochar application (F3B2). A total of 842 (421 up-/421 down-regulated) and 789 (415 up-/374 down-regulated) differential metabolites were identified in the F2B1 and F3B2 treatments, respectively. Nitrogen fertilizer reduction combined with biochar application significantly reshaped soil metabolomic profiles, with pronounced enrichment in eight key metabolic pathways, including ascorbate and aldarate metabolism pathways and arachidonic acid metabolism pathways. Streptomyces, Pseudomonas, and Afipia exhibited higher relative abundance levels in both F2B1 and F3B2 treatments. Redundancy analysis indicated that soil pH was the dominant influence on the variation of microbial communities. The topological complexity and stability of bacterial co-occurrence networks were significantly improved by F3B2. An upregulation of functional genes involved in soil nitrification (amoAB, hao, and nxrAB) resulted from F3B2. Furthermore, network analysis revealed significant correlations between microbial taxa and differential metabolites, with a preponderance of positive correlations. Our results indicate that nitrogen fertilizer reduction combined with biochar application significantly influences soil microbial metabolism, establishing a theoretical foundation for enhancing soil quality in Phoebe bournei woodlands and for the judicious use of nitrogen fertilizer and biochar in forestry.}, }
@article {pmid41242205, year = {2025}, author = {Li, X and Gao, X and Yu, S and Du, F and Liu, J and Kan, X and Liu, X and Yao, D}, title = {Rhizosphere microbiota diversity and salt stress-alleviating functional genes in coastal wild salt-tolerant plants.}, journal = {Microbiological research}, volume = {303}, number = {}, pages = {128397}, doi = {10.1016/j.micres.2025.128397}, pmid = {41242205}, issn = {1618-0623}, abstract = {Saline-alkali land significantly threatens global food security and ecological safety, and root-associated microorganisms help plants survive salt-alkali stress. However, the ecological functions and factors that influence the rhizosphere microbiomes of salt-tolerant plants remain poorly understood. In this study, we used high-throughput sequencing and metagenomics to reveal the microbial communities and functional traits of bulk and rhizosphere soil from salt-tolerant species (Suaeda glauca, Phragmites australis, and Spartina alterniflora) growing in saline soil. Bacterial and fungal taxa were significantly enriched in the rhizosphere soil compared to the non-rhizosphere soil. Metagenomic analyses revealed that metabolic pathways, including glycolysis and ABC transporters, were highly enriched in the rhizosphere. Functional profiling indicated that salt stress-related pathways were more abundant in the core genera Pseudomonas and Woeseia. The abundance of functional genes related to plant growth-promoting traits, including phosphate solubilization and salt adaptation pathways, was higher in the rhizosphere soil than in the non-rhizosphere soil, which was mainly driven by soil salinity, total nitrogen content, and total carbon content. Additionally, P. aeruginosa obtained from the rhizosphere of S. alterniflora exhibited high phosphorus solubilization efficiency (908.38 μg/mL), nitrogen fixation activity (2.84 μg/mL) and salt tolerance (≦ 5 % NaCl). These findings demonstrate that salt-tolerant plants shape microbial activities by controlling the rhizosphere microenvironment, mitigating salt stress, providing a scientific and practical foundation for the development of targeted microbial inoculants for saline-alkali land reclamation.}, }
@article {pmid41241245, year = {2025}, author = {Li, L and Yu, X and Wang, M and Sun, H and Zhu, J and Wang, X and Chen, S and Hu, S}, title = {Salicylic acid as a pathway inducer for improved bioremediation of oil-polluted saline-alkali soils by chemotactic S. Stutzeri M3.}, journal = {Bioresource technology}, volume = {441}, number = {}, pages = {133647}, doi = {10.1016/j.biortech.2025.133647}, pmid = {41241245}, issn = {1873-2976}, abstract = {The bioremediation would be inhibited by low-efficiency of mass transfer and persistent high-molecular weight polycyclic aromatic hydrocarbons (PAHs). In this study, chemotactic strain named as Stutzerimonas stutzeri M3 and salicylic acid were employed for enhancing biodegradation of petroleum hydrocarbon. The addition of salicylic acid significantly enhanced the activities of alkane hydroxylase and catechol 1,2-dioxygenase, as well as the biodegradation rate of petroleum hydrocarbons. Moreover, the inputs of salicylic acid reshaped microbial community, and obviously affected their cooperative metabolic process by increasing relative abundance of petroleum-degrading bacteria, such as Stutzerimonas, Pontibacillus, Halobacillus and Virgibacillus. Metagenomic analysis furtherly confirmed that overall metabolic pathways of microbial communities and expression of functional genes associated with petroleum degradation (e.g., fad, cat and nah) were enhanced. Furthermore, chemotactic gene expression in strain M3 was significantly increased, thereby facilitating petroleum hydrocarbons degradation. These findings provide a new regulating strategy for effective bioremediation in oil-contaminated sites.}, }
@article {pmid41241073, year = {2025}, author = {Du, JY and Qin, FL and Yang, RN and Chen, YL and Tan, GF and Li, WJ and Yang, L and Cai, J and Shen, DL and Zhu, HR and Yuan, ML and Zhang, W}, title = {Metagenomic analysis of the gut microbiota in major depressive disorder with different antidepressant efficacy: A prospective cohort study.}, journal = {Journal of affective disorders}, volume = {}, number = {}, pages = {120709}, doi = {10.1016/j.jad.2025.120709}, pmid = {41241073}, issn = {1573-2517}, abstract = {BACKGROUND: Major depressive disorder (MDD) is globally prevalent, with Selective Serotonin Reuptake Inhibitors (SSRIs) and Serotonin-Norepinephrine Reuptake Inhibitors (SNRIs) as first-line treatment. However, 30 %-40 % of patients have inadequate response, and early identification is difficult. Gut microbiota contributes to MDD pathogenesis through the gut-brain axis, but baseline differences between responders and non-responders to SSRIs or SNRIs remain unclear.<br><br>METHODS: 82 MDD individuals were initially screened. However, due to issues with the drug administration and fecal sample availability, a total of 43 people were eventually included. Based on 3-month Hamilton Depression Rating Scale (HAMD-17) changes, 29 patients were responders (39.12&#x202f;&#xb1;&#x202f;15.79&#x202f;years, 8 males), while 14 were non-responders (40.14&#x202f;&#xb1;&#x202f;17.28&#x202f;years, 5 males). Baseline assessments encompassed Depression Anxiety scales, demographics, and fecal metagenomic analysis (taxonomic/functional annotation, and differential analysis of microbial species and pathways).<br><br>RESULTS: Baseline demographic characteristics, lifestyle factors, and anxiety/depression scores were comparable. Non-responders had higher relative abundances of Bacteroidaceae and Bacteroide; LEfSe showed responders enriched Hungatella, Ligilactobacillus_ruminis, and non-responders enriched Anaerostipes, Bacteroides_faecis. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis identified 246 differentially expressed KEGG Orthologies and 13 pathways, with the steroid biosynthesis pathway (map00100) being enriched in non-responders and the D-amino acid metabolism pathway (map00470) enriched in responders. The study has limitations: small sample size and it lacks direct mechanism validation.<br><br>CONCLUSIONS: The composition and functional pathways of gut microbiota exhibit significant differences between responders and non-responders to SSRIs or SNRIs among MDD patients, providing clues for the development of new treatment strategies.}, }
@article {pmid41240828, year = {2025}, author = {Liu, J and Xie, S and Ji, Y and Fan, X and Luo, S and Xu, X and Wang, C and Zhu, L}, title = {Dual suppression of methanogenesis by dichloromethane and salinity: Competitive methyltransferase inhibition and energy-coupling disruption.}, journal = {Journal of hazardous materials}, volume = {500}, number = {}, pages = {140408}, doi = {10.1016/j.jhazmat.2025.140408}, pmid = {41240828}, issn = {1873-3336}, abstract = {The pervasive co-occurrence of dichloromethane (DCM), a prevalent chlorinated solvent, with high salinity in industrial wastewater poses a poorly understood combined ecological stress on anaerobic microbial ecosystems. This study deciphered the molecular mechanisms underlying the dual inhibition of methanogenesis under such combined stress. Metagenomic analysis revealed that methanogens (particularly Methanobacterium and Methanothrix) were more sensitive to DCM and salinity stress, while fermentative bacteria and acetogens exhibited better resilience. Under salinity stress, methanogens primarily expelled extra Na[+] was via the Na[+] pump coupled with methyltransferase (Mtr). However, density functional theory (DFT) calculations demonstrated that DCM competitively bound to the cobamide cofactor in Mtr (ΔG = -10.5 kcal/mol for DCM vs. +14.6 kcal/mol for methylated carrier), thereby impairing sodium extrusion (58 % downregulation in mtrH gene abundance) and subsequent ATP synthesis. Concurrently, elevated Na[+] levels forced a metabolic shift towards energy-intensive sodium extrusion pathways, as evidenced by the upregulation of mrpA (Na[+]/H[+] antiporter, +20 %) and natA/natB (ABC sodium transporters, +162 %). These disruptions culminated in a severe bioenergetic crisis, indicated by decreased coenzyme F420 activity (31.11 ± 1.58 vs. 48.66 ± 2.09 U/L in control) and suppression of methane yield (22.31 ± 3.63 CH4/g COD vs. 178.91 ± 1.28 mL CH4/g COD in control). Our findings uncovered a novel dual inhibition mechanism, combining molecular-level competitive enzyme inhibition with cellular-scale energy uncoupling, providing critical insights into the microbial toxicological effects of co-occurring chlorinated solvents and salinity.}, }
@article {pmid41240707, year = {2025}, author = {Fonseca, A and Kenney, S and Boney, J and Ganda, E}, title = {Mycobiome temporal and functional dynamics in broilers: Ecological perspective on bacterial-fungal correlations and the effect of feed additives.}, journal = {Poultry science}, volume = {104}, number = {12}, pages = {106092}, doi = {10.1016/j.psj.2025.106092}, pmid = {41240707}, issn = {1525-3171}, abstract = {The gut mycobiome (the fungal component of the microbiome) of chickens, though less abundant than bacterial populations, plays a vital role in gut ecology, yet remains underexplored. This study investigated the temporal, dietary, and ecological factors shaping the broiler chicken excreta-associated fungal communities and their correlation with bacterial microbiota. A total of 320 Cobb 500 (1-day-old) chicks were raised for 21 days in 32 randomly allocated cages. Treatments consisted of four experimental diets: a Basal Diet, a Basal Diet with an Antibiotic (bacitracin methylene disalicylate), an Essential oils blend (oregano oil, rosemary, and red pepper), or a Probiotic (Bacillus subtilis). Shotgun metagenomic sequencing was performed on excreta samples collected at days 1, 10, and 21 to evaluate fungal diversity, composition, cross-kingdom correlation and functional profiling. The fungal community was dominated by Ascomycota and Basidiomycota across all treatments and time points. While alpha diversity metrics did not differ significantly between treatments (P > 0.05), fungal richness and evenness increased significantly over time (P < 0.05), indicating age-driven ecological succession. Beta diversity analysis revealed distinct age-related clustering patterns, with early dominance by Candida albicans and later shifts toward genera such as Fusarium and Malassezia. Feed additives exerted limited influence on fungal composition or diversity metrics, although clustering patterns suggested subtle treatment-specific effects over time. Cross-kingdom correlation analysis identified co-occurring temporal dynamics between the two microbial communities. Candida was positively correlated with Streptococcus and Escherichia/Shigella but negatively associated with beneficial genera like Bifidobacterium and Faecalibacterium. Additionally, microbial functional characteristics were observed in each treatment exhibiting metabolic features. Overall, this study demonstrates that excreta fungal succession in the broiler gut is primarily driven by host age and highlights the temporal plasticity of concurrent changes in fungal and bacteria communities. The findings underscore the importance of multi-kingdom ecological approaches to better understand gut health in poultry production.}, }
@article {pmid39617895, year = {2024}, author = {Perrin, AJ and Dorrell, RG}, title = {Protists and protistology in the Anthropocene: challenges for a climate and ecological crisis.}, journal = {BMC biology}, volume = {22}, number = {1}, pages = {279}, pmid = {39617895}, issn = {1741-7007}, mesh = {*Climate Change ; *Eukaryota/physiology ; *Ecosystem ; Biodiversity ; }, abstract = {Eukaryotic microorganisms, or "protists," while often inconspicuous, play fundamental roles in the Earth ecosystem, ranging from primary production and nutrient cycling to interactions with human health and society. In the backdrop of accelerating climate dysregulation, alongside anthropogenic disruption of natural ecosystems, understanding changes to protist functional and ecological diversity is of critical importance. In this review, we outline why protists matter to our understanding of the global ecosystem and challenges of predicting protist species resilience and fragility to climate change. Finally, we reflect on how protistology may adapt and evolve in a present and future characterized by rapid ecological change.}, }
@article {pmid34286093, year = {2021}, author = {Cheng, CT and Jeng, ML and Tsai, JF and Li, CL and Wu, LW}, title = {Two mitochondrial genomes of Taiwanese rhinoceros beetles, Oryctes rhinoceros and Eophileurus chinensis (Coleoptera: Scarabaeidae).}, journal = {Mitochondrial DNA. Part B, Resources}, volume = {6}, number = {8}, pages = {2260-2262}, pmid = {34286093}, issn = {2380-2359}, abstract = {Two mitochondrial genomes of the dynastine beetles, Oryctes rhinoceros (Linnaeus, 1758) and Eophileurus chinensis (Faldermann, 1835), were assembled via high-throughput sequencing (HTS). Each of the mitogenomes has 37 genes, showing standard gene order and annotation as the other insects, except for the transfer genes, presenting tQ-tI-tM order. To examine their phylogenetic positions, 118 public mitogenomes of Scarabaeidae were used to infer a ML tree. Overall, our scarabaeid phylogeny reveals clear relationships with high nodal supports, and the two rhinoceros beetles are both grouped with the subfamily Dynastinae. The feeding habit of the two clades seems to represent coprophagous and phytophagous types. However, polyphyletic relationships were observed in the subfamily Melolothinae and in the tribes of Onthophagini and Oniticellini. Further systematic revision is needed.}, }
@article {pmid33898751, year = {2021}, author = {Jeng, ML and Chen, MY and Wu, LW}, title = {Two complete mitochondrial genomes of Papilio butterflies obtained from historical specimens (Lepidoptera: Papilionidae).}, journal = {Mitochondrial DNA. Part B, Resources}, volume = {6}, number = {4}, pages = {1341-1343}, pmid = {33898751}, issn = {2380-2359}, abstract = {Museum specimens are collected for education, exhibition, and various multiple scientific purposes. However, millions of specimens remain in their collection boxes for years without being analyzed. Historical specimens have been known to contain low-quality DNA; hence, it is difficult to utilize their sequence information in phylogenetic studies. However, recent advances in high-throughput sequencing (HTS) make these collections amenable to phylogenomic studies. In this study, two historical specimens (Papilio xuthus Linnaeus, 1767, and Papilio thoas Linnaeus, 1771) were sampled and DNA extracted for HTS via the Miseq platform. Two complete mitogenomes were assembled, even though the DNA quality of those specimens was highly fragmented, below 250 bp in length. The 37 genes of 60 mitogenomes were aligned and used for inferring the phylogenetic relationships of Papilioninae. These two newly sequenced mitogenomes are correctly grouped in the genus Papilio, and this result indicates that historical specimens show great potential for phylogenetic studies with HTS technology.}, }
@article {pmid32019036, year = {2020}, author = {Brandon, TA and Stamps, BW and Cummings, A and Zhang, T and Wang, X and Jiang, D}, title = {Poised potential is not an effective strategy to enhance bio-electrochemical denitrification under cyclic substrate limitations.}, journal = {The Science of the total environment}, volume = {713}, number = {}, pages = {136698}, doi = {10.1016/j.scitotenv.2020.136698}, pmid = {32019036}, issn = {1879-1026}, mesh = {Biofilms ; Bioreactors ; *Denitrification ; Nitrates ; Thiobacillus ; }, abstract = {Bio-electrochemical denitrification (BED) is a promising organic carbon-free nitrate remediation technology. However, the relationship between engineering conditions, biofilm community composition, and resultant functions in BED remains under-explored. This study used deep sequencing and variation partitioning analysis to investigate the compositional shifts in biofilm communities under varied poised potentials in the batch mode, and correlated these shifts to reactor-level functional differences. Interestingly, the results suggest that the proliferation of a key species, Thiobacillus denitrificans, and community diversity (the Shannon index), were almost equally important in explaining the reactor-to-reactor functional variability (e.g. variability in denitrification rates was 51% and 38% attributable to key species and community diversity respectively, with a 30% overlap), but neither was heavily impacted by the poised potential. The findings suggest that while enriching the key species may be critical in improving the functional efficiency of BED, poised potentials may not be an effective strategy to achieve the desired level of enrichment in substrate-limited real-world conditions.}, }
@article {pmid31974023, year = {2020}, author = {Gladding, PA and Legget, M and Fatkin, D and Larsen, P and Doughty, R}, title = {Polygenic Risk Scores in Coronary Artery Disease and Atrial Fibrillation.}, journal = {Heart, lung &amp; circulation}, volume = {29}, number = {4}, pages = {634-640}, doi = {10.1016/j.hlc.2019.12.004}, pmid = {31974023}, issn = {1444-2892}, mesh = {*Atrial Fibrillation/genetics/physiopathology/therapy ; *Coronary Artery Disease/genetics/physiopathology/therapy ; *Genetic Predisposition to Disease ; Genome-Wide Association Study ; Humans ; *Multifactorial Inheritance ; *Polymorphism, Single Nucleotide ; Risk Factors ; }, abstract = {Coronary artery disease (CAD) and atrial fibrillation (AF) are two highly prevalent cardiovascular disorders that are associated with substantial morbidity and mortality. Conventional clinical risk factors for these disorders may not be identified prior to mid-adult life when pathophysiological processes are already established. A better understanding of the genetic underpinnings of disease should facilitate early detection of individuals at risk and preventative intervention. Single rare variants of large effect size that are causative for CAD, AF, or predisposing factors such as hypertension or hyperlipidaemia, may give rise to familial forms of disease. However, in most individuals, CAD and AF are complex traits in which combinations of genetic and acquired factors play a role. Common genetic variants that affect disease susceptibility have been identified by genome-wide association studies, but the predictive value of any single variant is limited. To address this issue, polygenic risk scores (PRS), comprised of suites of disease-associated common variants have been devised. In CAD and AF, incorporation of PRS into risk stratification algorithms has provided incremental prognostic information to clinical factors alone. The long-term health and economic benefits of PRS-guided clinical management remain to be determined however, and further evidence-based data are required.}, }
@article {pmid31942825, year = {2020}, author = {Ho, J and Yeoh, YK and Barua, N and Chen, Z and Lui, G and Wong, SH and Yang, X and Chan, MC and Chan, PK and Hawkey, PM and Ip, M}, title = {Systematic review of human gut resistome studies revealed variable definitions and approaches.}, journal = {Gut microbes}, volume = {12}, number = {1}, pages = {1700755}, pmid = {31942825}, issn = {1949-0984}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/classification/*drug effects/*genetics ; Drug Resistance, Bacterial/*genetics ; Gastrointestinal Microbiome/*drug effects/*genetics ; Gastrointestinal Tract/microbiology ; Genes, Bacterial ; Humans ; }, abstract = {In this review, we highlight the variations of gut resistome studies, which may preclude comparisons and translational interpretations. Of 22 included studies, a range of 12 to 2000 antibiotic resistance (AR) genes were profiled. Overall, studies defined a healthy gut resistome as subjects who had not taken antibiotics in the last three to 12 months prior to sampling. In studies with de novo assembly, AR genes were identified based on variable nucleotide or amino acid sequence similarities. Different marker genes were used for defining resistance to a given antibiotic class. Validation of phenotypic resistance in the laboratory is frequently lacking. Cryptic resistance, collateral sensitivity and the interaction with repressors or promotors were not investigated. International consensus is needed for selecting marker genes to define resistance to a given antibiotic class in addition to uniformity in phenotypic validation and bioinformatics pipelines.}, }
@article {pmid31248111, year = {2019}, author = {Richardson, E and Dacks, JB}, title = {Microbial Eukaryotes in Oil Sands Environments: Heterotrophs in the Spotlight.}, journal = {Microorganisms}, volume = {7}, number = {6}, pages = {}, pmid = {31248111}, issn = {2076-2607}, support = {RES0021028, RES0043758, RES0046091//Natural Sciences and Engineering Research Council of Canada/ ; }, abstract = {Hydrocarbon extraction and exploitation is a global, trillion-dollar industry. However, for decades it has also been known that fossil fuel usage is environmentally detrimental; the burning of hydrocarbons results in climate change, and environmental damage during extraction and transport can also occur. Substantial global efforts into mitigating this environmental disruption are underway. The global petroleum industry is moving more and more into exploiting unconventional oil reserves, such as oil sands and shale oil. The Albertan oil sands are one example of unconventional oil reserves; this mixture of sand and heavy bitumen lying under the boreal forest of Northern Alberta represent one of the world's largest hydrocarbon reserves, but extraction also requires the disturbance of a delicate northern ecosystem. Considerable effort is being made by various stakeholders to mitigate environmental impact and reclaim anthropogenically disturbed environments associated with oil sand extraction. In this review, we discuss the eukaryotic microbial communities associated with the boreal ecosystem and how this is affected by hydrocarbon extraction, with a particular emphasis on the reclamation of tailings ponds, where oil sands extraction waste is stored. Microbial eukaryotes, or protists, are an essential part of every global ecosystem, but our understanding of how they affect reclamation is limited due to our fledgling understanding of these organisms in anthropogenically hydrocarbon-associated environments and the difficulties of studying them. We advocate for an environmental DNA sequencing-based approach to determine the microbial communities of oil sands associated environments, and the importance of studying the heterotrophic components of these environments to gain a full understanding of how these environments operate and thus how they can be integrated with the natural watersheds of the region.}, }
@article {pmid31226241, year = {2019}, author = {Roth, H and Gallo, S and Badger, P and Hillwig, M}, title = {Changes in microbial communities of a passive coal mine drainage bioremediation system.}, journal = {Canadian journal of microbiology}, volume = {65}, number = {10}, pages = {775-782}, doi = {10.1139/cjm-2018-0612}, pmid = {31226241}, issn = {1480-3275}, mesh = {Bacteria/genetics ; Biodegradation, Environmental ; *Coal Mining ; *Microbiota ; *Wetlands ; }, abstract = {Drainage from abandoned mines is one factor greatly affecting the streams and vegetation in and around Pittsburgh and the Appalachian Mountains where coal mining occurred. This drainage may be more acidic, alkaline, or metal based. Different methods for remediation exist. Passive remediation is one method used to naturally allow the metals to precipitate out and aid in cleaning up the water. The goal of this study is to sample different holding ponds in a sequential passive remediation system and determine microbial communities present at each site of an abandoned coal mine drainage site. Sequencing of the 16S rRNA gene of the sediment indicated the most abundant phyla at each of the 5 ponds and wetland area included Proteobacteria (36%-43%), Bacteroidetes (12%-37%), Firmicutes (3%-11%), and Verrucomicrobia (6%-11%). Analysis of genera between the first, and most polluted, pond included Solitalea, Pedosphaera, and Rhodocyclus, whereas the microbial community from the wetland site at the end of the remediation system included Ignavibacterium, Pelotomaculum, and Petrimonas. The results of our microbial community composition study of sediment from a passive treatment system are in line with organisms commonly found in sediment regardless of iron oxide precipitation, while others are preferentially found in the less polluted wetland site.}, }
@article {pmid30769763, year = {2019}, author = {,  and Singh, BR and Gupta, VK and Deeba, F and Bajpai, R and Pandey, V and Naqvi, AH and Upreti, DK and Gathergood, N and Jiang, Y and El Enshasy, HA and Sholkamy, EN and Mostafa, AA and Hesham, AE and Singh, BN}, title = {Non-Toxic and Ultra-Small Biosilver Nanoclusters Trigger Apoptotic Cell Death in Fluconazole-Resistant Candida albicans via Ras Signaling.}, journal = {Biomolecules}, volume = {9}, number = {2}, pages = {}, pmid = {30769763}, issn = {2218-273X}, mesh = {Antifungal Agents/chemistry/*pharmacology ; Candida albicans/cytology/*drug effects ; Cell Death ; Cell Survival/drug effects ; Drug Resistance, Fungal/*drug effects ; Fluconazole/chemistry/*pharmacology ; Lichens/chemistry/metabolism ; Metal Nanoparticles/*chemistry ; Particle Size ; Proto-Oncogene Proteins p21(ras)/*antagonists &amp; inhibitors/metabolism ; Reactive Oxygen Species/metabolism ; Signal Transduction/drug effects ; Silver/chemistry/*metabolism ; Surface Properties ; }, abstract = {Silver-based nanostructures are suitable for many biomedical applications, but to be useful therapeutic agents, the high toxicity of these nanomaterials must be eliminated. Here, we biosynthesize nontoxic and ultra-small silver nanoclusters (rsAg@NCs) using metabolites of usnioid lichen (a symbiotic association of algae and fungi) that exhibit excellent antimicrobial activity against fluconazole (FCZ)-resistant Candida albicans that is many times higher than chemically synthesized silver nanoparticles (AgNPs) and FCZ. The rsAg@NCs trigger apoptosis via reactive oxygen species accumulation that leads to the loss of mitochondrial membrane potential, DNA fragmentation, chromosomal condensation, and the activation of metacaspases. The proteomic analysis clearly demonstrates that rsAg@NCs exposure significantly alters protein expression. Most remarkable among the down-regulated proteins are those related to glycolysis, metabolism, free radical scavenging, anti-apoptosis, and mitochondrial function. In contrast, proteins involved in plasma membrane function, oxidative stress, cell death, and apoptosis were upregulated. Eventually, we also established that the apoptosis-inducing potential of rsAg@NCs is due to the activation of Ras signaling, which confirms their application in combating FCZ-resistant C. albicans infections.}, }
@article {pmid30278254, year = {2019}, author = {Wu, LW and Chiba, H and Lees, DC and Ohshima, Y and Jeng, ML}, title = {Unravelling relationships among the shared stripes of sailors: Mitogenomic phylogeny of Limenitidini butterflies (Lepidoptera, Nymphalidae, Limenitidinae), focusing on the genera Athyma and Limenitis.}, journal = {Molecular phylogenetics and evolution}, volume = {130}, number = {}, pages = {60-66}, doi = {10.1016/j.ympev.2018.09.020}, pmid = {30278254}, issn = {1095-9513}, mesh = {Animals ; Asia ; Butterflies/*classification/*genetics ; Genome, Insect/*genetics ; Genome, Mitochondrial/*genetics ; *Phylogeny ; }, abstract = {The phylogenetic relationships of the nymphalid butterfly tribe Limenitidini are best known for the genera Limenitis and Adelpha, model taxa for evolutionary processes such as Batesian mimicry and rapid adaptive radiations. Whereas these American limenitidines have received the most attention, phylogenetic relationships of their Asian relatives are still controversial and largely unexplored. Even one of the largest genera in Asia, Athyma, is polyphyletic. To clarify the phylogenetic relationships of these Asian Limenitidini, a total of 53 representatives were sampled; 37 have their mitogenomes sequenced for the first time. Our phylogenetic results confirm that mitogenomic data provides well-resolved relationships at most major levels of the phylogeny, even using different partition schemes or different inference methods. Interestingly, our results show that some Athyma taxa are embedded within the genus Limenitis, whereas the genus Tacola, previously considered to be a synonym of Athyma, needs to be recognized as a valid clade. Additionally, the other Limenitidini genera in Asia (namely Tarattia, Litinga, Sumalia, Pandita and Patsuia) are now grouped either within Athyma or Limenitis, so these genera need to be sunk. Importantly, we also show that the mainly Old World Limenitis and entirely New World Adelpha are sister groups, confirming the relevance of Asian lineages to global studies of Limenitis evolution.}, }
@article {pmid28105307, year = {2016}, author = {Ankenbrand, MJ and Terhoeven, N and Hohlfeld, S and Förster, F and Keller, A}, title = {biojs-io-biom, a BioJS component for handling data in Biological Observation Matrix (BIOM) format.}, journal = {F1000Research}, volume = {5}, number = {}, pages = {2348}, pmid = {28105307}, issn = {2046-1402}, abstract = {The Biological Observation Matrix (BIOM) format is widely used to store data from high-throughput studies. It aims at increasing interoperability of bioinformatic tools that process this data. However, due to multiple versions and implementation details, working with this format can be tricky. Currently, libraries in Python, R and Perl are available, whilst such for JavaScript are lacking. Here, we present a BioJS component for parsing BIOM data in all format versions. It supports import, modification, and export via a unified interface. This module aims to facilitate the development of web applications that use BIOM data. Finally, we demonstrate its usefulness by two applications that already use this component. Availability: https://github.com/molbiodiv/biojs-io-biom, https://dx.doi.org/10.5281/zenodo.218277.}, }
@article {pmid41240515, year = {2025}, author = {Wang, S and Xu, R and Xiao, M and Yu, J and Yu, L and Heng, Z and Li, Z and Du, Q and Zhou, Y and Li, Y and Zhu, G}, title = {Comammox ammonia oxidization and N2O production in vadose and saturated zone soils.}, journal = {Water research}, volume = {289}, number = {Pt B}, pages = {124899}, doi = {10.1016/j.watres.2025.124899}, pmid = {41240515}, issn = {1879-2448}, abstract = {Riparian zones are biogeochemical hotspots of N2O emission. The important role of ammonia oxidation in N2O production has been reported in rivers, even higher than heterotrophic denitrification, however, the mechanisms controlling riparian N2O production remain unknown. Here, we found that complete ammonia oxidation (comammox) process significantly contributes to ammonia oxidation and N2O production in subsurface riparian zone. The contribution of comammox to ammonia oxidation in surface soils (38.7 ± 6.5 %) is equivalent to that of bacterial ammonia oxidation (49.4 ± 6.9 %), and both processes are significantly more important than archaeal ammonia oxidation (11.9 ± 4.1 %). Moreover, comammox dominates ammonia oxidation in both vadose and saturated zone soils, especially in summer with the average contributions of over 67.9 %. However, as a biotic N2O production pathway, comammox produces more N2O in vadose (up to 72 %) and saturated zone (up to 100.0 %) soils, significantly higher than that produced by archaeal ammonia oxidation (32.0 ± 4.0 %) and bacterial ammonia oxidation (18.0 ± 5.7 %). We obtained the first metagenome-assembled genomes (MAGs) of comammox bacteria in a riparian profile, and metagenomic binning analysis revealed that the wide niche of comammox may attribute to its diverse metabolic pathways, which not only perform ammonia oxidation but also nitrate reduction to ammonia. This research enhances the understanding of the biogeochemical ammonia cycle in riparian zone systems and provides new insights for the control of nitrogen pollution in riparian zones.}, }
@article {pmid41240423, year = {2025}, author = {Alzeer, S and Almaghrabi, RS and Magrashi, A and Alzahrani, T and Bakheet, R and Alqasabi, A and Tayeb, H}, title = {Revealing co-infections in pneumonia: A case report on advancing diagnosis with metagenomic sequencing technologies.}, journal = {Journal of infection and public health}, volume = {19}, number = {1}, pages = {103036}, doi = {10.1016/j.jiph.2025.103036}, pmid = {41240423}, issn = {1876-035X}, abstract = {Pneumonia, a frequent and serious complication in kidney transplant recipients, is significantly increased by long-term immunosuppressive medication. This case report details a patient with lung cavitation, in which conventional microbiological methods revealed Escherichia coli as the principal pathogen. Metagenomic long-read sequencing also identified Klebsiella pneumoniae as a co-pathogen, underscoring the shortcomings of traditional diagnostic techniques. In identifying infectious pathogens, this case illustrates the superior diagnostic accuracy of long-read sequencing, offering crucial information that conventional methods might miss. The implementation of sophisticated sequencing technologies may overcome these diagnostic deficiencies, improving infection care in challenging and immunocompromised patients.}, }
@article {pmid41240163, year = {2025}, author = {Perez-Hernandez, C and Aldaroub, J and Barth, ZK and Aylward, FO}, title = {A novel lineage of large aquatic bacteriophages identified through metagenomics.}, journal = {Archives of virology}, volume = {170}, number = {12}, pages = {253}, pmid = {41240163}, issn = {1432-8798}, support = {#2141862//National Science Foundation/ ; }, mesh = {*Metagenomics ; *Bacteriophages/genetics/classification/isolation &amp; purification ; *Genome, Viral ; Phylogeny ; }, abstract = {"Jumbo phages" are tailed phages with genome sizes >200 kbp and physical dimensions reaching up to 0.45 μm. Although jumbo phages represent only a small fraction of the isolated phages to date, metagenomic surveys have shown that they are broadly distributed in a wide range of environments. In this study, we surveyed metagenomic data from aquatic systems and identified 25 genomes from a heretofore-undescribed lineage of jumbo phages with genomes reaching up to 307 kbp. We refer to these phages as "moraphages", from the Gaelic word 'mór', for large. Moraphages represent a diverse lineage with inter-genome average amino acid identity (AAI) ranging from 39 to 95%, and our pan-genomic analysis identified only 26 viral orthologous groups (VOGs) found in at least 80% of the genomes. Our phylogenomic analysis suggests that moraphages are distant relatives of a recently described lineage of huge phages from marine sediment. Moraphages lack much of the genetic machinery found in other lineages of large phages, but they have a range of genes that may be used to take over host cellular machinery and subvert host defenses, such as glutamine synthetases, antitoxin genes, and chaperones. The predicted hosts of most moraphages are members of the phylum Bacteroidota, and some encode homologs of the chaperones DnaK and DnaJ that bear evidence of recent gene transfer from members of the order Flavobacteriales. Our work sheds light on the emerging diversity of large phages that are found across the biosphere.}, }
@article {pmid41240088, year = {2025}, author = {V, C and Lal, SB and Mishra, DC and Sharma, A and Kumar, S and Chaturvedi, KK and Behera, BK}, title = {In Silico Identification of Enzymes Involved in Bioremediation from Metagenomic Sequence of River Ganga.}, journal = {Bulletin of environmental contamination and toxicology}, volume = {115}, number = {6}, pages = {64}, pmid = {41240088}, issn = {1432-0800}, mesh = {Biodegradation, Environmental ; *Rivers/chemistry/microbiology ; *Water Pollutants, Chemical/metabolism/analysis ; Metagenomics ; Computer Simulation ; Environmental Monitoring ; Metagenome ; }, abstract = {Environmental pollution, particularly in aquatic ecosystems, poses a major global threat. The Ganga River, vital to millions, suffers from severe contamination despite multiple remediation efforts. Bioremediation, especially enzyme-mediated approaches, offers an eco-friendly and efficient alternative to conventional methods. This study utilizes metagenomic reads to identify bioremediating enzymes, their host microorganisms, target pollutants, and enzyme abundance at two Ganga sites: Nawabganj, Kanpur (highly polluted), and Below Farakka Bridge, West Bengal (less polluted). In-silico analysis was conducted using RemeDB for enzyme identification and MG-RAST for microbial abundance. Enzyme abundance was determined by integrating microbial profiles with the RemeDB enzyme database. Key enzymes identified include Phenylacetaldehyde dehydrogenase (plastic), Biphenyl dioxygenase (hydrocarbons), and Catechol 1,2-dioxygenase (dyes). Results indicate higher bioremediating enzyme diversity in the more polluted Nawabganj site. The findings highlight the potential of native enzymes for pollutant degradation and support further exploration for environmental cleanup strategies.}, }
@article {pmid41239457, year = {2025}, author = {Kaczmarczyk, M and Kędzierska-Kapuza, K and Skonieczna-Żydecka, K and Surówka, A and Drożdżal, S and Lechowicz, K and Buszman, M and Szkudlarek, U and Cembrowska-Lech, D and Podsiadło, K and Samborowska, E and Łoniewski, I and Ciechanowski, K}, title = {Modulating effects of microbiota on synbiotic intervention outcomes for microbiota-derived trimethylamine, trimethylamine N-oxide and indoxyl sulfate in healthy young medical students: insights from a 12-week randomized clinical trial.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {1287}, pmid = {41239457}, issn = {1479-5876}, mesh = {Humans ; *Methylamines/blood ; *Synbiotics ; *Indican/blood ; Female ; Male ; Young Adult ; *Students, Medical ; *Microbiota ; Adult ; Gastrointestinal Microbiome ; *Healthy Volunteers ; }, abstract = {BACKGROUND: Microbiota-derived metabolites, trimethylamine-N-oxide (TMAO) and indoxyl sulfate (IS), have been implicated in cardiovascular, renal, and metabolic diseases. Synbiotic interventions are a promising strategy to modulate these metabolites, but their efficacy may vary depending on host-microbial characteristics. This study investigated whether a multi-strain synbiotic could reduce serum concentrations of trimethylamine (TMA), TMAO, and IS in healthy young adults, and whether baseline characteristics of the gut microbiota influence individual responses to the intervention.<br><br>METHODS: In a 12-week, double-blind, randomized, placebo-controlled trial, 38 healthy young medical students received either a synbiotic or placebo. Serum levels of TMA, TMAO, and IS were measured at baseline, 6 weeks, and week 12, two hours after consuming two eggs. Gut microbiota composition and function were assessed using 16&#xa0;S rRNA gene sequencing and predicted through metagenomic profiling (PICRUSt2). Weighted Gene Co-expression Network Analysis (WGCNA) was applied to identify groups of co-occurring bacterial taxa (ASVs) and functional orthologous groups - KEGG Orthologs (KOs).<br><br>RESULTS: The synbiotic intervention did not produce significant changes in TMA, TMAO, or IS levels across the entire study population. There were no significant changes in alpha diversity or microbiota composition during the intervention. However, baseline microbiota-related factors influenced individual responses to synbiotic therapy. Two taxonomic WGCNA modules, containing Lachnospiraceae and Ruminococcaceae, were associated with greater reductions in IS levels in participants receiving synbiotics. Also, a module containing Lachnospirales and Oscillospirales showed a potential modulatory effect on TMA levels. A KO module enriched in genes involved in bacterial secretion systems, sulfur metabolism, and methanogenesis pathways - including K14083 (mttB) and K14084 (mttC), both implicated in the conversion of TMA to methane - was significantly associated with reductions in TMA.<br><br>CONCLUSIONS: In this randomized, placebo-controlled trial in healthy young adults, the synbiotic did not produce a significant arm-wide effect on post-challenge serum TMA, TMAO, or indoxyl sulfate over 12 weeks. Exploratory moderation analyses suggest that baseline gut-microbiota features, taxonomic and functional, may modulate individual responses, particularly for IS and TMA, supporting a precision-nutrition framework. The translational significance of this study stems from the observation that primary prevention, which is particularly important in metabolic diseases, should be individualised based on the function of the microbiota.}, }
@article {pmid41239428, year = {2025}, author = {Chen, W and Zhang, Y and Gong, H and Cao, Z and Yang, K and Mi, J}, title = {Exploring diversity and distribution patterns of chicken gut bacteriophage community.}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {119}, pmid = {41239428}, issn = {2524-4671}, }
@article {pmid41239203, year = {2025}, author = {Wen, S and Sun, J and Zeng, W and Xiang, H and Zhao, M and Xiang, D}, title = {Effects of different arbuscular mycorrhizal fungi on tobacco seedling growth and their rhizosphere microecological mechanisms.}, journal = {BMC plant biology}, volume = {25}, number = {1}, pages = {1578}, pmid = {41239203}, issn = {1471-2229}, }
@article {pmid41239201, year = {2025}, author = {Akanmu, AM and Lawal, IB and Ibrahim, SL and Marle-Köster, EV and Hassen, A}, title = {Metagenomic data from the rumen of South African Mutton Merino sheep supplemented with crude or encapsulated Acacia tannin extracts.}, journal = {BMC genomic data}, volume = {26}, number = {1}, pages = {86}, pmid = {41239201}, issn = {2730-6844}, support = {SRUG2204254606//National Research Foundation/ ; }, mesh = {Animals ; *Rumen/microbiology ; *Tannins/pharmacology/administration &amp; dosage ; *Acacia/chemistry ; Sheep/microbiology ; *Metagenomics ; Gastrointestinal Microbiome ; *Plant Extracts/pharmacology ; Animal Feed ; Dietary Supplements ; }, abstract = {OBJECTIVES: This dataset was generated as part of a study investigating the impact of crude and encapsulated Acacia mearnsii tannin extracts on the rumen microbiota of South African Mutton Merino sheep. The aim was to provide high-quality metagenomic data to support methane mitigation strategies through dietary interventions targeting rumen microbial communities.<br><br>DATA DESCRIPTION: Rumen fluid was collected from 24 rams (six per treatment) fed a total mixed ration (TMR) supplemented with either distilled water (control), monensin (positive control), crude tannin, or microencapsulated tannin. However, one sample did not yield sufficient sequencing depth, resulting in 23 usable datasets. DNA was extracted and subjected to shotgun metagenomic sequencing on the Illumina NovaSeq 6000 platform. The dataset comprises paired-end reads deposited in the NCBI SRA under accession SRP480487. Taxonomic profiling reveals dominant phyla such as Bacteroidetes and Firmicutes, and the presence of archaeal genera such as Methanobrevibacter. This dataset provides insights into the structural and functional composition of the rumen microbiome and may be useful for comparative studies and biotechnology applications.}, }
@article {pmid41239026, year = {2025}, author = {Cao, D and Huang, W and Pang, M and Li, J and Huang, H and Ma, H and Li, D and Qin, Y and Peng, X and Fan, H}, title = {Investigation of the Alterations in the Gut Microbiota and Intestinal Mucosa in Mice Infected with Echinococcus multilocularis.}, journal = {Acta parasitologica}, volume = {70}, number = {6}, pages = {211}, pmid = {41239026}, issn = {1896-1851}, support = {No. 2020-ZJ-Y01//Key Laboratory Project of the Science and Technology Department of Qinghai Province/ ; Qinghai[2023]-125//The National Clinical Key Specialty Construction Project of Hepatobiliary Surgery (Hydatidosis) at Qinghai University Affiliated Hospital/ ; Qinghai Research Key Laboratory for Echinococcosis//The 2022 Science and Technology Plan Project of Qinghai Department of Science and Technology/ ; }, abstract = {PURPOSE: Alveolar echinococcosis (AE), a zoonotic parasitic disease caused by the larval metacestode of Echinococcus multilocularis (E. multilocularis), primarily affects the liver and can invide other organs. Given its extremely poor prognsis, witha 10-year mortality rate exceeding 90% in untreated cases, this study aimed to investigate the characteristics and compositional alterations of the intestinal microbiota in AE-infected hosts and evaluate associated intestinal mucosal damage.<br><br>METHODS: We established a mouse model of AE for analysis. Fecal samples were collected from 12 AE-infected mice and 12 age-matched healthy controls at 3 and 6 months post-infection. Gut microbiota composition was assessed by 16S rRNA gene sequencing. Intestinal tissues were subjected to histopathological exnamination using hematoxylin-eosin staining (H&amp;E staining), Alcian blue-glucogen staining (AB-PAS staining), and Lendrum's fluorescent peach red staining, to evaluate mucosal structural integrity and quantify the Paneth and goblet cells.<br><br>RESULTS: The analysis revealed significant alterations in intestinal microbiota diversity and composition in AE-infected mice compared with controls, with changes becoming more pronounced as the infection progressed. Minimal disruption in microbial ecology was observed at 3&#xa0;months, whereas substantial reductions in alpha diversity and distinct shifts in beta diversity emerged after 6&#xa0;months of chronic infection. Phylum-level analysis showed an early increase in Verrucomicrobiota, Bacteroidota, and Campylobacterota at 3&#xa0;months, followed by a marked enrichment of Verrucomicrobiota and Actinobacteriota at 6&#xa0;months when compared with controls. At the genus level, AE infection led to a rapid depletion of Ligilactobacillus and Lactobacillus between 3 and 6&#xa0;months, while Akkermansia abundance significantly increased. Histopathological examination of intestinal tissue further demonstrated severe mucosal damage, including villous atrophy, reduced crypt depth, a pronounced decrease in Paneth cell density (P&#x2009;<&#x2009;0.01), and reduced goblet cell counts (P&#x2009;<&#x2009;0.05), collectively indicating compromised intestinal barrier integrity.<br><br>CONCLUSION: AE infection induces progressive gut microbiota dysbiosis and compromises intestinal barrier integrity. The specific microbial shifts, particularly the depletion of Ligilactobacillus and enrichment of Akkermansia, represent promising diagnostic biomarkers and potential targets for probiotic supplementation or microbial modulation. To further clarify their roles, future research should incorporate multi-omics strategies, including metagenomics and metabolomics, within larger cohorts to better characterize microbiota-host metabolic interactions and to validate stage-specific microbial biomarkers in AE.}, }
@article {pmid41238915, year = {2025}, author = {Morad, G and Damania, AV and Melendez, B and Singh, BB and Veguilla, FJ and Soto, RA and Hoballah, YM and Sahasrabhojane, PV and Wong, MC and Ahmed, MM and Rico, RN and Lewis, KN and Wani, K and Shamsutdinova, DD and Lazcano Segura, RN and Ingram, DR and Goethe, EA and Day, A and Flores, II and McDaniel, LK and Chelvanambi, M and Johnson, SB and Dimitriou, F and Gupta, P and Oberai, S and Zal, MA and Doss, P and Jamal, MA and Hayase, E and Wathoo, C and Norberg, LM and Jenkins, SL and Nass, S and Gumin, J and Long, L and Yang, J and Bradley, GR and Bekal, MP and Dono, AG and Pichardo-Rojas, PS and Andrewes, SW and Ballester, LY and Losh, JS and Liang, J and Huo, L and Nielsen, DC and Parker Kerrigan, BC and Brastianos, PK and Fowlkes, NW and Chang, CC and Jenq, RR and Gomez-Manzano, C and Huse, JT and Davies, MA and Lazar, AJ and Bhat, KP and Tandon, N and Esquenazi, Y and Peterson, CB and Puduvalli, VK and Lang, FF and Johnston, CD and Bullman, S and Ajami, NJ and Ferguson, SD and Wargo, JA}, title = {Microbial signals in primary and metastatic brain tumors.}, journal = {Nature medicine}, volume = {31}, number = {11}, pages = {3675-3688}, pmid = {41238915}, issn = {1546-170X}, support = {R21 NS130323/NS/NINDS NIH HHS/United States ; F32 CA260769/CA/NCI NIH HHS/United States ; 1R01 CA227156-01//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; P50 CA221703/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; *Brain Neoplasms/microbiology/pathology ; RNA, Ribosomal, 16S/genetics ; Tumor Microenvironment ; Female ; *Glioma/microbiology/pathology ; Male ; Prospective Studies ; Middle Aged ; *Microbiota/genetics ; In Situ Hybridization, Fluorescence ; Aged ; Adult ; Bacteria/genetics ; }, abstract = {Gliomas and brain metastases are associated with poor prognosis, necessitating a deeper understanding of brain tumor biology and the development of effective therapeutic strategies. Although our group and others have demonstrated microbial presence in various tumors, recent controversies regarding cancer-type-specific intratumoral microbiota emphasize the importance of rigorous, orthogonal validation. This prospective, multi-institutional study included a total of 243 samples from 221 patients, comprising 168 glioma and brain metastases samples and 75 non-cancerous or tumor-adjacent tissues. Using stringent fluorescence in situ hybridization, immunohistochemistry and high-resolution spatial imaging, we detected intracellular bacterial 16S rRNA and lipopolysaccharides in both glioma and brain metastases samples, localized to tumor, immune and stromal cells. Custom 16S and metagenomic sequencing workflows identified taxa associated with intratumoral bacterial signals in the tumor microenvironment; however, standard culture methods did not yield readily cultivable microbiota. Spatial analyses revealed significant correlations between bacterial 16S signals and antimicrobial and immunometabolic signatures at regional, neighborhood and cellular levels. Furthermore, intratumoral 16S bacterial signals showed sequence overlap with matched oral and gut microbiota, suggesting a possible connection with distant communities. Together, these findings introduce microbial elements as a component of the brain tumor microenvironment and lay the foundation for future mechanistic and translational studies.}, }
@article {pmid41238729, year = {2025}, author = {Lee, KY and Shin, SH and Park, G and Kang, SH and Kang, HJ and Kim, J and Lee, JJ and Son, GH and Hong, JY}, title = {Shotgun metagenomics of the vaginal microbiome in cervical shortening and preterm birth risk.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {39988}, pmid = {41238729}, issn = {2045-2322}, support = {HI21C1624//Korea Health Industry Development Institute (KHIDI)/ ; HI21C1624//Korea Health Industry Development Institute (KHIDI)/ ; RS-2023-00252948//Korea government (the Ministry of Science and ICT, the Ministry of Trade, Industry and Energy, the Ministry of Health &amp; Welfare, the Ministry of Food and Drug Safety)/ ; }, mesh = {Female ; Humans ; *Vagina/microbiology ; *Premature Birth/microbiology ; *Microbiota/genetics ; Pregnancy ; *Metagenomics/methods ; Adult ; *Cervix Uteri/microbiology/pathology ; Risk Factors ; }, abstract = {Preterm birth (PTB), a leading cause of neonatal morbidity and mortality, is frequently associated with premature cervical remodeling and vaginal microbiome dysbiosis. Cervical shortening in mid-pregnancy is a well-established risk factor for spontaneous PTB (sPTB), yet the microbial signatures underlying this condition remain underexplored, especially in Asian populations. In this study, we conducted shotgun metagenomic analysis of vaginal samples from 35 East Asian pregnant women with a short cervix and 12 with normal cervical length. Species-level taxonomic profiling and functional pathway analysis revealed reduced Lactobacillus dominance, increased microbial diversity, and enrichment of non-optimal CST IV species, such as Fannyhessea vaginae, Bifidobacterium breve, and Mycobacterium canetti in the short cervix group. Functional profiling showed group differences in pathways related to folate biosynthesis, carbohydrate metabolism, and epithelial barrier regulation. Among women with a short cervix, those who delivered preterm had vaginal microbiomes enriched in opportunistic pathogens, including Peptoniphilus equinus, Treponema spp., and Staphylococcus hominis. Conversely, B. breve, Lactobacillus gasseri, and Lactobacillus paragasseri were associated with full-term delivery. Functions related to glycosylation, structural stability, and degradation of cervical mucin were enriched in the sPTB group. Network analysis identified distinct microbial interactions between Lactobacillus-dominated clusters and CST IV-associated taxa, providing ecological insights that may reflect competitive dynamics and potential influences on cervicovaginal barrier integrity. These findings enhance our understanding of the taxonomic and functional profiles of the vaginal microbiome linked to cervical shortening and sPTB, contributing to improved risk stratification and management strategies for PTB, particularly in women with cervical shortening.}, }
@article {pmid41238615, year = {2025}, author = {Wang, R and Wang, H and Jiang, J and Xu, S and Dong, M}, title = {Diagnostic value of metagenomic next-generation sequencing in the etiological diagnosis of lower respiratory tract infection.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {39987}, pmid = {41238615}, issn = {2045-2322}, support = {GXLIRMMKL-201916//Guangxi Key Laboratory of Molecular Medicine in Liver Injury and Repair/ ; }, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; Female ; Male ; *Respiratory Tract Infections/diagnosis/microbiology/drug therapy ; Middle Aged ; *Metagenomics/methods ; Aged ; Adult ; Bronchoalveolar Lavage Fluid/microbiology ; Aged, 80 and over ; }, abstract = {Metagenomic next-generation sequencing (mNGS) has been widely used in infectious diseases. However, reports on mNGS for lower respiratory tract infection (LRTI) diagnosis remain limited, potentially offering significant value for improving pathogen identification. This study evaluates the diagnostic performance and clinical value of mNGS compared to traditional methods in LRTI. We analyzed traditional and mNGS detection results from 165 patients with suspected LRTI using different specimens including bronchoalveolar lavage fluid (BALF), blood, tissue samples, and pleural effusion. We compared diagnostic differences and characteristics between mNGS and traditional methods, and evaluated the effect of mNGS results on antibiotic treatment.Among 165 cases, 146 (88.48%) patients with LRTI had microbial etiology finally identified. Compared with traditional diagnostic methods, mNGS showed significantly higher positive rate (143/165, 86.7% vs 69/165, 41.8%, P < 0.05). The diagnostic performance of mNGS was not affected by sample types. mNGS demonstrated significant advantage in detecting poly-microbial infections and rare pathogens. Twenty-nine kinds of pathogens were detected only by mNGS, including non-tuberculous mycobacteria (NTM), Prevotella, anaerobic bacteria, Legionella gresilensis, Orientia tsugamushi, and viruses. The pathogen spectrum differed between immunocompetent and immunocompromised individuals. mNGS resulted in treatment changes in 119 patients (72.13%), with 54 patients (32.73%) having reduced antibiotics. mNGS has obvious advantages over traditional detection methods with results unaffected by sample types. mNGS demonstrates significant value for pathogen detection and may provide guidance in clinical practice.}, }
@article {pmid41238538, year = {2025}, author = {Bilcke, G and Campese, L and Annunziata, R and Amadei Martínez, L and Borgonuovo, C and Rijsdijk, N and Chaerle, P and Van den Berge, K and D'hondt, S and Iudicone, D and Montresor, M and Ferrante, MI and Vandepoele, K and Vyverman, W}, title = {Conserved genetic markers reveal widespread diatom sexual reproduction in the global ocean.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {10029}, pmid = {41238538}, issn = {2041-1723}, support = {1228423N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; 11L2323N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; MARCO-BOLO (101082021)//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; AtlantECO (862923)//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; }, mesh = {*Diatoms/genetics/physiology ; Reproduction/genetics ; Genetic Markers/genetics ; Oceans and Seas ; Transcriptome ; Phytoplankton/genetics ; Gene Expression Profiling ; Salinity ; Metagenome ; Seawater ; }, abstract = {Sexual reproduction is a nearly universal characteristic of the eukaryotic life cycle, yet it is rarely observed in natural populations of micro-eukaryotes. Sex is particularly relevant for diatoms, a key group of marine and freshwater phytoplankton, where sexual reproduction counters a progressive cell size reduction due to cellular division. Here, we leveraged controlled sex transcriptome experiments of four diatom species to develop a robust method for in situ monitoring of sexual reproduction events. The resulting panel of conserved marker genes was validated for specificity and sensitivity using metatranscriptomic profiling of a natural estuarine community undergoing massive sexual reproduction of multiple species in response to increased salinity. Analysis of metatranscriptomic data linked with Metagenome-Assembled Genomes from the Tara Oceans expedition revealed widespread and coordinated expression of these markers across nine diatom genera, complemented by observations of sexual stages in automated imaging resources. Our results reveal that diatom sexual reproduction is more widespread in the global ocean than previously thought, encompassing both dominant bloom-forming species and rare taxa. Our panel of markers to detect sexual reproduction in natural environments paves the road to better understand the interplay between endogenous and environmental controls of this pivotal process, essential for the diatoms' evolutionary success.}, }
@article {pmid41238046, year = {2025}, author = {Oliveira, RDS and Oliveira Alves Filho, NC and Gomes Netto, WB and Silva, DC and Oliveira, MS and Oliveira, ACFM and Baraúna, RA and Graças, DAD and Silva, A and Oliveira Veras, AA}, title = {ContigPolishing: A User-Friendly Java GUI for contig extension and refinement in prokaryotic genomes.}, journal = {Gene}, volume = {}, number = {}, pages = {149893}, doi = {10.1016/j.gene.2025.149893}, pmid = {41238046}, issn = {1879-0038}, abstract = {To determine the gene content of an organism, the reads generated by the sequencing process must be assembled using an assembly strategy, either by reference or de novo. However, this process often results in multiple sequences called contigs, which, after the sorting steps, are grouped into scaffolds. The completion stage aims to obtain a single genomic sequence, called a complete genome, which is not a trivial task. Various analytical strategies have been developed to help in this process, many of which have been implemented in computer tools to obtain complete genomes or as close to this as possible, the so-called drafts. The manuscript presents ContigPolishing, a computational tool with a simple and intuitive graphical interface, developed to improve the assembly of prokaryotic genomes, such as bacteria and metagenomes. Despite existing software, there is a gap for solutions that combine simplicity and robustness. ContigPolishing addresses this need, featuring an integrated database that allows processing to be resumed at any time. The tool was validated with 90 NCBI datasets from genera such as Escherichia coli, Corynebacterium, and Nocardia, as well as raw reads from the SRA database to simulate real-world situations. The results showed improvement in the contiguity of the assemblies, with an increase in N50 and improvement in L50, and a reduction in the number of contigs, by extending the contigs using the similarity between their flanks. In some cases, the software was able to elevate the status of genomes from draft to complete, proving its efficiency. ContigPolishing is available at: https://github.com/allanverasce/contigpolishing.}, }
@article {pmid41237940, year = {2025}, author = {Borroni, D and Lo Monaco, F and Silvia, F and Mazzotta, C and Settino, M and Gabrielli, F and Papa, FT and Alfonsi, C and Di Pietro, F and Rizzuto, V and Stroffolini, G and Bonzano, C and Laganovska, G and Vanags, J and Rechichi, M and Rocha-de-Lossada, C and Ballesteros-Sánchez, A and Zeppieri, M and Gagliano, C}, title = {Ocular Surface Microbiota in Primary Open Angle Glaucoma.}, journal = {Experimental eye research}, volume = {}, number = {}, pages = {110734}, doi = {10.1016/j.exer.2025.110734}, pmid = {41237940}, issn = {1096-0007}, abstract = {Primary open-angle glaucoma (POAG) is a leading cause of irreversible blindness, yet the contribution of the ocular-surface (OS) microbiota remains poorly defined. We conducted a cross-sectional study including 27 POAG patients on chronic hypotensive therapy and 119 healthy Italian controls, profiled by 16S rRNA amplicon sequencing (Ion GeneStudio S5) and analyzed with QIIME2/phyloseq. POAG samples showed higher α-diversity (Shannon 4.23 vs 2.77; Observed richness 407 vs 154; Wilcoxon q < 1×10[-9]) and a distinct β-diversity profile (PERMANOVA p = 0.001; R[2] = 0.104). Compositional shifts included depletion of Firmicutes with loss of Staphylococcus in controls' place, and enrichment of Proteobacteria (e.g., Pseudomonas) together with unclassified Enterobacterales and a larger unclassified fraction. Differential-abundance testing identified numerous significant taxa separating groups, consistent with a more diverse yet less defined microbiota in POAG. These findings indicate an ocular-surface dysbiosis associated with POAG in a treatment-exposed cohort, supporting the relevance of host-microbe interactions and motivating longitudinal, treatment-naïve and functional studies before causal or translational inferences.}, }
@article {pmid41237902, year = {2025}, author = {Pitarch, A and Arribas, V and Gil, C}, title = {Omics and Multiomics-Based Diagnostics for Invasive Candidiasis: Toward Precision Medicine.}, journal = {Molecular &amp; cellular proteomics : MCP}, volume = {}, number = {}, pages = {101463}, doi = {10.1016/j.mcpro.2025.101463}, pmid = {41237902}, issn = {1535-9484}, abstract = {Invasive candidiasis (IC) is a serious, life-threatening, and costly fungal infection if not diagnosed early and treated appropriately. However, this healthcare-associated mycosis caused by Candida spp. is difficult to diagnose because of its nonspecific clinical signs and symptoms, and the lack of early and accurate detection methods. IC is also difficult to treat due to its late diagnosis, the limited antifungal arsenal, and the rapid emergence and spread of (multi)drug-resistant Candida strains. Therefore, early and accurate innovative methods for species and resistance identification in IC (candidemia and deep-seated candidiasis) are urgently needed to initiate timely and appropriate antifungal therapy, and reduce its high morbidity, mortality, and healthcare costs in hospitalized patients (in particular, severely immunocompromised or critically ill patients). The availability of the complete genome sequences of the most clinically relevant Candida species coupled with recent advances in high-throughput omics technologies have spurred an unprecedented era in the discovery and development of IC diagnostics at different levels of molecular complexity. Here we review the contribution of current and emerging omics technologies, including genomics, transcriptomics, proteomics, peptidomics, metabolomics, lipidomics, glycomics, immunomics (immunoproteomics, immunopeptidomics, and immunoglycomics), imiomics (imaging-omics), and microbiomics (metagenomics, metatranscriptomics, metaproteomics, and metabonomics), to the process of biomarker development for early diagnosis, antifungal susceptibility, prognosis, follow-up, and therapeutic monitoring in IC. We highlight the potential of integrating multiple omic data (through integromics, multiomics or panomics, together with systems biology and artificial intelligence) for the discovery of multidimensional biomarker signatures and computational algorithms for IC diagnosis. Finally, we discuss future challenges and prospects for their clinical implementation. These next-generation IC diagnostics promise to revolutionize medical practice by unraveling the complexity of biological systems at multiple levels. In addition, these could help clinicians make more precise and personalized clinical decisions through multiomics or panomics-based precision medicine approaches, rather than traditional one-size-fits-all approaches.}, }
@article {pmid41237728, year = {2025}, author = {Meng, Q and Wang, J and Li, K and Zhang, Y and Hu, Z and Wang, F and Pan, F and Fu, J and Dang, C}, title = {Low-dose chlorine disinfection poses a greater potential risk of antibiotic resistance genes and their pathogenic hosts.}, journal = {Water research}, volume = {289}, number = {Pt B}, pages = {124895}, doi = {10.1016/j.watres.2025.124895}, pmid = {41237728}, issn = {1879-2448}, abstract = {Identifying the responses of antibiotic resistance genes (ARGs) and their hosts to chlorine disinfection is necessary because it has been paradoxically reported to both amplify and suppress antibiotic resistance in water treatment processes. In this study, our integrated metagenomic and metatranscriptomic analysis of sequencing batch reactors under different chlorine disinfection conditions (0, 2, 6, and 10 mg/L) in activated sludge reveals that low-dose chlorine obviously increases ARG abundance, diversity, and transcriptional activity, particularly for multidrug, β-lactam, and tetracycline types, while higher doses reduce transcriptional diversity and activity. Acinetobacter johnsonii, a pathogen abundant and active under chlorine-addition conditions, poses a high risk of ARG transmission due to its multiple mobile genetic elements and potential involvement in horizontal gene transfer with non-pathogens. Notably, chlorine disinfection may simultaneously promote the co-transfer of chlorine resistance and antibiotic resistance genes, such as the qacE gene, with the involvement of plasmids and integrons. Overall, this study demonstrates that low-dose chlorine may promote greater ARG enrichment, mobility, and pathogenic potential in activated sludge. The findings highlight overlooked risks of low-concentration residual chlorine, urging reconsideration of disinfection strategies to protect public health.}, }
@article {pmid41237727, year = {2025}, author = {Zhao, Z and Zhao, Y and Hua, M and Yao, X and Hu, B}, title = {Deep metagenomic insights into the formation characteristics of the resistome in Pristine Saline Lakes.}, journal = {Water research}, volume = {289}, number = {Pt B}, pages = {124937}, doi = {10.1016/j.watres.2025.124937}, pmid = {41237727}, issn = {1879-2448}, abstract = {Pristine and isolated ecosystems remain underexplored in resistome research, leaving a major gap in understanding how antibiotic resistance genes (ARGs) persist and spread outside human influence. To address this, we performed the first long-term, systematic, ultra-deep metagenomic survey of four high-altitude pristine saline lakes in the Altun Shan National Nature Reserve-an uninhabited region of the Qinghai-Tibet Plateau-generating 1.8 terabases of sequencing data. We identified a total of 756 ARG subtypes spanning 28 ARG types in all sampled lakes, with the clinically relevant polymyxin resistance gene, ugd, accounting for 30.5 % of the total ARG abundance. Moreover, ugd showed high mobility potential, with 183 horizontal gene transfer (HGT) events identified across 18 genera, and was widely associated with mobile genetic elements (MGEs). Similarity analyses revealed that the ARG profiles of pristine saline lakes were most comparable to those of marine environments, suggesting that salinity is a key ecological driver shaping the prevalence of polymyxin resistance genes. These findings indicate that pristine saline lakes can act as previously underexplored reservoirs and exchange hubs for clinically important resistance genes. Our results reveal the abundance and dissemination potential of ugd in isolated ecosystems and provide new insights into how natural environmental factors independently shape the resistome, with implications for One Health antimicrobial resistance surveillance.}, }
@article {pmid41237724, year = {2025}, author = {Huang, P and Zhou, Y}, title = {Enhance H2 production by regulating acetyl-CoA supply and reducing equivalent diversion in an enriched purple phototrophic bacteria culture.}, journal = {Water research}, volume = {289}, number = {Pt B}, pages = {124910}, doi = {10.1016/j.watres.2025.124910}, pmid = {41237724}, issn = {1879-2448}, abstract = {Short-chain volatile fatty acids (VFAs) are promising carbon sources for biohydrogen production by purple phototrophic bacteria (PPB), given their high hydrogen conversion potential and low cost. However, most existing studies used a single VFA as the carbon source, providing only partial insights for practical applications, as VFAs in waste streams typically exist in mixtures. Furthermore, the metabolic responses of PPB to VFA mixtures, which determine H2 yield, and the metabolic mechanisms, remain largely unexplored. This study investigated the effects of co-feeding propionate with acetate or butyrate on PPB's hydrogen production and explored the associated metabolic responses through metagenomic and metatranscriptomic analyses. Results show that co-feeding butyrate with propionate (1:1 COD ratio) increased substrate conversion efficiency to 61 %, compared to 54 % from sole propionate. This improvement is linked to increased acetyl-CoA (Ac-CoA) availability, which, on one hand, activates the tricarboxylic acid (TCA) cycle and generates more electrons during carbon assimilation, and on the other hand, reduces the competitiveness of other electron sinks, thereby enhancing electron flow toward hydrogen. In contrast, co-feeding acetate with propionate results in a comparable conversion efficiency (∼50 %), where the increased Ac-CoA availability promotes carbon assimilation through the glyoxylate shunt instead. These findings reveal a synergistic metabolic impact from mixed VFAs and highlight the role of Ac-CoA in regulating carbon assimilation and electron dissipation. Understanding these interactions can guide the selection of waste streams and pretreatment processes to provide PPB with favorable VFA compositions, enabling more efficient and sustainable hydrogen production in practice.}, }
@article {pmid41237630, year = {2025}, author = {Hemmat-Jou, MH and Li, F and Wang, D and Gao, R and Xiao-Xia, Z and Chen, Y and Fang, L}, title = {Metagenomic analysis reveals global landscape of viruses in biogeochemical cycles and microbial resistance in paddy soils and wetlands.}, journal = {Journal of hazardous materials}, volume = {500}, number = {}, pages = {140469}, doi = {10.1016/j.jhazmat.2025.140469}, pmid = {41237630}, issn = {1873-3336}, abstract = {Paddy soils and wetlands form a critical soil-water interface that supports global crop production and biogeochemical cycling. Understanding the role of viruses in these ecosystems is vital for predicting ecosystem resilience. Considering the significance of viruses in microbial community structure and environmental pollution, we analyzed 163 metagenomes from 18 countries in Asia, Europe, America, and Australia. We characterized the global distribution and potential ecological functions of viruses through viral auxiliary metabolic genes (vAMGs), antibiotic resistance genes (vARGs), and metal(loid) resistance genes (vMRGs). We found viruses with globally consistent compositions and host profiles, characterized by high richness and a dominance of lysogenic families. We identified 497 vAMGs associated with carbon, phosphorus, nitrogen, and sulfur cycling, and detected 279 vARGs (conferring resistance to 10 antibiotic) and 141 vMRGs (against 7 metal(loids)). These genes exhibited strong co-localization and co-selection patterns, and their transduction can promote the emergence of multi-resistant microbes, reshaping microbial communities. Therefore, viruses are key mobile vectors for the environmental spread of these genes. By quantifying these pathways, we provide a crucial advancement for ecological risk identification and assessment. This meta-analysis provides a comprehensive overview of virus-mediated biogeochemical processes and resistance gene propagation. We demonstrate that viruses can disseminate antibiotic and metal(loid) resistance, a pollution-driven process that poses potential health risks. Furthermore, by regulating key metabolic pathways, viruses can influence greenhouse gas fluxes. Our findings underscore the necessity of integrating viruses into climate models, pollution mitigation strategies, and One Health policies to assess ecological risks and to protect ecosystem and public health.}, }
@article {pmid41237622, year = {2025}, author = {Liu, B and Wang, S and Ren, J and Zhang, Z and Ma, J and Li, T and Zhou, Q and Sun, J}, title = {Impacts of non-spherical polyethylene nanoplastics on microbial communities and antibiotic resistance genes in the rhizosphere of pea (Pisum sativum L.): An integrated metagenomic and metabolomic analysis.}, journal = {Journal of hazardous materials}, volume = {500}, number = {}, pages = {140425}, doi = {10.1016/j.jhazmat.2025.140425}, pmid = {41237622}, issn = {1873-3336}, abstract = {The ecological effects of nanoplastics (NPs) has become a growing concern; however, the influence of non-spherical NPs-which better represent real-world morphologies-remains poorly understood. This study investigated the impact of non-spherical polyethylene (PE) NPs on the growth of pea (Pisum sativum L.) and its rhizosphere microenvironment across different concentration levels (0, 20, and 200 mg/kg) using integrated metagenomics and metabolomics. Results showed that high-dose (200 mg/kg) exposure significantly inhibited plant growth. Although soil physicochemical properties remained unchanged, the rhizosphere microbial communities experienced significant restructuring, characterized by a marked enrichment of Pseudomonas and a reduction in beneficial Rhizobium populations. Metagenomic analysis revealed a concurrent increase in the abundance and diversity of antibiotic resistance genes (ARGs) under non-spherical PE-NP stress. This was accompanied by a shift in bacterial host composition, with a trend toward a higher prevalence of potentially pathogenic taxa such as Pseudomonas aeruginosa. Metabolomics analysis further revealed that non-spherical PE-NPs altered the rhizosphere metabolite profile, thereby significantly driving the succession of ARG hosts. Our integrated analysis enhances the understanding of how non-spherical PE-NPs disrupt microbial communities and elevate the risks of ARGs in rhizosphere soil, highlighting the significance of incorporating environmentally relevant NPs into environmental risk assessments.}, }
@article {pmid41236809, year = {2025}, author = {Shuvo, MSH and Kim, S and Jo, S and Rahim, MA and Barman, I and Hossain, MS and Jeong, Y and Jeong, H and Kim, S and Seo, H and Song, HY}, title = {Characterization of Gut Microbiota of Honey Bees in Korea.}, journal = {Polish journal of microbiology}, volume = {}, number = {}, pages = {}, doi = {10.33073/pjm-2025-025}, pmid = {41236809}, issn = {2544-4646}, abstract = {Korea's unique climate and agricultural environment suggest that the gut microbiome of honey bees may possess distinctive compositions influenced by regional factors. With the decline in honey bee populations and rising health challenges, understanding the role of gut microbiomes is essential for enhancing honey bee health and their resilience to environmental stressors. To explore caste-specific gut microbiota and identify microbial signatures associated with honey bee health, this study examined the gut microbial composition of worker bees, queen bees, and drones of Apis mellifera using 16S rRNA gene amplicon sequencing. Analysis of beta diversity and species richness demonstrated significant differences between worker bees and both drones and queens, with no significant differences identified between drones and queens. Notably, Lactobacillus dominated all groups, comprising 98.6% of the drones, 95.4% of the queens, and 68.3% of the workers. Additionally, Bombella was prominent in queens (4%), whereas Gilliamella (23%) and Frischella (4.7%) were notably enriched in workers. Drones and queens exhibited similar gut microbiome profiles, while workers displayed distinctly different compositions. These findings underscore the variation in gut microbiota composition and potential functional roles across honey bee castes. Such microbial distinctions may reflect caste-specific roles and physiological demands within the colony. Future research should investigate the physiological roles of gut microbiota and their contributions to environmental resilience, paving the way for microbiome-based strategies to promote honey bee health. This study lays a crucial scientific foundation for conserving the honey bee ecosystem and promoting sustainable agriculture.}, }
@article {pmid41236788, year = {2025}, author = {Artale, S and Filiali, F and Beretta, E and Arosio, F and Cazzaniga, F and Tersalvi, C and Sofia, M and Tagliabue, P and Pozzi, P and Colombo, A and Carbone, C and Pietrogiovanna, L and Verga, M and Nova, P and Calori, R and Renso, R and Rota, S and Aglione, S and Manfrida, I and Facendola, G and Trojani, A and Dazzani, MC and Basciani, S and Valsecchi, MG and Capitoli, G and Cocola, C and Consolandi, C}, title = {The Effects of a Modified Mediterranean Diet on Gut Microbiota and Chemotherapy Side Effects in Patients With Metastatic Colorectal Cancer Undergoing First-Line Chemotherapy With or Without Either Antiepidermal Growth Factor Receptor or Antivascular Endothelial Growth Factor Agent: Protocol for a Randomized Pilot Study in Italy.}, journal = {JMIR research protocols}, volume = {14}, number = {}, pages = {e72950}, doi = {10.2196/72950}, pmid = {41236788}, issn = {1929-0748}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Colorectal Neoplasms/drug therapy/pathology ; *Diet, Mediterranean ; Pilot Projects ; Italy ; Female ; Male ; Prospective Studies ; ErbB Receptors/antagonists &amp; inhibitors ; *Antineoplastic Agents/adverse effects/therapeutic use ; Middle Aged ; Aged ; Randomized Controlled Trials as Topic ; Adult ; }, abstract = {BACKGROUND: The gut microbiota is attracting increasing interest as a factor possibly impacting colorectal cancer risk, therapy toxicity, and, as a consequence, patient's quality of life. It has been observed that microbial imbalance in the gut and in cancer tissue is facilitated by a Western type of diet, rich in meat, sugars, and refined grains, while a Mediterranean diet, rich in low saturated fat and fibers, promotes gut eubiosis, and results in reduced risk of developing colorectal cancer. Specifically, a high fiber content diet has been associated with a reduced incidence of therapy related adverse events in patients with malignant melanoma.<br><br>OBJECTIVE: This study aimed to analyze and compare the gut microbiota of patients with metastatic colorectal cancer undergoing first-line chemotherapy with or without a biological agent (antiepidermal growth factor receptor or antivascular endothelial growth factor), and receiving either a free standard Western diet, or a modified Mediterranean diet, and the impact of microbiota on chemotherapy toxicity.<br><br>METHODS: This is a pilot nondrug, interventional prospective, randomized, controlled, single-center (Italian), open-label trial. Patients (n=40) living in Italy, and with a local style of life, will be randomized 1:1 to either a modified Mediterranean diet or a free Western-type diet. Blood and fecal samples will be collected at baseline and control visits, for metagenomic and metabolomic analysis. The primary endpoint is the Firmicutes:Bacteroidetes ratio after completion of the third cycle of first-line chemotherapy (time T1). Secondary endpoints are (1) the percentage of patients experiencing gastrointestinal side effects at T1, (2) the percentage of patients experiencing grade 3/4 gastrointestinal side effects at T1, and (3) changes in the Firmicutes:Bacteroidetes ratio, overall microbiome composition, and metabolome at T1, and after the sixth chemotherapy cycle (T2) versus baseline.<br><br>RESULTS: This pilot trial received ethics approval on July 24, 2024. By July 2025, a total of 17 participants have been recruited. The study will conclude with the visit at T2 for the last enrolled patient. Results are expected to be published in October 2028.<br><br>CONCLUSIONS: This study has the potential to provide critical insights into the role of diet in modifying the gut microbiota, diminishing chemotherapy-related side effects, and possibly enhancing the therapeutic efficacy in metastatic colorectal cancer by improving tolerability. In addition, data may pave the way for future research in immunotherapy, potentially influencing both clinical practice and public health strategies.<br><br>TRIAL REGISTRATION: Clinicaltrial.gov NCT06794931; https://clinicaltrials.gov/search?term=NCT06794931.<br><br>DERR1-10.2196/72950.}, }
@article {pmid41236769, year = {2025}, author = {Lima Filho, CM and Santos, AA and Lima, DVN and Silva, LO and Paranhos, RR and Branco, S and Pacheco, ABF and Azevedo, SMFO}, title = {Combining Ludwigia leptocarpa with the dried biomass of Pontederia crassipes for mitigating cyanobacteria: a sustainable way to use macrophyte waste.}, journal = {International journal of phytoremediation}, volume = {}, number = {}, pages = {1-13}, doi = {10.1080/15226514.2025.2579148}, pmid = {41236769}, issn = {1549-7879}, abstract = {Constructed Floating Wetlands (CFWs) with emergent macrophytes offer a low-cost, sustainable strategy to mitigate eutrophication. We evaluated the combined use of Ludwigia leptocarpa, a native macrophyte from the Americas, and dried biomass of Pontederia crassipes (DB Pc) as substrate in small-scale CFWs to suppress a natural cyanobacterial bloom. Ex-situ mesocosm experiments (40 L) were conducted over 16 days with treatments: L. leptocarpa with DB Pc (S+), L. leptocarpa alone (S-), DB Pc alone, and living P. crassipes as positive control. L. leptocarpa (S-) and P. crassipes reduced Soluble Reactive Phosphorus by >85%, but L. leptocarpa produced 10 times less biomass. Treatments with DB Pc increased nutrient and phenol concentrations. All treatments led to reduced chlorophyll-a and phytoplankton density, especially cyanobacteria, along with pH reduction. 16S rRNA sequencing revealed higher bacterial diversity in the L. leptocarpa rhizosphere than in the water, suggesting a role in phytoremediation. The combination of L. leptocarpa and DB Pc in CFWs shows potential for cyanobacterial control through nutrient uptake, allelopathy, and pH modulation. This method supports sustainable water management by utilizing a native, slow-growing macrophyte and repurposing waste biomass that would otherwise harm aquatic ecosystems.}, }
@article {pmid41236031, year = {2025}, author = {Kim, JR and Byun, JS and Jung, JK and Hong, SH and Lee, HJ}, title = {Altered oral microbiome diversity in patients with oral candidiasis.}, journal = {Archives of oral biology}, volume = {180}, number = {}, pages = {106430}, doi = {10.1016/j.archoralbio.2025.106430}, pmid = {41236031}, issn = {1879-1506}, mesh = {Humans ; *Candidiasis, Oral/microbiology/drug therapy ; *Microbiota/drug effects ; Male ; Saliva/microbiology ; Female ; *Fluconazole/therapeutic use/pharmacology ; Middle Aged ; *Antifungal Agents/therapeutic use/pharmacology ; RNA, Ribosomal, 16S/genetics ; *Mouth/microbiology ; Aged ; Adult ; Streptococcus salivarius/drug effects ; Real-Time Polymerase Chain Reaction ; }, abstract = {OBJECTIVE: Oral candidiasis is a common opportunistic infection caused by Candida albicans, particularly in individuals with local or systemic risk factors. This study aimed to investigate how antifungal therapy affects the composition of the oral bacterial microbiome.<br><br>DESIGN: Unstimulated saliva samples were collected from ten patients diagnosed with acute pseudomembranous oral candidiasis before and after fluconazole treatment. Microbiome profiles were assessed using 16S rRNA gene sequencing. Quantitative PCR was performed to validate changes in specific bacterial species.<br><br>RESULTS: Alpha diversity did not change significantly, whereas beta-diversity analyses indicated modest compositional shifts. Antifungal therapy was associated with an increase in Streptococcus salivarius, a commensal linked to mucosal health. The signal was confirmed by species-specific qPCR in paired samples.<br><br>CONCLUSIONS: Fluconazole treatment for oral candidiasis induces modest shifts in the oral bacterial community, particularly increasing the abundance of S. salivarius. These changes may reflect partial recovery of microbial homeostasis, supporting the role of microbiome monitoring and probiotic approaches in post-treatment care.}, }
@article {pmid41235937, year = {2025}, author = {Mills, S and Collins, G and Ijaz, UZ and Lens, PNL}, title = {Metagenome-assembled genomes from microbial communities in lab-scale anaerobic bioreactors treating simulated dairy wastewater.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0048725}, doi = {10.1128/mra.00487-25}, pmid = {41235937}, issn = {2576-098X}, abstract = {This dataset describes metagenome-assembled genomes from three lab-scale (4L) expanded granular sludge bed bioreactors treating synthetic dairy wastewater. The resulting MAGs encompass 60 phyla with average genome completeness of 78.68% and average contamination of 2.29%. These genomes represent a valuable resource for studying anaerobic bioreactors used in wastewater treatment.}, }
@article {pmid41235136, year = {2025}, author = {Wu, Y and Pan, S and Yin, C and Kong, Y and Huo, W and Wang, Q and Wu, J and Li, L and Wei, J and Lu, C and Han, L and Lu, Y}, title = {PSORI-CM02 Restores Epidermal Differentiation in Psoriasis via the Gut Microbiota-Sphingolipid Axis.}, journal = {Drug design, development and therapy}, volume = {19}, number = {}, pages = {9993-10010}, pmid = {41235136}, issn = {1177-8881}, mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; *Psoriasis/drug therapy/metabolism/pathology ; Mice ; Humans ; *Cell Differentiation/drug effects ; *Sphingolipids/metabolism ; *Epidermis/drug effects/pathology/metabolism ; Keratinocytes/drug effects/metabolism ; }, abstract = {BACKGROUND: Psoriasis is linked to gut dysbiosis and disturbed sphingolipid metabolism. PSORI-CM02 improves epidermal differentiation, yet its impact on the microbiota-sphingolipid axis remains unknown.<br><br>METHODS: Transcriptomics of patient keratinocytes, Carmofur inhibition in IMQ mice, and multi-omics (metabolomics, metagenomics) of skin, lymph nodes and gut were combined. SPF, PGF and GF mice underwent FMT to test microbiota dependency.<br><br>RESULTS: Psoriatic lesions showed sphingolipid pathway enrichment. Carmofur enhanced differentiation. PSORI-CM02 lowered PASI, spleen index, and tissue levels of ceramide, S1P, C1P and sphingomyelin while restoring Flg, Krt10 and Krt14. It reduced Turicibacter, Bacteroides, Bifidobacterium and Acetobacter. PSORI-CM02-derived microbiota reproduced therapeutic effects in all FMT settings.<br><br>CONCLUSION: PSORI-CM02 reshapes gut microbiota, normalizes sphingolipid metabolism and improves epidermal differentiation to treat psoriasis.}, }
@article {pmid41234773, year = {2025}, author = {Levé, M and Manghi, P and Bredon, M and Lefevre, A and Manara, S and Armanini, F and Emond, P and Planchais, J and Rolhion, N and Segata, N and Sokol, H}, title = {Metabolomics and metagenomics in mice reveal the role of the gut microbiota in tryptophan metabolism.}, journal = {iScience}, volume = {28}, number = {11}, pages = {113751}, pmid = {41234773}, issn = {2589-0042}, abstract = {Tryptophan metabolism plays a key role in host-microbiota interactions, producing a wide array of bioactive metabolites. However, our understanding of the interactions between tryptophan metabolites and the gut microbiota is still limited. Using targeted quantitative metabolomics and metagenomics in mice across various compartments, we showed that the cecal microbiota massively impacts tryptophan metabolism both in the gut and systemically. Grouping bacterial taxa in co-abundance guilds better reflected the links between gut microbes and tryptophan metabolites than single taxa taken individually and suggested the involvement of complex microbial interactions in tryptophan metabolism regulation. Finally, analyzing functional data, we shed light on the potential links between tryptophan metabolism and bacterial enzymes or metabolic pathways.}, }
@article {pmid41234739, year = {2025}, author = {Jin, L and Chen, S and Kang, R and Li, C and Yang, S and Yang, Q and Zhao, K and Zou, L}, title = {Variation and spread of resistomes in swine manure, manure slurries, and long-term manure-fertilized soils.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1683394}, pmid = {41234739}, issn = {1664-302X}, abstract = {BACKGROUND: Application of swine manure to soils exacerbates environmental antimicrobial resistance (AMR). However, a comprehensive evaluation of anaerobic digestion's (AD) mitigation potential against AMR and its influencing factors in swine manure-to-soil systems remains lacking.<br><br>METHODS: We employed mass spectrometry, metagenomics, and whole-genome sequencing (WGS) to investigate the fate of antibiotics, metals, and antibiotic resistance genes (ARGs) across manures, slurries, and soils from eight pig farms.<br><br>RESULTS: Anaerobic digestion reduced antibiotic and metal (except ciprofloxacin) content and risks in manure, but had limited effects on total ARG abundance, while increasing ARG network modularity. High-risk ARG abundance significantly increased from 404.7 in manure to 843.2 in slurries, with health-risk scores rising 1.88-fold during anaerobic digestion. Metagenomic analysis showed metal resistance gene (MRG) diversity and abundance decreased during anaerobic digestion, along with reduced ARG-MRG co-occurrence frequency, whereas mobile genetic element (MGE) diversity and ARG-MGE co-occurrence frequency increased. Escherichia coli was identified as the dominant ARG host. WGS of E. coli strains confirmed horizontal gene transfer (HGT) of nine ARGs (e.g., sul3 and blaTEM-1), and metagenomics suggested HGT of four ARGs (e.g., tet(M)) across different pathogens. Chromium concentrations, bacterial communities and MGEs were significantly associated with ARG profiles. Long-term slurry application resulted in elevated antibiotic, metal, and ARG concentrations in soils, with concomitant increases in high-risk ARGs and health risks.<br><br>CONCLUSION: This study demonstrates AD's limited effect on mitigating overall ARG abundance and highlights MGEs as critical drivers of ARG maintenance and dissemination from manure to soil process, guiding manure treatment optimization to reduce agricultural AMR risks.}, }
@article {pmid41234344, year = {2025}, author = {Yang, L and Zeng, J and Zhang, Y and Li, L}, title = {Purulent Meningitis Due to Porphyromonas endodontalis, Bacteroides heparinolyticus, Prevotella pleuritidis and Streptococcus constellatus from Oral and Maxillofacial Space Infection: A Case Report.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {5843-5851}, pmid = {41234344}, issn = {1178-6973}, abstract = {BACKGROUND: Purulent meningitis caused by polymicrobial oral anaerobes represents a rare but life-threatening clinical challenge, with Porphyromonas endodontalis, Bacteroides heparinolyticus, Prevotella pleuritidis, and Streptococcus constellatus being pfastidious organisms. Traditional diagnostic methods often fail to identify these fastidious organisms, leading to delayed or inappropriate therapy.<br><br>CASE PRESENTATION: We report a rare case of purulent meningitis resulting from a polymicrobial infection involving Porphyromonas endodontalis, Bacteroides heparinolyticus, Prevotella pleuritidis, and Streptococcus constellatus in a 76-year-old male patient who presented with a 40-day history of left facial pain. This case represents the first documented instance of these four oral anaerobes concurrently causing an infection of the central nervous system.<br><br>CONCLUSION: To the best of our knowledge, this case represents the first documented evidence of polymicrobial purulent meningitis caused by oral anaerobes, specifically Porphyromonas endodontalis, Bacteroides heparinolyticus, Prevotella pleuritidis, and Streptococcus constellatus. Our findings not only provide direct evidence for the oral-central nervous system (CNS) infection pathway but also validate that the valuable approach based on metagenomic next-generation sequencing (mNGS) offers significant clinical insights for diagnostic and therapeutic strategies.}, }
@article {pmid41233937, year = {2025}, author = {Zhang, P and Roque, B and Romero, P and Shapiro, N and Eloe-Fadrosh, E and Kebreab, E and Diamond, S and Hess, M}, title = {Red seaweed supplementation suppresses methanogenesis in the rumen, revealing potentially advantageous traits among hydrogenotrophic bacteria.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {231}, pmid = {41233937}, issn = {2049-2618}, mesh = {Animals ; *Rumen/microbiology/metabolism ; *Methane/metabolism/biosynthesis ; Cattle ; *Seaweed ; *Dietary Supplements ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; Animal Feed/analysis ; *Gastrointestinal Microbiome ; Fermentation ; Metagenome ; Metagenomics ; Hydrogen/metabolism ; }, abstract = {BACKGROUND: Macroalgae belonging to the genus Asparagopsis have shown to reduce methane (CH4) production during rumen fermentation, while increasing feed efficiency when added to the feed of cattle. However, little is known about how the rumen microbiome responds to Asparagopsis supplementation, and how changes in the microbiome may contribute to changes in rumen function and host phenotype. Here, we generated and analyzed metagenomic and metatranscriptomic data from the rumen microbiome from cows receiving (treatment) and not receiving (control) an Asparagopsis armata supplemented diet.<br><br>RESULTS: Using a combination of metatranscriptome and metagenome analysis, we found that reduction of CH4 emission from animals receiving A. armata was coupled to a significant reduction in the transcription of methanogenesis pathways. Additionally, a significant decrease in the transcription of genes for carbon catabolism and a reorganization of carbon catabolic gene expression occurred at the species level within the rumen microbiome of animals that received red seaweed with their diet. Increased H2 production, a consequence of methanogenesis suppression, was coupled to a significant increase in the transcription of hydrogenases that mediate hydrogenotrophic metabolism in the treatment group. Metatranscriptome analysis identified a single metagenome assembled genome (MAG) of a Duodenibacillus sp., a hitherto uncultured hydrogenotrophic bacterial species, as the dominant driver of this transcriptional change.<br><br>CONCLUSIONS: Comparative genomic analysis between the Duodenibacillus sp. and other hydrogenotrophic rumen organisms revealed metabolic traits that may provide Duodenibacillus sp. with a competitive advantage in H2 scavenging. Our findings provide an initial understanding of how the rumen microbiome responds to a promising CH4 reducing feed additive and serve as a model for alternative stable rumen microbiome states that produce less methane and increase animal productivity. Ultimately, insights from the work presented here might enable the development of advanced microbiome-based strategies to reduce enteric methane production.}, }
@article {pmid41233936, year = {2025}, author = {Modolon, F and N Garritano, A and J Hill, L and Duarte, G and Bendia, A and de Moura, R and Pellizari, V and Thomas, T and Peixoto, RS}, title = {Putative promiscuous symbionts in deep-sea corals and crinoids may contribute to nitrogen cycling.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {234}, pmid = {41233936}, issn = {2049-2618}, support = {141954/2019-1//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; ANP 21005-4//Shell, Brazil/ ; BAS/1/1095-01-01 and FCC/1/1976-40-01//KAUST/ ; }, mesh = {*Anthozoa/microbiology ; Animals ; *Symbiosis ; *Nitrogen Cycle ; Metagenomics/methods ; Microbiota ; Brazil ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; In Situ Hybridization, Fluorescence ; }, abstract = {BACKGROUND: Crinoids (feather stars) are frequently found in association with corals, yet the physiological and microbial interactions between these organisms remain poorly understood. Both corals and crinoids host symbiotic microorganisms, but the functional roles of these symbionts, particularly in deep-sea environments, are largely unexplored. This study characterizes the microbiomes of the deep-sea corals Desmophyllum pertusum and Solenosmilia variabilis and their associated crinoid Koehlermetra sp. (Thalassometridae) from the Campos Basin, Brazil, to investigate potential cross-host microbial interactions and their ecological implications. We used multiple approaches for this investigation, including amplicon sequencing surveys, genome-resolved metagenomics, and fluorescence in situ hybridization.<br><br>RESULTS: We found that the same endosymbiotic members of the families Endozoicomonadaceae and Nitrosopumilaceae inhabit both corals and the crinoids, suggesting promiscuity in host-symbiont relationships. Metagenomic analysis revealed a novel and dominant Endozoicomonas species (E. promiscua sp. nov.), whose genome encodes pathways for dissimilatory nitrate reduction to ammonia (DNRA). This metabolic capability could provide a substrate for ammonia-oxidizing archaea (Nitrosopumilaceae), indicating a potential cross-host nitrogen-cycling network. Shared microbial taxa between corals and crinoids further support the hypothesis of symbiont promiscuity, where metabolic redundancy may facilitate colonization across species.<br><br>CONCLUSIONS: Our findings suggest that nitrogen cycling plays a key role in structuring microbial symbioses in deep-sea coral-crinoid holobionts. The promiscuous distribution of symbionts across hosts implies that metabolic interactions, such as DNRA-driven ammonia provisioning, could underpin resilience in nutrient-limited environments. This study highlights the importance of microbial versatility in deep-sea ecosystems and provides new insights into how cross-host symbiosis may contribute to biogeochemical cycling in the ocean. Video Abstract.}, }
@article {pmid41233919, year = {2025}, author = {Vohsen, SA and Gruber-Vodicka, HR and Osman, EO and Saxton, MA and Joye, SB and Dubilier, N and Fisher, CR and Baums, IB}, title = {Deep-sea corals near cold seeps associate with sulfur-oxidizing chemoautotrophs in the family Ca. Thioglobaceae.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {232}, pmid = {41233919}, issn = {2049-2618}, support = {ECOGIG//Gulf of Mexico Research Initiative/ ; }, mesh = {Animals ; *Anthozoa/microbiology ; *Sulfur/metabolism ; Symbiosis ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Chemoautotrophic Growth ; Metagenomics/methods ; Seawater/microbiology ; }, abstract = {BACKGROUND: Corals are known for their symbiotic relationships, yet there is limited evidence of chemoautotrophic associations. This is despite some corals occurring near cold seeps where chemosymbiotic fauna abound including mussels that host sulfur-oxidizing chemoautotrophs from the SUP05 cluster (family Ca. Thioglobaceae). We investigated whether corals near cold seeps associate with related bacteria and report here that these associations are widespread.<br><br>RESULTS: We screened corals, water, and sediment for Thioglobaceae using 16S metabarcoding and found ASVs associated with corals at high relative abundance (10 - 91%). These ASVs were specific to coral hosts, absent in water samples, and rare or absent in sediment samples. Using metagenomics and transcriptomics, we assembled the genome of one phylotype associated with Paramuricea sp. B3 (ASV 4) which contained the genetic potential to oxidize sulfur and fix carbon, and confirmed that these pathways were transcriptionally active. Furthermore, its relative abundance was negatively correlated with the stable isotopic composition of its host coral's tissue suggesting some contribution of chemoautotrophy to the coral holobiont.<br><br>CONCLUSIONS: We propose that some lineages of Thioglobaceae may facultatively supplement the diet of their host corals through chemoautotrophy at seeps or may provide essential amino acids or vitamins. This is the first documented association between chemoautotrophic symbionts and corals at seeps and suggests that the footprint of chemosynthetic environments is wider than currently understood.}, }
@article {pmid41233799, year = {2025}, author = {Orschanski, D and Rubén Dandeu, LN and Rivero, MN and Labovsky, V and Fernández, EA}, title = {Dermatological implications of alignment-based de-hosting and bioinformatics pipelines on shotgun microbiome analysis.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {1276}, pmid = {41233799}, issn = {1479-5876}, abstract = {BACKGROUND: The skin microbiome is a critical component of dermatological health, with its dysbiosis implicated in conditions ranging from atopic dermatitis to cancer. Shotgun metagenomics offers an unparalleled resolution for comprehensive taxonomic and functional profiling, yet its application in dermatology is hampered by the high proportion of host DNA and the lack of consensus on best-practice bioinformatic pipelines. While Illumina's proprietary DRAGEN platform is widely used, its closed-source nature and cost limitations necessitate the validation of robust, open-source alternatives to democratize access and enable customization.<br><br>METHODS: This study evaluates the performance of Kraken-based open-source pipeline as a viable alternative to the DRAGEN platform as well as the effect of currently available alignment-based de-hosting methods-Bowtie2, BWA, and Rsubread-to remove human DNA, assuring the use of highly-curated human reference genome thus avoiding the limitations of potentially incomplete or contaminated k-mer-based databases. By using shotgun metagenomic data from 83 healthy individuals we systematically compared the impact of these de-hosting procedures prior to Kraken2/DRAGEN taxonomic classification and functional profiling using HUMAnN 3.0 to assess the influence of methodological choices on skin microbial community composition and metabolic pathway abundance interpretation.<br><br>RESULTS: Our analysis revealed marked discrepancies arising from the choice of de-hosting tool and taxonomic classifier, leading to substantial variability in microbial and functional profiles that could compromise clinical interpretation. Among the pipelines tested, Bowtie2 de-hosting combined with Kraken2 taxonomic classification and HUMAN functional profiling efficiently recovered well-established sex- and age-related bacterial associations in healthy skin that were missed by all other methods, including DRAGEN. This superior performance, together with its customizable features, underscores the value of this workflow for robust and clinically relevant dermatological metagenomic studies.<br><br>CONCLUSIONS: Our findings underscore the decisive impact of bioinformatic pipeline selection on skin microbiome analysis and offer actionable guidance for reproducible and clinically meaningful research. We present a customizable workflow that enhances reproducibility and transparency while improving the translational value of metagenomic data. This approach strengthens the reliability of microbiome studies and supports the development of precision diagnostics and personalized therapeutic strategies in dermatology.}, }
@article {pmid41233543, year = {2025}, author = {Aroney, STN and Newell, RJP and Tyson, GW and Woodcroft, BJ}, title = {Bin Chicken: targeted metagenomic coassembly for the efficient recovery of novel genomes.}, journal = {Nature methods}, volume = {}, number = {}, pages = {}, pmid = {41233543}, issn = {1548-7105}, support = {DP230101171//Department of Education and Training | Australian Research Council (ARC)/ ; FT210100521//Department of Education and Training | Australian Research Council (ARC)/ ; 2022070//National Science Foundation (NSF)/ ; 2022070//National Science Foundation (NSF)/ ; DE-SC0010580//U.S. Department of Energy (DOE)/ ; DE-SC0016440//U.S. Department of Energy (DOE)/ ; DE-SC0004632//U.S. Department of Energy (DOE)/ ; DE-SC0010580//U.S. Department of Energy (DOE)/ ; DE-SC0016440//U.S. Department of Energy (DOE)/ ; DE-SC0004632//U.S. Department of Energy (DOE)/ ; }, abstract = {The recovery of microbial genomes from metagenomic datasets has provided genomic representation for hundreds of thousands of species from diverse biomes. However, low-abundance microorganisms are often missed due to insufficient genomic coverage. Here we present Bin Chicken, an algorithm that substantially improves genome recovery through automated, targeted selection of metagenomes for coassembly based on shared marker gene sequences derived from raw reads. Marker gene sequences that are divergent from known reference genomes can be further prioritized, providing an efficient means of recovering highly novel genomes. Applying Bin Chicken to public metagenomes and coassembling 800 sample groups recovered 77,562 microbial genomes, including the first genomic representatives of 6 phyla, 41 classes and 24,028 species. These genomes expand the genomic tree of life and uncover a wealth of novel microbial lineages for further research.}, }
@article {pmid41233523, year = {2025}, author = {Dell, M and Kogawa, M and Streiff, AB and Shiraishi, T and Lotti, A and Meier, CM and Schorn, MA and Field, C and Cahn, JKB and Yokoyama, H and Yamada, Y and Peters, E and Egami, Y and Nakashima, Y and Tan, KC and Rückert, C and Alanjary, M and Kalinowski, J and Kuzuyama, T and Cardenas, P and Pomponi, S and Sipkema, D and Wright, A and Takada, K and Abe, I and Wakimoto, T and Takeyama, H and Piel, J}, title = {Chemical richness and diversity of uncultivated 'Entotheonella' symbionts in marine sponges.}, journal = {Nature chemical biology}, volume = {}, number = {}, pages = {}, pmid = {41233523}, issn = {1552-4469}, support = {22H05120//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 16H06279//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP21H02635//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP22H05128//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; }, abstract = {Marine sponges are the source of numerous bioactive natural products that serve as chemical defenses and provide pharmaceutical leads for drug development. For some of the compounds, symbiotic bacteria have been established as the actual producers. Among the known sponge symbionts, 'Candidatus Entotheonella' members stand out because of their abundant and variable biosynthetic gene clusters (BGCs). Here, to obtain broader insights into this producer taxon, we conduct a comparative analysis on eight sponges through metagenomic and single-bacterial sequencing and biochemical studies. The data suggest sets of biosynthetic genes that are largely unique in 14 'Entotheonella' candidate species and a member of a sister lineage named 'Candidatus Proxinella'. Four biosynthetic loci were linked in silico or experimentally to cytotoxins, antibiotics and the terpene cembrene A from corals. The results support widespread and diverse bacterial roles in the chemistry of sponges and aid the development of sustainable production methods for sponge-derived therapeutics.}, }
@article {pmid41233350, year = {2025}, author = {Kim, YJ and Kim, KE and Kim, HJ and Park, JS and Kim, MJ and Kim, SM and Lee, T and Jung, SW}, title = {Dynamics of the DNA Viral Community in Korean Coastal Waters.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1782}, pmid = {41233350}, issn = {2052-4463}, support = {RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science &amp; Technology promotion)/ ; RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science &amp; Technology promotion)/ ; RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science &amp; Technology promotion)/ ; RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science &amp; Technology promotion)/ ; RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science &amp; Technology promotion)/ ; RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science &amp; Technology promotion)/ ; RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science &amp; Technology promotion)/ ; RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science &amp; Technology promotion)/ ; }, mesh = {Republic of Korea ; *Seawater/virology ; *DNA Viruses/genetics/classification ; DNA, Viral ; *Virome ; Metagenomics ; Bacteriophages/genetics ; }, abstract = {Recent advances in metaviromics have revealed vast viral diversity across aquatic environments, yet coastal marine viromes remain underexplored compared to their open-ocean counterparts. In this study, we analyzed 49 surface water samples from 16 coastal sites around Korea, generating 265 gigabases of metagenomic sequence data. Following quality control, 754 DNA viral contigs of ≥10 kb (medium quality or higher) were recovered, with bacteriophages comprising 95% and nucleocytoplasmic large DNA viruses (NCLDVs) 5% of the total. Among these, Puniceispirillum phage HMO-2011 and Micromonas pusilla virus 12 T exhibited the highest relative abundance within their respective groups. In addition, we provided the dataset of environmental parameters such as water temperature, salinity, etc., as well as viral taxonomic profiling of contig-level metadata. This dataset provides a resource for the investigation of coastal DNA viral communities and supports comparative studies across marine environments.}, }
@article {pmid41233343, year = {2025}, author = {Lu, JN and Chao, Y and Tian, L and Zhong, X and Chen, Z and He, H and Huang, B and Li, M and Feng, Z and Feng, H and Hu, C and Zhou, S and Zhang, L and Yang, Y and Ruan, Z and Ding, K and Yang, Y and Yuan, K and Liu, W and Qi, H and Cao, Y and Fei, YH and Ling, N and Wang, S and Tang, YT and Luan, T and Xu, Z and Qiu, R}, title = {DNA viral community enhances microbial carbon fixation capacity via auxiliary metabolic genes in contaminated soils.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {9984}, pmid = {41233343}, issn = {2041-1723}, mesh = {*Carbon Cycle/genetics ; *Soil Microbiology ; Carbon/metabolism ; Soil/chemistry ; China ; *DNA Viruses/genetics/metabolism ; Metagenomics ; *Soil Pollutants/metabolism ; *DNA, Viral/genetics ; Metagenome ; Mining ; }, abstract = {Soil is the largest organic matter repository on land and the virosphere is an essential component of soil carbon cycling. While a few carbon-related auxiliary metabolic genes (AMGs) in viruses are reported to potentially influence the hosts, the effects of virus-host interactions on soil carbon fixation, particularly in carbon-deficient contaminated soils, need further validation. Here, we explore the impact of viruses on carbon fixation in contaminated soils from 58 metal mining areas across eastern China. Eleven different functional categories of carbon fixation AMGs are identified via metagenomic analysis in 323 contaminated soil samples. Enzymatic activities of three key AMGs (i.e., rbcL, ppdK and TKT) are experimentally characterized, indicating the positive role of these genes in carbon fixation. Furthermore, transcriptomic sequencing reveals that after active virus inoculation the carbon fixation genes significantly up-regulate (~73%, p < 0.05). In mesocosms with stable isotope labeling, the accumulation of [13]C-labeled organic carbon significantly increases (~10%, p < 0.01). Our results provide theoretical and experimental evidence for incorporating viral contributions into the assessments of carbon fixation, and improve the understanding of viral roles within the processes of carbon cycling.}, }
@article {pmid41233306, year = {2025}, author = {Wu, F and Wang, Y and Mai, Z and Xu, Z and Li, S and Li, Y and Yin, R and Li, J and Yu, Z and Wu, Y and Tian, X and Feng, X and Huo, X and Wang, C and Ma, X}, title = {Human intestinal fungus Clavispora lusitaniae attenuates colitis through Pyruvate decarboxylase-derived Indole-3-ethanol.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {9980}, pmid = {41233306}, issn = {2041-1723}, support = {82225048//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82204594//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82474340//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2024-MS-147 and 2025-YQ-13//Natural Science Foundation of Liaoning Province (Liaoning Provincial Natural Science Foundation)/ ; }, mesh = {Animals ; *Colitis/chemically induced/microbiology ; Mice ; Humans ; *Indoles/metabolism/pharmacology ; Gastrointestinal Microbiome ; Receptors, Aryl Hydrocarbon/metabolism/agonists ; Mice, Inbred C57BL ; *Hypocreales/metabolism/genetics ; Inflammatory Bowel Diseases/microbiology ; Male ; Female ; Feces/microbiology ; Disease Models, Animal ; Colon/microbiology/pathology ; Probiotics ; }, abstract = {Gut mycobiome dysbiosis has been implicated in inflammatory bowel disease (IBD). However, it remains unknown whether specific fungal species identified by sequencing directly contribute to IBD pathogenesis. Here, based on analysis of three fecal metagenome datasets of IBD cohorts and a previously established cultivated gut fungi catalog, we identify an IBD-depleted intestinal fungus Clavispora lusitaniae strain P4013B. We show P4013B attenuates DSS-induced colitis in wild-type, antibiotics-treated, and germ-free mice through activation of aryl hydrocarbon receptor (AHR). Using an activity-guided isolation strategy, we identify the P4013B metabolite indole-3-ethanol (IEt) as the AHR agonist mediating the anti-colitis activity. We further validate the role of IEt via engineering strains that overexpress pyruvate decarboxylases producing high yields of IEt. Tea polysaccharide enhanced the anti-colitis activity of P4013B by promoting its proliferation and colonization in the colon. Together, these results suggest that C. lusitaniae P4013B may be explored as a potential probiotic for the treatment and prevention of IBD.}, }
@article {pmid41232906, year = {2025}, author = {Kumar, S and Matra, S and Rajput, V and Ghode, H and Rathore, D and Kumar, S and Kamble, S and Dastager, S and Bajaj, A and Qureshi, A and Kapley, A and Dharne, M}, title = {Deciphering the antimicrobial resistomes and microbiome landscape of open drain wastewater using metagenomics in a progressive Indian state.}, journal = {Environmental research}, volume = {}, number = {}, pages = {123287}, doi = {10.1016/j.envres.2025.123287}, pmid = {41232906}, issn = {1096-0953}, abstract = {Antimicrobial resistance (AMR) is a growing environmental and public health concern, with wastewater systems are acting as a critical reservoirs for resistant microorganisms and genes. Open drains in densely populated and industrialized regions can accelerate AMR dissemination into the environment. Despite Maharashtra's high urban density and industrial activity, comprehensive metagenomic surveillance of its wastewater resistome is lacking. This study applied high-throughput nanopore sequencing to 138 wastewater samples collected from 23 open-drain sites across three regions of Maharashtra (Western, Mumbai, and Central). Bioinformatic pipelines were used to characterize microbial communities, resistance genes, mobile genetic elements (MGEs), and resistome risk scores. Microbial composition varied significantly across regions, with Mumbai and Central regions explaining up to 13% of variance at the family level. Thirty indicator taxa were identified through LEfSe analysis. Resistome profiling revealed 28 drug classes and 808 ARGs, dominated by multidrug (40.49%), macrolide-lincosamide-streptogramin (15.84%), beta-lactam (7.95%), and tetracycline (6.52%). WHO-priority pathogens such as Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa harbored high-abundance ARGs including sul1, mdr(ABC), and acrB. Resistome risk scores were highest in Mumbai, indicating elevated ecological and human health risks. These findings underscore wastewater as a hotspot for AMR persistence and spread. Integrating wastewater-based surveillance within a One Health framework enables systematic tracking of resistance trends, comprehensive assessment of environmental risks, and evidence-driven regional interventions. This integrated approach supports the development of targeted mitigation strategies to curb the spread of antibiotic-resistant contaminants across ecosystems.}, }
@article {pmid41232839, year = {2025}, author = {Fang, L and Jiaqi, L and Zhenwei, Z and Jingang, Z and Xiao, L and Yongdong, C}, title = {Remediation of soil contaminated by waste drilling slurry in oilfield with mixed bacteria immobilized by fly ash modified biochar.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {133644}, doi = {10.1016/j.biortech.2025.133644}, pmid = {41232839}, issn = {1873-2976}, abstract = {Organic and heavy metal combined pollution from large-scale landfill of waste drilling slurry in oilfields poses a significant remediation challenge. This study innovatively combined fly ash doping with physicochemical modification to regulate the morphology and functionalize the surface of reed straw biochar, developing a low-cost modified biochar-based carrier material. This material, validated through leachate adsorption experiments and characterization (SEM, FT-IR, BET, XRD, TEM-EDS), exhibited both high-efficiency organic pollutant adsorption capacity and strong microbial immobilization performance. To simulate practical conditions, pot experiments were conducted, with ICP-OES and metagenomic analyses used to investigate pollutant transformation and fate. Key findings showed that unmodified biochar and fly ash formed a "glass phase-carbon matrix" structure, and under optimal conditions (biochar-fly ash mass ratio 5:1, NaOH-H2O2-assisted ultrasonic modification, 700℃ calcination), the specific surface area of modified material increased by 158.60 % compared to unmodified biochar, with an organic pollutant adsorption capacity of 32.56 mg·g[-1]. When immobilized with specific degrading bacteria, this material achieved 80.54 % COD removal in contaminated soil over 63 days, a rate significantly higher than that of free bacterial or biochar-based material groups, thereby demonstrating stable degradation advantages. Mechanistically, the synergistic integration of high-efficiency adsorption and biodegradation leveraging local oilfield wastes highlights this as an engineerable, efficient, and low-cost strategy for remediating waste drilling slurry-contaminated sites, with broad implications for addressing legacy composite pollution in energy industries.}, }
@article {pmid41232286, year = {2025}, author = {Romero-Arguelles, R and Gómez-Govea, MA and Adame-Martinez, AE and Guzman-Velazco, A and Gonzalez-Rojas, JI and Ham-Dueñas, JG and Amezquita-Garcia, HJ and Rios-Del Toro, EE}, title = {Sulfammox in sediments of a natural wetland in northeastern Mexico: a sustainable approach to nitrogen and sulfur removal.}, journal = {The Science of the total environment}, volume = {1006}, number = {}, pages = {180920}, doi = {10.1016/j.scitotenv.2025.180920}, pmid = {41232286}, issn = {1879-1026}, abstract = {The simultaneous removal of nitrogenous and sulfate compounds in natural environments represents a major environmental challenge. The sulfammox process, a microbial pathway that couples anaerobic ammonium oxidation with sulfate reduction, has recently been proposed as a sustainable alternative for the removal of these pollutants. In this study, we evaluated for the first time the presence and activity of sulfammox microbial communities in sediments from a natural wetland in northeastern Mexico under controlled microcosm conditions. Physicochemical parameters, sediment composition, and ammonium dynamics were analyzed in two natural wetlands: Cachorritos pond (CHP) and Azul turqueza pond (AZP), during a four-week incubation period under controlled conditions. A decrease in ammonium concentration (up to 41.38 mM) was observed only in the CHP, with a stoichiometric NH4[+]/SO4[2-] ratio of 2.45 (92 %), confirming the activity of the sulfammox process. Metagenomic analysis revealed an enrichment of bacterial phylum associated with the sulfammox process, such as Chloroflexi, Chlorobi and Proteobacteria, which increased markedly in sulfate and ammonium treatments. This study represents the first report of sulfammox activity in a natural wetland in Mexico, highlighting the ecological potential of these ecosystems as natural treatment systems and supporting their consideration in sustainable bioremediation strategies.}, }
@article {pmid41232227, year = {2025}, author = {Sharma, V and Goel, S and Bisht, K and Kaura, T and Verma, S and Mewara, A and Grover, GS and Biswal, M}, title = {Unveiling the Presence of Coxiella-like bacteria in Rhipicephalus microplus Ticks from Punjab, North India: A 16S rRNA metagenomic study.}, journal = {Veterinary microbiology}, volume = {312}, number = {}, pages = {110783}, doi = {10.1016/j.vetmic.2025.110783}, pmid = {41232227}, issn = {1873-2542}, abstract = {In this study, using 16S rRNA gene-based metagenomics, we aimed to determine the presence of infectious bacteria in the ticks collected from Punjab state in north India. Tick samples were collected from the domesticated animals from the Patiala, Ropar, and Mohali districts of Punjab, India from February 2022- April 2022. DNA was extracted, and the library was prepared by targeting the V3-V4 hypervariable region of the 16S rRNA gene. The sequencing was conducted in Illumina using the 300 bp paired-end chemistry. Eight tick samples were analyzed from the Patiala, Ropar and Mohali districts of Punjab, India, revealing a diverse range of bacterial species within the tick microbiome. Seven out of eight samples were found to harbour Coxiella-like bacteria (46-181,607 reads; closely related to C. burnetii based on 16S rRNA [V3-V4] sequence similarity), indicating their abundance in the tick population. Furthermore, the analysis uncovered the presence of other pathogenic bacterial genera, including Staphylococcus, Streptococcus, Corynebacterium, Enterococcus, Pseudomonas, Bordetella, and Micrococcus in the tick microbiome, highlighting the abundance and diversity of infectious organisms within ticks. 16S rRNA gene-based metagenomics enables valuable insights into infectious agents in disease-transmitting vectors. Coxiella-like bacteria were found to be predominant bacterial species in the tick microbiomes in this study. The public health significance of this finding in animals and humans needs to be explored in this region. However, as 16S rRNA sequencing offers limited resolution for distinguishing closely related taxa, further confirmation using additional loci or whole-genome sequencing is warranted.}, }
@article {pmid41231980, year = {2025}, author = {Gelsinger, DR and Ronda, C and Ma, J and Kar, OB and Edwards, M and Huang, Y and Mavros, CF and Sun, Y and Perdue, T and Vo, PL and Ivanov, II and Sternberg, SH and Wang, HH}, title = {Metagenomic editing of commensal bacteria in vivo using CRISPR-associated transposases.}, journal = {Science (New York, N.Y.)}, volume = {390}, number = {6774}, pages = {eadx7604}, doi = {10.1126/science.adx7604}, pmid = {41231980}, issn = {1095-9203}, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome/genetics ; *Gene Editing/methods ; *Bacteroides/genetics/growth &amp; development ; Humans ; Metagenomics/methods ; *CRISPR-Cas Systems ; Symbiosis ; Mice, Inbred C57BL ; Metagenome ; Clustered Regularly Interspaced Short Palindromic Repeats ; }, abstract = {Although metagenomic sequencing has revealed a rich microbial biodiversity in the mammalian gut, methods to genetically alter specific species in the microbiome are highly limited. Here, we introduce Metagenomic Editing (MetaEdit) as a platform technology for microbiome engineering that uses optimized CRISPR-associated transposases delivered by a broadly conjugative vector to directly modify diverse native commensal bacteria from mice and humans with new pathways at single-nucleotide genomic resolution. Using MetaEdit, we achieved in vivo genetic capture of native murine Bacteroides by integrating a metabolic payload that enables tunable growth control in the mammalian gut with dietary inulin. We further show in vivo editing of segmented filamentous bacteria, an immunomodulatory small-intestinal microbial species recalcitrant to cultivation. Collectively, this work provides a paradigm to precisely manipulate individual bacteria in native communities across gigabases of their metagenomic repertoire.}, }
@article {pmid41231970, year = {2025}, author = {Coelho, C and Taborda, A and Lorena, C and Frazão, T and Veríssimo, A and Borges, PT and Brissos, V and Tiago, I and Martins, LO}, title = {Shotgun metagenomic mining reveals a new FAD-dependent D-lactate dehydrogenase in an isopod gut microbiome.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0148025}, doi = {10.1128/aem.01480-25}, pmid = {41231970}, issn = {1098-5336}, abstract = {UNLABELLED: Shotgun metagenomic sequencing has emerged as a powerful tool for exploring microbial diversity and uncovering genes encoding novel biocatalysts from complex environments. Here, we report the discovery and characterization of a new FAD-dependent D-lactate dehydrogenase (PdG-D-LDH) from the gut microbiome of the isopod Porcellio dilatatus. The enzyme was identified through in silico screening using BLAST and AlphaFold3 and functionally characterized as a homodimeric, thermoactive, and thermostable protein, demonstrating the robustness required for biotechnological applications. PdG-D-LDH exhibits a strong catalytic preference toward D-lactate and preferentially reduces quinones over cytochrome c or molecular oxygen. X-ray crystallography revealed a VAO/PCMH-like fold with a solvent-accessible active site that harbors both a FAD cofactor and an Fe(II) ion. Molecular docking studies provided insights into the structural determinants of its stereoselective substrate recognition. Under mild conditions, the enzyme catalyzed the oxidation of D-lactate to pyruvate with a 90% yield after 24 h of reaction, using molecular oxygen as the electron acceptor.<br><br>IMPORTANCE: This study illustrates how metagenomics, structural biology, and computational tools can jointly drive the discovery of new enzymes with valuable biotechnological applications aligned with circular economic principles. The newly identified D-lactate dehydrogenase, PdG-D-LDH, exhibits thermostability, stereoselectivity, and high catalytic efficiency, providing new insights into the structure-function relationships of lactate-metabolizing enzymes.}, }
@article {pmid41231285, year = {2025}, author = {Padur Sankaranarayanan, A and Dhanapal, S and Valliyappan, M and Shyu, DJH and Parthasarathy, TN}, title = {Intestinal microbiome diversity and disparity between wild and captive endangered Asian elephants (Elephas maximus indicus) in southern India.}, journal = {Antonie van Leeuwenhoek}, volume = {118}, number = {12}, pages = {191}, pmid = {41231285}, issn = {1572-9699}, support = {31950410559//National Natural Science Foundation [NSFC] of China/ ; }, mesh = {Animals ; *Elephants/microbiology ; *Gastrointestinal Microbiome/genetics ; India ; RNA, Ribosomal, 16S/genetics ; *Animals, Wild/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Endangered Species ; Biodiversity ; Phylogeny ; Animals, Zoo/microbiology ; Male ; DNA, Bacterial/genetics/chemistry ; Feces/microbiology ; Female ; }, abstract = {The gut microbiome affects the physical and mental wellbeing of an animal. Several factors, including diet, host physiology, age, sex, lifestyle, and environmental factors, influence the dynamic gut microbiome. We studied the gut microbiome composition of the endangered Asian elephants (Elephas maximus) kept under prolonged captive conditions (15.8 ± 3.9 years) and their wild counterparts, as both were exposed to two different environmental pressures. A total of 648,581 high-quality sequences were obtained, comprising 208 microbial families from 22 phyla and 97 orders, as determined by high-throughput 16S rRNA gene sequencing. Among them, 90% of the microbes belonged to the phyla Firmicutes, Proteobacteria and Bacteroidetes. Our analysis revealed a distinct variation in the gut microbiome between captive and wild elephants. The captive elephants had a higher abundance of the microbial phyla Kiritimatiellaeota, Tenericutes, Euryarchaeota, and Verrucomicrobia, which suggests that captivity alters the gut microbiome. These findings reveal distinct patterns of gut microbiome diversity between captive and wild elephants, underscoring the role of diet and environmental conditions in shaping the elephant gut microbiome.}, }
@article {pmid41231233, year = {2025}, author = {Absolon, DE and Jackson, VLN and Monier, A and Smith, AG and Helliwell, KE}, title = {Metagenomics of the MAST-3 stramenopile, Incisomonas, and its associated microbiome reveals unexpected metabolic attributes and extensive nutrient dependencies.}, journal = {Microbial genomics}, volume = {11}, number = {11}, pages = {}, doi = {10.1099/mgen.0.001510}, pmid = {41231233}, issn = {2057-5858}, mesh = {*Metagenomics/methods ; *Microbiota/genetics ; *Stramenopiles/genetics/metabolism/classification ; Bacteria/genetics/metabolism/classification ; Phylogeny ; }, abstract = {Protists are polyphyletic single-celled eukaryotes that underpin global ecosystem functioning, particularly in the oceans. Most remain uncultured, limiting the investigation of their physiology and cell biology. MArine STramenopiles (MASTs) are heterotrophic protists that, although related to well-characterized photosynthetic diatoms and parasitic oomycetes, are poorly studied. The Nanomonadea (MAST-3) species Incisomonas marina has been maintained in co-culture with a bacterial consortium, offering opportunities to investigate the metabolic attributes and nutritional dependencies of the community. Employing a metagenomics approach, the 68 Mbp haploid genome of I. marina was retrieved to an estimated completeness of 93%, representing the most complete MAST genome so far. We also characterized the diversity of, and assembled genomes for, 23 co-cultured bacteria. Auxotrophy of I. marina for B vitamins (B1, B2, B6, B7 and B12), but not vitamins C, B3, B5 and B9, was predicted. Several bacteria also lacked complete B-vitamin biosynthesis pathways, suggesting that vitamins and/or their precursors are exchanged in the consortium. Moreover, I. marina lacked the ability to synthesize half the protein amino acids, although genes encoding the complete urea cycle were identified, like diatoms; this may play a role in recycling organic nitrogen compounds. Unexpectedly, we also identified the gene DSYB for dimethylsulphoniopropionate biosynthesis. Biosynthesis of this important stress protectant and bacterial chemoattractant is typically found in photosynthetic eukaryotes and has not been identified before in heterotrophic stramenopiles. Together, our study reveals the metabolic attributes of a hitherto understudied organism, advancing knowledge of the evolution and adaptations of the stramenopiles and informing future culturing efforts.}, }
@article {pmid41231016, year = {2025}, author = {Wang, YL and Aghdam, SA and Brown, AMV and Deonarine, A}, title = {Global Survey of Mercury Methylation and Demethylation Microbial Communities in Wastewater and Activated Sludge.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c11448}, pmid = {41231016}, issn = {1520-5851}, abstract = {Wastewater treatment plants (WWTPs) are an understudied source of mercury methylating and demethylating microbes to downstream aquatic and terrestrial environments, where methylmercury production and subsequent bioaccumulation in the food web occur. To identify methylators and demethylators and evaluate their occurrence in WWTPs, metagenomic and metatranscriptomic analyses of raw sewage, activated sludge, and effluent samples from WWTPs across the globe were conducted. Results indicated that hgcA- and merB-carriers were widespread in WWTPs, with higher abundance in raw sewage and sludge compared to treated effluent. Bdellovibrionota were identified as merB-carriers, linking them to demethylation for the first time. Novel conserved motifs of hgcB and fused hgcAB were also identified. 30% of hgcA genes were colocalized with arsenic-resistance operons on the same contig, while all merB-carriers contained arsenic resistance genes (ars), though merB and arsR were not colocated. Antibiotic resistance genes were also present in the genomes of multiple hgcA- amd merB-carriers, including one sample where hgcA and the antiseptic/antibiotic resistant gene (qacG) were colocated on the same contig, suggesting possible coselection in environments containing antibiotics. Mobile genetic element-mediated horizontal gene transfer was identified as a mechanism facilitating the genetic transfer of hgcA. Overall, these findings highlight WWTPs as reservoirs of genes involved in mercury methylation and demethylation, with potential implications for mercury cycling in downstream environments.}, }
@article {pmid41230645, year = {2025}, author = {El-Mayet, FS and Moharam, I and El-Nahas, EM and El-Habbaa, AS and Najar, FZ and Stayton, E and El Nagar, EMS and Radi, M and Khalil, NW and Abaza, MA}, title = {First identification of concurrent infections with novel emerging duck astrovirus and duck hepatitis A virus type 3 (DHAV-3) in ducklings in Egypt using metagenomic next-generation sequencing (m-NGS).}, journal = {Avian pathology : journal of the W.V.P.A}, volume = {}, number = {}, pages = {1-17}, doi = {10.1080/03079457.2025.2581279}, pmid = {41230645}, issn = {1465-3338}, abstract = {First complete genome sequencing of a DHAV-3 strain from Egypt using m-NGS.Discovery of a novel duck astrovirus co-infecting with DHAV-3.Phylogenetic analysis reveals cross-border transmission links with Asian strains of both DHAV-3 and DAstV-5.}, }
@article {pmid41230492, year = {2025}, author = {Rodriguez-Fernandez, IA and Santiago-Rodriguez, TM and Figueroa-Pratts, PG and Cintrón-Berríos, K and Rodriguez-Cornier, ND and Toranzos, GA}, title = {Gut microbial community structure of the adult citrus root weevil Diaprepes abbreviatus.}, journal = {Frontiers in insect science}, volume = {5}, number = {}, pages = {1676003}, pmid = {41230492}, issn = {2673-8600}, abstract = {Diaprepes abbreviatus is an agricultural pest known to affect around 270 plant species across the Caribbean and the United States, posing significant challenges to pest management. Chemical control dominates management, but environmental and health concerns motivate microbiome-informed alternatives. However, limited information exists on the gut anatomy, physicochemical environment, and microbial composition of D. abbreviatus. In this study, we provide the first comprehensive characterization of the gut morphology, pH, and microbiota of adult D. abbreviatus in both females and males collected in Puerto Rico. Using dye-based gut tracing, we identified foregut, midgut, and hindgut or posterior gut compartments, and confirmed the presence of a muscular, sclerotized gizzard. Colorimetric analysis revealed a mildly acidic gut environment (approximately pH 4-5, based on qualitative ranges), consistent across sexes and regions. Shotgun metagenomic sequencing of dissected guts from males and females revealed microbial communities distinct from the leaf samples microbiota. While alpha and beta diversity did not differ significantly between sexes, co-occurrence analyses identified sex-specific correlation patterns among bacterial taxa. Notably, Enterobacter cloacae, Pantoea vagans, Lactococcus lactis, and Pseudomonas monteilii were repeatedly detected across individuals and generated metagenomic datasets, and some were localized to the hindgut, suggesting possible niche specialization. The presence of taxa, such as Enterobacter cloacae, previously reported as symbionts in other phytophagous insects further supports the hypothesis that certain bacteria may contribute to host digestion or adaptation. These findings establish a framework for understanding the gut environment and microbial community of D. abbreviatus, and highlight candidate taxa for future functional studies. More broadly, this work supports further research into the potential roles of gut microbiota in the ecology and management of this pest.}, }
@article {pmid41230491, year = {2025}, author = {Juhász, J and Ligeti-Nagy, N and Bodnár, B and Juhász, J and Pongor, S and Ligeti, B}, title = {ProkBERT PhaStyle: accurate phage lifestyle prediction with pretrained genomic language models.}, journal = {Bioinformatics advances}, volume = {5}, number = {1}, pages = {vbaf188}, pmid = {41230491}, issn = {2635-0041}, abstract = {MOTIVATION: Phage lifestyle prediction, i.e. classifying phage sequences as virulent or temperate, is crucial in biomedical and ecological applications. Phage sequences from metagenome or virome assemblies are often fragmented, and the diversity of environmental phages is not well known. Current computational approaches often rely on database comparisons that require significant effort and expertise to update. We propose using genomic language models (LMs) for phage lifestyle classification, allowing efficient direct analysis from nucleotide sequences without the need for sophisticated preprocessing pipelines or manually curated databases. We trained three genomic LMs (DNABERT-2, Nucleotide Transformer, and ProkBERT) on datasets of short, fragmented sequences. These models were then compared with dedicated phage lifestyle prediction methods in terms of accuracy, prediction speed, and generalization capability.<br><br>RESULTS: ProkBERT PhaStyle achieves accuracy comparable to, and in many cases higher than, state-of-the-art models across various scenarios. It demonstrates the ability to generalize to unseen data in our benchmarks, accurately classifies phages from extreme environments, and also demonstrates high inference speed.<br><br>Genomic LMs offer a simple and computationally efficient alternative for solving complex classification tasks, such as phage lifestyle prediction. ProkBERT PhaStyle's simplicity, speed, and performance suggest its utility in various ecological and clinical applications.}, }
@article {pmid41230489, year = {2025}, author = {Scherz, V and Nassirnia, S and Chaabane, F and Castelo-Szekely, V and Greub, G and Pillonel, T and Bertelli, C}, title = {zAMP and zAMPExplorer: reproducible scalable amplicon-based metagenomics analysis and visualization.}, journal = {Bioinformatics advances}, volume = {5}, number = {1}, pages = {vbaf255}, pmid = {41230489}, issn = {2635-0041}, abstract = {SUMMARY: To enable flexible, scalable, and reproducible microbiota profiling, we have developed zAMP, an open-source bioinformatics pipeline for the analysis of amplicon sequence data, such as 16S rRNA gene for bacteria and archaea or ITS for fungi. zAMP is complemented by two modules: one to process databases to optimize taxonomy assignment, and the second to benchmark primers, databases and classifier performances. Coupled with zAMPExplorer, an interactive R Shiny application that provides an intuitive interface for quality control, diversity analysis, and statistical testing, this complete toolbox addresses both research and clinical needs in microbiota profiling.<br><br>Comprehensive documentation and tutorials are provided alongside the source code of zAMP and zAMPExplorer software to facilitate installation and use. zAMP is implemented as a Snakemake workflow, ensuring reproducibility by running within Singularity or Docker containers, and is also easily installable via Bioconda. The zAMPExplorer application, designed for visualization and statistical analysis, can be installed using either a Docker image or from R-universe.}, }
@article {pmid41230409, year = {2025}, author = {Tian, Y and Xu, N and Chen, Y and Xu, Z and Zhou, JX and Zhang, L}, title = {Cost-effectiveness analysis of metagenomic next-generation sequencing versus traditional bacterial cultures for postoperative central nervous system infections in critical care settings: a prospective pilot study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1710412}, pmid = {41230409}, issn = {2235-2988}, mesh = {Humans ; *Cost-Benefit Analysis ; Pilot Projects ; Prospective Studies ; *High-Throughput Nucleotide Sequencing/economics/methods ; Female ; Male ; Middle Aged ; *Central Nervous System Infections/diagnosis/microbiology/economics ; *Metagenomics/economics/methods ; *Critical Care/economics ; Aged ; *Bacteria/genetics/isolation &amp; purification/classification ; Adult ; *Postoperative Complications/microbiology/diagnosis ; Intensive Care Units ; China ; *Bacteriological Techniques/economics/methods ; Cost-Effectiveness Analysis ; }, abstract = {BACKGROUND: Early and accurate pathogen identification is crucial for managing central nervous system infections (CNSIs). While Metagenomic Next-Generation Sequencing (mNGS) offers rapid and sensitive pathogen detection, its cost-effectiveness in postoperative neurosurgical patients in critical care settings remains underexplored. Our study aims to investigate the clinical health economic value of mNGS in detecting pathogens of CNSIs after neurosurgery.<br><br>METHODS: In this prospective pilot study, 60 patients with CNSIs at Beijing Tiantan Hospital ICU (March 2023-January 2024) were randomized 1:1 to mNGS or conventional pathogen culture groups. A decision-tree model compared cost-effectiveness using incremental cost-effectiveness ratios (ICERs). A decision-tree model was used to compare the cost-effectiveness between mNGS and traditional pathogen culture methods using incremental cost-effectiveness ratios (ICERs).<br><br>RESULTS: From March 2023 to January 2024, 60 patients were included. mNGS demonstrated superior diagnostic efficiency with shorter turnaround time (1 vs 5 days; _P_<0.001) and lower anti-infective costs (&#xa5;18,000 vs &#xa5;23,000; _P_=0.02). Despite higher detection costs (&#xa5;4,000 vs &#xa5;2,000; _P_<0.001), the ICER of &#xa5;36,700 per additional timely diagnosis suggested cost-effectiveness at China's GDP-based WTP threshold. No significant differences in hospitalization duration or total costs were observed (_P_>0.05).<br><br>CONCLUSION: mNGS improves diagnostic efficiency and reduces antimicrobial expenditure for postoperative CNSIs in critical care, demonstrating favorable cost-effectiveness when considering clinical outcome gains.}, }
@article {pmid41230408, year = {2025}, author = {Lin, L and Li, X and Li, J and Wu, B and Lin, Y and Li, W and Li, H and Guo, Y and Huang, C and Huang, Z and Zhang, W and Fang, X}, title = {Microbial culture vs. mNGS: diagnostic variations in periprosthetic joint infection.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1611332}, pmid = {41230408}, issn = {2235-2988}, mesh = {Humans ; *Prosthesis-Related Infections/diagnosis/microbiology ; Male ; Female ; Aged ; Middle Aged ; *High-Throughput Nucleotide Sequencing/methods ; *Bacteria/isolation &amp; purification/genetics/classification ; Aged, 80 and over ; *Metagenomics/methods ; *Microbiological Techniques/methods ; Retrospective Studies ; }, abstract = {OBJECTIVE: This study aimed to compare the diagnostic performance of conventional microbial culture and metagenomic next-generation sequencing (mNGS) in detecting pathogens in periprosthetic joint infection (PJI) and to identify factors contributing to discrepancies between these two methods.<br><br>METHODS: A total of 167 patients with suspected PJI (including PJI patients and aseptic failure patients) who underwent revision joint replacement at our center from September 2017 to April 2024 were enrolled. Demographic data, prior antibiotic use, and results of microbial culture and mNGS were documented. Joint fluid, periprosthetic tissue, or prosthetic ultrasonic fluid samples were collected, and at least one sample from each patient underwent both microbial culture and mNGS testing. In the light of the concordance between culture and mNGS results, patients were divided into the detection consistent and detection inconsistent groups. The differences in pathogen detection between the two models were compared, and factors contributing to discordant results were analyzed.<br><br>RESULTS: The prior antibiotic use (OR = 2.137, 95% CI = 1.069-4.272, P = 0.032), polymicrobial infections (OR = 3.245, 95% CI = 1.278-8.243, P = 0.013), infection caused by rare pathogens (OR = 2.735, 95% CI = 1.129-6.627, P = 0.026), and intraoperative tissue specimens (OR = 2.837, 95% CI = 1.007-7.994, P = 0.049) were identified as risk factors for discordance between microbial culture and&#xa0;mNGS results, particularly in cases with negative microbial culture but positive mNGS findings. Conversely, consistency in specimen type (OR = 0.471, 95%CI=0.254-0.875, P = 0.017) was identified as a protective factor against discordance.<br><br>CONCLUSION: Clinicians should optimize diagnostic strategies by tailoring microbial culture methods to the patient's clinical condition and integrating mNGS testing where appropriate. It is recommended to use tissue specimens from the same anatomical site across multiple tests while sampling from different regions when necessary. Although this approach may increase costs, it significantly enhances the accuracy of pathogen identification and facilitates more effective treatment.}, }
@article {pmid41229791, year = {2025}, author = {Wang, W and Mo, Q and Yu, Q and Ding, X}, title = {Clinical characteristics of Pneumocystis jirovecii pneumonia in 20 non-HIV-infected patients.}, journal = {Journal of thoracic disease}, volume = {17}, number = {10}, pages = {8904-8914}, pmid = {41229791}, issn = {2072-1439}, abstract = {BACKGROUND: Pneumocystis jirovecii pneumonia (PCP) is a life-threatening disease in clinics, commonly associated with human immunodeficiency virus (HIV) infected patients. Nowadays, with the increasing use of immunosuppressants, the incidence of PCP in non-HIV-infected patients is also on the rise. This study aimed to investigate the clinical diagnosis and treatment of PCP in non-HIV-infected patients.<br><br>METHODS: We collected and retrospectively analyzed 20 cases of PCP diagnosed in HIV-negative patients at Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University.<br><br>RESULTS: All cases were diagnosed using metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage (BAL). Of all 20 patients, 11 were men and nine were women. The median age was 66.5 (range, 18-83) years old. Three out of 20 patients had no immunosuppressive background, while 17 were exposed to immunosuppressants due to different diseases. Among them, four had solid malignancies, four had kidney disease, three had hematological malignancies, two had skin diseases, one had thrombocytopenia, one had rheumatoid arthritis, one had anaphylactoid purpura and one had knee arthritis. All patients had not received prophylactic drugs for PCP. All patients underwent antimicrobial treatment, 16 cases received glucocorticoid treatment, and seven underwent mechanical ventilation. A total of six out of 20 patients died. Bivariate Pearson's test revealed a negative correlation between patients' oxygenation index and age (r=-0.493, P=0.03). Serum lactate dehydrogenase (LDH) levels were positively correlated with serum creatinine levels (r=0.557, P=0.01). LDH levels were positively correlated with the time between symptom onset and oral administration of compound sulfamethoxazole (SMZ-TMP) (r=0.477, P=0.03). There was also a positive correlation between creatinine levels and the time to oral SMZ-TMP administration (r=0.607, P=0.005).<br><br>CONCLUSIONS: HIV-negative patients with PCP have atypical clinical symptoms and a high mortality rate. mNGS technology may facilitate early diagnosis based on its rapid turnaround time. To reduce mortality, SMZ-TMP drug treatment should be initiated promptly once PCP is considered clinically.}, }
@article {pmid41229688, year = {2025}, author = {Zhao, J and Zeng, R and Zhang, C and He, B and Zhang, Q and Zhou, Q and Gong, Z and Liu, H and Liu, S}, title = {Comparative analysis of soil properties before and after Morchella sextelata cultivation across various soil types.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1700246}, pmid = {41229688}, issn = {1664-302X}, abstract = {Morchella, a highly nutritious edible fungus, has been successfully cultivated through artificial means. However, as cultivation areas have expanded, declining yield have emerged more prominently. Soil physicochemical characteristics and microbial communities were critical to production on cultivating morels. In this study, our results reveals that cultivation significantly alters soil properties and microbial communities in a soil type-dependent manner. In sandy soil, pH and key nutrients (total nitrogen, total phosphorus, available phosphorus) increased, while potassium and calcium levels decreased. Microbial diversity decreased in sandy soil but increased in paddy soil, with the overall community structure in sandy soil being more drastically reshaped. Metagenomic profiling identified distinct differential taxa and functional shifts, showing that sandy soil exhibited greater enrichment of microbial genes, including soil-borne diseases. These findings demonstrate that M. sextelata cultivation induces considerable and contrasting changes in soil nutrient profiles and microbiome composition, with sandy soil being more susceptible to microbial restructuring and potential pathogen enrichment.}, }
@article {pmid41229344, year = {2025}, author = {Sures, K and Esser, SP and Bornemann, TLV and Moore, CJ and Soares, AR and Plewka, J and Figueroa-Gonzalez, PA and Ruff, SE and Moraru, C and Probst, AJ}, title = {Acquisition of Spacers from Foreign Prokaryotic Genomes by CRISPR-Cas Systems in Natural Environments.}, journal = {Genome biology and evolution}, volume = {17}, number = {11}, pages = {}, doi = {10.1093/gbe/evaf201}, pmid = {41229344}, issn = {1759-6653}, mesh = {*CRISPR-Cas Systems ; *Genome, Archaeal ; *Archaea/genetics ; Genome, Bacterial ; *Clustered Regularly Interspaced Short Palindromic Repeats ; *Bacteria/genetics ; Metagenome ; Evolution, Molecular ; *DNA, Intergenic/genetics ; }, abstract = {Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) systems of bacteria and archaea provide immunities against mobile genetic elements, like viruses. In addition, protospacer analyses revealed a very specific acquisition of CRISPR spacers derived from genomes of related species or from closely interacting episymbiont genomes as recently shown for subsurface archaea. However, the origin of most of the spacers that can be found in CRISPR-Cas systems from natural environments has not been deciphered. Here, by analyzing CRISPR-Cas systems of metagenome-assembled genomes (MAGs) from two subsurface environments spanning more than 1 Tb of sequencing data, we show that a substantial proportion of CRISPR spacers are acquired from DNA of other prokaryotes inhabiting the same environment. As such, we found that the number of respective spacers can be up to three times higher than the number of self-targeting spacers. Statistical analyses demonstrated that the acquisition of CRISPR spacers from other prokaryotic genomes is partly explained by the relative abundance of the MAG containing the protospacer, as well as by other factors, such as the total number of CRISPR arrays present in a MAG with the respective spacers. Further, we found that spacer acquisition from foreign prokaryotic DNA occurs in almost all types of CRISPR-Cas systems, but shows preferences for subtypes of CRISPR-Cas systems that differ across the investigated ecosystems. Taken together, our results shed new light on the diversity of CRISPR spacers in natural microbial communities and provide an explanation for some of the many unmatched spacers in public databases.}, }
@article {pmid41229166, year = {2025}, author = {Houttu, N and Mokkala, K and Lindgren, H and Lotankar, M and Benchraka, C and Pärnänen, K and Saros, L and Muhli, E and Vahlberg, T and Lahti, L and Laitinen, K}, title = {The Relationship Between Gut Microbiota During Pregnancy and the Level of Postpartum Adiposity.}, journal = {MicrobiologyOpen}, volume = {14}, number = {6}, pages = {e70128}, doi = {10.1002/mbo3.70128}, pmid = {41229166}, issn = {2045-8827}, support = {//This clinical trial was supported by the State Research Funding for university-level health research in the Turku University Hospital Expert Responsibility Area, Research Council of Finland (#258606), the Diabetes Research Foundation, the Juho Vainio Foundation, the Finnish Cultural Foundation, P&#xe4;ivikki and Sakari Sohlberg Foundation, Sigrid Juselius Foundation, and the Finnish Foundation for Cardiovascular Research. Funding to the University of Turku for the metagenomics analyses was provided by Janssen Research and Development, LLC. Himmi Lindgren was partially supported by the Finnish Doctoral Program Network in Artificial Intelligence (AI-DOC)./ ; }, mesh = {Humans ; Female ; Pregnancy ; *Gastrointestinal Microbiome ; *Adiposity ; *Postpartum Period ; Adult ; Body Mass Index ; *Obesity/microbiology ; Metagenomics ; Young Adult ; Bacteria/classification/genetics/isolation &amp; purification ; Overweight/microbiology ; Waist-Hip Ratio ; }, abstract = {Gut microbiota is linked with health, including obesity, in the general population. It is unknown whether adiposity at postpartum is influenced by gut microbiota already during pregnancy. We investigated the association between the gut microbiota's composition and predicted function by metagenomics during pregnancy and the women's adiposity (body mass index [BMI], waist-to-hip ratio [WHR], body fat%) assessed at 1-, 2-, and 5-6-years' postpartum in 257 women with overweight or obesity based on prepregnancy BMI values. Body fat% at 1-year, but not at 2- or 5-6-years' postpartum, was associated inversely with α-diversity during pregnancy. Bacterial species GGB3034 SGB4030 (family Erysipelotrichaceae) was higher in women with normal weight than those in women with obesity at 1-year postpartum (q = 0.02), other species being borderline statistically significant (q < 0.25). High WHR and body fat% at 1-year postpartum were associated with two species (q < 0.25). Considering predicted functions of bacteria, an association was detected for BMI, WHR, and body fat%, e.g., body fat% and glycogen biosynthesis I (q < 0.25). Gut microbiota during pregnancy predicted the BMI and body fat% at 1-year postpartum (ROC > 0.50, p < 0.02). Postpartum adiposity was associated with several species and α-diversity. Gut microbiota during pregnancy may be involved in the persistence of obesity and its comorbidities after pregnancy.}, }
@article {pmid41228422, year = {2025}, author = {Diotaiuti, P and Misiti, F and Marotta, G and Falese, L and Calabrò, GE and Mancone, S}, title = {The Gut Microbiome and Its Impact on Mood and Decision-Making: A Mechanistic and Therapeutic Review.}, journal = {Nutrients}, volume = {17}, number = {21}, pages = {}, doi = {10.3390/nu17213350}, pmid = {41228422}, issn = {2072-6643}, support = {MUR Decree n. 105123.06.2022 PNRR Missione 4 Componente 2 Investimento 1.5-CUP H33C22000420001//Project ECS0000024 "Ecosistema dell'innovazione-Rome Technopole" financed by EU NextGeneration EU plan/ ; }, mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Affect/physiology ; *Decision Making/physiology ; Animals ; Cognition ; Probiotics ; Dysbiosis/microbiology ; Fecal Microbiota Transplantation ; Prebiotics/administration &amp; dosage ; }, abstract = {Background/Objectives: The gut microbiome is increasingly recognized as a key modulator of central nervous system function through the gut-brain axis. Dysbiosis has been associated with neuropsychiatric disorders such as depression, anxiety, impulsivity, cognitive decline, and addiction. This review aims to synthesize mechanistic insights and therapeutic perspectives on how gut microbiota influence mood regulation, decision-making, and cognitive processes. Methods: A comprehensive narrative review was conducted using peer-reviewed articles retrieved from PubMed, Scopus, and Web of Science up to August 2025. Studies were included if they explored microbiota-related effects on behavior, mood, cognition, or decision-making using human or animal models. Emphasis was placed on molecular mechanisms, microbiome-targeted therapies, and multi-omics approaches. Results: Evidence indicates that gut microbiota modulate neurochemical pathways involving serotonin, dopamine, GABA, and glutamate, as well as immune and endocrine axes. Microbial imbalance contributes to low-grade systemic inflammation, impaired neuroplasticity, and altered stress responses, all of which are linked to mood and cognitive disturbances. Specific microbial taxa, dietary patterns, and interventions such as probiotics, prebiotics, psychobiotics, and fecal microbiota transplantation (FMT) have shown promise in modulating these outcomes. The review highlights methodological advances including germ-free models, metagenomic profiling, and neuroimaging studies that clarify causal pathways. Conclusions: Gut microbiota play a foundational role in shaping emotional and cognitive functions through complex neuroimmune and neuroendocrine mechanisms. Microbiome-based interventions represent a promising frontier in neuropsychiatric care, although further translational research is needed to define optimal therapeutic strategies and address individual variability.}, }
@article {pmid41228409, year = {2025}, author = {Xu, C and Cui, H and Fang, Q and Tu, P and Cui, X}, title = {Steamed Panax notoginseng Saponins Ameliorate Cyclophosphamide-Induced Anemia by Attenuating Gut-Liver Injury and Activating the cAMP/PI3K/AKT Signaling Pathway.}, journal = {Nutrients}, volume = {17}, number = {21}, pages = {}, doi = {10.3390/nu17213335}, pmid = {41228409}, issn = {2072-6643}, support = {202202AG050021//the Yunnan Major Scientific and Technological Projects/ ; }, mesh = {Animals ; *Saponins/pharmacology ; *Panax notoginseng/chemistry ; *Cyclophosphamide/adverse effects ; Signal Transduction/drug effects ; *Anemia/chemically induced/drug therapy ; Proto-Oncogene Proteins c-akt/metabolism ; Mice ; Cyclic AMP/metabolism ; Phosphatidylinositol 3-Kinases/metabolism ; Gastrointestinal Microbiome/drug effects ; Male ; Liver/drug effects/metabolism ; Colon/metabolism/drug effects ; }, abstract = {Background: Steamed Panax notoginseng saponins (SPNSs) can alleviate cyclophosphamide-induced anemia. However, the hepatointestinal effects of SPNSs and their role in ameliorating cyclophosphamide-induced anemia remain unexplored. Objective: To elucidate the hepatointestinal effects of SPNSs and their role in ameliorating cyclophosphamide-induced anemia. Methods: Blood samples were collected and analyzed on days 7 and 14. Liver tissues and small intestinal villi structures were observed via HE staining. Liver and colon content metabolites were detected by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Liver proteins were analyzed by using an Orbitrap Astral mass spectrometer. Colon content microbiota composition was assessed via metagenomics. Signaling pathway protein expression was analyzed via Western blotting (WB). Results: SPNSs significantly increased the red blood cell (RBC) count and hemoglobin (HGB) level by day 14 and alleviated hepatointestinal damage. Hepatic metabolomics revealed: the most abundant metabolites were fatty acids and stachyose on day 7 and amino acid and arachidonic acid derivatives on day 14. KEGG analysis implicated cAMP signaling. Proteomics revealed upregulated immune-related proteins and enhanced PI3K pathway activity (WB-validated). Colon content metabolomics showed increased daidzein, 3-(2,5-dimethoxyphenyl) propanoic acid, γ-CEHC, and adenosine in SPNS groups on day 14. Metagenomics indicated differential abundances of Heminiphilus faecis, Phocaeicola sartorii, and s-bacterium_J10.2018 on day 14. Multiomics integration demonstrated significant correlations between hepatic metabolites, hematopoietic proteins, colon content metabolites, and probiotic bacteria. Conclusions: SPNS alleviates cyclophosphamide-induced hepato-intestinal injury in anemic mice by modulating the gut microbiota and enhancing hepato-intestinal immune defense. Additionally, SPNSs ameliorate anemia in cyclophosphamide-treated mice by activating the cAMP/PI3K/AKT pathway, promoting hepatocyte proliferation, and increasing hematopoietic protein expression.}, }
@article {pmid41227654, year = {2025}, author = {Liscano, Y and Caicedo, N and Oñate-Garzón, J}, title = {Unlocking New Bioactive Peptides from Coffee Pulp: A Metagenomics and AI-Driven Discovery Paradigm.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {21}, pages = {}, pmid = {41227654}, issn = {2304-8158}, support = {call No. DGI-01-2025//Universidad Santiago de Cali/ ; }, abstract = {This perspective reframes Colombian coffee pulp from an environmental liability into a strategic asset by proposing a new discovery paradigm. We argue that the pulp's challenging chemical environment is not a barrier but its key advantage, having acted as a natural evolutionary filter that has sculpted a unique, highly resilient microbiome. Our vision is a technology pipeline that harnesses this natural pre-selection. By converging deep metagenomic data from the pulp's microbiome with generative artificial intelligence, we can create and validate novel, high-performance bioactive peptides and enzymes that are already pre-optimized for industrial robustness. This approach transcends traditional waste valorization, establishing a new framework for "biointelligence" in action. It offers a strategic roadmap for Colombia to generate knowledge-intensive value chains from its most iconic agricultural product, turning a national challenge into a global opportunity in the bioeconomy.}, }
@article {pmid41227630, year = {2025}, author = {Luo, Q and Li, X and Li, J and Lu, Y and Chen, J and Su, J and Zhao, D and Hu, J and Zhang, X and Zhao, P and Zhang, Z and Zhang, Q and Lei, X and Bai, J and Zheng, J and Zhao, X}, title = {Multi-Metaomics Unveils the Development Process of Microbial Communities During the Fermentation of Baobaoqu.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {21}, pages = {}, pmid = {41227630}, issn = {2304-8158}, support = {JUSRP202504012//Fundamental Research Funds for the Central Universities/ ; BK20233003//Jiangsu Basic Research Center for Synthetic Biology/ ; 32021005//Foundation for Innovative Research Groups of the National Natural Science Foundation of China/ ; }, abstract = {In order to understand the dynamic interaction process among species, enzymes, and metabolites during the fermentation process of Baobaoqu, which is a representative Daqu starter for Chinese baijiu, the intimate connection between the progression of microbial communities and the diversities and activities of enzymes was examined by metagenomics, metatranscriptomics and metaproteomics. It was found that while 5211 species of microorganisms were detected by metagenomics, only 1774 active species were detected by metatranscriptomics, which indicated that only a small proportion (34.04%) were active. The metabolic routes associated with the breakdown of substrates and synthesis of metabolites were redesigned, and the special functional microorganisms for lactate, pyrazines and phenylethyl alcohol production were isolated. It was found that the progression of the microbial community was highly coupled with the components of enzymes and flavor substrates, precisely corresponding to the three stages of the Baobaoqu fermentation process, and were regulated by multiple physical factors. During the Baobaoqu-making process of the fermentation, microorganisms with different functions work together to complete metabolism in different stages. These findings will aid us in gaining a deeper and clearer understanding of the "species-enzyme-metabolite" system within the Daqu starter culture, thus offering valuable perspectives for developing artificial synthetic communities and the production of high-quality Baobaoqu.}, }
@article {pmid41227601, year = {2025}, author = {Hou, Y and Jia, R and Zhou, L and Li, B and Zhu, J}, title = {The Presence of Stone Moroko (Pseudorasbora parva) Drives Divergent Sediment Resistome Profiles in Chinese Mitten Crab (Eriocheir sinensis) Polyculture Pond.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {21}, pages = {}, pmid = {41227601}, issn = {2304-8158}, support = {CARS-45//China Agriculture Research System of MOF and MARA/ ; 31802302//National Natural Science Foundation of China/ ; 2023TD64//Central Public-Interest Scientific Institution Basal Research Fund, CAFS/ ; BK20231140//Jiangsu Provincial Natural Science Foundation of China/ ; 2019YFD0900305//National Key R&amp;D Program of China/ ; }, abstract = {The propagation of antibiotic resistance genes (ARGs) in aquatic environments poses a significant threat to global health. This study compared sediment resistome profiles in river crab (Eriocheir sinensis) polyculture systems with and without stone moroko (Pseudorasbora parva). The results showed that, compared to the control group (MC group), the sediment from the polyculture system containing stone moroko (PC group) exhibited significant reductions in the total abundances of ARGs, metal resistance genes (MRGs), biocide resistance genes (BRGs), and mobile genetic elements (MGEs). Crucially, the total abundance and composition of MGEs in pond sediment were substantially correlated with ARGs, MRGs, and BRGs, respectively. Co-occurrence network analysis revealed that there was only one edge between ARGs and MGEs in the PC group, whereas the MC group had eight edges. Additionally, the proportion of mobile ARGs in the PC group was significantly lower than that in the MC group. Alterations in resistome profiles were markedly associated with decreased levels of total carbon (TC) and phosphate in the sediment. All of the findings demonstrated that the introduction of stone moroko in the river crab polyculture system effectively mitigated the sediment resistome primarily by altering environmental factors and suppressing MGEs, thereby disrupting the horizontal transfer network of resistance genes. This study highlights the potential of leveraging aquatic biota as a novel biological strategy for the in situ management of environmental antimicrobial resistance.}, }
@article {pmid41227457, year = {2025}, author = {Soto-López, JD and Fernández-Soto, P and Muro, A}, title = {Bacterial Composition Across Bat Species: A Human Health Perspective.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {21}, pages = {}, pmid = {41227457}, issn = {2076-2615}, abstract = {Bats are widely recognized as reservoirs of diverse bacterial pathogens with important implications for human health. Recent zoonotic disease outbreaks have intensified interest in bat microbiomes, with high-throughput sequencing increasingly used to assess microbial diversity. In this article, we review literature from the past five years on bacterial species associated with bats and their potential clinical relevance. Using automated searches and manual filtering, we extracted data from 47 peer-reviewed studies. Most research has focused on guano samples, though interest in skin microbiomes is rising, particularly in relation to Pseudogymnoascus destructans, the agent of white-nose syndrome. China leads in the number of publications, followed by the United States, and amplicon sequencing remains the predominant metagenomic method. Across studies, 4700 bacterial species were reported, including several known human pathogens capable of aerosol transmission or opportunistic infections in immunocompromised individuals. Many of these taxa are classified as global priority targets for antimicrobial drug development by the World Health Organization and the U.S. Centers for Disease Control and Prevention. Given the clinical severity of diseases linked to some species, bats should be integrated into epidemiological surveillance systems. However, the lack of standardized reporting practices significantly limits the comparability and utility of bat microbiome data for robust ecological and epidemiological analyses.}, }
@article {pmid41227433, year = {2025}, author = {Yang, B and Shen, P and Xu, Z and Yang, J and Song, B and Jiang, H and Chai, J and Zhao, J and Deng, F and Li, Y}, title = {Functional and Compositional Changes in Ileal Microbiota in Piglets During the Nursing Period Revealed by 16s rRNA Gene and Metagenomics.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {21}, pages = {}, pmid = {41227433}, issn = {2076-2615}, support = {2023YFE0124400//the National Key Research and Development Program of China/ ; 2023B10564001//the Specific University Discipline Construction Project/ ; 2022A1515110819//Youth Project of Guangdong Foshan joint fund of the Guangdong Natural Science Foundation/ ; No. 32202715//the National Natural Science Foundation of China/ ; }, abstract = {In piglets, the gut microbiota matures in a segment-specific manner during the nursing period, while fecal-based studies provide limited functional resolution across intestinal sites. We profiled the ileum using 16s rRNA gene sequencing and assessed segmental functions by shotgun metagenomics at selected ages. Ileal species richness and diversity were relatively stable across days. Lactobacillus were prominent from day 7, with stage-associated taxa including Lactobacillus johnsonii, Lactobacillus delbrueckii, Ligilactobacillus salivarius, and Limosilactobacillus pontis. Through metagenomic functional analysis, at 21 days, genes were enriched in butanoate metabolism, and Limosilactobacillus pontis as a potential probiotic played an important role in it. At day 28, metagenomic analysis indicated higher relative abundance in the ileum of pathways linked to cysteine and methionine metabolism and lysine biosynthesis, largely carried by Limosilactobacillus mucosae, Limosilactobacillus oris, and Limosilactobacillus pontis. These data describe the composition and function of the ileum in the intestines of piglets and indicate a differentiation period around day 21 to day 28.}, }
@article {pmid41227430, year = {2025}, author = {Deng, L and Yao, Y and Li, H and Lu, Q and Wu, R}, title = {Effects of Antimicrobial Peptides on the Growth Performance of Squabs Were Investigated Based on Microbiomics and Non-Targeted Metabolomics.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {21}, pages = {}, pmid = {41227430}, issn = {2076-2615}, support = {2023B02036//Xinjiang Uygur Autonomous Region Key Research and Development Project/ ; XJARS-12-01//Xinjiang Uygur Autonomous Region Modern Agricultural Industrial Technology System/ ; 2025XJJQ-z-01//Xinjiang Uygur Autonomous Region Modern Livestock and Poultry Breeding Industry Promotion Project/ ; }, abstract = {This study aims to investigate the effects of dietary supplementation with AMPs on the growth performance, antioxidant capacity, and intestinal health of squabs. Furthermore, metagenomic and metabolomic approaches were employed to identify key differential bacterial species and metabolites associated with growth performance, and thereby the potential mechanisms underlying the enhancement of squab growth and development by AMPs being elucidated. One hundred and twenty pairs of healthy adult White Carneau pigeons (2 years old) were randomly divided into two groups, the control group (CK, fed with basal diet) and antimicrobial peptide group (AP, fed with basal diet +200 mg/kg antimicrobial peptide), with 10 replicates per group and 6 pairs of breeding pigeons per replicate. The experiment lasted for 53 days, including 7 days of prefeeding, 18 days of incubation and 28 days of feeding. In this study, squabs were weighed at 0 and 28 days of age to evaluate growth performance. At 28 days of age, duodenal contents were collected to assess digestive enzyme activities, while jejunal and liver tissues were harvested to determine antioxidant capacity. Intestinal morphology was examined using tissue samples from the duodenum, jejunum, and ileum. Finally, ileal contents were collected for a comprehensive analysis of microbial composition and metabolite profiles in the two experimental groups, employing high-throughput sequencing and LC-MS/MS techniques. The results showed that body weight, liver total antioxidant capacity (T-AOC), jejunal malondialdehyde (MDA) content, jejunum and ileum villus height-to-crypt depth ratio (VH/CD) were significantly increased, and jejunal crypt depth (CD) was significantly decreased in the AP group at 28 days of age (p < 0.05). In addition, the microbiome data showed that Lactobacillus in the AP group was a biomarker with significant differences (p < 0.05). Metabolomics analysis showed that the steroid hormone biosynthesis pathway was significantly different between the two groups (p < 0.01). In addition, the content of potentially beneficial metabolites (Biotin, beta-Tocotrienol, 7-Chloro-L-tryptophan and Dihydrozeatin) was significantly increased in the AP group (p < 0.05). These results indicate that dietary AMPs can significantly improve the body weights, liver antioxidant capacity and jejunum and ileum VH/CD of squabs.}, }
@article {pmid41227427, year = {2025}, author = {Lu, H and Wang, H and Li, B and Lv, Z and Li, S and Xia, Y and Wang, L}, title = {Effects of Soybean Meal Replacement on Growth Performance, Rumen Fermentation, Rumen Microorganisms, and Metabolites in Dumont Lambs.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {21}, pages = {}, pmid = {41227427}, issn = {2076-2615}, support = {BR231520//Basic Research Operating Funds of Universities under the Direct Administration of the Inner Mongolia Autonomous Region/ ; project No. BR22-13-13//Basic Research Fund for Universities in Inner Mongolia Autonomous Region/ ; YLXKZX-NND-007//Inner Mongolia Education Department Special Research Project For First Class Disciplines/ ; }, abstract = {This study investigated the effects of replacing part of the soybean meal in the diet of Dumont lambs with urea, rapeseed meal, and cottonseed meal on their growth performance and rumen fermentation and combined rumen microbial metagenomics and metabolomics to explain the reasons for the changes in phenotypic data. Twenty-four healthy male Dumont lambs were divided into four groups: soybean meal group (T1, control group), group with 1.5% urea replacing 6.4% soybean meal (T2), group with 1% urea replacing 4.3% soybean meal (T3), and group with 1% urea + 6.6% cottonseed meal +5% rapeseed meal replacing all soybean meal (19%) (T4), following the principle of equal energy and nitrogen. Urea, rapeseed meal, and cottonseed meal have different degradation rates in the rumen, primarily stimulating arginine biosynthesis, sulphur metabolism, and carbon fixation in photosynthetic organisms through Prevotella genus mediation, thereby influencing the accumulation of metabolites such as 9,10-DiHOME, DG (PGJ2/a-15:0/0:0), isonicotinate and taxifolin, affecting rumen fermentation. Compared with the T1 group, the T2 group showed significantly increased ammonia nitrogen (NH3-N) and microbial protein (MCP) content (p < 0.01) and improved fructose and mannose metabolic capacity (p < 0.05). The T3 group showed a significant increase in total volatile fatty acids (TVFA) and MCP content (p < 0.01), which facilitated the absorption of subsequent nutrients. In the T4 group, different degradation rates of nitrogen resources and rapeseed meal + cottonseed meal contained abundant and complementary amino acids, which improved rumen fermentation, enhanced rumen microbial and metabolite diversity, and optimized the synergistic metabolic efficiency of carbon, nitrogen and sulphur. However, the specific mechanisms of post-rumen metabolism and absorption require further investigation.}, }
@article {pmid41227163, year = {2025}, author = {Armbruster, J and Thomas, B and Stengel, D and Spranger, N and Gruetzner, PA and Hackl, S}, title = {Managing Nonunions and Fracture-Related Infections-A Quarter Century of Knowledge, and Still Curious: A Narrative Review.}, journal = {Journal of clinical medicine}, volume = {14}, number = {21}, pages = {}, pmid = {41227163}, issn = {2077-0383}, abstract = {Nonunions and fracture-related infections represent a significant complication in orthopedic and trauma care, with their incidence rising due to an aging, more comorbid global population and the escalating threat of multi-resistant pathogens. This narrative review highlights pivotal advancements in diagnostics and therapeutic approaches, while also providing an outlook on future directions. Diagnostic methodologies have significantly evolved from traditional cultures to sophisticated molecular techniques like metagenomic next-generation sequencing and advanced imaging. Simultaneously, therapeutic strategies have undergone substantial refinement, encompassing orthoplastic management for infected open fractures and the innovative application of antibiotic-loaded bone substitutes for local drug delivery. The effective integration of these possibilities into daily patient care critically depends on specialized centers. These institutions play an indispensable role in managing complex cases and fostering innovation. Despite considerable progress over the past 25 years, ongoing research, interdisciplinary collaboration, and a steadfast commitment to evidence-based practice remain crucial to transforming management for the future.}, }
@article {pmid41226831, year = {2025}, author = {Stoyancheva, G and Mihaylova, N and Gerginova, M and Krumova, E}, title = {Endometrial Microbiome and Reproductive Receptivity: Diverse Perspectives.}, journal = {International journal of molecular sciences}, volume = {26}, number = {21}, pages = {}, doi = {10.3390/ijms262110796}, pmid = {41226831}, issn = {1422-0067}, support = {&#x41a;&#x41f;-06-&#x41d;83/6//Scientific Research Fund at the Ministry of Education and Science, Bulgaria/ ; }, mesh = {Humans ; Female ; *Endometrium/microbiology ; *Microbiota ; *Embryo Implantation ; Dysbiosis/microbiology ; *Reproduction ; }, abstract = {The human endometrium, previously considered a sterile environment, is now recognized as a low-biomass but biologically active microbial niche critical to reproductive health. Advances in sequencing technologies, particularly shotgun metagenomics, have provided unprecedented insights into the taxonomic and functional complexity of the endometrial microbiome. While 16S rRNA sequencing has delineated the distinction between Lactobacillus-dominant and non-dominant microbial communities, shotgun metagenomics has revealed additional diversity at the species and strain level, uncovering microbial signatures that remain undetected by amplicon-based approaches. Current evidence supports the association of Lactobacillus dominance with endometrial homeostasis and favorable reproductive outcomes. Dysbiosis, characterized by increased microbial diversity and enrichment of anaerobic taxa such as Gardnerella, Atopobium, Prevotella, and Streptococcus, is linked to chronic endometritis, implantation failure, and adverse IVF results. Beyond compositional differences, the endometrial microbiome interacts with the host through immunological, metabolic, and epigenetic mechanisms. These interactions modulate cytokine signaling, epithelial barrier integrity, and receptivity-associated gene expression, ultimately influencing embryo implantation. However, discrepancies between published studies reflect the lack of standardized protocols for sampling, DNA extraction, and bioinformatic analysis, as well as the inherent challenges of studying low-biomass environments. Factors such as geography, ethnicity, hormonal status, and antibiotic exposure further contribute to interindividual variability. Culturomics approaches complement sequencing by enabling the isolation of viable bacterial strains, offering perspectives for microbiome-based biotherapeutics. Emerging 3D endometrial models provide additional tools to dissect microbiome-host interactions under controlled conditions. Taken together, the growing body of data highlights the potential of endometrial microbiome profiling as a biomarker for reproductive success and as a target for personalized interventions. Future research should focus on integrating multi-omics approaches and functional analyses to establish causal relationships and translate findings into clinical practice. This review gives a new insight into current knowledge on the uterine microbiome and its impact on implantation success, analyzed through the lenses of microbiology, immunology, and oxidative stress.}, }
@article {pmid41226812, year = {2025}, author = {Kondo, T and Kondo, S and Nakayama-Imaohji, H and Tada, A and Tabassum, N and Munyeshyaka, E and Koyano, K and Nakamura, S and Kusaka, T and Kuwahara, T}, title = {Comparative Analysis of Mucosa-Associated and Luminal Gut Microbiota in Pediatric Ulcerative Colitis.}, journal = {International journal of molecular sciences}, volume = {26}, number = {21}, pages = {}, doi = {10.3390/ijms262110775}, pmid = {41226812}, issn = {1422-0067}, support = {24K14726//JSPS KAKENHI/ ; 23K28020//JSPS KAKENHI/ ; }, mesh = {Humans ; *Colitis, Ulcerative/microbiology/pathology ; *Gastrointestinal Microbiome/genetics ; Child ; Male ; Female ; *Intestinal Mucosa/microbiology/pathology ; Adolescent ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Child, Preschool ; Dysbiosis/microbiology ; }, abstract = {Inflammatory bowel diseases (IBD), including ulcerative colitis (UC) and Crohn's disease, are chronic disorders relating to gut microbiota dysbiosis. Despite severe pancolitis being more prevalent in pediatric UC than in adults, alterations in the colon mucosa-associated microbiota (MAM) and their association with disease severity remain to be elucidated. The present study aimed to compare the gut microbiota in colon lavage fluids (CLFs) and fecal samples from 19 pediatric UC and 19 non-IBD patients. The community structure of MAM inferred by 16S metagenomic analysis was similar throughout the colon regardless of disease type. Bacterial compositions between MAM and feces were significantly different in non-IBD, while no difference was observed in pediatric UC, indicating a compromised mucous layer that could not sufficiently separate the MAM and luminal microbiota in UC. In pediatric UC, homogenous distribution of MAM was gradually disordered with increases in disease activity or mucosal inflammation, and bacterial groups of upper digestive tract or environmental origin were more abundant in MAM. Monitoring key bacterial markers in MAM, which include Lactobacillus and Enterococcus or Faecalibacterium and Blautia as increased or reduced members in pediatric UC, respectively, might be useful for evaluation of patient prognosis.}, }
@article {pmid41226502, year = {2025}, author = {Kuo, TH and Wu, PH and Liu, PY and Chuang, YS and Tai, CJ and Kuo, MC and Chiu, YW and Lin, YT}, title = {Identification of Gut Microbiome Signatures Associated with Serotonin Pathway in Tryptophan Metabolism of Patients Undergoing Hemodialysis.}, journal = {International journal of molecular sciences}, volume = {26}, number = {21}, pages = {}, doi = {10.3390/ijms262110463}, pmid = {41226502}, issn = {1422-0067}, support = {MOST 111-2314-B-037-032-MY3//Ministry of Science and Technology, Taiwan/ ; MOST 111-2314-B-037 -083 -MY3//Ministry of Science and Technology, Taiwan/ ; KMUH-DK(C)113003//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH-DK(B)110003-4//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH112-2M08//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH112-2R21//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH112-2R76//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH111-1M60//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH111-1R73//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH110-0M73//Kaohsiung Medical University Hospital, Taiwan/ ; NHRIKMU-111-I003-2//Kaohsiung Medical University, Taiwan/ ; NHRIKMU-113-I005//Kaohsiung Medical University, Taiwan/ ; NYCUKMU-112-I006//Kaohsiung Medical University, Taiwan/ ; KT112P012//Kaohsiung Medical University, Taiwan/ ; KT113P006//Kaohsiung Medical University, Taiwan/ ; NHRIKMU-114-I001//Kaohsiung Medical University, Taiwan/ ; S11209//Kaohsiung Medical University, Taiwan/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Tryptophan/metabolism ; *Serotonin/metabolism ; Male ; Female ; Middle Aged ; *Renal Dialysis ; Aged ; Melatonin/metabolism ; Metagenomics/methods ; Adult ; }, abstract = {Serotonin, a tryptophan metabolite, exerts a significant influence on both brain and gut functionality. While previous research has elucidated the intricate dynamics of the gut-brain axis, the interplay between serotonin pathway metabolites and gut microbiota in individuals undergoing hemodialysis remains largely unexplored. Therefore, this study aimed to investigate gut microbiota composition corresponding to serotonin pathway metabolite levels among patients with hemodialysis. A total of 85 patients undergoing hemodialysis were selected. Their gut microbiota was analyzed using shotgun metagenomic sequencing profiling. The serotonin pathway metabolites, including 5-hydroxytryptophan (5-HTP), serotonin, 5-methoxytryptophan (5-MTP), 5-methoxytryptamine, melatonin, and 6-hydroxymelatonin, were analyzed with the liquid chromatograph-tandem mass spectrometer. The robust linear discriminant analysis Effect Size (LEfSe) was employed to reveal the gut microbiota signature according to levels of serotonin pathway metabolites. A significant β-diversity difference in 5-Methoxytryptamine (p = 0.037) was found, while no variance in α-diversity was detected. Using LefSe analysis, we identified an enriched Tannerellaceae family in the high-hydroxytryptophan (5-HTP) group, the Odoribacteraceae family in the high-serotonin group, the Eubacteriales order in the high-5-methoxytryptophan (5-MTP) group, the Prevotella copri species in the high-5-Methoxytryptamine group, and the Clostridium genus in the high-melatonin group. In contrast, an enriched Clostridiaceae family in the low-5-HTP group, the Clostridiaceae family in the low-serotonin group, and the Bacteroides ovatus species in the low-5-MTP group were found. Distinct gut microbiota signatures linked to serotonin pathway metabolites were identified in patients undergoing hemodialysis. These findings provide insights for future gut-brain axis research and may guide methods to modulate gut microbiota to influence serotonin metabolites.}, }
@article {pmid41225603, year = {2025}, author = {Rong, H and Wu, Z and Zhao, K and Ding, Y and Ning, S and Tian, Y and Wang, X and Qiao, Q and Zhu, X and Wu, T and Ge, Y and Chu, H and Cui, L}, title = {Identification and characterization of Jingmen tick virus in Jiangsu, China.}, journal = {Virology journal}, volume = {22}, number = {1}, pages = {372}, pmid = {41225603}, issn = {1743-422X}, support = {BK20231374//Natural Science Foundation of Jiangsu Province/ ; 2023YFC2605100, 2023YFC2605104//National Key Research and Development Program of China/ ; }, mesh = {China ; Phylogeny ; Animals ; Genome, Viral ; *Flaviviridae/isolation &amp; purification/genetics/classification ; Genetic Variation ; Sequence Analysis, DNA ; *Ticks/virology ; *Ixodidae/virology ; }, abstract = {Jingmen virus (JMV) is a group of viruses that belong to the Flaviviridae family. These viruses have been shown to cause widespread infections in various hosts and can lead to febrile illnesses in humans. Jingmen tick virus (JMTV) as an important member of the JMV group, has been detected in multiple countries worldwide and poses a significant threat to public health. This study utilized metagenomic sequencing technology to detect JMV in tick samples collected in Jiangsu Province. The results demonstrated the presence of JMTV in Jiangsu and identified two complete genomes (ZJ-7-4-2 and ZJ-7-9) from Haemaphysalis campanulate ticks. These gene sequences exhibited the highest sequence similarity to the known Japanese isolate of JMTV. Phylogenetic analysis showed that the JMTV identified in this study clustered within the same clade as the Japanese JMTV. In summary, this study reported for the first time that JMTV is prevalent in Jiangsu Province, China. These findings expand the known geographic distribution and genetic diversity of JMTV, providing new insights into its epidemiology and viral evolution.}, }
@article {pmid41225454, year = {2025}, author = {Ohmichi-Tomiwa, M and Kato-Kogoe, N and Kudo, A and Fujita, D and Sakaguchi, S and Tsuda, K and Omori, M and Hayashi, E and Nakamura, S and Nakano, T and Ohmichi, M and Tamaki, J and Ueno, T}, title = {Exploratory study of the oral microbiota in pregnant women with hypothyroidism and their infants.}, journal = {BMC pregnancy and childbirth}, volume = {25}, number = {1}, pages = {1198}, pmid = {41225454}, issn = {1471-2393}, mesh = {Humans ; Female ; Pregnancy ; *Hypothyroidism/microbiology ; *Microbiota ; *Mouth/microbiology ; Adult ; Prospective Studies ; Infant ; Infant, Newborn ; *Pregnancy Complications/microbiology ; Case-Control Studies ; Postpartum Period ; }, abstract = {BACKGROUND: Hypothyroidism is a metabolic disorder associated with potentially adverse maternal and neonatal outcomes. Emerging evidence suggests a link between thyroid function and the microbiota; however, little is known about the oral microbiota of pregnant women with hypothyroidism and its potential impact on that of their offspring. This study aimed to characterize the oral microbiota of pregnant women with hypothyroidism and their children as part of the Oral Microbiome Prospective Unicenter Cohort Study (OMPU-CS).<br><br>METHODS: Pregnant women with hypothyroidism (Hypothyroid group, n&#x2009;=&#x2009;31) and those with normal thyroid function (Control group, n&#x2009;=&#x2009;30) were selected from participants in the ongoing OMPU-CS. Oral samples were collected from the women during pregnancy and at one month postpartum, and from their one-month-old infants. Microbiota composition was analyzed using 16&#xa0;S rRNA metagenomic sequencing.<br><br>RESULTS: Compared with pregnant women in the Control group, those in the Hypothyroid group exhibited significantly reduced richness and evenness of the oral microbiota (observed operational taxonomic units, p&#x2009;=&#x2009;0.034; Shannon index, p&#x2009;=&#x2009;0.034). The overall structure of the oral microbiota differed significantly between groups at all phases-in pregnant women, postpartum women, and their infants (unweighted UniFrac distances, p&#x2009;=&#x2009;0.002, p&#x2009;=&#x2009;0.049, and p&#x2009;=&#x2009;0.019, respectively). Linear discriminant analysis effect size (LEfSe) identified several differentially abundant taxa, including a consistently reduced abundance of members of the Rhizobiaceae family in the Hypothyroid group across all three phases compared with that in the Control group.<br><br>CONCLUSIONS: The oral microbiota of pregnant women with hypothyroidism and their one-month-old infants exhibited disease-specific characteristics. These findings suggest that maternal hypothyroidism may influence the oral microbiota of offspring, underscoring the importance of monitoring oral microbiota in mothers with hypothyroidism and their children.}, }
@article {pmid41225248, year = {2025}, author = {Bignami, G and Monzón-Atienza, L and Leuzzi, D and Scicchitano, D and Candela, M and Gómez-Mercader, A and Jlidi, M and Gustinelli, A and Tedesco, P and Fioravanti, ML and Castro, PL and Acosta, F}, title = {"Effects of Bacillus Velezensis D-18 on Health Status of European Seabass (Dicentrarchus labrax) Experimentally Challenged with Vibrio harveyi".}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {41225248}, issn = {1867-1314}, support = {28740//Horizon 2020/ ; }, abstract = {In recent years, the use of probiotics as a possible alternative to antibiotics has generated a growing interest in the global aquaculture field. In this study, the probiotic Bacillus velezensis D-18 was evaluated for its potential protective effect against the marine pathogen Vibrio harveyi. The probiotic was administered through the diet of European seabass (Dicentrarchus labrax) for 30 days, followed by an in vivo challenge with V. harveyi to assess whether the D-18 strain could enhance host resistance to infection. Biofilm formation in tanks was also investigated to analyze its composition and if there are antagonistic interactions between the two bacterial species. From a histological perspective, significant changes were observed in intestinal morphological parameters after infection, the area and base of the villi appeared to increase in the probiotic-fed groups as did the number of goblet cells and in the serum antibacterial activity which was increased in the infected group that received the probiotic compared to baseline levels. The intestinal microbiome was also analyzed to monitor the composition and determine whether different diets before and after infection induced any changes. Although no significant differences were found in the metagenomics of the tank biofilm and the gut microbiome, mortality rates showed that the probiotic provided effective protection against the pathogen. These findings support the potential of B. velezensis D-18 as a viable alternative to antibiotics, particularly when included in the diet prior to disease onset.}, }
@article {pmid41225104, year = {2026}, author = {Kars, G and Alkebsi, BLA and Keleş, S and Altan, H and Özer, H and Holyavkin, C and Karaselek, MA}, title = {Recent Insights on Dental Caries Microbiota in Pediatric Patients with Inborn Errors of Immunity.}, journal = {Advances in experimental medicine and biology}, volume = {1492}, number = {}, pages = {291-313}, pmid = {41225104}, issn = {0065-2598}, mesh = {Humans ; *Dental Caries/microbiology/immunology ; *Microbiota/immunology ; Child ; Dysbiosis/immunology/microbiology ; *Mouth/microbiology/immunology ; }, abstract = {Inborn errors of immunity (IEIs) are genetic disorders that impair immune defense and regulation, increasing susceptibility to infections, including those in the oral cavity. The oral microbiota plays a vital role in maintaining oral health, and in pediatric patients with IEIs, disruptions in this balance can lead to dental caries and other oral diseases. This chapter provides a comprehensive analysis of the relationship between immune deficiencies and oral microbiota dysbiosis, focusing on dental caries in children with IEIs. Omics technologies, particularly metagenomics, have enhanced understanding of the microbial diversity and metabolic activities within the oral microbiota of the patients. Key findings reveal that compromised immune responses in children with IEIs disrupt the balance of oral bacteria, making them more prone to dental caries. The chapter highlights the importance of an interdisciplinary approach, integrating microbiology, immunology, dentistry, and bioinformatics, to uncover the complex interactions between the oral microbiome and the immune system. The insights gained from this research will contribute to the development of personalized therapeutic strategies, improving the dental and overall health of pediatric patients with IEIs.}, }
@article {pmid41225090, year = {2026}, author = {Ziaei, H and Rezaei, N}, title = {Introduction to Oral Immunity.}, journal = {Advances in experimental medicine and biology}, volume = {1492}, number = {}, pages = {3-21}, pmid = {41225090}, issn = {0065-2598}, abstract = {The oral immune system functions as a primary line of defense, composed of oral epithelial barriers, salivary antimicrobial factors, and various innate and adaptive immune components to prevent pathogen entry. Resident immune cells in oral tissues help maintain tolerance to commensal microorganisms while simultaneously responding to harmful external stimuli and contributing to systemic immune regulation. This chapter provides a comprehensive overview of the immunological components and their functions in the oral cavity, emphasizing the dual role of maintaining tolerance to commensal microbes and dietary antigens while initiating protective responses against pathogens. Any disruptions in this balance, such as oral dysbiosis or immune dysregulation, can lead to the development of local inflammatory conditions; it may also contribute to systemic immune disturbances and related pathologies. Immune mechanisms also regulate craniofacial development and postnatal bone remodeling and regeneration, mainly through cytokine-mediated signaling pathways and interactions between stem cells and immune cells. Several local and systemic immunological pathways are often dysregulated in oral inflammatory conditions, which makes them important therapeutic targets. Therapeutic strategies targeting these pathways include immune checkpoint inhibitors, microbiome-directed interventions, stem cell-based therapies, and salivary diagnostics for real-time and noninvasive immune profiling. These offer promising approaches for restoring oral and systemic immune balance. Finally, this chapter has reviewed recent technological advances, such as single-cell RNA sequencing (scRNA-seq), spatial transcriptomics, metagenomics, and multi-omics integration, in the context of oral immunity. These novel techniques are transforming oral immunology, since they enable high-resolution characterization of cellular, microbial, and molecular interactions, and support the transition toward establishing more precise diagnosis and treatment plans. These findings suggest that oral immunity plays a critical role in linking local mucosal defense and systemic immune responses. Therefore, understanding oral immune mechanisms in health and inflammatory conditions is important for revealing disease pathogenesis and guiding targeted interventions.}, }
@article {pmid41224996, year = {2025}, author = {Nadel, O and Hanna, R and Rozenberg, A and Shitrit, D and Tahan, R and Pekarsky, I and Béjà, O and Kleifeld, O and Lindell, D}, title = {Viral NblA proteins negatively affect oceanic cyanobacterial photosynthesis.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {41224996}, issn = {1476-4687}, abstract = {Marine picocyanobacteria are abundant photosynthetic organisms of global importance. They coexist in the ocean with cyanophages-viruses that infect cyanobacteria. Cyanophages carry many auxiliary metabolic genes acquired from their hosts that are thought to redirect host metabolism for the phage's benefit[1-5]. One such gene is nblA, which is present in multiple cyanophage families[2,6-8]. Under nutrient deprivation cyanobacterial NblA is responsible for inducing proteolytic degradation of the phycobilisome[9-11], the large cyanobacterial photosynthetic light-harvesting complex. This increases the pool of amino acids available for essential tasks[11], serving as a survival mechanism[12]. Ectopic expression of different cyanophage nblA genes results in host pigment protein degradation[6,8,13]. However, the benefit of the virus-encoded NblA for cyanophages and the broader impact on the host are unclear. Here, using a recently developed genetic manipulation system for marine cyanophages[14], we reveal that viral NblA significantly accelerates the cyanophage infection cycle, directs degradation of the host phycobilisome and other proteins, and reduces host photosynthetic light-harvesting efficiency. Metagenomic analysis revealed that cyanophages carrying nblA are widespread in the oceans and comprise 35% and 65% of oceanic T7-like cyanophages in surface and deep photic zones, respectively. Our results show a large benefit of NblA to the cyanophage, while it exerts a negative effect on the host photosynthetic apparatus and host photosynthesis. These findings suggest that cyanophage NblA has an adverse global impact on light harvesting by oceanic picocyanobacteria.}, }
@article {pmid41224779, year = {2025}, author = {Secaira-Morocho, H and Jiang, X and Zhu, Q}, title = {Augmenting microbial phylogenomic signal with tailored marker gene sets.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {9943}, pmid = {41224779}, issn = {2041-1723}, support = {RFGA2023-008-15//ADHS | Arizona Biomedical Research Commission (ABRC)/ ; }, abstract = {Phylogenetic marker genes are traditionally selected from a fixed collection of whole genomes representing major microbial phyla, covering only a small fraction of gene families. However, most microbial diversity resides in metagenome-assembled genomes, which exhibit taxonomic imbalance and harbor gene families that do not fit the criteria for universal orthologs. To address these limitations, we introduce TMarSel, a software tool for automated, free-from-expert opinion, and tailored marker selection for deep microbial phylogenomics. TMarSel allows users to select a variable number of markers and copies based on KEGG and EggNOG gene family annotations, enabling a systematic evaluation of the phylogenetic signal from the entire gene family pool. We show that an expanded marker selection tailored to the input genomes improves the accuracy of phylogenetic trees across simulated and real-world datasets of whole genomes and metagenome-assembled genomes compared to previous markers, even when metagenome-assembled genomes lack a fraction of open reading frames. The selected markers have functional annotations related to metabolism, cellular processes, and environmental information processing, in addition to replication, translation, and transcription. TMarSel provides flexibility in the number of markers, copies, and annotation databases while remaining robust against taxonomic imbalance and incomplete genomic data.}, }
@article {pmid41224755, year = {2025}, author = {Gupta, S and Almeida, A}, title = {Integration of metagenome-assembled genomes with clinical isolates expands the genomic landscape of gut-associated Klebsiella pneumoniae.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {9959}, pmid = {41224755}, issn = {2041-1723}, support = {MR/W016184/1//RCUK | Medical Research Council (MRC)/ ; }, abstract = {Klebsiella pneumoniae is an opportunistic pathogen causing diseases ranging from gastrointestinal disorders to severe liver abscesses. While clinical isolates of K. pneumoniae have been extensively studied, less is known about asymptomatic variants colonizing the human gut across diverse populations. Developments in genome-resolved metagenomics have offered unprecedented access to metagenome-assembled genomes (MAGs), expanding the known bacterial diversity within the gut microbiome. Here we analysed 656 human gut-derived K. pneumoniae genomes (317 MAGs, 339 isolates) from 29 countries to investigate the population structure and genomic landscape of gut-associated lineages. Over 60% of MAGs were found to belong to new sequence types, highlighting a large uncharacterized diversity of K. pneumoniae missing among sequenced clinical isolates. In particular, integrating MAGs nearly doubled gut-associated K. pneumoniae phylogenetic diversity, and uncovered 86 MAGs with >0.5% genomic distance compared to 20,792 Klebsiella isolate genomes from various sources. Pan-genome analyses identified 214 genes exclusively detected among MAGs, with 107 predicted to encode putative virulence factors. Notably, combining MAGs and isolates revealed genomic signatures linked to health and disease and more accurately classified disease and carriage states compared to isolates alone. These findings showcase the value of metagenomics to understand pathogen evolution and diversity with implications for public health surveillance strategies.}, }
@article {pmid41224035, year = {2025}, author = {Wu, X and Wang, C and Wang, D and Yu, Z and Meng, F}, title = {Microbiota ecology upon moderate concentrations of total ammoniacal nitrogen enhances methane production of anaerobic membrane bioreactor.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {133630}, doi = {10.1016/j.biortech.2025.133630}, pmid = {41224035}, issn = {1873-2976}, abstract = {In this study, the ecological responses of microbial community of anaerobic membrane bioreactor (AnMBR) upon exposure to moderate concentration total ammoniacal nitrogen (TAN) were studied to unveil the underlying mechanisms of reactor performance variation. The 16S rRNA gene and community assembly analysis indicated that the moderate ammonia concentration imposed limited selection pressure on the methanogenic community. Instead, the community assembly was governed by the random birth, death, and reproduction of community members. Network analysis further suggested that the moderate concentration of TAN established strong cooperative linkage between hydrogenotrophic methanogens (HM) and syntrophic acetate oxidizing bacteria (SAOB) in AnMBR. Metagenome sequencing analysis provided convergent evidence that there were enriched genes responsible for the SAOB-HM pathway as well as direct interspecific electron transfer. Moreover, the morphology of anaerobic granular sludge (AnGS) suggested that the decreased particle size enhanced substrate mass transfer efficiency among community members and the methanogens in inner layer of AnGS received more protection from its neighbors in moderate TAN phases. Consequently, the biogas production, methane (CH4) yield and specific methanogenic activity (SMA) of granular sludge in moderate TAN phases were significantly increased compared to the low TAN phase. Together, this study has expanded our understanding of facilitation of moderate concentration TAN-containing wastewater treatment on AnMBR process.}, }
@article {pmid41223797, year = {2025}, author = {Xu, YY and Tan, X and Dang, CC and Liu, LY and Wang, X and Zhao, ZC and Ren, NQ and Wu, YN and Xie, GJ}, title = {Thermophilic Sulfide-Driven autotrophic Denitrification: High-Rate nitrogen removal and metagenomic insights into microbial cooperation.}, journal = {Environment international}, volume = {205}, number = {}, pages = {109918}, doi = {10.1016/j.envint.2025.109918}, pmid = {41223797}, issn = {1873-6750}, abstract = {Sulfide-driven autotrophic denitrification (SDAD) plays a pivotal role in linking nitrogen and sulfur cycles, particularly in thermophilic environments. However, the performance and metabolic mechanisms of thermophilic SDAD systems remain underexplored. This study successfully enriched thermophilic sulfide-oxidizing denitrifiers from hot spring sediments (60 °C) in an expanded granular sludge bed (EGSB) reactor, achieving a stable nitrate removal rate of 250 mg N L[-][1] d[-][1]. This thermal system demonstrated a higher tolerance threshold for sulfides (250 mg TDS L[-1]) than mesophilic processes. The influent sulfide-to-nitrate (S/N) molar ratio critically influenced nitrogen removal efficiency with nitrite accumulation at low S/N ratios (1:1), whereas higher ratios (2:1) restored complete nitrate reduction. Microbial community analysis demonstrated Thermus (52.89 %) as the predominant genus in the SDAD system, marking the first report of its dominance in thermophilic nitrogen-sulfur coupling, alongside uc_Aquificales (21.78 %). Metagenomic insights further revealed two high-quality genomes: Thermus scotoductus exclusively executed complete sulfide-to-sulfate oxidation via the Sox system and partially catalyzed denitrification (narGHI); while Aquificaeae_UBA11096 adopted Sox-independent enzyme system and complete denitrification. Strikingly, Thermus scotoductus encoded nrfH, and it might be the overlooked " nitrogen retainer" in geothermal ecosystems. This work elucidates the cooperative and competitive interactions between thermophilic denitrifiers, and establishes a multi-level thermal adaptability analysis. These findings advance understanding of their biogeochemical roles in geothermal ecosystems, and provide a sustainable strategy for nitrogen removal in high-temperature wastewater treatment.}, }
@article {pmid41223750, year = {2025}, author = {Yao, S and Luo, Y and Zhou, Y and Wang, Y and Yang, L and Kong, Q and Zhang, H}, title = {Microbial functional shifts in a paradigmatic petrochemical brownfield: Mechanisms of adaptation in soil and groundwater.}, journal = {Ecotoxicology and environmental safety}, volume = {306}, number = {}, pages = {119380}, doi = {10.1016/j.ecoenv.2025.119380}, pmid = {41223750}, issn = {1090-2414}, abstract = {The long-term presence of pollutants from the petrochemical industry, including benzene, nitro compounds, and amine-based aromatics, poses a significant threat to soil and groundwater, resulting in shifts in microbial community structures. In this study, 48 soil and groundwater samples from contaminated environments were analyzed using metagenomic technology and gas chromatography-mass spectrometry to examine the metabolic strategies employed by microorganisms in response to these pollutants. The results revealed that microbial community composition was significantly influenced by varying contamination levels, primarily determined by the distance from contamination sources and the diffusion characteristics of the environmental media. In highly contaminated areas, specific bacterial genera, including Pseudomonas and Stutzerimonas, became dominant, suggesting an adaptation toward pollutant degradation. Soil and groundwater microorganisms exhibited distinct adaptive mechanisms: in soils, enhanced motility, metabolism, and toxicant transport were associated with the expression of genes such as mcp, tktA, and pleD, while in groundwater, pollutant degradation and the maintenance of cellular function were driven by genes including xylA, dmpB, nfnB, and glnA. These findings emphasise the capacity of microbes to adapt to pollutants from petrochemical industry environments, thus providing valuable insights into microbial remediation strategies for environmental pollution management.}, }
@article {pmid41223625, year = {2025}, author = {Yang, B and Wang, H and Yan, Y and Bao, P and Feng, Q and Chen, B and Jia, Y and Shu, WS and Lu, H}, title = {Coupling Microalgae-based Biochar with MBGS Enhances Microbial Synergy and Multi-Pollutant Removal from Saline Aquaculture Wastewater.}, journal = {Water research}, volume = {289}, number = {Pt B}, pages = {124881}, doi = {10.1016/j.watres.2025.124881}, pmid = {41223625}, issn = {1879-2448}, abstract = {The microalgal-bacterial granular sludge (MBGS) system has gained attention as an energy-efficient, multifunctional approach for wastewater treatment, yet its stability and pollutant removal under combined salinity and antibiotic stress remain unclear. In this study, we developed an MBGS system integrated with nitrogen-rich microalgae-derived biochar to enhance removal of organic matter, nutrients, and enrofloxacin (ENR) from saline aquaculture wastewater. The biochar-coupled MBGS achieved high removal efficiencies: 94.2±4.8% COD, 87.1±3.6% NH4[+]-N, 60.3±4.6% PO4[3-]-P, and 60.1±3.5% ENR. Microbial community analysis revealed enrichment of ammonia-oxidizing bacteria (Nitrosomonas, 3.3-9.7%), nitrite-oxidizing bacteria (Nitrospira, 2.3-6.4%), denitrifiers (Thauera, 14.9-27.6%), phosphate-accumulating organisms (Acinetobacter, 0.8-7.7%), and photosynthetic microalgae (Chlorophyceae, 1.4-23.6%). Fluorescence in situ hybridization (FISH) confirmed that biochar enhanced the spatial organization of these functional microbes within MBGS. Metagenomics revealed increased abundance of genes associated with carbon (porCD, CS, korD), nitrogen (amoAB, narGHI, norBC), phosphorus (ppk, phaA, acs), and photosynthesis-related (petABCD, psaA) genes, indicating improved metabolic capacity and synergy. Genome-resolved metagenomics further identified Nitrosomonas europaea, Acinetobacter sp002296655, Thauera aminoaromatica, and Chlorobium sp013334435 as core taxa driving carbon, nitrogen, and phosphorus cycling and energy flow, promoting synergistic interactions and enhancing pollutant removal under stress. Coupling MBGS with microalgae-based biochar improves resilience and multi-pollutant removal, offering a robust, sustainable strategy for advanced aquaculture wastewater treatment.}, }
@article {pmid41223471, year = {2025}, author = {Zhang, Y and Gao, M and Zhang, X and Tang, A and Wang, S and Wang, X}, title = {How microalgae-bacteria consortia adapt sulfamethoxazole pressure: Insights from physiological and genetic responses.}, journal = {Journal of hazardous materials}, volume = {500}, number = {}, pages = {140406}, doi = {10.1016/j.jhazmat.2025.140406}, pmid = {41223471}, issn = {1873-3336}, abstract = {Microalgae-bacteria consortia (MBC) are regarded as an energy-saving alternative for wastewater treatment process, while their reliability is challenged under long-term antibiotic pressure. Unfortunately, the underlying physiological and genetic mechanisms enabling adaptation to such prolonged antibiotic pressure remain largely unknown. This study systematically investigates the adaptive responses of MBC systems to sulfamethoxazole (SMX) pressure during two exposure stages (100 and 200 μg/L). While the system remained stable at 100 μg/L SMX (stage I), its performance declined at 200 μg/L (stage II), with COD and ammonium removal decreasing by 7.5 % and 8.8 %, respectively. This was accompanied by adverse physiological responses, including a 36.3 ± 3.2 % decrease in photosynthetic oxygen production, a 96.2 ± 9.7 % increase in ROS levels, and a 49.0 ± 5.3 % reduction in EPS content. Remarkably, both pollutant removal and physiological state were fully restored following a 100-day recovery period. This resilience may be attributed to the enrichment of microbial communities such as Chlorophyta and Bacillariophyta, whose presence strongly correlated with reduced antibiotic resistance gene (ARG) dissemination. Genetic analysis further indicated that suppressed ATP synthase and electron transfer within the oxidative phosphorylation pathway may represent important adaptive costs. Fortunately, the response regulators within the two-component system functioned as central mediators, coordinating both extracellular EPS secretion and intracellular antioxidant activity. Overall, this study advances current understandings of adaptive mechanism and offers insights for facilitating stable operation under long-term antibiotic pressure.}, }
@article {pmid41222958, year = {2025}, author = {Yang, Y and Li, Q and Xiao, Y and Shen, Y and Zhang, Y and Zhang, W and Lei, N and Pei, X and Xie, Y}, title = {Elucidating the Mechanism of PFOA Regulation of Biofilms in Aquatic Systems at Gene and Metabolic Levels.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c06467}, pmid = {41222958}, issn = {1520-5851}, abstract = {Perfluorooctanoic acid (PFOA) is prevalent in aquatic ecosystems and exhibits significant toxicity to aquatic organisms. Microorganisms can adhere to the surfaces of submerged plants, forming complex extracellular structures referred to as attached biofilms. However, the mechanisms underlying the regulation of biofilm formation by PFOA remain unclear. This study cultured plant-attached biofilms under PFOA stress to investigate the mechanisms by which PFOA regulates biofilm formation, utilizing metagenomics and metabolomics. Results show that the biofilm structure was significantly altered under PFOA exposure, characterized by an increase in polysaccharide and protein content. Furthermore, PFOA bound to proteins within extracellular polymeric substances contributes to a reduction in PFOA toxicity. PFOA regulates biofilm formation by modifying the content of signaling molecules and the abundance of genes (bapA and ABC.PE.S) associated with quorum sensing, establishing a natural barrier against the toxic effects of PFOA. In addition, PFOA was found to inhibit the metabolism of linoleic and linolenic acids, thus indirectly promoting the formation of biofilms, which allowed microbial aggregation and coresistance to the toxic effects of exogenous pollutants. This study provides a comprehensive understanding on the mechanisms by which PFOA regulates biofilm formation, which is crucial for enhancing our understanding of microbial processes in aquatic ecosystems.}, }
@article {pmid41222645, year = {2025}, author = {Rana, S and Das, KK and Singh, SK and Bhattacharyya, D}, title = {Deciphering Fungal Communities in Three Species of Phlogacanthus Nees (Acanthaceae) Using Amplicon-Metagenomic Analysis.}, journal = {Current microbiology}, volume = {83}, number = {1}, pages = {16}, pmid = {41222645}, issn = {1432-0991}, abstract = {Fungal communities play vital roles in plant health, nutrient cycling, and ecological balance. Species of Phlogacanthus Nees, valued for their medicinal and ecological importance, harbor diverse fungal microbiomes that may influence growth, resilience, and metabolite production. This study investigated fungal communities associated with three Phlogacanthus species-P. tubiflorus Nees (SKS-1), P. thyrsiformis (Roxb. ex Hardw.) Mabb. (SKS-2), and P. curviflorus (Wall.) Nees (SKS-3)-using high-throughput amplicon-metagenomic sequencing of the ITS2 region on the Illumina MiSeq platform. A total of 153 operational taxonomic units (OTUs) were identified, with SKS-2 showing the highest richness (129 OTUs), followed by SKS-1 (112) and SKS-3 (95). Seventy OTUs were shared across all species, while 10, 22, and 8 were unique to SKS-1, SKS-2, and SKS-3, respectively. Alpha diversity indices (Chao1, ACE, Shannon, Simpson, Inverse Simpson, Fisher's alpha) confirmed SKS-2 as the most species-rich fungal habitat. A high proportion of unclassified taxa in SKS-2, along with dominance of Pleosporales, suggests the presence of novel fungi with ecological and biotechnological significance. Beta diversity analysis using Bray-Curtis dissimilarity and Principal Coordinate Analysis revealed significant differences among the fungal communities of the three species. Overall, SKS-2 emerged as the most diverse habitat, while SKS-3 supported a unique but less diverse assemblage. This is the first report profiling fungal microbiomes of Phlogacanthus species. The results highlight their potential as reservoirs of endophytes with applications in plant growth promotion, stress tolerance, biocontrol, enzyme production, and bioactive metabolite discovery, offering leads for sustainable agriculture and biotechnology.}, }
@article {pmid41222234, year = {2025}, author = {Sinno, A and Baghdadi, R and Narch, R and El Rayes, S and Tokajian, S and Al Khoury, C}, title = {Charting the virosphere: computational synergies of AI and bioinformatics in viral discovery and evolution.}, journal = {Journal of virology}, volume = {}, number = {}, pages = {e0155425}, doi = {10.1128/jvi.01554-25}, pmid = {41222234}, issn = {1098-5514}, abstract = {The advancement of metagenomic sequencing has revealed a vast viral diversity while simultaneously exposing limitations of homology-based tools such as BLAST and HMMER, which often fail to detect highly divergent viral genomes. The integration of artificial intelligence (AI) into viromics has transformed this landscape, introducing machine learning and deep learning models-including convolutional neural networks (CNNs), recurrent neural networks (RNNs), and transformers-that extend viral discovery beyond sequence similarity constraints. Structure-based frameworks such as AlphaFold, ESMFold, and Foldseek further enable annotation of divergent viral proteins through conserved 3D folds, while graph neural networks (GNNs) model host-virus interaction and explainable AI enhances interpretability of prediction. Despite their high sensitivity and scalability, AI-driven approaches face notable challenges: computational burden, data set bias, limited explainability, and elevated false discovery rates. This review traces the evolution of computational virology from traditional methods to AI-based and hybrid frameworks. We examine landmark AI tools while underscoring the continuing importance of phylogenetics and functional annotation in contextualizing AI predictions. We propose an integrated workflow that combines AI pattern recognition with classical bioinformatics to enhance both scalability and interpretability. By addressing the limitations of solely AI-driven or traditional approaches, this review presents a unified computational strategy to accelerate viral discovery, enhance evolutionary insights, and strengthen global preparedness for emerging infectious diseases.}, }
@article {pmid41222171, year = {2025}, author = {Lazov, CM and Larsen, LE and Johnston, CM and Rasmussen, TB and Hjulsager, CK}, title = {Announcement of two complete coding genomes of mink coronavirus and one partial coding genome of mink enteric calicivirus from mink in Denmark.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0045925}, doi = {10.1128/mra.00459-25}, pmid = {41222171}, issn = {2576-098X}, abstract = {Two complete coding genomes of mink coronavirus and one partial coding genome of the sapovirus mink enteric calicivirus were assembled from metagenomic sequencing data from mink on different farms with diarrhea outbreaks in 2015 in Denmark.}, }
@article {pmid41222160, year = {2025}, author = {Liu, W and Nagasaka, K and Wu, J and Ban, H and Mimick, E and Meng, L and Neches, RY and Moniruzzaman, M and Yoshida, T and Nishimura, Y and Endo, H and Okazaki, Y and Ogata, H}, title = {Giant viruses specific to deep oceans show persistent presence and activity.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0093225}, doi = {10.1128/msystems.00932-25}, pmid = {41222160}, issn = {2379-5077}, abstract = {Giant viruses (GVs) of the phyla Nucleocytoviricota and Mirusviricota are large double-stranded DNA viruses that infect diverse eukaryotic hosts and impact biogeochemical cycles. Their diversity and ecological roles have been well studied in the photic layer of the ocean, but less is known about their activity, population dynamics, and adaptive strategies in the aphotic layers. Here, we conducted eight seasonal time-series samplings of the surface and mesopelagic layers at a coastal site in Muroto, Japan, and integrated 18S metabarcoding, metagenomic, and metatranscriptomic data to investigate mesopelagic GVs and their potential hosts. The analysis identified 48 GV genomes including six that were exclusively detected in the mesopelagic layer. Notably, these mesopelagic-specific GVs showed persistent activity across seasons. To further investigate the distribution and phylogenomic features of GVs at a global scale across broader depths, we compiled 4,473 species-level GV genomes from the OceanDNA MAG project and other resources and analyzed 1,890 marine metagenomes. This revealed 101 deep-sea-specific GVs, distributed across the GV phylogenetic tree, indicating that adaptation to deep-sea environments has occurred in multiple lineages. One clade enriched with deep-sea-specific GVs included a GV genome identified in our Muroto data, which displayed a wide geographic distribution. Seventy-six KEGG orthologs and 74 Pfam domains were specifically enriched in deep-sea-specific GVs, encompassing functions related to the ubiquitin system, energy metabolism, and nitrogen acquisition. These findings support the scenario that distinct GV lineages have adapted to hosts in aphotic marine environments by altering their gene repertoire to thrive in this unique habitat.IMPORTANCEGiant viruses are widespread in the ocean surface and are key in shaping marine ecosystems by infecting phytoplankton and other protists. However, little is known about their activity and adaptive strategies in deep-sea environments. In this study, we performed metagenomic and metatranscriptomic analyses of seawater samples collected from a coastal site in Japan and discovered giant virus genomes showing persistent transcriptional activity across seasons in the mesopelagic water. Using a global marine data set, we further uncovered geographically widespread and vertically extensive groups of deep-sea-specific giant viruses and characterized their distinctive gene repertoire, which likely facilitates adaptation to the limited availability of light and organic compounds in the aphotic zone. These findings expand our understanding of giant virus ecology in the dark ocean.}, }
@article {pmid41222147, year = {2025}, author = {Vogel, H and Weiss, B and Rama, F and Rinklef, A and Engl, T and Kaltenpoth, M and Vilcinskas, A}, title = {A multi-partner symbiotic community inhabits the emerging insect pest Pentastiridius leporinus.}, journal = {mBio}, volume = {}, number = {}, pages = {e0310325}, doi = {10.1128/mbio.03103-25}, pmid = {41222147}, issn = {2150-7511}, abstract = {The planthopper Pentastiridius leporinus has emerged as a severe crop pest, rapidly expanding both its host plant range and the affected areas in central Europe. Originating as a monophagous herbivore of reed grass, P. leporinus recently adopted polyphagous feeding and is now a pest of sugar beet, potato, carrot, and onion, suggesting rapid ecological niche expansion. P. leporinus vectors two bacterial pathogens: the γ-proteobacterium Candidatus Arsenophonus phytopathogenicus (CAP) and the stolbur phytoplasma Candidatus Phytoplasma solani (CPS), which are responsible for a range of disease syndromes, including syndrome basses richesses in sugar beet. We used long-read metagenomic sequencing to characterize the genomes of microbes associated with P. leporinus, resulting in the complete sequences of CAP and CPS, as well as obligate symbionts of the genera Purcelliella, Karelsulcia, and Vidania, and facultative symbionts Rickettsia and Wolbachia. The obligate symbionts are inferred to provide or contribute to the biosynthesis of 10 essential amino acids and to B vitamin. The genomes of CPS and CAP encode numerous pathogenicity factors, enabling the colonization of different hosts. Bacterial fluorescence in situ hybridization revealed the tissue distribution, cellular localization, relative abundance, and transmission patterns of these bacteria. The intracellular presence of all obligate symbionts in bacteriomes, the intracellular presence of Wolbachia, and the intranuclear localization of Rickettsia suggest vertical transmission. CPS was restricted to salivary glands, suggesting strict horizontal, plant-mediated transmission, whereas CAP colonized all tissue types, allowing for horizontal and vertical transmission. Our data suggest that P. leporinus hosts an exceptionally broad range of symbionts, encompassing mutualistic, commensal, and pathogenic interactions.IMPORTANCEThe planthopper Pentastiridius leporinus has recently expanded its host plant range and emerged as a severe pest of sugar beet and potato crops in central Europe, which is exacerbated by its capacity to vector bacterial pathogens to its host plants. Because microbial symbionts may play an important role for both the host plant shifts and the transmission of pathogens, we used metagenomic sequencing and fluorescence in situ hybridization to characterize the microbial community associated with P. leporinus. We detected three bacteriome-localized obligate symbionts that together provision all essential amino acids and several B-vitamins to the host, as well as two intracellular bacteria with a broader tissue distribution. In addition, we infer localization, transmission, and putative pathogenicity factors for the two major phytopathogens that are vectored by P. leporinus. Our results reveal a complex community of symbiotic bacteria that likely shapes the interaction of this emerging pest with its host plants.}, }
@article {pmid41222145, year = {2025}, author = {Koo, H and Heber, K and Tian, S and Connolly, ST and Hao, F and Zhao, J and Swencki-Underwood, B and Patterson, AD and Townsend, GE and Bisanz, JE}, title = {A synthetic gut microbiota provides an understanding of the maintenance and functional impact of phage.}, journal = {mBio}, volume = {}, number = {}, pages = {e0234125}, doi = {10.1128/mbio.02341-25}, pmid = {41222145}, issn = {2150-7511}, abstract = {UNLABELLED: Phages are under intense study as therapeutics and mediators of microbial community behavior; however, tractable models are needed to study phages in the context of the mammalian gut. To address this gap, we isolated phages against members of a synthetic gut microbial community (sFMT), identifying the Bacteroides uniformis JEB00023 (DSM 6597) phage HKP09. While resistance to HKP09 was observable within hours of infection in monoculture, high titers of HKP09 were maintained in vitro and in gnotobiotic mouse models over extended periods. Sequencing of resistant B. uniformis lines revealed phase variation upstream of a capsular polysaccharide locus driving the generation of resistant and sensitive subpopulations, thus demonstrating a mechanism allowing stable coexistence of both virus and bacterial host. Communities infected in vitro and in vivo with HKP09 showed transiently reduced loads of B. uniformis DSM 6597. Its impact in the gut was distinct from communities constructed without its host B. uniformis strain (sFMT∆JEB00023). Rather than a compensatory increase in closely related Bacteroides strains, the most significant impacts were observed on distantly related strains, demonstrating that phage perturbations more broadly impact community structure in ways not easily predicted by phylogeny or simple strain exclusion. Metabolomic analyses of the feces of HKP09-infected sFMT-colonized gnotobiotic animals demonstrated altered abundances of amino acids and microbial fermentation products compared to uninfected mice and those colonized with sFMT∆JEB00023. Taken together, these data provide a controlled model for studying phages in the context of the mammalian gut, providing mechanistic insights into phage-host dynamics and their consequences on the function of microbial communities.<br><br>IMPORTANCE: Phages are key members of the gut microbiome, but the understanding of their biological significance for host health lags behind their bacterial hosts. In this study, we demonstrate the use of a phage-infection model using defined, synthetic microbial communities that colonize the intestinal tract of mice. We uncovered that spontaneous inversions in the genome of Bacteroides uniformis perpetually generate subpopulations, which are either sensitive or resistant to phage infection, allowing for the coexistence of predator and prey in this species. Phage infection demonstrated broad impacts on community structure and metabolism in animals, which are not easily predicted by the exclusion of the viral host. This research demonstrates a tractable approach through which the impacts of phage on both the microbiome and mammalian host can be deciphered.}, }
@article {pmid41222144, year = {2025}, author = {Ericsson, AC and McAdams, ZL and Dorfmeyer, RA and Hart, ML and O'Neill-Blair, A and Amos-Landgraf, J and Franklin, CL}, title = {Dominant effects of the immediate environment on the gut microbiome of mice used in biomedical research.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0111225}, doi = {10.1128/msystems.01112-25}, pmid = {41222144}, issn = {2379-5077}, abstract = {Studies using genetically engineered mouse (GEM) models are often performed over extended periods. The microbiomes of GEM colonies are expected to retain some of the microbial features present in the founder mice used to generate each GEM model and to acquire new features through dietary and environmental sources. The rate at which these processes occur over time likely varies between institutions. To assess the relative effect size of environment on the microbiome of GEMs used in biomedical research, we performed 16S rRNA metabarcoding of fecal samples from 275 distinct GEM lines (n = 351) maintained by 139 different laboratories at 84 different research institutions in 34 U.S. states or districts and seven other countries, and compared intra-strain, inter-strain, inter-lab, and inter-institution similarities. Reference data from mice harboring supplier-origin (SO) microbiomes (n = 1,171) were used to determine the relative contribution and nature of microbes from known and unknown sources. Paradoxically, the data indicate that the immediate laboratory-level environment is the dominant factor shaping the microbiome of GEM models, but that the microbiome of GEMs develops similarities in beta-diversity, regardless of other factors. Related to this, we detected an unexpectedly high prevalence and abundance of Helicobacter spp. in GEM microbiomes, the abundance of which correlated significantly with the abundance of multiple resident taxa colonizing the mucosa. These findings suggest a higher prevalence of Helicobacter spp. in laboratory mice than previously appreciated, and the possibility of positive and negative interactions with other taxa is found to affect GEM model phenotypes.IMPORTANCEThere are concerns regarding the reproducibility and predictive value of mouse models of human disease. Notwithstanding those legitimate concerns, genetically engineered mouse (GEM) models provide an invaluable platform to investigate gene function or effects of environmental factors in a biological system. The microbiome of GEM models significantly influences model phenotypes and thus represents a possible source of poor reproducibility. While the microbiome is often incorporated in research investigating disease mechanisms using GEMs, limited information is available regarding the similarity of the microbiome of GEM models within and between research labs at the same institution, or across institutions. Moreover, while the microbiome of founder mice from different suppliers is known to differ, the degree to which features present in supplier-origin microbiomes are retained in GEM colonies throughout experimentation is unclear. These data demonstrate the robust effect of lab-level environment and the need for sample collection concurrent with phenotyping.}, }
@article {pmid41222143, year = {2025}, author = {Liu, P and Zhang, R and Meng, F and Zhang, C and Roberts, AP and Wang, Y and Zhu, K and Cao, Z and Pan, Y and Li, J}, title = {Deep-branching magnetotactic bacteria form intracellular carbonates enriched in trace metals.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0113125}, doi = {10.1128/msystems.01131-25}, pmid = {41222143}, issn = {2379-5077}, abstract = {UNLABELLED: Microbial biomineralization is a fundamental driver of global biogeochemical cycles, yet the ability of prokaryotes to form intracellular carbonates remains rarely documented. Here, we report three ecotypes of magnetotactic bacteria (MTB) affiliated with the Pseudomonadota and the deep-branching Nitrospirota phyla that concurrently synthesize magnetite magnetosomes and intracellular calcium carbonate inclusions enriched in Ba, Mg, and Ni. These carbonate granules are typically spherical and contrast with the highly ordered morphology of magnetite crystals. Comparative genomic analyses reveal that these MTB encode multiple metal-permease systems (e.g., GDT1, CorA, ZnuA2), which suggests both a capacity for selective uptake of divalent cations from their environment and a process likely linked to intracellular carbonate precipitation. By uncovering new examples of bacterial intracellular calcification, our findings expand the known diversity and genetic basis of prokaryotic biomineralization. Moreover, they highlight a potential role of MTB in mediating heavy-metal cycling and provide a refined framework for understanding microbially driven carbonate formation.<br><br>IMPORTANCE: Intracellular biomineralization is a hallmark of animals and algae, yet among prokaryotes, it has traditionally been associated with a limited range of lineages and minerals. This study reveals that magnetotactic bacteria (MTB) from both the Pseudomonadota and the deep-branching Nitrospirota phyla are capable of intracellularly forming carbonate granules enriched in diverse divalent cations, including environmentally scarce trace metals Ba&#xb2;&#x207a; and Ni&#xb2;&#x207a;, and biologically essential Mg&#xb2;&#x207a;. These findings significantly expand the known taxonomic and functional diversity of prokaryotic intracellular calcifiers. By integrating electron microscopy, metagenomics, and structural protein modeling, we propose a potential metal-selective transport system that facilitates trace element accumulation and carbonate precipitation. This work establishes a previously underappreciated role for MTB in trace metal biogeochemical cycling (i.e., Ba&#xb2;&#x207a; and Ni&#xb2;&#x207a;) and suggests that intracellular calcification may be a more widespread bacterial trait than previously assumed.}, }
@article {pmid41221535, year = {2025}, author = {Xie, K and Zhang, Y and Tan, S and Luo, J and Ou, X and Tan, S}, title = {Gut microbiota involvement in the alteration of inflammatory cell infiltration and gut barrier integrity in liver cirrhosis.}, journal = {Biomedical reports}, volume = {23}, number = {6}, pages = {193}, pmid = {41221535}, issn = {2049-9442}, abstract = {The gut microbiota is essential for the development and regulation of the immune and intestinal homeostasis of the host. The present study aimed to investigate the composition, diversity and functional features of the microbiota in patients with liver cirrhosis. and healthy volunteers using high-throughput sequencing of the 16S rRNA gene, and evaluated inflammatory cell infiltration and the gut barrier in both the colonic mucosa and liver sections using histological analysis. Diversity and metagenome function of the gut microbiota significantly differed between healthy volunteers and patients with liver cirrhosis. Patients with cirrhosis showed decreased microbial richness, evenness, and diversity, with functional prediction indicating enrichment of phosphotransferase and membrane transport pathways, while amino acid and energy metabolism pathways were predominant in healthy controls. Furthermore, gut microbial dysbiosis associated with liver cirrhosis augmented inflammatory cell infiltration in the colonic mucosa and liver sections, impaired gut barrier function and enhanced intestinal permeability and bacterial translocation. The gut microbiota contributes to the pathophysiology of liver cirrhosis, which may impact prevention and treatment strategies for patients with liver cirrhosis.}, }
@article {pmid41221508, year = {2025}, author = {Siljanen, HMP and Manoharan, L and Hilts, AS and Bagnoud, A and Alves, RJE and Jones, CM and Kerou, M and Sousa, FL and Hallin, S and Biasi, C and Schleper, C}, title = {Targeted metagenomics using probe capture detect a larger diversity of nitrogen and methane cycling genes in complex microbial communities than traditional metagenomics.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf183}, pmid = {41221508}, issn = {2730-6151}, abstract = {Microorganisms are key players in the global cycling of nitrogen and carbon, controlling their availability and fluxes, including the emissions of the powerful greenhouse gases nitrous oxide and methane. Standard sequencing methods often reveal only a limited fraction of their diversity, because of their low relative abundance, the insufficient sequencing depth of traditional metagenomes of complex communities, and limitations in coverage of DNA amplification-based assays. Here, we developed and tested a targeted metagenomics approach based on probe capture and hybridization to simultaneously characterize the diversity of multiple key metabolic genes involved in inorganic nitrogen and methane cycling. We designed comprehensive probe libraries for each of the 14 target marker genes comprising 264 111 unique probes. In validation experiments with mock communities, targeted metagenomics yielded gene profiles similar to the original communities. Only GC content had a small effect on probe efficiency, as low GC targets were less efficiently detected than those with high GC, within the mock communities. Furthermore, the relative abundances of the marker genes obtained using targeted or traditional shotgun metagenomics were significantly correlated. In addition, using archaeal amoA genes as a case-study, targeted metagenomics identified a substantially higher taxonomic diversity and a larger number of sequence reads per sample, yielding diversity estimates 28 or 1.24 times higher than shotgun metagenomics or amplicon sequencing, respectively. Our results show that targeted metagenomics complements current approaches to characterize key microbial populations and functional guilds in biogeochemical cycles in different ecosystems, enabling more detailed, simultaneous characterization of multiple functional genes.}, }
@article {pmid41221507, year = {2025}, author = {Clinton, CK and Jackson, FLC}, title = {Persistent human-associated microbial signatures in burial soils from the 17th and 18th century New York African burial ground.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf181}, pmid = {41221507}, issn = {2730-6151}, abstract = {Understanding the long-term persistence of human-associated microbial signatures in burial soils offers a untapped insights into historical human health, decomposition, and ecological transformation. This study investigates whether centuries-old burial soils retain distinguishable microbial evidence of human decomposition using 16S rRNA gene sequencing on 81 samples from the New York African Burial Ground (NYABG), a 17th and 18th century cemetery for free and enslaved Africans. Comparative analyses against six control soils from nearby urban parks were conducted using QIIME2, ALDEx2, and ANCOM. Burial soils exhibited significantly greater alpha diversity (Faith's PD, Shannon, observed ASVs; P < .01) and distinct beta diversity patterns (Bray-Curtis, UniFrac; PERMANOVA P = .001). Enrichment of Firmicutes, Actinobacteriota, and gut-associated genera such as Bacillus and Ruminococcus characterized burial soils, whereas oligotrophic taxa dominated controls. Tentative identifications of human-associated pathogenic genera (e.g. Fusobacterium periodonticum, Prevotella pleuritidis) were observed exclusively in burial soils, suggesting their origin from the interred individuals but requiring further validation. These findings demonstrate that soil microbiomes reflect host-associated microbial communities long after decomposition, providing a scalable, nondestructive approach for reconstructing ancient microbial communities and host-associated health signatures. This work establishes the NYABG burial soil microbiome as a valuable model for microbial archaeology and introduces a replicable framework for integrating environmental microbiology, bioarchaeology, and historical epidemiology through the lens of postmortem microbial ecology.}, }
@article {pmid41221399, year = {2025}, author = {Huang, Y and Zhou, Q and Gui, M and Guo, D and Cheng, J and Ma, W and Shu, P and Liu, X}, title = {Dynamic multi-omics mechanisms underpinning retinol tolerance: stage-specific reconstruction of skin barrier function and host-microbiome metabolic interactions.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1668712}, pmid = {41221399}, issn = {1664-302X}, abstract = {BACKGROUND: Retinol remains an essential component in anti-aging skincare; however, a subset of users develop intolerance, characterized by compromised barrier integrity and inflammation. The temporal dynamics of how skin microbiota and host metabolism co-evolve during retinol tolerance establishment remain poorly understood.<br><br>METHODS: We conducted a prospective 28-day longitudinal study with 18 Chinese women (aged 25-40): 9 retinol-intolerant subjects monitored at baseline, adverse reaction phase, and tolerance establishment, while baseline data from 9 retinol-tolerant individuals served as controls. We integrated cutaneous phenotypic measurements, metagenomic sequencing, and untargeted metabolomics.<br><br>RESULTS: In the intolerant group, skin phenotype assessment revealed a distinct biphasic response-an acute phase marked by increased stratum corneum hydration, reduced sebum secretion, lower skin pH, and improved wrinkle metrics, followed by a re-equilibration phase characterized by sustained barrier restoration. Metagenomic profiling of 969 microbial species demonstrated that, although overall microbial &#x3b1;-diversity remained stable across time points in both groups, key taxa in the intolerant group exhibited transient "rise-and-fall" dynamics. At baseline, the intolerant group exhibited overrepresentation of Cutibacterium acnes, whereas the tolerant group was enriched in potentially protective species, including Sphingomonas hankookensis and Acinetobacter johnsonii. Untargeted metabolomics showed marked temporal fluctuations with an initial phase of metabolic turbulence, followed by partial recovery. During the early adverse reaction phase in intolerant subjects, lipid and fatty acid metabolic pathways-specifically, glycerophospholipid, linoleic acid, &#x3b1;-linolenic acid, and ether lipid metabolism-were significantly upregulated, concomitant with the suppression of TCA cycle and sphingolipid activity. Conversely, as tolerance was established, enhanced activity in the TCA cycle, sphingolipid, ascorbate, and pentose metabolism pathways-coupled with a reduction in pro-inflammatory arachidonic acid derivatives-indicated metabolic reconstitution and restoration of barrier integrity.<br><br>DISCUSSION: Integrated multi-omics correlation analyses further underscored the tightly interconnected regulation of host-microbe energy metabolism, antioxidant defenses, and membrane repair in response to retinol-induced stress. These findings elucidate the temporal interplay between host and microbial processes underpinning retinol tolerance and highlight baseline biomarkers that may facilitate personalized skincare interventions.}, }
@article {pmid41221168, year = {2025}, author = {Yu, X and Cheng, J and He, J and Wu, X and Wang, W and Chen, M and Zhuo, B and Ge, Y}, title = {First Documented Case of Pneumonia with Nocardia africana and SARS-CoV-2 Co-Detection in Mainland China.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {5721-5730}, pmid = {41221168}, issn = {1178-6973}, abstract = {Nocardia spp. are zoonotic pathogens that can cause infections ranging from localized lesions to systemic dissemination, primarily via pulmonary inhalation or percutaneous inoculation. We report the first confirmed case of Nocardia africana pneumonia with SARS-CoV-2 co-detection in mainland China, diagnosed through bronchoalveolar lavage fluid (BALF) analysis using metagenomic next-generation sequencing (mNGS) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). A 76-year-old male presented with persistent cough and fever, accompanied by radiographic evidence of progressive pneumonia. Targeted antimicrobial therapy with trimethoprim-sulfamethoxazole and amoxicillin-clavulanate resulted in clinical resolution within 12 days. This case underscores three critical implications for post-COVID-19 pandemic medicine: the requirement for heightened vigilance for opportunistic pathogens (eg, Nocardia species) in pneumonia patients with recurrent fever, the essential role of advanced diagnostics (eg, mNGS and MALDI-TOF MS) in identifying fastidious organisms like actinomycetes, and the potential for antimicrobial resistance in N. africana, which necessitates susceptibility-guided therapy.}, }
@article {pmid41220843, year = {2025}, author = {Kwon, K and Kim, M and Jung, Y and Yoon, MY and Lee, JY and Yoon, SS and Rho, M and Chung, YW and Ryu, JH}, title = {Intestinal Dysbiosis Caused by Epithelial Fabp6 Gene Disruption Exacerbates Gut Inflammatory Disease.}, journal = {Immune network}, volume = {25}, number = {5}, pages = {e35}, pmid = {41220843}, issn = {1598-2629}, abstract = {Ileal lipid binding protein (Ilbp), encoded by Fabp6 gene, plays a critical role in intracellular transport of bile acids (BAs) from apical to basolateral side of ileal enterocytes, maintaining BA homeostasis within enterohepatic circulation. However, pathophysiological consequences of Ilbp deficiency remain largely unexplored. Here, we demonstrate that disruption of BA balance, caused by intestinal epithelial cell (IEC)-specific Fabp6 gene knockout (Fabp6 [ΔIEC]), exacerbates dextran sulfate sodium (DSS)-induced gut inflammation. Fecal microbiota transplantation from Fabp6 [ΔIEC] mice to germ free recipient mice replicated the adverse effects observed in Fabp6 [ΔIEC] mice, which were mitigated when these mice were co-housed with control (Fabp6 [f/f]) mice. Metagenomic analysis identified Ligilactobacillus murinus as a primarily diminished strain in Fabp6 [ΔIEC] mice. Oral administration of L. murinus isolated from feces of Fabp6 [f/f] mice ameliorated DSS-induced colitis in Fabp6 [ΔIEC] mice by restoring epithelial barrier integrity and lowering pro-inflammatory cytokines IL-1β, IL-6 and TNF-α. Furthermore, daily administration of taurodeoxycholic acid-one of the BAs reduced in Fabp6 [ΔIEC] mice and that promotes the growth of L. murinus in an in vitro growth assay-also exhibited a protective effect against DSS-induced colitis through a similar mechanism. These findings suggest that deficiency of specific BAs due to epithelial Fabp6 deletion leads to gut dysbiosis, predisposing the host to inflammatory disease.}, }
@article {pmid41220286, year = {2025}, author = {Lee, JY and Yoo, JH and Kim, JE and Bae, JW and Lee, CK}, title = {Translating Gut Microbiota into Diagnostics: A Multidimensional Approach for the Diagnosis of Inflammatory Bowel Disease.}, journal = {Gut and liver}, volume = {}, number = {}, pages = {}, doi = {10.5009/gnl250360}, pmid = {41220286}, issn = {2005-1212}, abstract = {The gut microbiota has emerged as a key factor in the pathophysiology of inflammatory bowel disease (IBD), providing novel opportunities for diagnostic innovation. Traditional biomarkers, such as C-reactive protein and fecal calprotectin, are widely used in clinical practice; however, their ability to reflect disease complexity and microbial dysregulation remains limited. Recent advances in metagenomics and multi-omics integration have enabled high-resolution profiling of microbial communities and their functional capacities and associated metabolites. Differential abundance analysis and machine learning models have been used to identify microbial biomarkers that can distinguish patients with IBD from healthy individuals. Multicohort studies integrating microbiome and metabolomic data have further improved diagnostic accuracy and generalizability. Transcriptomic and proteomic analyses provide complementary insights into host-microbe interactions and disease mechanisms. In this review, we explored the potential of metagenomic biodata as diagnostic markers for IBD, with an emphasis on a multidimensional analytical approach. We highlight the recent developments in sequencing technologies, computational pipelines for microbial feature selection, and machine learning strategies applied to biomarker discovery. The integration of multi-omics data deepens our understanding of host-microbe interactions and facilitates the development of microbiota-informed diagnostic tools. As multidimensional microbial profiling evolves, its clinical utility for the diagnosis and stratification of IBD requires further investigation.}, }
@article {pmid41219964, year = {2025}, author = {George, NA and Zhou, Z and Anantharaman, K and Hug, LA}, title = {Discarded diversity: novel megaphages, auxiliary metabolic genes, and virally encoded CRISPR-Cas systems in landfills.}, journal = {Virology journal}, volume = {22}, number = {1}, pages = {370}, pmid = {41219964}, issn = {1743-422X}, support = {R35GM143024/GM/NIGMS NIH HHS/United States ; 2016-03686//Natural Sciences and Engineering Research Council of Canada/ ; Tier II chair//Canada Research Chairs/ ; }, abstract = {BACKGROUND: Viruses are the most abundant microbial entities on the planet, impacting microbial community structure and ecosystem services. Despite outnumbering bacteria and archaea by an order of magnitude, viruses have been comparatively underrepresented in reference databases. Metagenomic examinations have illustrated that viruses of bacteria and archaea have been specifically understudied in engineered environments. Here we employed metagenomic and computational biology methods to examine the diversity, host interactions, and genetic systems of viruses predicted from 27 samples taken from three municipal landfills across North America.<br><br>RESULTS: We identified numerous viruses that are not represented in reference databases, including the third largest bacteriophage genome identified to date (~&#x2009;678 kbp), and noted a large diversity of viruses in landfills that has limited overlap across landfills and is distinct from viromes in other systems. Host-virus interactions were examined via host CRISPR spacer to viral protospacer mapping which captured hyper-targeted viral populations and six viral populations predicted to infect hosts across multiple phyla. Auxiliary metabolic genes (AMGs) were identified with the potential to augment hosts' methane, sulfur, and contaminant degradation metabolisms, including AMGs not previously reported in the literature. CRISPR arrays and CRISPR-Cas systems were identified from predicted viral genomes, including the two largest bacteriophage genomes to contain these genetic features. Some virally encoded Cas effector-like proteins appear distinct relative to previously reported Cas effectors and are interesting targets for potential genome editing tools.<br><br>CONCLUSIONS: Our observations indicate landfills, as heterogeneous contaminated sites with unique selective pressures, are key locations for diverse viruses and atypical virus-host dynamics.}, }
@article {pmid41219190, year = {2025}, author = {Chung, D and Brask, N and Matar, S and Gallot-Lavallée, L and Pringle, ES and Duguay, BA and Blais, C and Latimer, J and Haro, R and Slamovits, CH and Leyland, B and Rest, JS and Collier, JL and McCormick, C and Archibald, JM}, title = {Persistent mirusvirus infection in the marine protist Aurantiochytrium.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {9922}, pmid = {41219190}, issn = {2041-1723}, support = {GBMF5782//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; }, abstract = {Mirusviruses are abundant and broadly distributed double-stranded (ds) DNA viruses recently discovered in marine metagenomic data. Their host range and ecological impact are unclear. The protist Aurantiochytrium limacinum possesses two mirusvirus-like genomic elements, one a circular episome (AurliV-1) and the other (AurliV-2) a chromosomal integrant. Here we show that genes in both genomes are expressed and viral particles containing mainly AurliV-1 DNA are produced under starvation conditions and when cells are cultured in standard growth medium. We detected viral particles of ~140 nm in the nucleus, in cytoplasmic vesicles, between the plasma membrane and cell wall, and in the extracellular environment. Of 67 AurliV-1-encoded proteins detected using proteomics, 45 are enriched under starvation conditions, including the structurally important major capsid and triplex proteins. Our results establish Aurantiochytrium as a model system for elucidating mirusvirus-host interactions and demonstrate persistent viral infection in a microbial eukaryote.}, }
@article {pmid41218604, year = {2025}, author = {Lyu, L and Fan, Y and Bryrup, T and Clos-Garcia, M and Brix, S and Eiken, M and Stankevic, E and Lund, AB and Knop, FK and Jørgensen, NR and Vestergaard, H and Hansen, T and Hansen, T and Nielsen, T and Pedersen, O}, title = {Glucocorticoid-induced changes of the gut microbiota and metabolic markers in healthy young men: Outcome of a randomized controlled trial.}, journal = {Cell reports. Medicine}, volume = {}, number = {}, pages = {102426}, doi = {10.1016/j.xcrm.2025.102426}, pmid = {41218604}, issn = {2666-3791}, abstract = {Glucocorticoids induce insulin resistance and suppress immunity, but their impact on gut microbiota, which may modulate metabolism and immunity remains under explored. In this 7-day trial, we assess glucocorticoid-induced changes in gut microbiota and metabolic markers in 56 healthy men, randomly assigned to three interventions: oral prednisolone (PO group), intramuscular methylprednisolone acetate (IM group), or saline (CTL group). Shotgun metagenomics reveal that PO glucocorticoid causes shifts in bacterial abundance, increasing Blautia and Collinsella, while decreasing Dysosmobacter welbionis and Anaerotignum faecicola, linked with insulin resistance and immunosuppression markers. Additionally, PO treatment alters microbial pathways and enzymes related to glycolysis and lipid metabolism, with changes in predicted metabolites such as hypoxanthine and phenylacetate. IM treatment results in minimal microbiota changes. These findings underscore the route-dependent effects of glucocorticoids on gut microbiota and their potential impact on host metabolism and immunity. The trial was approved by the Danish Medicine Agency (EudraCT protocol number: 2016-001850-16).}, }
@article {pmid41214576, year = {2025}, author = {Feng, Y and Zhang, R and Wen, G and Xie, L and Chen, T and Liu, W}, title = {The role of gut microbiota tyrosine decarboxylases in levodopa pharmacokinetics: insights from a levodopa challenge test.}, journal = {BMC neurology}, volume = {25}, number = {1}, pages = {460}, pmid = {41214576}, issn = {1471-2377}, support = {822QN459//Youth Project of Hainan Natural Science Foundation/ ; 82371268//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: The gut microbiota is known to influence levodopa metabolism in the intestinal tract, primarily through the action of tyrosine decarboxylase, an enzyme encoded by the tyrosine decarboxylase gene (tyrDC). However, the effect of the abundance of the tyrDC gene on levodopa pharmacokinetics remains unclear.<br><br>METHODS: The aim of this study was to investigate this relationship in Parkinson&#x2019;s disease (PD) patients undergoing a levodopa challenge test. Our study enrolled 12 PD patients with a good response to levodopa. Plasma levodopa pharmacokinetics were determined via liquid chromatography&#x2012;tandem mass spectrometry, while tyrDC gene abundance in faecal samples was assessed via metagenomic shotgun sequencing.<br><br>RESULTS: A total of 12 PD patients (age: 58.00&#x2009;&#xb1;&#x2009;8.80 years) with an Hoehn and Yahr stage of 2.25 (2.0&#x2013;3.0) and a disease duration of 8.46&#x2009;&#xb1;&#x2009;4.94 years were enrolled. After levodopa administration, the MDS-UPDRS-III score decreased 71.28%&#xb1;17.09%. We found no significant association between tyrDC gene abundance and levodopa pharmacokinetics.<br><br>CONCLUSION: These findings indicate that the influence of the intestinal microbiota on PD patients with a good response to levodopa during the levodopa challenge test may be minimal, which may provide new insight into levodopa therapy.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12883-025-04428-6.}, }
@article {pmid41206538, year = {2025}, author = {Hall, MB and Zhou, C and Coin, LJM}, title = {Genome size estimation from long read overlaps.}, journal = {Bioinformatics (Oxford, England)}, volume = {41}, number = {11}, pages = {}, doi = {10.1093/bioinformatics/btaf593}, pmid = {41206538}, issn = {1367-4811}, support = {FSPGN000045//Australian Government Medical Research Future Fund (MRFF) Genomics Health Futures Mission (GHFM) Flagships-Pathogen Genomics/ ; //META-GP/ ; //DELIVERING A CLINICAL METAGENOMICS PLATFORM FOR AUSTRALIA/ ; }, abstract = {MOTIVATION: Accurate genome size estimation is an important component of genomic analyses such as assembly and coverage calculation, though existing tools are primarily optimized for short-read data.<br><br>RESULTS: We present LRGE, a novel tool that uses read-to-read overlap information to estimate genome size in a reference-free manner. LRGE calculates per-read genome size estimates by analysing the expected number of overlaps for each read, considering read lengths and a minimum overlap threshold. The final size is taken as the median of these estimates, ensuring robustness to outliers such as reads with no overlaps. Additionally, LRGE provides an expected confidence range for the estimate. We validate LRGE on a large, diverse bacterial dataset and confirm it generalizes to eukaryotic datasets. On bacterial genomes, LRGE outperforms k-mer-based methods in both accuracy and computational efficiency and produces genome size estimates comparable to those from assembly-based approaches, like Raven, while using significantly less computational resources.<br><br>Our method, LRGE (Long Read-based Genome size Estimation from overlaps), is implemented in Rust and is available as a precompiled binary for most architectures, a Bioconda package, a prebuilt container image, and a crates.io package as a binary (lrge) or library (liblrge). The source code is available at https://github.com/mbhall88/lrge and an archive at https://doi.org/10.5281/zenodo.17183812 under an MIT license.}, }
@article {pmid41218490, year = {2025}, author = {Qingrui, L and Hongyang, L and Guijun, W and Yiqiao, Z and Yue, C and Changqun, D and Chang'e, L}, title = {Synergistic ecotoxicity of nanoscale zero-valent iron and cadmium in soil: Insights from Eisenia fetida.}, journal = {Ecotoxicology and environmental safety}, volume = {306}, number = {}, pages = {119381}, doi = {10.1016/j.ecoenv.2025.119381}, pmid = {41218490}, issn = {1090-2414}, abstract = {Nano-zero-valent iron (nZVI) has been extensively applied as a soil conditioner in remediation practices. However, studies have suggested that excessive doses of nZVI can adversely affect soil organisms and even exacerbate the toxicity of contaminants such as cadmium (Cd) in earthworms. This study investigated whether nZVI induces stress and exacerbates Cd toxicity in Eisenia fetida under controlled laboratory conditions. Four treatments were established: control (no nZVI or Cd), nZVI (10 g∙kg[-1]), Cd (30 mg∙kg[-1]), and Cd-nZVI (30 mg∙kg[-1] Cd + 10 g∙kg[-1] nZVI). Survival rate, biomass, Cd bioaccumulation, enzyme activity, and other indicators were measured. On day 7 of exposure, reactive oxygen species (ROS) levels in the nZVI, Cd, and Cd-nZVI groups were 1.4-, 1.5-, and 1.6-fold higher than those in the control group, respectively (P < 0.05). Over time, both survival rate and biomass declined, with the lowest survival rate and greatest biomass loss observed in the Cd-nZVI group on day 28. Histological staining revealed that under Cd or nZVI stress, the circular muscle layer of the earthworms was loosened, intestinal tissue was partially detached, and the number of villi decreased. Metagenomic sequencing indicated significant alterations in the community structure of the earthworm intestinal microbiota under different treatments. Both 30 mg∙kg[-1] Cd and 10 g∙kg[-1] nZVI disrupted gut microbial balance, which was further exacerbated by combined exposure.}, }
@article {pmid41218435, year = {2025}, author = {Ren, J and Wang, J and Dong, Y and Xiao, L and Wang, L and Ji, J and Liu, Y}, title = {Microbial community dynamics and its relationship with biogeochemical processes under geochemical perturbations.}, journal = {Water research}, volume = {289}, number = {Pt B}, pages = {124889}, doi = {10.1016/j.watres.2025.124889}, pmid = {41218435}, issn = {1879-2448}, abstract = {Environmental microbial communities are crucial in regulating ecosystem functions and are increasingly affected by human-induced geochemical perturbations. While microbial communities are known to shift under such perturbations, the explicit link between these shifts and corresponding biogeochemical processes remains unclear. Here, we conducted time-series sediment incubation experiments under elevated nitrate conditions, combining 16S rRNA gene sequencing, qPCR, and metagenomics to track microbial taxonomic and functional dynamics. We further developed a gene-centric, process-based biogeochemical model to quantitatively connect microbial community structure to geochemical reaction kinetics. Our results revealed that functional metagenomics provided a broader view of functional diversity than qPCR and enabled detailed analysis of gene co-occurrence. Through modeling, we uncover a quantitative coupling between functional gene abundance and reaction rates under geochemical perturbations. However, this relationship can be obscured by redox-driven abiotic processes affected by perturbations and the nonlinear nature of enzyme-mediated reactions, making it difficult to resolve using standard statistical approaches. Together, these findings improve our understanding of the linkage between microbial function and biogeochemical processes, and underscore the value of gene-centric, process-based models for predicting ecosystem behavior under geochemical stress.}, }
@article {pmid41218045, year = {2025}, author = {Kitsanayanyong, L and Chongprachavat, N and Rairat, T and Keetanon, A and Wimanhaemin, P and Chuchird, N}, title = {Exploring the gut microbiota of Pacific white shrimp (Litopenaeus vannamei) suffering pale shrimp disease.}, journal = {PloS one}, volume = {20}, number = {11}, pages = {e0336700}, doi = {10.1371/journal.pone.0336700}, pmid = {41218045}, issn = {1932-6203}, abstract = {Pale shrimp disease is an emerging threat in Thailand, characterized by pale body coloration in Pacific white shrimp (Litopenaeus vannamei). Although the etiology had been identified as Photobacterium damselae subsp. damselae, the disease effects on gut microbiome remain poorly understood. This study investigated changes in the gut microbiota of Pacific white shrimp suffering from pale shrimp disease (diseased group) compared to disease-free shrimp (healthy group) collected from Surat Thani Province, Thailand. DNA extracted from the intestinal samples was subjected to 16S rRNA metagenomic sequencing, followed by taxonomic identification, diversity analyses, and functional prediction of the metabolic pathways. Despite a limited number of biological replicates, the occurrence of pale shrimp disease was able to reveal alterations in intestinal microbial composition, diversities, and functional features compared to the healthy shrimp. In most cases, the intestinal microbiota of the diseased shrimp were dominated by only 2 genera of bacteria, i.e., Photobacterium (54.63-70.53%) and Vibrio (24.94-26.12%), which together accounted for 79.58-95.47% of the total bacterial community. α-diversity, as indicated by the observed features, Shannon, and Simpson indices, was significantly decreased, and dominance was significantly increased in the diseased shrimp compared to healthy shrimp. Likewise, β-diversity was significantly different between groups; PCoA of un-weighted and weighted UniFrac clearly distinguished intestinal microbiota of the shrimp into 2 clusters, and ANOSIM of these data revealed statistical differences between groups, suggesting different microbiota communities between healthy and diseased shrimp. Moreover, diseased shrimp had significantly higher predicted functional features associated with bacterial virulence factors and antibacterial resistance. These exploratory findings suggest an association among pale shrimp disease, gut microbiota dysbiosis, and the proliferation of opportunistic taxa, particularly Photobacterium.}, }
@article {pmid41217732, year = {2025}, author = {Boutin, S and Klein, S and Untergasser, G and Loka, TP and Jakob, S and Caf, Y and Khatamzas, E and Knabl, L and Wrettos, G and Knobloch, H and Nurjadi, D}, title = {Evaluating Seqstant LiveGene Analysis in real-time assessment of metagenomic next-generation sequencing (mNGS) data from respiratory samples.}, journal = {Infection}, volume = {}, number = {}, pages = {}, pmid = {41217732}, issn = {1439-0973}, abstract = {BACKGROUND: The detection of pathogens causing infections by conventional diagnostic methods can be challenging and next-generation sequencing (NGS) technology offers a promising alternative method. In this study, we evaluated the performance of real-time metagenomic next-generation sequencing (rt-mNGS) for the detection of pathogens in respiratory samples.<br><br>METHOD: We used rt-mNGS, using the Seqstant LiveGene Analysis platform, on 335 respiratory samples in comparison to conventional culture results.<br><br>RESULTS: We observed an overall good concordance in 71.64% (240/335) of the methods. The rt-mNGS outperformed the gold standard culture in 16.12% (54/335) of the samples, while the culture was superior in detecting the clinically relevant pathogen in 12.24% (41/335) of the samples. The non-inferiority of rt-mNGS was statistically significant (&#x3b4;&#x2009;=&#x2009;10, &#x3b1;&#x2009;=&#x2009;0.05, 1&#x2009;-&#x2009;&#x3b2;&#x2009;=&#x2009;0.8). We also observed that the real-time analysis of NGS data is beneficial in obtaining reliable, timely results, as the initial report at cycle 46 exhibits a Positive Predictive Value (PPV) of 93.75% at the species-level with a sensitivity of 32.09%.<br><br>CONCLUSION: Overall, our study showed the non-inferiority of rt-mNGS compared to the standard-of-care microbiology for respiratory samples with statistical significance. Moreover, the rt-mNGS method exhibited superior sensitivity and superior overall performance. It also uniquely detected certain organisms that are typically hard to culture. However, rt-mNGS reported a higher number of false positives and faced limitations in detecting Aspergillus spp. In conclusion, the study highlights the potential of rt-mNGS as a powerful tool in clinical diagnostics of respiratory infections and beyond.}, }
@article {pmid41217690, year = {2025}, author = {Nguyen, HN and Kim, OTP and Tran, TT}, title = {Metagenomic analysis of microbial communities and associated resistance genes, virulence genes, and mobile genetic elements in natural honey from Mu Cang Chai, Vietnam.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {41}, number = {11}, pages = {445}, pmid = {41217690}, issn = {1573-0972}, support = {B2023-SPH17; VINIF.2021.TS.127//The Ministry of Education and Training, Vietnam; PhD Scholarship Programme of Vingroup Innovation Foundation (VINIF)/ ; B2023-SPH17; VINIF.2021.TS.127//The Ministry of Education and Training, Vietnam; PhD Scholarship Programme of Vingroup Innovation Foundation (VINIF)/ ; }, abstract = {Natural honey is preferred over honey from farmed bees in Vietnam, often commanding higher prices; therefore, it needs proper guidance. Environmental DNA from natural honey can be used to monitor its safety and authenticate its quality, as it contains DNA traces from various organisms. In this study, shotgun metagenomic sequencing was employed to identify risk factors in three natural honey samples from Mu Cang Chai, one of the central honey-producing regions in Northwest Vietnam. Our data revealed that more than 95% of the identified DNA belonged to bacteria in all three samples. Some opportunistic pathogenic bacteria, such as Klebsiella pneumoniae, Burkholderia contaminans, and Ralstonia picketti, were found dominant in the examined samples. Moreover, the bacteria in these honey samples carried numerous antibiotic resistance genes (ARGs), as well as virulence genes (VGs). The resistome profiles revealed the detection of 491 ARG sequences across three honey samples, belonging to 43 gene families that encode various resistance proteins. The most frequently encountered drug classes associated with these ARGs were cephalosporins, fluoroquinolones, and tetracyclines. On the other hand, the virulome profiles showed a rich composition of VGs: a total of 94 unique VGs linked to 25 virulence factors. They included nutritional factors, secretion systems, biofilm formation, exotoxins, and immunomodulation; the nutritional factors were the most prevalent function of these VGs. Mobilome profiles showed that only a small fraction of ARGs (0.6%) and VGs (15%) were located on mobile genetic elements (MGEs) such as plasmids and proviruses, suggesting most were chromosomally encoded; however, the presence of MGEs carrying these determinants (ARGs and VGs) still indicates a latent potential for horizontal gene transfer. Although these results are based on a case study of only three samples of natural honey collected in Mu Cang Chai, they highlight the need for a broader examination and the importance of monitoring the risk of pathogenicity in unprocessed foods, such as natural honey.}, }
@article {pmid41217278, year = {2025}, author = {Zhang, C and Chang, N and Yin, G and Shen, W and Lu, L and Bao, M and Guan, D and Zhang, S and Wang, R and Zhang, H}, title = {Drivers of Metal Resistance-Virulence Co-Selection in Landfill Leachates.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxaf275}, pmid = {41217278}, issn = {1365-2672}, abstract = {AIMS: Metal resistance genes (MRGs) and virulence factor genes (VFGs) are driven by environmental factors and host immunity, respectively, and they are traditionally considered to evolve independently. However, their co-selection dynamics in landfill leachates remain poorly characterized. In this study, a multi-regional metagenomic assessment integrating environmental gradients was first presented to reveal how heavy metals shape MRG-VFG interactions and associated ecological risks in landfill leachates.<br><br>METHODS AND RESULTS: Landfill leachates were collected from 13 landfills spanning six regions in China. Multi-regional metagenomic sequencing combined with co-occurrence network analysis was applied to examine pathogen-gene relationships. The results revealed pronounced regional disparities in pathogen, MRG, and VFG distribution, alongside shared features. Staphylococcus aureus and Pseudomonas aeruginosa were identified as dominant pathogens. tufA and gyrA emerged as conserved VFGs, whereas arsB and copA represented dominant MRGs. Network analysis revealed Escherichia coli, Salmonella enterica, and Acinetobacter baumannii as central nodes carrying overlapping functional genes, forming a "metal resistance-virulence" synergy module. Redundancy analysis revealed that specific heavy metals (Cu, Zn, Cr, and As) were crucial for the formation and stability of "pathogen-MRG-VFG" functional assemblies.<br><br>CONCLUSIONS: This study addresses a critical knowledge gap by integrating multi-regional metagenomic evidence with environmental selection pressures. MRGs conferred survival advantages and synergized with VFGs to enhance pathogen infectivity. These findings provide insight into MRG-VFG co-selection mechanisms in landfill leachates and guide targeted monitoring to mitigate environmental and health risks.}, }
@article {pmid41217198, year = {2025}, author = {Valade, M and Le Bideau, M and Grimaldier, C and Boschi, C and Colson, P and La Scola, B}, title = {Development of cell combos micromethod to isolate respiratory viruses not detected by molecular techniques.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0257125}, doi = {10.1128/spectrum.02571-25}, pmid = {41217198}, issn = {2165-0497}, abstract = {Virological diagnosis of respiratory infections relies mainly on molecular methods but can be overlooked in cases of unexpected or unknown emerging viruses. In this case, modern approaches use mainly metagenomics without a priori. The other approach to detecting new viruses is based on their isolation in cell culture using virus-specific cells and culture conditions. Unfortunately, inoculation on several lines and metagenomics requires a large volume of clinical sample, while the initial sample has already been largely used to carry out multiplexed RT-PCR. Herein, we aimed to develop micro-methods to inoculate combos of cell lines to isolate respiratory viruses missed by molecular techniques. Ten cell lines were selected, and then five cell combos of two cell lines each were developed. Strains of 15 respiratory virus species were inoculated, and viral growth was assessed by cytopathic effect detection and RT-PCR assays. Among these, all grew on at least one combo. The Caco-2/MRC5 combo was the most promising. As proof-of-concept, 859 human respiratory samples found negative by multiplex RT-PCR panels were inoculated into these five cell combos and monitored for the appearance of cytopathic effects. The efficiency of this approach was evidenced by isolating 12 herpes simplex or varicella-zoster viruses not detected by respiratory multiplex PCR assays. In conclusion, this updated approach can detect known but, most importantly, likely emerging respiratory viruses. It could be used to investigate undiagnosed respiratory infection outbreaks especially if optimized with an approach allowing for the detection of viral multiplications with minor or no cytopathic effects.IMPORTANCEThe detection of respiratory viruses relies on a range of laboratory methods each of which has distinct advantages in terms of speed, practicality, and sensitivity. Current molecular methods for respiratory virus detection, such as multiplex PCR, may fail to identify unexpected, genetically divergent, or emerging viruses. This study presents an innovative approach using micromethods inoculating combinations of cell lines (cell combos) to enhance the isolation of a broad panel of respiratory viruses, including those undetected by standard molecular techniques. This strategy revives and modernizes classical virology techniques for use in contemporary diagnostics, particularly during unexplained respiratory outbreaks. It opens up new possibilities for detecting both known and unknown viruses across different sample types.}, }
@article {pmid41217051, year = {2025}, author = {Alam, SS and Mehdi, A and Zafar, A and Ali, S and Rehman, AU and Liaqat, I and Peng, L and Kanwal, F and Afzal, S and Haq, IU and Aftab, MN}, title = {Advances in microbial biofuel production by metabolic and enzyme engineering, synthetic biology, metagenomics, and genome editing applications.}, journal = {Emerging topics in life sciences}, volume = {}, number = {}, pages = {}, doi = {10.1042/ETLS20240002}, pmid = {41217051}, issn = {2397-8554}, abstract = {Microorganisms are the primary source of genetic diversity on earth due to their unparalleled metabolic and functional variability. With the depletion of fossil fuels, a sustainable alternative approach is the use of biofuels, where plant biomass as feedstock is essentially degraded to sugars with the aid of microbe-derived enzymes, followed by the conversion of those sugars to biofuels. Several cellulolytic and non-cellulolytic enzymes are involved in biofuel synthesis. Molecular cloning, along with the advancements in genetic and metabolic engineering in microbial cells, plays a significant contribution to biofuel overproduction. Advanced molecular technologies such as metagenomics and synthetic biology approaches are also being used to construct effective microorganisms for biofuel manufacturing. Obtaining novel enzymes from undiscovered microbial consortia and functional gene analysis is possible through a metagenomics approach. While synthetic biology provides engineered biological systems to generate required biofuel productivity, the CRISPR-Cas genome editing tool is another revolutionary tool being utilized for efficient biofuel production. This article provides a brief overview of different methods of biofuel production using microorganisms.}, }
@article {pmid41216332, year = {2025}, author = {Facciotti, F and Di Stefano, G and Maragno, P and Ferraro, C and Dridi, D and Somigliana, E and Viganò, P and Vercellini, P and Casalechi, M}, title = {Microbiome dysbiosis and endometriosis: a systematic scoping review of current literature and knowledge gaps.}, journal = {Human reproduction open}, volume = {2025}, number = {4}, pages = {hoaf061}, pmid = {41216332}, issn = {2399-3529}, abstract = {STUDY QUESTION: What is the evidence available concerning gut and reproductive tract microbiomes in patients with endometriosis and what are the methodological approaches employed in microbiome studies on endometriosis?<br><br>SUMMARY ANSWER: The taxonomic profiles exhibited pronounced heterogeneity within women with and also within women without endometriosis across reviewed studies for all the anatomical districts evaluated.<br><br>WHAT IS KNOWN ALREADY: Both human and animal studies support differences in the microbiome composition of individuals with and without endometriosis. Endometriosis onset occurs with variable symptoms and manifestations. The microbiome composition at different sites may contribute to this variability.<br><br>STUDY DESIGN SIZE DURATION: We used the scoping review methodology. Systematic searches of studies from the PubMed, EMBASE, and Web of Science databases published between 1 January 2016 and 1 November 2024 addressing endometriosis microbiome characterization in: (i) gut, (ii) vaginal fluid, (iii) cervical fluid, (iv) peritoneal fluid, (v) uterine fluid, (vi) ovarian cyst fluid, (vii) oropharyngeal fluid, and (viii) eutopic and (ix) ectopic tissues were performed using a combination of MeSH terms. References from relevant publications were systematically screened.<br><br>Results were reported in accordance with the PRISMA-ScR guidelines. Studies that did not report original data, not written in English or providing a review of the field were excluded. From the 2182 publications retrieved, 36 papers were selected and analyzed, focusing on sample characterization (patients, controls, tissues, and fluids) and methodologies used.<br><br>Sound evidence is lacking to support a specific gut dysbiosis profile in women with endometriosis. The largest metagenome study performed using shotgun sequencing and controlling for multiple hypotheses testing did not detect significant differences between women with and without the disease. For eutopic and ectopic tissue microbiomes, the literature is too scant to draw any conclusion. Some data suggest a possible enrichment of Streptococcus sp. in cervical fluid and of Pseudomonas sp. in peritoneal fluid and a depletion of Lachnospira sp. in stool/anal fluid of endometriosis patients. However, these findings may be explained by confounders or by intrinsic patient or population characteristics. We appraised the limitations of the studies and proposed suggestions for optimizing sequencing techniques and experimental designs.<br><br>The number of participants per study greatly varied and, with few exceptions, was typically low. Incomplete information on methodological approaches was broadly observed. The impact of participants' menstrual cycle phase, diet, and drug assumption was frequently not considered.<br><br>Standardization of research protocols to allow reproducibility is required, as well as collaborations to harmonize data analysis, interpretation, and, more importantly, health outcome prediction or improvement.<br><br>The review was funded by the Italian Ministry of Health: RF-2019-12369460, and Current Research IRCCS. P.Vi. serves as co-editor in Chief of Journal of Endometriosis and Uterine Disorders. E.S. serves as Editor in Chief of Human Reproduction Open and discloses research grants from Ferring, Ibsa, Gedeon Richter, and Theramex, and honoraria from Ibsa and Gedeon Richter. P.Ve. serves as Associate Editor for Human Reproduction Open; is a member of the Editorial Board of the Journal of Obstetrics and Gynaecology Canada, of the Italian Journal of Obstetrics and Gynaecology, and of the International Editorial Board of Acta Obstetricia et Gynecologica Scandinavica; has received royalties from Wolters Kluwer for chapters on endometriosis management in the clinical decision support resource UpToDate; and maintains both a public and private gynecological practice. All other authors declare they have no conflict of interest.<br><br>REGISTRATION NUMBER: 10.17605/OSF.IO/X6HBT at https://osf.io/registries.}, }
@article {pmid41216322, year = {2025}, author = {Li, C and Hou, J and Datry, T and Adyel, TM and Zhou, W and Wu, J and You, G and Jin, T and Deng, Y and Miao, L}, title = {How river drying influences greenhouse gas emissions: insights from species and gene shifts.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf187}, pmid = {41216322}, issn = {2730-6151}, abstract = {Drying is threatening global river ecosystems due to climate change, altering community composition and function even upon flow resumption. This mesocosm study investigated the greenhouse gas emissions fluxes and underlying mechanisms from benthic habitats prone to 20-100 days of drying. Results show that CO2 and N2O emissions from biofilms did not increase when drying increased, due to the changes in functional communities and genes. Notable is the transformation of biofilm from carbon source to sink following prolonged drying (mean emission fluxes ranged from 804.78 to -305.55 mg m[2] h[2]). This was mainly due to strong increases in the abundance of genes involved in the Calvin-Benson-Bassham cycle (2.82 × 10[-5] to 7.12 × 10[-5]), and functional taxa such as gemmatimonadota and pseudomonadota. These findings reveal a potential mitigation effect of drying on greenhouse gas emissions from rivers and streams, which could be relevant in the face of climate change.}, }
@article {pmid41216321, year = {2025}, author = {Hawthorne, SEG and Tsola, SL and Carrión, O and Todd, JD and Eyice, &#xd6;}, title = {Active microorganisms and potential metabolic pathways mediating anaerobic degradation of DMSP in anoxic saltmarsh sediment.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf180}, pmid = {41216321}, issn = {2730-6151}, abstract = {Dimethylsulfoniopropionate (DMSP) is a globally abundant organosulfur compound produced by marine organisms, where it plays key physiological roles in stress protection and serves as a major source of carbon, sulfur, and energy for microbial communities. Importantly, DMSP degradation contributes to the formation of the climate-active gas dimethyl sulfide (DMS), which can drive the production of potent greenhouse gases, methane and carbon dioxide, in anoxic environments. While aerobic DMSP degradation is well studied, its fate under anoxic conditions remains poorly understood, and the microbial populations and metabolic pathways underlying these biotransformations are virtually unknown. Here, we present the first detailed investigation of microbial DMSP cycling in anoxic saltmarsh sediments. Our sediment samples had high in situ DMSP concentrations (up to 7.7 μmol/g) and the conversion efficiencies of DMSP to DMS under anoxic conditions (~68%) were comparable to those in oxic environments. Furthermore, using [13]C-labelled DMSP in stable isotope probing (SIP) experiments, combined with 16S rRNA gene sequencing and metagenomics, we identified Amphritea (Oceanospirillales) as a key active DMSP degrader, likely operating via the dddD-encoded lysis pathway. Additional taxa, including Geopsychrobacter, were implicated as potential secondary consumers, while Arcobacteraceae may contribute to sulfur cycling rather than direct DMSP catabolism. This study uncovers a previously overlooked route for DMSP transformation via anaerobic metabolism, expands the known metabolic roles of saltmarsh microorganisms and highlights the potential for DMSP to drive climate-active gas production in anoxic coastal ecosystems.}, }
@article {pmid41216320, year = {2025}, author = {González-Rosales, C and Rezaei Somee, M and Buck, M and Bertilsson, S and Mehrshad, M and Dopson, M}, title = {A global deep terrestrial biosphere core microbiome.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf176}, pmid = {41216320}, issn = {2730-6151}, abstract = {The deep biosphere encompasses life beneath the Earth's surface and constitutes a substantial portion of the planet's microbial biomass. This study analyzed nucleic acid datasets from low-carbon and low-energy deep terrestrial subsurface groundwaters across four continents and revealed four core global populations. These populations exhibited metabolic strategies and adaptations reflecting depth and environmental constraints. Erythrobacter featured heterotrophic metabolism; Thiobacillus demonstrated sulfur oxidation coupled to denitrification along with carbon and nitrogen fixation; Methanobacteriaceae were methanogenic autotrophs using the Wood-Ljungdahl pathway (WL); and Candidatus Desulforudis audaxviator functioned as a sulfate-reducer also encoding the WL pathway. Depth-related adaptations suggested heterotrophic dominance at shallower depths with increasing contributions from autotrophy with depth. Finally, comparative genomics revealed minimal evolutionary changes among these populations, suggesting functional conservation since diverging from their ancestral lineages. These findings underscore a global deep biosphere core community.}, }
@article {pmid41216181, year = {2025}, author = {Song, Z and Huang, T and Jiang, X and Hu, M and Wu, H and Wang, J}, title = {A case report of Staphylococcus saccharolyticus bloodstream infection in a non-implanted host diagnosed by mNGS: Mechanism and pathogenesis analysis.}, journal = {IDCases}, volume = {42}, number = {}, pages = {e02408}, pmid = {41216181}, issn = {2214-2509}, abstract = {BACKGROUND: Staphylococcus saccharolyticus is an obligate anaerobic skin commensal that is rarely implicated in bloodstream infections, particularly in immunocompetent individuals without implanted medical devices. Due to its low virulence and fastidious growth requirements, it is often overlooked or dismissed as a contaminant. This report describes a rare case of S. saccharolyticus bacteremia and explores the underlying pathogenic mechanism.<br><br>CASE PRESENTATION: A 50-year-old immunocompetent female presented with recurrent low-grade fever and oral mucosal ulceration. Pathogen detection was performed using plasma-based metagenomic next-generation sequencing (mNGS), which identified S. saccharolyticus at a relative abundance of 15&#x202f;% (seven species-specific reads). The result was corroborated by anaerobic blood culture. Laboratory assessment revealed severe vitamin D deficiency (25-hydroxyvitamin D: 11.6&#x202f;ng/mL). Initial treatment with ceftriaxone was ineffective. Following the initiation of intravenous moxifloxacin and oral vitamin D supplementation (cholecalciferol 2000 IU/day), the patient's fever resolved within five days, and high-sensitivity C-reactive protein (hsCRP) levels decreased markedly from 88.3&#x202f;mg/L to 12.0&#x202f;mg/L. Mechanistically, the combination of mucosal barrier disruption due to oral ulceration and vitamin D deficiency may have facilitated translocation of the anaerobic pathogen into the bloodstream.<br><br>CONCLUSIONS: This case underscores the diagnostic value of mNGS in detecting low-biomass anaerobic infections and proposes a synergistic "mucosal barrier disruption-pathogen translocation" model. It also highlights the potential role of host-directed adjunctive therapy in managing bloodstream infections not associated with prosthetic material.}, }
@article {pmid41215794, year = {2025}, author = {Onile-Ere, O and Name, PE and Tibiri, EB and Tiendrébéogo, F and Pita, J and Mohammed, IU and Nkere, CK and Oranusi, S and Eni, A}, title = {Dataset of rolling circle amplification (RCA) enriched metagenome of Cassava obtained through nanopore sequencing.}, journal = {Data in brief}, volume = {63}, number = {}, pages = {112204}, pmid = {41215794}, issn = {2352-3409}, abstract = {The dataset presented here was obtained by sequencing selected historic herbarium cassava samples collected across Nigeria. Total DNA was extracted from the samples using the CTAB method, after which the samples were enriched by Rolling Circle Amplification (RCA) and then sequenced on the MinION. The dataset consists of raw sequencing data in FASTQ format reflecting microbial diversity in cassava leaf samples. Taxonomic classification of the samples using the Kraken2 PlusPFP-16 database revealed 12 kingdoms, 36 phyla, 67 classes, 154 orders, 273 families, 524 genera, and 895 species across the dataset, with a substantial proportion (77.9%) of reads remaining unclassified following host removal. The data is beneficial for exploring the microbiome diversity of cassava leaves across Nigeria, as well as serving as a reference for future microbial discovery, given the large number of unidentified reads in the dataset.}, }
@article {pmid41214992, year = {2025}, author = {Li, C and Yang, F and Han, Y and Yang, C and Qin, X and Zheng, H and Chen, L and Lu, J and Zhang, C and Lu, F and Wang, L}, title = {Aldehyde metabolism in Maotai-flavor Baijiu: insights from integrated metagenomic and metaproteomic analyses.}, journal = {Food research international (Ottawa, Ont.)}, volume = {221}, number = {Pt 3}, pages = {117518}, doi = {10.1016/j.foodres.2025.117518}, pmid = {41214992}, issn = {1873-7145}, abstract = {Acetaldehyde and acetal are crucial to the flavor of Maotai-flavor Baijiu, affecting aroma release and sauce-aroma traits. Targeted control of acetaldehyde metabolic flux is critical for stabilizing base liquor quality. However, the diversity of acetaldehyde-metabolizing enzymes and their microbial drivers remain uncharacterized, critically impeding precision control. This study selected the third production round to systematically investigate acetaldehyde accumulation dynamics and metabolic mechanisms. Time-resolved profiling showed that acetaldehyde and acetal concentrations display an initial rise, followed by a decline and stabilization. By integrated metagenomic and metaproteomic analyses, we confirmed that the metabolic network comprised two biosynthetic and three conversion pathways. The dominant biosynthetic pathway featured pyruvate decarboxylase (PDC)-catalyzed decarboxylation, while ethanolamine ammonia-lyase contributed minimally. Among conversion pathways, NADH-dependent alcohol dehydrogenase (NADH-ADH) reduction to ethanol predominated, with lower-flux oxidation to acetate and acetyl-CoA. Dynamic enzyme profiling revealed that PDC activity preceded the activation of NADH-ADH during stacking fermentation, resulting in a temporal mismatch between aldehyde production and consumption, which led to metabolic retention. During pit fermentation, acetaldehyde was more efficiently converted to ethanol through upregulation of NADH-ADH and NADH/NAD[+] ratio. As main contributors of PDC and NADH-ADH, Schizosaccharomyces pombe and Saccharomyces cerevisiae exhibited dual regulatory roles in acetaldehyde metabolism, with their metabolic mode shifts governed by dissolved oxygen and the NADH/NAD[+] ratio. Microbial interaction analysis and simulated fermentation confirmed that Pichia kudriavzevii synergized with Saccharomyces cerevisiae and Schizosaccharomyces pombe, driving rapid acetaldehyde accumulation during the stacking fermentation. These findings establish a theoretical framework for optimizing brewing processes and enhancing base liquor quality.}, }
@article {pmid41214941, year = {2025}, author = {Kahraman Ilıkkan, &#xd6; and Cerit, ZG and Baloglu, MC and Yılmaz, R}, title = {Microbial monitoring and Resistome analysis in white cheese production at a dairy plant: MALDI-TOF MS and shotgun metagenomics approaches.}, journal = {Food research international (Ottawa, Ont.)}, volume = {221}, number = {Pt 3}, pages = {117432}, doi = {10.1016/j.foodres.2025.117432}, pmid = {41214941}, issn = {1873-7145}, abstract = {This study presents a comprehensive microbiological evaluation of white cheese production in a small-scale dairy facility in northern Türkiye, integrating culture-dependent and culture-independent methods. Ten samples, including raw milk, milk with starter culture added, curd, clot, final cheese product, and environmental samples such as milk truck, cheese vessel, stirrer, cutting wire, and cheesecloth, were analyzed. Pathogenic bacteria were identified using MALDI-TOF MS, while shotgun metagenomics enabled a detailed investigation of microbial communities, antibiotic resistance genes (ARGs), and functional properties. The analysis using MALDI-TOF MS revealed ten pathogenic species, among which Staphylococcus aureus and Escherichia coli were the most dominant. Shotgun metagenomics corroborated the prevalence of S. aureus in dairy samples and Salmonella spp. on equipment surfaces, particularly the cheese vessel, stirrer, and cutting wire. The highest E. coli contamination was detected on cheesecloth, underscoring a critical point of concern. Across 15 antibiotic classes, 974 ARGs were identified, with equipment samples harboring significantly higher ARG loads than dairy products. Resistance mechanisms included β-lactamase enzymes, RND efflux pumps, and ribosomal protection proteins. Equipment samples showed an enrichment of carbohydrate-active enzymes (CAZymes), notably glycoside hydrolases and glycosyl transferases, suggesting microbial biofilm development and increased spoilage potential. Functional gene profiling revealed distinct metabolic signatures between dairy and equipment samples, with enriched pathways related to virulence and antimicrobial resistance in environmental samples. These findings underscore the limitations of conventional thermal treatment and the necessity of stringent sanitation practices, particularly for reusable equipment such as cheesecloth. The combined use of MALDI-TOF MS and shotgun metagenomics offers an effective strategy for microbial risk assessment in traditional cheese production systems.}, }
@article {pmid41214546, year = {2025}, author = {Su, YS and Tsai, WH and Wu, HC and Chiu, YT and Jiang, NR and Lee, CY and Cheng, SH and Huang, CT and Chi, CY and Lin, EJ and Kuo, YP and Tsai, WT and Tien, CF and Liao, YC and Lee, KL and Chen, FJ and Yu, GY}, title = {Multiplex metagenomic sequencing for rapid viral pathogen identification and surveillance in clinical specimens.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {1531}, pmid = {41214546}, issn = {1471-2334}, abstract = {BACKGROUND: Rapid and accurate viral detection is essential for clinical diagnosis and effective outbreak surveillance. Traditional methods, including culture-based isolation and antigen tests, are time-consuming and limited by tissue tropism. Multiplex PCR panels, although faster, are constrained by predefined targets, limiting their ability to detect novel or unexpected viral strains.<br><br>METHODS: We applied Oxford Nanopore Technology sequencing (ONT-Seq), a long-read, real-time, and multiplex metagenomic platform, to 85 clinical specimens using a sequence-independent, single-primer amplification (SISPA) workflow. Sequencing results were compared with routine clinical diagnostics for concordance and for identification of co-infections RESULTS: ONT-Seq achieved 80% concordance with clinical diagnostics and identified co-infections in 7% of cases missed by routine testing, including influenza C virus (ICV), and Sapporovirus. Among 58 adenovirus-positive cases, 31 samples with over 80% genome coverage at 20&#xd7; depth were used for phylogenetic analysis, revealing adenovirus B3 as the predominant circulating strain.<br><br>CONCLUSIONS: ONT-based metagenomic sequencing enhances the detection of both known and emerging viruses in clinical specimens. Its ability to provide real-time, unbiased data supports its utility in improving diagnostic accuracy and viral surveillance.<br><br>CLINICAL TRIAL: Not applicable.}, }
@article {pmid41212644, year = {2025}, author = {Acosta, DJ and Barth, DR and Bondy, J and Appler, KE and De Anda, V and Ngo, PHT and Alper, HS and Baker, BJ and Marcotte, EM and Ellington, AD}, title = {Plastic degradation by enzymes from uncultured deep sea microorganisms.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {41212644}, issn = {1751-7370}, abstract = {Polyethylene terephthalate (PET)-hydrolyzing enzymes (PETases) are a recently discovered enzyme class capable of plastic degradation. PETases are commonly identified in bacteria; however, pipelines for discovery are often biased to recover highly similar enzymes. Here, we searched metagenomic data from hydrothermally impacted deep sea sediments in the Guaymas Basin (Gulf of California) for PETases. A broad diversity of potential proteins were identified and 22 were selected based on their potential thermal stability and phylogenetic novelty. Heterologous expression and functional analysis of these candidate PETases revealed three candidates capable of depolymerizing PET or its byproducts. One is a PETase from a Bathyarchaeia archaeon (dubbed GuaPA, for Guaymas PETase Archaeal) and two bishydroxyethylene terephthalate-hydrolyzing enzymes (BHETases) from uncultured bacteria, Poribacteria, and Thermotogota. GuaPA is the first archaeal PETase discovered that is able to depolymerize PET films and originates from a specific enzyme class which has endowed it with predicted novel structural features. Within 48 h, GuaPA released ~3-5 mM of terephthalic acid and mono-(2-hydroxyethyl) terephthalate from low crystallinity PET. PET co-hydrolysis containing GuaPA and one of the newly discovered BHETases further improves the hydrolysis of untreated PET film by 68%. Genomic analysis of the PETase- and BHETase-encoding microorganisms reveals that they likely metabolize the products of enzymatic PET depolymerization, suggesting an ecological role in utilizing anthropogenic carbon sources. Our analysis reveals a previously uncharacterized ability of these uncultured microorganisms to catabolize PET, suggesting that the deep ocean is a potential reservoir of biocatalysts for the depolymerization of plastic waste.}, }
@article {pmid41212311, year = {2025}, author = {Slobodkin, AI and Rusanov, II and Slobodkina, GB and Chernyh, NA and Stroeva, AR and Merkel, AY}, title = {A culture-independent study of the structure, functions and methane oxidation activity of microbial communities of geothermal springs in Dagestan.}, journal = {Extremophiles : life under extreme conditions}, volume = {29}, number = {3}, pages = {42}, pmid = {41212311}, issn = {1433-4909}, abstract = {Microbial communities inhabiting geothermal springs in the Republic of Dagestan, Russia, have not been studied by culture-independent methods. We have investigated the taxonomic composition, metabolic potential and rates of methane oxidation of microbial communities in two geothermal springs with methane emission (Artuzen and Miatli) located in Dagestan. Methane oxidation rates measured by the radiotracer technique varied from 3.7 to 96.5 nmol CH4 cm[- 3] day[- 1]. 16S rRNA gene amplicon sequencing indicates that in the Artuzen hot springs (54 °C), with a salinity of 2.5%, the primary production of organic matter is performed by mesophilic cyanobacteria, while in the freshwater Miatli hot springs (58 °C) primary producers are thermophilic cyanobacterium Thermosynechococcus and photosynthetic members of Chloroflexi. Analysis of metabolic capabilities of the metagenome assembled genomes in one of Artuzen samples shows that anaerobic bacteria belonging to Anaerolineae and Marinisomatota are the key decomposers of complex organic substances. The main terminal electron-accepting process in the sediment is acetoclastic methanogenesis carried out by the genus Methanocrinis. The presence of "Candidatus Methanospirareceae" (ANME-1) suggests the involvement of anaerobic archaea in methane oxidation. Thus, our study extends the current knowledge of the phylogenetic and metabolic diversity and activity of the prokaryotes inhabiting terrestrial hydrothermal environments.}, }
@article {pmid41211992, year = {2025}, author = {Wang, Y and Tian, F and Zhang, J and Xu, S and Li, M and Tong, Y}, title = {Identification and characterization of a novel plaque-invisible lytic single-stranded RNA phage.}, journal = {Journal of virology}, volume = {}, number = {}, pages = {e0163724}, doi = {10.1128/jvi.01637-24}, pmid = {41211992}, issn = {1098-5514}, abstract = {The RNA phages offer promising applications in biotechnology, including vaccine development and drug delivery. However, their potential remains underexplored due to the limited number of known RNA phages, partly because conventional methods fail to identify plaque-invisible lytic phages that do not form plaques. Here, we introduced a novel method that combines RNA-inclusive metagenomic studies and quantitative reverse transcription-PCR (RMS-RT-qPCR) to identify and characterize active RNA phages from environmental samples. This study led to the discovery of a new active Qbeta-like phage, named Cute. Genomic analysis revealed that Cute is a new member of the Qubevirus genus. Although Cute does not form plaques, it can be observed to continuously release into the supernatant when co-cultured with the host by RT-qPCR detection. This discovery underscores the potential diversity of RNA phages in nature and the limitations of traditional culture-dependent techniques. Our findings suggest that RMS-RT-qPCR could aid in the discovery of active RNA phages with significant biotechnological applications.IMPORTANCEThe discovery and characterization of RNA phages might be historically constrained by traditional culture-based methods. Our study provides a powerful tool for identifying active RNA phages by combining RNA-inclusive metagenomic analysis with RT-qPCR. This method expands our understanding of the diversity and ecological roles of RNA phages, which are often overlooked in microbiome studies. This research highlights the importance of RNA phages in natural ecosystems and their potential applications in biotechnology and medicine, such as antimicrobial therapies and vaccine development. By expanding our understanding of RNA phage diversity, this study opens new avenues for their utilization in various fields, emphasizing the need for continued exploration of these versatile biological entities.}, }
@article {pmid41211985, year = {2025}, author = {Hypša, V and Martinů, J and Mahmood, S and Gupta, S and Nováková, E and Roth, S and Balvín, O}, title = {Dynamic but constrained: repeated acquisitions of nutritional symbionts in bed bugs (Heteroptera: Cimicidae) from a narrow taxonomic pool.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0124725}, doi = {10.1128/msystems.01247-25}, pmid = {41211985}, issn = {2379-5077}, abstract = {Bed bugs (Heteroptera: Cimicidae) harbor obligate bacterial symbionts that supplement their blood diet with missing nutrients, especially B vitamins. The primary symbiont, transovarially transmitted Wolbachia, is notable for a horizontally acquired biotin operon. Additional maternally inherited bacteria, including Symbiopectobacterium and Tisiphia, have been detected but are considered facultative and nonessential. However, nearly all current knowledge is derived from the human-associated Cimex lectularius, leaving symbiont diversity across more than 100 bed bug species largely unknown. Using amplicon and metagenomic data, we identified Wolbachia, Symbiopectobacterium, Sodalis, Serratia, and Tisiphia as candidate symbionts, with at least 16 independent acquisition events across the cimicid species, sometimes involving multiple strains per host. Phylogenetic comparisons indicated that some of these origins were followed by cospeciation. Wolbachia was present in most hosts except Cacodminae, where Symbiopectobacterium occurred as the sole symbiont, suggesting its obligate role. Analysis of 23 draft genomes revealed heterogeneity in size and gene content, consistent with varying stages of symbiotic reduction. Most lineages lost many biosynthetic pathways; only riboflavin and lipoic acid synthesis remained universally conserved. Our survey reveals a dynamic evolution of bed bug symbioses, with repeated symbiont acquisitions, cospeciation, and frequent coinfections. Despite independent origins, most symbionts belong to Wolbachia, Symbiopectobacterium, or Sodalis, implying unknown mechanisms shaping host specificity. Two points merit further study. First, Symbiopectobacterium as the sole obligate symbiont in Cacodminae suggests broader sampling may uncover greater symbiotic diversity. Second, uncertainties in biotin synthesis function call for deeper investigation into the evolution of this pathway in symbiotic bacteria.IMPORTANCEBed bugs are obligate blood-feeding insects that depend on bacterial partners to supply nutrients missing from their diet. Most previous research has focused on the human-associated species Cimex lectularius, leaving little known about symbiont diversity across other species. By surveying a broad phylogenetic range, we found that bed bugs have repeatedly acquired different bacteria as symbionts, including lineages not previously recognized as essential. Notably, finding Symbiopectobacterium as the sole symbiont in one subfamily shows that the nutritional partnerships in bed bugs are more dynamic than previously thought. At the same time, the majority of the 16 independent acquisitions involve only four bacterial genera, suggesting efficient mechanisms that constrain and shape bed bug-symbiont specificity.}, }
@article {pmid41211947, year = {2025}, author = {Calvez, E and Quétel, I and Saint-Alban, L and Gutiérrez-Bugallo, G and Dollin, C and Ramdini, C and Vega-Rúa, A}, title = {Contrasted impacts of commercial diets and rearing water on Aedes aegypti fitness and microbiota.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0054325}, doi = {10.1128/msphere.00543-25}, pmid = {41211947}, issn = {2379-5042}, abstract = {Mosquito rearing optimization in laboratory conditions is crucial for both vector research and control. Although the addition of nutrients is important for Aedes aegypti development from immature stages to adult mosquitoes, little is known about the nutrient composition of commercial diets used for mosquito rearing and their influence on Ae. aegypti life traits. Here, we evaluated the influence of four commercial diets commonly used to rear Ae. aegypti in the laboratory on its fitness, lifespan, and microbiota. We also compared the effect of these diets on this mosquito when combined with two different rearing waters (laboratory versus field-collected waters). Our investigations demonstrated that higher levels of protein and lipid in commercial diets promote better Ae. aegypti development, lifespan, and size in both water. Metagenomic analysis revealed specific modulations of adult microbiota composition according to both diet and rearing water. Chryseobacterium dominated the microbiota of female mosquitoes reared in laboratory water, except for yeast condition, where a more diverse microbiota was observed. When reared in larval site water, the microbiota diversity was overall higher despite diet addition, except for fish food, which promoted Sphingobacterium dominance. Given the pivotal influence of diet addition during the larval stage on Ae. aegypti microbiota and life traits, rearing conditions should be carefully chosen according to the goals of the research (i.e., vectorial capacity estimations) or vector control intervention.IMPORTANCEAedes aegypti is the main vector of arbovirus, such as dengue, yellow fever, and chikungunya viruses. Vector research and control are primarily carried out in laboratories, with larval stage rearing conducted using commercial diet. If many nutrients are essential for Ae. aegypti development, gaining insight into the influence of these diets and their nutrient levels is important to promote optimized rearing worldwide. In this study, our results indicated a significant impact of commercial diet on Ae. aegypti development, lifespan, size, and microbiota related to contrasted protein, lipid, and carbohydrate levels in these diets. This study will help people working with Ae. aegypti raise awareness in staff working with Ae. aegypti to select optimized diets for their specific purpose.}, }
@article {pmid41211940, year = {2025}, author = {Roberts, WR and Parks, M and Ashner, M and Ashworth, MP and Denne, N and Ruck, EC and Spiliotopoulos, E and Wang, A and Amin, SA and Schaack, S and Wickett, NJ and Alverson, AJ}, title = {Reference genome for the benthic marine diatom Psammoneis japonica: Bacterial associations and repeat-driven genome size evolution in diatoms.}, journal = {Journal of phycology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jpy.70101}, pmid = {41211940}, issn = {1529-8817}, support = {1150213//Division of Molecular and Cellular Biosciences/ ; 1353131//Division of Environmental Biology/ ; 1353152//Division of Environmental Biology/ ; 2331644//Division of Environmental Biology/ ; 2336342//Division of Environmental Biology/ ; }, abstract = {We sequenced the genome, transcriptome, and bacterial metagenome of Psammoneis japonica, a benthic, chain-forming, and araphid marine diatom. This combination of traits fills several gaps in genome sequencing coverage across diatoms. The nuclear genome (QPGO00000000) is an estimated 91.4 Mb in length, with 11,047 genes that comprise 18% of the total genome. Repetitive elements account for 33% of the genome, and other noncoding sequences comprise the remaining 49% of the genome. A global analysis of diatom genomes showed that repetitive elements are the principal driver of genome size variation in diatoms. Four complete genomes of Planctomycetota, ɑ-proteobacteria, and Bacteroidota were also recovered, and each had only moderate similarity to previously sequenced bacterial genomes. This finding supports the idea that bacterial species richness in the phycosphere is under-described and far exceeds the number of diatom host species, which themselves number in the tens to hundreds of thousands of species.}, }
@article {pmid41211921, year = {2025}, author = {Wang, Q and Bao, H}, title = {Integrated metagenomics and metabolomics reveal the dynamic mechanism in the rhizosphere soil of Morus alba L. and Fraxinus mandshurica Rupr. with Inonotus hispidus.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0125125}, doi = {10.1128/aem.01251-25}, pmid = {41211921}, issn = {1098-5336}, abstract = {Inonotus hispidus is a medicinal fungus that grows on Morus alba L., Fraxinus mandshurica Rupr., and Ziziphus jujuba Mill. However, there have been no reports on the comparative study of microbial diversity and metabolites in the rhizosphere soil of different tree species, specifically M. alba and F. mandshurica, growing with I. hispidus. Therefore, this study conducts a multi-omics joint analysis utilizing metagenomics and metabolomics to explore the differences in the synergistic mechanisms between different hosts of I. hispidus. Using metagenomics technology, a total of 177 phyla and 2,651 genera were identified as significantly different. At both the phylum and genus levels, Actinomycetota and Pseudomonadota as well as Solirubrobacter and Bradyrhizobium emerged as the predominant phyla and genera, respectively. In the Kyoto Encyclopedia of Genes and Genomes database, carbohydrate and amino acid metabolisms were identified as the primary metabolic pathways. Differential analysis of these metabolic pathways revealed that glucokinase and pyruvate kinase were downregulated. Additionally, metabolomics analysis identified 558 differential metabolites, with tyrosine metabolism being the foremost metabolic pathway involved. This pathway included five differential metabolites, among which salidroside, 3,4-dihydroxyphenylpropanoate, rosmarinate, and homovanillate were significantly upregulated in M. alba in association with I. hispidus. Furthermore, correlation analysis indicated that Enhydrobacter was positively correlated with 10 differential metabolites, while Gaiella, Haladaptatus, Jiangella, and Prauserella showed negative correlations. This study lays a solid foundation for elucidating the interactions between I. hispidus and its hosts, as well as for the effective utilization of I. hispidus resources across different tree species.IMPORTANCEInonotus hispidus, which is traditionally recognized as the authentic source of the medicinal fungus, primarily grows on Morus alba L. It is commonly found in ancient regions along the Yellow River, including Linqing, Xiajin, and Wudi in Shandong, as well as Chengde in Hebei Province and Aksu in Xinjiang. In traditional Chinese medicine, it is known as "Sanghuang" and has a long history of medicinal use. In addition to M. alba, I. hispidus also grows on other broad-leaved species, such as Ulmus macrocarpa, Acer truncatum, and Fraxinus mandshurica. The lack of fundamental research on its multi-host and -source diversity has hindered its industrial development and medicinal value. Consequently, this study employs metagenomics and metabolomics to investigate the rhizosphere soil microbial diversity and differential metabolites associated with the different host plants of I. hispidus, specifically M. alba and F. mandshurica, with the aim of providing a reference for its resource conservation and development.}, }
@article {pmid41211880, year = {2025}, author = {Duan, C and Zang, Z and Xu, Y and He, H and Li, S and Liu, Z and Lei, Z and Zheng, JS and Li, SZ}, title = {FGeneBERT: function-driven pre-trained gene language model for metagenomics.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {6}, pages = {}, doi = {10.1093/bib/bbaf592}, pmid = {41211880}, issn = {1477-4054}, support = {2022ZD0115101//National Science and Technology Major Project/ ; U21A20427//National Natural Science Foundation of China/ ; WU2022A009//National Natural Science Foundation of China/ ; WU2023C019//Center of Synthetic Biology and Integrated Bioengineering of Westlake University/ ; //InnoHK program and Ant Group through CAAI-Ant Research Fund/ ; }, abstract = {Metagenomic data, comprising mixed multi-species genomes, are prevalent in diverse environments like oceans and soils, significantly impacting human health and ecological functions. However, current research relies on K-mer, which limits the capture of structurally and functionally relevant gene contexts. Moreover, these approaches struggle with encoding biologically meaningful genes and fail to address the one-to-many and many-to-one relationships inherent in metagenomic data. To overcome these challenges, we introduce FGeneBERT, a novel metagenomic pre-trained model that employs a protein-based gene representation as a context-aware and structure-relevant tokenizer. FGeneBERT incorporates masked gene modeling to enhance the understanding of inter-gene contextual relationships and triplet enhanced metagenomic contrastive learning to elucidate gene sequence-function relationships. Pre-trained on over 100 million metagenomic sequences, FGeneBERT demonstrates superior performance on metagenomic datasets at four levels, spanning gene, functional, bacterial, and environmental levels and ranging from 1 to 213 k input sequences. Case studies of ATP synthase and gene operons highlight FGeneBERT's capability for functional recognition and its biological relevance in metagenomic research.}, }
@article {pmid41211879, year = {2025}, author = {}, title = {Retraction and replacement of: FGeneBERT: function-driven pre-trained gene language model for metagenomics.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {6}, pages = {}, doi = {10.1093/bib/bbaf591}, pmid = {41211879}, issn = {1477-4054}, }
@article {pmid41210936, year = {2025}, author = {Xu, Y and Miao, J and Chen, J and Ye, L and Yang, K and Wang, H}, title = {Metagenomic next-generation sequencing facilitates precision treatment and prognostic improvement in pulmonary cryptococcosis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1638215}, pmid = {41210936}, issn = {2235-2988}, abstract = {BACKGROUND: The early diagnosis of pulmonary cryptococcosis (PC) remains challenging due to the low sensitivity and prolonged turnaround time of conventional diagnostic methods. Despite the broad-spectrum pathogen detection capability of metagenomic next-generation sequencing (mNGS), its clinical utility in the diagnosis and therapeutic management of pulmonary cryptococcosis remains underexplored.<br><br>METHODS: In this retrospective study, 31 patients diagnosed with Cryptococcus infection through mNGS at The First Affiliated Hospital of Zhengzhou University between July 2023 to March 2025 were included. data on clinical characteristics, treatment regimens, and patient prognosis were systematically collected.<br><br>RESULTS: Compared to conventional pathogen detection methods, mNGS demonstrated superior sensitivity, shorter turnaround time (1.00 d vs. 4.50 d, p = 0.002), and significantly reduced interval from admission to clinical decision-making (3.50 d vs. 9.00 d, p = 0.002). Among 31 patients with mNGS-identified cryptococcal infection, only 12 underwent fungal culture, with merely 1 case yielding positive results (positivity rate: 8.33%). Antimicrobial therapy was optimized for all patients based on mNGS findings. During post-discharge follow-up of 27 cases, 1 patient experienced disease recurrence, 1 died from tumor metastasis, and 1 was lost to follow-up.<br><br>CONCLUSION: Our retrospective analysis revealed that mNGS facilitated treatment optimization, improved clinical outcomes, and provided crucial evidence supporting the precision management of pulmonary cryptococcosis.}, }
@article {pmid41210414, year = {2025}, author = {Hu, L and Li, S and Gao, F and Diao, S and Liu, X and Qiu, J}, title = {Silent Threat: Multi-Organ Failure in Neonatal Scrub Typhus Without Traditional Markers.}, journal = {Clinical case reports}, volume = {13}, number = {11}, pages = {e71352}, pmid = {41210414}, issn = {2050-0904}, abstract = {Scrub typhus, an acute zoonotic disease from Orientia tsutsugamushi, is uncommon in newborns and presents atypical symptoms. Untimely diagnosis and treatment can lead to a prolonged and potentially fatal course. Early diagnosis and treatment are essential for better patient outcomes. Metagenomic next-generation sequencing can rapidly and accurately diagnose pathogens, aiding precise treatment.}, }
@article {pmid41210074, year = {2025}, author = {Lin, L and You, W and Liao, Y and Wu, B and Lin, H and Huang, Z and Zeng, J and Zhang, Z and Huang, C and Li, W and Fang, X}, title = {Impact of Antibiotic Exposure Duration on Pathogen Detection in Periprosthetic Joint Infection.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {5661-5670}, pmid = {41210074}, issn = {1178-6973}, abstract = {OBJECTIVE: Antibiotic exposure affects pathogen detection in periprosthetic joint infection (PJI). This study evaluated the impact of antibiotic duration before sampling on the diagnostic performance of microbiological cultures and metagenomic next-generation sequencing (mNGS).<br><br>METHODS: We conducted a retrospective analysis of 153 patients with PJI treated at our center between January 2013 and March 2024. Patients who had discontinued antibiotics for at least 7 days before sampling and those with no history of antibiotic use were classified into the antibiotic-withdrawal group (AWD group). Based on the duration of antibiotic exposure, those who received antibiotics for &#x2264;7 days before sampling was assigned to the short-term antibiotic group (STA group), while those with >7 days of continuous antibiotic use were included in the long-term antibiotic group (LTA group). By comparing microbiological culture and mNGS results across these groups, we analyzed how antibiotic duration before sampling affects etiological diagnosis in PJI patients.<br><br>RESULTS: In the AWD group, microbial culture positivity (86.3%, 44/51) was comparable to mNGS (92.2%, 47/51; P=0.338). However, mNGS demonstrated superior positivity rates in both the STA (86.7% vs 70.0%, P=0.027) and LTA groups (76.2% vs 54.8%, P=0.039). Prolonged antibiotic use (>7 days) markedly reduced culture positivity (86.3% to 54.8%, P=0.001), whereas the decline in mNGS sensitivity was smaller (92.2% to 76.2%, P=0.032), indicating its greater resistance to antibiotic effects. Among culture-negative PJI cases, mNGS maintained robust diagnostic performance across all groups (CN-AWD: 57.1%; CN-STA: 66.7%; CN-LTA: 57.9%), with no significant differences observed.<br><br>CONCLUSION: Antibiotic use before sampling significantly impacts PJI pathogen detection. We recommend either: (1) sampling after &#x2265;7 days without antibiotics, or (2) for patients on prolonged antibiotics (>7 days), combining microbial culture with routine mNGS to improve diagnostic accuracy.}, }
@article {pmid41209715, year = {2025}, author = {Yadav, P and Kumar, A and Ram, K and Kumar, A and Gupta, RK and Dufossé, L}, title = {Microbial degradation of microplastics: Effectiveness, challenges, and sustainable solutions.}, journal = {Current research in microbial sciences}, volume = {9}, number = {}, pages = {100495}, pmid = {41209715}, issn = {2666-5174}, abstract = {Microplastics (MPs), defined as plastic particles ranging from 1 µm to 5 mm, have emerged as pervasive contaminants in both terrestrial and aquatic environments, posing significant ecological and human health risks. Their sources are broadly categorized as primary, such as microbeads, microfibres, paints and pharmaceutical additives, and secondary, which result from the degradation of larger plastic products. This growing concern of MPs led to development of different mitigation techniques but the recent advancements in microbial biodegradation present a promising approach to mitigating MPs pollution. Thus, microbial biodegradation could play a crucial role in developing sustainable solutions to tackle global MPs pollution. This review explores the potential of various microorganisms, including bacteria, fungi, and algae, in degrading MPs through enzymatic processes, thereby shortening the half-life of these pollutants. A detailed examination of the degradation mechanisms of commonly used polymers such as polyethylene, polystyrene, and polyvinyl chloride highlights the efficacy and limitations of microbial biodegradation. Despite the promising capabilities of certain strains, the overall weight loss rate of MPs remains quite low, typically ranging from 0 to 15%, necessitating further investigation into optimizing enzymatic activity and environmental conditions. Advancements in metagenomics and enzyme engineering offer pathways to enhance degradation efficiency, potentially achieving up to 90% degradation within 10 hrs under optimized conditions. This review underscores the need for comprehensive research to identify key microbial strains and enzymes involved, understand their degradation pathways, and investigate the influence of different environmental matrices on biodegradation processes.}, }
@article {pmid41208101, year = {2025}, author = {Paul, JK and Akter, A and Jewel, NA and Rolin, MH and Karim, D and Niloy, RK and Mondal, SI}, title = {Exploration of Human Skin Phageome to Reveal Endolysins and Novel Antimicrobial Peptides for Therapeutic Applications.}, journal = {MicrobiologyOpen}, volume = {14}, number = {6}, pages = {e70115}, doi = {10.1002/mbo3.70115}, pmid = {41208101}, issn = {2045-8827}, support = {//The study was supported by the SUST Research Center (Grant number: LS/2023/1/05)./ ; }, abstract = {The global rise of antibiotic-resistant pathogens has intensified the search for alternative therapeutics. Bacteriophage-derived endolysins are emerging as promising candidates. They exhibit strong potential due to their target specificity, rapid bactericidal action, and low tendency to induce bacterial resistance. This study presents a comprehensive metagenomic analysis of the human skin phageome using 1564 samples from 10 metagenomic projects. Our analysis led to the classification of 696 phage genomes into clusters and singletons. These genomes displayed considerable variation in size, GC content (average 56%), and coding efficiency (72%). A total of 968 endolysins were identified, including 75 SAR variants, with diverse domain architectures such as CHAP, Amidase, and SH3, suggesting host-specific adaptations. Notably, we identified 37 previously unreported endolysin-derived antimicrobial peptides (AMPs), several of which exhibited nontoxic, antifungal, and antiviral properties. Molecular dynamics and docking studies revealed strong binding affinity and stability of peptides EP-464 and EP-519 to key virulence factors, including Staphylococcus epidermidis autolysin (PDB: 4EPC), beta-lactamase VIM-2 (PDB: 5O7N), and AHL synthase LasI (PDB: 1RO5). These interactions suggest potential for disrupting bacterial virulence, resistance mechanisms, and quorum sensing. This study provides the first large-scale functional characterization of the human skin phageome focused on therapeutic endolysins and their novel AMP derivatives, offering promising candidates for the development of next-generation antimicrobial agents. However, further experimental validation is essential to assess their clinical efficacy in treating skin-related infections.}, }
@article {pmid41207803, year = {2025}, author = {You, TY and Chen, YW and Chen, SY and Jan, HE and Lee, NY and Ko, WC}, title = {Etiological identification of Rickettsia typhi and Coxiella burnetii by metagenomic next-generation sequencing among adults with acute febrile illness in southern Taiwan.}, journal = {Journal of the Formosan Medical Association = Taiwan yi zhi}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jfma.2025.11.012}, pmid = {41207803}, issn = {0929-6646}, }
@article {pmid41207298, year = {2025}, author = {Zhai, Z and Che, X and Shen, W and Zhang, Z and Li, Y and Pan, J}, title = {HLRMDB: a comprehensive database of the human microbiome with metagenomic assembly, taxonomic classification, and functional annotation by analysis of long-read and hybrid sequencing data.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkaf1152}, pmid = {41207298}, issn = {1362-4962}, support = {32470699//National Natural Science Foundation of China/ ; //Chongqing Medical University/ ; }, abstract = {The human microbiome harbours an immense diversity of uncultivated microbes; short-read metagenomic sequencing has elucidated much of this diversity, but fragment repeats and mobile elements constrain strain-level resolution. Fortunately, long-read metagenomic sequencing can generate reads spanning tens of kilobases with single-molecule accuracies exceeding 99%, enabling near-complete genome and gene cluster recovery in a cultivation-independent manner. However, systematic resources that aggregate and standardise long-read outputs remain limited. Here, we present HLRMDB (http://www.inbirg.com/hlrmdb/), a comprehensive database of human microbiome datasets derived from long-read and hybrid metagenomic sequencing. We curated 1672 publicly available metagenomes (1291 long reads; 381 hybrids) spanning 38 studies, 39 sampling contexts and 42 host health states. A uniform assembly and binning pipeline reconstructed >98 Gb of contigs and yielded 18 721 metagenome-assembled genomes (MAGs). These MAGs span 21 phyla and 1323 bacterial species, with 6339 classified as near-complete and 5609 as medium-quality. HLRMDB integrates these genome-resolved data with extensive gene-centric functional profiles and antimicrobial resistance annotations. An interactive web interface supports flexible access to both sample-level and genome-level results, with multiple visualisations linking raw reads to assembled genomes. Overall, HLRMDB offers a harmonised, long-read-oriented repository that supports reproducible, strain-resolved comparative genomics and context-sensitive ecological investigations of the human microbiome.}, }
@article {pmid41207243, year = {2025}, author = {Kumalo, PC and Amoah, ID and Pierneef, RE and Ismail, A and Bux, F and Kumari, S}, title = {Unveiling the role of aeration systems in the bioaerosol emission rate, particle size and microbial composition from wastewater treatment plants.}, journal = {Journal of hazardous materials}, volume = {500}, number = {}, pages = {140394}, doi = {10.1016/j.jhazmat.2025.140394}, pmid = {41207243}, issn = {1873-3336}, abstract = {Wastewater treatment plants (WWTPs) are important sources of bioaerosols; however, the influence of aeration on emission characteristics, particle size distribution, and microbial composition remains poorly studied. This study investigates how surface aeration (SA) and diffused aeration (DA) systems affect bioaerosol emission rates, particle size distribution, and microbial diversity using an 8-stage Andersen cascade impactor and shotgun metagenomics. Bioaerosol emission rates were estimated by combining measured particle concentrations with system-specific airflow rates. Abiotic factors were analysed through redundancy analysis to determine their influence on community structure. SA consistently generated higher emission rates, particularly in respirable particles (0.43-2.1 µm), which are capable of deep respiratory deposition. Dominant taxa included Rhodococcus, Pseudomonas, Bacillus, Meyerozyma, and Siphoviridae, with SA showing higher relative abundance of opportunistic pathogens even in smaller particle sizes. In contrast, DA systems exhibited a lower emission rate but broader microbial diversity, reflecting more stable aeration conditions. The study indicated that activated sludge was the main source of microbial populations, with a larger bioaerosol -activated sludge overlap in SA than DA. Redundancy analysis revealed that wind speed (WS) and relative humidity (RH) significantly influenced bacterial and viral populations, while WS and air temperature (AT) affected eukaryotes. Notably, SA emissions decreased with distance (100 m), while DA emissions increased. By quantifying emission rates rather than concentrations and integrating high-throughput metagenomics, this study provides a comprehensive framework for characterising bioaerosol hazards in WWTPs. These findings highlight the need for mitigation strategies in WWTPs, especially near SA systems.}, }
@article {pmid41207031, year = {2025}, author = {Ren, Y and Li, Y and Lei, Y and He, R and Fu, J and Ma, D and Zhong, G}, title = {Deciphering microbial and metabolite dynamics in rice noodle fermentation: A metagenomic and untargeted metabolomic approach.}, journal = {Food chemistry}, volume = {497}, number = {}, pages = {147011}, doi = {10.1016/j.foodchem.2025.147011}, pmid = {41207031}, issn = {1873-7072}, abstract = {Inoculated fermentation accelerates rice noodle production and improves quality, but the underlying microbe-metabolite dynamics remain unclear. This study employed metagenomic and non-targeted metabolomic profiling to investigate microbial succession and metabolic transformations during fermentation. Lacticaseibacillus rhamnosus, Lactococcus cremoris, and Saccharomyces cerevisiae were identified as dominant strains, with Lacticaseibacillus rhamnosus rapidly outcompeting other microbes and suppressing Klebsiella pneumoniae and Salmonella enterica by over 70 %. At 6 h, rice noodle hardness and springiness improved markedly, driven by microbial shifts and metabolic outputs. Metabolomic analysis identified 1405 metabolites, of which 57 showed significant changes: aspartic and citric acid levels declined by 14.99 % and 33.16 %, while citrulline, γ-aminobutyric acid, lactate, and Cinnamic acid increased by 16.38 %, 8.96 %, 70.69 %, and 63.90 %, respectively. Enzyme annotation indicated α-amylase and glycogen synthase regulate starch degradation and amylose synthesis. These findings provide insights into the microbial and metabolic mechanisms that enhance the quality of fermented rice noodles.}, }
@article {pmid41206939, year = {2025}, author = {Yu, H and Xu, Y and Chen, D and Gong, M and Sun, W and Liu, M and Zhang, T and Xue, J}, title = {The application of mNGS of bronchoalveolar lavage fluid in dissecting pulmonary infections in patients with CTD-ILD.}, journal = {Rheumatology (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/rheumatology/keaf571}, pmid = {41206939}, issn = {1462-0332}, abstract = {OBJECTIVES: To evaluate the application of metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) in the diagnosis of pulmonary infection in patients with connective tissue disease-associated interstitial lung disease (CTD-ILD).<br><br>METHODS: Patients with CTD-ILD who had been evaluated for suspected pulmonary infection by mNGS of BALF were identified, and were then categorized either as pulmonary infection or non-infectious disease progression of CTD-ILD based on clinical composite assessment. The performance of mNGS in the diagnosis of pulmonary infection was compared with that of conventional microbiological tests (CMTs).<br><br>RESULTS: In the 48 patients with CTD-ILD who had been evaluated for pulmonary infection by mNGS of BALF, the majority (66.67%) were patients with idopathic inflammatory myopathy-associated ILD (IIM-ILD). According to the clinical composite assessment, 36 patients were classified as pulmonary infection and 12 as non-infectious disease progression. Cytomegalovirus (CMV), pneumocystis jirovecii, and aspergillus were among the most common causative pathogens. While mNGS was superior in identifying bacteria, viruses, and pneumocystis jirovecii, CMTs identified more aspergillus and cryptococcus. Decreased albumin, reduced immunoglobulin M, and increased lactate dehydrogenase (LDH) were predictors for pulmonary infections in CTD-ILD. Short disease duration, decreased lymphocytes, and reduced immunoglobulins were predictive of infection with pneumocystis jirovecii. Older age and increased serum ferritin were more common in patients with aspergillus infection.<br><br>CONCLUSION: Pulmonary infections are common in patients with CTD-ILD. mNGS has the advantages of rapidly detecting more bacteria, viruses, and pneumocystis jirovecii. However, infection with aspergillus should be more rigorously evaluated in combination with CMTs.}, }
@article {pmid41206936, year = {2025}, author = {Borman, T and Sannikov, A and Finn, RD and Limborg, MT and Rogers, AB and Kale, V and Hanhineva, K and Lahti, L}, title = {HoloFoodR: a statistical programming framework for holo-omics data integration workflows.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btaf605}, pmid = {41206936}, issn = {1367-4811}, abstract = {SUMMARY: Holo-omics is an emerging research area that integrates multi-omic datasets from the host organism and its microbiome to study their interactions. Recently, curated and openly accessible holo-omic databases have been developed. The HoloFood database, for instance, provides nearly 10,000 holo-omic profiles for salmon and chicken under controlled treatments. However, bridging the gap between holo-omic data resources and algorithmic frameworks remains a challenge. Combining the latest advances in statistical programming with curated holo-omic data sets can facilitate the design of open and reproducible research workflows in the emerging field of holo-omics.<br><br>HoloFoodR R/Bioconductor package and the source code are available under the open-source Artistic License 2.0 at the package homepage https://doi.org/10.18129/B9.bioc.HoloFoodR.<br><br>SUPPLEMENTARY INFORMATION: Available in the package vignette https://ebi-metagenomics.github.io/HoloFoodR/articles/case_study.html.}, }
@article {pmid41206740, year = {2025}, author = {Lage, OM and Godinho, O and García-Domínguez, R and Øvreås, L and Devos, DP}, title = {A century of research on Planctomycetota bacterial phylum, previously known as Planctomycetes.}, journal = {FEMS microbiology reviews}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsre/fuaf056}, pmid = {41206740}, issn = {1574-6976}, abstract = {100 years after Planctomycetes were discovered and fifty years since the first isolate was successfully cultured, this bacterial phylum remains enigmatic in many ways. In the last few decades, a significant effort to characterize new isolates has resulted in over 150 described species, allowing a more comprehensive analysis of their features. However, metagenomic studies reveal that a diverse group of Planctomycetes has yet to be cultured and characterized, and that many biological surprises are yet to bee revealed. This is the case for the recently discovered phagotrophic Candidatus Uabimicrobium, which challenges our understanding of the distinction between prokaryotes and eukaryotes. The unique biology of Planctomycete cells, such as their ability to divide without the FtsZ protein, their complex structure and characteristic morphology, their relatively large genomes containing many genes with unknown function, and their variable metabolic capabilities, imposes significant barriers for researchers. Although ubiquitous, the precise ecological roles of Planctomycetes in various environments are still not fully understood. However, their distinctive metabolism opens the door to a great potential of biotechnological applications, which are beginning to be unveiled. In this article, we first review the historical milestones in Planctomycetes research and describe the pioneers of the field. We then describe the controversies and their resolutions, we highlight the past discoveries and current interrogations related to Planctomycetes and discuss the ongoing challenges that hinder a comprehensive understanding of their biology. We end up with directions for exploring the biology and ecological roles of these fascinating organisms.}, }
@article {pmid41206659, year = {2025}, author = {Siddiqui, R and Maciver, SK and Khan, NA}, title = {Beyond Predation: Potential Metabolic Roles of Intracellular Bacteria in Acanthamoeba Ecology.}, journal = {FEMS microbiology letters}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsle/fnaf124}, pmid = {41206659}, issn = {1574-6968}, abstract = {Although Acanthamoeba is well known as a reservoir and "Trojan horse" for other microbes, its relationship with intracellular organisms may extend beyond protection. Here, we discuss that certain bacteria contribute metabolically to the host, breaking down complex substrates and providing nutrients that expand its ecological adaptability. The proposed model reframes amoebae not only as predators and shelters, but also as metabolic consortia, with implications for environmental microbiology, protist ecology, and the evolution of opportunistic pathogens. Further studies using integrated multi-omics and co-culture approaches, combining metagenomic and metabolomic profiling of Acanthamoeba-bacteria interactions and transcriptomic analyses will help identify bidirectional metabolic exchange and functional gene expression within the symbiosis.}, }
@article {pmid41206461, year = {2025}, author = {Kifushi, M and Nishikawa, Y and Hosokawa, M and Anai, T and Takeyama, H}, title = {Strain-level dissection of complex rhizoplane and soil bacterial communities using single-cell genomics and metagenomics.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {}, number = {}, pages = {}, doi = {10.1093/dnares/dsaf032}, pmid = {41206461}, issn = {1756-1663}, abstract = {Root exudates shape root-associated microbial communities that differ from those in soil. Notably, specific microorganisms colonize the root surface (rhizoplane) and strongly associate with plants. Although retrieving microbial genomes from soil and root-associated environments remains challenging, single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) are essential for studying these microbiomes. This study compared SAGs and MAGs constructed from short-read metagenomes of the same soil samples to clarify their advantages and limitations in soil and root-associated microbiomes, and to deepen insights into microbial dynamics in rhizoplane. We demonstrated that SAGs are better suited than MAGs for expanding the microbial tree of life in soil and rhizoplane environments, due to their greater gene content, broader taxonomic coverage, and higher sequence resolution of quality genomes. Metagenomic analysis provided sufficient coverage in the rhizoplane but was limited in soil. Additionally, integrating SAGs with metagenomic reads enabled strain-level analysis of microbial dynamics in the rhizoplane. Furthermore, SAGs provided insights into plasmid-host associations and dynamics, which MAGs failed to capture. Our study highlights the effectiveness of single-cell genomics in expanding microbial genome catalogs in soil and rhizosphere environments. Integrating high-resolution SAGs with comprehensive rhizoplane metagenomes offers a robust approach to elucidating microbial dynamics around plant roots.}, }
@article {pmid41205488, year = {2025}, author = {Lv, AP and Ying-Han,  and Fang, BZ and Wang, GZ and Liu, MC and Bian, BR and Zheng, ZH and Li, K and Li, BY and Jiao, JY and Liu, L and Dong, L and Chen, LQ and Yang, F and Li, WJ}, title = {Metagenome-assembled genomes reveal Pseudogracilibacillus amylolyticus sp. nov., a functional uncultured microorganism in high-temperature Daqu.}, journal = {Systematic and applied microbiology}, volume = {48}, number = {6}, pages = {126667}, doi = {10.1016/j.syapm.2025.126667}, pmid = {41205488}, issn = {1618-0984}, abstract = {Daqu, a traditional fermentation starter for Chinese liquor production, harbors a complex microbial community that plays a pivotal role in shaping the flavor and quality of the final product of Baijiu. This study characterized three metagenome-assembled genomes (MAGs) from high-temperature Daqu of Jiang-flavor Baijiu, revealing a novel taxon within the genus Pseudogracilibacillus. Phylogenomic analysis demonstrated that three MAGs (A3-12A_bin_9[TS], M2-6-2A_bin_27 and M2-7-9A_bin_18) formed a distinct monophyletic clade, supported by the threshold value of ANI recommended for bacterial species, while showing significant divergence from other related type species within the genus Pseudogracilibacillus. Functional annotation revealed the metabolic versatility of this taxon, including starch and aromatic compound degradation (potentially contributing to flavor formation), biosynthetic capacity and adaptive traits such as oxidative phosphorylation flexibility and ABC transporter diversity, underscoring its ecological role in Daqu fermentation. Based on genomic and phylogenetic characteristics, these MAGs should be classified as representing a new taxon of this genus, for which the name Pseudogracilibacillus amylolyticus sp. nov. is proposed following the rules of the published Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). This discovery expands the diversity of the family Bacillaceae in Baijiu fermentation and provides insights into the functional potential of uncultured microbes in traditional food ecosystems.}, }
@article {pmid41205408, year = {2025}, author = {Bao, C and Ma, Y and Li, M and Li, Y and Zhang, C and Liu, X and Fan, R and Cui, W and Fan, X and Zheng, F and Duan, F and Liu, J}, title = {Assessment of glymphatic dysfunction in ulcerative colitis using DKI-ALPS: An innovative imaging biomarker.}, journal = {Journal of neuroradiology = Journal de neuroradiologie}, volume = {53}, number = {1}, pages = {101402}, doi = {10.1016/j.neurad.2025.101402}, pmid = {41205408}, issn = {0150-9861}, abstract = {PURPOSE: Ulcerative colitis (UC) is associated with higher anxiety, depression, and cognitive disorders linked to brain glymphatic dysfunction. In this study, we used along-the-perivascular-space (ALPS) index (based on DTI and DKI) to determine if UC relates to glymphatic dysfunction and explore how microbiota dysbiosis and inflammation affect brain glymphatic function.<br><br>MATERIALS AND METHODS: In this study, 63 patients with UC and 68 healthy controls underwent 3-Tesla MRI scans to evaluate DTI-ALPS and DKI-ALPS index. The protocol included diffusion-weighted imaging (DWI) and diffusion kurtosis imaging (DKI) sequences to calculate the ALPS index, which quantifies glymphatic system function. All participants completed cognitive (MMSE) and depression (SAS/SDS) assessments (SAS/SDS). Patients with UC also underwent assessment for inflammation and gut microbiota (based on metagenomic analysis). Data analysis was performed using correlation analysis and linear regression.<br><br>RESULTS: Patients with UC showed lower DTI-ALPS index (1.25) and DKI-ALPS index (1.40) compared to controls (1.40 vs. 1.69; P < 0.001). In multi-adjusted linear regression models, UC was associated with lower DTI-ALPS index and DKI-ALPS index (&#x3b2; =-0.142 vs.-0.284), with DKI-ALPS showing higher sensitivity. The results remained significant even after stratification by age and sex. The Mayo score correlated negatively with DTI and DKI-ALPS index. The ALPS index correlates with gut microbiota, particularly those involved in butyrate and short-chain fatty acid (SCFA) production. DTI-ALPS index was significantly correlated with ESR (&#x3b2; =-0.003), CRP (&#x3b2; =-0.035), SII (&#x3b2; =-0.062), INFLA (&#x3b2; =-0.010), and SIRI (&#x3b2; =-0.058). We also observed significant correlations between DKI ALPS index and ESR (&#x3b2; =-0.006), CRP (&#x3b2; =-0.051), SII (&#x3b2; =-0.130), INFLA (&#x3b2; =-0.017), SIRI (&#x3b2; =-0.095), IL-6 (&#x3b2; =-0.081) and NLR (&#x3b2; =-0.108).<br><br>CONCLUSIONS: UC is associated with brain glymphatic dysfunction, correlating with inflammation level. DKI-ALPS serves as a more sensitive method than DTI-ALPS, offering a new approach for managing ulcerative colitis through glymphatic dysfunction.}, }
@article {pmid41205292, year = {2025}, author = {Smallbone, JA and Gregson, BH and McGenity, TJ and Holland, RD and Whitby, C and Cameron, TC and Chamberlain, J and Clift, LG and Hynes, C and McKew, BA}, title = {Effects of the 2023 Poole Harbour oil spill on sediment bacterial communities and ecosystem functioning.}, journal = {Marine pollution bulletin}, volume = {222}, number = {Pt 3}, pages = {118904}, doi = {10.1016/j.marpolbul.2025.118904}, pmid = {41205292}, issn = {1879-3363}, abstract = {In March 2023, approximately 27 t of fluid from an oil and gas reservoir (containing approximately 85 % water and 15 % crude oil spilt from a fractured pipeline beneath Ower Bay creek, entering Poole Harbour (Dorset, UK). This event provided a unique opportunity to investigate the impacts of hydrocarbon contamination on microbial communities in-situ in a temperate coastal, shallow, fine sediment environment. Our aims were to quantify hydrocarbon concentrations (via gas chromatography mass spectrometry (GC-MS)) and effects on microbial community structure and functional potential (via metagenomic sequencing) to understand the capacity for microbial biodegradation across the impacted region. Hydrocarbon contamination was localised to the Spill Site (approximately an area of 1500 m[2]) at the head of the creek, with minimal impact at the Mid Point (164 m from the Spill Site) and End Point (387 m from the Spill Site) and with no indication of contamination at Brownsea Island located in the heart of the harbour. By October 2023, n-alkane and 4-5 ring PAH concentrations had declined to background levels, highlighting the combined effects of the remediation response and natural hydrocarbon biodegradation at the Spill Site. Clear changes in bacterial community structure were observed in the seven months following the spill, with notable hydrocarbon-degrading bacteria i.e. Anaerolinea, Thiobacillus and Dechloromonas favouring the Spill Site, suggesting a significant increase in anaerobic biodegradation occurred as a result of significant increase in assA (anaerobic alkylsuccinate synthase), abcA (anaerobic benzene carboxylase) and ahyA (anaerobic alkane hydroxylase) genes. Overall, 24 alkane and aromatic hydrocarbon degradation genes, from both aerobic and anaerobic degradation pathways, were identified from contigs throughout the study site, being present within 48 out of 221 Metagenome-Assembled Genomes (MAGs), highlighting the sites capacity for hydrocarbon biodegradation under both aerobic and anaerobic conditions.}, }
@article {pmid41205042, year = {2025}, author = {Zolkefli, N and Shui, X and Ma, K and Mustapha, NA and Maeda, T}, title = {Unveiling the Impact of Indole Derivatives on Methanogenic Archaea and Microbial Functions in Anaerobic Digestion of Waste Sewage Sludge.}, journal = {Applied biochemistry and biotechnology}, volume = {}, number = {}, pages = {}, pmid = {41205042}, issn = {1559-0291}, abstract = {As an interspecies-signaling molecule, indole that is also regulating the microbial community quorum sensing (QS) can be an indispensable factor in influencing the performance of an anaerobic digestion process. Mainly released by Gram-negative bacteria, the impact of indole regulation on methane production in such a system is hardly exposed. This research intends to analyze the methane production affected by the microbial community fluctuations in the waste sewage sludge (WSS) in response to QS repression by indole and its analogs: 4-fluoroindole (4-FI), 5-fluoroindole (5-FI), 6-fluoroindole (6-FI), 3-indoleacetic acid (3-IAA), and 3-indoleacrylic acid (3-IARA). Illumina MiSeq platform was utilized to delve into the active microbes, with ribonucleic acid (RNA) used as the template to generate the 16S metagenomic library. As results, all of them inhibit methane generation even with substrates (acetic acid) availability, and this phenomenon can be led by the slight imbalance of Gram-positive/negative bacterial composition and the inactivation of the viable core fermenters: Firmicutes, Proteobacteria, and Chloroflexi. Plus, the following compounds, indole, 3-IAA, and 6-FI directly disrupted methane production by both acetoclastic and hydrogenotrophic methanogenic archaea. Methanosarcina acetivorans C2A, as a prominent methane synthesizer, was also characterized in terms of its viability and methane synthesis activity against them. Notably, Methanosarcina acetivorans C2A was non-viable in the presence of indole and 6-FI, thus lowering methane production. From here, the affirmation of the direct and indirect inhibitions of methanogenic archaea by indole and its derivatives will pave the way for a valuable future exploration of QS mechanism mapping in archaea during methanogenesis.}, }
@article {pmid41204634, year = {2025}, author = {Yuan, L and Li, Y and Wang, Z and Xie, X and Wu, Q}, title = {Gut Microbiota-Mediated Antihypertensive Effects of Probiotic Fermented Milk: A Multi-Omics Study.}, journal = {Journal of food science}, volume = {90}, number = {11}, pages = {e70654}, doi = {10.1111/1750-3841.70654}, pmid = {41204634}, issn = {1750-3841}, support = {21977020//National Natural Science Foundation of China/ ; 2022B1111070006//the Key-Area Research and Development Program of Guangdong Province/ ; 2020GDASYL-20200102003//GDAS' Project of Science and Technology Development/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Probiotics/pharmacology ; Rats, Inbred SHR ; *Antihypertensive Agents/pharmacology ; Rats ; *Hypertension/diet therapy ; Male ; Blood Pressure/drug effects ; *Cultured Milk Products/microbiology ; Fermentation ; Lactobacillus plantarum/metabolism ; Renin-Angiotensin System/drug effects ; Metabolomics ; Multiomics ; }, abstract = {The precise molecular mechanisms through which gut microbiota mediate the antihypertensive effects of probiotic fermented milk (PFM) remain largely unexplored. This study aimed to elucidate these mechanisms by employing a multi-omics approach, combined with metagenomic deep sequencing technology, non-targeted metabolomics technology, and antibody chip protein detection technology to elucidate the potential mechanisms behind the antihypertensive effects of milk fermented by Lactiplantibacillus plantarum SR37-3 (PFM-SR37-3) in spontaneously hypertensive rats (SHR). Our findings demonstrate that PFM-SR37-3 intervention significantly reduces blood pressure in SHR and is associated with partial inactivation of the renin-angiotensin system (RAS). Notably, long-term administration of PFM-SR37-3 inhibited the progressive rise in systolic blood pressure (SBP), with final measurements of 187.17 ± 3.61 mmHg in the model group versus 172.21 ± 11.81 mmHg in the PFM-SR37-3-treated group after 4 weeks (p < 0.01). PFM-SR37-3 modulates key host metabolic pathways (especially arachidonic acid metabolism) by reshaping the gut microbiota (such as enrichment of Lactobacillaceae), with concomitant reductions in the levels of proinflammatory cytokines (such as ICAM-1 and Fractalkine). This "gut-immune" pathway is an important complement to its partial inhibition of the RAS. Collectively, these data highlight strong associations between PFM-induced gut microbial shifts and antihypertensive effects, providing a multi-faceted view of the potential mechanisms and underscoring the therapeutic potential of PFM in managing hypertension.}, }
@article {pmid41204581, year = {2025}, author = {Zhuang, Q and Xu, R and Sun, X and Pan, X and Wan, L and Li, S and Chen, H and Yu, X and Zheng, L and Yu, Y and Deng, Z and Zheng, X and Chen, Z}, title = {Performance of metagenomic next-generation sequencing in bronchoalveolar lavage fluid for pathogen detection in patients with acute exacerbations of bronchiectasis.}, journal = {Medicine}, volume = {104}, number = {45}, pages = {e45606}, doi = {10.1097/MD.0000000000045606}, pmid = {41204581}, issn = {1536-5964}, support = {FYQM-LC-202003//The Affiliated Hospital of Medical School of Ningbo University Youth Talent Cultivation Program/ ; 2021Y13//Ningbo Medical Science and Technology Program/ ; 2015C50012//Ningbo Social and Scientific Development Fund/ ; 2020SWSQNGG-05//Ningbo Health Youth Technical Key Talents Training Special Project/ ; 2018A610271&#xe3;&#x20ac;2017A610250//the Natural Science Foundation of Ningbo/ ; 2022ZYC-Z31//Clinical Medicine Special Fund Project of Zhejiang Medical Association/ ; Normal project No.6//Special Project on Scientific and Technological Research of COVID-19 Infection Diseases/ ; 2016KYB268//Medical Health Science and Technology Project of Zhejiang Provincial Health Commission/ ; }, mesh = {Humans ; *Bronchiectasis/microbiology ; *Bronchoalveolar Lavage Fluid/microbiology ; Male ; Retrospective Studies ; Female ; Middle Aged ; *High-Throughput Nucleotide Sequencing/methods ; Aged ; *Metagenomics/methods ; Pseudomonas aeruginosa/isolation &amp; purification ; Sensitivity and Specificity ; }, abstract = {This study aimed to evaluate the diagnostic value of metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) in detecting pathogens among bronchiectasis patients with acute exacerbations. A retrospective analysis was conducted on 89 bronchiectasis patients who were treated for acute exacerbations at the First Affiliated Hospital of Ningbo University from April 1, 2021, to September 30, 2023. Among the 89 patients, 88 were diagnosed with pulmonary infection, of which 15.9% (14/88) were cases of mixed infections. The sensitivity of BALF-mNGS for detecting pathogens in bronchiectasis patients during acute exacerbations was significantly higher than that of BALF culture (93.2% vs 28.4%; P < .001). All cases of mixed infection were fully identified by BALF-mNGS. The most common pathogens in patients with bronchiectasis were Pseudomonas aeruginosa, nontuberculous mycobacteria, Haemophilus influenzae, and Aspergillus. In conclusion, compared with the traditional microbial culture method, BALF-mNGS significantly improves the accuracy of diagnosis for detecting pathogens associated with bronchiectasis infections.}, }
@article {pmid41204496, year = {2025}, author = {Tian, J and Dong, J and Yu, G and Guan, W}, title = {Bronchoscopy-associated dissemination of pulmonary nocardiosis caused by Nocardia terpenica in an immunocompetent patient with bronchiectasis: A case report.}, journal = {Medicine}, volume = {104}, number = {45}, pages = {e45875}, doi = {10.1097/MD.0000000000045875}, pmid = {41204496}, issn = {1536-5964}, mesh = {Humans ; Female ; *Nocardia Infections/drug therapy/diagnosis/etiology/microbiology ; Middle Aged ; *Bronchoscopy/adverse effects ; *Bronchiectasis/complications ; *Nocardia/isolation &amp; purification ; Anti-Bacterial Agents/therapeutic use/administration &amp; dosage ; Bronchoalveolar Lavage/adverse effects ; Trimethoprim, Sulfamethoxazole Drug Combination/therapeutic use/administration &amp; dosage ; Bronchoalveolar Lavage Fluid/microbiology ; Immunocompetence ; }, abstract = {RATIONALE: Bronchoscopy with bronchoalveolar lavage (BAL) is essential for diagnosing pulmonary infections; however, its potential to iatrogenically disseminate a localized Nocardia infection represents a severe and unreported risk. This case aims to alert clinicians to this danger and underscore essential therapeutic lessons for disseminated disease.<br><br>PATIENT CONCERNS: A 51-year-old immunocompetent woman with longstanding bronchiectasis presented with 1-day of hemoptysis and a 40-year history of chronic cough and sputum production. These symptoms had worsened over the preceding 2 months despite broad-spectrum antibiotic therapy.<br><br>DIAGNOSES: Bronchiectasis was diagnosed based on chronic respiratory symptoms and characteristic computed tomography findings. Nocardia terpenica infection was confirmed by BAL fluid culture and metagenomic next-generation sequencing. Within 24 hours post-BAL, the patient developed fever, respiratory failure, and new bilateral consolidations on computed tomography, indicating procedure-related disseminated nocardiosis.<br><br>INTERVENTIONS: Diagnostic bronchoscopy with BAL was performed. Therapeutically, the patient received a total of 24 days of intensive combination therapy with intravenous imipenem/cilastatin and oral trimethoprim-sulfamethoxazole (TMP-SMX), followed by sequential long-term oral TMP-SMX monotherapy.<br><br>OUTCOMES: The initial 10-day course of combination therapy led to rapid clinical improvement, with resolution of fever and respiratory failure within 3 days, and normalization of C-reactive protein levels by day 10. Radiographic improvement was also evident. However, relapse (recurrent fever and malaise) occurred promptly within 3 days after de-escalation to TMP-SMX monotherapy. After reinstitution of imipenem/cilastatin plus TMP-SMX for an additional 14 days (totaling 24 days of intensive therapy), the patient achieved sustained clinical and radiographic remission. She was successfully discharged on long-term TMP-SMX monotherapy and remained well at the 2-month follow-up.<br><br>LESSONS: This is the first report suggesting that bronchoscopy, particularly BAL, can disseminate a localized airway Nocardia infection, causing acute disseminated pulmonary nocardiosis. Extreme caution is warranted when performing bronchoscopy in bronchiectasis patients with suspected or confirmed nocardiosis. For disseminated pulmonary nocardiosis, intensive combination therapy for at least 3 weeks is mandatory to prevent relapse, regardless of a rapid initial response.}, }
@article {pmid41203618, year = {2025}, author = {Moriel, N and Jones, L and Harpenas, E and Rakow, N and Shmorak, S and Eventov Friedman, S and Ofek Shlomai, N and Yassour, M}, title = {Development of the preterm infant gut and gastric residuals microbiome.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {9848}, pmid = {41203618}, issn = {2041-1723}, mesh = {Humans ; *Infant, Premature ; Infant, Newborn ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Female ; Male ; Intensive Care Units, Neonatal ; Metagenomics ; Bacteria/classification/genetics/isolation &amp; purification ; *Stomach/microbiology ; Gestational Age ; Enteral Nutrition ; }, abstract = {Prematurity, defined as birth before 37 weeks of gestation, is the leading cause of mortality in children under five, affecting ~11% of live births worldwide (≈15 million annually). Despite advances in neonatal care, preterm infants remain at high risk of complications. In neonatal intensive care units, gastric residuals (GRs) are routinely monitored to guide enteral feeding, yet their microbial composition remains poorly understood. We performed metagenomic sequencing of 199 stool and 69 GR samples from 39 preterm infants during hospitalization to characterize stomach and gut microbiomes. To our knowledge, this is the first metagenomic sequencing of the GR in premature infants. We identified 11 GR microbial clusters, commonly dominated by Staphylococcus, Streptococcus, and Klebsiella, with microbial diversity correlating with aspiration frequency. Colonization was dynamic: early GR samples were enriched with Staphylococcus epidermidis and Bradyrhizobium, while later samples featured Escherichia coli, Staphylococcus hominis, and Streptococcus thermophilus. Stool samples formed eight microbial clusters, frequently enriched with Enterobacteriaceae. S. epidermidis was linked to higher gestational age and lower richness, whereas Bifidobacterium breve, a beneficial commensal, appeared later. Comparative analysis showed overlap between gut and gastric microbiota, with GR samples more dynamic and less subject-specific. Strain-level analysis revealed both individual-specific and widely shared taxa, including a pathogenic Klebsiella aerogenes strain associated with bacteremia, detectable a week before clinical isolation. These findings provide new insights into microbial colonization dynamics of preterm infants.}, }
@article {pmid41203352, year = {2025}, author = {Tonoli, A and Dalby, PA and Hailes, HC and Jeffries, JWE}, title = {Transketolase enzyme discovery and engineering.}, journal = {Methods in enzymology}, volume = {722}, number = {}, pages = {343-368}, doi = {10.1016/bs.mie.2025.07.002}, pmid = {41203352}, issn = {1557-7988}, mesh = {*Transketolase/genetics/metabolism/chemistry/isolation &amp; purification ; Substrate Specificity ; *Protein Engineering/methods ; Directed Molecular Evolution/methods ; Ribosemonophosphates/metabolism ; Metagenomics/methods ; Pyruvates ; }, abstract = {Transketolases (TKs) are important C-C bond forming enzymes that in vivo transfer a two carbon ketol unit to the acceptors d-ribose-5-phosphate or d-erythrose-4-phosphate. There is significant interest in biocatalytic applications where frequently the donor β-hydroxypyruvic acid is used. In recent years there has been interest in the discovery of new TKs with unique or robust properties that are an excellent starting point for mutagenesis, or that are able to accept new acceptors or donors. Similarly, TK mutagenesis has led to TKs with alternative substrate profiles. In this chapter, firstly an overview of the substrates accepted by TKs is briefly summarized. Then, metagenomic strategies for the discovery of unique TKs and how this approach has developed with an early example, and a more recent study on the discovery of 'split'-TKs, are described with methods. Finally, enzyme evolution methods and approaches to develop a wide range of TKs with modified substrate acceptance and improved stabilities are detailed.}, }
@article {pmid41203168, year = {2025}, author = {Vangah, SJ and Kermani, AA and Vali, H and Noghabi, KA and Zahiri, HS}, title = {Engineering Saccharomyces cerevisiae for the secretion of an acidic, halotolerant, and cold-adapted xylanase derived from the camel rumen metagenome: Enzyme characterization and strain assessment.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {148805}, doi = {10.1016/j.ijbiomac.2025.148805}, pmid = {41203168}, issn = {1879-0003}, abstract = {This study reports the development of a recombinant Saccharomyces cerevisiae strain engineered to produce and secrete a novel xylanase (rXylM) derived from the camel rumen metagenome. The recombinant enzyme exhibited optimal activity at 35 °C, pH 5.0, and retained 58 % of its activity even at 5 °C. The enzyme activity was not significantly affected by high sodium chloride (NaCl) concentrations up to 5 M. These properties characterize rXylM as an acidic, halotolerant, and cold-adapted xylanase. The combination of these adaptive traits in a single enzyme offers substantial advantages for industrial applications. Enzyme kinetic analysis was performed at 35 °C and pH 5.0 using beechwood xylan, wheat bran, and high-extraction wheat flour as substrates, yielding specific activities of 1190 U/mg, 1029 U/mg, and 383 U/mg respectively. Scanning electron microscopy (SEM) revealed noticeable morphological alterations indicating substantial degradation of the substrates following treatment with rXylM. The engineered strain, CEN.PK-Xyl, was assessed as a leavening agent for baking applications. Rheological analysis of the dough demonstrated a significant reduction in elasticity and viscous resistance, improving dough handling and kneading properties. Correspondingly, the resulting bread exhibited a significant decrease in hardness, gumminess, and chewiness, indicating an improvement in texture and overall quality. Cytotoxicity evaluation using the MTT assay showed that rXylM did not affect the viability of L929 mouse fibroblast cells under the tested conditions. The favorable biochemical properties and non-toxicity of rXylM, together with the established safety of S. cerevisiae, highlight CEN.PK-Xyl as a promising platform for applications in food, feed, bioprocessing, and fermentation.}, }
@article {pmid41203007, year = {2025}, author = {Li, H and Wang, X and Zhang, X and Mu, H and Hao, R and Li, Y and Liu, Q and Chi, R and Zhai, D}, title = {Disrupted Microbiome-Metabolome Networks Underlie Gut Barrier and Immune Imbalance in Severe Fever with Thrombocytopenia Syndrome.}, journal = {Microbes and infection}, volume = {}, number = {}, pages = {105586}, doi = {10.1016/j.micinf.2025.105586}, pmid = {41203007}, issn = {1769-714X}, abstract = {Severe fever with thrombocytopenia syndrome (SFTS) is a life-threatening tick-borne viral infection with a high mortality rate and limited treatment options. While gastrointestinal symptoms are common, the contribution of gut microbiome disruption to disease progression remains unclear. Previous studies have noted taxonomic shifts in SFTS-associated microbiota, but their functional and metabolic consequences have not been systematically characterized. We conducted an integrated metagenomic and metabolomic analysis of fecal samples from 20 SFTS patients and 20 healthy controls. At the time of admission, patients with SFTS exhibited acute-stage infection, characterized by symptoms such as fever, thrombocytopenia, and gastrointestinal disturbances. Metagenomic sequencing was used to assess the microbial gene content, taxonomic composition, and functional potential. Untargeted metabolomics analysis using liquid chromatography-tandem mass spectrometry (LC-MS/MS) was performed to profile fecal metabolites. The SFTS patients showed a significantly reduced microbial gene richness, alpha diversity, and compositional stability. Short-chain fatty acid (SCFA)-producing genera (e.g., Faecalibacterium and Roseburia) were depleted, while mucin-degrading and opportunistic taxa (e.g., Pseudomonas and Akkermansia) were enriched. Functionally, biosynthetic and homeostatic pathways were suppressed; while stress-adaptive, biofilm-forming, and virulence-associated pathways were elevated. Metabolomic profiling revealed depletion of anti-inflammatory metabolites (e.g., bile acids and curcumin sulfate) and enrichment of proinflammatory compounds (e.g., porphyrins and beta-tyvelose). Multi-omic correlation highlighted strong links between microbial disruption and altered metabolite production. In conclusion, SFTS is associated with significant alterations in the gut microbiome and its metabolic profile, which is characterized by the loss of beneficial microbial taxa and functions, alongside the emergence of virulence factors and stress-related signatures. These findings underscore the role of microbiome dysfunction in SFTS and suggest that microbiota-targeted strategies may offer supportive benefits, particularly in alleviating SFTS-associated gastrointestinal disturbances and secondary microbial imbalance.}, }
@article {pmid41202935, year = {2025}, author = {Wu, B and Cheng, Y and Gu, J and Yuan, H and Murphy, JD}, title = {Toward sustained and efficient n-caproate production: Insights into magnetite-encapsulated biochar mediated microbial chain elongation.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {133617}, doi = {10.1016/j.biortech.2025.133617}, pmid = {41202935}, issn = {1873-2976}, abstract = {Decarbonization of the chemical sector may be facilitated by microbial chain elongation, through conversion of organic waste into chemical products. Challenges in efficient interspecies electron transfer is a barrier to this technology. Here we introduce a magnetite-encapsulated biochar (Fe@biochar) amendment strategically integrated with chain elongation to facilitate sustained and efficient n-caproate production. This strategy increased n-caproate yields to 13.92 g COD/L, 199 % and 71 % higher than the control (4.66 g COD/L) and biochar (8.13 g COD/L) groups, respectively. Most importantly, Fe@biochar consistently enhanced n-caproate production after recycle, a continuity not observed with biochar. This difference may be attributed to the inhibitory effects of high concentrations of undissociated n-caproic acid (up to 9.06 mM or 2.32 g COD/L) on functional microbes in the biochar group. Microbial community analysis identified Clostridium_sensu_stricto as the key genus involved in n-caproate production. Comparative metagenomic and microbial activity analyses revealed the energy metabolism, where Fe@biochar promoted extracellular iron-based electron transfer, and further accelerated intracellular electron sinks. This is substantiated by a 3.6 fold increase in electron transfer system activity and evaluated relative abundances of key genes encoding acetyl-CoA synthetase (15.0 % increase), cytochrome c biosynthesis (28.7 % increase) and NADH dehydrogenase (48.0 % increase). This study offers a new paradigm for sustained n-caproate production.}, }
@article {pmid41202544, year = {2025}, author = {Zhang, H and Sun, H and Pan, X and Wu, D and Liang, H and Tang, J and Fang, H and Wu, X}, title = {Sediment archives urban-rural divergence in antibiotic resistance gene contamination within a freshwater lake.}, journal = {Journal of hazardous materials}, volume = {500}, number = {}, pages = {140322}, doi = {10.1016/j.jhazmat.2025.140322}, pmid = {41202544}, issn = {1873-3336}, abstract = {Freshwater lakes are critical ecosystems for sustaining biodiversity and human well-being, yet increasing anthropogenic activities threaten their ecological safety through pollution such as antibiotic resistance genes (ARGs). Previous studies on ARG pollution in aquatic systems have largely overlooked the distinct impacts of urban versus rural landscapes, limiting targeted mitigation strategies. Here, we investigate the urban-rural heterogeneity of ARG pollution in Chaohu lake, a major urban-rural junction lake in China, using shotgun metagenomic sequencing and Bayesian source-tracking approaches. Our findings reveal significant spatiotemporal variations in ARG abundance, with urban-adjacent regions (western lake) exhibiting 1.22- to 1.25-fold higher ARG levels than rural-adjacent areas (eastern lake) in water and sediments, respectively. Notably, a significant distance-decay relationship of ARG profiles was observed in sediments, highlighting that sediments act as a stable environmental archive recording the urban-rural divergence. Agricultural activities were identified as the dominant source lake-wide, contributing over 60 % of the total ARG load, thereby surpassing urban sewage inputs. Meanwhile, the abundance of mobile genetic elements (MGEs), particularly transposases, was significantly higher in the western lake, indicating a greater potential for horizontal gene transfer. The presence of multidrug-resistant, ARG-carrying pathogens, such as Stenotrophomonas maltophilia and Pseudomonas putida, was significantly enriched in these areas, correlating with higher ecological and health risks as quantified by the antibiotic resistome risk index. These results underscore the urgent need for landscape-specific management strategies to curb ARG dissemination, prioritizing agricultural non-point source control in urban-rural transitional zones to safeguard freshwater ecosystems and human health.}, }
@article {pmid41202381, year = {2025}, author = {Jiang, CH and Zhang, SJ and Li, P and Miao, H and Zhao, YY}, title = {Natural products targeting TGF-β/Smad signaling in renal fibrosis: Multiomics-based novel molecular mechanisms and therapeutic strategies.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {148}, number = {}, pages = {157496}, doi = {10.1016/j.phymed.2025.157496}, pmid = {41202381}, issn = {1618-095X}, abstract = {BACKGROUND: Renal diseases including acute kidney injury (AKI) and chronic kidney disease (CKD) have become one of the major global public health challenges. Regardless of the underlying aetiology, renal fibrosis is a common pathological endpoint in the progression of diverse kidney diseases to end-stage renal disease. Increasing studies have highlighted that emerging multi-omics techniques (metagenomics, transcriptomics, proteomics and metabolomics) have been used for elucidating the pathogenesis of kidney disease and underlying molecular mechanism of renal fibrosis. However, few reviews provide a comprehensive and systematic presentation of multi-omics signaling-mediated TGF-β/Smad pathway in both AKI and CKD as well as therapeutic strategies for targeting signaling cascades by natural products.<br><br>PURPOSE AND STUDY DESIGN: This review summarizes multi-omics signaling-mediated TGF-&#x3b2;/Smad pathway and therapeutic strategies of natural products by targeting this signaling axis in patients and animal models with kidney disease.<br><br>METHODS: All the available information is searched by several electronic database such as Web of Science, Pubmed, ScienceDirect, Splinker, Google Scholar, etc., that covered approximately 1000 publications from 2015 to 2025.<br><br>RESULTS: Ample evidence has indicated that transforming growth factor-&#x3b2; (TGF-&#x3b2;)/suppressor of mothers against decapentaplegic (Smad) signaling pathway plays a central role in renal fibrosis. Based on the multi-omics techniques, a variety of novel mediators are identified and affects kidney diseases by regulating TGF-&#x3b2;/Smad pathway. Therefore, targeting TGF-&#x3b2;/Smad pathway is an important and promising antifibrotic therapy. This review summarizes TGF-&#x3b2;/Smad pathway in both AKI and CKD, elaborate on the multidimensional regulatory mechanisms in renal fibrosis by crosstalk between TGF-&#x3b2;/Smad pathway and novel multi-omics signaling-associated mechanisms including microbial dysbiosis, dysregulating non-coding ribonucleic acids including long non-coding RNAs and microRNAs and metabolite disorder and shed light on the latest therapeutic effects of natural products such as terpenoids, anthraquinones, xanthones and flavonoids as well as natural polysaccharides by targeting multi-omics signaling-mediated TGF-&#x3b2;/Smad pathway.<br><br>CONCLUSION: This review presents a multiomics-driven therapeutic strategy for the development of effective and precise antifibrotic therapies.}, }
@article {pmid41201920, year = {2025}, author = {Soni, S and Mittal, P and Lo, JH and Yang, Y and Smbatyan, G and Lee, K and Wan, J and Kumagai, H and Yen, K and Mehta, HH and Miller, B and Torres-Gonzalez, L and Battaglin, F and Shah, UH and Bartolini, M and Zhang, W and Craig, DW and Millstein, J and Cohen, P and Lenz, HJ}, title = {Age-diet interactions significantly influence intratumoral gene expression, gut microbiome signature and tumor microenvironment in colorectal cancer.}, journal = {Neoplasia (New York, N.Y.)}, volume = {70}, number = {}, pages = {101245}, doi = {10.1016/j.neo.2025.101245}, pmid = {41201920}, issn = {1476-5586}, mesh = {*Colorectal Neoplasms/pathology/etiology/genetics/metabolism/microbiology ; Animals ; *Gastrointestinal Microbiome ; Mice ; *Tumor Microenvironment/genetics ; Humans ; *Diet ; *Gene Expression Regulation, Neoplastic ; Disease Models, Animal ; Age Factors ; Male ; *Aging ; }, abstract = {Colorectal Cancer (CRC) is the third most prevalent malignancy, leading to significant morbidity and mortality globally. Epidemiological studies suggest that chronological age and diet are among the major contributing factors correlated with the incidence of CRC. Our study aimed to provide insights into the association between age, diet, and gut microbiome in CRC using molecular techniques including RNA sequencing, cytokine analysis, and metagenomic analysis. We used syngeneic MC38 mice model divided into two age groups (old and young) and three diet groups (standard chow, calorie-restricted and high-fat). The major findings of this study are that age and diet impact intratumoral gene signaling (nuclear and mitochondrial), and hub genes we identified are associated with prognosis in CRC. Fecal microbiome analysis showed that old microbiomes have higher alpha diversity compared to young mice. Our results demonstrate that interactions between host (age) and external (diet) factors regulate tumor growth mediated by cytokines, mitochondrial derived proteins, and the gut microbiome. Collectively, our findings advance current understanding of the mechanisms by which aging, diet and gut microbiota impact CRC onset and progression though further investigation is warranted.}, }
@article {pmid41201839, year = {2025}, author = {da Silva Fong, D and Abrantes, J and Moura, T and Serra-Pereira, B and Xavier, R and Veríssimo, A and Varsani, A and Neves, F}, title = {Identification and characterization of a novel papillomavirus in thornback skate (Raja clavata).}, journal = {Microbial genomics}, volume = {11}, number = {11}, pages = {}, doi = {10.1099/mgen.0.001541}, pmid = {41201839}, issn = {2057-5858}, mesh = {Animals ; Phylogeny ; Genome, Viral ; *Skates, Fish/virology ; *Papillomaviridae/genetics/isolation &amp; purification/classification ; *Papillomavirus Infections/virology/veterinary ; Sequence Analysis, DNA ; DNA, Viral/genetics ; }, abstract = {Papillomaviruses are non-enveloped, double-stranded DNA viruses capable of infecting a wide range of vertebrates, from chondrichthyans to mammals. In this study, we report for the first time the identification and complete genome of a papillomavirus in the thornback skate (Raja clavata), named Raja clavata papillomavirus 1 (RclaPV1). The genomic sequence was determined using a metagenomic approach and subsequently confirmed by PCR. The RclaPV1 genome is 5,539 bp in length and displays the typical organization of papillomaviruses, encoding 4 core proteins on a single DNA strand: two early genes (E1 and E2) and two late genes (L1 and L2). Maximum likelihood phylogenetic analyses of the L1 and E1 genes indicate that RclaPV1 belongs to the Secondpapillomavirinae subfamily, clustering with fish and amphibian papillomaviruses and showing closer evolutionary relationships to amphibians than to fish.}, }
@article {pmid41201733, year = {2025}, author = {Saleh, RM and Hassan, OM}, title = {The infectome framework: linking polymicrobial ecology and biofilm dynamics to precision diagnostic approaches.}, journal = {Infection}, volume = {}, number = {}, pages = {}, pmid = {41201733}, issn = {1439-0973}, abstract = {Chronic infections are a persistent global health problem and are frequently sustained by polymicrobial communities rather than by a single pathogen. This review brings together current evidence for the infectome concept, defined as the dynamic set of pathogenic or pathobiont taxa in the host, their shared functional capacities, and the interactions that connect them. We analyze how community-level processes promote persistence, cause diagnostic failure, and drive therapeutic resistance, with emphasis on multispecies biofilms, quorum sensing, horizontal gene transfer, metabolic cooperation, and immune modulation. We also highlight advances in multi-omics and computational integration that now permit high-resolution infectome profiling and reveal taxa and interspecies networks that are not captured by routine culture. Clinical examples such as periodontitis, bacterial vaginosis, chronic rhinosinusitis, device-associated infections, and recurrent urinary tract infections show the translational value of this shift. On the therapeutic side, we discuss infectome-informed options including antivirulence agents, biofilm-disrupting enzymes, bacteriophages and lysins, community-wide susceptibility-guided regimens, and microbiome-restoration strategies. Finally, we identify the main requirements for the field: standardized sampling and analytic workflows, reproducible infectome signatures linked to clinical outcomes, and trial designs able to capture ecological dynamics and meet regulatory expectations for community-targeted interventions. Adopting an infectome perspective can enable precision infectiology and reshape the management of chronic and recurrent infections.}, }
@article {pmid41201496, year = {2025}, author = {Ren, QD and Li, MR and Farag, MA and Qiu, LL and Wang, YA and Liu, D and Liu, HR and Sun, JY and Li, NY and Liu, C}, title = {Pomegranate peel extract alleviates diabetic retinopathy by suppressing the PI3K/AKT/HIF-1α/VEGF pathway and gut microbiota modulation.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2025.10.048}, pmid = {41201496}, issn = {2090-1224}, abstract = {INTRODUCTION: Diabetic retinopathy (DR) is a severe microvascular complication of diabetes mellitus. Pomegranate peel extract (PPE) has shown potential in mitigating various diabetic complications, yet its role in DR remains unexplored.<br><br>OBJECTIVE: To investigate the beneficial effects and underlying action mechanisms of PPE in managing DR.<br><br>METHODS: PPE was extracted using 50&#xa0;% ethanol. The effects and underlying mechanisms of PPE on DR were evaluated in streptozotocin (STZ)-induced DR rats and high-glucose-incubated adult retinal pigment epithelial cell line (ARPE-19) cells. Phenotypic parameters, network pharmacology (NP), and gut microbiota metagenomic analysis were employed to elucidate the impact and mechanisms of PPE in DR.<br><br>RESULTS: In DR rats, oral administration of PPE significantly mitigated retinal damage. NP analysis indicated potential mechanisms, involving the hypoxia-inducible factor-1/vascular endothelial growth factor (HIF-1/VEGF), phosphoinositide 3-kinase/protein kinase B (PI3K/AKT), and reactive oxygen species (ROS) pathways. PPE suppressed oxidative stress and inhibited the activation of PI3K/AKT/HIF-1&#x3b1;/VEGF pathway in the retina of DR rats and high-glucose-incubated ARPE-19 cells. Moreover, PPE improved gut microbiota dysbiosis in DR rats, particularly increasing Akkermansia muciniphila, which likely contributed to reduced inflammation and oxidative stress.<br><br>CONCLUSION: PPE exhibited therapeutic effects in DR by directly alleviating retinal damage via the suppression of oxidative stress and inhibition of PI3K/AKT/HIF-1&#x3b1;/VEGF pathway, as well as indirectly modulating gut microbiota. These findings suggested that PPE may serve as a promising nutraceutical for DR management.}, }
@article {pmid41201223, year = {2025}, author = {Zha, Y and Xiang, M and Zuo, Y and Liu, D and Wang, Q}, title = {High-dose Dietary Fibre Supplementation Enhances the Gut Microbiome, Health, and Athletic Performance of College Basketball Players.}, journal = {International journal for vitamin and nutrition research. Internationale Zeitschrift fur Vitamin- und Ernahrungsforschung. Journal international de vitaminologie et de nutrition}, volume = {95}, number = {5}, pages = {37069}, doi = {10.31083/IJVNR37069}, pmid = {41201223}, issn = {0300-9831}, support = {2019YFF0301702//National Key R&amp;D Program of China/ ; XJ2022000601//Doctoral Research Fund/ ; }, mesh = {Humans ; Male ; *Gastrointestinal Microbiome/drug effects ; *Basketball/physiology ; *Athletic Performance/physiology ; Young Adult ; *Dietary Fiber/administration &amp; dosage ; Adolescent ; *Dietary Supplements ; Adult ; Body Composition ; Athletes ; Universities ; }, abstract = {BACKGROUND: Prolonged or intense exercise can disrupt gastrointestinal (GI) function and gut microbiota, impairing athletic performance. Dietary fibre supplementation may enhance gut microbiota diversity, improve body composition, and promote recovery in athletes. This study aimed to explore the effects of dietary fibre supplementation at two doses for 8 weeks on these aspects in college basketball players.<br><br>METHODS: Twenty male college basketball players (aged 17-25 years) were randomly assigned to a high-dose group (HDG; 10 participants; 6.84 g/day dietary fibre) or a low-dose group (LDG; 10 participants; 3.24 g/day dietary fibre). The participants consumed fibre-enriched meals daily while maintaining their regular training schedules. The outcome measures included gut microbiota diversity (metagenomic sequencing), body composition, fatigue recovery markers, glucose and lipid metabolism, and athletic performance. Statistical analyses included paired and independent t tests for within- and between-group comparisons and Spearman's correlation analysis to assess the relationships between gut microbiota and biochemical markers.<br><br>RESULTS: One participant in the high-dose group withdrew, and nineteen ultimately completed the study. Both groups showed significant within-group improvements (p < 0.05) in body weight (HDG: -2.77 &#xb1; 0.76 kg; LDG: -2.40 &#xb1; 0.67 kg), body fat percentage (HDG: -1.87 &#xb1; 0.69; LDG: -1.49 &#xb1; 0.45), cortisol (HDG: -6.79 &#xb1; 4.26 &#x3bc;g/dL; LDG: -4.5 &#xb1; 4.84 &#x3bc;g/dL), maximum power (HDG: 27.16 &#xb1; 9.77 W; LDG: 14.50 &#xb1; 9.43 W), maximal oxygen uptake (HDG: 8.78 &#xb1; 0.97; LDG: 6.90 &#xb1; 1.37), and half-court triangle run times (HDG: -0.48 &#xb1; 0.36 s; LDG: -0.25 &#xb1; 0.20 s). Meanwhile, fasting blood glucose significantly decreased (0.91 &#xb1; 0.55 mmol/L; p = 0.001), and the gut microbiome changes were more stable in the HDG, whereas the LDG presented greater shifts in microbial diversity. No significant between-group differences were observed.<br><br>CONCLUSIONS: Dietary fibre supplementation improved the gut microbiome composition, body composition, fatigue recovery, and athletic performance of college basketball players, regardless of dosage. Further studies are needed to evaluate higher doses and specific fibre types.}, }
@article {pmid41200800, year = {2025}, author = {Quarton, S and Livesey, A and Jeff, C and Hatton, C and Chen, CH and Scott, A and Parekh, D and Thickett, D and McNally, A and Sapey, E}, title = {Metagenomics in the diagnosis of pneumonia: a systematic review.}, journal = {Infectious diseases (London, England)}, volume = {}, number = {}, pages = {1-25}, doi = {10.1080/23744235.2025.2580954}, pmid = {41200800}, issn = {2374-4243}, abstract = {BACKGROUND: Pneumonia is a major cause of morbidity and mortality, yet causative organisms are rarely identified. Metagenomic next-generation sequencing (mNGS) may improve this, however the impact on outcomes is uncertain and the relative utility in pneumonia subtypes or different clinical samples is unclear.<br><br>METHODS: This systematic review compared mNGS with conventional microbiology, assessing pathogen identification, turnaround time and clinical impact. It also reviewed&#xa0;difference related to the pneumonia subtype, or sample used. We searched EMBASE, MEDLINE, Scopus, and the Cochrane Central Register of Controlled Trials (CENTRAL) for studies comparing mNGS with conventional microbiology, in patients with pneumonia. All study types were included (excluding case reports of <10 people). Eligibility assessment and data extraction was performed by two independent reviewers, and risk of bias assessed using the QUADAS-2.<br><br>RESULTS: We identified 74 studies including 10,566 people, with all studies having high risk of bias or applicability concerns in at least one domain. Conventional tests identified a pathogen in 43.2% of cases (3559/8229) compared to 78.9% for mNGS (6242/7980). mNGS had faster turnaround times than conventional microbiology (MD -73.6h, CI-111.36 - -35.73&#x2009;hrs) but meta-analysis was not possible for other outcomes. Most studies did not specify the pneumonia subtype. 92%of studies used exclusively or predominantly bronchoalveolar lavage fluid (BALF), and the utility of other sample types could not be established.<br><br>CONCLUSIONS: mNGS may identify possible pathogens with greater frequency than standard techniques although bias in study design limits definite conclusions, and the clinical relevance of this remains unresolved. There is a need for studies assessing&#xa0;clinical outcomes, and the differential impact in pneumonia subtypes and in samples other than BALF.}, }
@article {pmid41200470, year = {2025}, author = {Maldonado, M and Pita, L and Erpenbeck, D and Hentschel, U and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and ,  and ,  and ,  and ,  and , }, title = {The chromosomal genome sequence of the sponge, Corticium candelabrum Schmidt, 1862 and its associated microbial metagenome sequences.}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {535}, pmid = {41200470}, issn = {2398-502X}, abstract = {We present a genome assembly from a specimen of Corticium candelabrum (sponge; Porifera; Homoscleromorpha; Homosclerophorida; Plakinidae). The genome sequence has a total length of 185.49 megabases. Most of the assembly (99.4%) is scaffolded into 22 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 18.19 kilobases in length. Gene annotation of this assembly on Ensembl identified 26,198 protein-coding genes. The metagenome of the specimen was also assembled, and 53 binned bacterial genomes were identified, including 44 high-quality MAGs that were typical of high microbial abundance sponge and included, besides the phyla Chloroflexota (class Dehalococcoidia), Acidobacteriota (order Acidomicrobiales), Alpha- and Gammaproteobacteria, also representatives of several candidatus phyla (Candidatus Latescibacterota, Binatota, Poribacteria).}, }
@article {pmid41200317, year = {2025}, author = {Kazemzadeh, S and Korneeva, O and Shabunin, S and Syromyatnikov, M}, title = {Antibiotic resistance in mastitis-causing bacteria: Exploring antibiotic-resistance genes, underlying mechanisms, and their implications for dairy animal and public health.}, journal = {Open veterinary journal}, volume = {15}, number = {9}, pages = {3980-4006}, pmid = {41200317}, issn = {2218-6050}, mesh = {Animals ; *Mastitis, Bovine/microbiology/drug therapy ; Female ; Cattle ; *Drug Resistance, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; Public Health ; *Bacteria/drug effects/genetics ; Dairying ; Humans ; Milk/microbiology ; }, abstract = {The development and spread of superbugs, which are bacterial strains resistant to several types of antibiotics, threatening the lives of myriad people and animals worldwide, is one of the most concerning issues facing both global and animal health. Dairy animals are considered to be key reservoirs of antibiotic-resistant bacteria, which are closely correlated with the widespread and inappropriate application of antibiotics in agriculture and veterinary medicine, particularly for mastitis treatment. Although antimicrobial agents are administered in dairy farming for various conditions beyond mastitis, such as respiratory infections and digestive disorders, as well as prophylaxis and growth promotion, the most common reason for antimicrobial use in this industry is mastitis treatment. Since raw milk can be contaminated with opportunistic pathogens carrying antimicrobial resistance genes, these pathogens increase the gene pool from which pathogenic bacteria can acquire resistance traits. Indeed, these resistance genes may be horizontally transferred from livestock to human pathogens through mobile genetic elements through the consumption of raw milk. This phenomenon poses a global health threat, emphasizing the necessity of applying the "One Health" approach in global health and medicine to safeguard animal health and public health. Given the high prevalence and economic impact of mastitis and the evidence supporting mastitis as a major driver of antimicrobial use in dairy farming, this review summarizes recent genomic and metagenomic studies on major mastitis-causing pathogens (Staphylococcus aureus, Escherichia coli, Streptococcus spp., and Pseudomonas spp.) in dairy animals, detailing their primary resistance mechanisms. We highlight advanced surveillance tools, such as metagenomics, whole-genome sequencing, and quantitative polymerase chain reaction, for the rapid detection of resistance genes and mobile elements in the dairy chain.}, }
@article {pmid41199950, year = {2025}, author = {Sang, Z and Zhang, Y and Kao, E and Zhu, T and Yang, J and Xu, ZZ and Huang, S and Teng, F and Wang, W}, title = {Decoding oral leukoplakia: microbiome dysbiosis and inflammatory dynamics unveiled in a rat model.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1613165}, pmid = {41199950}, issn = {1664-302X}, abstract = {INTRODUCTION: Oral leukoplakia (OLK) is an oral precancerous lesion associated with oral microbiome dysbiosis and systemic inflammation. However, the longitudinal changes of the microbiome and its causal relationship with inflammation remain unclear, and traditional sequencing struggles to detect low-biomass samples.<br><br>METHODS: A 4-nitroquinoline-1-oxide (4-NQO)-induced rat OLK model was used. The oral microbiome was analyzed via 2bRAD-M sequencing; serum levels of tumor necrosis factor-&#x3b1; (TNF-&#x3b1;) and interleukin-6 (IL-6) were measured. Additionally, functional pathway analysis of the microbiome and its correlation with inflammation were conducted.<br><br>RESULTS: In OLK, we observed significant shifts in the oral microbial diversity, marked by elevated abundances of Streptococcus, Glaesserella, and Pseudomonas aeruginosa. Moreover, shifts in the microbiota precede the manifestation of clinical symptoms of OLK. Functional pathway analysis highlighted enrichment in metabolism, quorum sensing, and cancer-associated microRNA pathways. Serum levels of inflammatory markers (TNF-&#x3b1; and IL-6) were significantly elevated in OLK and significantly correlated with specific bacterial taxa.<br><br>DISCUSSION: This study demonstrates the utility of 2bRAD-M sequencing in overcoming traditional metagenomic limitations, offering a high-resolution view of microbiome dynamics in low-biomass environments such as the oral mucosa. These findings establish the oral microbiota as candidate early biomarkers for OLK screening and prevention, opening avenues for precision diagnostics and targeted therapies to mitigate cancer risk associated with OLK.}, }
@article {pmid41199948, year = {2025}, author = {Vasanthrao, R and Nidhin, IK and Taj, Z and Chattopadhyay, I}, title = {Comprehensive whole metagenomics analysis uncovers microbial community and resistome variability across anthropogenically contaminated soils in urban and suburban areas of Tamil Nadu, India.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1649872}, pmid = {41199948}, issn = {1664-302X}, abstract = {INTRODUCTION: Environmental contamination by heavy metals and hydrocarbons significantly impacts microbial diversity and soil functionality.<br><br>METHODS: This study employs whole-genome metagenome sequencing to analyse microbial compositions, antibiotic resistance genes (ARGs), heavy metal resistance genes (HMRs), and virulence genes (VGs) in soil samples from diverse locations, including gardens, poultry farms, cattle sheds, markets, hospitals, thermal power plants, paper industries, and waste disposal sites.<br><br>RESULTS: The findings indicate that heavy metal concentrations (Pb, Cr, Cd, and Cu) and hydrocarbons (heptadecane, triacontane, docosane, and heneicosane) were positively correlated with several microbial phyla with relatively high abundances in these contaminated sites, such as Actinobacteria, Proteobacteria, Basidiomycota, Ascomycota, Euryarchaeota, and Apicomplexa. The prevalence of multidrug resistance genes, including MexD, MexC, MexE, MexF, MexT, CmeB, MdtB, MdtC, and OprN, was significant, facilitating antibiotic resistance primarily via efflux pump mechanisms (42%), followed by antibiotic inactivation (23%) and changes in antibiotic targets (18%). Virulence genes such as espR, regX3, sigA/rpoV, bap, and sugB were significantly prevalent in contaminated locations, indicating microbial pathogenic potential in polluted ecosystems. The functional gene analysis revealed significant metabolic pathways related to protein metabolism, carbohydrates, amino acids and their derivatives, metabolism, and DNA metabolism, highlighting the microbial adaptation processes engaged in pollution degradation and resource utilisation.<br><br>DISCUSSION: This study establishes a clear link between environmental pollution, microbial adaptations, and functional resilience, emphasizing the ecological significance of microbial bio-remediation in shaping targeted remediation strategies and long-term ecological recovery. Understanding these microbial interactions is essential for developing targeted remediation techniques and assessing long-term ecological recovery in contaminated regions.}, }
@article {pmid41199944, year = {2025}, author = {Dai, L and Guo, XR and Chen, XR and Ma, MH and Liu, ZH and Lai, J and Lu, J and Feng, M and Liu, XX and Yang, SH}, title = {A review of the mechanism, diagnosis, and treatment of Naegleria fowleri infection.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1686695}, pmid = {41199944}, issn = {1664-302X}, abstract = {Naegleria fowleri is a rare pathogen responsible for primary amoebic meningoencephalitis (PAM), a fatal central nervous system infection characterized by rapid clinical progression and an extremely high mortality rate. The existing diagnostic methods are insufficiently sensitive, and therapeutic options are minimal, making early recognition and intervention extremely challenging. This review systematically examines the biological characteristics and pathogenic mechanisms of this pathogen, as well as current diagnostic and treatment strategies, with a particular focus on the groundbreaking applications of emerging technologies such as metagenomic next-generation sequencing (mNGS) in the diagnosis of difficult-to-treat infections. The aim is to provide theoretical support and practical guidance for rapid identification, accurate diagnosis, and timely intervention in clinical practice, serving as a reference for the prevention and treatment of N. fowleri infections.}, }
@article {pmid41199943, year = {2025}, author = {Zhang, M and Di, H and Wang, S and Ning, Z}, title = {Column experiment reveals high natural attenuation potential for toluene in iron-rich aquifers but significant concomitant secondary Fe pollution risk.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1687219}, pmid = {41199943}, issn = {1664-302X}, abstract = {INTRODUCTION: Iron mineral reduction mediated by indigenous microbes represents a crucial natural attenuation mechanism for organic contaminants like toluene in anaerobic aquifers, yet the partitioning of generated Fe(II) species and associated secondary pollution risks remain poorly constrained.<br><br>METHODS: This study employed controlled column experiments simulating an iron-rich aquifer (ferrihydrite-amended quartz sand) to track the biogeochemical dynamics of toluene degradation coupled with iron transformation. Over 43 days, we quantified spatiotemporal changes in toluene concentrations, dissolved/solid-phase iron species, and microbial community structure through high-frequency hydrochemical monitoring and metagenomic sequencing.<br><br>RESULTS AND DISCUSSION: Results demonstrated that iron-reducing consortia (notably Thiobacillus and Pseudomonas) drove > 99% toluene degradation within 10 cm flow distance, effectively containing plume migration. However, Fe(III) reduction generated Fe(II) predominantly (98%) as immobile solid-phase minerals, with only 1%-2% manifesting as dissolved Fe[2+]. This dissolved fraction accumulated progressively across space and time, exceeding China's groundwater quality threshold (0.3 mg/L) at 90% of monitoring points by experiment termination despite near-complete toluene removal. The study confirms that iron-rich aquifers provide significant natural attenuation capacity for petroleum hydrocarbons but concurrently pose substantial secondary contamination risks through highly mobile Fe[2+] generation. Therefore, it is recommended to include solidphase ferrous iron [Fe(II)] as an indicator in natural attenuation assessments and to take into account biogeochemical by-products such as Fe[2+] in risk assessment efforts.}, }
@article {pmid41199942, year = {2025}, author = {Zeng, W and Yang, L and Cui, L and Liang, C and Zhu, D and Fang, Y and Zhang, Y and Liu, H}, title = {Virome analysis and detection of ticks and tick-borne viruses in Shanghai, China.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1699705}, pmid = {41199942}, issn = {1664-302X}, abstract = {INTRODUCTION: Ticks are well-known ectoparasites and vectors responsible for transmitting a diverse range of pathogens, including viruses, bacteria, and protozoa, many of which pose substantial risks to public health and livestock. In recent decades, the incidence and diversity of tick-borne diseases have increased globally, with several novel tick-borne viruses (TBVs) being discovered.<br><br>METHODS: This study aimed to characterize the virome of ticks collected from various locations in Shanghai, China, using next-generation sequencing (NGS). A total of 2,568 ticks belonging to three dominant species-Haemaphysalis flava, Haemaphysalis longicornis, and Rhipicephalus sanguineus sensu lato-were collected and analyzed through metagenomic sequencing.<br><br>RESULTS: The sequencing analysis identified 214 viral contigs classified into 32 viral families, including Chrysoviridae, Phenuiviridae, Partitiviridae, Nairoviridae, Dicistroviridae, Reoviridae, Botourmiaviridae, and Flaviviridae. Several TBVs with potential relevance to human and animal health, such as Cheeloo Jingmen-like virus (CJLV), Songling virus (SGLV), brown dog tick phlebovirus 1 (BDTPV1), brown dog tick phlebovirus 2 (BDTPV2), and Wuhan mosquito virus 1 (WMV1), were detected. Significant differences in virome composition among tick species based on geographical locations were also observed.<br><br>DISCUSSION: These findings highlight the influence of environmental factors on viral diversity in ticks and underscore the need for ongoing surveillance of TBVs. Implementation of longitudinal virome monitoring across tick developmental stages in Shanghai will provide critical insights for early warning systems, disease prevention strategies, and public health interventions.}, }
@article {pmid41199613, year = {2025}, author = {Kagemasa, S and Kuroda, K and Nakai, R and Sato, M and Li, YY and Kubota, K}, title = {Metabolic Potential of Candidatus Saccharimonadia Including Rare Lineages in Activated Sludge.}, journal = {Environmental microbiology reports}, volume = {17}, number = {6}, pages = {e70231}, doi = {10.1111/1758-2229.70231}, pmid = {41199613}, issn = {1758-2229}, support = {JP18H01564//Japan Society for the Promotion of Science/ ; JP21H01460//Japan Society for the Promotion of Science/ ; JP23H02545//Japan Society for the Promotion of Science/ ; JP23K27236//Japan Society for the Promotion of Science/ ; JP23K19153//Japan Society for the Promotion of Science/ ; JP24H00328//Japan Society for the Promotion of Science/ ; JP21J11654//Japan Society for the Promotion of Science/ ; //Tohou University - AIST matching fund/ ; //MEXT WISE Program for Sustainability in Dynamic Earth (SyDE), Japan/ ; }, mesh = {*Sewage/microbiology ; Phylogeny ; Genome, Bacterial ; Metagenomics ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; Wastewater/microbiology ; }, abstract = {Candidatus Saccharimonadia is a class-level lineage of ultrasmall bacteria within the phylum Minisyncoccota (formerly Candidate Phyla Radiation or Ca. Patescibacteria), commonly found in activated sludge processes treating municipal wastewater. In this study, we aimed to elucidate the metabolic potential of Ca. Saccharimonadia by using shotgun metagenomic sequencing combined with a filtration-based size-fractionation approach for activated sludge from five wastewater treatment plants. A total of 65 high-quality metagenomic bins were recovered, belonging to four orders and 19 families of Ca. Saccharimonadia, including previously unreported lineages in activated sludge. These bins had small genomes (approximately 0.46-1.73 Mbp) with limited metabolic capabilities, indicating dependency on other microorganisms. Notably, the order Ca. Saccharimonadales retained a type IV secretion system and effector gene cluster for parasitic interactions with the hosts, suggesting that Ca. Saccharimonadales bacteria may exhibit a parasitic lifestyle. Co-occurrence network analysis showed that members of the order Ca. Saccharimonadales were significantly correlated with multiple lineages, including Actinobacteriota, for which a parasitic relationship has been previously demonstrated. Our results shed light on the potential ecophysiology of the diverse members of Ca. Saccharimonadia, providing a comprehensive understanding of Ca. Saccharimonadia in activated sludge.}, }
@article {pmid41199348, year = {2025}, author = {Ghozlane, A and Thirion, F and Plaza Oñate, F and Gauthier, F and Le Chatelier, E and Annamalé, A and Almeida, M and Ehrlich, SD and Pons, N}, title = {Accurate profiling of microbial communities for shotgun metagenomic sequencing with Meteor2.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {227}, pmid = {41199348}, issn = {2049-2618}, support = {ANR-11-DPBS-0001//Metagenopolis/ ; }, mesh = {*Metagenomics/methods ; Animals ; Mice ; Humans ; *Microbiota/genetics ; *Bacteria/genetics/classification ; *Metagenome ; *Gastrointestinal Microbiome/genetics ; *Software ; Computational Biology/methods ; }, abstract = {BACKGROUND: The characterization of complex microbial communities is a critical challenge in microbiome research, as it is essential for understanding the intricate relationships between microorganisms and their environments. Metagenomic profiling has advanced into a multifaceted approach, combining taxonomic, functional, and strain-level profiling (TFSP) of microbial communities. Here, we present Meteor2, a tool that leverages compact, environment-specific microbial gene catalogues to deliver comprehensive TFSP insights from metagenomic samples.<br><br>RESULTS: Meteor2 currently supports 10 ecosystems, gathering 63,494,365 microbial genes clustered into 11,653 metagenomic species pangenomes (MSPs). These genes are extensively annotated for KEGG orthology, carbohydrate-active enzymes (CAZymes) and antibiotic-resistant genes (ARGs). In benchmark tests, Meteor2 demonstrated strong performance in TFSP, particularly excelling in detecting low-abundance species. When applied to shallow-sequenced datasets, Meteor2 improved species detection sensitivity by at least 45% for both human and mouse gut microbiota simulations compared to MetaPhlAn4 or sylph. For functional profiling, Meteor2 improved abundance estimation accuracy by at least 35% compared to HUMAnN3 (based on Bray-Curtis dissimilarity). Additionally, Meteor2 tracked more strain pairs than StrainPhlAn, capturing an additional 9.8% on the human dataset and 19.4% on the mouse dataset. Furthermore, in its fast configuration, Meteor2 emerges as one of the fastest available tools for profiling, requiring only 2.3&#xa0;min for taxonomic analysis and 10&#xa0;min for strain-level analysis against the human microbial gene catalogue when processing 10&#xa0;M paired reads - operating within a modest 5&#xa0;GB RAM footprint. We further validated Meteor2 using a published faecal microbiota transplantation (FMT) dataset, demonstrating its ability to deliver an extensive and actionable metagenomic analysis. The unified database design also simplifies the integration of TFSP outputs, making it straightforward for researchers to interpret and compare results.<br><br>CONCLUSIONS: These results highlight Meteor2 as a robust and versatile tool for advancing microbiome research and applications. As an open-source, easy-to-install, and accurate analysis platform, Meteor2 is highly accessible to researchers, facilitating the exploration of complex microbial ecosystems.}, }
@article {pmid41198952, year = {2025}, author = {Makarova, KS and Shmakov, SA and Wolf, YI and Mutz, P and Altae-Tran, H and Beisel, CL and Brouns, SJJ and Charpentier, E and Cheng, D and Doudna, J and Haft, DH and Horvath, P and Moineau, S and Mojica, FJM and Pausch, P and Pinilla-Redondo, R and Shah, SA and Siksnys, V and Terns, MP and Tordoff, J and Venclovas, &#x10c; and White, MF and Yakunin, AF and Zhang, F and Garrett, RA and Backofen, R and van der Oost, J and Barrangou, R and Koonin, EV}, title = {An updated evolutionary classification of CRISPR-Cas systems including rare variants.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {41198952}, issn = {2058-5276}, support = {Intramural funds//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; }, abstract = {The known diversity of CRISPR-Cas systems continues to expand. To encompass new discoveries, here we present an updated evolutionary classification of CRISPR-Cas systems. The updated CRISPR-Cas classification includes 2 classes, 7 types and 46 subtypes, compared with the 6 types and 33 subtypes in our previous survey 5 years ago. In addition, a classification of the cyclic oligoadenylate-dependent signalling pathway in type III systems is presented. We also discuss recently characterized alternative CRISPR-Cas functionalities, notably, type IV variants that cleave the target DNA and type V variants that inhibit the target replication without cleavage. Analysis of the abundance of CRISPR-Cas variants in genomes and metagenomes shows that the previously defined systems are relatively common, whereas the more recently characterized variants are comparatively rare. These low abundance variants comprise the long tail of the CRISPR-Cas distribution in prokaryotes and their viruses, and remain to be characterized experimentally.}, }
@article {pmid41198823, year = {2025}, author = {Navarro Marcos, C and Gutiérrez-Rivas, M and Goiri, I and García-Rodríguez, A and González-Recio, &#xd3;}, title = {The association of the rumen virome with methane emissions in dairy cattle.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {1534}, pmid = {41198823}, issn = {2399-3642}, mesh = {Animals ; Cattle ; *Methane/metabolism/biosynthesis ; *Rumen/virology/microbiology/metabolism ; *Virome ; Female ; Viruses/genetics/classification ; Metagenome ; Bacteria/metabolism ; Metagenomics ; }, abstract = {Enteric methane production in ruminants is a major environmental concern, yet its association with the ruminal virome remains largely unexplored. Here, we conduct a bioinformatic analysis on previously published ruminal metagenomes from 448 Holstein cows to investigate the virome and its association with methane production. We identify 8933 viral operational taxonomic units (vOTUs), including bacteriophages, archaeophages, megaviruses, and virophages. Differences between high- and low-emitting cows are observed. Low emitters show greater abundance (mean log-FC = 0.72, Padj ≤ 0.049) of some vOTUs infecting bacteria like Prevotella, whereas greater abundance (mean log-FC = 0.70, Padj ≤ 0.047) of archaeophages and megaviruses infecting Methanobrevibacter, ciliates, and fungi, all microorganisms linked to methane production, are observed in high emitters. Associations between viruses and microorganisms might suggest viruses influence methane emissions by modulating key microbial populations. Although mechanisms remain unclear, rumen viruses could serve as biomarkers for selecting low-emission animals or developing microbial interventions.}, }
@article {pmid41197746, year = {2025}, author = {Yu, PF and Jiang, DL and Wang, D and Ma, XG and Jun-Li,  and Han, LY and Wang, A and Fu, YB and Jin, X}, title = {Manganese cycle-mediated synchronous bacteria-algae/anammox coupled denitrification system under low-temperature conditions: Performance and mechanisms.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {133593}, doi = {10.1016/j.biortech.2025.133593}, pmid = {41197746}, issn = {1873-2976}, abstract = {The treatment of high-nitrogen complex wastewater in an efficient, economical, and environmentally friendly manner has attracted growing attention in recent years. However, slow reaction rates remain a significant obstacle to its broad application. This study investigated the addition of Mn@BC to enhance the low-temperature resistance of an anaerobic ammonia oxidation (anammox) process coupled with denitrification. The results demonstrated that under 17℃ conditions, the average nitrogen removal efficiency increased to 82% with the addition of Mn@BC, representing a 9% improvement compared to the addition of BC alone. Moreover, Mn@BC promoted the secretion of extracellular polymeric substances and diversified the microbial community structure.The incorporation of microalgae created a synergistic microalgal-bacterial system that maintained a phosphorus removal rate of 50% and reduced the reliance on external organic carbon, as confirmed by TOC analysis.The underlying intra- and extracellular metabolic pathways, formed by functional genes including mtrC, nirS/K, and c-Cyts, were elucidated using metagenomic sequencing. Therefore, the development of a high-efficiency nitrogen and phosphorus removal process capable of synchronizing microalgal-bacterial interactions, overcoming low-temperature inhibition, enhancing microbial synergy, and reducing carbon source dependency holds practical application value for treating high-nitrogen and low-temperature wastewater, while also providing theoretical support for constructing microalgal-bacterial synergistic systems to achieve efficient autotrophic nitrogen removal.}, }
@article {pmid41197744, year = {2025}, author = {Li, Y and Wang, G and Yang, Y and Liu, L and Dang, X and Li, YY and Chen, R}, title = {Operational thresholds and microbial mechanisms in high-solid anaerobic membrane bioreactors treating swine wastewater: from process performance to metabolic pathways.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {133596}, doi = {10.1016/j.biortech.2025.133596}, pmid = {41197744}, issn = {1873-2976}, abstract = {This study investigated swine wastewater treatment using a high-solid anaerobic membrane bioreactor (HSAnMBR), focusing on microbial adaptive mechanisms and process stability under stepwise-increased organic loading rates (OLRs: 5-26 g COD/L/d). The HSAnMBR achieved high efficiency at OLRs ≤ 17 g COD/L/d, with COD removal > 96 % and optimal methane yield (0.28 L CH4/g CODremoved). However, OLR elevation to 26 g COD/L/d induced volatile fatty acid (VFA) accumulation (5.57 g/L), causing acute methanogenic inhibition that reduced methane yield efficiency by 39 %. System functionality was rapidly restored within 10 days after OLR reduction to 21 g COD/L/d. Microbial analysis revealed divergent diversity dynamics: bacterial alpha diversity peaked at 14 g COD/L/d before declining, while archaeal diversity increased continuously, enhancing functional redundancy. Sludge acclimation enriched key functional taxa (such as Clostridium_sensu_stricto and hydrogenotrophic methanogens), forming a resilient "metabolic complementarity-functional substitution" network that maintained process stability under VFA stress. Metagenomic evidence confirmed metabolic pathway restructuring, including upregulation of hydrogenotrophic methanogenesis genes (e.g., coenzyme F420 biosynthesis) and a decline in acetoclastic dominance. This work deciphers the microbial mechanisms enabling high-load operation of HSAnMBRs, establishing the foundation for energy-efficient swine wastewater valorization.}, }
@article {pmid41197631, year = {2025}, author = {Klag, K and Ott, D and Tippetts, TS and Nicolson, RJ and Tatum, SM and Bauer, KM and Stephen-Victor, E and Weis, AM and Bell, R and Weagley, J and Maschek, JA and Vu, DL and Heaver, S and Ley, R and O'Connell, R and Holland, WL and Summers, SA and Stephens, WZ and Round, JL}, title = {Dietary fat disrupts a commensal-host lipid network that promotes metabolic health.}, journal = {Cell metabolism}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cmet.2025.10.007}, pmid = {41197631}, issn = {1932-7420}, abstract = {The microbiota influences metabolic health; however, few specific microbial molecules and mechanisms have been identified. We isolated a Turicibacter strain from a community of spore-forming bacteria that promotes leanness in mice. Human metagenomic analysis demonstrates reduced Turicibacter abundance in individuals with obesity. Similarly, a high-fat diet reduces Turicibacter colonization, preventing its weight-suppressive effects, which can be overcome with continuous Turicibacter supplementation. Ceramides accumulate during a high-fat diet and promote weight gain. Transcriptomics and lipidomics reveal that the spore-forming community and Turicibacter suppress host ceramides. Turicibacter produces unique lipids, which are reduced during a high-fat diet. These lipids can be transferred to host epithelial cells, reduce ceramide production, and decrease fat uptake. Treatment of animals with purified Turicibacter lipids prevents obesity, demonstrating that bacterial lipids can promote host metabolic health. These data identify a lipid metabolic circuit between bacteria and host that is disrupted by diet and can be targeted therapeutically.}, }
@article {pmid41197619, year = {2025}, author = {Forbes, M and Ng, DYK and Boggan, RM and Frick-Kretschmer, A and Durham, J and Lorenz, O and Dave, B and Lassalle, F and Scott, C and Wagner, J and Lignes, A and Noaves, F and Jackson, DK and Howe, K and Harrison, EM}, title = {Benchmarking of human read removal strategies for viral and microbial metagenomics.}, journal = {Cell reports methods}, volume = {}, number = {}, pages = {101218}, doi = {10.1016/j.crmeth.2025.101218}, pmid = {41197619}, issn = {2667-2375}, abstract = {Human reads are a key contaminant in microbial metagenomics and enrichment-based studies, requiring removal for computational efficiency, biological analysis, and privacy protection. Various in silico methods exist, but their effectiveness depends on the parameters and reference genomes used. Here, we assess different methods, including the impact of the updated telomere-to-telomere (T2T)-CHM13 human genome versus GRCh38. Using a synthetic dataset of viral and human reads, we evaluated performance metrics for multiple approaches. We found that the usage of high-sensitivity configuration of Bowtie2 with the T2T-CHM13 reference assembly significantly improves human read removal with minimal loss of specificity, albeit at higher computational cost compared to other methods investigated. Applying this approach to a publicly available microbiome dataset, we effectively removed sex-determining SNPs with little impact on microbial assembly. Our results suggest that our high-sensitivity Bowtie2 approach with the T2T-CHM13 is the best method tested to minimize identifiability risks from residual human reads.}, }
@article {pmid41197616, year = {2025}, author = {Gao, P and Yuan, H and Mei, Z and Yin, X and Zeng, Y and Liu, Z and Yang, X and Xue, J and Liu, Z and Jiang, Y and Ye, W and Lu, M and Suo, C and Chen, X}, title = {The comprehensive oral microbiome landscape unveils its interplay with poor oral health in esophageal squamous cell carcinoma risk.}, journal = {Cell reports. Medicine}, volume = {}, number = {}, pages = {102431}, doi = {10.1016/j.xcrm.2025.102431}, pmid = {41197616}, issn = {2666-3791}, abstract = {Growing evidence links poor oral health to an increased esophageal squamous cell carcinoma (ESCC) risk, with the oral microbiome recognized as a key contributor. However, human-based evidence remains limited. Here, we analyze salivary shotgun metagenomic data from 390 ESCC case-control pairs and 16S rRNA sequencing data from 206 incident esophageal cancer (EC) case-control pairs. We identify 50 bacterial species altered in ESCC (e.g., enriched Porphyromonas catoniae and depleted Campylobacter rectus) and disruptions in 54 biochemical pathways (e.g., inosine 5'-phosphate degradation). These features potentially mediate the association between poor oral health and ESCC. Notably, this association is stronger among individuals with lower Streptococcus mitis levels, implicating pathways related to thiamine salvage and energy metabolism. Consistent findings in the validation dataset further support the interplay between the oral microbiome and oral health in EC risk. Our results highlight the promise of precision-targeted microbial interventions to improve oral health for ESCC prevention and management.}, }
@article {pmid41197513, year = {2025}, author = {Luo, J and Hou, C and Wang, Z and Gui, N and Wang, YX and Jiang, X and Mu, Y and Shen, J}, title = {Simultaneous removal of nitrate and ammonia at the sulfur/pyrite-microbe interface: A novel insight of pyrite in wastewater polishing treatment for nitrogen metabolism.}, journal = {Journal of hazardous materials}, volume = {500}, number = {}, pages = {140316}, doi = {10.1016/j.jhazmat.2025.140316}, pmid = {41197513}, issn = {1873-3336}, abstract = {The development of advanced nitrogen removal technologies for municipal wastewater effluents is critical to meeting increasingly stringent discharge standards. We present a sulfur/pyrite-microbe interfacial system that optimizes nitrogen-transformation pathways to achieve simultaneous removal of NO3[-]-N and NH4[+]-N with reduced sulfate production. This overcomes the drawbacks of conventional sulfur autotrophy (poor NH4[+] removal and excessive sulfate production) and stand-alone iron systems (low denitration rate and easy passivation), delivering synchronous ammonia and nitrate elimination in a single step. A comprehensive analysis of the microstructure and composition of the bio-abiotic interface was performed to elucidate the regulatory role of pyrite in electron transfer and substance transformation. The formation of secondary minerals, structural alterations in extracellular proteins, and enhanced activity of redox-active proteins collectively activated both intracellular and extracellular electron transfer channels. Pyrite-induced quorum sensing promoted iron transport and stimulated microbial metabolic functions. Driven by Fe(II)/Fe(III) redox cycling, nitrate-dependent Fe(II) oxidation (NDFO) and Fe(III)-mediated ammonium oxidation (Feammox) reduced sulfate production and suppressed sulfur disproportionation. Metagenomic analysis further confirmed that Feammox, rather than conventional Anammox, served as the dominant pathway for NH4[+]-N conversion. Pilot-scale validation demonstrated robust nitrogen removal (TN > 90 %) and low sulfate production with a treatment cost 40 % lower than conventional carbon-driven systems. This study offers a sustainable, low-carbon alternative for advanced nitrogen polishing and provides mechanistic insights into bio-abiotic interface engineering for wastewater treatment.}, }
@article {pmid41197508, year = {2025}, author = {Wen, M and Deng, C and Lei, J and Yang, X and Li, J and Al-Dhabi, NA and Wen, S and Tang, W and Feng, B and Zhang, P}, title = {Amoxicillin effects on pollutant removal, cyanophycin synthesis, and the proliferation of antibiotic resistance genes (ARGs) in the algal-bacterial biofilm.}, journal = {Journal of hazardous materials}, volume = {500}, number = {}, pages = {140363}, doi = {10.1016/j.jhazmat.2025.140363}, pmid = {41197508}, issn = {1873-3336}, abstract = {The algal-bacterial wastewater treatment process is characterized by its efficiency in water quality purification and bioresource recovery. This study investigated the effects of amoxicillin (AMX) on pollutant removal, cyanophycin synthesis, and the proliferation of antibiotic resistance genes (ARGs) within the algal-bacterial biofilm. AMX significantly suppressed ammonia and phosphorus removal by inhibiting nitrogen and phosphorus assimilation in cyanobacteria. A total of 72 metagenomic assembled genomes carrying cyanophycin biosynthetic genes were identified, with Pantanalinema and Planktothrix being the primary cyanophycin-producing species. AMX concentrations of 0.5 and 1 mg/L suppressed both cyanobacterial growth and cyanophycin synthesis, with the inhibitory effect intensifying as AMX concentration increased. AMX also promoted the proliferation of sul1, OXA-101, VEB-3, and qacEdelta1, while decreased the abundance of OXA-36, erm(F), and tet types. Pseudomonadota and Bacteroidota were the primary hosts for ARGs proliferation and dissemination, with bacA and tetX1 actively spreading within the algal-bacterial biofilm. Cyanobacteria played a negligible role in the propagation of ARGs. This study offers new insights into the spread of ARGs and bioresource recovery in algal-bacterial systems, focusing on both gene and strain levels.}, }
@article {pmid41197330, year = {2025}, author = {Ke, T and Jiang, T and Li, H and Dong, X and Khoo, HE}, title = {Probiotic-fermented milk alleviates hypertension in preeclampsia rats and is associated with increases in branched fatty acid esters of hydroxy fatty acids.}, journal = {Nutrition research (New York, N.Y.)}, volume = {144}, number = {}, pages = {1-15}, doi = {10.1016/j.nutres.2025.10.004}, pmid = {41197330}, issn = {1879-0739}, abstract = {Branched fatty acid esters of hydroxy fatty acids (FAHFAs), a newly-discovered class of endogenous lipids closely associated with obesity, cardiovascular disease, and aging, are potential drug candidates or targets for the prevention and treatment of related conditions. The antihypertensive potential of probiotic-fermented milk has been recognized, but its relevance to preeclampsia (PE) is unclear. It was hypothesized that probiotic-fermented milk could reduce blood pressure in PE rats and influence the contents of FAHFAs, with FAHFAs potentially playing a critical role in this process. To test this hypothesis, the PE rat model was constructed using L-NAME (125 mg/kg), and probiotic-fermented milk (20 mg/kg) was administered for a total of 21 d. Metagenomic sequencing and LC-MS/MS based metabolomics were used. Probiotic-fermented milk substantially attenuated hypertension in PE rats, with an efficacy comparable to that of labetalol (4 mg/kg). Probiotic-fermented milk significantly increased the contents of specific FAHFAs (e.g., 18:0/20:2, 16:0/18:2) in the gut and serum (P < .05) and FAHFAs was negatively correlated with blood pressure (P < .05). Probiotic-fermented milk regulated the composition of gut microbiota (increasing Lactiplantibacillus and Staphylococcus and decreasing Methanobrevibacter and Limosilactobacillus), and down-regulated purine, glyoxylate/dicarboxylate, and amino metabolism, and the one-carbon pool produced by folate. These metabolic shifts were strongly correlated with the gut microbiota and FAHFAs. These results indicate that probiotic-fermented milk alleviates hypertension in PE rats, potentially mediated by FAHFAs. This study provides foundational evidence for the antihypertensive mechanism of probiotic-fermented milk in preeclampsia and supports the development of novel strategies for its prevention and treatment.}, }
@article {pmid41196658, year = {2025}, author = {Verna, G and De Santis, S and Islam, BN and Sommella, EM and Licastro, D and Zhang, L and De Almelda Celio, F and Miller, EN and Merciai, F and Caponigro, V and Xin, W and Campiglia, P and Pizarro, TT and Chieppa, M and Cominelli, F}, title = {A missense mutation in Muc2 promotes gut microbiome- and metabolome-dependent colitis-associated tumorigenesis.}, journal = {The Journal of clinical investigation}, volume = {}, number = {}, pages = {}, doi = {10.1172/JCI196712}, pmid = {41196658}, issn = {1558-8238}, abstract = {Colitis-associated cancer (CAC) arises from a complex interplay between host and environmental factors. In this report, we investigated the role of the gut microbiome using Winnie mice, a UC-like model with a missense mutation in the Muc2 gene. Upon rederivation from a conventional (CONV) to a specific-pathogen-free (SPF) facility, Winnie mice developed severe colitis and, notably, spontaneous CAC that progressively worsened over time. In contrast, CONV Winnie showed only mild colitis but no tumorigenesis. By comparison, when rederived into germ-free (GF) conditions, SPF Winnie mice were protected from colitis and colon tumors, indicating an essential role for the gut microbiome in the development of CAC in these mice. Using shotgun metagenomics, metabolomics, and lipidomics, we identified a distinct pro-inflammatory microbial and metabolic signature that potentially drives the transition from colitis to CAC. Fecal microbiota transplantation (FMT), using either SPF Winnie or WT (Bl/6) donors into GF Winnie recipients, demonstrated that while colitis developed regardless of the donor, only FMT from SPF Winnie donors resulted in CAC. Our studies present a relevant model of CAC, providing strong evidence that the microbiome plays a key role in its pathogenesis, thereby challenging the concept of colon cancer as a strictly non-transmissible disease.}, }
@article {pmid41196057, year = {2025}, author = {Fait Kadlec, T and Ilett, EE and da Cunha-Bang, C and Sengeløv, H and Brieghel, C and Gulay, A and Rafiq, S and Ravn, HB and Zheng, C and Nielsen, RV and Sørensen, SS and Zargari Marandi, R and Niemann, CU}, title = {Explainable machine learning to identify chronic lymphocytic leukemia and medication use based on gut microbiome data.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0094425}, doi = {10.1128/spectrum.00944-25}, pmid = {41196057}, issn = {2165-0497}, abstract = {Medication, particularly antibiotics, significantly alters gut microbiome composition, often reducing microbial diversity and affecting host health. Given that the gut microbiome may influence cancer progression, we integrated clinical, shotgun metagenomic, and medication data to assess microbiome composition across diseased and healthy cohorts, as well as the impact of medication on microbiome variation. The study cohorts included patients with chronic lymphocytic leukemia (CLL, n = 85), acute myeloid leukemia (AML, n = 61), myeloid dysplastic syndrome (MDS), and other severe hematological malignancies (n = 104); patients scheduled for elective cardiac surgery (n = 89); and kidney donors (n = 9), all collected as part of a consecutive microbiome sampling effort at Copenhagen University Hospital, Denmark; and healthy individuals (N = 59). First, our analyses revealed similarities in both diversity and composition between microbiomes of patients with CLL and patients prior to elective cardiac surgery, whereas patients with AML and MDS exhibited the least diverse and most distinct microbiomes. Second, when we quantified sources of microbiome variation, the combination of medication, disease, age, and sex accounted for 4% of variation between all cohorts and 10.4% of variation between CLL and pre-cardiac surgery patients only; the two cohorts selected for comparison due to their similar microbiomes. Notably, this left 90%-95% of the variation unexplained, emphasizing the need for better identification of the parts of the microbiome variation impacting health and disease. Third, using a machine learning approach, we validated and further refined the CLL-associated microbiome pattern from our previous studies. Overall, our data provide a foundation for further investigation into disease-specific microbial signatures and the potential interactions between medication, underlying disease, and the microbiome, with the ultimate goal to improve our understanding and clinical management of CLL.IMPORTANCEThis study reveals how disease and medication influence the gut microbiome in patients with chronic lymphocytic leukemia (CLL) when compared to other more severe hematological malignancies, a cohort of patients scheduled for elective cardiac surgery representing a severely diseased nonhematological cohort, and a cohort of healthy individuals. We found that patients with CLL and those scheduled for cardiac surgery had the most similar microbiome diversity and composition. Similarities across very different disease contexts suggest that disease status alone has limited impact. Consistently, across all cohorts, medication, disease, age, and sex together explained only less of microbiome variation, leaving 90%-95% unexplained. This underscores the important need for better identification of factors shaping the microbiome. In addition, we validated a previously published, machine learning-based CLL-associated microbiome signature, demonstrating the robustness of our previous findings differentiating the microbiome signature for CLL as compared to healthy individuals. The findings expand knowledge on how disease states and medical treatments shape gut microbiome composition and diversity, potentially leading to new ways of managing CLL and improving patient outcomes through microbiome signatures.}, }
@article {pmid41196055, year = {2025}, author = {Plaza Oñate, F and Quinquis, B and Thirion, F and Gilles, M and Morabito, C and Valeille, K and Martin, R and Guidet, B and Kern, C and Pécastaings, S}, title = {Assessment of protocols for characterization of the human skin microbiome using shotgun metagenomics and comparative analysis with 16S metabarcoding.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0173225}, doi = {10.1128/spectrum.01732-25}, pmid = {41196055}, issn = {2165-0497}, abstract = {The skin microbiome includes bacteria, fungi, and viruses, with composition varying significantly across body sites. Although 16S rRNA gene sequencing is common, it excludes non-prokaryotic taxa and offers limited functional data. Shotgun metagenomics provides broader taxonomic and functional insights but is challenging for low-biomass skin samples due to limited microbial DNA and high host contamination. In this study, we characterized the microbiome of the forehead and armpits in healthy individuals using shotgun metagenomics and assessed the strategies to improve sequencing success. We compared collection kits, DNA extraction protocols, and tested multiple displacement amplification (MDA). We found that sampling with D-Squame discs followed by an in-house DNA extraction protocol was the most effective combination to maximize DNA yields. MDA introduced significant compositional biases and is not recommended. Shotgun sequencing, without MDA, produced microbial compositions and diversity indices broadly consistent with 16S rRNA metabarcoding, although it showed discrepancies in the relative abundance of some genera. Consistent with prior studies, the armpit microbiome was dominated by Staphylococcus spp., whereas the forehead microbiome was dominated by Cutibacterium spp. Critically, shotgun sequencing provided additional insights into viral and eukaryotic microorganisms and revealed the functional potential of microbial communities, demonstrating its clear advantages over 16S rRNA metabarcoding for comprehensive skin microbiome research.IMPORTANCEWith growing evidence of the role of microorganisms in maintaining healthy skin, accurately characterizing the skin microbiome remains a significant challenge. In this study, we demonstrate that shotgun sequencing, carried out with adapted wet lab protocols, provides deep insights into the microbiome composition of specific areas, such as the forehead or the armpits. Notably, it enables the characterization of fungi and viruses while offering direct functional insights into microbial communities, providing a clear advantage over 16S ribosomal RNA gene sequencing. Our findings highlight the potential of shotgun metagenomics as a powerful tool for comprehensive skin microbiome analysis. They emphasize the importance of tailored protocols for low-biomass samples, improving the reliability of shotgun sequencing and paving the way for more robust clinical studies focused on the skin microbiome.}, }
@article {pmid41196050, year = {2025}, author = {Lee, S and Raza, S and Lee, E-J and Chang, Y and Ryu, S and Kim, H-L and Kang, S-H and Kim, H-N}, title = {Metagenome-assembled genomes reveal microbial signatures and metabolic pathways linked to coronary artery disease.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0095425}, doi = {10.1128/msystems.00954-25}, pmid = {41196050}, issn = {2379-5077}, abstract = {Gut microbiota has emerged as a critical factor influencing cardiovascular disease (CVD) risk, particularly coronary artery disease (CAD) development. Using fecal metagenomic shotgun sequencing, we investigated gut microbiota signatures associated with CAD and provided strain-resolved insights through metagenome-assembled genome (MAG) reconstruction. We analyzed 14 patients with CAD and 28 propensity score-matched healthy controls. Differential abundance analysis identified 15 CAD-associated bacterial species. Members of the Lachnospiraceae family, previously associated with trimethylamine-N-oxide production, were significantly enriched in patients with CAD. Conversely, short-chain fatty acid-producing bacteria Slackia isoflavoniconvertens and Faecalibacterium prausnitzii were depleted, suggesting a potential contribution to gut-mediated inflammation and metabolic dysregulation. Metabolic pathway analysis revealed significant urea cycle and L-citrulline biosynthesis enrichment in CAD cases, with Alistipes and Coprococcus as key contributors. Among predicted metabolites, inosine, which is implicated in coronary artery relaxation, was elevated in patients with CAD, whereas C18:0e MAG and α-muricholate were depleted. A random forest model achieved a mean AUC of 0.89 for CAD classification, with improved performance when integrating microbial taxa and metabolites. CAD-derived MAGs showed metabolic signatures linked to inflammatory dysbiosis and cardiovascular dysfunction, such as enriched N2 fixation and sulfite reduction. Strain-resolved comparative genomic analysis of MAGs revealed distinctive functional characteristics between CAD-derived and control-derived strains of Akkermansia muciniphila and Megamonas fumiformis. F. prausnitzii MAG from the control group carried non-trimethylamine-producing gene, mtxB, suggesting its potential protective role in CAD pathophysiology. These findings provide insights into gut microbial alterations in CAD and highlight potential targets for microbiome-based therapeutic interventions to reduce CVD risk.IMPORTANCEGut microbiota plays a pivotal role in cardiovascular disease; however, its specific contribution to coronary artery disease (CAD) remains underexplored. This study identified distinct microbial signatures associated with CAD, including the enrichment of pro-inflammatory bacterial taxa and depletion of short-chain fatty acid-producing bacteria, which may contribute to systemic inflammation and metabolic dysregulation. Perturbations in key pathways, such as the urea cycle and glycolysis, suggest metabolic links between the gut microbiota and CAD. Additionally, the metagenome-assembled genome-based analysis revealed strain-resolved functional heterogeneity that shapes host-microbe interactions and may contribute to CAD pathophysiology. These findings provide novel insights into gut dysbiosis in CAD and highlight the potential of microbiome-targeted therapeutic strategies in precision medicine.}, }
@article {pmid41195400, year = {2025}, author = {Zhili, G and Jie, L and Peihao, Y}, title = {Macro- and metabolome-based characterization between gut microbiota and metabolites in patients with colorectal adenomas.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1628315}, pmid = {41195400}, issn = {1664-302X}, abstract = {OBJECTIVE: The gut microbiota has been recognized as a significant regulator in the development and progression of colorectal adenoma (CRA). However, few studies have investigated the presence and association of resident microbial species and metabolites in patients with CRA. Our aim was to analyze differences in gut microbiome composition and metabolites, as well as to evaluate their diagnostic potential for CRA.<br><br>METHODS: We conducted metagenomic and metabolomic analyses on fecal samples from 90 subjects, including 60 patients with CRA (CRA group) and 30 healthy subjects who served as normal controls (NC group). By integrating fecal metagenomic and metabolomic data, we identified gut microbiota-associated metabolites that showed significant abundance changes in CRA patients. Furthermore, we explored whether these metabolites and microbial species could distinguish CRA patients from healthy individuals.<br><br>RESULTS: 16S rRNA gene sequencing and untargeted metabolomics analysis revealed microbial changes that distinguished CRA patients from controls. Microbial population analysis showed that the CRA group formed distinct clusters from the controls, with significant &#x3b2;-diversity (PCA and PCoA analyses, p < 0.05). At the phylum level, the dominant taxa in terms of relative abundance included Firmicutes, Ascomycota, Mycobacteria, Actinobacteria, and Clostridia. Differential analysis of the gut flora based on species abundance revealed significant differences in taxonomic composition between healthy individuals and CRA patients. KEGG functional enrichment analysis indicated that the differential flora were primarily involved in metabolic pathways, including metabolic pathways, biosynthesis of secondary metabolites, microbial metabolism in diverse environments, amino acid biosynthesis, and cofactor biosynthesis. In this study, three microbial species-Fusobacterium mortiferum, Alistipes, and Bacteroides fragilis-were validated as discriminators between healthy individuals and CRA patients, with Alistipes showing higher classification efficacy. Metabolomic analysis revealed differences in tryptophan metabolism, protein degradation products, amides, and phenolic acid metabolites. KEGG enrichment results indicated that metabolic pathways were the most significantly enriched. Differential metabolites were mainly associated with the biosynthesis of plant secondary metabolites. Procrustes and Venn analyses were performed on functional entries of the two omics datasets, highlighting enriched pathways including Metabolic pathways, Glycerophospholipid metabolism, Sphingolipid metabolism, and Alpha-linolenic acid metabolism. A review of the literature confirmed that the differential flora and metabolites are associated with adenoma growth.<br><br>CONCLUSION: In this study, metagenomic and metabolomic analyses were conducted in subjects with CRA. The findings based on fecal metagenomic and metabolomic assays suggest that intestinal microecology is altered in CRA patients, leading to changes in gut cellular structure.}, }
@article {pmid41195399, year = {2025}, author = {, }, title = {Correction: Metagenomic insights reveal the differences in the community composition and functional characteristics of the sea turtle microbiomes based on host species and tissue region.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1721706}, doi = {10.3389/fmicb.2025.1721706}, pmid = {41195399}, issn = {1664-302X}, abstract = {[This corrects the article DOI: 10.3389/fmicb.2025.1652229.].}, }
@article {pmid41195309, year = {2025}, author = {Xu, Z and Li, X and Yuan, X and Sun, C and Zhang, M and Chen, R and Wei, H and Chen, L and Du, H and Li, G and Yang, Y and Chen, X and Cui, L and Fang, X and Wu, J and Li, Q and Luo, F}, title = {HLA-C⁣ [∗] 0304 Associates With Beneficial Gut Microbiota and Later Onset of Type 1 Diabetes in Pediatric Cohorts.}, journal = {Pediatric diabetes}, volume = {2025}, number = {}, pages = {3013063}, pmid = {41195309}, issn = {1399-5448}, mesh = {Humans ; *Diabetes Mellitus, Type 1/genetics/microbiology/epidemiology/immunology ; *Gastrointestinal Microbiome/genetics ; Child ; Male ; Female ; Cross-Sectional Studies ; Adolescent ; Child, Preschool ; Age of Onset ; Cohort Studies ; Infant ; }, abstract = {OBJECTIVE: To investigate whether human leukocyte antigens (HLAs) influence gut microbiota composition and contributes to delayed type 1 diabetes mellitus (T1DM) onset in children.<br><br>METHODS: This multicenter cross-sectional study included 106 newly diagnosed pediatric T1DM patients (age <18 years) and 69 healthy controls from nine Chinese cities. Gut microbiota was profiled via whole-metagenome shotgun sequencing, and HLA alleles were genotyped by PCR sequence-based typing. Participants were stratified by HLA-risk scores. Statistical analyses included &#x3b1;/&#x3b2;-diversity metrics, linear discriminant analysis effect size analysis (LEfSe), and Spearman correlation adjusted for confounders.<br><br>RESULTS: Principal coordinates analysis (PCoA) exposed discernible disparities in gut microbiota structures within the high-HLA-risk T1DM cohort relative to both high- and low-HLA-risk control groups (R [2]&#x2009;=&#x2009;0.0562, p=0.003 and R [2]&#x2009;=&#x2009;0.0343, p=0.003). HLA-C [&#x2217;] 0304 carriers exhibited delayed T1DM onset compared to noncarriers (adjusted R [2]&#x2009;=&#x2009;0.225, p=0.017). High-HLA-risk T1DM patients showed distinct microbiota divergence from controls (R [2]&#x2009;=&#x2009;0.0562, p=0.003), driven by reduced Lachnospiraceae and Blautia (butyrate producers) in noncarriers. Conversely, HLA-C [&#x2217;] 0304-positive T1DM patients had enriched Blautia (p=0.005) and Lachnospiraceae (p=0.039), alongside lower opportunistic pathogens (Citrobacter; p < 0.05). High-HLA-risk patients also displayed lower fasting C-peptide levels than low-risk counterparts (0.19&#x2009;&#xb1;&#x2009;0.14 vs. 0.26&#x2009;&#xb1;&#x2009;0.19&#x2009;&#xb5;g/mL, p=0.029).<br><br>CONCLUSIONS: Our study demonstrates that specific HLA class I subtypes (e.g., C [&#x2217;] 0304) may modulate T1DM onset through selective enrichment of beneficial gut microbiota. Elucidating the mechanisms by which HLA variants regulate mucosal immunity and coordinate HLA-microbiota-immune interactions holds significant potential for developing targeted interventions against T1DM pathogenesis.}, }
@article {pmid41194765, year = {2025}, author = {Li, J and Zhao, S and Guo, F and Zhang, W and Chen, M and den Haan, R and Xin, F and Jiang, Y and Jiang, M}, title = {Strategies to Improve the Efficiency of Enzymatic Carbon Dioxide Conversion In Vitro.}, journal = {ACS synthetic biology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acssynbio.5c00760}, pmid = {41194765}, issn = {2161-5063}, abstract = {With the rapid industrial development, massive fossil fuel use has caused excessive carbon dioxide (CO2) emissions, triggering global warming and environmental issues. Thus, CO2 recovery and reuse have become a research focus, among which artificially designed in vitro biocatalytic pathways for converting CO2 into high-value chemicals show promise, with advantages like shorter routes, higher efficiency and lower energy consumption compared to natural pathways. However, challenges remain due to natural enzymes' issues in specificity, affinity, efficiency, stability and oxygen sensitivity. To tackle these problems, extensive research efforts have been undertaken. These include elucidating the mechanisms and catalytic efficiencies of carbon-fixing enzymes from diverse sources, as well as developing and refining novel in vitro carbon fixation pathways. Moreover, significant progress has been made in computer-aided investigations of enzyme structure, function, and engineering optimization, alongside advancements in enzyme immobilization strategies, cofactor regeneration systems, and the development of artificial cofactors. By summarizing the latest research progress in recent years, we can identify the current bottlenecks and challenges in in vitro enzymatic CO2 conversion, propose effective methods to enhance the efficiency of CO2 conversion, and thus promote the development of research in related fields.}, }
@article {pmid41194716, year = {2025}, author = {Liu, YH and Sheng, SY and Hu, HB and Wang, Y and Zhang, LW and Feng, YF and Feng, YY}, title = {Effects of drought on the thermal adaptation of soil microbial respiration: A review.}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {36}, number = {10}, pages = {2965-2977}, doi = {10.13287/j.1001-9332.202510.032}, pmid = {41194716}, issn = {1001-9332}, mesh = {*Droughts ; *Soil Microbiology ; Climate Change ; Soil/chemistry ; *Adaptation, Physiological/physiology ; Ecosystem ; Carbon Cycle ; }, abstract = {Drought induced by global climate change affects the thermal adaptation of soil microbial respiration, which has complex consequences on the carbon (C) cycle. Drought can either enhance C emissions and create a positive feedback loop, or promote C sequestration and generate a negative feedback effect. We reviewed the effects of drought on microbial thermal adaptation, analyzed the underlying mechanisms, and summarized current research findings and related debates. Drought significantly influences microbial thermal adaptation through altering soil aggregate structure, organic carbon molecular composition, and microbial community structure. Due to variations in climatic zones, ecosystem types, and soil conditions, the impacts of drought on microbial thermal adaptation exhibit regional variety and complexity. Future research should focus on experimental designs that simulate natural environments, utilizing diverse organic substrates (e.g., cellulose, oxalic acid and xylan) to generate more accurate data and explore the synergistic effects of drought with other environmental factors (e.g., elevated CO2 concentrations, increased ultraviolet radiation, and nitrogen deposition) to reveal their combined impacts on microbial thermal adaptation. Advanced techniques like metagenomics and DNA-stable isotope probing should be warranted to further reveal the microbial mechanisms involved in the regulation of drought on microbial thermal adaptation.}, }
@article {pmid41194562, year = {2025}, author = {Martínez-Mercado, MA and Latisnere-Barragán, H and Ramírez-Arenas, PJ and Vázquez-Juárez, R and García-Maldonado, JQ and López-Cortés, A}, title = {Genome-Resolved Approach of Guerrero Negro Hypersaline Microbial Mats Reveals the Metabolic Potential of Key Players in a Stratified Community.}, journal = {Environmental microbiology}, volume = {27}, number = {11}, pages = {e70199}, doi = {10.1111/1462-2920.70199}, pmid = {41194562}, issn = {1462-2920}, support = {CF-2019-848287//Consejo Nacional de Humanidades Ciencia y Tecnolog&#xed;a/ ; }, mesh = {*Archaea/genetics/metabolism/classification/isolation &amp; purification ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; *Genome, Bacterial ; Metagenome ; *Microbiota ; Sulfur/metabolism ; *Geologic Sediments/microbiology ; Salinity ; Genome, Archaeal ; Carbon/metabolism ; Nitrogen/metabolism ; Phylogeny ; }, abstract = {Hypersaline microbial mats at Guerrero Negro harbor a stratified, highly diverse community with diel metabolic changes. While oxygenic photosynthesis and sulfate reduction are the dominant bacterial metabolic processes, methylotrophic methanogenesis is the main archaeal pathway. Although these metabolic processes have been biochemically characterized, the identity and encoded metabolism of the microorganisms have been inferred only from gene-marker data. Here, a genome-resolved approach in both environmental, as well as experimental dark condition samples (control, H2/CO2, TMA, and H2/CO2-TMA) was used to stimulate less-known anaerobic strategies, determine the metabolic potential of the main microbial players, and analyze the community. Representative metagenome-assembled genomes (170 MAGs) were obtained, encompassing 25 bacterial and 4 archaeal phyla. The metabolic analyses of three basic elements (carbon, sulfur, nitrogen) encoded in the MAGs suggested that in environmental samples, phototrophic taxa were the main source of the organic matter that fueled most of the community. Different sulfur species acting as electron acceptors led to the metabolism of partially degraded organic matter in the lower layers of the mat. These results link and clarify the biochemical processes and microbial players, adding a novel genomic component for the ecological understanding of the microbial mats of Guerrero Negro.}, }
@article {pmid41194295, year = {2025}, author = {Breukers, E and Kim, H and Banihashem, F and Andersson, K and Leijon, M and Westin, R and Sjölund, M and Zohari, S}, title = {The first detection of swine orthopneumovirus in a pig farm in Sweden: a case report.}, journal = {Porcine health management}, volume = {11}, number = {1}, pages = {56}, pmid = {41194295}, issn = {2055-5660}, abstract = {BACKGROUND: Respiratory diseases are globally a major challenge in today's pig production. Despite the efforts to manage the disease, the number of pigs affected is still increasing, indicating gaps in the current knowledge. In 2016, a novel pneumovirus, swine orthopneumovirus, was detected in the USA. Since then, the virus has been detected in a few European countries and in South Korea. However, the wider distribution of the virus is still greatly unknown, as well as its clinical relevance.<br><br>CASE PRESENTATION: This report describes the first detection of swine orthopneumovirus in a Swedish pig herd. The virus was detected as the result of an investigation conducted between September 2023 to June 2024, where all clinical samples (n&#x2009;=&#x2009;682) sent to the Swedish Veterinary Agency for diagnostic purposes from 112 Swedish pig farms exhibiting clinical signs of respiratory disease were screened for the presence of swine orthopneumovirus. The virus was detected in one piglet producing farm that had a respiratory disease outbreak in autumn 2023, which presented with cough and nasal discharge. In November 2023, 11 nasal swabs were collected, of which 9 were PCR-positive for swine orthopneumovirus. In addition, each sample was also PCR-positive for Mesomycoplasma hyorhinis and Pasteurella multocida, and 2 samples were PCR-positive for Actinobacillus pleuropneumoniae, indicating a polymicrobial respiratory infection.<br><br>CONCLUSIONS: This report emphasises the importance of ongoing efforts to identify emerging pathogens and determine their clinical significance. Therefore, further research is needed to assess the distribution and potential clinical relevance of swine orthopneumovirus.}, }
@article {pmid41194257, year = {2025}, author = {Parsons, C and Fournier, GP}, title = {Horizontal transfer of matrix metalloproteinase genes links early animal and microbial evolution.}, journal = {Biology direct}, volume = {20}, number = {1}, pages = {107}, pmid = {41194257}, issn = {1745-6150}, support = {EAR-1615426//National Science Foundation/ ; }, mesh = {*Gene Transfer, Horizontal ; Animals ; *Bacteria/genetics/enzymology ; Phylogeny ; *Matrix Metalloproteinases/genetics ; *Evolution, Molecular ; Archaea/genetics/enzymology ; *Biological Evolution ; Metagenome ; }, abstract = {BACKGROUND: The early evolution of animals is characterized by the emergence of complex tissues, organs, and integument, made possible in part by the diversification of groups of structural proteins. The abundance of this new kind of organic material in the environment would have provided novel nutrient opportunities for microbes, as part of the beginnings of animal-microbial coevolution. Indeed, a diverse ensemble of extant microbial groups appear to possess the enzymatic ability to cleave collagen, the most abundant animal-specific protein, through the use of matrix metalloproteinases (MMPs). In animals, MMPs serve to reshape the extracellular matrix in the course of development, but their prevalence in the microbial world has been largely overlooked.<br><br>RESULTS: MMPs have extensive diversity in Bacteria, Eumetazoa, and Streptophyta. We show that in marine metagenomes, MMP abundance is highly correlated with chitinase abundance, implying that even microbial MMPs are associated with animal-derived substrates. Reconstructing the phylogeny of MMP proteins reveals a history of rapid diversification, as well as multiple interkingdom and interdomain horizontal gene transfers. Included among these is a transfer to the ancestral lineage of the archaeal family Methanosarcinaceae, constraining this group to postdate the evolution of collagen, and therefore animal diversification.<br><br>CONCLUSIONS: MMPs have an unusual genetic history, marked by multiple instances of gene transfer between bacteria and multicellular eukaryotes, a smoking gun for some of the earliest coevolution between prokaryotes and metazoans. By calculating an end-Permian divergence of Methanosarcina, we demonstrate that the phylogenies of substrate-specific enzymes can provide valuable older-bound age calibrations for improving molecular clock age estimates across the Tree of Life.}, }
@article {pmid41194238, year = {2025}, author = {Ellis, VA and Theodosopoulos, A and Sharma, I and Bardil, A and Stjernman, M and Hellgren, O}, title = {Simultaneous population genomics of hosts and their parasites with selective whole genome amplification.}, journal = {Parasites &amp; vectors}, volume = {18}, number = {1}, pages = {448}, pmid = {41194238}, issn = {1756-3305}, support = {NIH/NIGMS P20 GM103446, S10 OD028725/GF/NIH HHS/United States ; DEL00854, NE1943, NE2443//USDA Hatch/ ; VR 2021-03663//Swedish Research Council/ ; }, mesh = {Animals ; *Haemosporida/genetics ; *Host-Parasite Interactions/genetics ; *Protozoan Infections, Animal/parasitology ; *Bird Diseases/parasitology ; *Genome, Protozoan ; DNA, Protozoan/genetics ; Genomics ; *Passeriformes/parasitology/genetics ; Metagenomics/methods ; }, abstract = {BACKGROUND: Generating parasite genomes is challenging when little of the DNA in infected host tissue is from the parasite. We used selective whole genome amplification (SWGA) to generate genomic data from wildlife samples of the avian haemosporidian Haemoproteus majoris (lineage PARUS1) and its host, the blue tit (Cyanistes caeruleus).<br><br>METHODS: We used SWGA to amplify the parasite DNA in nine avian blood samples collected between 1996 and 2021, and subsequently performed short-read sequencing and bioinformatically separated the host and parasite reads in each sample.<br><br>RESULTS: SWGA increased the percentage of parasite reads significantly. Sequencing to a depth of about 56 million reads (forward and reverse) per sample resulted on average (&#xb1; standard error [SE]) in 11.3X&#x2009;&#xb1;&#x2009;1.85 for the host genome and 1.17X&#x2009;&#xb1;&#x2009;0.446 mean depth of coverage for the host and parasite, respectively, after SWGA. Furthermore, about 74% of the host genome (genome size approx. 1.2&#xa0;Gb) and 33% of the parasite genome (approx. 23.9&#xa0;Mb) had at least 1X coverage on average; two samples had 1X coverage of approximately 60% of the parasite genome. Parasite sequencing success was positively correlated with parasitemia. When comparing the parasite sequences in the four best samples, we identified 9895 sites (minimum 5X coverage) that varied among the infections. When filtering the full dataset to at least six samples per variant, we identified 14,512,339 and 7068 sites that varied among samples in the host and parasite populations, respectively, revealing variation among samples and years.<br><br>CONCLUSIONS: SWGA facilitates dual host-parasite population genomics in this system and will greatly expand our understanding of host-parasite interactions over space and time.}, }
@article {pmid41194219, year = {2025}, author = {Liu, Y and Yu, M and Chen, X and Ran, L and Zhang, XH}, title = {Diversity, metabolic potential and global distribution of the anaerobic fermentative bacteria Phylum Candidatus Cloacimonadota.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {136}, pmid = {41194219}, issn = {2524-6372}, support = {32370118//National Natural Science Foundation of China/ ; 202172002//Fundamental Research Funds for the Central Universities/ ; 2022QNLM030004-3, LSKJ202203201 and LSKJ202203206//Scientific and Technological Innovation Project of Laoshan Laboratory/ ; }, abstract = {BACKGROUND: The phylum Candidatus Cloacimonadota (formerly known as Cloacimonetes, WWE 1) is a group of strictly anaerobic organisms that frequently associated with engineering and wastewater systems. At present, it cannot be cultured using traditional cultivation methods, and the taxonomic position within this phylum remains unclear, with only one class, Candidatus Cloacimonadia. Furthermore, the diversity and metabolic characteristics of Candidatus Cloacimonadota members in marine environments have yet to be explored. Therefore, the taxonomy and metabolism of the phylum Candidatus Cloacimonadota require further investigation.<br><br>RESULTS: In this study, six high-quality metagenome-assembled genomes (MAGs) of Candidatus Cloacimonadota were acquired from the anoxic zone of the Yongle Blue Hole (YBH), potentially representing new taxa. Additionally, 483 Candidatus Cloacimonadota genomes from global databases were downloaded, and all genomes were analyzed and compared. Candidatus Cloacimonadota is widely distributed across diverse environments worldwide, and its class, Candidatus Cloacimonadia, can be divided into two clades, Clade A and Clade B, the latter of which contains six YBH-derived MAGs. The Clade A and Clade B showed distinct genomic features, metabolic strategies and evolutionary histories, which are associated with their environments. For instance, they employ different anaerobic respiratory pathways: Clade B utilizes heterodisulfide reductase (HdrABC)-[NiFe]-hydrogenase (MvhADG) complex (NiFe/MvhADG-HdrABC), while Clade A utilizes Hnd/FeFe Group A3 hydrogenase complex for hydrogen utilization. Furthermore, YBH-derived MAGs have unique metabolic genes, such as those encoding chitinase and &#x3b1;-galactosidase, and the chitinase activity in MAG213-F140 from YBH was confirmed by heterologous expression. Divergence time analysis revealed that YBH-derived MAGs diverged around 3.36 million years ago.<br><br>CONCLUSION: This study enhances the understanding of the diversity, metabolic potential, and global distribution of Candidatus Cloacimonadota. We found this phylum could be divided into Clades A and B, revealing significant differences in genetic traits and metabolic capabilities between the two clades, and focusing on their ecological roles in marine environments. Moreover, this research holds substantial value for the development and utilization of marine resources, as well as for advancing the understanding of biogeochemical cycles, further highlighting the crucial role of microorganisms in these key ecological processes.}, }
@article {pmid41194006, year = {2025}, author = {Ivanova, A and Buzova, V}, title = {A novel enzymatic approach for a targeted fungal growth inhibition.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {719}, pmid = {41194006}, issn = {1471-2180}, support = {03-ZP23-087//SkyLab AG/ ; 03-ZP23-087//SkyLab AG/ ; }, abstract = {BACKGROUND: Dandruff represents a complex, multifactorial disorder characterized by impaired barrier function, altered lipid composition, and microbial imbalance. The principal pathogenic mechanism, however, involves excessive colonization by Malassezia species, notably M. furfur, M. restricta and M. globosa, on the scalp. Standard antifungal options often lead to undesirable effects, including itching and irritation, and may negatively impact the scalp microbiome. This study evaluates combination of chitinase and chitosanase, targeting fungal cell wall chitin and chitosan, as a promising targeted approach for scalp Malassezia spp.<br><br>METHODS: The in vitro antifungal activities of chitinase (100 U/g) and chitosanase (200 U/g) were evaluated against Malassezia furfur, Malassezia restricta, and Malassezia globosa at concentrations ranging from 0.125% to 5% w/w. Their efficacy was compared to that of conventional antifungal agents, including climbazole, piroctone olamine, selenium sulfide, zinc pyrithione, and propanediol caprylate. Cytotoxicity was assessed using fibroblast cell lines via MTT assay and fluorescence microscopy. A clinical study (n&#x2009;=&#x2009;18) evaluated the impact of a solution containing 0.25% chitinase and 0.25% chitosanase on scalp M. furfur and M. restricta DNA and RNA levels using quantitative PCR (qPCR). A metagenomic analysis was conducted to assess the impact of enzymatic treatment on bacterial composition and diversity.<br><br>RESULTS: Individually, 0.25% chitinase and 0.25% chitosanase inhibited Malassezia spp. growth by 23.85% and 26.15%, respectively (p&#x2009;<&#x2009;0.05). When combined at 0.25%, they achieved 98.38% inhibition (p&#x2009;<&#x2009;0.05), with complete suppression observed at 0.5%. In a clinical study, a 3-hour scalp treatment with a solution containing 0.25% chitinase and 0.25% chitosanase followed by quantitative PCR of post-treatment samples demonstrated significant reductions in DNA and RNA levels of M. furfur and M. restricta. DNA content decreased 2.4- and 1.9-fold, and RNA levels declined 2.4- and 4.6-fold, respectively. Cytotoxicity was detected only at concentrations&#x2009;&#x2265;&#x2009;7.6%, well above the effective antifungal doses. The metagenomic analysis demonstrated that a three-hour scalp treatment with chitinase - chitosanase solution increased alpha diversity (Chao1 index) and doubled the number of identifiable operational taxonomic units (OTUs).<br><br>CONCLUSIONS: The chitinase-chitosanase combination offers a promising targeted approach for scalp Malassezia spp. control without broad antimicrobial effects.}, }
@article {pmid41193697, year = {2025}, author = {Chica Cardenas, LA and Leonard, MM and Baldridge, MT and Handley, SA}, title = {Gut virome dynamics: from commensal to critical player in health and disease.}, journal = {Nature reviews. Gastroenterology &amp; hepatology}, volume = {}, number = {}, pages = {}, pmid = {41193697}, issn = {1759-5053}, abstract = {The gut virome is a complex ecosystem characterized by the interplay of diverse viral entities, predominantly bacteriophages and eukaryotic viruses. The gut virome has a critical role in human health by shaping microbial community profiles, modulating host immunity and influencing metabolic processes. Different viral metagenomics approaches have revealed the remarkable diversity of the gut virome, showing individual-specific patterns that evolve over time and adapt dynamically to environmental factors. Perturbations in this community are increasingly associated with chronic immune and inflammatory conditions, metabolic disorders and neurological conditions, highlighting its potential as a diagnostic biomarker and therapeutic target. The early-life gut virome is particularly influential in establishing lifelong health trajectories through its interactions with diet, immune pathways and others, thereby contributing to inflammatory and metabolic regulation. This Review synthesizes current knowledge of gut virome composition, dynamics and functional relevance, critically evaluating evidence distinguishing causal from correlative roles in disease pathogenesis. The interactions of the virome with other microbiome components and host immunity are examined, and emerging translational applications, including phage therapy and biomarker development, are discussed. Integrating these insights while acknowledging methodological challenges provides a comprehensive framework for understanding the complex roles of the gut virome in health and disease.}, }
@article {pmid41193636, year = {2025}, author = {Hug, LA and Hatzenpichler, R and Moraru, C and Soares, AR and Meyer, F and Heyder, A and ,  and Probst, AJ}, title = {Author Correction: A roadmap for equitable reuse of public microbiome data.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41564-025-02212-3}, pmid = {41193636}, issn = {2058-5276}, }
@article {pmid41193635, year = {2025}, author = {Weinheimer, AR and Brown, JM and Thompson, B and Leonaviciene, G and Kiseliovas, V and Jocys, S and Munson-McGee, J and Gavelis, G and Mascena, C and Mazutis, L and Poulton, NJ and Zilionis, R and Stepanauskas, R}, title = {Single-particle genomics uncovers abundant non-canonical marine viruses from nanolitre volumes.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {41193635}, issn = {2058-5276}, support = {991222//Simons Foundation/ ; }, abstract = {Viruses and other extracellular genetic elements play essential roles in marine communities. However, methods to capture their full diversity remain limited by the constraints of bulk sequencing assemblers or pre-sorting throughput. Here we introduce environmental micro-compartment genomics (EMCG), which vastly improves the throughput and efficiency of single-particle genomic sequencing obtained from nanolitre volumes by compartmentalizing particles of a sample into picolitre-sized, semi-permeable capsules for in-capsule DNA amplification and barcoding. From 300 nanolitres of seawater, EMCG obtained genomic sequences of 2,037 particles. The microbiome composition agreed with other methods, and the virus-like assembly lengths indicated that most were near complete. Many viral assemblies belonged to the Naomiviridae, lacked metagenomic representation and aligned to outlier contigs of abundant, putative host lineages, suggesting their use of non-canonical DNA and overlooked ecological importance. This approach provides opportunities for high-throughput, quantitative and cost-effective genome analyses of individual cells and extracellular particles across complex microbiomes.}, }
@article {pmid41192565, year = {2025}, author = {Tóth, GE and Petersen, M and Chevenet, F and Sikora, M and Tomazatos, A and Bialonski, A and Baum, H and Horváth, B and Siriyasatien, P and Heitmann, A and Jansen, S and Offergeld, R and Lachmann, R and Schmidt, M and Schmidt-Chanasit, J and Cadar, D}, title = {Blood donors as sentinels for genomic surveillance of West Nile virus in Germany using a sensitive amplicon-based sequencing approach.}, journal = {The Journal of infection}, volume = {}, number = {}, pages = {106647}, doi = {10.1016/j.jinf.2025.106647}, pmid = {41192565}, issn = {1532-2742}, abstract = {BACKGROUND: West Nile virus (WNV) has emerged as a public health concern in Germany since its first detection in 2018, with evidence of expanding geographic spread. Genomic surveillance is critical for tracking viral evolution, identifying introductions, and monitoring local transmission. However, genome recovery from low-viremia samples such as those obtained through blood donor screening remains technically challenging.<br><br>AIM: To develop and validate a sensitive amplicon-based sequencing protocol optimized for WNV lineage 2 and apply it to low-titer samples to support genomic surveillance in Germany.<br><br>METHODS: A novel primer scheme was designed for WNV lineage 2 and applied to 43 nucleic acid testing (NAT)-positive blood donor samples collected between 2020 and 2024. Amplicon-based sequencing performance was benchmarked against metagenomic next-generation sequencing (mNGS). Recovered genomes were subjected to phylogenomic analysis to assess viral diversity and transmission dynamics.<br><br>RESULTS: The amplicon protocol enabled genome recovery (>70% coverage) from samples with viral loads as low as ~10&#xb9; RNA copies/&#xb5;L, outperforming metagenomic NGS (mNGS). Of the 43 samples, 30 yielded complete or near-complete genomes. Six distinct WNV subclades (2A-2F), including German strains, were identified, indicating multiple introductions into Germany from Central Europe. Subclade 2F emerged as the dominant and widely distributed group. Berlin, Brandenburg, Saxony, and Saxony-Anhalt were identified as persistent transmission hubs.<br><br>CONCLUSION: This study highlights blood donors as valuable sentinels for WNV genomic surveillance. The validated amplicon-based sequencing approach enables sensitive, scalable genome recovery from low-viremia samples, and when integrated with routine blood donor screening, provides a robust framework for early detection, transmission dynamics, and public health preparedness.}, }
@article {pmid41192489, year = {2025}, author = {Meng, F and Wang, L and Xu, J and Li, X and Hao, J}, title = {Enhanced electron transfer mediated by surface functional groups of targetedly modified sludge-based biochar for sustainable microbial chain elongation.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {133600}, doi = {10.1016/j.biortech.2025.133600}, pmid = {41192489}, issn = {1873-2976}, abstract = {While unmodified sludge-based biochar (SBBC) exhibits limited electron transfer capacity in chain elongation (CE), its surface functional groups are recognized as critical factor influencing direct interspecies electron transfer (DIET). This study employed three modification methods, i.e., H2O2, HNO3, and anthraquinone sulfonate (AQS), to explore the effects of modified SBBC on CE process. Results indicated that the AQS-modified SBBC (SBBC-AQS) exhibited optimal electron transfer properties and electrochemical activity. Thus, SBBC-AQS greatly promoted DIET-mediated CE, leading to 62% higher caproate production compared to no biochar. Further recycling experiments confirmed the reusability of SBBC-AQS, along with the biofilm formation. Lastly, metagenomic analysis revealed that modified SBBC improved the abundance of CE bacteria such as Clostridium kluyveri, and introduced electron-transferring bacteria such as Petrimonas, so as to reinforce ethanol oxidation and medium-chain fatty acids production. This study offers novel insights into the sustainable material and microbes synergistic regulation to achieve an efficient CE system.}, }
@article {pmid41192488, year = {2025}, author = {Chen, W and Yang, Y and Chang, S and Zhang, K and Xu, T and Li, J and Liang, X and Xu, Y and Nghiem, LD and Johir, MAH and Wei, Y}, title = {Microbial necromass analogues reshape composting humification pathways.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {133583}, doi = {10.1016/j.biortech.2025.133583}, pmid = {41192488}, issn = {1873-2976}, abstract = {Microbial necromass is increasingly recognized as a key driver of soil carbon stabilization, yet its mechanistic role in compost humification remains elusive. Here, by integrating metagenomics, quantitative necromass tracing, and partial least squares structural equation modeling (PLS-SEM), the regulatory effects of two microbial necromass analogues-N-acetyl-d-glucosamine (GlcNAc) and chitin-on pig manure composting were systematically investigated. Both analogues significantly altered the physicochemical properties, microbial community composition, and necromass dynamics during composting. Chitin addition markedly enhanced early microbial biomass and bacterial diversity but inhibited humic acid (HA) formation, while promoting fulvic acid (FA) accumulation and resulting in humic substances (HS) with lower molecular complexity. In contrast, GlcNAc selectively stimulated bacterial proliferation during the maturation phase, reduced both bacterial and fungal diversity, and led to increased FA content, accompanied by reduced HS molecular complexity. Metagenomic and PLS-SEM analyses revealed that both analogues fundamentally reprogrammed humification metabolic pathways: chitin suppressed genes involved in complex precursor metabolism, whereas GlcNAc narrowed the functional repertoire and shifted humification toward simpler pathways. These analogue-driven microbial metabolic shifts decoupled necromass accumulation from stable HA formation and favored the accumulation of simpler humic fractions. This study provides the first mechanistic evidence that targeted regulation of necromass transformation can precisely optimize humification efficiency and molecular characteristics, laying a theoretical foundation for improved organic waste utilization and process control in composting.}, }
@article {pmid41192424, year = {2025}, author = {Li, P and Sun, J and Geng, Y and Jiang, Y and Li, YZ and Zhang, Z}, title = {Assessment of enzyme diversity in the fermented food microbiome.}, journal = {Cell systems}, volume = {}, number = {}, pages = {101430}, doi = {10.1016/j.cels.2025.101430}, pmid = {41192424}, issn = {2405-4720}, abstract = {Microbial bioactivity is essential for the flavor, appearance, quality, and safety of fermented foods. However, the diversity and distribution of enzymatic resources in fermentation remain poorly understood. This study explored 10,202 metagenome-assembled genomes from global fermented foods using machine learning, identifying over 5 million enzyme sequences grouped into 98,693 homologous clusters, representing over 3,000 enzyme types. Functional analysis revealed that 84.4% of these clusters were unannotated in current databases, with high novelty in terpenoid and polyketide metabolism enzymes. Peptide hydrolases exhibited broad environmental adaptability based on predicted optimal temperatures and pH, and niche breadth calculations indicated 31.3% of enzyme clusters displayed food-type specificity. Additionally, we developed a machine learning model to classify fermented food sources by enzyme clusters, highlighting key enzymes differentiating habitats. Our findings emphasize the untapped potential of fermented food environments for enzyme resource exploration, offering valuable insights into microbial functions for future food research. A record of this paper's transparent peer review process is included in the supplemental information.}, }
@article {pmid41192191, year = {2025}, author = {Zhou, G and Wang, YS and Zhang, GF and Zhang, SY and Wen, X and Cui, ZB and Shi, QS and Xie, XB}, title = {Gut microbiota composition and antibiotic resistance ontology landscape in Micropterus salmoides: Insights from metagenomic and metabolomic analyses.}, journal = {Comparative biochemistry and physiology. Part D, Genomics &amp; proteomics}, volume = {57}, number = {}, pages = {101666}, doi = {10.1016/j.cbd.2025.101666}, pmid = {41192191}, issn = {1878-0407}, abstract = {Micropterus salmoides, a pivotal aquaculture species in China, faces critical challenges including high disease susceptibility and insufficient characterization of gut microbiota-associated antibiotic resistance ontology (ARO). This study integrated metagenomic and metabolomic approaches to systematically characterize the compositional dynamics, diversity patterns, and spatiotemporal distribution of gut microbiota and AROs in M. salmoides across four developmental stages, while clarifying their interactions with metabolic pathways. Metagenomic profiling identified Proteobacteria, Firmicutes, and Fusobacteria as the dominant bacterial phyla, with Acinetobacter baumannii and Alcanivorax profundi exhibiting stage-specific abundance patterns. A total of 150 distinct ARO subtypes were identified, among which tetracycline- and glycopeptide-resistance genes (e.g., tetA and vanR) showing high abundance, with their resistance primarily mediated by efflux-driven mechanisms. Untargeted metabolomics uncovered 4459 metabolites, with robust correlations observed between core microbial genera (e.g., Flavobacterium and Herbaspirillum) and lipid/amino acid metabolic pathways. Co-occurrence network analysis further demonstrated significant interconnections between ARO subtypes and lineages of Proteobacteria/Firmicutes. Our multi-omics framework provides comprehensive insights into the gut microbiota-ARO-metabolism nexus in M. salmoides, thereby establishing a correlative framework for developing precision interventions to control the dissemination of antimicrobial resistance and improve disease management in sustainable aquaculture systems.}, }
@article {pmid41192179, year = {2025}, author = {Wu, GG and Jin, JA and Han, NN and Guo, WL and Fan, NS and Jin, RC}, title = {Multiomic insights into the regulatory mechanism of anammox consortia: Interspecies cooperation, degradation and self-adaptation to plasticizer stress.}, journal = {Journal of hazardous materials}, volume = {500}, number = {}, pages = {140319}, doi = {10.1016/j.jhazmat.2025.140319}, pmid = {41192179}, issn = {1873-3336}, abstract = {Phthalates are prevalent in wastewater treatment systems and pose a potential threat to microbial communities. In this study, it was found that the nitrogen removal efficiency of anaerobic ammonium oxidation (anammox) process remained at 92.5 ± 2.4 % after the long-term exposure to di-(2-ethylhexyl) phthalate (DEHP). Although the relative abundance of Candidatus Kuenenia decreased by 5.5 %, that of other denitrifying functional bacteria increased to maintain the system stability. The adaptation of anammox consortia to DEHP mainly depended on microbial cooperation and molecular regulation. Combined with metagenomic and metatranscriptomic analyses, Bacillus subtilis functioned as the DEHP-degrading species and exhibited a collaborative relationship with other degrading microorganisms. The expression levels of carbon metabolism, two-component system and quorum sensing related genes were significantly (p < 0.05) upregulated by 0.4-6.6 folds. The structural equation model further proved that biodegradation was the main contributor to mitigating DEHP inhibition. Notably, Ca. Kuenenia and transposons were the host of most antibiotic resistance genes (ARGs) and the main mobile genes elements, respectively. DEHP also triggered oxidative stress and resistance dissemination in anammox consortia. These findings provide molecular insights into the microbial regulatory mechanism in responding to plasticizer stress and drive the expansion of anammox process application.}, }
@article {pmid41192168, year = {2025}, author = {Skalny, AV and Korobeinikova, TV and Morozova, G and Menshikova, IV and Gritsenko, VA and Zhang, F and Mak, DV and Guo, X and Sotnikova, TI and Aschner, M and Tinkov, AA}, title = {Serum trace element and mineral levels and fecal microbiota in relation to cartilage damage in rheumatoid arthritis patients.}, journal = {Journal of trace elements in medicine and biology : organ of the Society for Minerals and Trace Elements (GMS)}, volume = {92}, number = {}, pages = {127787}, doi = {10.1016/j.jtemb.2025.127787}, pmid = {41192168}, issn = {1878-3252}, abstract = {UNLABELLED: The objective of the present study was to evaluate serum trace element and mineral levels as well as taxonomic characteristics of gut microbiota and their association with cartilage damage in patients with rheumatoid arthritis (RA).<br><br>MATERIALS AND METHODS: Serum trace element and mineral levels in 41 healthy controls and 41 RA patients were assessed using inductively-coupled plasma mass-spectrometry. Taxonomic characteristics of fecal microbiota were assessed using 16S metagenomic sequencing. RA patients were characterized by increased cartilage oligomeric matrix protein (COMP) and complement component 3 (C3) levels, indicative of cartilage damage and inflammation.<br><br>RESULTS: Serum Ca, Fe, Se, and Zn levels in RA patients were lower, whereas circulating Cr, Cu, and Mo concentrations exceeded the respective control values. 16S metagenomic sequencing of fecal samples revealed lower relative abundance of Firmicutes and Actinomycetota with a reduction in Firmicutes-to-Bacteroidetes ratio in RA patients. At the class level, the relative abundance of Bacilli, Coriobacteria, and Clostridia in RA patients was lower, whereas that of Bacteroidia and Negativicutes was higher compared to the control group. Tight negative association between serum Zn levels and the abundance of Bacteroidetes and Bacteroidia was observed, whereas correlation between Zn and Firmicutes-to-Bacteroidetes ratio was positive. Multiple linear regression analysis demonstrated that serum COMP level was inversely associated with serum Fe and Se levels, as well as relative abundance of Bacilli and Clostridia, being positively associated with serum Ca and C3 levels.<br><br>CONCLUSION: These novel findings demonstrate a multilateral relationship between trace element metabolism, gut microbiota, and cartilage damage in RA.}, }
@article {pmid41192067, year = {2025}, author = {Świderek, K and Arafet, K and de Sousa Batista, V and Grajales-Hernández, D and López-Gallego, F and Moliner, V}, title = {Insights into the Catalytic Activity of a Metagenome-Derived Urethanase.}, journal = {Journal of the American Chemical Society}, volume = {}, number = {}, pages = {}, doi = {10.1021/jacs.5c13147}, pmid = {41192067}, issn = {1520-5126}, abstract = {The discovery of urethanases shows an opportunity to access the biotechnological recycling of polyurethane-based plastics (PURs), widely used in the manufacture of everyday materials. However, the mechanistic understanding of these enzymes remains under debate. In this work, we report a QM/MM-based mechanistic study of the metagenome-derived urethanase UMG-SP2 catalyzing the degradation of a urethane-like model compound, 4-nitrophenyl benzylcarbamate (pNC). A high-quality structural model generated with AlphaFold2, prior to the availability of the crystal structure, accurately captured the Ser-Ser-Lys catalytic triad characteristic of amidase signature enzymes. Highly accurate constant-pH nonequilibrium molecular dynamics and Monte Carlo (neMD/MC) simulations provided the full titration curve of active site Lys, explaining the need for alkaline media for the enzyme to be active. The generation of the free energy landscape, obtained by means of free energy perturbation methods with the M06-2X DFT functional describing the QM region of the full system, reveals an esterase-like three-step mechanism of UMG-SP2, i.e., acylation, hydrolysis, and decarboxylation, with all steps being kinetically feasible. Our computational results show very good agreement with experimental kinetic data, with a calculated free energy barrier of 21.2 kcal·mol[-1] for the rate-determining step compared to 22.9 kcal·mol[-1] derived from the experimentally measured turnover frequency (TOF). The present results also open the door for the final decarboxylation occurring in the solution after the release of the product of the hydrolysis step or within the active site. These findings provide an atomistic insight into the urethanase function and establish a robust framework for the future design of biocatalysts targeting polyurethane degradation.}, }
@article {pmid41192043, year = {2025}, author = {Kumar, A and Xu, C and Dakal, TC}, title = {Microbiome based precision medicine through integrated multiomics and machine learning.}, journal = {Microbiological research}, volume = {303}, number = {}, pages = {128384}, doi = {10.1016/j.micres.2025.128384}, pmid = {41192043}, issn = {1618-0623}, abstract = {Gut microbiome (GME) is a dynamic ecosystem composed of diverse microorganisms with extensive functional potential that influence host physiology, endocrinology, and neurology. This review explores how multiomics (m[OMICS]) and machine learning (ML) enhance understanding of the GME and its implications for human disease and therapy. Integrating metagenomics, metatranscriptomics, metaproteomics, and metabolomics with ML enables the linkage of microbial composition and function to clinical outcomes. Combined m[OMICS] approaches elucidate species and strain dynamics, metabolic pathways, and metabolite production within the gut environment. Techniques such as shotgun metagenomics, metagenome-assembled genomes, and pathway mapping reveal associations between dysbiosis and diseases including inflammatory bowel disease, colorectal cancer, cardiometabolic, and neurological disorders. Mechanistic insights highlight short-chain fatty acids in immune regulation, bile acid transformations in metabolic signaling, and trimethylamine N-oxide in cardiovascular risk. ML models trained on heterogeneous datasets identify disease-related microbial modules, improve patient stratification, and predict therapeutic responses, such as differentiating IBD subtypes and detecting cancer-linked microbial signatures. Network analyses uncover gut microbial interaction patterns influencing host physiology. Emerging integrative tools like MOFA+ , DIABLO, and MintTea strengthen cross-modal analysis and biomarker discovery. Standardized workflows addressing quality control, assembly, binning, annotation, and visualization ensure reproducibility. Together, m[OMICS] and ML establish a robust framework for translating GME ecology into clinically relevant biomarkers and precision interventions. To enhance reliability, GME studies should adopt uniform sampling protocols, correct compositional biases, employ interpretable models, and validate findings across multi-site cohorts to advance microbiome-based diagnostics and therapeutics in precision medicine.}, }
@article {pmid41192026, year = {2025}, author = {Chen, Y and Kong, X and Mao, X and Fan, X and Yuan, J}, title = {Unlocking methanogenesis at 45°C: Synergistic roles of Zero-Valent iron and magnetite in Restoring cellulose anaerobic digestion.}, journal = {Waste management (New York, N.Y.)}, volume = {210}, number = {}, pages = {115225}, doi = {10.1016/j.wasman.2025.115225}, pmid = {41192026}, issn = {1879-2456}, abstract = {Anaerobic digestion (AD) operated at transitional temperature is a promising technology for treating de-oiled food waste (FW). However, under such conditions, the metabolic activity of methanogens will be significantly negatively affected compared to conventional mesophilic or thermophilic conditions, which limits its practical application. In this study, the AD of cellulose at 45 °C were investigated, and the synergistic effects of zero-valent iron (ZVI) and magnetite (Fe3O4) on enhancing methanogenesis were explored. The results indicated that the combination of ZVI and Fe3O4 played a crucial role in promoting cellulose methanogenesis during AD at 45 °C. Specifically, the methane yield reached 300.1 mL/g VS, representing a 58 % increase compared to the control group. Further analysis revealed that ZVI + Fe3O4 enhanced the levels of coenzyme F420 and acetate kinase. Firmicutes and Methanosarcina were the dominant microbial groups involved in normal methanogenesis at 45 °C, and a positive correlation between these two groups was observed. Metagenomic sequencing further demonstrated that the combination of ZVI and Fe3O4 synergistically increased the abundance of genes associated with both acetate cleavage and CO2 reduction methanogenic pathways. The dominant pathways achieved a dynamic equilibrium, functioning according to the available substrates at different stages within the reactor. Life Cycle Assessment (LCA) results indicated that coupling ZVI and Fe3O4 could effectively reduce carbon emissions and fossil resource depletion. The study provided theoretical evidence for the application of AD in treating cellulose-based substrates at transitional temperatures.}, }
@article {pmid41191113, year = {2025}, author = {Cheng, J and Yang, F and Zhang, L and Zhao, J and Zhang, X and Qiao, H and Yan, Z and Luo, Y and Dai, Y}, title = {Genomic Analysis, Metabolite Characterization, and Wheat Seedling Growth Promotion of Variovorax Endophyticus sp. nov., A Novel Endophyte from Wheat Root Tissue.}, journal = {Current microbiology}, volume = {83}, number = {1}, pages = {2}, pmid = {41191113}, issn = {1432-0991}, support = {41877042//National Natural Science Foundation of China/ ; 2023YB007//Hebei Normal University of Science and Technology/ ; 2022JDTD0027//Science and Technology Department of Sichuan Province/ ; }, mesh = {*Triticum/microbiology/growth &amp; development ; *Plant Roots/microbiology/growth &amp; development ; *Endophytes/genetics/isolation &amp; purification/classification/metabolism ; Phylogeny ; *Comamonadaceae/genetics/isolation &amp; purification/classification/metabolism/physiology ; RNA, Ribosomal, 16S/genetics ; *Seedlings/growth &amp; development/microbiology ; Base Composition ; Fatty Acids/chemistry/analysis ; DNA, Bacterial/genetics ; Genome, Bacterial ; Bacterial Typing Techniques ; Genomics ; }, abstract = {A bacterial strain CY25R-8[T] (= CGMCC 1.16908[T] = KACC 21250[T]) was isolated from the root tissues of wheat. It is aerobic, motile (with a single flagellum), Gram-negative, rod-shaped and yellow, and capable of growing at 10-40 ℃, pH 3.0-10.0 and NaCl 0.0-5.0%; its major fatty acids were C16:0, C17:0 cyclo, summed feature 8 and 3; its genomic DNA G + C content was 69.5%. Its respiratory quinone was ubiquinone-8 and major polar lipids were phosphatidylethanolamine, phosphatidylglycerol diphospatidylglycerol and unidentified aminophospholipid. Strain CY25R-8[T] exhibited the highest 16S rRNA gene sequence similarity (99.0%-99.6%) with the type strains of several Variovorax species. However, the dDDH and ANI values between strain CY25R-8[T] with these type strains were 28.6%-29.5% and 84.65%-86.0%, respectively. These values indicated that strain CY25R-8[T] represents a novel species of the genus Variovorax. The name Variovorax endophyticus sp. nov. is proposed. Furthermore, genomic comparisons with uncharacterized isolates and uncultured strains (metagenome-assembled genomes) revealed no close relatives of CY25R-8[T], suggesting this species is novel and potentially aquatic. Through LC-MS, NMR, and MS data, 25 metabolites were identified in strain CY25R-8[T], with cyclo (L-Phe-L-Ser), cyclo (L-Phe-D-4-OH-Pro), H-DPro-β[3]-Glu-NH2 1-ααβ and pGlu-His-Pro-OH being the major compounds. Notably, strain CY25R-8[T] is the first reported natural producer of H-DPro-β[3]-Glu-NH2 1-ααβ. As an endophyte of wheat, strain CY25R-8[T] also demonstrated the ability to enhance wheat seedling growth by promoting main root elongation in vivo. These findings suggest that V. endophyticus CY25R-8[T] has potential applications in biotechnology and agriculture.}, }
@article {pmid41190884, year = {2025}, author = {van Scheijen, S and Neerincx, AH and Weersink, EJM and Altenburg, J and Majoor, C and van Muijlwijk-Koezen, JE and Maitland-van der Zee, AH and Abdel-Aziz, MI and , }, title = {Metagenomics approach to predict antibiotic resistance genes in sputum samples of adult people with cystic fibrosis: a pilot study.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0229924}, doi = {10.1128/spectrum.02299-24}, pmid = {41190884}, issn = {2165-0497}, abstract = {UNLABELLED: Lung infections in people with cystic fibrosis (CF) cause lung damage, which is the leading factor in the morbidity and mortality of CF. Prescription of antibiotics to treat these infections is essential to maintain a higher quality of life and increase life expectancy. Determination of antibiotic susceptibility (ABS) is done by culture-dependent, phenotypic methods. These procedures take several days, while timely intervention is key. The analysis of antibiotic resistance genes by use of shotgun metagenomics might offer a time-sensitive alternative. Twenty people with CF with a homozygous Phe508del mutation provided 68 sputum samples during different visits over a period of roughly a year. After shotgun sequencing, the samples were analyzed using the deep learning tool deepARG. These results were compared with the results from routine ABS testing. The performance was determined by area under the curve-receiver operating characteristics (AUCROC) and sensitivity. Significant results were obtained for the following antibiotic classes: aminoglycoside (AUCROC = 0.81 [95% CI: 0.67-0.95, sensitivity = 73%]), cephalosporin (AUCROC = 0.70 [95% CI: 0.54-0.86, sensitivity = 95%]), and fluoroquinolone (AUCROC = 0.73 [95% CI: 0.56-0.89, sensitivity = 88%]). For other antibiotic classes, results were not significant. Using antibiotic class-specific cut-offs for positive reads of ARGs, a metagenomics approach potentially offers a culture-independent and more time-efficient manner to predict ABS for commonly prescribed antibiotic classes for sputum samples of adult people with CF. The use of metagenomics and artificial intelligence in clinical care will add to more personalized care for people with CF as well as better antibiotic stewardship.<br><br>IMPORTANCE: Damage induced by lung infections in people with cystic fibrosis (CF) is the leading factor to the mortality and morbidity of CF. To treat bacterial infections, people with CF are prescribed antibiotics. Routine antibiotic susceptibility (ABS) testing relies on culture-dependent, phenotypic techniques. These take several days up to more than a week, while timely intervention is key. To bridge this time gap, physicians in CF care use patient history of ABS data to start antibiotics, with risk of resistance to it. This pilot study explores a time saving alternative: the possibility to predict antibiotic resistance genes using shotgun metagenomics and artificial intelligence. By quicker prediction of ABS, people with CF can receive more adequate care, which results in the possible prevention of chronic infections and contributes to antibiotic stewardship.}, }
@article {pmid41190675, year = {2025}, author = {McHugh, O and Ayilaran, E and Jung, Y}, title = {Maple sap microbial communities and tubing sanitation: dominance of Pseudomonas species.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0069325}, doi = {10.1128/mra.00693-25}, pmid = {41190675}, issn = {2576-098X}, abstract = {Shotgun metagenomic data from maple (Acer saccharum) sap collected via 3/16-inch tubing (new, unsanitized, or sanitized with 400 ppm calcium hypochlorite) during weeks 1 and 5 revealed 317 species. Applying a 5% relative abundance cutoff, 20 dominant species were identified. Pseudomonas_E proteolytica and/or Pseudomonas_E lurida were abundant across conditions.}, }
@article {pmid41190646, year = {2025}, author = {Brown, KM and Beall, BFN and Bullerjahn, GS and Finlay, JC and Glavina Del Rio, T and Small, GE and Sterner, RW and McKay, RM}, title = {Depth-resolved paired metagenomes and metatranscriptomes from the Lake Erie 'dead zone'.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0101325}, doi = {10.1128/mra.01013-25}, pmid = {41190646}, issn = {2576-098X}, abstract = {Metagenomes and metatranscriptomes were generated from the surface mixed layer and hypolimnion at a NOAA-Great Lakes Environmental Research Laboratory Real-Time Coastal Observation Network (ReCON) site in Lake Erie's central basin during the onset of hypolimnetic hypoxia. Here, we describe the sequencing of the samples, metagenome assembly, and binning of microbial taxa.}, }
@article {pmid41190270, year = {2025}, author = {Li, W and Li, X and Cheng, J and Liu, J and Liu, J and Wang, Y and Yuan, W and Ren, E}, title = {Lung microbiota of raccoon dogs (Nyctereutes procyonoides) using high-throughput sequencing.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1677761}, pmid = {41190270}, issn = {1664-302X}, abstract = {Pneumonia frequently causes mass mortality in raccoon dogs, resulting in significant economic loss. Additionally, raccoon dogs carry various zoonotic pathogens. This study systematically assessed pulmonary pathogens in raccoon dogs and their potential public health implications utilizing 2bRAD microbiome sequencing (2bRAD-M) and viral metagenomics. We analyzed 30 lung tissue samples for microbial composition. Sequencing revealed Pseudomonadota, Ascomycota, and Actinobacteria as dominant phyla and Acinetobacter, Escherichia, and Klebsiella as predominant genera. The most abundant species were Acinetobacter baumannii, Escherichia coli, and Klebsiella pneumoniae. In total, 158 species across 84 genera were identified, including 49 potentially zoonotic species. Viral metagenomics revealed Peduoviridae, Rountreeviridae, and Parvoviridae as dominant families, with Valbvirus ValB1MD2, Andhravirus andhra, and Amdoparvovirus carnivoran3 comprising over 80% of the viral composition. These findings highlight the pathogenic complexity of raccoon dog pneumonia and its zoonotic risks, providing crucial insights for disease control and public health management.}, }
@article {pmid41190207, year = {2025}, author = {You, Y and Liu, X and Wang, L and Khalid, M and Wang, X and Jiang, L and Wang, F and Pang, Z and Peng, Y and Zhao, X}, title = {Integrated metagenomic and soil chemical analyses revealed shifts of microbial nutrient cycling with poplar plantation age.}, journal = {Frontiers in plant science}, volume = {16}, number = {}, pages = {1513281}, pmid = {41190207}, issn = {1664-462X}, abstract = {INTRODUCTION: Poplar (Populus spp.) is widely recognized as an ideal model system for studying plant-microbial interactions due to its rapid growth, genetic tractability, and ecological importance in afforestation programs. Leveraging these advantages, we investigated how poplar cultivation reshapes soil microbial communities and their nutrient cycling functions. Although plant roots are known to profoundly influence microbial community structure and functionality, comprehensive studies systematically linking poplar-induced microbiome shifts to nutrient cycling remain limited.<br><br>METHODS: Here, we employed an integrative approach combining metagenomic sequencing with soil nutrient analyses to assess poplar-induced changes in microbial community and metabolic activities at the root-soil interface.<br><br>RESULTS: Our analyses revealed three major findings: (1) poplar cultivation significantly altered the composition of microbial communities-including bacteria, fungi, and archaea-and reduced the complexity of microbial interaction networks, as revealed by co-occurrence analysis; (2) poplar cultivation enhanced microbial genetic potential related to degradation pathways for starch, lignin, and aromatic compounds, as well as carbon (C) fixation, while suppressing cellulose/hemicellulose decomposition; and (3) soil nutrient cycling processes involving nitrogen (N), phosphorus (P), and sulfur (S) were reprogrammed through changes in both gene abundance (e.g., nifH, pqqC, aprA) and nutrient availability (e.g., NO3-, P). Moreover, specific microbial taxa showed strong correlations with these functional shifts, i.e., Bacteroidota correlated with P metabolism in roots/soil, Actinobacteria and Firmicutes with organic C turnover, and Gemmatimonadetes and Nitrospirae with nitrate cycling dynamics.<br><br>DISCUSSION: By integrating poplar's roles as both a model species and a driver of ecological change, this study elucidates how afforestation shapes soil ecosystems through complex plant-microbe-environment interactions. These findings provide critical insights for sustainable land management strategies.}, }
@article {pmid41190090, year = {2025}, author = {Watkinson, JI}, title = {Habitat Disturbance Promotes Shifts in the Abundance of Major Fungal Phyla in the Roots of a Native Orchid, Tipularia discolor.}, journal = {Plant-environment interactions (Hoboken, N.J.)}, volume = {6}, number = {6}, pages = {e70096}, pmid = {41190090}, issn = {2575-6265}, abstract = {Orchids are a widely distributed group of flowering plants with important roles in ecosystems around the globe. However, many species are in decline due, in part, to human-driven changes in their habitat. It is well established that orchids are reliant on specific groups of mycorrhizal fungi for growth and reproduction and that these fungi can vary across the range in which an orchid species resides. Recent studies have shown that the orchid fungal mycobiome (mycobiome) includes a diverse array of non-mycorrhizal endophytic fungi that may also contribute to growth and resilience and that can vary across a particular orchid's range. The communities of mycorrhizal and non-mycorrhizal species that make up the orchid mycobiome may be altered by habitat disturbance, which could affect the ability of these plant species to thrive in different environments. Here a metagenomic approach is used to provide a snapshot of the root mycobiome of Tipularia discolor in habitats defined as disturbed or undisturbed. While amplicon sequence variant (ASV) richness and evenness were similar, the structure of the mycobiome differed between the two sites. Orchids growing in disturbed locations were associated with a greater abundance of Basidiomycota and Glomeromycota, while orchids in undisturbed habitats were associated with Ascomycota and Mucoromycota. The overall abundance of mycorrhizal families was similar across the two habitats. The data indicate that habitat disturbance induces a change in the composition of the fungal mycobiome of T. discolor , suggesting that the community of root fungi could be key to the ability of orchids to successfully adapt to different environments.}, }
@article {pmid41189926, year = {2025}, author = {Chen, X and Qin, H and Song, Y and Lian, Y and Long, Q}, title = {Metagenomics next-generation sequencing for diagnosis of invasive fungal diseases in patients with hematological diseases.}, journal = {IJID regions}, volume = {17}, number = {}, pages = {100780}, pmid = {41189926}, issn = {2772-7076}, abstract = {OBJECTIVES: To investigate the clinical characteristics and risk factors of invasive fungal disease (IFD) in patients with hematological disorders.<br><br>METHODS: From January 2023 to January 2025, 67 patients with blood diseases hospitalized at the Hematology Department who were suspected of infection with IFD underwent metagenomic next-generation sequencing (mNGS) and fungal pathogen detection. Their clinical characteristics and laboratory examinations were retrospectively analyzed.<br><br>RESULTS: A cohort of 67 patients was enrolled in the study, among which 32 cases were diagnosed with IFD through mNGS and etiological culture, while no fungal pathogens were detected in the remaining 35 cases. The diagnostic yield of mNGS for fungal infection detection (47.76%) demonstrated superior sensitivity compared to conventional pathogenic microbial culture (14.93%), &#x3b2;-D-glucan assay (11.94%), and galactomannan assay (2.99%). Within the IFD cohort, Candida species constituted the most prevalent etiology (46.88%, n = 15), followed by Aspergillus (18.75%, n = 6), Penumocystis (12.5%, n = 4), and Rhizomucor (12.5%, n = 4), with other fungal species accounting for the remaining cases (9.37%, n = 3). Multivariate logistic regression analysis revealed six independent risk factors associated with IFD in patients with hematological disorders: cluster of differentiation 4+ T cell count <400 cells/&#xb5;L (odds ratio [OR] = 9.45, P = 8.9&#xd7;10[-5]), elevated C-reactive protein (OR = 3.18, P = 0.027), elevated interleukin (IL)-6 (OR = 5.75, P = 0.001), elevated IL-10 (OR = 3.31, P = 0.033), hypoproteinemia (OR = 42.17, P = 0.013), and neutropenia lasting for more than 10 days (OR = 4.11, P = 0.015).<br><br>CONCLUSIONS: mNGS has high sensitivity in detecting IFD in patients with hematological diseases. Cluster of differentiation 4+ cell count below 400/uL, increased level of C-reactive protein, IL-6, and IL-10, hypoproteinemia, and neutropenia lasting for more than 10 days are independent risk factors for IFD in patients with hematological diseases.}, }
@article {pmid41189709, year = {2025}, author = {Chen, Y and Zhang, R and Wen, J and Zhao, J and Zhang, J}, title = {Metagenomic analysis of blood microbiota alterations: insights into HIV progression and immune restoration.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1619059}, pmid = {41189709}, issn = {2235-2988}, mesh = {Humans ; *HIV Infections/immunology/drug therapy/microbiology/blood/virology ; Metagenomics ; Male ; Female ; Adult ; *Microbiota ; Middle Aged ; Disease Progression ; Viral Load ; *Bacteria/classification/genetics/isolation &amp; purification ; *Immune Reconstitution ; *Blood/microbiology ; CD4-CD8 Ratio ; }, abstract = {INTRODUCTION: Emerging evidence suggests that the blood microbiome may influence the progression of HIV infection and immune restoration. This study aims to comprehensively characterize blood microbiota alterations associated with HIV infection and antiretroviral therapy (ART), and to evaluate their potential as microbial indicators for assessing infection status and immune restoration.<br><br>METHODS: We recruited 91 participants, including 31 treatment-na&#xef;ve HIV-infected individuals, 30 ART-treated individuals with undetectable viral loads, and 30 healthy controls. Blood samples were collected for metagenomic sequencing and immunological profiling.<br><br>RESULTS: HIV infection profoundly disrupted blood microbiota diversity and composition, with a marked reduction in &#x3b1;-diversity and enrichment of opportunistic pathogens such as Pseudomonas aeruginosa, Acinetobacter baumannii and Stenotrophomonas maltophilia, alongside depletion of beneficial taxa like Bifidobacterium longum. ART partially restored microbial diversity but did not fully reestablish a healthy microbiota. Correlation analysis revealed that Acinetobacter pittii, Xanthomonas campestris and Diaphorobacter nitroreducens were significantly associated with viral load, suggesting their potential role in HIV progression. Additionally, after ART, Acinetobacter junii and Pseudomonas putida were significantly correlated with the CD4/CD8 ratio, indicating their potential role in immune restoration.<br><br>DISCUSSION: These findings provide new insights into the interactions between blood microbiota and HIV progression. The identified blood microbiota may serve as potential indicators for evaluating HIV infection status and treatment efficacy, offering a basis for microbial-based diagnostic and therapeutic strategies.}, }
@article {pmid41189593, year = {2025}, author = {Huang, Y and Wei, X and Huang, X and Peng, C and Lin, B and Ren, X and He, G and Zhang, X and Jiang, C and Huang, L and Gu, S}, title = {Pneumocystis jirovecii associated with Lung Virome in patients with severe pneumonia.}, journal = {iScience}, volume = {28}, number = {11}, pages = {113710}, pmid = {41189593}, issn = {2589-0042}, abstract = {Pneumocystis jirovecii (P. jirovecii) threatens immunocompromised patients, yet its role in the lung microbiome remains unclear. We performed metagenomic sequencing on bronchoalveolar lavage fluid from two retrospective cohorts: a multicenter study of 1,737 patients with pneumonia and a validation cohort of 72 intubated ICU patients. Participants were categorized into P. jirovecii infection, colonization, or negative groups based on qPCR and clinical characteristics. Our analysis revealed minimal bacterial differences but significant viral and fungal variations. Notably, negative patients with P. jirovecii exhibited the lowest viral diversity. Even after adjusting for potential confounders, including immunosuppression and disease severity, P. jirovecii status remained most strongly associated with virome alterations. Furthermore, in cytomegalovirus-positive individuals, P. jirovecii positivity was significantly associated with higher 28-day mortality. These findings suggest that P. jirovecii colonization represents a distinct intermediate state in the lung microbial ecosystem between infection and negative, shedding light on its potential role in pneumonia pathogenesis and outcomes.}, }
@article {pmid41189414, year = {2025}, author = {Zheng, Z and Zhao, L and Liu, Y and Wang, W and Zheng, K and Chen, X and Zhang, S and Sun, Y and Ma, Z and Shao, H and Sung, YY and Mok, WJ and Wong, LL and McMinn, A and Wang, M and Gao, C and Sun, L and Liang, Y}, title = {Identification and Genomic Analysis of a New Viral Species With Low Similarity to Existing Viruses.}, journal = {Environmental microbiology}, volume = {27}, number = {11}, pages = {e70201}, doi = {10.1111/1462-2920.70201}, pmid = {41189414}, issn = {1462-2920}, support = {LSKJ202203201//Laoshan Laboratory/ ; 42120104006//National Natural Science Foundation of China/ ; 42176111//National Natural Science Foundation of China/ ; 42306111//National Natural Science Foundation of China/ ; //Ocean Negative Carbon Emissions/ ; 2025M770867//China Postdoctoral Science Foundation/ ; 202172002//Fundamental Research Funds for the Central Universities/ ; 201812002//Fundamental Research Funds for the Central Universities/ ; 202072001//Fundamental Research Funds for the Central Universities/ ; }, mesh = {*Genome, Viral ; Metagenomics ; *Bacteriophages/genetics/isolation &amp; purification/classification ; Phylogeny ; *Pseudoalteromonas/virology ; Genomics ; *Viruses/genetics/classification/isolation &amp; purification ; }, abstract = {Viruses are among the most abundant and diverse biological entities on Earth. Over the past decades, metagenomic sequencing has revealed thousands of viral genomes. However, viral isolation methods remain indispensable for discovering viruses that are missed by metagenomic sequencing due to limitations like low abundance (1, 2). Here, a novel phage, vB_PshM_Y4, which infects Pseudoalteromonas shioyasakiensis, an economically important, opportunistic marine pathogen was isolated. A comparison of vB_PshM_Y4 with over 15 million viral genomes, including both cultivated and uncultivated viruses in the NCBI and IMG/VR v4 datasets, found no closely related genome. This study provides evidence that traditional isolation methods can detect viruses that cannot be identified through metagenomic sequencing. In addition, a comparison of virus isolates deposited in the NCBI database with uncultured viruses in the IMG/VR viral database shows that approximately only half of the isolates can be detected using metagenomic approaches. Notably, viruses that are not able to be detected by metagenomic sequencing often exhibit low abundance and possess unique genomes. These results suggest that traditional viral isolation methods remain important for obtaining rare, low-abundance viruses and underscore the significance of traditional experimental methods in the era of metagenomes.}, }
@article {pmid41189006, year = {2025}, author = {Popall, RM and Roland, A and Davidson, S and Combet-Blanc, Y and Price, RE and Quéméneur, M and Postec, A and Erauso, G}, title = {Cultivating microbial communities from the serpentinite-hosted Prony Bay hydrothermal field on different carbon sources in hydrogen-fed bioreactors.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {135}, pmid = {41189006}, issn = {2524-6372}, support = {19-CE02-0020-02//Agence Nationale de la Recherche/ ; 19-CE02-0020-02//Agence Nationale de la Recherche/ ; 19-CE02-0020-02//Agence Nationale de la Recherche/ ; 19-CE02-0020-02//Agence Nationale de la Recherche/ ; 19-CE02-0020-02//Agence Nationale de la Recherche/ ; 19-CE02-0020-02//Agence Nationale de la Recherche/ ; 19-CE02-0020-02//Agence Nationale de la Recherche/ ; 19-CE02-0020-02//Agence Nationale de la Recherche/ ; }, abstract = {BACKGROUND: The primary source of carbon is one of the most fundamental questions regarding the development of microbial communities in serpentinite-hosted systems. The hydration of ultramafic rock to serpentinites releases large amounts of hydrogen and creates hyperalkaline conditions that deplete the environment of dissolved inorganic carbon. Metagenomic studies suggest that serpentinite-hosted microbial communities depend on the local redissolution of bicarbonate and on small organic molecules produced by abiotic reactions associated with serpentinization.<br><br>METHODS: To verify these bioinformatic predictions, microbial consortia collected from the Prony Bay hydrothermal field were enriched under anoxic conditions in hydrogen-fed bioreactors using bicarbonate, formate, acetate, or glycine as the sole carbon source.<br><br>CONCLUSIONS: With the exception of glycine, the chosen carbon substrates allowed the growth of microbial consortia characterized by significant enrichment of individual taxa. Surprisingly, these taxa were dominated by microbial genera characterized as aerobic rather than anaerobic as expected. Our results indicate the presence of both autotrophic and heterotrophic taxa that may function as foundation species in serpentinite-hosted shallow subsurface ecosystems. We propose that an intricate feedback loop between these autotrophic and heterotrophic foundation species facilitates ecosystem establishment. Bicarbonate-fixing Meiothermus and Hydrogenophaga, as well as formate-fixing Meiothermus, Thioalkalimicrobium, and possibly a novel genotype of Roseibaca might produce organic compounds for heterotrophs at the first trophic level. In addition, the base of the trophic network may include heterotrophic Roseibaca, Acetoanaerobium, and Meiothermus species producing CO2 from acetate for a more diverse community of autotrophs. The cultivated archaeal community is expected to recycle CH4 and CO2 between Methanomicrobiales and Methanosarcinales with putative Woesearchaeales symbionts.}, }
@article {pmid41188784, year = {2025}, author = {Luo, H and Wu, P and Yang, H and Zhang, B and Zheng, M and Kuang, W and Li, W and Li, X and Zhang, X and Huang, J and Fan, Q and He, S}, title = {Clinical analysis of Pneumocystis jirovecii pneumonia in children with malignant disease.}, journal = {BMC pediatrics}, volume = {25}, number = {1}, pages = {906}, pmid = {41188784}, issn = {1471-2431}, mesh = {Humans ; *Pneumonia, Pneumocystis/diagnosis/drug therapy/complications ; Male ; Female ; Retrospective Studies ; Child ; Child, Preschool ; *Pneumocystis carinii/isolation &amp; purification ; Adolescent ; *Neoplasms/drug therapy/complications ; Glucocorticoids/therapeutic use/adverse effects ; Trimethoprim, Sulfamethoxazole Drug Combination/therapeutic use ; Antifungal Agents/therapeutic use ; Immunocompromised Host ; Tomography, X-Ray Computed ; }, abstract = {OBJECTIVE: To characterize Pneumocystis jirovecii pneumonia (PJP) in pediatric malignancy patients receiving chemotherapy or glucocorticoids, and provide guidance for timely diagnosis and effective treatment.<br><br>METHODS: A retrospective analysis of clinical features, laboratory findings, radiological characteristics, treatment approaches, and outcomes in pediatric malignancy patients who developed PJP.<br><br>RESULTS: Ten patients (1:1 male-to-female ratio; median age 6.50 years, range 2.83-14.58 years) were followed for a median of 14 months (range 6-53 months). Eight developed PJP during chemotherapy and two post-completion. Nine received glucocorticoids in their chemotherapy regimen. PJP prophylaxis was either absent (n&#x2009;=&#x2009;4) or discontinued&#x2009;>&#x2009;1 month prior (n&#x2009;=&#x2009;5). Clinical presentations included fever, dyspnea, and wheezing, often without significant cough. Laboratory findings showed elevated (1,3)-&#x3b2;-D-glucan(BDG)in 7 cases. Chest CT typically revealed bilateral diffuse patchy infiltrates, ground-glass opacities, and nodular shadows. All cases had a positive metagenomic next-generation sequencing (mNGS) or targeted next-generation sequencing (tNGS) result for P. jirovecii from sputum or bronchoalveolar lavage fluid (BALF) samples.Treatment included Trimethoprim-sulfamethoxazole(TMP/SMZ) with/without caspofungin and adjunctive corticosteroids. Eight patients required PICU admission (median stay 7.5 days, range 0-45 days) for respiratory support. Nine patients survived PJP, with one PJP-related death and one death from underlying disease.<br><br>CONCLUSION: High clinical suspicion for PJP is warranted in pediatric malignancy patients presenting with fever, dyspnea, elevated BDG, and characteristic imaging findings, particularly in those with inadequate prophylaxis. Early pathogen detection and treatment initiation are crucial. While TMP/SMZ remains first-line therapy, combination with caspofungin may improve outcomes. Short-term adjunctive corticosteroids may benefit moderate to severe cases.}, }
@article {pmid41184794, year = {2025}, author = {Chen, J and Chen, C and Xie, Y and Xu, G and Lin, M and Gong, X and Zhang, X and Chen, X and Chen, J and Zhang, L and He, G}, title = {Clinical value of quantitative PCR in diagnosis of suspected mycobacterial pulmonary infections.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {1476}, pmid = {41184794}, issn = {1471-2334}, abstract = {BACKGROUND: Due to the difficulty in clinically distinguishing pulmonary infections caused by Mycobacterium tuberculosis (MTB) and Non-tuberculous mycobacteria (NTM), the study utilizes quantitative PCR (qPCR) technology to simultaneously detect MTB, Mycobacterium abscessus complex (MABC), Mycobacterium avium complex (MAC), and Mycobacterium kansasii(M. kansasii),to explore its clinical value in diagnosing of patients suspected mycobacterial pulmonary infections.<br><br>METHODS: A retrospective analysis was conducted on a cohort of 102 patients suspected of mycobacterial pulmonary infections. Samples of sputum and bronchoalveolar lavage fluid were extracted for testing with acid-fast staining (AFS), qPCR, and metagenomic next-generation sequencing (mNGS). Assess the diagnostic performance of AFS, qPCR, and mNGS for four types of mycobacteria based on comprehensive pulmonary tuberculosis (PTB) CRS composite criteria, non-tuberculous mycobacteria (NTM) diagnostic and treatment guidelines, as well as clinical observations.<br><br>RESULTS: The sensitivity, specificity, positive predictive value, negative predictive value, and AUC of qPCR for mycobacteria (MTB, MABC, MAC) were 90.00% (76.33&#x2013;97.20), 100.00% (94.22&#x2013;100.00), 100.00% (99.90&#x2013;100.00), 93.93% (85.95&#x2013;97.51), and 0.950 (0.888&#x2013;0.983), respectively. For mNGS, the corresponding estimates were 87.50% (73.19&#x2013;95.81), 96.77% (88.82&#x2013;99.60), 94.59%(81.66&#x2013;98.56),92.30% (84.07&#x2013;96.46), and 0.921(0.851&#x2013;0.965), respectively. The research showed that the sensitivity and specificity of qPCR and mNGS method for detecting mycobacteria are higher than AFS; and there was no statistical difference in the diagnostic performance for mycobacteria between qPCR and mNGS, but qPCR was superior to mNGS in specific values.<br><br>CONCLUSION: Compared with AFS, qPCR has higher sensitivity and specificity but statistical significance needs to be assessed with larger sample sizes for mycobacteria identification. In this regard, qPCR and mNGS demonstrate exhibit similar performance. However, qPCR is less expensive and more convenient for pathogen detection, which make it a promising lower-cost alternative diagnostic method for patients suspected of mycobacterial pulmonary infections in resource-limited settings.}, }
@article {pmid41188680, year = {2025}, author = {Falk, NW and Smith, H and Papudeshi, B and Martin, B and Qian, G and Gerson, AR and Prasad, A and Harmer, SL and Dinsdale, EA}, title = {Metagenomics reveals water, biofilm, and sediment microbial communities exhibit distinct responses and functions in neutral and metalliferous drainage (NMD).}, journal = {Environmental geochemistry and health}, volume = {47}, number = {12}, pages = {547}, pmid = {41188680}, issn = {1573-2983}, support = {CRC TiME project 3.10 and Teck Resources Limited//CRCTiME/ ; }, abstract = {Neutral and metalliferous drainage (NMD) poses an environmental risk for both operating and legacy mine sites. Near-neutral pH distinguishes NMD from more acidic conditions of acid and metalliferous drainage (AMD), however NMD contains elevated levels of metals that necessitate strict management. Microbial communities are key indicators of ecological conditions and play important roles in NMD biogeochemical cycling, often exhibiting distinct dynamics compared to AMD. Shotgun sequencing and metagenome assembled genomes (MAGs) were used to characterize microbial diversity and functional potential across water, biofilm, and sediment microbiomes along a flow path at a historical lead-zinc mine in Western Australia. Zn levels peaked upstream and declined downstream, corresponding to shifts in microbial diversity. In water microbiomes, a Polynucleobacter MAG became dominant where Zn concentrations dropped below known toxicity thresholds. The genomic traits of Polynucleobacter, including a streamlined genome, Zn- (LpxC) and heat-responsive membrane genes, and enriched lipid metabolism pathways, enabled survival under metal and nutrient stress. Photosynthetic biofilms, dominated by cyanobacteria such as Synechococcaceae and Leptolyngbyaceae, played a central role in ecosystem function. These biofilms contained genes for photosynthesis, metal transport, and motility, and likely contributed organic carbon and sulfur intermediates that supported heterotrophs like Polynucleobacter and Sediminibacterium. Coordinated microbial sulfur metabolism across habitats was evident, with sulfur oxidation occurring in water and biofilms and sulfate reduction localized to sediment, evidenced with ZnS mineral phases associated with increased DsrMKJOP gene abundance. These findings are vital for mine closure and land reclamation, offering knowledge on key microbial adaption and syntrophy in NMD systems.}, }
@article {pmid41188618, year = {2025}, author = {Saini, K and Kumar, SS and Kumar, V and Bajar, S}, title = {Enhanced biodegradation of ibuprofen using bacterial consortia isolated from landfill leachate.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {12}, pages = {1295}, pmid = {41188618}, issn = {1573-2959}, support = {SR/PURSE/2022/126(G)//Department of Science and Technology (DST), New Delhi, India, under the PURSE grant/ ; }, mesh = {*Ibuprofen/metabolism/analysis ; Biodegradation, Environmental ; *Water Pollutants, Chemical/metabolism/analysis ; *Microbial Consortia ; *Bacteria/metabolism ; *Anti-Inflammatory Agents, Non-Steroidal/metabolism/analysis ; RNA, Ribosomal, 16S ; }, abstract = {The widespread use of non-steroidal anti-inflammatory drugs (NSAIDs), like ibuprofen, has led to a persistent occurrence across various environmental matrices, raising concern regarding potential human health and ecological impacts. The potentially detrimental risks of ibuprofen exposure highlight the need for exploring effective and cost-efficient remediation techniques. The microbial degradation of ibuprofen represents a significant technological and economical approach. The present study investigates the biodegradation of ibuprofen using two distinct microbial consortia (MC I and MC II) isolated from landfill leachate using Postgate media and acclimated with ibuprofen. Batch mode experiments were conducted to assess the removal of 500 mg/L ibuprofen in the presence and absence of a carbon source (glucose and acetate). MC I and MC II achieved complete removal of ibuprofen within 78 h and 60 h, respectively, under substrate-free conditions. When supplemented with glucose, the removal time was reduced to 54 h for MC I and 36 h for MC II, whereas acetate addition resulted in removal extended to 60 h and 48 h, respectively. The metagenomics analysis (16S rRNA sequencing) of microbial consortia revealed Firmicutes (Bacillota), Actinobacteria (Actinomycetota), Proteobacteria, Bacteroidetes, and Thermotogae as the dominant phyla and GC-MS analysis confirmed the presence of significant metabolites (endpoint of the bioassay) in the biodegradation of ibuprofen, i.e., 2-hydroxy ibuprofen, 1,4-hydroquinone, and 2-hydroxy-1,4-quinol. The findings of the study highlight the potential of microbial consortia for efficient ibuprofen biodegradation and provide insights into their metabolic pathway.}, }
@article {pmid41188566, year = {2025}, author = {Kondratov, IG and Ogarkov, OB and Sinkov, VV and Suzdalnitsky, AE and Koshcheyev, ME and Orlova, EA and Belkova, NL and Zhdanova, SN and Rychkova, LV and Kolesnikova, LI}, title = {Prediction of Metabolic Profile and Virulence Factors of Facultative-Anaerobic Bacteria from Tuberculous Necrosis Foci Based on Whole-Genome Sequencing Data.}, journal = {Bulletin of experimental biology and medicine}, volume = {}, number = {}, pages = {}, pmid = {41188566}, issn = {1573-8221}, abstract = {Metagenomics of bacterial communities in tuberculosis caseous necrotic mass indicates the predominance of facultative anaerobes. Nine strains isolated from the tuberculosis necrosis were identified to species and whole-genome sequencing was performed: Staphylococcus hominis (3 strains), S. epidermidis (3 strains), Corynebacterium ureicelerivorans (2 strains), and C. kefirresidentii (1 strain). Prediction of metabolic pathways and virulence factors showed that Corynebacterium and Staphylococcus possess gene sets that are absent in Mycobacterium tuberculosis: lipases and proteases for the degradation of caseous necrosis, glutamate and polysaccharide capsules, ureases capable of increasing pH of the caseum; and Fe(III) uptake systems. The isolated species can form a bacterial consortium with M. tuberculosis at the early (Corynebacterium) and later (Staphylococcus) stages of necrotization of the tuberculosis focus in the lungs.}, }
@article {pmid41188334, year = {2025}, author = {Kang, R and Yu, Z and Kim, H and Seo, J and Kim, M and Park, T}, title = {Manually weighted taxonomy classifiers improve species-specific rumen microbiome analysis compared to unweighted or average weighted taxonomy classifiers.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {38587}, pmid = {41188334}, issn = {2045-2322}, mesh = {*Rumen/microbiology ; Animals ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Species Specificity ; Metagenomics/methods ; *Bacteria/classification/genetics ; }, abstract = {Previous research has demonstrated that applying taxonomic weights to shotgun metagenomic data can improve species identification in 16S rRNA gene-based microbiome analysis. However, such an approach does not allow for accurate analysis of samples collected from less studied habitats, such as rumen. In the present study, we developed a method to incorporate taxonomic weights based on relative abundance of species identified from shotgun sequencing and amplicon sequencing data derived from rumen. Using this weighting method, we evaluated latest versions of five prominent databases-SILVA, Greengenes2 (GG2), RDP, NCBI RefSeq, and GTDB-against the BLAST 16S rRNA database, assessing classification counts, fully classified ratios (proportion of ASVs classified to a known genus and species), and error rates. Our results indicated that providing taxonomic weights partially increased classification counts and fully classified ratios, although the extent of improvement varied across databases. A reduction in error rates was also observed compared to the unweighted taxonomy classifier (P < 0.05). While GG2 and SILVA struggled with accurate classification at the species level owing to their inherent database characteristics, GTDB consistently improved all metrics using the manually weighted taxonomy classifier, achieving up to an 8% error rate reduction at the species level. NCBI RefSeq and RDP also exhibited remarkable improvement in the classification counts and fully classified ratios, along with error rate reductions by up to 47% at the species level. These findings demonstrate that amplicon sequencing datasets can enhance rumen microbiome analyses through effective weighting methods. While SILVA is commonly used in metataxonomic analyses of the rumen microbiome, we recommend NCBI RefSeq for species-level classification due to its superior accuracy and minimal ambiguous classification (e.g., "uncultured" or "sp.") in future metataxonomic studies.}, }
@article {pmid41188324, year = {2025}, author = {Kwak, MS and Cha, JM and Kim, CW and Won, KY and Hwang, CI}, title = {Integrative multi-omics deciphers the potential mechanism and microbial biomarkers for lymph node metastasis in colorectal cancer.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {38611}, pmid = {41188324}, issn = {2045-2322}, support = {NRF- 2022R1A2C100309913//National Research Foundation of Korea/ ; 2022//Medical Science Research Institute grant, Kyung Hee University Hospital at Gangdong/ ; R37CA249007/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; *Colorectal Neoplasms/genetics/pathology/microbiology ; *Lymphatic Metastasis/genetics ; DNA Methylation ; Male ; Female ; *Biomarkers, Tumor/genetics ; Middle Aged ; *Gastrointestinal Microbiome ; Aged ; Transcriptome ; Gene Expression Regulation, Neoplastic ; Gene Expression Profiling ; Multiomics ; }, abstract = {Understanding and accurate diagnosis of lymph node metastasis (LNM) for patients with colorectal cancer (CRC) is essential to determine treatment and follow-up strategies. Therefore, in this study, we aimed to elucidate the biological process and identify the potential biomarker for LNM in CRC.A total of 30 patients who received a histologically confirmed diagnosis of CRC with Stage I to III and a curative surgery between November 2020 and July 2021 at Kyung Hee university hospital at Gangdong were included. We performed multi-omics approach integrating the data on somatic mutation, transcriptomic expression, DNA methylation, and microbiome with tumor and adjacent matched normal tissues of each patient. In total, 12 significant DEGs between the patients with and without LNM were identified, consisting of significantly upregulated S100A8 gene, a proinflammatory gene. The GSEA revealed that gene sets involving "MULTI CANCER INVASIVENESS" in terms related to epithelial-mesenchymal transition was significantly upregulated in the patients with LNM. Integrated functional analysis of DNA methylation with transcriptome profile shows that significantly hypomethylated promoters of the genes are enriched for LNM. The phylum Proteobacteria, unassigned (p_PU) presented significantly higher proportions in cancer tissues from the adjacent normal tissues. Notably, when compared to the patients without LNM, the gut microbiota of those with LNM appears to exhibit a significantly lower abundance of the p_PU, indicating its potential as promising biomarker for LNM in CRC. We explained the mechanism of tumor spreading using multi-omics analysis and identified the relevant metagenomic biomarker to predict the LNM in CRC by the recognition of host-microbial interaction, thereby can make the cancer surveillance of the patients more individualized and convincing.}, }
@article {pmid41188219, year = {2025}, author = {Ndiaye, M and Bonilla-Rosso, G and Mazel, F and Engel, P}, title = {Phage diversity mirrors bacterial strain diversity in the honey bee gut microbiota.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {9738}, pmid = {41188219}, issn = {2041-1723}, mesh = {Animals ; *Bacteriophages/genetics/classification/physiology ; *Gastrointestinal Microbiome/genetics ; Bees/microbiology/virology ; *Bacteria/genetics/classification/virology ; Biodiversity ; Metagenomics ; Metagenome ; }, abstract = {Bacteriophages (phages) play a crucial role in shaping bacterial communities. Documenting the relationship between phage and bacterial diversity in natural systems is fundamental to understand eco-evolutionary dynamics that shape community composition, such as host specificity, emergence of phage resistance and phage-driven microbial diversification. However, our current understanding of this relationship is still limited, particularly in animal-associated microbiomes. Here, we analyze paired bacterial and viral metagenomics data from the gut microbiota of 49 individual honeybees and reconstruct the phage-bacteria interaction network by leveraging CRISPR spacer matches and genome homology. The resulting interaction network displays a highly modular structure with nested phage-bacteria interactions within each module. Viral and bacterial alpha and beta diversity are correlated, particularly at the bacterial strain level and when considering the interaction network. Overall, our results suggest that the most relevant approach to study phage-bacteria diversity patterns should rely on strain-level resolution and the explicit use of the interaction network. This may explain why previous studies have obtained mixed results when testing for phage-bacteria diversity correlations. Finally, we call for further studies building up on these correlation patterns to probe the underlying mechanisms by considering both bottom-up and top-down regulatory mechanisms in microbiome assembly.}, }
@article {pmid41187758, year = {2025}, author = {Yilmaz, B and Baertschi, I and Meier, KHU and Le Gac, C and Jordi, SBU and Black, C and Li, J and Lindholm, AK and ,  and König, B and Sauer, U and Stelling, J and Macpherson, AJ}, title = {A global survey of taxa-metabolic associations across mouse microbiome communities.}, journal = {Cell host &amp; microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2025.10.010}, pmid = {41187758}, issn = {1934-6069}, abstract = {Host-microbiota mutualism is rooted in the exchange of dietary and metabolic molecules. Microbial diversity broadens the metabolite pool, with each taxon contributing distinct compounds in varying proportions. In the human microbiome, high variability in consortial composition is largely compensated by similar metabolic functions across different taxa. However, the extent of compensation in lower diversity mouse models, and whether vivaria are metabolically equivalent, is unknown. We provide a searchable resource of microbiome composition variability across 51 murine vivaria and 12 wild mouse colonies worldwide, with vivarium-specific variants mapped according to predicted 3D structures for each microbial species. Our matched metabolomics data show that realized metabolic potential has relatively low variability, providing functional evidence for metabolic compensation. Additionally, variability is related to taxonomic composition rather than vivarium, revealing taxa-metabolite associations that are potentially relevant to phenotypic differences between vivaria. Collectively, this resource offers tools to strengthen microbiome studies and collaborative science.}, }
@article {pmid41187361, year = {2025}, author = {Zhang, T and Xia, Q and Wang, Y and Sun, Y and Pan, D and Cao, J and Zhou, C}, title = {The molecular mechanism of Rhodotorula mucilaginosa on the accumulation of γ-glutamyl peptides and taste development of dry-cured ham: the insights of metagenomics and metabolomics.}, journal = {International journal of food microbiology}, volume = {445}, number = {}, pages = {111511}, doi = {10.1016/j.ijfoodmicro.2025.111511}, pmid = {41187361}, issn = {1879-3460}, abstract = {To explore the mechanism of Rhodotorula mucilaginosa on the accumulation of γ-glutamyl peptides and taste development in Jinhua ham, the influences of R. mucilaginosa on fungal community structure, functional enzyme gene expression, key enzyme activities, γ-glutamyl peptides accumulation and taste attributes were investigated during the dry-ripening. In comparison with Pichia kudriavzevii XS-5 (PK), Rhodotorula mucilaginosa XZY63-3 (RX) and no inoculation (CK), the inoculation with Rhodotorula mucilaginosa EIODSF019 (RE) showed the highest overall acceptance and richness. Metagenomics revealed that RE inoculation inhibited Aspergillus abundance, and the profile of Rhodotorula reached 45.94 % at genus level. The treatment of RE increased the gene abundance of amino acid metabolism pathways; the expression levels of γ-glutamyl transpeptidase gene in RE were increased by 83.27 % compared with CK, and the activities of γ-glutamyl transpeptidase increased from 214 U/g proteins of CK to 567 U/g proteins of RE. LC-MS/MS analysis revealed the total contents of γ-glutamyl peptides increased from 136.40 μg/g of CK to 518.18 μg/g of RE. Partial least squares regression and correlation analysis indicated that γ-Glu-Cys and γ-Glu-Gln were mainly responsible for the improvement of overall acceptance and richness of Jinhua ham with RE inoculation.}, }
@article {pmid41187181, year = {2025}, author = {Xu, P and Huang, Z}, title = {Omadacycline treatment of severe Chlamydia psittaci pneumonia with septic shock diagnosed via metagenomic next-generation sequencing.}, journal = {Journal of infection in developing countries}, volume = {19}, number = {10}, pages = {1570-1576}, doi = {10.3855/jidc.21299}, pmid = {41187181}, issn = {1972-2680}, mesh = {Humans ; *Chlamydophila psittaci/genetics/isolation &amp; purification/drug effects ; High-Throughput Nucleotide Sequencing ; *Anti-Bacterial Agents/therapeutic use ; *Psittacosis/drug therapy/diagnosis/microbiology ; *Shock, Septic/drug therapy/diagnosis/microbiology ; *Tetracyclines/therapeutic use ; Metagenomics ; Male ; Treatment Outcome ; Doxycycline/therapeutic use ; }, abstract = {INTRODUCTION: Parrot fever, caused by Chlamydia psittaci, is a zoonotic disease typically treated with tetracyclines. Omadacycline, a novel aminomethyl tetracycline, has limited reports on its efficacy in severe Chlamydia psittaci pneumonia in the literature.<br><br>CASE PRESENTATION: We present a case of a patient with severe Chlamydia psittaci pneumonia showing symptoms of chills, high fever, shock, hepatic and renal insufficiency, and acute respiratory failure with copious yellow watery sputum. Chlamydia psittaci was confirmed by metagenomic next-generation sequencing (mNGS). Despite initial treatment with moxifloxacin and doxycycline, the patient did not improve and was subsequently discharged after receiving omadacycline.<br><br>CONCLUSIONS: Our findings highlight the potential of mNGS for rapid diagnosis of Chlamydia psittaci pneumonia and suggest omadacycline as a potential therapeutic option for severe cases that do not respond to conventional treatment.}, }
@article {pmid41187070, year = {2025}, author = {De Vivo, G and Pelletier, E and Feuda, R and D'Aniello, S}, title = {An Ocean of Opsins.}, journal = {Genome biology and evolution}, volume = {17}, number = {11}, pages = {}, doi = {10.1093/gbe/evaf189}, pmid = {41187070}, issn = {1759-6653}, support = {//Stazione Zoologica Anton Dohrn/ ; UF160226//Royal Society University Research Fellowship/ ; URF/R/221011//Royal Society University Research Fellowship/ ; RGF\R1\181012//Royal Society/ ; RGP009/2023//Human Frontier Science Program/ ; }, mesh = {*Opsins/genetics ; Animals ; Phylogeny ; *Evolution, Molecular ; Oceans and Seas ; Vertebrates/genetics ; }, abstract = {In this study, we explored the diversity and evolution of opsins using meta-omic data from the Tara Oceans and Tara Polar Circle expeditions, one of the largest marine datasets available. By using sequence similarity methods and phylogenetic analyses, we identified opsins across the different metazoan groups. Our results indicate that most of the opsin sequences belong to arthropods and vertebrates. We also detected sequences from all known opsin subfamilies, including r-opsin, c-opsin, xenopsin, and Group-4 opsins. Despite the broad taxonomic scope, no new opsin families were discovered; however, we provide valuable taxonomic insights into known opsin subfamilies and reinforce existing phylogenetic hypotheses. Additionally, we present novel opsin sequences from less-studied taxa, such as chaetognaths, rotifers, acoelomates, and tunicates, and which may serve as a valuable resource for future research into opsin function and diversity.}, }
@article {pmid41186403, year = {2025}, author = {Lugli, GA and Argentini, C and Tarracchini, C and Longhi, G and Mancabelli, L and Bianchi, MG and Taurino, G and Amaretti, A and Candeliere, F and Bussolati, O and Milani, C and Turroni, F and Ventura, M}, title = {Host interactions of Lactococcus lactis and Streptococcus thermophilus support their adaptation to the human gut microbiota.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0154725}, doi = {10.1128/aem.01547-25}, pmid = {41186403}, issn = {1098-5336}, abstract = {UNLABELLED: Within the human gut microbiota, lactic acid bacteria (LAB) play a crucial role in host health by producing lactic acid, which has been shown to shape microbial interactions and support intestinal homeostasis. However, despite their importance, there are limited insights regarding how LAB species interact with the host and other gut commensals. In this study, the investigation of the human gut microbiota of 10,000 healthy adults allowed the identification of Lactococcus lactis and Streptococcus thermophilus as commonly detected food bacteria. Further in silico analyses led to the identification of reference strains of the L. lactis and S. thermophilus species within the human gut, represented by PRL2024 and PRL2025 strains, respectively, which can represent nomadic bacteria. In vitro experiments revealed that both strains are ecologically adapted to survive and interact within the human gastrointestinal tract, while also highlighting their metabolic capacity to utilize a broad range of carbon sources. Specifically, the lactose metabolism was investigated, revealing that S. thermophilus PRL2025, despite high lactic acid output, incompletely metabolizes galactose, whereas L. lactis PRL2024 ensures full galactose utilization with lower acid production.<br><br>IMPORTANCE: The identification and functional characterization of Lactococcus lactis PRL2024 and Streptococcus thermophilus PRL2025 as human-adapted reference strains provide a valuable foundation for further in vivo experimentation. Given their ecological resilience, metabolic versatility, and interaction potential with beneficial gut microbes, these strains represent promising candidates as microbiota-targeted functional foods.}, }
@article {pmid41186329, year = {2025}, author = {Liu, Y and Liu, X and Hu, Y and Gao, F and Yu, W and Cheng, F}, title = {Evaluating untargeted metabolomics pipelines for sports nutrition research: a review.}, journal = {Analytical methods : advancing methods and applications}, volume = {}, number = {}, pages = {}, doi = {10.1039/d5ay01484k}, pmid = {41186329}, issn = {1759-9679}, abstract = {Untargeted metabolomics has emerged as a transformative approach in sports nutrition research, offering an unbiased means to characterize the complex biochemical responses to exercise, training, and dietary interventions. Unlike targeted assays restricted to predefined metabolites, untargeted strategies capture broad metabolic perturbations across lipid, carbohydrate, amino acid, and nucleotide pathways, enabling the discovery of novel biomarkers and unanticipated physiological mechanisms. This review critically evaluates the design and application of untargeted metabolomic pipelines in the context of exercise and nutrition science, from pre-analytical sample handling and analytical platforms such as NMR, LC-MS, and GC-MS, to data processing using tools like XCMS, MZmine, and MS-DIAL, and subsequent statistical and bioinformatic interpretation. Key applications include delineating acute metabolic shocks induced by endurance exercise, identifying athlete-specific metabolic phenotypes shaped by chronic training, and assessing the impact of nutritional interventions such as fruit intake, amino acid supplementation, or polyphenol-rich foods on exercise recovery and oxidative stress. The integration of metabolomics with other omics, particularly microbiome metagenomics and lipidomics, highlights the potential for systems-level insights into host-microbe-diet interactions. Nonetheless, significant challenges remain, including the reproducibility of findings, difficulties in metabolite identification, and the translational gap between large datasets and actionable nutritional strategies. By synthesizing current strengths, limitations, and controversies, this review emphasizes that the future of sports metabolomics lies in methodological standardization, multi-omics integration, and validation of candidate biomarkers in independent cohorts. Collectively, these efforts position untargeted metabolomics as a cornerstone for advancing precision nutrition and personalized performance monitoring in athletes.}, }
@article {pmid41186225, year = {2025}, author = {Chuang, H-Y and Chen, W-Y and Chen, S-H and Shao, Y-H and Wu, J-H}, title = {Metagenome-assembled genome sequence of Candidatus Loosdrechtia sp. KJ reconstructed from an alkaline anammox reactor.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0102425}, doi = {10.1128/mra.01024-25}, pmid = {41186225}, issn = {2576-098X}, abstract = {Candidatus Loosdrechtia sp. KJ is an anaerobic ammonium-oxidizing bacterium enriched from a bioreactor operated under alkaline conditions (pH 9.2 ± 0.4). We report its 3.39 Mb draft genome, containing 3,065 predicted coding sequences, 47 tRNA genes, and a single rrn operon.}, }
@article {pmid41186205, year = {2025}, author = {Li, Z and Zhang, X and Peng, L and Fang, Y and Liu, H and Zhou, Y and Wang, J and Lu, W}, title = {Response of Bovine Uterine Microbiota to Staphylococcus aureus Infection.}, journal = {American journal of reproductive immunology (New York, N.Y. : 1989)}, volume = {94}, number = {5}, pages = {e70178}, doi = {10.1111/aji.70178}, pmid = {41186205}, issn = {1600-0897}, support = {U20A2053//National Natural Science Foundation of China/ ; 2024BBF01007//Key R&amp;D Program of Ningxia Hui Autonomous Region/ ; CARS-37//China Agriculture Research System of MOF and MARA/ ; }, mesh = {Animals ; Female ; Cattle ; *Staphylococcus aureus/physiology ; *Staphylococcal Infections/microbiology/immunology/veterinary ; *Microbiota ; *Uterus/microbiology/immunology ; *Endometritis/microbiology/immunology/veterinary ; *Cattle Diseases/microbiology/immunology ; }, abstract = {BACKGROUND: Endometritis is a highly prevalent reproductive disorder in cows, causing serious adverse effects on reproductive performance, which brings huge economic losses to the livestock industry. Staphylococcus aureus is detected in a high proportion of endometritis pathogens (alone or in combinations of infections). Uterine microbial composition plays an important role in endometritis.<br><br>OBJECT AND METHOD: In order to determine the role of S. aureus in endometritis, we established an endometritis model using this bacterium and utilized metagenomics to detect the structure and function of the bovine uterine microbiota.<br><br>RESULTS: We found that S. aureus infection significantly increased the relative abundance of bacteria such as Escherichia coli, Trueperella pyogenes, and Streptococcus spp., while reducing the relative abundance of Akkermansia and Prevotella bacteria. The functions of microorganisms in the uterus are mainly manifested in metabolic levels, including carbohydrate metabolism, amino acid metabolism, energy metabolism, and lipid metabolism processes. The number of genes continues to increase with the duration of S. aureus infection, which disrupts the balance that maintains the bovine uterine flora.<br><br>CONCLUSION: This study provides a descriptive analysis of changes in the uterine microbiota of cows infected with S. aureus, which contributes to a new understanding of uncultured or unidentified pathogenic bacteria.}, }
@article {pmid41186087, year = {2025}, author = {Bortoletto, E and Rosani, U}, title = {Domoic Acid Risk and the Potential of Meta-Omics for Environmental Surveillance.}, journal = {Global change biology}, volume = {31}, number = {11}, pages = {e70593}, doi = {10.1111/gcb.70593}, pmid = {41186087}, issn = {1365-2486}, support = {101186013//HORIZON EUROPE European Innovation Council/ ; }, }
@article {pmid41185941, year = {2025}, author = {Al-Husseini, A and Komijani, M and Sabah, R}, title = {Impact of Dust Storms on Airborne Bacteria, Heavy Metals, and Inflammatory Markers in Asthmatic Patients.}, journal = {MicrobiologyOpen}, volume = {14}, number = {6}, pages = {e70109}, doi = {10.1002/mbo3.70109}, pmid = {41185941}, issn = {2045-8827}, support = {//The authors received no specific funding for this work./ ; }, mesh = {Humans ; *Asthma/blood/microbiology ; *Metals, Heavy/analysis ; *Bacteria/classification/isolation &amp; purification/genetics ; Iraq ; *Dust/analysis ; Female ; Male ; Biomarkers/blood ; Adult ; *Air Microbiology ; Cytokines/blood ; Metagenomics ; Middle Aged ; Young Adult ; Adolescent ; Child ; }, abstract = {Asthma, a chronic bronchial disorder prevalent in children/adolescents, is exacerbated under environmental conditions like dust storms. The current study investigated heavy metal levels, airborne bacteria, and serum IL-4/IL-8 in asthmatics during before/after dust storms in Iraq's Al-Anbar, Baghdad, and Kirkuk provinces. Airborne heavy metals were quantified by ICP-MS, serum cytokines by ELISA, and bacterial communities via metagenomics. Statistical analysis was performed using GraphPad Prism (p < 0.05 significant). ICP-MS revealed considerably elevated post-storm concentrations of As, Ag, B, Ba, Co, Hg, Mg, Mn, Ni, Sn, S, Ti, and V. Asthmatic subjects presented with considerably elevated IL-4 and IL-8 post-storm (p < 0.05) compared to controls (p > 0.05). Metagenomics revealed storm-induced bacterial alterations: Al-Anbar contained elevated Burkholderiaceae, Methylophilaceae, and Rhodobacteraceae; Kirkuk contained elevated Ilumatobacteraceae, Microbacteriaceae, Burkholderiaceae, and Rhodobacteraceae. Baghdad's most prevalent species included Rhodocyclaceae (50%), Burkholderiaceae (17%), and Arcobacteraceae (4.5%). Al-Anbar was significantly richer in microbes (Chao1) and more diverse (Shannon) than other regions following the dust storm (p < 0.0001). These findings indicate that dust storms raise heavy metals, alter airborne bacteria, and increase inflammatory cytokines in asthma sufferers, and these emphasize their role in exacerbating asthma in Iraq.}, }
@article {pmid41185633, year = {2025}, author = {Villarreal, CX and Chan, DD}, title = {Multiomic Integration Reveals Taxonomic Shifts Correlate to Serum Cytokines in an Antibiotics Model of Gut Microbiome Disruption.}, journal = {Cellular and molecular bioengineering}, volume = {18}, number = {5}, pages = {369-385}, pmid = {41185633}, issn = {1865-5025}, abstract = {PURPOSE: The gut microbiome interacts with many systems throughout the human body. Microbiome disruption reduces bone tissue mechanics but paradoxically slows osteoarthritis progression. The microbiome also mediates inflammatory and immune responses, including serum cytokines. Towards our long-term goal of studying how the gut microbiome interacts with synovial joint health and disease, we examined how antibiotics-induced changes to microbial taxa abundance associated to serum cytokine levels.<br><br>METHODS: Mice (n&#x2009;=&#x2009;5&#x2009;+&#x2009;) were provided ad libitum access to water containing antibiotics (1 g/L neomycin, 1 g/L ampicillin, or 1 g/L ampicillin with 0.5 g/L neomycin) or control water from 5- to 16-weeks old, corresponding in skeletal development to&#x2009;~&#x2009;10 to&#x2009;~&#x2009;25 years in humans. At humane euthanasia, we collected cecum contents for 16S metagenomics and blood for serum cytokine quantification for comparison to control and among antibiotic groups. We used dimensional reduction techniques, multiomic integration, and correlation to discriminate antibiotic groups and identify specific relationships between high-abundance taxa and serum cytokines.<br><br>RESULTS: Antibiotic treatment significantly lowered diversity, altered phylum relative abundance, and resulted in significant association with specific taxa. Dimensional reduction techniques and multiomic integration revealed distinct antibiotic-associated clusters based on genera relative abundance and cytokine serum concentration. Cytokines IL-6, MIP-1B, and IL-10 significantly contributed to antibiotic discrimination, significantly different among antibiotic treatments, and had significant correlations with specific taxa.<br><br>CONCLUSIONS: Antibiotic treatment resulted in heterogenous response in gut microbiome and serum cytokines, allowing significant microbe-cytokine links to emerge. The relationships identified here will enable further investigation of the gut microbiome's role in modifying joint health and disease.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12195-025-00861-2.}, }
@article {pmid41185359, year = {2025}, author = {Cao, R and Zhou, Q and Ma, Y and Yan, X and Li, A and Du, H and Xu, Y}, title = {Multimodal integration: Mechanisms of temperature dynamics and quality formation critical period in Daqu.}, journal = {Food research international (Ottawa, Ont.)}, volume = {221}, number = {Pt 4}, pages = {117622}, doi = {10.1016/j.foodres.2025.117622}, pmid = {41185359}, issn = {1873-7145}, mesh = {*Fermentation ; Machine Learning ; Metagenomics ; *Temperature ; Microbiota ; Hot Temperature ; Quality Control ; *Food Microbiology ; }, abstract = {The quality of medium-high temperature Daqu, the core starter for strong-aroma Baijiu, is regulated by the synergistic mechanisms of temperature, physicochemical properties, and microbial activity. In this study, we aimed to integrate dynamic monitoring of indicators, metagenomic analysis, and machine learning modeling to establish a multimodal approach. The systematic analysis of the differential contributions of spatiotemporal factors to Daqu fermentation temperature highlighted the dynamic changes in physicochemical and microbial processes during Daqu fermentation, as well as the critical period for quality control. The influence of temporal factors on Daqu temperature was significantly higher than that of spatial heterogeneity. Additionally, the temperature difference generated by the interaction of dual pathways between environmental changes and microbial metabolic heat production could regulate the Daqu fermentation through a heat-flow positive feedback mechanism. By combining temperatural and physicochemical data, machine learning models identified and validated the early fermentation stage (S2-S3) as the critical period for Daqu quality formation. Consequently, the quality control of Daqu can be effectively predicted and guided through monitoring the temperature in the early stage of fermentation. Metagenomic analysis revealed the two-phase characteristics of medium-high temperature Daqu fermentation: the core microbiota construction was completed in the S1-S3 stages, and the microbiota function then entered a stable period in the S4-S6 stages. This explains the dynamic change regularity of Daqu quality critical period formative from a microscopic perspective.}, }
@article {pmid41185305, year = {2025}, author = {Ying, H and Yang, J and Yu, L and Wei, J and Sheng, Q and Yuan, Y and Yue, T}, title = {Metagenomics and GC-IMSanalyses reveal microbial community differences and flavor characteristics among three types of Feng flavor Daqu.}, journal = {Food research international (Ottawa, Ont.)}, volume = {221}, number = {Pt 4}, pages = {117551}, doi = {10.1016/j.foodres.2025.117551}, pmid = {41185305}, issn = {1873-7145}, mesh = {*Metagenomics/methods ; *Taste ; Fermentation ; *Microbiota ; Fungi/classification/genetics/metabolism ; *Alcoholic Beverages/microbiology/analysis ; China ; Bacteria/classification/genetics/metabolism ; *Food Microbiology ; Gas Chromatography-Mass Spectrometry ; Flavoring Agents ; }, abstract = {Feng flavor Baijiu is one of the four famous Baijiu in China, and its quality and flavor are closely related to the microbial flora. Daqu is a saccharifying agent and starter for the production of Feng flavor Baijiu. Different styles of Daqu (Hong-Xin Daqu, Huai-Rang Daqu, Qing-Cha Daqu) reflect different microbial community structures and functions. Understanding the relationship between the microbial characteristics of Daqu and flavor is challenging yet vital for improving Baijiu fermentation. This study used metagenomics combined with GC-IMS to systematically analyze the microbial characteristics and flavor features of three different styles of Feng flavor Daqu. The bacteria mainly include Bacillus, Lactococcus, Lactobacillus and Leuconostoc. Fungi mainly include Aspergillus, Rhizopus, Saccharomyces, Paecilomyces and Rasamsonia. Actinobacteria mainly included Saccharopolyspora and Streptomyces. The community structure and function of microorganisms in different styles of Daqu exhibited strong functional complementarity. The results indicated that the content of esters and alkenes in Qing-Cha Daqu was higher, mainly related to carbon metabolism and amino acid metabolism, and generated aromatic compounds through esterification reactions. While there were more aldehydes, ketones, and esters in Huai-Rang Daqu, mainly participating in enzymatic reactions and biosynthesis of cofactors, generating precursor substances for various aroma compounds. Moreover, the content of ethyl acetate and alkenes in Hong-Xin Daqu was higher, mainly participating in the glycolysis and tricarboxylic acid cycle, generating various alcohols and organic acids. This study revealed the complementary roles of the three styles of Daqu in Feng flavor Baijiu fermentation, providing valuable insights for product enhancement.}, }
@article {pmid41185132, year = {2025}, author = {Lonsing, A and Martens, GA and Resteu, A and Kizina, J and Wilkie, I and Bahr, A and Harder, J}, title = {Anaerobic Limonene Metabolism in a Methanogenic Enrichment Involves a Glycine Radical Enzyme.}, journal = {Environmental microbiology}, volume = {27}, number = {11}, pages = {e70192}, doi = {10.1111/1462-2920.70192}, pmid = {41185132}, issn = {1462-2920}, support = {//Max Planck Society/ ; }, mesh = {*Limonene/metabolism ; *Methane/metabolism ; Anaerobiosis ; *Bacteria/genetics/metabolism/enzymology/classification ; *Archaea/genetics/metabolism/enzymology/classification ; *Terpenes/metabolism ; Metagenome ; *Glycine/metabolism ; *Cyclohexenes/metabolism ; Phylogeny ; Metagenomics ; Bacterial Proteins/metabolism/genetics ; }, abstract = {Limonene is a natural monoterpene omnipresent in human environments. It enters wastewater and is also metabolised in methanogenic digesters. A stable limonene-degrading methanogenic enrichment culture was investigated by metagenomic, metatranscriptomic and metaproteomic data sets to characterise the microbial community and identify the limonene degradation pathway. Thirty-two metagenome-assembled genomes revealed a complex community of bacteria and methanogenic archaea dominated by Candidatus Velamenicoccus archaeovorus as the top predator, contributing two-thirds of the reads in the metagenome. The presence of several fermenting bacteria (Anaerolineaceae, Aminidesulfovibrio, Smithellaceae, Lentimicrobium) indicated the recycling of necromass in a microbial loop. Only one hydrocarbon-activating enzyme system was expressed, a member of the alkyl- and arylsuccinate synthase family which is a glycine radical enzyme that adds fumarate to hydrocarbons. The limonenylsuccinate synthase gene encodes a modified substrate binding pocket with two smaller amino acids, suggesting an adaptation for the larger structure of limonene. The limonenylsuccinate synthase operon and a ring cleavage operon, as well as genes for the final syntrophic fermentation to acetate, hydrogen and formate were encoded in a Syntrophobacteraceae genome. Almost all genes for this degradation pathway were highly transcribed and expressed, demonstrating a catalytic role for glycine radical enzymes in methanogenic systems degrading limonene.}, }
@article {pmid41185061, year = {2025}, author = {Mekuria, Z and Deblais, L and Ojeda, A and Mummed, B and Singh, N and Gebreyes, W and Havelaar, AH and Rajashekara, G and , }, title = {Host clustering of Campylobacter species and enteric pathogens in a longitudinal cohort of infants, family members and livestock in rural Eastern Ethiopia.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {225}, pmid = {41185061}, issn = {2049-2618}, support = {OPP11755487//Bill and Melinda Gates Foundation/ ; OPP11755487//Bill and Melinda Gates Foundation/ ; OPP11755487//Bill and Melinda Gates Foundation/ ; }, mesh = {Animals ; Humans ; *Campylobacter/classification/genetics/isolation &amp; purification ; Infant ; *Campylobacter Infections/microbiology/epidemiology/veterinary ; Ethiopia/epidemiology ; *Livestock/microbiology ; Rural Population ; Longitudinal Studies ; Female ; Male ; Chickens/microbiology ; Feces/microbiology ; Metagenomics/methods ; Gastrointestinal Microbiome ; Adult ; Cluster Analysis ; Family ; Child, Preschool ; }, abstract = {BACKGROUND: Livestock are recognized as major reservoirs for Campylobacter species and other enteric pathogens, posing infection risks to humans. High prevalence of Campylobacter during early childhood has been linked to environmental enteric dysfunction and stunting, particularly in low-resource settings.<br><br>METHODS: A total of 280 samples from Campylobacter positive households with complete metadata were analyzed by shotgun metagenomic sequencing followed by bioinformatic analysis via the CZ-ID metagenomic pipeline (Illumina mNGS Pipeline v7.1). Further statistical analyses in JMP PRO 16 explored the microbiome, emphasizing Campylobacter and other enteric pathogens. Two-way hierarchical clustering and split k-mer analysis examined host structuring, patterns of co-infections and genetic relationships. Principal component analysis was used to characterize microbiome composition across the seven sample types.<br><br>RESULTS: The study identified that microbiome composition was strongly host-driven, with more than 3844 genera detected, and two principal components explaining 62% of the total variation. Twenty-one dominant (based on relative abundance) Campylobacter species showed distinct clustering patterns for humans, ruminants, and broad hosts. The broad-host cluster included the most prevalent species, C. jejuni, C. concisus, and C. coli, present across sample types&#xa0;and a sub-cluster within C. jejuni involving humans, chickens, and ruminants. Campylobacter species from chickens showed strong positive correlations with mothers (r&#x2009;=&#x2009;0.76), siblings (r&#x2009;=&#x2009;0.61) and infants (r&#x2009;=&#x2009;0.54), while co-occurrence analysis found a higher likelihood (Pr&#x2009;>&#x2009;0.5) of pairs such as C. jejuni with C. coli, C. concisus, and C. showae. Analysis of the top 50 most abundant microbial taxa showed a distinct cluster uniquely present in human stool and absent in all livestock. The study also found frequent co-occurrence of C. jejuni with other enteric pathogens such as Salmonella, and Shigella, particularly in human and chicken. Additionally, instances of Candidatus Campylobacter infans (C. infans) were identified co-occurring with Salmonella and Shigella species in stool samples from infants, mothers, and siblings.<br><br>CONCLUSIONS: A comprehensive analysis of Campylobacter diversity in humans and livestock in a low-resource setting revealed that infants can be exposed to multiple Campylobacter species early in life. C. jejuni is the dominant species with a propensity for co-occurrence with other notable enteric bacterial pathogens, including Salmonella, and Shigella, especially among infants. Video Abstract.}, }
@article {pmid41183495, year = {2025}, author = {Hu, CY and Dai, CY and Anh, PNT and Tsai, HY and Chen, YC}, title = {Tetragenococcus halophilus A003 altered microbiota and repressed the accumulation of biogenic amines in the fermentation of fish Sauce.}, journal = {Letters in applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/lambio/ovaf128}, pmid = {41183495}, issn = {1472-765X}, abstract = {Fish sauce, a seasoning commonly utilized in East Asian cuisine, is produced from fish combined with a substantial quantity of salt. However, biogenic amines (BAs) accumulation poses safety concerns in fermented fish sauce during fermentation. This study characterized Tetragenococcus halophilus A003, isolated from fish sauce, which exhibited the weakest decarboxylase gene activation and lowest BA production among the tested strains. Starter inoculation with A003 yielded minimal chemical alteration compared to natural fermentation. Cadaverine levels were substantially lower (19.1 ± 1.49 mg/L) than those in sauce fermented without a starter or with T. halophilus BCRC12250. Histamine and tyramine were undetectable in isolate A003-inoculated samples. Metagenomic analysis revealed an enrichment of low BA-producing taxa, notably Tetragenococcus and Staphylococcus, comprising 97.91% of the community. These findings suggest T. halophilus A003 confers a selective advantage for low BA microbiota during fish sauce fermentation.}, }
@article {pmid41183487, year = {2025}, author = {Xu, Q and He, N and Tian, Y and Wu, Z and Wang, H and Liu, B and Yang, Z and Zhang, H and Luo, Q and Zhong, Y and Xiao, L and Li, S and Zou, Y}, title = {Lactobacillus gasseri TF08-1 ameliorate high-fat diet induced Nonalcoholic fatty liver disease and regulates gut microbiota in mice.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxaf271}, pmid = {41183487}, issn = {1365-2672}, abstract = {AIMS: This study aimed to investigate the therapeutic potential of Lactobacillus gasseri TF08-1, a gut bacterium isolated from healthy adolescents, in alleviating high-fat diet (HFD)-induced non-alcoholic fatty liver disease (NAFLD). This followed our discovery of lipid metabolism-related genes in its complete genome.<br><br>METHODS AND RESULTS: The high-precision complete genome map of L. gasseri TF08-1 was constructed for the first time, revealing enriched lipid metabolism pathways, including bile salt hydrolase activity and short-chain fatty acid (SCFA) production. After supplementing Lactobacillus gasseri TF08-1 for 8 weeks in mice fed with a high-fat diet, the serum triglyceride (TG) level decreased by 41.95%, the hepatic total cholesterol (TC) level decreased by 35.09%, and the TNF-&#x3b1; level decreased by 42.91%. Meanwhile the NAS score decreased by 3.66 points. The treatment significantly reduced hepatic lipid accumulation, lowered pro-inflammatory cytokines, and improved steatosis scores. Metagenomic analyses showed L. gasseri TF08-1 restored gut microbiota balance, significantly increasing the abundance of beneficial bacteria such as Faecalibacterium prausnitzii and Phocaeicola vulgatus, while also enriching fatty acid degradation pathways.<br><br>CONCLUSIONS: L. gasseri TF08-1 demonstrates probiotic efficacy against NAFLD through dual mechanisms: direct metabolic modulation and gut microbiota restoration. The lipid metabolism capacity encoded by its genome likely contributes to therapeutic effects.}, }
@article {pmid41183417, year = {2025}, author = {Liu, S and Xiang, Y and Liu, P and Deng, J and He, J and Chen, H and Liao, S and Lu, Y and Zhang, Z and Xu, J and Zhang, Z}, title = {Application of metagenomic next-generation sequencing in the precise and rapid diagnosis of spinal infections.}, journal = {Diagnostic microbiology and infectious disease}, volume = {114}, number = {2}, pages = {117165}, doi = {10.1016/j.diagmicrobio.2025.117165}, pmid = {41183417}, issn = {1879-0070}, abstract = {OBJECTIVE: To evaluate the comparative diagnostic efficacy of metagenomic next-generation sequencing (mNGS) versus conventional microbiological culture in spinal infections.<br><br>METHODS: A retrospective analysis was conducted in a cohort of 80 patients with suspected spinal infections who underwent concurrent testing via metagenomic next-generation sequencing (mNGS), microbial culture, and histopathological examination. Diagnostic performance of mNGS and microbial culture was compared using a composite clinical reference standard (definitive diagnosis integrating histopathology, clinical history, and laboratory findings) as the diagnostic gold standard.<br><br>RESULTS: Pathogens were detected in 64 cases (80 %) by mNGS, compared to 34 cases (42.5 %) via conventional microbial culture, demonstrating a statistically significant difference in detection rates (P < 0.001). Using clinical diagnosis (histopathology combined with medical history and laboratory findings) as the gold standard, mNGS exhibited superior sensitivity, accuracy, positive predictive value (PPV), and negative predictive value (NPV) in tissue specimens. Conversely, microbial culture showed higher specificity. In pus specimens, mNGS maintained advantages in sensitivity, accuracy, and PPV, while culture demonstrated higher specificity and NPV.<br><br>CONCLUSION: Compared to conventional microbial culture, mNGS demonstrates superior diagnostic performance in spinal infections, with significantly higher pathogen detection rates and enhanced sensitivity, accuracy PPV and NPV. mNGS exhibits significant advantages over culture in identifying both common pathogens and fastidious organisms, while also demonstrating robust fungal detection capabilities. Additionally, in tissue specimens, mNGS demonstrates relatively pronounced advantages compared to conventional microbial culture. For purulent specimen testing, comprehensive sensitivity and specificity in diagnosis can be achieved through a combined strategy of mNGS and microbial culture.}, }
@article {pmid41183305, year = {2025}, author = {Yang, R and Ma, J and Abebe, H and Tu, Y}, title = {Divergent Responses of Soil Microbiome Structure and Function to Salinity and Depth Gradients.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.5c08498}, pmid = {41183305}, issn = {1520-5118}, abstract = {Soil salinization profoundly threatens agricultural ecosystems by disrupting soil microbial communities and functions, yet the interplay of salinity and depth on microbiome structure and function is unclear. In the present experiment, soils from two depths (0-20 and 20-40 cm) across a low (LS), medium (MS), and high (HS) salinity gradient were collected. The results indicated that the soil electrical conductivity, available sodium, and available potassium were significantly elevated in HS soil. 16S rRNA gene sequencing identified three key microorganisms associated with soil salinity, including Sphingomonas, Bradyrhizobium, and Chloracidobacterium. Metagenomic analysis indicated that the abundances of carbon and nitrogen cycle genes such as amyA, xylA, nifH, nirK, narG and amoA were significantly upregulated in LS soils. In conclusion, the experiment systematically elucidated the intricate restructuring of soil microbiome responses across distinct salinity gradients and depths, providing new theoretical support for the remediation of soil salinization.}, }
@article {pmid41183096, year = {2025}, author = {Lv, JX and Pei, YY and Yang, C and Liu, X and Ju, MJ and Holmes, EC and Chen, YM and Zhu, TY and Zhang, YZ}, title = {Extensive diversity of unusual microorganisms associated with severe pneumonia in kidney transplant recipients.}, journal = {PLoS pathogens}, volume = {21}, number = {11}, pages = {e1013667}, doi = {10.1371/journal.ppat.1013667}, pmid = {41183096}, issn = {1553-7374}, abstract = {Although pneumonia is a common lung disease with a high morbidity and mortality, aside from well-known pathogens little is known about why, which and how many microorganisms are associated with the disease, particularly in immunocompromised individuals. We enrolled 32 kidney transplant cases with severe pneumonia admitted to Shanghai Zhongshan Hospital between 2019 and 2025, and performed both metagenomic and metatranscriptomic sequencing on the bronchoalveolar lavage fluid (BALF) and blood samples from each case. Comprehensive analyses of immune cells and cytokines, as well as BALF and blood metatranscriptomes, revealed that both adaptive and innate immunity inside and outside of their lungs were severely suppressed. Notably, a high diversity of unusual microorganisms were present in BALF samples, including bacteria and DNA viruses that are rare or absent in healthy individuals, as well as RNA viruses and fungi. Of these, 17 bacteria, 46 DNA viruses, eight RNA viruses and two fungi, which were at high abundance, were considered to be responsible for the lung infections. Remarkably, the majority of these patients experienced co-infections of multiple bacteria, DNA and RNA viruses and fungi, reaching 32 virus species in one individual. In sum, these data indicate that the prosperity or overgrowth of accidental, opportunistic and rare microorganisms within the lungs of these kidney transplant patients substantially altered their lung microbiota, with multiple co-infections further exacerbating the severity of pneumonia.}, }
@article {pmid41182689, year = {2025}, author = {de Kroon, RR and van Wesemael, AJ and van Kaam, AH and Savelkoul, PHM and Boon, M and Budding, AE and Niemarkt, HJ and de Meij, TGJ}, title = {A Novel Untargeted Molecular Detection Technique for Rapid Fecal Microbiota Profiling in Very Preterm Infants: Optimization, Genus-Level Comparison, and Application.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {39}, number = {21}, pages = {e71207}, doi = {10.1096/fj.202502006RR}, pmid = {41182689}, issn = {1530-6860}, mesh = {Humans ; *Feces/microbiology ; Infant, Newborn ; RNA, Ribosomal, 16S/genetics ; *Infant, Premature ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; Intensive Care Units, Neonatal ; *Bacteria/genetics/classification ; }, abstract = {Gut microbiota profiling shows potential for improving care in the neonatal intensive care unit (NICU). However, common techniques, including 16S rRNA gene and metagenomic sequencing, have limited bedside applicability. The IS-pro microbiota assay provides species-level abundances within 5 h. We aimed to optimize the taxa annotation for preterm infants (phase 1), compare its findings to 16S sequencing on the genus level (phase 2), and apply the assay in a preterm cohort (phase 3). 1445 fecal samples from 479 preterm infants (24-30 weeks gestation) across 10 NICUs were analyzed with IS-pro. For phase 1 (optimization), IS-pro amplicons of 32 fecal samples were additionally analyzed with nanopore sequencing to expand the IS-pro matching database. For phase 2 (comparison), 41 samples were compared to 16S sequencing. In phase 3 (application), the optimized IS-pro assay was applied to the total cohort. Following phase 1, a mean relative abundance of 82.5% was successfully annotated. In phase 2, IS-pro showed high concordance with 16S sequencing, with a strong positive correlation between the two techniques (Pearson's correlation coefficient: 0.77, SD 0.24). In phase 3, IS-pro analysis of the full cohort revealed Staphylococcus, Klebsiella, Enterococcus, Escherichia-Shigella, and Streptococcus as the predominant genera in the first 4 weeks of life. Our findings demonstrate that the IS-pro microbiota assay effectively detects and quantifies key bacterial taxa in fecal samples of preterm infants, with outcomes highly concordant with 16S sequencing. Unlike traditional techniques, IS-pro is a rapid tool, illustrating its potential for clinical practice. Future studies should explore its applications in the NICU.}, }
@article {pmid41182549, year = {2025}, author = {Dandare, SU and Dabai, IA and Kumaresan, D and Allen, CCR}, title = {A Novel Salicylaldehyde Dehydrogenase from Alpine Soil Metagenome Reveals a Unique Catalytic Mechanism.}, journal = {Applied biochemistry and biotechnology}, volume = {}, number = {}, pages = {}, pmid = {41182549}, issn = {1559-0291}, support = {NGCA-2014-78//Commonwealth Scholarship Commission/ ; }, abstract = {Metagenomic approaches have revolutionised the discovery of novel enzymes with ecological and biotechnological significance from different environments. Here, we report the comprehensive characterisation of a novel salicylaldehyde dehydrogenase (SALDAP) obtained from an alpine soil metagenome. Phylogenetic analysis revealed that SALDAP is the first experimentally characterised Alphaproteobacterial SALD, forming a distinct evolutionary clade among known bacterial enzymes. The recombinant enzyme exhibited strict specificity for NAD[+] and exceptional catalytic efficiency toward aromatic aldehydes, with benzaldehyde as the preferred substrate. Kinetic analyses showed catalytic efficiencies exceeding 10[6] M[-1] s[-1] for aromatics, whereas aliphatics were oxidised with much lower efficiency, consistent with ecological specialisation for aromatic catabolism in alpine soils enriched in lignin-derived compounds. SALDAP was most active under mildly alkaline conditions (optimum pH 8.0) and tolerated a range of chemical environments, though high concentrations of certain metals and solvents were inhibitory. Differential scanning fluorimetry demonstrated that the enzyme was stabilised by ligand binding, with maximal thermal stability observed when both substrate and cofactor were present. Structural alignment with Pseudomonas NahF and docking analyses revealed that SALDAP employs a distinctive catalytic configuration involving ASN-137, ARG-145, GLU-238, and CYS-272, highlighting a non-canonical role for ASN-137 in substrate binding and stabilisation. Based on these findings, we propose a mechanistic model for SALDAP that expands the catalytic diversity of the aldehyde dehydrogenase superfamily. This study establishes a new paradigm for aromatic aldehyde oxidation, underscores the ecological significance of SALDAP in alpine soil microbiomes, and provides a foundation for engineering novel biocatalysts for bioremediation and synthetic biology applications.}, }
@article {pmid41182235, year = {2025}, author = {Bisschop, K and Goel, N and Coone, M and Vanoverberghe, I and Greffe, A and Asselman, J and Decaestecker, E}, title = {Host-microbiota matching and epigenetic modulation drive Daphnia magna responses to cyanobacterial stress.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf247}, pmid = {41182235}, issn = {1751-7370}, abstract = {Microbial communities are crucial in host adaptation to stressors, particularly in dynamic ecosystems. In aquatic environments, Daphnia magna is ideal for studying host-microbiome interactions due to its ecological importance and sensitivity. Adaptation to toxins, such as those produced by cyanobacteria, may involve both host and microbial gene repertoires. Yet, the influence of microbiota composition and function on host performance remains poorly understood. Because epigenetic mechanisms such as DNA methylation regulate gene expression and mediate adaptive responses, we also investigated whether these associations are reflected in DNA methylation levels. To address this, we conducted a fully factorial transplant experiment using microbiota-depleted Daphnia colonised with microbiota from the same or different genotype, previously exposed to toxic or non-toxic diets, or left uncolonised. We assessed life-history traits, microbial composition (16S rRNA genes), functional profiles (whole-genome-resequencing), and DNA methylation (colorimetric quantification). Daphnia fed non-toxic diets grew larger and reproduced more. Increased methylation occurred when microbiota donors differed from the host genotype and was strongest under toxic diet. Dysbiosis and reduced performance were noted in individuals colonised with toxic-diet microbiota from another genotype, where Limnohabitans spp. was reduced or absent. Signs of hormesis emerged when Daphnia received microbiota from their own genotype reared on non-toxic diets. DNA methylation of both host and microbiota was associated with functional pathways, including increased mitochondrial fatty acid biosynthesis. These findings highlight the importance of host-microbiota matching and microbial environmental history in shaping host performance and epigenetic responses, emphasizing the need to consider host-microbe-environment interactions in evolutionary and ecological studies.}, }
@article {pmid41181472, year = {2025}, author = {Iftikhar, F and Iftikhar, A and Khalid, M and Talha, M and Waafira, A}, title = {Gut microbial signatures in autoimmune hepatitis: unlocking diagnostic and therapeutic potential.}, journal = {Annals of medicine and surgery (2012)}, volume = {87}, number = {10}, pages = {6868-6869}, pmid = {41181472}, issn = {2049-0801}, abstract = {Autoimmune hepatitis (AIH) is a chronic inflammatory liver disease with unclear etiology but likely results from a complex interplay of genetic susceptibility and environmental triggers. Emerging evidence highlights the role of gut microbiota in AIH pathogenesis, with specific genera such as Veillonella, Lactobacillus, and Oscillospira demonstrating diagnostic value. Dysbiosis-associated biomarkers like lipopolysaccharide and aspartate aminotransferase further support a microbial role in disease onset and progression. Despite these promising developments, rare AIH variants remain poorly characterized due to methodological and population-level limitations. Moving forward, large-scale, longitudinal studies integrating metagenomics, metabolomics, and host genomic data are needed to establish subtype-specific microbial markers and assess the efficacy of targeted interventions such as probiotics and bacteriophage therapy.}, }
@article {pmid41181328, year = {2025}, author = {Jo, JW and Kim, SK and Byun, JY and Hong, SM and Kim, BS}, title = {The association between the adenoid microbiome and chronic otitis media with effusion in children differs according to age.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1660939}, pmid = {41181328}, issn = {2235-2988}, mesh = {Humans ; *Otitis Media with Effusion/microbiology ; Child ; *Adenoids/microbiology ; Male ; Female ; Child, Preschool ; Age Factors ; Chronic Disease ; *Microbiota ; Feces/microbiology ; Streptococcus pneumoniae/isolation &amp; purification ; Haemophilus influenzae/isolation &amp; purification ; Gastrointestinal Microbiome ; Metagenomics ; Bacteria/classification/genetics/isolation &amp; purification ; Infant ; }, abstract = {INTRODUCTION: Chronic otitis media with effusion (COME) can adversely affect childhood development, and while the adenoid has been considered a reservoir for bacterial pathogens contributing to the pathogenesis of COME, the role of the adenoid microbiome in COME remains unclear. This study analyzed both the adenoid and gut microbiome in children with and without COME to identify their potential roles in the disease's pathogenesis.<br><br>METHODS: Adenoid samples were collected during surgery for adenoid microbiome analysis, while fecal samples were collected for gut microbiome analysis. Microbiome was analyzed using whole metagenome sequencing and subsequent bioinformatic analysis.<br><br>RESULTS: A significant association between the adenoid microbiome and COME was detected, while no such association observed for the gut microbiome. The adenoid microbiome varied by age in the control group, but this age-dependent variation was perturbed in the COME group. Notably, in children aged 6-12 years, the adenoid microbiome was significantly associated with COME based on the type of middle ear fluid, where Streptococcus pneumoniae and Haemophilus influenzae were prominent indicators in the mucoid form of COME. The proliferation of these species in mucoid COME group was correlated with indicators for the serous COME group. The altered microbiome in COME patients may influence immune responses through the synthesis of spermidine and acetate, contributing to disease development.<br><br>DISCUSSION: This study highlights the age-dependent contribution of the adenoid microbiome-particularly in children aged 6 to 12 years-to the pathogenesis of COME.}, }
@article {pmid41181319, year = {2025}, author = {Wang, Z and Song, L and Li, D and Jin, Y}, title = {From commensalism to pathogenesis: the hidden role of the respiratory virome.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1693796}, pmid = {41181319}, issn = {2235-2988}, mesh = {Humans ; *Virome ; *Microbiota ; *Symbiosis ; *Respiratory System/virology/microbiology ; Bacteriophages ; *Viruses/classification/genetics ; Animals ; Metagenomics ; Host-Pathogen Interactions ; Respiratory Tract Infections/virology ; }, abstract = {The respiratory virome, encompassing both eukaryotic viruses and bacteriophages, is an essential but often overlooked component of the airway microbiome. Recent advances in metagenomics have revealed that a diverse viral community exists even in healthy individuals, contributing to immune regulation and microbial balance. However, the field faces several challenges: the baseline composition of the respiratory virome remains incompletely defined, its immunomodulatory functions are not fully understood, and its contributions to respiratory diseases are only beginning to be elucidated. This mini-review summarizes current knowledge of the respiratory virome under physiological conditions, highlights emerging insights into how resident viruses and phages shape host immunity, and discusses alterations observed in asthma, chronic obstructive pulmonary disease, pulmonary fibrosis, and pneumonia. By integrating evidence across these conditions, we emphasize the significance of the virome in both health and disease. A deeper understanding of its dynamics may yield novel diagnostic markers and therapeutic strategies, underscoring the importance of future longitudinal and mechanistic studies in this rapidly evolving field.}, }
@article {pmid41181040, year = {2025}, author = {Jeyaraman, M and Balasubramanian, E and Jeyaraman, N and Nallakumarasamy, A and Muthu, S}, title = {Metagenomic analysis of gut microbiome and spondyloarthropathy: A systematic review.}, journal = {World journal of orthopedics}, volume = {16}, number = {10}, pages = {108374}, pmid = {41181040}, issn = {2218-5836}, abstract = {BACKGROUND: Spondyloarthritis (SpA), a prevalent chronic inflammatory disorder, predominantly impacts the axial skeleton, including the spine and sacroiliac joints. Emerging evidence implicates gut dysbiosis in the pathogenesis of SpA.<br><br>AIM: To evaluate the association between gut microbiome alterations and SpA through metagenomic sequencing analyses.<br><br>METHODS: A systematic review was conducted by querying English-language databases, including PubMed, EMBASE, and Google Scholar, spanning 2000 to 2023. From an initial pool of 150 studies, four articles meeting stringent inclusion and exclusion criteria were selected for analysis.<br><br>RESULTS: The reviewed studies identified an enrichment of opportunistic pathogenic bacterial species, such as Clostridium spp., Prevotella spp., and Bacteroides spp., alongside viral families including Gratiaviridae and Quimbyviridae, in individuals with ankylosing spondylitis compared to healthy controls. Dysregulated metabolic pathways were highlighted as potential mediators of chronic inflammation and arthritic manifestations. Notably, treatment with tumor necrosis factor inhibitors demonstrated efficacy in mitigating SpA symptoms and restoring gut microbial balance.<br><br>CONCLUSION: The findings underscore a significant presence of pathogenic gut microbiota in SpA patients, suggesting a pivotal role in disease progression. Future investigations should focus on species-specific microbial targets to develop innovative therapies for preventing and managing SpA and associated gut dysbiosis.}, }
@article {pmid41180884, year = {2025}, author = {Sharma, P and Kapoor, N and Langer, S}, title = {Comparative Analysis of Gut Bacterial Communities in Fish and Shellfish of Great Himalayan River System.}, journal = {Indian journal of microbiology}, volume = {65}, number = {3}, pages = {1734-1747}, pmid = {41180884}, issn = {0046-8991}, abstract = {The gut microbiota comprises a unique micro-ecosystem and plays important role in various metabolic functions of the host. Cirrhinus mrigala and Maydelliathelphusa masoniana are two important species of fish and shellfish found in Chenab and Ravi rivers of Himalayan river system. This is the first report on the core gut microbiota of M. masoniana and C. mrigala using Illumina Miseq Sequencing. Gut bacterial diversity of crabs and fishes are studied from the rivers as well as farms. The core microbiome of crab gut samples consists of genera: Bacteroides, Dysgonomonas, Lactobacillus, Leptotrichia, Acinetobacter, Prevotella, Prevotella 1, Pseudomonas, Fusobacterium and Streptococcus. The core microbiome of fish gut samples consists of genera: Acinetobacter, Lactobacillus, Methanosaeta, Prevotella and Pseudomonas. The result shows higher relative abundance of Bacteroides and Lactobacillus in river Ravi than Chenab. Gut bacterial diversity of fishes and crabs of river Chenab is comparatively lower than the river Ravi. Three genera (Bacteroides, Oceanobacillus and Lactococcus) show significant variation (p value < 0.05) in fishes and crabs. Our study generated sequencing data on the gut microbiota of M. masoniana and C. mrigala can establish a base for the development of therapeutic approaches in dealing with the health conditions of diseased fishes and crabs. Gut microbial characterization will not only help in growth and development of the host but also helps in minimizing the disease susceptibility.}, }
@article {pmid41180871, year = {2025}, author = {Kumari, A and Rao, KVB}, title = {Exploring the Bacterial Diversity of Rajgir Hot Spring in India and its Antibacterial Potential.}, journal = {Indian journal of microbiology}, volume = {65}, number = {3}, pages = {1490-1497}, pmid = {41180871}, issn = {0046-8991}, abstract = {UNLABELLED: Hot springs naturally produce geothermally heated water and are renowned for their diverse microbial communities. Metagenomics studies unveil this microbial diversity. In this study, the bacterial community, along with thermophilic actinobacteria from the Rajgir hot spring, located in Bihar, India, was analyzed using 16S rRNA gene metagenomics sequencing. The sediment temperature was recorded at 45 °C. Investigation of the hot spring ecology revealed the presence of 16 bacterial phyla, with actinobacteria being abundant. Streptomyces, Sphingomonas, Gemmatimonas, Paracoccus, Aeromicrobium, and Actinomyces were among the most common genera found in the sediment samples. These six genera exhibited the highest abundance, with Streptomyces being the most prevalent at 19%, followed by other genera at 13%, 11%, 11%, 10%, and 9%, respectively. Actinobacteria isolated from the hot spring samples were further examined for their antibacterial activities against pathogenic bacteria. Isolates from the Rajgir hot spring demonstrated potential antibacterial activity based on their inhibition zones on agar plates. The results of the antimicrobial screening revealed that AIBRSS1 exhibited the most significant inhibition zone, measuring 26 mm, against Listeria monocytogenes.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12088-025-01482-z.}, }
@article {pmid41180687, year = {2025}, author = {Muhammad Abdur Rehman, A and Rizwan, MH and Khalid, M and Talha, M and Waafira, A}, title = {Revolutionizing endocarditis diagnosis: AI meets metagenomics for rare Bartonella detection.}, journal = {Annals of medicine and surgery (2012)}, volume = {87}, number = {11}, pages = {7772-7773}, pmid = {41180687}, issn = {2049-0801}, abstract = {Bartonella endocarditis is notoriously challenging to diagnose due to its insidious onset, nonspecific symptoms, and the limitations of conventional culture-based techniques. Artificial intelligence (AI)-driven metagenomic next-generation sequencing (mNGS) represents a transformative diagnostic approach by integrating machine learning algorithms with culture-independent sequencing data to improve accuracy and sensitivity. This technique overcomes barriers such as culture bottlenecks and post-surgical sample limitations, achieving high diagnostic specificity while enabling the detection of rare or novel pathogens. Despite challenges including limited reference databases, contamination risks, and cost-related barriers in low-resource settings, AI-enhanced metagenomics offers a promising path toward faster and more precise diagnosis of Bartonella endocarditis. Its integration into clinical workflows, supported by continuous algorithm development, cost optimization, and standardized protocols, has the potential to improve patient outcomes in rare infectious diseases.}, }
@article {pmid41180610, year = {2025}, author = {Deng, Q and Yang, Y and Gao, S and Lu, M and Zhao, Y and Wang, Z}, title = {Integrated Molecular Diagnostics Unmask Legionella Pneumophila and Fungal Coinfection in an Immunocompromised Host: A Case Study of Precision Antimicrobial Stewardship.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {5549-5556}, pmid = {41180610}, issn = {1178-6973}, abstract = {BACKGROUND: Legionella pneumophila poses significant diagnostic challenges in immunocompromised hosts due to its fastidious growth requirements and nonspecific clinical presentation. Conventional culture methods have limited sensitivity (30-80%), while molecular diagnostics require multi-platform validation to ensure reliability.<br><br>CASE DESCRIPTION: A 57-year-old woman with rheumatic heart disease, chronic renal failure, and immunosuppression presented with acute respiratory failure. Initial investigations revealed leukocytosis (19.03&#xd7;10[9]/L), hyponatremia (127 mmol/L), elevated procalcitonin (42.55 ng/mL), and bilateral pulmonary infiltrates. Bronchoalveolar lavage fluid (BALF) analysis employed three molecular methods: isothermal amplification for screening (positive for L. pneumophila on ICU admission), digital PCR (dPCR, 4,455 copies/mL after 10-fold dilution) reconfirmed L. pneumophila infection, and metagenomic next-generation sequencing (mNGS; 384,661 Legionella reads alongside 3,474 Candida glabrata reads). Subsequent fungal &#x3b2;-D-glucan testing (674.8 pg/mL) and culture validated Candida glabrata coinfection. Antimicrobial therapy from targeted moxifloxacin/azithromycin to co-infection therapy with carbapenem escalated from Imipenem-cilastatin to sulbactam/cefoperazone for suspected gram-negative coinfection and fluconazole escalated to amphotericin B for resistant candidiasis guided by CRP/PCT trends.<br><br>CONCLUSION: Integrated molecular diagnostics enable rapid pathogen identification in critically ill immunocompromised hosts. Multi-platform verification (isothermal amplification/dPCR/mNGS) overcomes technical limitations of single methods, while serial biomarker monitoring optimizes antimicrobial stewardship for mixed infections.}, }
@article {pmid41180402, year = {2025}, author = {Chen, C and Xu, D and Jiang, B and Lu, X and Yu, C and Wang, Y and Wang, H and Li, J and Zhu, J}, title = {Precipitation-driven restructuring of rhizosphere microbiota enhances alpine plant adaptation.}, journal = {Frontiers in plant science}, volume = {16}, number = {}, pages = {1641511}, pmid = {41180402}, issn = {1664-462X}, abstract = {INTRODUCTION: Climate-driven precipitation changes are increasingly threatening alpine ecosystems, yet the adaptive responses of soil microbiomes to rainfall variability remain poorly characterized. This knowledge gaphinders our ability to predict ecosystem resilience under future climate scenarios.<br><br>METHODS: We combined metagenomic sequencing with detailed physicochemical analyses to examine how natural precipitation events reshape the microbial communities in both rhizosphere and bulk soils associated with Poa alpigena in the alpine sandy ecosystems of Qinghai Lake.<br><br>RESULTS: Rainfall significantly reduced bacterial alpha diversity, particularly in bulk soils, and triggered a compositional shift from drought-resistant taxa (e.g., Geobacter, Pseudomonas) to moisture-adapted genera (e.g., Azospirillum, Methylobacterium). Actinobacteria remained consistently dominant (31.56-34.62%), while Proteobacteria abundance decreased markedly in the rhizosphere post-rainfall. Metabolic reconstruction revealed a transition from pre-rainfall carbohydrate catabolism to post-rainfall anaerobic energy production and carbon fixation pathways. The rhizosphere microbiome uniquely displayed drought-induced biofilm formation and rainfall-enhanced branched-chain amino acid metabolism. Soil moisture and total carbon were identified as primary drivers of microbial restructuring in bulk soils, whereas root exudates conferred stability to rhizosphere communities against hydrological fluctuations.<br><br>DISCUSSION: These results elucidate microbiome-mediated adaptive strategies to precipitation changes in alpine sandy ecosystems, highlighting the critical buffering role of plant-microbe interactions. The study provides a mechanistic basis for predicting and restoring climatevulnerable wetlands under increasingly variable hydrological regimes.}, }
@article {pmid41180097, year = {2025}, author = {Jin, S and Meng, S and Huang, Q and Xie, H and Zheng, J and Wang, R}, title = {Joint application of multiplex drop-off digital PCR, droplet digital PCR, and metagenomic next-generation sequencing for the diagnosis of suspected infectious diseases: A retrospective cohort study.}, journal = {Journal of intensive medicine}, volume = {5}, number = {4}, pages = {407-418}, pmid = {41180097}, issn = {2667-100X}, abstract = {BACKGROUND: Critically ill patients in ICUs are highly vulnerable to infectious diseases. Early and accurate identification of pathogens is vital for initiating appropriate antimicrobial therapy. To evaluate the diagnostic effectiveness in patients with suspected infectious diseases; three different molecular technologies and conventional microbiological tests were used.<br><br>METHODS: A total of 97 individuals suspected of having infectious diseases were retrospectively enrolled from July 2023 to January 2024 at Shanghai General Hospital. Samples were collected for metagenomic next-generation sequencing (mNGS), droplet digital polymerase chain reaction (ddPCR), multiplex drop-off digital polymerase chain reaction (MDO-dPCR), and conventional microbiological tests (CMTs) for suspected pathogen detection. The diagnostic efficacies of the three molecular technologies and CMTs were compared, and the effects of their joint application on clinical outcomes were evaluated. Intergroup comparisons were performed using the Kruskal-Wallis test, with a P-value <0.05 considered statistically significant.<br><br>RESULTS: Joint detection exhibited a high negative predictive value. The sensitivity of MDO-dPCR, ddPCR, and mNGS was 52.6%, 48.5%, and 96.6%, respectively; and the corresponding specificity was 72.5%, 73.3%, and 50.0%. A positive correlation was observed between pathogen copies detected using MDO-dPCR and procalcitonin (Pearson's &#x3c1;=0.21, P=0.039), acute physiology and chronic health evaluation II (Pearson's &#x3c1;=0.24, P =0.018), and sequential organ failure assessment (Pearson's &#x3c1;=0.25, P=0.012). Therapeutic regimens were adjusted in 51.5% of the patients (50/97) based on the results of the combination tests.<br><br>CONCLUSIONS: In the present study, we highlighted the significance of molecular technologies for the early diagnosis of patients with suspected infections. These technologies can serve as a complement to CMTs and should be implemented promptly to guide clinicians in providing timely and effective anti-infective treatments. Future studies should aim to confirm these findings in large-scale clinical trials to refine diagnostic protocols, while also incorporating cost-utility analyses.}, }
@article {pmid41179961, year = {2025}, author = {Schnabel, E and Xavier, CAD and Whitfield, AE and Dubrow, Z and Pham, G and Cieniewicz, E}, title = {Exploring the Virome of Blackberry and Wild Rubus spp. in South Carolina.}, journal = {Phytobiomes journal}, volume = {9}, number = {1}, pages = {80-94}, pmid = {41179961}, issn = {2471-2906}, abstract = {Numerous viruses infect blackberry, and they are associated with virus disease complexes with complicated etiologies. Blackberry virus diseases limit the lifespan of blackberry production in the Southeastern United States. Although some previous research has been conducted to understand which viruses are prevalent in South Carolina, a comprehensive study on the virome of blackberry has not been done in this region. Additionally, the role of wild Rubus as a virus inoculum source is likely underappreciated and represents a potential opportunity for disease management. We took a comprehensive approach to characterize viral genome sequences from known and novel viruses using metatranscriptomic sequencing of blackberry and wild Rubus spp. leaf samples collected in 2021 from eight sites across South Carolina. We detected 17 known and 6 novel plant viruses and describe relevant genome sequence information. Although the etiologies of these novel viruses are yet to be elucidated, they should be considered part of the blackberry/wild Rubus virome and further studied. We describe instances of potential connectivity of virus populations between cultivated blackberry and wild Rubus for several viruses at several sites. In addition to plant viruses, we describe numerous viruses likely associated with foliar fungi, referred to as Rubus leaf-associated viruses. This study revealed a diverse landscape of both known and novel viruses in blackberry and wild Rubus in South Carolina and has stimulated topics for future research, such as temporal analyses of virus spread at the landscape scale and investigating potential vectors and the biological relevance of novel viruses.}, }
@article {pmid41179353, year = {2025}, author = {Carboni, S and Poirier, AC and Peralta-Aguilar, AP and Watsa, M and Erkenswick, G and Melin, AD}, title = {The Scent Gland Microbiomes of Wild Tamarins Provide New Insight Into Microbial Contributions to Olfactory Communication.}, journal = {Ecology and evolution}, volume = {15}, number = {11}, pages = {e72335}, pmid = {41179353}, issn = {2045-7758}, abstract = {The microbiome of mammalian scent glands is thought to contribute to the production of odorant compounds involved in sensory communication. Yet, the extent to which glandular microbiomes contain bacteria relevant to odor production and vary by host species, scent marking behavior, or gland morphology remains poorly understood, particularly in wild animals. We sampled microbes collected from skin swabs of suprapubic and sternal scent glands in wild Peruvian saddleback tamarins (Leontocebus weddelli; n = 19) and emperor tamarins (Tamarinus imperator; n = 20) to better understand glandular microbial communities. We aimed to: (1) profile glandular microbiomes of both species, focusing on odor-related taxa and metabolic pathways, and (2) determine whether suprapubic glands, more often in contact with the external environment, had higher diversity and distinct composition of odor-related taxa and pathways compared to sternal glands. We generated metagenomic reads using short-read DNA shotgun sequencing from glandular swabs. We identified 18 odor-associated microbial taxa in both tamarin species, mainly Staphylococcus and Corynebacterium, and 26 pathways, including pyruvate fermentation and amino acid metabolism. Suprapubic glands had lower Shannon alpha diversity relative to sternal glands, especially in L. weddelli. The glands of L. weddelli also differed in taxonomic composition, with odor-related taxa more abundant in suprapubic glands. Our results provide evidence for the involvement of scent gland microbiomes in host communication biology. Glandular specializations differed not only between closely related tamarin species but also between gland types within the same individuals, suggesting a nuanced pattern of host-microbe coevolution that may shape interactions important for olfactory communication.}, }
@article {pmid41179309, year = {2025}, author = {Yan, L and He, B and Deng, Q and Qiu, Y and Lin, L and Shi, B and Wang, J and Chen, F}, title = {Is systemic inflammation a missing link between oral microbiome and oral squamous cell carcinoma? Results from multi-omics integration analyses.}, journal = {Journal of oral microbiology}, volume = {17}, number = {1}, pages = {2574326}, pmid = {41179309}, issn = {2000-2297}, abstract = {OBJECTIVES: To investigate whether systemic inflammation mediates the relationship between oral microbiome alterations and oral squamous cell carcinoma (OSCC) through multi-omics integration analyses.<br><br>METHODS: Metagenomic sequencing of unstimulated saliva samples from 65 OSCC patients and 65 matched controls was performed. Plasma levels of 34 inflammatory cytokines were profiled using Luminex assay. Six machine learning models identified potential diagnostic microbial markers. Mediation analysis assessed whether inflammation serves as a mechanistic link between oral microbiota and OSCC.<br><br>RESULTS: OSCC patients exhibited reduced species richness and significant beta diversity alterations. Among 155 differential species identified, 25 were enriched in OSCC, including Capnocytophaga sputigena, Gemella haemolysans, Staphylococcus aureus, and several Streptococcus species, with higher abundance in poor oral hygiene conditions. The Boruta-CatBoost model achieved exceptional diagnostic performance (bootstrap AUC&#x2009;=&#x2009;0.991; 5-fold cross-validation AUC&#x2009;=&#x2009;0.947). Functional profiling revealed 22 metabolic pathways over-represented in OSCC, notably lipopolysaccharide biosynthesis. Nine circulating cytokines (IL-22, IL-6, IL-2, CCL5, GM-CSF, IL-1&#x3b2;, TNF-&#x3b1;, IL-18, IFN-&#x3b1;) were significantly elevated in OSCC patients. Mediation analysis revealed that IL-22 partially mediated the effect of Staphylococcus aureus on OSCC risk, while CCL5 mediated associations of Gemella haemolysans and Streptococcus species with OSCC (mediation proportions: 29.9-50.1%).<br><br>CONCLUSION: Our multi-omics integration suggests that systemic inflammation, particularly through IL-22 and CCL5 upregulation, serves as a mechanistic link between specific oral bacteria and OSCC risk, which could provide new strategies for OSCC prevention and early intervention.}, }
@article {pmid41178975, year = {2025}, author = {Li, B and Xu, W and Wang, W and Mao, M and Huang, X and Zhang, E}, title = {Discrepancies in gut microbial communities and serum metabolites of Hu sheep with different backfat thickness.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1667088}, pmid = {41178975}, issn = {1664-302X}, abstract = {Although market demand for lean meat continues to rise, the regulatory mechanisms governing backfat thickness (BFT) metabolism remain poorly understood. This study employed a multi-omics approach to investigate BFT-associated differences in Hu sheep with distinct fat deposition phenotypes. From 160 genetically similar Hu sheep, we selected 12 individuals with non-significant weight differences (P > 0.05) but extreme divergence in BFT [6 high-BFT (HBF) and 6 low-BFT (LBF) individuals]. Using integrated metagenomics and metabolomics, we systematically compared ileal microbial community structure and serum metabolic profiles between the two groups. HBF sheep showed significantly increased adiposity and altered ileal microbiota composition, characterized by elevated abundances of Carnobacterium, Parabacteroides distasonis, Lactiplantibacillus, and Bifidobacterium. Serum metabolomics identified key differential glycerophospholipids-1-(9Z-octadecenoyl)-2-(11Z-eicosenoyl)-glycero-3-phosphate, PE-NMe(15:0/20:3(5Z,8Z,11Z)), PE-NMe2(18:1(9Z)/20:0), and PE-NMe2(18:1(9Z)/22:1(13Z))-all enriched in glycerophospholipid metabolism pathways. Integrated correlation analysis revealed strong associations between P. distasonis abundance and these phospholipids. These results demonstrate BFT-related adaptive remodeling of the serum metabolome and gut microbiota, identifying P. distasonis as a potential modulator of the host-microbe metabolic axis in ovine adiposity regulation.}, }
@article {pmid41178973, year = {2025}, author = {Teixeira, MJ and Barbosa, DJ and Dinis-Oliveira, RJ and Freitas, AR}, title = {Redefining postmortem interval estimation: the need for evidence-based research to bridge science and justice.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1646907}, pmid = {41178973}, issn = {1664-302X}, abstract = {Classical methods for postmortem interval (PMI) estimation have been applied for nearly a century. Contrary to the notion of being simple or easily accessible, these approaches require highly specialized training, including a medical degree, postgraduate specialization in forensic pathology, and extensive practical experience. Classical PMI estimation relies on observable physical and chemical changes in the human cadaver, such as rigor mortis, livor mortis, algor mortis, and transformative processes during decomposition. These methods are fundamental in medicolegal practice but remain largely influenced by environmental and individual variability. Recent advances in forensic research, particularly in microbiology and biochemistry, have introduced innovative approaches that complement traditional methods, offering greater accuracy and reliability, though resource-intensive. Emerging approaches leverage the predictable postmortem succession of microbial communities (thanatomicrobiome) and biochemical alterations in cadaver fluids and tissues. Techniques such as metagenomics, metatranscriptomics, and metabolomics enable detailed analysis of these changes, while computational models and machine learning further refine PMI estimates. Despite advancements, challenges persist, including variability due to environmental factors and limited access to human decomposition data. Integrating multi-omics approaches and artificial intelligence offers a path forward, addressing these limitations and enhancing the accuracy of PMI estimation. This review provides a comprehensive overview of PMI estimation, critically examining classical approaches and highlighting cutting-edge methodologies rooted in thanatomicrobiology and thanatochemistry. We emphasize the transformative potential of multi-omics integration and artificial intelligence in improving PMI accuracy. Importantly, we propose a paradigm shift: redefining PMI estimation through evidence-based, interdisciplinary research that bridges scientific rigor and judicial application. Transdisciplinary collaboration and standardized methodologies will be essential to translate emerging knowledge into robust forensic tools that serve both science and justice.}, }
@article {pmid41178971, year = {2025}, author = {Du, H and Hao, X and Lin, B and Zhu, Y and Yang, Y and Tang, M and Wu, W and Wang, D and Lin, B and Liang, Y and Tang, W and Xu, H and Li, J and Gao, F and Du, X}, title = {Exploring the role of intestinal microbiota in mitigating acute radiation-induced intestinal injury through high-energy X-ray FLASH radiotherapy via metagenomic analysis.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1601244}, pmid = {41178971}, issn = {1664-302X}, abstract = {OBJECTIVES: This study preliminarily examines the potential correlation between the gut microbiome and the protective effects of FLASH radiotherapy (FLASH-RT) on intestinal tissue using metagenomic analysis.<br><br>METHODS: Compact single high-energy X-ray source (CHEXs) FLASH-RT was employed for FLASH irradiation, while EBT3 radiochromic film and a fast current transformer were used to measure the absolute dose and the pulsed beam characteristics. Sham radiotherapy (control), FLASH-RT (333&#x202f;Gy/s), and Conventional dose rate radiotherapy (CONV-RT, 0.07&#x202f;Gy/s) were performed on whole abdomen of normal C57BL/6J female mice (10&#x202f;Gy, 12&#x202f;Gy, 14&#x202f;Gy). At 72&#x202f;h post-irradiation, intestinal contents from normal C57BL/6J female mice were collected for metagenomic analysis. The survival status, body weight, and damage to normal tissues were observed.<br><br>RESULTS: At 28&#x202f;days post-whole abdomen irradiation with doses of 12&#x202f;Gy, the survival rate of the FLASH group was higher than that of the CONV group (p&#x202f;<&#x202f;0.05). Histological analysis of intestinal tissues by H&amp;E staining revealed significantly less acute intestinal damage and inflammation in the FLASH group compared to the CONV group. Further macrobiome analysis using LEfSe indicated that the abundance of beneficial bacteria, including Weissella, Lactobacillus ruminis and Lactobacillus taiwanensis was significantly higher in the FLASH group than in the CONV group. Moreover, compared to the CONV group, the FLASH group exhibited significant upregulation of several signaling pathways, including the glycosaminoglycan degradation, PI3K/Akt and arabinogalactan biosynthesis Mycobacterium signaling pathway.<br><br>CONCLUSION: Compared to CONV-RT, high-energy X-ray FLASH irradiation exerts radioprotective effects on normal intestinal tissue. Alterations in the gut microbiota and associated signaling pathways may be linked to the protective effects of FLASH.}, }
@article {pmid41178960, year = {2025}, author = {Abildinova, GZ and Benberin, VV and Vochshenkova, TA and Mussin, NM and Afshar, A and Tamadon, A}, title = {Distinct gut microbial species, but not phylum-to-genus composition, associate with insulin resistance: a unique perspective from the Kazakh population.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1683885}, pmid = {41178960}, issn = {1664-302X}, abstract = {OBJECTIVES: Links between gut microbiota and insulin resistance (IR) vary across populations. We profiled the fecal microbiota of Kazakh adults to test whether community composition associates with IR at broad (phylum → genus) and species levels.<br><br>METHODS: In a cross-sectional case control study (N&#x202f;=&#x202f;200; IR&#x202f;=&#x202f;183, controls&#x202f;=&#x202f;17), TyG indexed IR status. 16S rRNA sequencing (two primer pools; nine hypervariable regions) characterized taxa. After CSS normalization, we compared presence/absence across groups (&#x3c7;[2]) and modeled species with univariate and multivariable logistic regressions, using absence of each species as the predictor.<br><br>RESULTS: High-level composition did not differ between IR and controls (phylum, class, family, genus; all p&#x202f;>&#x202f;0.05). In contrast, several species differed. In univariate models, absence of Actinomyces odontolyticus (OR&#x202f;=&#x202f;25.55, p&#x202f;=&#x202f;0.010), Bifidobacterium kashiwanohense (OR&#x202f;=&#x202f;12.69, p&#x202f;=&#x202f;0.015), Lactobacillus sp. (OR&#x202f;=&#x202f;5.71, p&#x202f;=&#x202f;0.020), and Streptococcus lactarius (OR&#x202f;=&#x202f;6.27, p&#x202f;=&#x202f;0.044) associated with higher IR odds, suggesting protection when present; whereas absence of Alistipes onderdonkii (OR&#x202f;=&#x202f;0.30, p&#x202f;=&#x202f;0.044) and Prevotella copri (OR&#x202f;=&#x202f;0.19, p&#x202f;=&#x202f;0.003) associated with lower IR odds, suggesting risk when present. In multivariable models, these signals persisted: absence of P. copri (OR&#x202f;=&#x202f;0.146, p&#x202f;=&#x202f;0.003) and Roseburia inulinivorans (OR&#x202f;=&#x202f;0.143, p&#x202f;=&#x202f;0.011) predicted lower IR odds (risk alignment), while absence of Lactobacillus sp. (OR&#x202f;=&#x202f;8.29, p&#x202f;=&#x202f;0.016) and Coprococcus catus (OR&#x202f;=&#x202f;7.04, p&#x202f;=&#x202f;0.004) predicted higher IR odds (protective alignment).<br><br>CONCLUSION: In this Kazakh cohort, no broad compositional signal emerged, but species-specific associations were strong and bidirectional. Findings highlight population-specificity and identify candidate species associated with IR that may serve as hypothesis-generating targets for future validation. Any attempt to modulate these taxa for insulin resistance is unproven and requires function-resolved, diet-measured longitudinal studies and randomized trials before clinical application. The IR:control imbalance (183:17) increases uncertainty for low-prevalence taxa; species-level findings are hypothesis-generating and require validation in a more balanced design. Because 16S rRNA profiling does not measure gene functions or metabolites, these species-IR associations are hypothesis-generating and warrant validation using shotgun metagenomics and metabolomics.}, }
@article {pmid41177622, year = {2026}, author = {Sun, C and Zhao, W and Yue, W and Cheng, H and Long, A and Yin, J and Sun, F and Wang, Y}, title = {Degradation of polymeric carbohydrates coupled with cellular motility driving microbial niche separation in the Pearl River Estuary surface sediment.}, journal = {Journal of environmental sciences (China)}, volume = {160}, number = {}, pages = {414-423}, doi = {10.1016/j.jes.2025.04.032}, pmid = {41177622}, issn = {1001-0742}, mesh = {*Geologic Sediments/microbiology/chemistry ; *Estuaries ; Rivers/microbiology ; Carbohydrates ; Metagenome ; *Carbohydrate Metabolism ; }, abstract = {Estuaries are key areas for organic carbon cycling, where polymeric carbohydrates are abundant and chemically diverse. The recycling of these polymers by microbes depends on a variety of carbohydrate-active enzymes (CAZymes). However, it remains unclear whether other gene traits, particularly those related to cell motility toward polymeric carbohydrates, are intertwined with carbohydrate depolymerization and niche specialization in estuarine sediment soils. In this study, estuarine sediments were incubated with four prevalent polymeric carbohydrates (laminarin, fucan, cellulose, and chitin) under anaerobic conditions. Based on metagenomic analysis, we identified potential responses to the degradation and utilization of polymeric carbohydrate substrates from the perspectives of CAZymes and sugar transporters. The analysis of metagenomic gene data also revealed a positive correlation between chemotaxis and the abundance of CAZymes genes. Furthermore, metagenomes-assembled genomes (MAGs) that exhibited higher abundance in polysaccharide-treated samples compared to controls also featured elevated copies of genes involved in polysaccharide utilization loci (PULs), chemotaxis, as well as those associated with flagellar or gliding movement. SprB and CTDs associated with gliding proteins genes are essential for type IX secretion system-mediated secretion of CAZymes and gliding motility in Bacteroidota. The enhanced potential for mobility, coupled with the ability to degrade polymeric carbohydrates, may enable these bacteria to exploit nutrients beyond carbon sources, thereby potentially broadening their ecological niches.}, }
@article {pmid41177619, year = {2026}, author = {Yang, R and Wei, Y and Jiang, J and Kong, X and Wu, S and Tang, Q and Liu, Y and Luo, L and Ali, EAE and Chen, H}, title = {Adaptation of microbial gene polymorphisms of the partial nitritation-anammox process for maintaining denitrification performance and robustness under salinity stress.}, journal = {Journal of environmental sciences (China)}, volume = {160}, number = {}, pages = {39-50}, doi = {10.1016/j.jes.2025.04.028}, pmid = {41177619}, issn = {1001-0742}, mesh = {*Denitrification ; *Salt Stress ; Bioreactors/microbiology ; *Waste Disposal, Fluid/methods ; Wastewater ; Salinity ; Ammonium Compounds/metabolism ; Nitrification ; Bacteria/genetics ; }, abstract = {To explore the adaptive mechanisms of the partial nitritation-anammox (PNA) process under high salinity stress during kitchen wastewater treatment, focusing on their physiological and molecular responses through metagenomic analysis. An airlift inner-circulation partition bioreactor (AIPBR) was developed, featuring an inner cylinder and a flow guide tube to create distinct oxygen gradients, facilitating the study of microbial adaptation under varying salt conditions. The AIPBR was operated with synthetic wastewater containing ammonium concentrations of 1800 ± 100 mg/L and salinity gradients ranging from 1 to 10 g/L, followed by a fixed salinity period at 6 g/L, with ammonium concentrations approximately 850 mg/L. High-throughput metagenomic analysis revealed shifts in functional genes and metabolic pathways in response to salinity stress. Anammox bacteria adapted by enriching genes involved in the synthesis of osmoprotective compounds and activating energy-producing pathways like the tricarboxylic acid cycle (TCA). These adaptations, along with modifications in membrane composition, were essential for sustaining system stability under elevated salinity. Under prolonged high salinity stress, anaerobic ammonium oxidizing (AnAOB) exhibited improved salt tolerance, maintaining a total nitrogen removal efficiency above 85 % and stabilizing after an adaptation phase. The metagenomic data revealed a marked enrichment of genes associated with ion transport, stress response mechanisms, and DNA repair pathways. Changes in microbial community composition favored salt-tolerant species, supporting system stability. These findings highlight the applicability of the developed bioreactor for scaling up the PNA process to handle high-salinity wastewater, providing a promising avenue for sustainable nitrogen removal in challenging environments.}, }
@article {pmid41177609, year = {2026}, author = {Lu, N and Du, Z and Feng, G and Xin, X and Che, M and Jia, R and Chu, W}, title = {Metagenomic investigations of microbial community response and antibiotic resistance genes in river sediments polluted by perfluoroalkyl acids.}, journal = {Journal of environmental sciences (China)}, volume = {160}, number = {}, pages = {300-307}, doi = {10.1016/j.jes.2025.04.024}, pmid = {41177609}, issn = {1001-0742}, mesh = {*Fluorocarbons/analysis/toxicity ; *Water Pollutants, Chemical/analysis/toxicity ; *Geologic Sediments/microbiology/chemistry ; Rivers/microbiology/chemistry ; *Drug Resistance, Microbial/genetics ; China ; *Environmental Monitoring ; Metagenomics ; *Microbiota/drug effects ; Caprylates/toxicity ; }, abstract = {Liquid-solid phase transfer promotes the interaction of perfluoroalkyl acids (PFAAs) with the microbial system of river sediments, which may affect the environmental behavior of antibiotic resistance genes (ARGs) contained in benthic environments. Sediments collected from the receiving water of the largest fluoropolymer production facility in China were analyzed to investigate the impact of PFAAs on microbial communities and ARG profiles. The main contributors to the PFAAs were perfluorooctanoic acid and perfluorobutanoic acid, whose proportions (86.9 %-93.4 %) in the downstream surface sediments affected by industrial effluents were significantly higher than in the corresponding upstream samples (53.3 %). A reduction in microbial diversity and richness was observed in the presence of high concentrations of PFAAs at the downstream sites. 144 ARG subtypes, including three high-risk subtypes (bacA, aac (6')-I and aadA), were identified in sediment samples. The discharge of fluorochemical effluents also results in a reduction of ARG diversity at subtype level. PFAAs exert a pronounced influence on the profile of ARGs in sediment. PFAAs and water quality parameters (e.g. pH and total phosphorus) were key drivers of the microbial community composition in the sediment. The regulation of microbial communities by PFAAs may represent an important pathway by which these compounds affect ARG profiles.}, }
@article {pmid41177409, year = {2025}, author = {Lin, S and Pan, M and Ma, Y and Chen, Z and Lyu, T and Dong, R and Ruan, R and Liu, S}, title = {Microalgae-mediated shaping of bacterial communities enhances antibiotic removal and antibiotic resistance control.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {133577}, doi = {10.1016/j.biortech.2025.133577}, pmid = {41177409}, issn = {1873-2976}, abstract = {The microalgae-bacteria symbiosis sludge (MBSS) system offers a promising strategy for efficient wastewater treatment and nutrients upcycling. However, maintaining stable and effective performance facing antibiotic stress remains a significant challenge. This study explored the regulation strategy of microbial succession towards sulfadiazine (SDZ)-containing wastewater remediation while controlling antibiotic resistance genes (ARGs) spread in MBSS system. The MBSS achieved efficient SDZ removal of up to 99.8%, with an optimal microalgae-to-activated sludge inoculation ratio of 1:3. However, the highest nutrient upcycling efficiencies (33.7% for nitrogen and 98.6% for phosphorus) were observed at an inoculation ratio of 1:1. Metagenomics analysis revealed that genera Chlorella and Micractinium of Chlorophyta were strongly positively correlated with SDZ removal. Moreover, microalgae inoculation significantly modulated the microbial community structure, promoting the dominance of genera Rhodanobacter and Dokdonella in MBSS. This microbial succession could potentially facilitate bacterial co-degradation of SDZ and contribute to a substantially reduced level of ARGs (with the relative abundance of sul1 and sul2 decreasing to 22.9% post-treatment). Overall, the strategy of regulating microalgae inoculation in the MBSS significantly enhanced antibiotic removal and nutrient recovery while controlling the proliferation and spread of ARGs by directing microbial community succession.}, }
@article {pmid41177051, year = {2025}, author = {Guo, Y and Lin, X and Song, B and Zhao, C and Riaz, M and Ishfaq, M}, title = {Biochar remodeled rhizosphere microbial community structure and function to alleviate sugar beet under fomesafen phytotoxicity.}, journal = {Journal of environmental management}, volume = {395}, number = {}, pages = {127821}, doi = {10.1016/j.jenvman.2025.127821}, pmid = {41177051}, issn = {1095-8630}, abstract = {Residual fomesafen in soybean field soil can adversely affect subsequent sugar beet crops. Biochar has been shown to alleviate this damage, the regulatory mechanisms by which it influences the rhizosphere microbial community and its functions in the presence of fomesafen residues remain unclear. This study employed plant physiological assessments, amplicon sequencing, and metagenomic analysis to investigate root physiology, the rhizosphere soil microbial community, and their functional responses to fomesafen toxicity with biochar addition. By comparing sterilized soil with normal soil, that all measured indices in the sterilized soil were reduced, confirming that biochar mitigates fomesafen phytotoxicity through soil microorganisms. Biochar increased root biomass by 37.50 % under fomesafen residue stress, reduced malondialdehyde content in sugar beet roots, enhanced antioxidant enzyme activity, and improved soil multifunctionality by 13.95 %. Furthermore, biochar significantly restored the richness and diversity of rhizosphere fungi and bacteria under fomesafen residue stress. The relative abundance of Dehalococcoidia, a potential herbicide-degrading bacterium, increased significantly under fomesafen stress (90.32 %) and peaked under biochar mitigation treatment (94.02 %), suggesting its potential as a biomarker for fomesafen residues. Biochar alleviated fomesafen's impact on the microbial network, restoring it to a molecular ecological network similar to the control. Metagenomic analysis revealed that biochar increased the Calvin-Benson-Bassham cycle (29.87 %), the nitrogen fixation pathway (21.42 %), and the phosphate transport pathway (10.60 %). By enhancing soil multifunctionality and reshaping rhizosphere microbial communities, biochar improves the stress resistance of sugar beet roots and mitigates damage caused by fomesafen. This finding is significant for maintaining the microecological balance of the rhizosphere.}, }
@article {pmid41177050, year = {2025}, author = {Su, F and Li, Y and Zhu, C and Gurmesa, GA and Fang, Y}, title = {Impact of freeze-thaw cycle on metagenomics in subsurface wastewater infiltration systems: Ecological implications for greenhouse gas emissions.}, journal = {Journal of environmental management}, volume = {395}, number = {}, pages = {127839}, doi = {10.1016/j.jenvman.2025.127839}, pmid = {41177050}, issn = {1095-8630}, abstract = {Nitrous oxide (N2O) is a potent greenhouse gas, with a global warming potential 273 times that of carbon dioxide (CO2) and is a significant byproduct of wastewater treatment. Subsurface wastewater infiltration systems (SWIS) effectively treat nitrate-rich wastewater but can also contribute to N2O emissions, particularly during freeze-thaw cycles. This study used metagenomics and [15]N isotope tracing to investigate the impacts of freeze-thaw on microbial ecology and nitrogen transformation in SWIS. Results show that freeze-thaw significantly increased abundances of denitrifying bacteria (Bradyrhizobium, Streptomyces and Nocardioides), on average, by 16-63 %. Denitrification genes (nirK and norB) were also increased by 40 ± 16 % and 22 ± 5 %, while the N2O reductase gene (nosZ) decreased by 19 ± 0.46 %. These impacts collectively increased N2O emissions by more than 20 %. During freezing, about one-third of the added [15]NO3[-]-N was recovered as gas (25 % as N2O and 13 % as N2), increasing to 43 % during thawing (29 % N2O and 15 % N2). This study underscores the need for targeted strategies N2O emission in SWIS, particularly under freeze-thaw conditions, to maximize their sustainability in wastewater treatment.}, }
@article {pmid41177031, year = {2025}, author = {Faghihinezhad, M and Eshghdoostkhatami, Z and Bernstein, A and Cupples, AM}, title = {Identification of the dominant methanotrophs in trichloroethene degrading enrichment cultures from multiple sources.}, journal = {Journal of hazardous materials}, volume = {499}, number = {}, pages = {140268}, doi = {10.1016/j.jhazmat.2025.140268}, pmid = {41177031}, issn = {1873-3336}, abstract = {The current study examined the potential of bioremediation to clean up trichloroethene (TCE) contaminated sites using co-metabolic TCE biodegradation in methanotrophic enrichment cultures. Methanotrophic cultures were developed from both uncontaminated soils (agricultural soils) and impacted sediment from two sites. Following the enrichment of methanotrophs, the cultures were tested for their ability to degrade TCE. Whole genome sequencing data indicated the dominance of the genus Methylocystis and, to a lesser extent, the genera Methylobacter and Methylomicrobium. Fourteen Methylocystis, Methylobacter and Methylomicrobium metagenome assembled genomes (MAGs) were obtained. Twelve particulate methane monooxygenase operons (pmoCAB) were also obtained. The collected operons contained sequences similar to those classifying within the genera Methylocystis, Methylobacter and Methylomicrobium phylotypes. Three operons (mmoXYBZDC) were obtained for soluble methane monooxygenase, with mmoX classifying most closely to other Methylocystis mmoX genes. The newly obtained sequences were compared to commonly used primers for the biomarkers pmoA (A189f and mb661r) and mmoX (536 f and 898r). In summary, TCE degrading methanotrophic cultures were easily developed from both uncontaminated soils and impacted sediments and whole genome sequencing data indicated the importance of the genus Methylocystis across many of the methanotrophic enrichments.}, }
@article {pmid41177025, year = {2025}, author = {Singh, DP and Bijalwan, V and Poonam, J and Lal, R and Palkhade, R and Viramgami, A and Vidhani, H and Kumar, A and Bishnoi, M and Das, S}, title = {Bisphenol-A at an environmentally plausible dose caused gut microbiota-led impaired cognitive performances in adult mice.}, journal = {Journal of hazardous materials}, volume = {499}, number = {}, pages = {140254}, doi = {10.1016/j.jhazmat.2025.140254}, pmid = {41177025}, issn = {1873-3336}, abstract = {Omnipresent Bisphenol-A (BPA) exposure is linked to neurobehavioral deficits and gut dysbiosis. However, studies assessed its impact on cognitive performance at environmentally unrealistic doses. Nevertheless, the exact mechanism underlying the neurobehavioral phenotype, linking the role of gut microbiota is poorly understood. Here, we evaluated the effects of environmentally plausible dose of BPA-exposure on cognitive task performances with the functional analysis of gut metagenome to elucidate the role of microflora-gut-brain axis in behavioural regulation. Swiss albino mice were exposed to BPA for 5 weeks assessed for working and spatial navigation task performances. qRT-PCR based gene expression, histological investigation, gut permeability, molecular and biochemical markers of neuro-inflammation, leaky gut, oxido-nitrosative stress and 16 s rRNA gene based metagenomics with functional analysis were performed. BPA exposure altered the cognitive task performances (mean difference for transfer latency in elevated plus maze 20.84 ± 5.64 sec in and -13.12 ± 3.53 in Morris' water maze), changed serotonin levels (-70.95 ± 21.43) and acetylcholinesterase activity (0.0032 ± 0.0008), enhanced ileal permeability (12.36 ± 3.56) and systemic and tissue level inflammation (increased brain LPS, TNF-a, IL-1b, IL-6 and circulating TNF-a and IL-1b), coupled with reduced SCFAs levels (acetate; 32.48 ± 8.48, and butyrate; 28.16 ± 9.86). Faecal microbial transplant cohort replicated similar behavioural, biochemical and molecular patterns, suggesting the role of gut-microbiota in the phenotype determination. Functional pathways prediction suggested altered serotonin, dopamine, SCFAs metabolism and LPS biosynthesis. BPA at a much lower but environmentally relevant dose altered the cognitive performances, which has potential linkage to gut-microbiota mediated pathways.}, }
@article {pmid41176044, year = {2025}, author = {Sodré, IC and Prist, PR and Mancini, MCS and Bettoni-Rodríguez, G and de Andreazzi, CS and Tambosi, LR and Dos Santos, AFA and da Costa, MDF and Bueno, MG}, title = {Forest cover influences the fecal virome of Oligoryzomys nigripes in Atlantic Forest remnants, Brazil.}, journal = {Acta tropica}, volume = {}, number = {}, pages = {107894}, doi = {10.1016/j.actatropica.2025.107894}, pmid = {41176044}, issn = {1873-6254}, abstract = {Landscape changes driven by human activities can alter host-pathogen interactions, favoring generalist mammal species that act as reservoirs for zoonotic pathogens, potentially leading to spillover events and outbreaks. Here, we investigated how forest cover influences viral diversity in Oligoryzomys nigripes, a generalist rodent known to harbor zoonotic viruses in the Brazilian Atlantic Forest. We employed high-throughput sequencing to explore the fecal virome of 20 specimens collected across three landscapes with varying forest cover (20%, 40%, and 60%) within Atlantic Forest fragments in São Paulo state. We identified 48 viral families, predominantly bacteriophages and vertebrate-associated viruses. Some, found for the first time in this host, exhibited zoonotic potential, including Papillomaviridae, Herpesviridae, Polyomaviridae, Adenoviridae, Alloherpesviridae, Arenaviridae, Paramyxoviridae, Peribunyaviridae, and Picornaviridae. Alpha and beta diversity indices were used to assess the viral community structure. Although alpha diversity indices did not show a statistically significant difference among landscapes, a significant compositional difference in viral community was detected through beta diversity index (Jaccard dissimilarity), indicating that forest cover may shape the composition of viral families present. The presence of a core virome shared across all landscapes, including families with pathogenic potential, reinforces O. nigripes role as a natural reservoir. While forest cover influences viral community structure, it doesn't necessarily reflect greater ecological complexity within fragments, indicating that other landscape-related factors must also be considered. This pioneering study characterizes the fecal virome of O. nigripes, revealing how forest cover may shape viral communities in wild rodents and underscoring their potential for zoonotic virus surveillance.}, }
@article {pmid41175772, year = {2025}, author = {Eshghdoostkhatami, Z and Li, Z and Faghihinezhad, M and Cupples, AM}, title = {Characterization of propanotrophic enrichments from agricultural soils capable of 1,4-dioxane biodegradation to sub-μg/L levels.}, journal = {The Science of the total environment}, volume = {1005}, number = {}, pages = {180824}, doi = {10.1016/j.scitotenv.2025.180824}, pmid = {41175772}, issn = {1879-1026}, abstract = {Major challenges to 1,4-dioxane bioremediation concern chemical characteristics that result in migration and persistence, often resulting in large and dilute plumes. In this study, the objectives were to 1) develop propanotrophic enrichment cultures from agricultural soils and determine if they could degrade high and low concentrations of 1,4-dioxane, 2) investigate the feasibility of bioaugmentation for 1,4-dioxane biodegradation in laboratory microcosms and 3) identify dominant propanotrophs and propane monooxygenase genes in the propanotrophic enrichments. Agricultural soils were selected as inocula as they commonly contain microorganisms capable of the biodegradation of a wide range of agricultural chemicals. Propanotrophic enrichment cultures were established from three soils by repeatedly amending propane. Following this, the biodegradation trends for high (3 mg/L) and low (∼200 μg/L) concentrations of 1,4-dioxane were investigated. The experiments also involved bioaugmentation to impacted site sediment microcosms. Prior to their use in bioaugmentation, DNA was extracted from the propanotrophic cultures for shotgun sequencing and analyses with KBase. The easy development of propanotrophic enrichments from agricultural soils suggests a natural abundance of propanotrophs in the soils. Rapid (often <2 weeks) 1,4-dioxane biodegradation was observed in the enrichment cultures at high or low 1,4-dioxane concentrations. 1,4-Dioxane was degraded close to or below the limit of detection (0.46 μg/L) following bioaugmentation. Eighteen propanotrophic metagenome assembled genomes, classifying as Methylibium, Mycobacterium, Rhodococcus opacus, Rhodococcus wratislaviensis and Mesorhizobium, contained full propane monooxygenase operons. Sequences for twenty-two propane monooxygenase operons were retrieved. Sequences for one subunit (prmA) were compared to the closest matches in GenBank. Overall, the developed cultures have potential for use in bioaugmentation to address in situ 1,4-dioxane contamination.}, }
@article {pmid41147335, year = {2025}, author = {Gurnani, B and Kaur, K}, title = {Advancing diagnostics in Pythium insidiosum keratitis: the emerging role of point-of-care imaging and biosensor-based detection devices.}, journal = {Expert review of medical devices}, volume = {}, number = {}, pages = {1-6}, doi = {10.1080/17434440.2025.2582616}, pmid = {41147335}, issn = {1745-2422}, abstract = {INTRODUCTION: Pythium insidiosum keratitis (PIK) is a rapidly progressive, aggressive corneal infection that closely mimics fungal keratitis but fails to respond to conventional antifungal therapy. Misdiagnosis and delayed intervention frequently result in poor outcomes, including high rates of therapeutic keratoplasty and irreversible vision loss. Timely and accurate identification is therefore vital, yet conventional microbiological methods are slow, and histopathology is invasive and often inconclusive. Recent advances in imaging, molecular diagnostics, and biosensor technology are revolutionizing diagnostic possibilities.<br><br>AREAS COVERED: Modern tools such as anterior segment optical coherence tomography (AS-OCT) and in vivo confocal microscopy(IVCM) permit rapid, noninvasive visualization of characteristic stromal patterns. Molecular platforms, including PCR, loop-mediated isothermal amplification (LAMP), recombinase polymerase amplification (RPA), and multiplex panels, provide precise results within hours. Innovative lateral flow immunoassays (LFIA), aptamer-based electrochemical biosensors, and artificial intelligence (AI)-assisted image interpretation expand point-of-care capabilities, while metagenomic sequencing aids in culture-negative cases.<br><br>EXPERT OPINION: The integration of imaging, molecular, and biosensor modalities marks a paradigm shift in PIK diagnostics. PortableAS-OCT, handheld IVCM, and rapid multiplex panels promise to reduce diagnostic delay, minimize unnecessary antifungal use, lower keratoplasty rates, and improve visual prognosis. Collaborative validation and affordable access remain essential for global impact.}, }
@article {pmid41175763, year = {2025}, author = {Lv, Z and Liu, Z and Li, D and Cai, M and Liu, J and Zhang, XH and Shi, X}, title = {Anthropogenic PAHs reshape sedimentary microbiomes and ecotoxicological risks in polar regions: A pan-Arctic/Antarctic metagenomic study.}, journal = {Journal of hazardous materials}, volume = {499}, number = {}, pages = {140321}, doi = {10.1016/j.jhazmat.2025.140321}, pmid = {41175763}, issn = {1873-3336}, abstract = {The analysis of the composition and functional gene responses of sedimentary microbial communities to polycyclic aromatic hydrocarbons (PAHs) is essential for evaluating the pollution status of PAHs in polar regions. PAH concentrations and microbiome characteristics are quantified using advanced instrumental detection combined with metagenomic analysis. Overall, PAHs exhibit relatively high levels of contamination in polar regions, whereas variations in the abundance of functional genes indicate potential degradation propensities among different sedimentary microbial communities. The PAHs in the study area are primarily attributed to fossil fuel combustion, with local anthropogenic emissions considered the main drivers of contaminant accumulation. Sedimentary bacterial communities and their functions are significantly influenced by PAH contamination. Correlation analysis identifies 4H-Naphthalene, Naphthalene, 1-Indanone, Anthracene, Benzo[c]phenanthrene and 1,4-Naphthoquinone as the most critical compounds affecting microbial communities. The co-occurrence of PAH degradation genes with nitrogen- and sulfur-cycling genes in several MAGs suggests that PAH biodegradation may be enhanced through the utilization of nitrate and sulfate as electron acceptors. Within a pan-Arctic and Antarctic framework, the responses of sedimentary microbiomes to PAH contamination are examined, providing novel insights into the comprehensive evaluation of PAH pollution levels and associated ecological risks in polar regions.}, }
@article {pmid41175752, year = {2025}, author = {Ding, W and Chen, B and Song, M and Liu, M and Lv, B and Qiu, D and Zhu, Y and Zhang, Z and Zhang, M and Zhang, R and Lu, T and Qian, H}, title = {Different effects of heterocyclic compounds on the diversity and functions of soil microbiota.}, journal = {Journal of hazardous materials}, volume = {499}, number = {}, pages = {140318}, doi = {10.1016/j.jhazmat.2025.140318}, pmid = {41175752}, issn = {1873-3336}, abstract = {Heterocyclic compounds are extensively used in pharmaceuticals and agrochemicals, yet their persistence and bioavailability in soil may disrupt microbial functions and ecosystem health. To address these impacts, we performed a metagenomic sequencing to assess the impact of three such compounds--cefapirin, pyrimethanil, and quinclorac on soil microbial communities at 15 and 30 d exposure. Our results revealed distinct compound-specific and time-dependent effects. Cefapirin initially induced minimal changes at 15 days but significantly reduced eukaryotic diversity and functional potential by 30 days, while also enriching virulence factors. Pyrimethanil strongly perturbed the community at 15 days, suppressing metabolic pathways and elevating the abundance of antibiotic resistance genes (ARGs) and virulence factors, along with consistently enriching mobile genetic elements (MGEs) associated with these genes-though some effects diminished by 30 days. Quinclorac exerted comparatively milder inducing subtle shifts in virulence factor profiles and exerting limited influence on antibiotic resistance gene abundance. Spearman correlation analysis linked compound-induced shifts in dominant microbial phyla (notably Pseudomonadota and Actinomycetota) to the dynamics of ARGs and virulence factors. These results underscore that the ecological risks of heterocyclic compounds depend critically on both compound properties and exposure duration. Our findings provide valuable insights for guiding risk assessment and sustainable practices to mitigate the ecological risks of agrochemicals.}, }
@article {pmid41175696, year = {2025}, author = {Li, N and Zhang, Y and Qu, Z and Xu, J and Ming, A and Sun, H and Huang, L}, title = {Rhizosphere resilience: Exploring microbial diversity and metabolic responses in long-term eucalyptus plantations.}, journal = {Microbiological research}, volume = {303}, number = {}, pages = {128381}, doi = {10.1016/j.micres.2025.128381}, pmid = {41175696}, issn = {1618-0623}, abstract = {The large-scale cultivation of eucalyptus has led to significant ecological challenges, such as declines in soil microbial diversity and soil degradation. To address these issues, management practices incorporating nitrogen-fixing species and adjusted rotation periods have been proposed. However, their impacts on rhizosphere soil microorganisms and metabolites remain insufficiently understood. This study employed metagenomic and untargeted metabolomics techniques to investigate the response of rhizosphere microorganisms and metabolites in eucalyptus plantations under different management regimes: monoculture plantation, plantation mixed with a nitrogen-fixing tree species, monoculture second-generation plantation, and second-generation mixed plantation. The results revealed that mixed plantation increased microbial diversity compared to continuous cropping. In contrast, second-generation monoculture led to a loss of unique microbial species and reduced microbial community stability compared to the first-generation monoculture. In nutrient-poor pure second-generation plantations, the bacterium Gemmatimonadetes (relative abundance: PF: 0.13 %, PS: 0.39 %, MF: 0.14 %, MS: 0.21 %)-which plays a key role in soil phosphorus cycle-was enriched. Although continuous cropping improved the organic phosphorus mineralization function, it decreased the abundance of genes related to carbon (rbcL and ppc) and phosphorus cycle (phoP and ppk2). The metabolite fluocinolone is negatively correlated with carbon, nitrogen and phosphorus cycle gene components in our dataset, while echinocystic acid and bezitramide are positively correlated. These findings highlight that mixed plantations enhance the ecological niche of eucalyptus rhizosphere by altering the interaction between rhizosphere microbial composition, function, and host plant metabolism.}, }
@article {pmid41175632, year = {2025}, author = {Patel, AB and Jain, KR and Gupta, V and Lal, R and Madamwar, D}, title = {Structural and functional responses of microbial communities in coastal sediments towards anthropogenic pollution caused by ship breaking activities.}, journal = {Marine environmental research}, volume = {213}, number = {}, pages = {107665}, doi = {10.1016/j.marenvres.2025.107665}, pmid = {41175632}, issn = {1879-0291}, abstract = {Coastal ecosystems, like many others on the planet, face chronic threats from anthropogenic activities. The Alang-Sosiya Ship Breaking Yard (ASSBY) located near Bhavnagar in Gujarat, India, represents one such ecosystem impacted by decades of ship-breaking activities. This study aimed to assess the differences in microbial community composition between polluted coastal samples and pristine samples through high-throughput sequencing. Additionally, microbial co-occurrence networks and genes related to antibiotic and heavy metal resistance were predicted using metagenome mining. The analysis confirmed elevated heavy metal concentrations, particularly iron, in polluted samples. In non-polluted sites, alpha diversity indices showed a high microbial diversity compared to polluted sites. The bacterial communities from Deltaproteobacteria at non-polluted sites noticeably shifted to Gammaproteobacteria at polluted sites. Unclassified reads constituted a significant portion of the bacterial diversity. LEfSe (Linear discriminant analysis Effect Size) analysis identified potential bacterial biomarkers, including Pseudomonas, Halomonas and Rhodovulum, which were differentially abundant at polluted sites and may play roles in the biodegradation of xenobiotic compounds. Moreover, Co-occurrence network analysis validated these bacterial biomarkers from polluted sites and revealed their habitat-specific nature. Polluted metagenomes were enriched with genes related to aromatic compound degradation and stress responses, particularly genes for heavy metal and antibiotic resistance. These findings suggest that chronic pollution from ship-breaking activities has led to a shift in microbial communities, leading to an increased presence of resistance mechanisms in the polluted coastal environment to adapt to prolonged heavy pollution.}, }
@article {pmid41175494, year = {2025}, author = {Ramirez Pavon, JA and Aparecido da Silva Neves, N and de Oliveira Martins, A and Pinho, JB and Juscineide de Souza, V and Patroca da Silva, S and Ribeiro Cruz, AC and Barbosa de Almeida Medeiros, D and Teixeira Nunes, MR and Slhessarenko, RD}, title = {Viral diversity in vertebrates from Alto Pantanal, Mato Grosso, 2019.}, journal = {Virology}, volume = {614}, number = {}, pages = {110729}, doi = {10.1016/j.virol.2025.110729}, pmid = {41175494}, issn = {1096-0341}, abstract = {The Alto Pantanal is a key yet unexplored Brazilian wetland for studying vertebrate viral profiles. This study presents viral taxonomic profiles from vertebrate sera sampled in May, June and October of 2019 in Porto São Luiz and Pirizal, Alto Pantanal. A total of 13 frogs, 19 bats, 23 caimans, 36 equids, 20 domestic hens, 140 birds and 16 humans were sampled. After nucleic acid extraction, individual samples were pooled by species and subjected to a metagenomic approach. Viral reads accounted for less than 0.2 % in each pool, except in domestic hens (35.8 %), yielding an overall viral abundance variation among pools of 48.83 %. In total, twenty-nine viral genomic sequences were retrieved from five pools. In equids, two coding-complete genomes were identified belonging to species Copiparvovirus ungulate8 and Mutorquevirus equid2. In domestic hens, four coding-complete genomes of species Alpharetrovirus avileu were detected, along with partial genomes of three gyroviroviruses of species Gyrovirus homsa1, Gyrovirus galga1 and a putative novel unclassified gyrovirus. In humans, 15 genomes of known human anelloviruses were identified, as well as partial sequences of Orthoflavivirus ilheusense and Erythroparvovirus primate species. In caimans, a partial genome belonging to genus Betadintovirus was detected. In frogs, one partial sequence of a putative novel pegivirus, and a coding-complete sequence of an unclassified retrovirus (Rhinella marina endogenous retrovirus) were found. These findings provide valuable insights into viral circulation within the diverse Pantanal biome, and support viral genomic surveillance efforts in the region.}, }
@article {pmid41175489, year = {2025}, author = {Fan, Z and Wu, H and Feng, Y and Sun, L and Yuan, L and Muhammad, T}, title = {Biochar mitigates biodegradable microplastic-induced greenhouse gas emissions in lake sediments: Unraveling microbial mechanisms and particle-size effects.}, journal = {Journal of environmental management}, volume = {395}, number = {}, pages = {127799}, doi = {10.1016/j.jenvman.2025.127799}, pmid = {41175489}, issn = {1095-8630}, abstract = {Accumulation of biodegradable microplastics (MPs) in freshwater sediments exacerbates greenhouse gas (GHG) emissions, though effective mitigation strategies are still poorly understood. This study investigated the potential of biochar (BC) for carbon sequestration and its role in suppressing MP-induced GHG emissions. Herein, we elucidated the effects of biodegradable MPs Poly (butylene-adipate-co-terephthalate) (PBAT) and different-sized (bulk- and nano-) BC on carbon dioxide (CO2) and methane (CH4) emissions. Results revealed that PBAT significantly reduced sediment pH and oxidation-reduction potential while increasing carbon content, leading to a 50.5 % rise in CO2 and 487.9 % in CH4 emissions. Nano-BC alone reduced CO2 emissions by 46.8 %, whereas no inhibitory effect was observed under MPs pollution. Critically, bulk- and nano-BC strongly inhibited cumulative CH4 emissions in MP-polluted sediment by 14.7 % and 50.6 %, respectively. BC countered PBAT-induced increases in sedimentary amino acids and humic substances by limiting key bacterial phyla involved in organic matter decomposition. Furthermore, BC reduced the abundance of MP-enriched microbes such as p_Firmicutes, f_Methanoregulaceae, and f_Methanotrichaceae, suppressed microbial metabolic functions and carbohydrate-active enzymes, and promoted CH4 oxidation and carbon fixation via genes including cutL, coxL, and coxA. Simultaneously, BC diminished methanogenic gene expression (mcrB, mcrA2). This work demonstrates the pronounced stimulatory effect of biodegradable MPs on sediment carbon mineralization and establishes the multi-level mechanism through which BC (particularly nano-BC) mitigates climate change effectively.}, }
@article {pmid41175312, year = {2025}, author = {Miller, BC and Haggler, JA and Chaudhari, DS and Shukla, R and Kumar, V and Mishra, SP and Masternak, MM and Holland, P and Labyak, C and Golden, A and Dangiolo, M and Arikawa, AY and Kociolek, J and Fraser, A and Williams, C and Agronin, M and Aymat, M and Pledger, W and Yadav, H and Jain, S}, title = {Gut microbiome signatures predict cognitive impairment in older cancer survivors.}, journal = {GeroScience}, volume = {}, number = {}, pages = {}, pmid = {41175312}, issn = {2509-2723}, support = {22A17//Florida Department of Health/ ; }, abstract = {Cancer treatments are improving, and the population of cancer survivors is steadily increasing. However, many survivors experience long-term side effects, including chemobrain and other age-related geriatric disorders like cognitive impairment (CI), severely impacting their quality of life. Emerging studies suggest that the gut microbiome plays a central role in cognitive health. However, the long-term effects of cancer treatments on the microbiome, and how these changes impact cognitive health in survivors, remain largely unknown. Shotgun metagenomic data from 150 older adults (≥ 60 years old, including 49 cancer survivors and 101 controls) from the Microbiome in Aging Gut and Brain (MiaGB) consortium revealed that Tyzzerella, Eggerthella lenta, and Bacteroides vulgatus were specific markers of the cancer survivor gut and could differentiate cancer survivorship in this cohort. Microbiome signatures were distinct in cancer survivors with CI compared to those without and differed from those seen in non-cancer individuals with CI. Bacterial taxa including Streptococcus thermophilus and Firmicutes bacterium CAG 114 were significantly reduced in cancer survivors and strongly associated with CI. Importantly, metabolic pathway analysis revealed that microbial neurotransmitter synthesis was significantly depleted in the gut of cancer survivors, suggesting a mechanistic link to CI. Our results suggest that microbiome signatures predict cancer survivorship and the risk of CI in older adults, potentially by depleting neurotransmitter synthesis in the gut. These findings aid in establishing the role of the microbiome in predicting cancer survivorship and CI risk, which is valuable in the development of novel therapies to support the growing population of cancer survivors.}, }
@article {pmid41175161, year = {2025}, author = {Demin, KA and Kulikova, DB and Kulikov, MP and Mazanko, MS and Prazdnova, EV}, title = {Gellan gum-based media recover more diverse microbial communities from soil material.}, journal = {Archives of microbiology}, volume = {207}, number = {12}, pages = {338}, pmid = {41175161}, issn = {1432-072X}, support = {Strategic Academic Leadership Program "Priority 2030"//Ministry of Science and Higher Education of the Russian Federation/ ; }, mesh = {*Polysaccharides, Bacterial/chemistry ; *Soil Microbiology ; *Culture Media/chemistry ; *Bacteria/isolation &amp; purification/classification/genetics/growth &amp; development ; *Microbiota ; }, abstract = {Soil microbial communities contain a huge proportion of microorganisms that cannot be cultured using standard microbiological media and are accessible only through molecular methods. These uncultivable microbes may include producers of biologically active compounds valuable for medicine, biotechnology, and agriculture. Development of approaches for cultivation of such groups is of paramount importance. Here we successfully replicate and confirm the accumulated observations on the fact that replacing agar with gellan gum as gelling agent and using nutrient-poor media leads to the more frequent recovery and enrichment of rare and hard-to-culture microbial phyla representatives. We also show that altering the gas mixture in the incubation chamber may promotes the isolation of specific microbial groups. Replacing agar with gellan gum is suggested as a strategy to recover new microbial species.}, }
@article {pmid41174950, year = {2025}, author = {Vega-Abellaneda, S and Román, E and Soler, Z and Ortiz, M&#xc0; and Rossi, G and Biagini, L and Sánchez, E and Pons-Tarin, M and Laghi, L and Mengucci, C and Kaur, N and Poca, M and Cuyàs, B and Serrano-Gomez, G and Alvarado, E and Manichanh, C and Soriano, G}, title = {A Metagenomics Approach to Frailty in Patients With Cirrhosis Undergoing a Multifactorial Intervention.}, journal = {Liver international : official journal of the International Association for the Study of the Liver}, volume = {45}, number = {12}, pages = {e70418}, pmid = {41174950}, issn = {1478-3231}, support = {PI19/00275//Instituto de Salud Carlos III/ ; PR-455/2020//Col.legi Oficial d'Infermeres i Infermers de Barcelona/ ; //MENDES SA/ ; //Infisport/ ; }, mesh = {Humans ; *Liver Cirrhosis/complications/therapy/microbiology ; *Frailty/therapy/microbiology ; Male ; Metagenomics ; *Gastrointestinal Microbiome ; Female ; *Probiotics/therapeutic use ; Middle Aged ; Aged ; Feces/microbiology ; Amino Acids, Branched-Chain/therapeutic use ; }, abstract = {The relationship between frailty and gut microbiota has not been previously addressed in patients with cirrhosis. We studied by metagenomic shotgun sequencing the faecal microbiota composition associated with frailty in 29 patients with cirrhosis from a previous study (Román, Hepatol Commun 2024). Frail and prefrail patients were randomised to a multifactorial intervention (home exercise, branched-chain amino acids and a multistrain probiotic) or control for 12 months. We observed a positive correlation between the abundance of Rothia dentocariosa and the Liver frailty index (LFI), and between Bacteroides faecis and gait speed. After the multifactorial intervention, LFI improved and the main changes in the microbiota composition were a decrease in the abundance of Akkermansia muciniphila, and an increase in Streptococcus thermophilus, Lactobacillus acidophilus and several species of Bifidobacterium. We conclude that frailty in patients with cirrhosis was associated with a distinct microbiome signature. After a long-term multifactorial intervention, frailty improved in parallel with changes in microbiome composition. Trial Registration: ClinicalTrials.gov identifier: NCT04243148.}, }
@article {pmid41174628, year = {2025}, author = {Wei, M and Ai, X and Gu, D and Zhang, S and Xu, K and Li, S and Mao, S and Li, M}, title = {Ultra-broad hybrid capture-based targeted next-generation sequencing for sensitive plasma pathogen cfDNA detection in bloodstream infections.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {1203}, pmid = {41174628}, issn = {1479-5876}, support = {2025YFC3409100//National Key Research and Development Program/ ; 24SF1903500//Science and Technology Innovation Plan Of Shanghai Science and Technology Commission/ ; 23YF1431300//Science and Technology Innovation Plan Of Shanghai Science and Technology Commission/ ; }, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Cell-Free Nucleic Acids/blood/genetics ; Female ; Male ; Middle Aged ; Aged ; *Sepsis/microbiology/blood ; Adult ; Retrospective Studies ; }, abstract = {BACKGROUND: The limited genomic targeting range of current targeted next-generation sequencing (tNGS) workflows results in limited detection of pathogen-derived cell-free DNA (cfDNA), making it challenging to apply this approach to bloodstream infections (BSIs). Here, we developed an ultra-broad hybrid capture-based tNGS method to detect plasma pathogen-derived cfDNA and evaluate its suitability for the diagnosis of BSI.<br><br>METHODS: This study introduced an ultra-broad hybrid capture-based tNGS method featuring an ultra-broad pathogen panel (1872 pathogens) and high-density probe coverage. To adequately evaluate its performance, we conducted retrospective tests in 208 suspected BSI patients (139 immunocompromised), comparing tNGS results with mNGS, conventional microbiological testing (CMT), and comprehensive clinical diagnoses.<br><br>RESULTS: In pathogen detection, the concordance between ultra-broad hybrid capture-based tNGS and mNGS results was 93.75%. The diagnostic accuracy of tNGS in BSI was comparable to mNGS (76.44% vs. 75.00%) and significantly higher than CMT (45.67%, p&#x2009;<&#x2009;0.0001). In immunocompromised populations, the diagnostic accuracy of tNGS was similar to mNGS (77.70% vs. 76.98%). tNGS detected 92.09% (163/177) of pathogens identified by mNGS. Two of the missed pathogens were not included in the 1872 pathogens panel, and both were from the immunocompromised group.<br><br>CONCLUSIONS: Ultra-broad hybrid capture-based tNGS exhibits sensitivity and accuracy comparable to mNGS, effectively covering a relatively wide range of pathogens, and may serve as an economic screening tool for BSI in the future.}, }
@article {pmid41174528, year = {2025}, author = {Sharma, D and Valmiki, H and Chayal, P and Kumar, S and Chhotaray, S}, title = {Microbiome study of Murrah buffalo mastitis milk with emphasis on Acinetobacter species.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {703}, pmid = {41174528}, issn = {1471-2180}, }
@article {pmid41174518, year = {2025}, author = {Das, R and Thatal, B and Thakur, N and Kumar, R and Tamang, B}, title = {Metagenomic report of element-microbe synergy and xenobiotic detoxification in the sacred waters of Khecheopalri lake, Eastern Himalaya.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {704}, pmid = {41174518}, issn = {1471-2180}, mesh = {*Lakes/microbiology/chemistry ; *Metagenomics/methods ; India ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; *Xenobiotics/metabolism ; Microbiota ; Metagenome ; Inactivation, Metabolic ; }, abstract = {BACKGROUND: Khecheopalri Lake, a sacred freshwater body and recently recognized Ramsar Wetland site in Sikkim, India, holds both ecological and cultural significance. The ecological health of this lake is influenced by elemental inputs and environmental parameters, yet its microbial and functional diversity remain poorly characterized. In this study, we employed a multi-omics approach combining shotgun metagenomics, inductively coupled plasma mass spectrometry (ICP-MS), and culture-dependent analyses to provide an integrated understanding of the lake's microbial ecosystem. Shotgun metagenomics revealed taxonomic diversity and functional gene profiles, ICP-MS quantified elemental composition and its potential role in shaping microbial communities, while culture-dependent methods complemented metagenomic insights by isolating representative taxa. Together, these approaches highlight the interactions between microbes and elemental dynamics, offering new perspectives on the ecological functioning of this Himalayan wetland and its potential vulnerability to environmental change.<br><br>RESULTS: ICP-MS analysis revealed phosphorus (P) as the most abundant element, followed by iron (Fe), sodium (Na), magnesium (Mg), and potassium (K). Elevated BOD and COD levels in sample KES4 indicated organic pollution and coincided with the dominance of Microcystis aeruginosa, a cyanobacterium indicative of eutrophication. Shotgun metagenomic sequencing generated approximately 213 million reads, with bacteria constituting 98.85% of the community. Dominant phyla included Pseudomonadota and Cyanobacteria. Culturable isolates confirmed the presence of genera such as Limnohabitans, Microcystis, and Mycolicibacterium. Functional gene profiling showed that metabolism was the most enriched category (71.64%), with several genes (e.g., xylB, pchF, clcD) associated with xenobiotic degradation pathways.<br><br>CONCLUSION: This first comprehensive metagenomic assessment of Khecheopalri Lake reveals diverse microbial populations involved in nutrient cycling and pollutant detoxification. The presence of genes linked to aromatic hydrocarbon degradation highlights the ecological potential of native microbes in mitigating environmental stress.}, }
@article {pmid41174459, year = {2025}, author = {Tian, Z and Koak, NH and Kinanti, B and Eun, JB and Kim, YM and Zhao, C}, title = {Integration of metagenomics and targeted metabolomics reveals the flavor metabolism network of the microbial community in traditional watermelon soybean paste.}, journal = {Food research international (Ottawa, Ont.)}, volume = {221}, number = {Pt 2}, pages = {117386}, doi = {10.1016/j.foodres.2025.117386}, pmid = {41174459}, issn = {1873-7145}, mesh = {*Metabolomics/methods ; *Citrullus/microbiology ; *Metagenomics/methods ; *Glycine max/microbiology ; *Taste ; Fermentation ; *Microbiota ; Food Microbiology ; Flavoring Agents/metabolism ; Bacteria/metabolism/classification/genetics ; }, abstract = {Watermelon soybean paste (WSP) is an important traditional Chinese condiment known for its unique flavor and nutritional value. However, the correlation between microbial communities and metabolites, especially flavor-related metabolites, as well as the underlying fermentation mechanisms, remains poorly understood. The microbial synthesis pathways of flavor-related metabolites and the composition of microbial communities in traditional watermelon soybean paste during fermentation were investigated through integrated metagenomic and targeted metabolomic analyses. The results demonstrated that Glu, Asp, Pro, Tyr, Ser, Leu, Phe, Val, and 73 metabolites were characterized as the key differential metabolites. An increase in the number of differential metabolites was observed as fermentation progressed. Aspergillus, Klebsiella, Enterococcus, and Weissella were identified as the dominant genus species in WSP samples. Functional composition analysis using both the eggNOG and KEGG databases revealed that valine, leucine, and isoleucine biosynthesis, starch and sucrose metabolism, glycolysis/gluconeogenesis, and pyruvate metabolism were identified as the predominant metabolic pathways. In contrast, GT4 and CBM were identified as the predominant enzyme families. Additionally, correlation analysis and key metabolic pathway investigation revealed that lactic acid bacteria (e.g., Weissella, Lactococcus, Lactobacillus) and Aspergillus were associated with the synthesis of flavor compounds (e.g., vanillin) and nutrient enrichment through amino acid metabolism and isoflavone biosynthesis pathways. This study offers a scientific basis for optimizing starter cultures and improving the flavor quality, contributing to improved quality control of WSP production.}, }
@article {pmid41174397, year = {2025}, author = {Zhang, L and Li, D and Zhou, L and Zhu, L and Zhang, R and Hong, Q and Liu, S and Li, C}, title = {Characterization of flavor profile and microbial community dynamics in naturally fermented sour watermelon.}, journal = {Food research international (Ottawa, Ont.)}, volume = {221}, number = {Pt 2}, pages = {117319}, doi = {10.1016/j.foodres.2025.117319}, pmid = {41174397}, issn = {1873-7145}, mesh = {*Citrullus/microbiology/chemistry ; *Fermentation ; *Taste ; *Fermented Foods/microbiology/analysis ; Volatile Organic Compounds/analysis ; *Microbiota ; Acetic Acid/analysis ; Odorants/analysis ; Cresols/analysis ; *Food Microbiology ; Flavoring Agents/analysis ; Bacteria/classification/metabolism/genetics ; Gas Chromatography-Mass Spectrometry ; China ; }, abstract = {Sour watermelon (DFSW) is a distinctive fermented food that originated in Hainan, China, known for its unique and pungent flavor. Despite its cultural significance, the microbial dynamics and flavor formation mechanisms of DFSW remain poorly understood. This study employed multi-omics approaches, including HS-SPME-GC-MS and metagenomic sequencing, to analyze the physicochemical properties, volatile flavor compounds, and microbial community structure during DFSW fermentation. Results revealed that p-cresol, acetic acid, ethanol, hexaldehyde, and ethyl acetate were the dominant flavor compounds, endowing DFSW floral, fruity and spicy flavors, with p-cresol being the primary cause of pungent odors. The microbial community was primarily composed of Limosilactobacillus, Lactiplantibacillus, and Lactobacillus, which together made up over 83 % of the total abundance and were closely linked to flavor production. The correlation coefficient values (R) for Lactiplantibacillus and Lactobacillus with p-cresol, lactic acid, and acetic acid were consistently greater than 0.6. Metabolic pathway analysis highlighted the role of microbial carbohydrate and amino acid metabolism in flavor development. The synthesis of p-cresol was mainly related to the metabolism of tyrosine and L-phenylalanine, while the synthesis and metabolism of lactic acid and acetic acid were mainly related to the dominant bacterial genera in the fermentation system. These findings provide valuable insights for the biotechnological optimization of DFSW production, supporting the development of a consistent flavor profile and improved product stability.}, }
@article {pmid41174177, year = {2025}, author = {Simmonds, P and Butković, A and Grove, J and Mayne, R and Mifsud, JCO and Beer, M and Bukh, J and Drexler, JF and Kapoor, A and Lohmann, V and Smith, DB and Stapleton, JT and Vasilakis, N and Kuhn, JH}, title = {Taxonomic expansion and reorganization of Flaviviridae.}, journal = {Nature microbiology}, volume = {10}, number = {11}, pages = {3026-3037}, pmid = {41174177}, issn = {2058-5276}, support = {MC_UU_00034/1//Department of Health | National Health and Medical Research Council (NHMRC)/ ; 107653/Z/15/Z//Wellcome Trust (Wellcome)/ ; NIHR203338)//DH | National Institute for Health Research (NIHR)/ ; }, mesh = {Phylogeny ; *Flaviviridae/classification/genetics/enzymology ; RNA-Dependent RNA Polymerase/genetics ; Evolution, Molecular ; Genome, Viral ; Host Specificity ; Viral Proteins/genetics ; RNA Helicases/genetics ; }, abstract = {Flaviviridae is a family of non-segmented positive-sense RNA viruses that includes major pathogens such as hepatitis C virus, dengue viruses and yellow fever virus. Recent large-scale metagenomic surveys have identified many RNA viruses related to members of this family, such as orthoflaviviruses and pestiviruses. These viruses diverge by having different genome lengths and configurations, and host range. Here we performed an analysis of RNA-directed RNA polymerase (RdRP) hallmark gene sequences of flaviviruses and 'flavi-like' viruses. We uncovered four divergent clades and multiple lineages that are congruent with phylogenies of their helicase genes, protein profile hidden Markov model profiles, and evolutionary relationships based on predicted RdRP protein structures. These results support their classification into three families (Flaviviridae, Pestiviridae and Hepaciviridae) and 12 genera in the established order Amarillovirales, with groupings correlating with genome properties and host range. This taxonomy provides a framework for future evolutionary studies on this important viral family.}, }
@article {pmid41174125, year = {2025}, author = {Dobrzyński, J and Jakubowska, Z}, title = {Pseudomonas protegens as a biocontrol agent against phytopathogenic fungi - mini review.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {41}, number = {11}, pages = {428}, pmid = {41174125}, issn = {1573-0972}, mesh = {*Plant Diseases/microbiology/prevention &amp; control ; *Pseudomonas/metabolism/physiology/genetics ; *Biological Control Agents/metabolism ; *Fungi/pathogenicity ; Antifungal Agents/metabolism/pharmacology ; Phloroglucinol/analogs &amp; derivatives/metabolism ; Secondary Metabolism ; Chitinases/metabolism ; Phenols ; Pyrroles ; }, abstract = {Pseudomonas protegens, a member of the P. fluorescens complex, is an important biocontrol agent with high potential in sustainable agriculture. It produces diverse secondary metabolites, including 2,4-diacetylphloroglucinol (DAPG), pyoluteorin (PLT), orfamides, and protegenins, as well as hydrolytic enzymes such as chitinases, which contribute to antifungal activity, fungal cell wall degradation, and induction of systemic resistance (ISR) in plants. Despite these insights, gaps remain in understanding the regulation of metabolite biosynthesis, variability of ISR across crops, and the field efficacy of P. protegens. Future research should employ omics approaches (metagenomics, transcriptomics) to optimize biocontrol strategies, explore natural inducers of metabolite production, and evaluate colonization efficiency under field conditions. This review synthesizes current knowledge on P. protegens, highlighting its importance, mechanisms of action, existing knowledge gaps, and directions for future research.}, }
@article {pmid41173910, year = {2025}, author = {Bednarski, OJ and Lehman, SB and Mzinza, D and Kazinga, C and Namazzi, R and Opoka, RO and Ren, J and Tran, TM and Taylor, TE and Seydel, KB and John, CC and Conroy, AL and Schmidt, NW}, title = {Gut bacterial dysbiosis in pediatric severe malaria associates with post-discharge mortality.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {9658}, pmid = {41173910}, issn = {2041-1723}, support = {R01NS055349//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; D43TW010928//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; T32GM148382//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; }, mesh = {*Dysbiosis/microbiology/mortality/complications ; Humans ; *Gastrointestinal Microbiome/genetics ; Child, Preschool ; *Malaria/mortality/microbiology/complications ; Female ; Male ; Infant ; Feces/microbiology ; Child ; Escherichia coli/isolation &amp; purification/genetics ; Metagenome ; Enterobacteriaceae/isolation &amp; purification/genetics ; Patient Discharge ; }, abstract = {Gut microbiota have been implicated in severe malaria in murine models, but their contribution to the pathogenesis of severe malaria in children is unknown. Here we show through analysis of gut bacteria in stool samples from two separate African studies enrolling children with severe malaria, and children from local communities, that children with severe malaria have gut bacteria dysbiosis. Among children with severe malaria, there is increased abundance of Enterobacteriaceae that associates with multiple clinical complications of severe malaria. Moreover, increased abundance of Escherichia coli was a predictor of post-discharge mortality. Metagenome analysis identify elevated metabolic pathways and genes supporting the utilization of host-derived molecules in children with severe malaria that have the potential to promote the survival and growth of Enterobacteriaceae. Treatments that target Enterobacteriaceae may have the potential to reduce post-discharge mortality in children with severe malaria.}, }
@article {pmid41173905, year = {2025}, author = {Adhikary, R and Alkhatib, AEA and Hazra, S}, title = {Resistome profiling and bacterial community structure of semi-urban gutter ecosystems of India.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {38127}, pmid = {41173905}, issn = {2045-2322}, mesh = {India ; Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects/classification ; RNA, Ribosomal, 16S/genetics ; *Ecosystem ; *Drug Resistance, Bacterial/genetics ; beta-Lactamases/genetics/metabolism ; Gastrointestinal Microbiome ; Metagenomics/methods ; Humans ; Microbiota ; Metagenome ; }, abstract = {Environmental factors contribute to antimicrobial resistance, a global health threat. Contaminated gutter water in urban areas spreads resistant bacteria, disrupting ecosystems and promoting biofilm formation, causing widespread concern. This study aimed to evaluate antibiotic-resistant bacterial populations across six gutter ecosystems in Roorkee, Uttarakhand, India during summer against different classes of antibiotics, identify presence of beta-lactamase, and explores total bacterial communities, and predicting metabolic pathways through 16S rRNA based metagenomic approach of V3 region. The highest resistant bacterial population was found in HL_NS-6, and HL_NS-2, with highly resistance to Penicillin (ampicillin and oxacillin), Cephalosporin (Cephalothin), aminoglycoside (Kanamycin), fluoroquinolone (ciprofloxacin), and Antifolate (Trimethoprim) class antibiotics. Beta-lactamase activity was detected in all samples except HL_NS-5, indicated by nitrocefin hydrolysis. The microbial community in the six samples were composed with the major families enterobacteriaceae (15.4%) and pseudomonadaceae (8.29%), covering 23.7% of the total population. The highest taxa were found in HL_NS-2 and HL_NS-4, while the largest genera were Pseudomonas (8.3%), Escherichia (8.2%), Hydrogenophaga (6.85%), and Candidatus Moranella (5.4%). There were 21.25% common bacterial genera were present as core microbiome and rest were signified the population diversity among the six-gutter microbiome. The coexistence of common metabolic pathways (citric acid cycle, carbon, nitrogen metabolism etc.), and streptomycin, glycosphingolipid, lipopolysaccharide, cyanoamino acid metabolism pathways might be induced the development of antibiotic resistance in gutter microbiome. This study suggests the presence of antibiotic-resistant bacteria with antibiotic resistant metabolic pathways, and beta-lactamase genes in urban gutter water, which could be harmful to both human health and environmental ecosystems.}, }
@article {pmid41173568, year = {2025}, author = {Díaz Perdigones, CM and Hinojosa Nogueira, D and Rodríguez Muñoz, A and Subiri Verdugo, A and Vilches-Pérez, A and Mela, V and Tinahones, FJ and Moreno Indias, I}, title = {Taxonomic and functional characteristics of the gut microbiota in obesity: A systematic review.}, journal = {Endocrinologia, diabetes y nutricion}, volume = {72}, number = {9}, pages = {501624}, doi = {10.1016/j.endien.2025.501624}, pmid = {41173568}, issn = {2530-0180}, mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Obesity/microbiology/metabolism ; Bacteria/classification ; }, abstract = {Obesity is a growing public health problem. In recent decades, scientific evidence has linked gut microbiota to obesity. This systematic review summarizes current knowledge on the composition and functional differences in gut microbiota between individuals with obesity and those with normal weight. Following PRISMA 2020 recommendations, studies published in adult populations between January 2014 and May 2024 were reviewed. PubMed, Web of Science, and Scopus databases were searched for observational studies that had used advanced sequencing methods, such as 16S rRNA and shotgun metagenomics, to assess gut microbiota. The quality of these studies was also analyzed using the Newcastle-Ottawa scale. Our review of 16 studies shows a reduction in microbial diversity in individuals with obesity. In addition, a higher relative abundance of the phylum Firmicutes, the families Enterobacteriaceae, Gemellaceae, Prevotellaceae, Streptococcaceae and Veillonellaceae, as well as the genera Blautia, Butyricimonas, Collinsella, Megamonas, and Streptococcus, while beneficial bacteria such as the families Porphyromonadaceae and Rikenellaceae, and the genera Bifidobacterium spp. and Faecalibacterium prausnitzii, were depleted. Functional analysis showed a tendency to an increase in metabolic pathways associated with carbohydrate and lipid metabolism, with reduced pathways related to short-chain fatty acid production. Obesity is associated with altered gut microbiota composition and function. However, the variability across studies regarding population characteristics, dietary pattern, and sequencing techniques limits the comparability of findings. Future research should prioritize standardized methodologies and confounding factors to elucidate the role of the gut microbiome in obesity.}, }
@article {pmid41173365, year = {2025}, author = {Liu, H and Qu, Y and Yue, Y and Cui, X and Wang, X and Wang, C and Geng, Z and Zhang, L and Sun, M and Huo, M}, title = {Low-dose chlorite drives stable nitrite accumulation for partial denitrification.}, journal = {Environmental research}, volume = {}, number = {}, pages = {123234}, doi = {10.1016/j.envres.2025.123234}, pmid = {41173365}, issn = {1096-0953}, abstract = {Achieving stable and efficient nitrite accumulation in partial denitrification (PD) requires precise control techniques, which poses a challenge to its practical application. This study introduces a new strategy using chlorite (ClO2[-]) as a regulatory factor to halt denitrification at the nitrite stage, ensuring stable and efficient PD. The effectiveness of this approach was assessed in a continuously operated PD biofilter. At different ClO2[-] concentrations, the nitrite accumulation rate (NTR) reached its peak at 97.6% at 1.00 mg/L ClO2[-], with effluent nitrate-nitrogen (NO3[-]-N) as low as 0.61 mg/L. The chlorite-regulated PD filter exhibited a rapid start-up period, reaching optimal performance within 7 days and maintaining stable operation for over 30 days. Moreover, this PD biofilter sustained a nitrite accumulation rate above 67.5% across a wide range of carbon/nitrogen ratios (C/N) (2-4) and remained efficient at an extremely short hydraulic retention time of 30 min. Additionally, ClO2[-] easily degrade into non-toxic chloride ion (Cl[-]) and oxygen (O2) in the environment, thereby preventing secondary pollution. Metagenomic analysis identified Thauera (16.4%), Simplicispira (14.7%), and Flavobacterium (14.0%) as key contributors to nitrite accumulation. Furthermore, according to the real-time quantitative polymerase chain reaction (qPCR) results, chlorite exposure upregulated the nitrate reductase gene (nar) and downregulated the nitrite reductase gene (nir). Finally, the final effluent Total Inorganic Nitrogen (TIN) concentration of 10.26 mg/L was achieved through the Partial denitrification/Anammox (PD/A) coupling process. This study provides new insights into nitrite accumulation in PD/A and presents valuable guidance for optimizing the PD/A process in engineering applications.}, }
@article {pmid41173342, year = {2025}, author = {Vanbiervliet, Y and Aerts, R and Maessen, L and Wauters, J and Maertens, J and Lagrou, K}, title = {Laboratory innovations to diagnose invasive mould infections - what is relevant, what is not?.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cmi.2025.10.017}, pmid = {41173342}, issn = {1469-0691}, abstract = {BACKGROUND: Invasive mould infections (IMI) carry high morbidity and mortality. Conventional diagnostics - histopathology, culture and microscopy - rely on invasive sampling and lack sensitivity, particularly during early phases of infection. Rare and mixed mould infections are frequently diagnosed too late or missed.<br><br>OBJECTIVES: To provide a narrative review of recent innovations in diagnosing IMIs, highlighting advances, identifying areas where progress remains limited, and assessing gaps in current diagnostic algorithms to guide future directions.<br><br>SOURCES: We performed a literature search regarding diagnostic methods for IMIs without date restrictions, including experimental and clinical studies, systematic reviews and meta-analyses.<br><br>CONTENT: Rapid lateral-flow assays and single-sample chemiluminescent immunoassays for detecting Aspergillus antigens in blood and BALF now complement enzyme immunoassays (EIA). Novel targets, such as urinary glycans and siderophores in various biological matrices, show potential to diagnose IMI. Targeted PCRs for Aspergillus and Mucorales enable earlier detection than conventional methods and rapid detection of resistance in case of A. fumigatus, though isolated Aspergillus PCR positivity is challenging to interpret. Metagenomic next-generation sequencing (mNGS) expands pathogen detection but is limited by costs and technical and interpretative challenges. A shift towards assays based on the host immune response (functional immune assays and biochemical markers) shows promise but remains investigational.<br><br>IMPLICATIONS: Due to different commercially available test formats, Aspergillus antigen detection assays can now be implemented in many hospitals. Implementation of Mucorales PCR tests improves the diagnosis of mucormycosis also in the setting of coinfections. Multimodal pathogen-based strategies that integrate antigen assays, targeted PCRs, and, in select cases, mNGS enable earlier, more accurate, and comprehensive diagnosis of IMIs ultimately improving clinical outcomes; but the need for rapid, accurate, non-invasive diagnostic tests for IMIs remains. Host-response based assays are not yet clinic-ready. Prospective multicentre studies are needed to standardize diagnostic thresholds, validate novel diagnostic markers and to evaluate impact on patient outcomes and cost-effectiveness.}, }
@article {pmid41173130, year = {2025}, author = {Gonzalez, G and Carr, MJ and Byrne, H and Colgan, A and Hare, D and Sawa, H and De Gascun, CF and Matthijnssens, J and Yandle, Z}, title = {Complex evolutionary dynamics including reassortment drive genome diversity in human rotavirus species a circulating in Ireland.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {}, number = {}, pages = {105848}, doi = {10.1016/j.meegid.2025.105848}, pmid = {41173130}, issn = {1567-7257}, abstract = {Rotavirus A (RVA), belonging to the species Rotavirus alphagastroenteritidis, is among the most frequently diagnosed viral causes of gastroenteritis. The inclusion of RVA vaccines in the primary childhood immunisation schedules of multiple countries has led to significant reductions in yearly-reported cases. Nevertheless, such interventions may exert selective pressures that could result in the emergence of novel vaccine escape variants. RVA classification has traditionally focused on two of eleven gene segments encoding the capsid proteins, VP4 and VP7, which limits evolutionary assessments of genomic diversity and reassortments involving the other segments. A viral metagenomics approach (NetoVIR) was employed to investigate the genomic diversity of RVA in Ireland. The analysis focused on clinical samples (n = 140) collected from patients between 2015 and 2021. Besides the Wa-like or DS-1-like genotype constellations, 4/140 genomes (3 %) were identified as reassortant, with an NSP2 genotype 1 in a DS-1-like constellation. Also, we confirmed the circulation of OP354-like P[8] strains in six G9P[8] samples. Notably, these strains show dissimilarity in the antigenic epitopes of the VP4 protein compared to the Rotarix vaccine. Furthermore, we detected strains with an equine-like G3 (EQL-G3) VP7 gene within a DS-1-like constellation (n = 5/140, 4 %) and the unusual combination of G1P[8] with a DS-1-like constellation in 6/22 (27 %) of the G1P[8] samsples. Our study supports using a viral metagenomic approach for RVA genetic characterisation to determine pathogen diversity and reassortments. The public health implications of the identified reassortant RVA strains, requires investigations for any potential impacts on vaccine efficacies.}, }
@article {pmid41172871, year = {2025}, author = {Lalucat, J and Busquets, A and Mulet, M and Riesco, R and García-Valdés, E and Gomila, M}, title = {Genome insights into Hydrogenophaga taeniospiralis and its R-body genetic determinants.}, journal = {Systematic and applied microbiology}, volume = {48}, number = {6}, pages = {126664}, doi = {10.1016/j.syapm.2025.126664}, pmid = {41172871}, issn = {1618-0984}, abstract = {The genome of Hydrogenophaga taeniospiralis 2K1[T], the type and only strain of the species, was analysed. The genes encoding elements involved in autotrophic and chemolithotrophic growth that oxidize H2 in addition to other metabolic traits, such as potential nitrogen fixation capability, are described. A phylogenomic analysis of the taxonomy of members of the genus reveals a high number of species not yet described in the genus, especially if the numerous metagenomes obtained from environmental samples are included. The differences from the closest related genera, Malikia and Serpentinimonas, are highlighted and the delineation of the genus Hydrogenophaga is discussed based on phylogenomic analysis. Furthermore, a survey of metagenomes available in public databases demonstrates the wide environmental and geographic distribution of Hydrogenophaga strains. H. taeniospiralis 2K1[T] is the first free-living bacterium described for its ability to synthesize R- bodies, which are intracytoplasmic extendable protein ribbons associated mainly with toxic effects. The genetic determinants of R-body synthesis are analysed and compared with those found in other Hydrogenophaga genomes and strains from other genera.}, }
@article {pmid41172852, year = {2025}, author = {Chen, T and Li, S and Xiao, J and Peng, R and Sha, M and Wang, J and Ma, J and Wang, W and Ma, M and Li, S and Cao, Z and Liu, S}, title = {Carbohydrate-metabolizing gastrointestinal bacteria mediate resistome divergence in high feed efficiency Holstein dairy calves.}, journal = {Journal of hazardous materials}, volume = {499}, number = {}, pages = {140283}, doi = {10.1016/j.jhazmat.2025.140283}, pmid = {41172852}, issn = {1873-3336}, abstract = {Improvements in feed efficiency often involve alterations in nutrient metabolism mediated by gastrointestinal microorganisms. These microorganisms serve as carriers of antibiotic resistance genes (ARGs); therefore, metabolic changes may influence the dissemination of ARGs. In this study, we investigated the variations in gastrointestinal ARGs between female Holstein calves exhibiting low residual feed intake (LRFI) with high feed efficiencies and those exhibiting high residual feed intake (HRFI) with low feed efficiencies. Metagenomics was conducted to analyze the underlying factors driving these differences. The LRFI calves exhibited 16.6 % higher ruminal ARG abundance but had reduced fecal ARG diversity. The abundance of Erysipelotrichaceae enrichment in LRFI rumen drove resistance functions and elevated carbohydrate-active enzymes (CAZymes) expression. Correlation analysis linked LRFI rumen enriched bacteria Erysipelotrichaceae and Coprobacillaceae to CAZymes, which were positively associated with multidrug, fluoroquinolone, and MLS resistance functions. Weighted Gene Co-Expression Network Analysis confirmed these resistance functions were dominant in LRFI calves. CAZymes improved substrate utilization, enhanced bacterial efflux resistance, promoted bacterial proliferation, and upregulated resistance genes. Rumen microbes and their resistomes systemically alter microbiota and ARG profiles in the feces. The contributions of fecal microbial abundance and diversity, mobile genetic elements (MGEs), and starch to the differences in ARGs were 14.92 %, 11.18 %, 8.90 %, and 10.25 %, respectively. In summary, LRFI calves require more CAZymes to reshape gut microbiota and ARG carrier populations, which lead to shifts in gastrointestinal ARG abundance/diversity shifts.}, }
@article {pmid41172529, year = {2025}, author = {Lima, JD and Rivadavea, WR and Calgaro, LC and Alberton, O and Costa, MSSM and Lima, JC and Monteiro, PHR and Kuhn, EV and Silva, GJ}, title = {Biological dynamics of no-tillage soils in the western region of Paraná.}, journal = {Brazilian journal of biology = Revista brasleira de biologia}, volume = {85}, number = {}, pages = {e298630}, doi = {10.1590/1519-6984.298630}, pmid = {41172529}, issn = {1678-4375}, mesh = {*Soil Microbiology ; *Soil/chemistry ; Brazil ; Nitrogen/analysis ; *Agriculture/methods ; Biomass ; Biodiversity ; Fungi/classification ; Carbon/analysis ; }, abstract = {This study investigates soil dynamics on farms in the western region of Paraná, Brazil, highlighting the importance of biological parameters in agriculture. In particular, focusing on the interaction of management practices with soil biodiversity and biological functions, the aim is to understand and promote sustainable and efficient agricultural practices. To do this, we collected soil samples from 15 farms close to Toledo, Paraná, Brazil. These samples were then analyzed to determine biological and physicochemical parameters using techniques such as carbon and nitrogen microbial biomass, metabolic coefficient, basal respiration, bacterial and fungal biomass, and length of the hyphae. The most contrasting soils were evaluated for physicochemical composition and metagenomic analyses. The results showed significant differences in biological parameters between 2020 and 2021, including fungal biomass, hyphae length, and soil basal respiration. Statistical analyzes revealed strong relationships between biological variables, notably the correlation between fungal hyphae and total nitrogen. Climate changes and management practices appear to influence the microbial composition and biological functions of the soil over the years. Soil P9 stood out with superior biological activity and richer microbial diversity, contrasting with soil P13. These differences reflect the influence of management and climatic conditions on soil composition and biological functions. The microbial comparison of the soils emphasized the need for continuous and careful agricultural management, highlighting the importance of biodiversity and ecological functionality of the soil for agricultural sustainability. So, the study underscores the relevance of considering soil biological parameters, in addition to physicochemical aspects, to optimize soil health and productivity.}, }
@article {pmid41172139, year = {2025}, author = {Yang, S and Zhang, J and Ou, Y and Liu, W and Tian, X and Hou, LJ and Dong, HP}, title = {Ammonia oxidation by aerobic methanotrophs as a source of marine nitrous oxide.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf242}, pmid = {41172139}, issn = {1751-7370}, abstract = {Aerobic methanotrophs encode a hydroxylamine oxidoreductase, which facilitates the oxidation of ammonia to nitrite or nitric oxide, potentially leading to nitrous oxide production. Aerobic methane oxidation has been documented in shallow marine waters or the water column of the open ocean. However, little is known about the distribution pattern of marine aerobic methanotrophs containing hydroxylamine oxidoreductase and their contribution to marine nitrous oxide emissions. Here, by analyzing global marine metagenomes, we show that hydroxylamine oxidoreductase-containing aerobic methanotrophs were widely distributed across diverse marine habitats, with higher abundances in methane seep systems and estuary regions than in other environments. Among these, aerobic methanotrophs belonging to Gammaproteobacteria were the most widely distributed and abundant functional group. We also identified a second order within Gammaproteobacteria (Ga0077536) potentially capable of aerobic methanotrophy, and a complete repertoire of denitrification genes in a gammaproteobacterial methanotroph, expanding the phylogenetic and functional diversity of marine aerobic methanotrophs. By using enrichments of estuarine methanotrophs in combination with 15N stable isotope tracing and metatranscriptomic analysis, we indicate that marine aerobic methanotrophs take part in ammonia oxidation and nitrous oxide production. The ammonia oxidation can persist for approximately 6 days, and the nitrous oxide produced is at least partially derived from the hydroxylamine oxidation. Given the prevalence of denitrification genes in aerobic methanotrophs, methane oxidation may also be coupled to NOx- reduction under anoxic marine conditions, potentially contributing to nitrous oxide production. The intrinsic nature of aerobic methanotrophs could partially offset the mitigation of global warming achieved through the methane consumption.}, }
@article {pmid41171744, year = {2025}, author = {Jia, X and Peng, J and Lv, J and Li, Y and Luo, Z and Xiang, J and Hou, Y and Zheng, Q and Han, B}, title = {Metagenomic analysis reveals the abundance changes of bacterial communities and antibiotic resistance genes in the influent and effluent of hospital wastewater.}, journal = {PloS one}, volume = {20}, number = {10}, pages = {e0335723}, pmid = {41171744}, issn = {1932-6203}, mesh = {*Wastewater/microbiology ; *Metagenomics/methods ; *Bacteria/genetics/drug effects/classification ; Hospitals ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; *Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Metagenome ; Sewage/microbiology ; }, abstract = {The presence of substantial quantities of antibiotics and their metabolites in hospital wastewater can lead to the accumulation of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs). Research on the influent and effluent sewage of hospitals is crucial for understanding the effectiveness of wastewater treatment systems in inactivating ARB and ARGs. Key features of microbial communities and ARGs in influent and effluent wastewater - including taxonomic diversity and relative abundance - were assessed via metagenomic sequencing. The treatment process resulted in a reduction of the overall bacterial count in hospital wastewater. However, a notable increase in relative abundance was observed for three phyla, 16 genera, and 21 species post-treatment. Bacteria harboring ARGs were predominantly identified as belonging to Pseudomonadota and Bacillota. A total of 354 ARGs were detected in the influent, while 331 were identified in the effluent samples, with a general decrease in absolute abundance. Nevertheless, the relative abundance of certain ARGs, such as mphG, fosA8, and soxR, was found to increase in the effluent across all samples. Seasonal fluctuations also played a role in the distribution of microbial communities and ARGs. These findings underscore the role of hospital wastewater treatment systems in reducing the discharge of ARB and ARGs into the environment, while also revealing potential shortcomings in the wastewater treatment process that necessitate further improvement for more effective removal of these ARGs.}, }
@article {pmid41171541, year = {2025}, author = {Joseph, JS and Selvamani, SB and Thiruvengadam, V and Ramasamy, GG and Subramanian, S and Menon, G and Sivakumar, G and Manjunath, C}, title = {Gut microbiota profiling of Apis cerana indica across biodiversity hotspots in the Western Ghats, India.}, journal = {Molecular biology reports}, volume = {53}, number = {1}, pages = {35}, pmid = {41171541}, issn = {1573-4978}, mesh = {Bees/microbiology ; Animals ; *Gastrointestinal Microbiome/genetics ; India ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; Bacteria/genetics/classification ; High-Throughput Nucleotide Sequencing/methods ; Phylogeny ; }, abstract = {BACKGROUND: The gut microbiome of honey bees plays a crucial role in regulating key physiological traits and metabolic processes, including digestion, detoxification, nutrient assimilation, development and immunity. However, information on the gut bacterial diversity of Apis cerana indica bee populations in India remains limited. This study aims to address this critical knowledge gap in Western Ghats, India with outcomes that may provide valuable insights for improving beekeeping practices in the region.<br><br>METHODS AND RESULTS: To fill this gap, we investigated and characterized the gut bacteriome of A. cerana indica collected from two ecologically distinct regions within the Western Ghats. We employed a combination of next-generation sequencing (NGS) using the Oxford Nanopore platform and traditional culture-based methods targeting the 16S rRNA gene to analyze the microbial communities. Our results revealed that the gut bacterial communities of foraging A. cerana indica bees from both locations displayed unique and overlapping microbiome profiles. A total of 225 bacterial species across 30 bacterial orders were identified via 16S rRNA amplicon sequencing, with 92 species shared between the two sites. Prominent symbiotic bacterial groups included Gammaproteobacteria, Betaproteobacteria, Flavobacteria, Actinobacteria, Firmicutes, Proteobacteria, and Actinomycetota. Notably, core bee-associated symbionts exhibited a negative correlation with pathogenic bacterial taxa.<br><br>CONCLUSION: These findings offer valuable insights into the ecological and functional roles of the gut microbiome in A. cerana indica, a native honeybee species of the Western Ghats. The presence of shared bacterial species across regions suggests their potential significance in formulating conservation strategies for indigenous bee populations.}, }
@article {pmid41171444, year = {2025}, author = {U, A and Chacko, A and Priyadarshini, M and P P, R}, title = {Utilization of Chlorella vulgaris biomass in microbial fuel cell as a feed and the study on its degradation pathway.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {92}, number = {8}, pages = {1104-1117}, pmid = {41171444}, issn = {0273-1223}, support = {//Cochin University of Science and Technology/ ; }, mesh = {*Chlorella vulgaris/metabolism ; *Bioelectric Energy Sources/microbiology ; *Biomass ; Waste Disposal, Fluid/methods ; }, abstract = {Microbial fuel cells (MFCs) represent an advanced and environmentally friendly bioenergy technology with significant potential for simultaneous power generation and wastewater treatment. This study specifically compared the anodic performance of MFCs with Chlorella vulgaris versus those fed with acetate. Dual-chamber MFCs were constructed for simultaneous electricity generation and wastewater treatment. In addition, microbial communities of both the MFCs and the gene function of MFC-Ch were analyzed through metagenomic sequencing. When comparing all the electrochemical parameters produced from MFCs, MFC-Ch is slightly more efficient than MFC-A. Metagenomic analysis showed that Proteobacteria was the predominant phylum in MFC-A, whereas Bacteroidota was predominant in MFC-Ch. COG (Clusters of Orthologous Groups) analysis of the primary metabolic pathways in the anolyte of MFC-Ch revealed a relatively high abundance of genes associated with several metabolic pathways during MFC operation, including amino acid transport and metabolism, carbohydrate transport and metabolism, and coenzyme transport and metabolism. The study on carbohydrate and protein degradation indicated that protein metabolism occurred to a greater extent than carbohydrate metabolism. This aligns with the known ability of some bacteria present in the sludge to promote amino acid metabolism in MFCs, a finding further supported by the positive correlation observed in the COG analysis.}, }
@article {pmid41171134, year = {2025}, author = {Sun, Y and Chen, Q and Fan, G and Sun, Q and Zhou, Q and Zhang, J and Nie, J and Ma, J and Wu, L}, title = {gcMeta 2025: a global repository of metagenome-assembled genomes enabling cross-ecosystem microbial discovery and function research.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkaf1115}, pmid = {41171134}, issn = {1362-4962}, support = {2021YFA0717001//National Key R&amp;D Program of China/ ; XDB0830000//Chinese Academy of Sciences/ ; 153211KYSB201900211//Chinese Academy of Science/ ; //Chinese Academy of Sciences/ ; }, abstract = {The rapid growth of metagenomic sequencing has generated an unprecedented wealth of metagenome-assembled genomes (MAGs), transforming opportunities for microbial discovery and functional characterization. Yet, full utilization of these resources has been constrained by heterogeneous data generation practices and inconsistent analytical pipelines. The gcMeta database addresses this gap by compiling MAGs through both public acquisition and de novo assembly. This release integrates over 2.7 million MAGs from 104 266 samples spanning various biomes, covering human, animal, plant, marine, freshwater, and extreme environments. It establishes 50 biome-specific MAG catalogues comprising 109 586 species-level clusters, of which 63% (69 248) represents previously uncharacterized taxa, and annotates >74.9 million novel genes. By linking functional traits with microbial co-occurrence networks, gcMeta identifies keystone taxa central to biogeochemical cycling and environmental adaptation. The platform further supports cross-ecosystem functional comparisons, revealing niche-specific metabolic pathways and stress-response genes. Moreover, gcMeta provides standardized, AI-ready datasets encompassing microbial enzymes, anti-phage defense systems, and other functional modules, enabling advanced machine learning applications. By bridging microbial "sequence discovery" with "functional utilization," gcMeta establishes a foundation for ecological research, industrial biotechnology, and novel gene mining. The platform is freely accessible at https://gcmeta.wdcm.org/.}, }
@article {pmid41171126, year = {2025}, author = {She, J and Qian, PY and Wu, L}, title = {DOO: integrated multi-omics resources for deep ocean organisms.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkaf1096}, pmid = {41171126}, issn = {1362-4962}, support = {2021HJ01//Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; HJRC2022001//Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; SMSEGL24SC01//Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; CCRS25SC01//Otto Poon Center for Climate Resilience and Sustainability/ ; 26104824//Early Career Scheme/ ; JCYJ20220530151207016//Technology Innovation Committee of Shenzhen/ ; 26104824//Technology Innovation Committee of Shenzhen/ ; }, abstract = {The deep ocean is one of Earth's most vast and least explored frontiers, characterized by extreme conditions such as high pressure, limited light, and nutrient scarcity. These environments pose unparalleled challenges to life, making them invaluable for studying genetic and molecular adaptations to extreme conditions. Emerging omics resources have recently provided significant insights into the advanced understanding of deep ocean ecosystems and evolution. However, a centralized resource for deep ocean multi-omics data remains lacking. To bridge this gap, the Deep Ocean Omics (DOO, https://DeepOceanOmics.org) database, a multi-omics atlas for deep ocean organisms, is presented. DOO integrates diverse omics resources from 68 species across seven phyla and 16 classes, encompassing 72 genomes, 950 bulk transcriptomes, 15 single-cell transcriptomes, and 1112 metagenomes, alongside functional support toolkits for functional and comparative analysis. DOO provides a systematic view of genomic information, including genome assembly, phylogeny, gene annotation, BUSCO genes, transcription factors/ubiquitin family, gene clusters, symbiont and mitochondrial genomes, and fossil records. Moreover, DOO offers co-expression networks with expression views across different tissues, and developmental stages and micro- and macrosynteny analyses to elucidate the pan-evolutionary features of genome structure. As the first comprehensive multi-omics resource dedicated to deep ocean organisms, DOO serves as a pivotal platform for uncovering multi-omics underpinnings of deep ocean organisms and offering insights into the understanding of deep ocean biodiversity, evolution, and genetic adaptation under extreme conditions.}, }
@article {pmid41171125, year = {2025}, author = {Kuhn, M and Schmidt, TSB and Ferretti, P and Głazek, A and Robbani, SM and Akanni, W and Fullam, A and Schudoma, C and Cetin, E and Hassan, M and Noack, K and Schwarz, A and Thielemann, R and Thomas, L and von Stetten, M and Alves, R and Iyappan, A and Kartal, E and Kel, I and Keller, MI and Maistrenko, O and Mankowski, A and Nishijima, S and Podlesny, D and Schiller, J and Schulz, S and Van Rossum, T and Bork, P}, title = {Metalog: curated and harmonised contextual data for global metagenomics samples.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkaf1118}, pmid = {41171125}, issn = {1362-4962}, support = {668031//Horizon 2020/ ; ERC-AdG-669830/ERC_/European Research Council/International ; 101059915//European Union's Horizon Europe research and innovation programme/ ; NNF15OC0016692//MicrobLiver/ ; //Novo Nordisk Foundation/ ; //Deutsche Forschungsgemeinschaft/ ; 460129525//German Research Foundation/ ; //Ministry of Science/ ; //MWK/ ; //German Federal Ministry of Research, Technology and Space/ ; //European Molecular Biology Laboratory/ ; }, abstract = {Metagenomic sequencing enables the in-depth study of microbes and their functions in humans, animals, and the environment. While sequencing data is deposited in public databases, the associated contextual data is often not complete and needs to be retrieved from primary publications. This lack of access to sample-level metadata like clinical data or in situ observations impedes cross-study comparisons and meta-analyses. We therefore created the Metalog database, a repository of manually curated metadata for metagenomics samples across the globe. It contains 80 423 samples from humans (including 66 527 of the gut microbiome), 10 744 animal samples, 5547 ocean water samples, and 23 455 samples from other environmental habitats such as soil, sediment, or fresh water. Samples have been consistently annotated for a set of habitat-specific core features, such as demographics, disease status, and medication for humans; host species and captivity status for animals; and filter sizes and salinity for marine samples. Additionally, all original metadata is provided in tabular form, simplifying focused studies e.g. into nutrient concentrations. Pre-computed taxonomic profiles facilitate rapid data exploration, while links to the SPIRE database enable genome-based analyses. The database is freely available for browsing and download at https://metalog.embl.de/.}, }
@article {pmid41171124, year = {2025}, author = {Lv, J and Ma, S and Ma, C and Liu, F and Duan, X and Huang, X and Geng, Q and Liu, F and Li, G and Li, Y and Wang, J and Li, C and Zheng, H and Zhang, Y and Sun, Z and Wang, J and Fan, G and Huang, S and Zhang, L and Bao, Z and Wang, S}, title = {Ocean-M: an integrated global-scale multi-omics database for marine microbial diversity, function and ecological interactions.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkaf1098}, pmid = {41171124}, issn = {1362-4962}, support = {2024YFC2816000//National Key Research and Development Program of China/ ; LSKJ202202804//Marine S&amp;T Fund of Shandong Province for Laoshan Laboratory/ ; 2025B1111180001//Guangdong Provincial Key Areas R&amp;D Program Project/ ; SOLZSKY2025013//Hainan Province Science and Technology Special Fund/ ; 32573498//Natural Science Foundation of China/ ; 32222085//Natural Science Foundation of China/ ; QDLYY-2024011//Blue Seed Industry Science and Technology Innovation Project/ ; GZB20250215//Postdoctoral Fellowship Program of CPSF/ ; }, abstract = {Multi-omics analyses have significantly advanced the understanding of complex marine microbial communities and their interactions. Despite notable progress from recent large-scale ocean meta-analysis efforts, the effective integration and accessibility of these diverse datasets remain challenging. To address this, we introduce Ocean-M (http://om.qnlm.ac), a comprehensive and publicly accessible platform for marine microbial multi-omics data integration, analysis, and visualization. Ocean-M provides a systematic view of 54 083 high-quality metagenome-assembled genomes, including genome assembly statistics, genome clustering, gene annotation, and interactive tools for global-scale taxonomic profiling. The platform also incorporates microbial community networks, host-microbiome interactions, and environmental DNA datasets to support an integrated ecological framework for studying microbial interactions and ecosystem functions. Additionally, Ocean-M enables large-scale mining of ecologically and biotechnologically important genes, with curated catalogs of 151 798 biosynthetic gene clusters, 52 699 antibiotic resistance genes, and millions of carbohydrate-active enzymes and plastic-active enzymes. By combining multi-omics data with environmental metadata, Ocean-M serves as a valuable resource for advancing marine microbial ecology, global biogeography, and functional gene discovery.}, }
@article {pmid41170985, year = {2025}, author = {Gamage, C and Graves, A and Li, G and Thieulent, CJ and Balasuriya, UBR and Morrow, J and Vissani, A and Parreño, V and Matthijnssens, J and Carossino, M}, title = {Coding-complete genome sequences of group B equine rotavirus from central Kentucky, USA, reveal circulation of a single genome constellation.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0074425}, doi = {10.1128/mra.00744-25}, pmid = {41170985}, issn = {2576-098X}, abstract = {Equine rotavirus B (ERVB) has caused foal diarrhea in central Kentucky since 2021. Coding-complete genome sequences from 14 strains circulating in 2024 revealed >99% nucleotide identity to the 2021 prototype ERVB strain RVB/Horse-wt/USA/KY1518/2021, with a conserved genomic constellation (G3-P[3]-I3-R3-C3-M3-A4-N3-T3-E3-H3).}, }
@article {pmid41170455, year = {2025}, author = {Ruan, L and Chen, S and Zhang, J and Peng, G}, title = {Infected left atrial myxoma with Streptococcus gordonii: case report and literature review.}, journal = {Frontiers in oncology}, volume = {15}, number = {}, pages = {1635642}, pmid = {41170455}, issn = {2234-943X}, abstract = {Cardiac myxoma is a relatively common type of benign heart tumor, but infectious myxoma is rare. The symptoms of non-infected cardiac myxoma and infected cardiac myxoma are similar and mostly nonspecific, which can easily lead to delayed diagnosis, missed diagnosis, and delayed treatment. A 57-year-old male patient presented with nonspecific systemic symptoms such as anorexia, fever, and cough, and was initially considered to have gastrointestinal disease or pulmonary infection. Preoperative bacterial culture was negative, and imaging features were consistent with cardiac myxoma. A small amount of vegetation was found attached to the surface of the tumor. Postoperative blood culture, surgical specimen culture, and postoperative blood metagenomic next-generation sequencing (mNGS) examination all showed positive results for Streptococcus gordonii, confirming the diagnosis of infectious left atrial myxoma. For patients with febrile cardiac myxoma, it is crucial to be vigilant against concurrent infections. Blood cultures should be performed before administering antibiotics. In cases where blood cultures are negative, a combination of mNGS, PCR, and transesophageal echocardiography (TEE) should be utilized for differential diagnosis, with particular attention paid to the characteristics of vegetations on the tumor surface.}, }
@article {pmid41170433, year = {2025}, author = {Zhang, S and Chu, M and Sun, X}, title = {The arms race in bacteria-phage interaction: deciphering bacteria defense and phage anti-defense mechanisms through metagenomics.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1687307}, pmid = {41170433}, issn = {1664-302X}, abstract = {Bacteriophages are viruses that specifically infect bacteria and co-evolve with their hosts through mutual interactions. They represent one of the most significant drivers of microbial diversity, influencing its evolution, generation, and maintenance. To counter bacteriophage infection, bacteria have developed sophisticated immune systems, including both passive adaptations, such as inhibiting phage adsorption and preventing DNA entry, and active defense systems such as restriction-modification systems and CRISPR-Cas systems. The ongoing arms race between bacteriophages and bacteria has left distinct evolutionary signatures in their genomic sequences. Advances in large-scale genomic and metagenomic sequencing technologies, coupled with bioinformatics approaches, have greatly enhanced our understanding of bacteria-phage interaction mechanisms, driving progress in bacteriophage biology. This review systematically analyses the diverse immune strategies bacteria employ against phage infection, elucidates the coordination and interrelationships among different anti-phage mechanisms, and highlights potential directions for future research.}, }
@article {pmid41170420, year = {2025}, author = {Guo, Y and Zhang, N and Pei, D}, title = {Gut microbiota heterogeneity in non-alcoholic fatty liver disease: a narrative review of drivers, mechanisms, and clinical relevance.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1645298}, pmid = {41170420}, issn = {1664-302X}, abstract = {Non-alcoholic fatty liver disease (NAFLD), a prevalent metabolic disorder, is increasingly recognized as a complex condition influenced by gut microbiota dysbiosis. However, the heterogeneity in findings across studies has hindered the clinical translation of microbiota-based interventions. In this narrative review, we synthesize current evidence on gut microbial alterations in patients with NAFLD, with a focus on the sources of variability that contribute to inconsistent results. We included human studies (2000-2024) that compared gut microbiota profiles between NAFLD patients and healthy controls using 16S rRNA or metagenomic sequencing; key drivers of microbial changes include clinical factors (metabolic comorbidities, disease progression), biological variables (diet, genetics), and methodological biases (sequencing platform differences, diagnostic criteria variability). Emerging evidence highlights the role of non-bacterial components (fungi, viruses) in modulating bacterial communities and disrupting host metabolic pathways, exacerbating hepatic inflammation and lipid accumulation. To overcome current limitations, we propose integrating multi-omics approaches (metagenomics, metabolomics, and proteomics) with a longitudinal study design to capture dynamic microbiota-host interactions. Precision microbiota therapies, including strain-specific probiotics, engineered microbial consortia, and fecal microbiota transplantation tailored to individual dysbiosis profiles, are emerging as promising strategies for targeted interventions. Addressing these challenges is essential to identifying reliable microbial biomarkers and developing personalized strategies for NAFLD prevention and treatment. Future research should harmonize methodologies, validate causal mechanisms, and optimize microbiota-based therapies to bridge experimental findings and clinical application.}, }
@article {pmid41170165, year = {2025}, author = {Shi, Y and Lin, Z and Chen, Z and Ye, C and Yu, J and Xi, J and Geng, Y and Zou, M and Ren, H and Wang, L and Wang, B and Xu, F and Zheng, X and Xiang, G}, title = {High-throughput and Efficient Assay for Central Nervous System Infection with Targeted Nanopore Sequencing Technology.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {5461-5471}, pmid = {41170165}, issn = {1178-6973}, abstract = {INTRODUCTION: Central nervous system (CNS) infections represent a significant global public health concern and are characterized by high morbidity and mortality rates. In this study, we developed an integrated diagnostic approach for CNS infections by combining high-throughput nanopore sequencing with multiplex PCR amplification, designated targeted nanopore sequencing (tNPS).<br><br>METHODS: The tNPS assay employed a dual detection strategy incorporating pathogen-specific primers targeting 17 prevalent CNS pathogens (seven bacteria, one fungus and nine DNA viruses), with universal primers for the comprehensive amplification of full-length 16S ribosomal RNA (16S rRNA) and internal transcribed spacer (ITS) regions.<br><br>RESULTS: Analytical validation of tNPS was successfully carried out using the 12 positive reference strains (seven bacteria, one fungus, and four DNA viruses) individually, the ZymoBIOMICS microbial community (eight bacteria and two fungi), the laboratory synthetic community of bacteria and fungi (seven bacteria and one fungus), and the laboratory synthetic community of viruses (five DNA viruses). With accelerated turnaround time within 8&#xa0;h, the tNPS also assayed 11 clinical cerebrospinal fluid (CSF) samples, which further confirmed the feasibility of precise identification of CNS pathogens compared to CSF culture and metagenomic next-generation sequencing.<br><br>DISCUSSION: Our tNPS as a culture-independent diagnostic assay offered enhanced efficiency, high-throughput capability, and an expanded pathogen detection spectrum, facilitating potential implementation in molecular diagnosis of CNS infection.}, }
@article {pmid41169729, year = {2025}, author = {Osogo, AK and Muyekho, F and Were, H and Okoth, P}, title = {Unveiling Common Bean (Phaseolus vulgaris L) RNA- and DNA-Based Virome in Western Kenya: Insights From Metatranscriptomic and Metagenomic Signatures.}, journal = {Advances in virology}, volume = {2025}, number = {}, pages = {6690945}, pmid = {41169729}, issn = {1687-8639}, abstract = {Common bean (Phaseolus vulgaris L) is Kenya's second most important agricultural product after maize, serving as a vital source of protein for many rural families in Western Kenya. However, viral diseases caused by RNA and DNA viruses greatly impair bean productivity, often leading to yield losses of up to 100%, thus contributing to food insecurity. Global research has isolated 168 viruses of plants that have detrimental effects on common beans; however, no extensive profiling of these viruses has been done in Western Kenya. The scope of this study was to delineate the whole virome that infects common beans through a comprehensive disease diagnostic survey. Sixty-one diseased samples were collected, and nucleic acids were extracted using standard extraction protocols (DNA &amp;RNA Qiagen) and sequenced on the Illumina platform. Metagenomic analysis revealed several DNA-based viruses, such as Badnavirus spp, Caulimovirus maculatractylodei, Pandanus badnavirus, Okra enation leaf curl virus, and Paper mulberry vein-banding virus, while metatranscriptomic analysis uncovered viruses like Tomato leaf curl Cameroon alphasatellite, Physalis Rugose Mosaic Virus, Citrus endogenous paretrovirus, Natevirus nate, and Bracoviriform facetosae. To the best of our knowledge, this study provides a comprehensive inventory of viral entities associated with common beans not documented in Africa. This information is essential for defining plant defense mechanisms, guiding crop protection strategies, lowering agriculture-related risks, strengthening resistance, and advancing resilience.}, }
@article {pmid41168883, year = {2025}, author = {Gabashvili, E and Küsel, K and Pratama, AA and Wang, H and Taubert, M}, title = {Growth of candidate phyla radiation bacteria in groundwater incubations reveals widespread adaptations to oxic conditions.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {224}, pmid = {41168883}, issn = {2049-2618}, support = {390713860//Deutsche Forschungsgemeinschaft/ ; B 715-09075//Th&#xfc;ringer Ministerium f&#xfc;r Wirtschaft, Wissenschaft und Digitale Gesellschaft/ ; 2016 FGI 0024 "BIODIV"//Th&#xfc;ringer Ministerium f&#xfc;r Wirtschaft, Wissenschaft und Digitale Gesellschaft,Germany/ ; }, mesh = {*Groundwater/microbiology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/growth &amp; development/genetics/classification/isolation &amp; purification/metabolism ; *Microbiota/genetics ; Phylogeny ; DNA, Bacterial/genetics ; Adaptation, Physiological ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: The candidate phyla radiation (CPR) comprises a widespread but poorly understood group of bacteria with limited cultured representatives, largely due to their metabolic dependencies on microbial hosts. In laboratory incubations, CPR often decline sharply in relative abundance, even when samples originate from natural environments where they dominate, such as groundwater, where they can represent over 50% of the microbiome. Suitable enrichment conditions and host interactions remain poorly defined.<br><br>RESULTS: Here, we analyzed 16S rRNA gene amplicon data from 397 groundwater incubation samples across 31 treatments, including 22 under oxic conditions, to identify factors that promote CPR survival and growth. Despite an initial decline, CPR abundances recovered over longer incubation times, reaching up to 11-30% of the microbial community. In total, we detected 1410 CPR amplicon sequence variants (ASVs), spanning six major CPR classes commonly found in groundwater. Enrichment success was treatment-specific: Cand. Saccharimonadia dominated in incubations with polysaccharides (up to 31.4%), while Cand. Parcubacteria were enriched (>&#x2009;23%) in treatments stimulating methylotrophs and autotrophs. ASV-specific growth rates based on quantitative PCR showed that some CPR doubled within 1-2&#xa0;days, comparable to faster-growing non-CPR groundwater bacteria, while most CPR had doubling times around 15&#xa0;days. Strikingly, although the relative abundance of many CPR ASVs showed positive correlation with anoxic conditions, overall CPR reached higher absolute abundances under oxic conditions than under anoxic conditions. Metabolic network analysis based on metagenome-assembled genomes revealed that up to 62% of annotated genes were associated with functions linked to oxic conditions. In fact, 25 CPR genomes encoded enzymes that directly utilize oxygen, challenging the long-standing view of CPR as strictly anaerobic, fermentative organisms.<br><br>CONCLUSIONS: Our findings demonstrate that diverse CPR lineages not only survive but actively grow in groundwater incubations, even under oxic conditions. The discovery of genes for oxygen-dependent reactions and substantial CPR enrichment in oxic treatments reveals unexpected metabolic flexibility, helping to explain their persistence and ecological success across a wide range of environments.}, }
@article {pmid41168882, year = {2025}, author = {Bowers, RM and Bennett, S and Riley, R and Villada, JC and Da Silva, IR and Woyke, T and Frank, AC}, title = {Host species and geographic location shape microbial diversity and functional potential in the conifer needle microbiome.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {222}, pmid = {41168882}, issn = {2049-2618}, support = {10.46936/10.25585/60000936//U.S. Department of Energy/ ; DEB-1442348//Directorate for Biological Sciences/ ; }, mesh = {*Microbiota/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; Metagenomics/methods ; *Tracheophyta/microbiology ; Metagenome ; Phylogeny ; *Plant Leaves/microbiology ; Pinus/microbiology ; }, abstract = {BACKGROUND: The aerial surface of plants, known as the phyllosphere, hosts a complex and dynamic microbiome that plays essential roles in plant health and environmental processes. While research has focused on root-associated microbiomes, the phyllosphere remains comparatively understudied, especially in forest ecosystems. Despite the global ecological dominance and importance of conifers, no previous study has applied shotgun metagenomics to their phyllosphere microbiomes.<br><br>RESULTS: This study uses metagenomic sequencing to explore the microbial phyllosphere communities of subalpine Western conifer needle surfaces from 67 trees at six sites spanning the Rocky Mountains, including 31 limber pine, 18 Douglas fir, and 18 Engelmann spruce. Sites span&#x2009;~&#x2009;1,075&#xa0;km and nearly 10&#xb0; latitude, from Glacier National Park to Rocky Mountain Biological Laboratory, capturing broad environmental variation. Metagenomes were generated for each of the 67 samples, for which we produced individual assemblies, along with three large coassemblies specific to each conifer host. From these datasets, we reconstructed 447 metagenome-assembled genomes (MAGs), 417 of which are non-redundant at the species level. Beyond increasing the total number of extracted MAGs from 153 to 294, the three coassemblies yielded three large MAGs, representing partial sequences of host genomes. Phylogenomics of all microbial MAGs revealed communities predominantly composed of bacteria (n&#x2009;=&#x2009;327) and fungi (n&#x2009;=&#x2009;117). We show that both microbial community composition and metabolic potential differ significantly across host tree species and geographic sites, with site exerting a stronger influence than host.<br><br>CONCLUSIONS: This dataset offers new insights into the microbial communities inhabiting the conifer needle surface, laying the foundation for future research on needle microbiomes across temporal and spatial scales. Variation in functional capabilities, such as volatile organic compound (VOC) degradation and polysaccharide metabolism, closely tracks shifts in taxonomic composition, indicating that host-specific chemistry, local environmental factors, and regional microbial source pools jointly shape ecological roles. Moreover, the observed patterns of mobile genetic elements and horizontal gene transfer suggest that gene exchange predominantly occurs within microbial lineages, with occasional broader transfers dispersing key functional genes (e.g., those involved in polysaccharide metabolism), which may facilitate microbiome adaptation.}, }
@article {pmid41168776, year = {2025}, author = {Heng Wu,  and Dong, T and Li, A and Chen, J and Zhang, H and Lv, H and Yang, C and Guo, X and Yang, X and Qiu, L and Miao, C and Yao, Y}, title = {An innovative strategy for overcoming ultra-high ammonia nitrogen inhibition on anaerobic methanogenesis via stepwise domestication.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {223}, pmid = {41168776}, issn = {2049-2618}, mesh = {*Methane/biosynthesis/metabolism ; Anaerobiosis ; *Ammonia/metabolism ; Animals ; Cattle ; Methanosarcina/metabolism/genetics ; *Nitrogen/metabolism ; Bioreactors/microbiology ; Bacteria/metabolism/classification/genetics ; Manure/microbiology ; Domestication ; Metagenomics/methods ; }, abstract = {BACKGROUND: The world is facing both an increasingly severe energy crisis and a growing problem of agricultural pollution. The utilization of agricultural waste by anaerobic digestion (AD), has received increasing attention. AD using representative waste cow dung results in total ammonia nitrogen (TAN) accumulation and inhibition of methanogens resulting in reduced CH4 production. However, there is a lack of highly efficient in-situ biological domestication strategies to enhance the TAN tolerance of methanogens in AD systems.<br><br>RESULTS: In this study, an incremental approach to gradually increasing the TAN concentration has been used for overcoming the problem. The results showed that at an ultra-high concentration of 6124.09&#xa0;mg/L TAN, a 48-day domesticated AD system functioned stably and the cumulative CH4 production reached 72.81&#xa0;mL/g volatile solids, whereas the undomesticated AD system failed to produce CH4. After domestication, the lactate dehydrogenase concentration decreased to 96.44&#xa0;ng/L and the adenosine triphosphate concentration increased to 48.77&#xa0;nmol/L, confirming that microbial activity improved. Hydrolytic and acidogenic bacteria were enriched, with Methanosarcina (79.73%) dominating the domesticated AD system, primarily Methanosarcina mazei. Metagenomic analysis showed that with two-component system enrichment, the key inhibited steps from glycerate-1,3P2 to pyruvate (2.498&#x2030;), and from acetyl-CoA and acetyl phosphate to acetic acid (1.141&#x2030; and 0.798&#x2030;), as well as vital methanogenic genes mcrA (0.128&#x2030;), mcrB (0.127&#x2030;), and mcrG (0.065&#x2030;), were both enriched, which favored a stable methanogenic system. More importantly, this ultra-high resistance AD system also showed the potential to increase the CH4 production per unit substrate at the Minhe biogas plant with 24,000&#xa0;m[3] operation scale in Shandong Province, China.<br><br>CONCLUSIONS: Stepwise increase the TAN concentration is a novel method that was demonstrated to be a practical and sustainable way to overcome ultra-high TAN inhibition (6124.09&#xa0;mg/L). During domestication, the two-component system may regulate the microbial collaborative network to ensure microbial activity and high abundance enrichment, thus potentially constructing a methanogenic system dominated by hydrogenotrophic and acetoclastic methanogenesis, holding a promising application prospect. This study helped recognize the potential of methanogens in tolerating ultra-high inhibition and developed an achievable AD technology for robustly treating fecal residue and wastewater in practice.}, }
@article {pmid41168702, year = {2025}, author = {Lakamp, A and Adams, S and Kuehn, L and Snelling, W and Wells, J and Hales, K and Neville, B and Fernando, S and Spangler, ML}, title = {Prediction accuracy for feed intake and body weight gain using host genomic and rumen metagenomic data in beef cattle.}, journal = {Genetics, selection, evolution : GSE}, volume = {57}, number = {1}, pages = {64}, pmid = {41168702}, issn = {1297-9686}, support = {2022-33522-38219//National Institute of Food and Agriculture/ ; 2023-68015-40015//National Institute of Food and Agriculture/ ; 2024-33522-43699//National Institute of Food and Agriculture/ ; 2018-67015-27496//National Institute of Food and Agriculture/ ; }, mesh = {Animals ; Cattle/genetics/physiology ; *Rumen/microbiology ; *Metagenome ; *Weight Gain/genetics ; *Eating/genetics ; Metagenomics/methods ; Animal Feed ; Phenotype ; Genomics/methods ; Diet/veterinary ; Gastrointestinal Microbiome ; }, abstract = {BACKGROUND: Host genomic and rumen metagenome data can predict feed efficiency traits, supporting management decisions and increasing profitability. This study estimated the proportion of variation of average daily dry matter intake and average daily gain explained by the rumen metagenome in beef cattle, evaluated prediction accuracy using genomic data, metagenomic data, or their combination, and explored methods for modelling the rumen metagenome to improve phenotypic prediction accuracy. Data from 717 animals on four diets (two concentrate-based and two forage-based) were analyzed. Animal genotypes consisted of 749,922 imputed sequence variants, while metagenomic data comprised 16,583 open reading frames from ruminal microbiota. The metagenome was modelled using six (co)variance matrices, based on combinations of two creation methods and three modifications. Nineteen mixed linear models were used per trait: one with genomic effects only, six with metagenomic effects, six combining genomic and metagenomic effects, and six adding interaction effects. Two cross-validation schemes were applied to evaluate prediction accuracy: fourfold cross-validation balanced for diet type with 5 replicates and leave-one-diet-out cross-validation, where three diets served as training and the fourth as testing. Prediction accuracy was measured as the correlation between an animal's summed random effects and its adjusted phenotype.<br><br>RESULTS: Although minimal, differences existed in parameter estimates and validation accuracy depending on how the metagenome effect was modelled. Median phenotype prediction accuracy ranged from -0.01 to 0.28. No specific set of model characteristics consistently lead to the highest accuracies. Models which combined genome and metagenome data outperformed those using either data source alone. Models where the rumen metagenome (co)variances matrix was scaled within each diet composition generally led to lower prediction accuracies in this study.<br><br>CONCLUSIONS: The rumen metagenome can explain a significant proportion of variation in beef cattle feed efficiency traits. Those traits can also be predicted using either host genome or rumen metagenome, though using both sources of information proved more accurate. Multiple methods of forming the metagenome (co)variance matrix can lead to similar prediction accuracies.}, }
@article {pmid41168432, year = {2025}, author = {Ginnan, NA and Custódio, V and Gopaulchan, D and Ford, N and Salas-González, I and Jones, DH and Wells, DM and Moreno, &#xc2; and Castrillo, G and Wagner, MR}, title = {Precipitation legacy effects on soil microbiota facilitate adaptive drought responses in plants.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {41168432}, issn = {2058-5276}, support = {IOS-2016351//National Science Foundation (NSF)/ ; IOS-2016351//National Science Foundation (NSF)/ ; IOS-2016351//National Science Foundation (NSF)/ ; BB/V011294/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/V011294/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/V011294/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/V011294/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/V011294/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/V011294/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/V011294/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; }, abstract = {Drought alters the soil microbiota by selecting for functional traits that preserve fitness in dry conditions. Legacy effects or ecological memory refers to how past stress exposure influences microbiota responses to future environmental challenges. How precipitation legacy effects impact soil microorganisms and plants is unclear, especially in the context of subsequent drought. Here we characterized the metagenomes of six prairie soils spanning a precipitation gradient in Kansas, United States. A microbial precipitation legacy, which persisted over a 5-month-long experimental drought, mitigated the negative physiological effects of acute drought for a native wild grass species, but not for the domesticated crop species maize. RNA sequencing of roots revealed that soil microbiota with a low precipitation legacy altered expression of plant genes that mediate transpiration and intrinsic water-use efficiency during drought. Our results show how historical exposure to water stress alters soil microbiota, with consequences for future drought responses of some plant species.}, }
@article {pmid41168431, year = {2025}, author = {Jabbar, KS and Priya, S and Xu, J and Das Adhikari, U and Pishchany, G and Mohamed, ATM and Johansen, J and Thurimella, K and McCabe, C and Vlamakis, H and Okello, S and Delorey, TM and Lankowski, A and Mosepele, M and Siedner, MJ and Plichta, DR and Kwon, DS and Xavier, RJ}, title = {Human immunodeficiency virus and antiretroviral therapies exert distinct influences across diverse gut microbiomes.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {41168431}, issn = {2058-5276}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 HL141053/HL/NHLBI NIH HHS/United States ; K24 HL166024/HL/NHLBI NIH HHS/United States ; DK120485//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; }, abstract = {Human immunodeficiency virus (HIV) infection alters gut microbiota composition and function, but the impact of geography and antiretroviral therapy remains unclear. Here we determined gut microbiome alterations linked to HIV infection and antiretroviral treatment in 327 individuals with HIV and 260 control participants in cohorts from Uganda, Botswana and the USA via faecal metagenomics. We found that while HIV-associated taxonomic differences were mostly site specific, changes in microbial functional pathways were broadly consistent across the cohorts and exacerbated in individuals with acquired immunodeficiency syndrome. Microbiome perturbations associated with antiretroviral medications were also geography dependent. In Botswana and Uganda, use of the non-nucleoside reverse transcriptase inhibitor efavirenz was linked to depletion of Prevotella, disruption of interspecies metabolic networks, exacerbation of systemic inflammation and atherosclerosis. Efavirenz-associated Prevotella depletion may occur through cross-inhibition of prokaryotic reverse transcriptases involved in antiphage defences, as shown by computational and in vitro experiments. These observations could inform future geography-specific and microbiome-guided therapy.}, }
@article {pmid41168291, year = {2025}, author = {Arjmand, E and Moghadam, A and Afsharifar, A and Faghihi, MM and Izadpanah, K and Taghavi, SM}, title = {Metagenome analysis of Citrus sinensis rhizosphere infected with Candidatus liberibacter asiaticus reveals distinct structure in bacterial communities.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {37987}, pmid = {41168291}, issn = {2045-2322}, mesh = {*Rhizosphere ; *Plant Diseases/microbiology ; *Metagenome ; *Microbiota/genetics ; *Citrus sinensis/microbiology ; *Rhizobiaceae ; Plant Roots/microbiology ; Soil Microbiology ; *Bacteria/genetics/classification ; Phylogeny ; *Liberibacter ; High-Throughput Nucleotide Sequencing ; }, abstract = {The rhizosphere microbiome plays crucial roles in different root-associated biological functions, especially regulating plant defense systems. Huanglongbing (HLB) disease, caused by Candidatus Liberibacter species, is a disaster threat to the global citrus industry. This study investigates changes in rhizosphere bacterial communities of Citrus sinensis trees infected by Candidatus Liberibacter asiaticus (CLas). We performed the high-throughput sequencing of the rhizosphere-associated bacterial metagenome and identified taxonomic profiles. Alpha diversity based on Shannon and Chao1 indices, and beta diversity based on Bray-Curtis dissimilarity and the UniFrac indices, revealed significant differences in the composition and structure of the rhizosphere microbiome between CLas-infected and CLas-free trees. We achieved significant relative abundance at the phylum and family, and genus levels. The abundance of Pseudomonas, Chryseobacterium, and an unknown genus belonging to Aurantimonadaceae was significantly suppressed in infected trees, while Planococcus and an unknown genus belonging to Caulobacteraceae were significantly enriched. These results confirm that CLas have dramatically altered the structure and composition of the rhizosphere microbiome. These changes discovered some valuable biomarkers related to this disease. These clues might be applied in microbial engineering of the rhizosphere to control HLB.}, }
@article {pmid41167954, year = {2025}, author = {Chen, T and Jin, D and Ye, H}, title = {[Balamuthia mandrillaris amebic encephalitis in children: a case report].}, journal = {Zhongguo xue xi chong bing fang zhi za zhi = Chinese journal of schistosomiasis control}, volume = {37}, number = {4}, pages = {447-450}, doi = {10.16250/j.32.1915.2024285}, pmid = {41167954}, issn = {1005-6661}, support = {2019xkj175//Anhui Medical University Scientific Research Fund/ ; }, mesh = {Humans ; *Balamuthia mandrillaris/isolation &amp; purification/physiology/genetics ; Male ; *Encephalitis/diagnosis/parasitology ; *Amebiasis/diagnosis/parasitology ; Child ; Child, Preschool ; Female ; *Infectious Encephalitis/diagnosis/parasitology ; }, abstract = {Balamuthia mandrillaris amebic encephalitis is a rare but highly fatal parasitic disease in the central nervous system caused by amebae infections. This disease is characterized by complex, diverse and non-specific clinical manifestations and high difficulty in diagnosis, resulting in a high likelihood of missing diagnosis and misdiagnosis. This article presents the diagnosis and treatment of a child with definitive diagnosis B. mandrillaris amebic encephalitis as revealed by metagenomic next-generation sequencing of cerebrospinal fluids, so as to provide insights into clinical diagnosis and treatment of B. mandrillaris amebic encephalitis.}, }
@article {pmid41167953, year = {2025}, author = {Xue, T and Du, W and Zhao, Y and Xu, J}, title = {[Metagenomic next - generation sequencing technology and its application in diagnosis of Pneumocystis jirovecii infection: a review].}, journal = {Zhongguo xue xi chong bing fang zhi za zhi = Chinese journal of schistosomiasis control}, volume = {37}, number = {4}, pages = {434-446}, doi = {10.16250/j.32.1374.2024277}, pmid = {41167953}, issn = {1005-6661}, support = {32200168//National Natural Science Foundation of China/ ; BYJL044//Shanxi Medical University Science and Technology Guidance Project for Higher Education in Shangxi Province/ ; 2020150//Shanxi Provincial Traditional Chinese Medicine Research Project/ ; 2023RC-2-7//Lvliang Municipal Talent Introduction Program/ ; 2020-BS-268//Liaoning Provincial Department of Science and Technology Doctoral Startup Project/ ; XD1905//Shanxi Medical University Doctoral Research Startup Fund/ ; 2020L0223//Shanxi Provincial Higher Education Science and Technology Innovation Project/ ; }, mesh = {Humans ; *Pneumocystis carinii/genetics/isolation &amp; purification ; *High-Throughput Nucleotide Sequencing/methods ; *Pneumonia, Pneumocystis/diagnosis/microbiology ; *Metagenomics/methods ; }, abstract = {Pneumocystis jirovecii is an opportunistic fungal pathogen causing fatal Pneumocystis jirovecii pneumonia (PJP) among immunocompromised patients. Conventional pathogen detection Methods have limitations, which hinders early diagnosis and treatment of PJP, resulting in misdiagnosis and underdiagnosis, and high mortality rates. Metagenomic next-generation sequencing (mNGS), which is high in sensitivity and specificity for pathogen detection, enables accurate detection of P. jirovecii and P. jirovecii co-infection with other pathogens, which facilitates timely diagnosis and treatment of PJP. This review summarizes the advances in mNGS technology and its application in diagnosis of PJP, highlighting its critical clinical value in improving diagnostic effectiveness, guiding clinical therapy, and preventing nosocomial transmission of PJP.}, }
@article {pmid41167483, year = {2025}, author = {Cao, Y and Zhu, Y and He, W and Zou, Z and Chen, J and Yang, M and Yu, Y}, title = {Fe2O3 nanoparticles drive enhanced composting humification by modulating bacteriophage-bacteria interactions.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {133575}, doi = {10.1016/j.biortech.2025.133575}, pmid = {41167483}, issn = {1873-2976}, abstract = {Although bacteria are responsible for decomposing organic matter and forming humic substances (HS) during composting, the role of bacteriophages in carbon metabolism cannot be ignored. In this study, integrated metagenomics and untargeted metabolomic analysis were used to explore the interaction mechanism between bacteriophages and bacteria on the humification process in composting with added Fe2O3 nanoparticles (NPs). The results showed that Fe2O3 NPs optimized the function of the bacterial community by maintaining a high relative abundance of Bacillota, promoting organic matter degradation, and significantly increasing the HS concentration by 27 % on day 30 of composting. Specifically, the higher Bacillota relative abundance directly enhanced the relative abundance of cellulose phosphorylase (GH94), activated the glycolysis pathway, and led to a significant enrichment of metabolites such as phenols, organic acids, and amino acids on day 14 of composting, thereby strengthening energy metabolism. Furthermore, lysis of the host (Bacillota) by bacteriophages released cellular contents, providing key precursors for HS condensation. Concurrently, lysis by bacteriophages interrupted metabolism of the host, preventing complete mineralization of some carbon, thereby converting easily mineralizable carbon into sequestered HS carbon. Fe2O3 NPs also accelerated lignin depolymerization, enriching aromatic precursors and providing core structural units for humification. This study reveals that Fe2O3 NPs stimulate the synergistic action of the functional bacterium Bacillota and remodeling of the microbial-virus interaction network to drive efficient lignocellulose degradation and humification, thus providing a new strategy for optimizing composting processes based on viral regulation.}, }
@article {pmid41167475, year = {2025}, author = {Hamelin, B and Hosch, S and Neidhöfer, C and Ruf, MT and Haslbauer, JD and Field, CM and Schläpfer, P and Manzo, M and Neumayr, A and Kuenzli, E and Mancuso, M and Sachs, M and Mensah, N and Bernhard, R and Klaus-Wirthner, B and Concu, M and Nienhold, R and Kuehl, R and Baettig, V and Weisser-Rohacek, M and Gosert, R and Tzankov, A and Tschudin-Sutter, S and Khanna, N and Leuzinger, K and Keller, PM and Mertz, KD}, title = {Unbiased DNA pathogen detection in tissues: Real-world experience with metagenomic sequencing in pathology.}, journal = {Laboratory investigation; a journal of technical methods and pathology}, volume = {}, number = {}, pages = {104254}, doi = {10.1016/j.labinv.2025.104254}, pmid = {41167475}, issn = {1530-0307}, abstract = {Pathogen detection in formalin-fixed paraffin-embedded (FFPE) tissue remains challenging. We implemented metagenomic next-generation sequencing (mNGS) in our clinical diagnostic workflow to evaluate its feasibility, diagnostic yield, and pathogen spectrum in routine infectious pathology cases. Between November 2021 and April 2025, we analyzed 623 FFPE tissue samples using a low-depth mNGS workflow on the Thermo Fisher Ion Torrent platform with a CLC Genomics Workbench bioinformatics pipeline. Our assay was designed to detect DNA pathogens. When possible, results were validated by orthogonal methods including species-specific PCRs, 16S/ITS PCR, and immunohistochemistry on tissue sections. Among 623 samples analyzed, at least one potentially pathogenic and plausible microorganism was identified in 229 samples (36.8%), while 334 (53.6%) were negative and 60 (9.6%) were uninterpretable due to quality control failures or suspected contamination. Of the 229 positive samples, 145 (63.3%) involved bacteria, 37 (16.2%) viruses, 28 (12.2%) fungi, and 9 (3.9%) parasites; mixed infections with more than one pathogen were detected in 10 (4.4%) samples. The most frequently identified bacterial family was Mycobacteriaceae (n=27), including Mycobacterium xenopi (n=8), which is not routinely covered by syndromic multiplex PCR panels. Notable viral and fungal detections included a novel human circovirus and Coccidioides posadasii. Despite variable sample quality and DNA input, mNGS yielded reliable results in a wide range of tissue types. Metagenomic NGS is a feasible, valuable addition to routine infectious pathology diagnostics, particularly in complex or inconclusive cases. The assay improved the diagnostic yield compared to conventional PCR, expanded the range of detectable pathogens, and proved robust even in low-quality FFPE samples. These results support broader adoption of mNGS in tissue-based pathogen diagnostics.}, }
@article {pmid41167355, year = {2025}, author = {Feng, Y and Liu, S and Huang, X and Geng, Y and Mou, C and Zhao, H and Zhou, J and Li, Q and Deng, Y}, title = {Ferroptosis Triggered by Gill Dysbiosis Mediates Immune Failure in Grass Carp Overwintering Syndrome.}, journal = {Fish &amp; shellfish immunology}, volume = {}, number = {}, pages = {110965}, doi = {10.1016/j.fsi.2025.110965}, pmid = {41167355}, issn = {1095-9947}, abstract = {Overwintering syndrome (OWS) causes massive mortality in grass carp (Ctenopharyngodon idella) during early spring, yet its pathogenesis beyond the "low-temperature-pathogen" paradigm remains unclear. This study investigates the cascade mechanism through integrated multi-omics analyses on gill tissues of healthy and OWS-affected grass carp. Gill histopathology revealed progressive necrotizing inflammation in OWS-affected grass carp. Transcriptomics identified 962 differentially expressed genes, highlighting upregulation of cytokine signaling, porphyrin metabolism, and ferroptosis alongside downregulation of adrenergic pathways. Ferroptosis was confirmed through the suppression of glutathione peroxidase 4 (GPX4) and the accumulation of iron in necrotic lamellae. Mucous cell depletion and eosinophil disintegration compromised the mucosal barriers of the gills. Metagenomic analysis first revealed a state of microbial dysbiosis, marked by bacterial dominance comprising 92.21% of the community, along with an enrichment of biofilm and exotoxin genes and a reduction in immune modulation, all exacerbating barrier dysfunction. Subsequent integrated correlation analysis linked the specifically enriched bacteria taxa, including Caldilinea sp. CFX5 and Ilumatobacter sp., to the upregulation of metabolic and virulence pathways, while also revealing significant microbiota-gene interactions that modulate gill immune and metabolic functions. Although previously reported pathogens like Flavobacterium and Aeromonas showed increased abundance in OWS-affected fish, their overall abundance remained low. Based on these findings, we propose a "Dysbiosis-Ferroptosis-Collapse" axis, in which microbiota-driven barrier disruption promotes iron overload and the suppression of GPX4, triggering non-resolving inflammation and ion dyshomeostasis. Targeting this cascade provides a novel theoretical framework for intervening in and developing new treatments for OWS.}, }
@article {pmid41167204, year = {2025}, author = {Donovan, J and Cresswell, FV and Figaji, A and Thwaites, GE}, title = {Integrating metagenomic sequencing into diagnostic pathways for tuberculous meningitis - Authors' reply.}, journal = {The Lancet. Infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/S1473-3099(25)00628-0}, pmid = {41167204}, issn = {1474-4457}, }
@article {pmid41167203, year = {2025}, author = {Lin, SY and Chen, CJ and Lu, PL}, title = {Integrating metagenomic sequencing into diagnostic pathways for tuberculous meningitis.}, journal = {The Lancet. Infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/S1473-3099(25)00627-9}, pmid = {41167203}, issn = {1474-4457}, }
@article {pmid41167188, year = {2025}, author = {Cha, JH and Kim, N and Ma, J and Lee, S and Koh, G and Yang, S and Beck, S and Byeon, I and Lee, B and Lee, I}, title = {A high-quality genomic catalog of the human oral microbiome broadens its phylogeny and clinical insights.}, journal = {Cell host &amp; microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2025.10.001}, pmid = {41167188}, issn = {1934-6069}, abstract = {The oral microbiome is increasingly linked to human health. To further examine this microbial community, we present the human reference oral microbiome (HROM), with 72,641 high-quality genomes from 3,426 species, including 2,019 previously unidentified species, improving metagenomic sequence read classification over existing catalogs. Notably, HROM unveils 1,137 previously uncharacterized candidate phyla radiation (CPR) species, establishing Patescibacteria as the most prevalent phylum in the oral microbiota and distinct from environmental Patescibacteria. Additionally, an oral CPR subclade is associated with periodontitis, complementing Porphyromonas gingivalis in predicting disease. Finally, comparing HROM with reference genomes of the gut microbiome reveals taxonomic and functional divergence between these microbiomes. HROM contains 42 ectopic oral species, and their relative abundance in gut microbiota is predictive of intestinal, cardiovascular, and liver diseases. Thus, HROM offers an expanded view of the oral microbiome and highlights the clinical importance of further examining the links between oral microbes and systemic disorders.}, }
@article {pmid41166605, year = {2025}, author = {Huang, XC and Zheng, SJ and Hu, YL and Cao, YE and Liu, YY and Dai, K and Zeng, RJ and Zhang, F}, title = {Comprehensive Insights into the Role of Hydrogen Bonds in the Anaerobic Fermentation of Insoluble Exopolysaccharides in Waste Activated Sludge: Taking Chondroitin Sulfate as an Example.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c11116}, pmid = {41166605}, issn = {1520-5851}, abstract = {The hydrogen bond confers the structural recalcitrance of insoluble exopolysaccharides, but its role in the anaerobic fermentation of waste activated sludge (WAS) is seldom reported. As a typical high-molecular-weight exopolysaccharide with poor solubility, chondroitin sulfate (CS) was used to elucidate the role of hydrogen bonds in WAS fermentation. The chondroitin sulfate-degrading consortium (CSDC) was enriched for 180 days, but the methane production was limited (∼18%). The methane production was significantly improved by 88.2%, and extracellular enzyme activity increased by 11.8% after the fast acidic pretreatment of CS. The disruption of the hydrogen bond was confirmed by combining 41.6% reduction of particle size, 46.7% decrease of surface height, blue shifts in the O-H vibrational spectra, and 38.1% decline of interfacial free energy. The molecular dynamics simulation further showed that the hydrogen bond number after the fast acidic pretreatment was reduced from 51.4 ± 2.7 to 44.9 ± 2.1. Co-occurrence network analysis identified Thermovirga as a keystone taxon to facilitate microbial cooperation. The metagenomics and metaproteomics analyses revealed that Proteiniphilum and Mariniphaga served as key producers of extracellular CS-degrading enzymes, primarily CS lyase (EC 4.2.2.5). Above all, these findings demonstrate that the hydrogen bond represents a non-negligible structural constraint on the degradability of insoluble exopolysaccharides.}, }
@article {pmid41166306, year = {2025}, author = {Zhang, ZF and Huang, JE and Phurbu, D and Qu, ZS and Liu, F and Cai, L}, title = {A deep metagenomic atlas of Qinghai-Xizang Plateau lakes reveals their microbial diversity and salinity adaptation mechanisms.}, journal = {Cell reports}, volume = {44}, number = {11}, pages = {116483}, doi = {10.1016/j.celrep.2025.116483}, pmid = {41166306}, issn = {2211-1247}, abstract = {The Qinghai-Xizang Plateau (QXP), harboring the planet's highest density of plateau lakes, offers an exceptional biogeographic environment for studying extremophilic microbial communities and their adaptation to salinity. Through deep metagenomic sequencing, we construct the Qinghai-Xizang Lake Sediment Genome (QXLSG) catalog, a high-resolution genomic catalog comprising 5,866 metagenome-assembled genomes (MAGs), 58.16 million non-redundant protein encoding genes, and 19,008 biosynthetic gene clusters. Notably, 80.78% of the 2,742 species-level MAGs represent undescribed taxa, significantly expanding the known microbial diversity. Salinity emerges as the primary environmental factor influencing microbial community. Functional annotation highlights that the "salt-out" strategy, particularly the uptake of glycine betaine, is the main mechanism for salinity tolerance. This strategy is prevalent in both hypersaline lake communities and the dominant microbial phyla. Overall, this study provides a crucial genetic resource for future bioprospecting and deepens our understanding of the fundamental mechanisms of microbial adaptation to extreme saline environments.}, }
@article {pmid41166145, year = {2025}, author = {Ding, W and Zhang, H and Wen, J and Xiong, G and Cheng, M and Liu, J and Zhao, Y and Miao, Q and Deng, H and Xu, Z and Mi, L and Tan, Z and Su, L and Long, Y and Ning, K}, title = {A multi-omics analysis reveals a gut microbiome-LPC metabolic axis driving postoperative inflammation in cardiopulmonary bypass patients.}, journal = {Shock (Augusta, Ga.)}, volume = {}, number = {}, pages = {}, doi = {10.1097/SHK.0000000000002722}, pmid = {41166145}, issn = {1540-0514}, abstract = {BACKGROUND: Patients undergoing cardiac surgery with cardiopulmonary bypass (CSCPB) are at substantial postoperative risk, which may be influenced by alterations in gut microbiota and metabolites. The roles of these biological changes in postoperative outcomes remain inadequately explored.<br><br>METHODS: We collected 54 preoperative samples and 33 postoperative samples from 60 CSCPB patients. Metagenomic and metabolomic sequencing were performed to identify the gut microbiota and serum and fecal metabolites. We examined the dynamics pattern of these microbiota and metabolites, as well as their associations with the postoperative risk. Additionally, we developed a predictive model for postoperative risk based on preoperative microbiome and metabolome data.<br><br>RESULTS: We revealed significant alterations of gut microbiota (P = 0.012), serum metabolites (P = 3.50e-10) and fecal metabolites (P = 0.0081) in patients following CSCPB, among which lysophosphatidylcholines (LPCs) exhibited notable changes. Particularly, we identified a potential regulatory function of the microbiota on LPC metabolism, which further influence the postoperative risk. The predictive model for ICU stay duration achieved a mean absolute error (MAE) of 1.27 days and an R&#xb2; of 0.63, suggesting its utility in assessing postoperative risk. Also, our study provides a valuable resource (catalogue GM3C) for further investigation into potential medical targets in CSCPB patients, comprising more than 2,000 metagenome-assembled genomes and 3 million unigenes.<br><br>CONCLUSIONS: Our study reveals that the gut microbiome and LPC-centered metabolism form a functional network influencing postoperative risk in CSCPB patients. These findings underscore the role of gut-derived signals in modulating non-infectious inflammatory responses and host imbalance, offering a multi-omics framework for decoding systemic complications beyond classical sepsis paradigms.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov (NCT04032938). Registered 25 July 2019, https://clinicaltrials.gov/study/NCT04032938#study-record-dates.}, }
@article {pmid41165913, year = {2025}, author = {de Farias, BO and Dos Santos Lopes, E and Pereira, BC and Pimenta, RL and Parente, CET and Seldin, L and Saggioro, EM}, title = {Poultry slaughterhouse wastewater as a driver of bacterial community shifts and the spread of antibiotic resistance genes in aquatic ecosystems.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {11}, pages = {1268}, pmid = {41165913}, issn = {1573-2959}, mesh = {*Wastewater/microbiology ; Animals ; *Abattoirs ; *Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Poultry ; Genes, Bacterial ; Waste Disposal, Fluid ; RNA, Ribosomal, 16S ; Environmental Monitoring ; Anti-Bacterial Agents ; *Water Microbiology ; Microbiota ; }, abstract = {Poultry slaughterhouse wastewater (PSW) is a source of environmental pollutants, harboring pathogens and antibiotic resistance genes (ARGs). This study aimed to assess the effects of conventional biological treatment of PSW on the bacterial community and its efficiency in removing ARGs, as well as to evaluate the impact of its discharge on the receiving river. Samples were collected from raw sewage, treated effluent, and upstream and downstream river sites. Total metagenomic DNA was extracted for real-time PCR quantification of 16S rRNA, yccT gene (Escherichia coli), and ARGs, which were selected based on their ability to confer resistance to clinically relevant antibiotics and their prevalence in poultry-associated environments, including resistance to tetracyclines (tetM), beta-lactams (blaTEM), sulfonamides (sul1), and quinolones (qnrS). Amplicon sequencing of 16S rRNA V3-V4 region was used to assess bacterial community structure. Treated effluent significantly altered the downstream microbiome, reducing bacterial richness by up to 72.3% and diversity by 25.4%. Effluent-associated phyla such as Pseudomonadota (37%), Bacillota (28%), and Bacteroidota (26%) became dominant in the downstream river samples. Enterobacterales increased after treatment, and E. coli increased by 2.93 logs downstream. All ARGs increased after treatment and remained elevated downstream, with qnrS and sul1 rising by 3.77 and 3.87 logs, respectively. These findings highlight PSW treatment plants as a potential point of selection and dissemination of antimicrobial resistance (AMR)-related bacteria and genes. Inefficient treatment contributes to shifts in river bacterial communities and the spread of AMR.}, }
@article {pmid41165328, year = {2025}, author = {Eshak, MIY and Breithaupt, A and Tews, BA and Luttermann, C and Franzke, K and Scheibe, M and Woelke, S and Beer, M and Rubbenstroth, D and Pfaff, F}, title = {Wǔhàn sharpbelly bornavirus infects and persists in cypriniform cells.}, journal = {Journal of virology}, volume = {}, number = {}, pages = {e0132225}, doi = {10.1128/jvi.01322-25}, pmid = {41165328}, issn = {1098-5514}, abstract = {Our recent study using in silico data mining identified novel culterviruses (family: Bornaviridae) in fish, including a variant of Wuhan sharpbelly bornavirus (WhSBV) in grass carp kidney and liver cell lines. Here, metagenomic sequencing of different fish cell lines revealed WhSBV in two cell lines from grass carp (Ctenopharyngodon idella; order: Cypriniformes). Using these cell lines, we investigated the ability of WhSBV to infect and establish persistent infection in other cell lines from bony fish (Cypriniformes, Chichliformes, Salmoniformes, Centrarchiformes, and Spariformes), reptiles (Testudines and Squamata), birds (Galliformes), and mammals (Primates and Rodentia). WhSBV showed efficient replication and a time-dependent increase in viral RNA levels in cypriniform cells, whereas replication was limited, confined to single cells, and lacked a clear time-dependent increase in cells from other bony fish and reptiles. No replication was detected in avian and mammalian cells. In situ hybridization and electron microscopy confirmed the presence of viral RNA and particles in infected cypriniform cells. Transcriptomic sequencing revealed minimal innate immune activation during early stages of infection and antiviral response only at later stages, suggesting that WhSBV establishes persistence by evading early immune recognition. In addition, we identified polycistronic viral mRNAs regulated by specific transcriptional start and termination sites and RNA splicing. Viral proteins were detected, confirming previous in silico predictions. These findings provide insights into the potential infectivity, persistence mechanisms, and transcriptional strategies of WhSBV. This study validates previous findings from in silico data mining, further reinforcing its effectiveness as a powerful tool for discovering hidden viruses.IMPORTANCEUnderstanding the diversity and host range of viruses is crucial for assessing their ecological role, associated diseases, and zoonotic potential. However, many newly discovered viruses are characterized using sequence data alone because isolates are often difficult to obtain. Using cell culture models, this study characterizes Wuhan sharpbelly bornavirus (WhSBV), a member of the genus Cultervirus. Here, we demonstrate its ability to establish persistent infection in cypriniform fish cell lines, while exhibiting restricted replication in certain non-cypriniform fish. The identification of polycistronic transcription, splicing events, and immune evasion mechanisms advances our understanding of the molecular biology of WhSBV and culterviruses in general. By validating in silico predictions, this study highlights the power of computational approaches in uncovering viral diversity. As cypriniform fish include economically important species such as carp, understanding the dynamics of WhSBV host range and infection biology may be crucial for future aquaculture health management.}, }
@article {pmid41164885, year = {2025}, author = {Hosseinkhani, F and Chevalier, C and Marizzoni, M and Park, R and Bos, S and Dunjko, AK and van Duijn, CM and Harms, AC and Frisoni, GB and Hankemeier, T}, title = {Plasma and feces multiomics unveil cognition-associated perturbations of chronic inflammatory pathways of the gut-microbiota-brain axis.}, journal = {Alzheimer's &amp; dementia : the journal of the Alzheimer's Association}, volume = {21}, number = {10}, pages = {e70844}, doi = {10.1002/alz.70844}, pmid = {41164885}, issn = {1552-5279}, support = {184.034.019//Dutch Research Council (NWO)/ ; 175.2019.032//Dutch Research Council (NWO)/ ; //Private Foundation of Geneva University Hospitals: A.P.R.A.-Association Suisse pour la Recherche sur la Maladie d'Alzheimer, Gen&#xe8;ve/ ; //Fondation Segr&#xe9;, Gen&#xe8;ve/ ; //Race Against Dementia Foundation, London, UK/ ; //Fondation Child Care, Gen&#xe8;ve/ ; //Fondation Edmond J. Safra, Gen&#xe8;ve/ ; //Fondation Minkoff, Gen&#xe8;ve/ ; //Fondazione Agusta, Lugano/ ; //McCall Macbain Foundation, Canada/ ; //Nicole et Ren&#xe9; Keller, Gen&#xe8;ve/ ; //Fondation AETAS, Gen&#xe8;ve/ ; //Clinical Research Center, University Hospital and Faculty of Medicine/ ; //Italian Ministry of Health (Ricerca Corrente)/ ; //H&#xf4;pitaux Universitaires de Gen&#xe8;ve/ ; 175.2019.032//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Feces/microbiology/chemistry ; Male ; Female ; *Dysbiosis/metabolism ; *Cognitive Dysfunction/metabolism/microbiology ; Aged ; *Inflammation/metabolism ; *Brain/metabolism ; Cytokines/blood ; Multiomics ; }, abstract = {INTRODUCTION: Gut-microbiota dysbiosis has been linked to cognitive decline. Given its role in metabolism, immunity, and environmental interactions, broader molecular signaling alterations are likely.<br><br>METHODS: We analyzed gut microbiota composition, plasma and fecal metabolites, and inflammatory cytokines across cognitive stages, from healthy controls to dementia.<br><br>RESULTS: Alpha diversity declined with increasing cognitive impairment severity. Short-chain fatty acid-producing Firmicutes and Bacteroidota decreased from 76% and 17% in controls to 59% and 11% in dementia, respectively. Proteobacteria (e.g., Escherichia-Shigella) rose from&#xa0;<&#xa0;2% to 4%, and Verrucomicrobiota from 3% to 11%. Despite overall Firmicutes decline, Ruminococcus gnavus, a mucus-degrading species, increased in dementia. These shifts correlated with elevated plasma cytokines, suggesting a link between gut dysbiosis and systemic inflammation. Bacteria-associated metabolites, including bile acids, trimethylamine N-oxide, oxylipins, sugars, and fatty acids were significantly altered. Changes were seen as early as subjective cognitive decline.<br><br>DISCUSSION: Larger studies are needed to validate these findings and explore microbiome-based interventions.<br><br>HIGHLIGHTS: Examined gut microbiota, inflammation, and metabolic changes in cognitive impairment stages Early metabolic changes in feces detected before plasma alterations Observed shifts in gut microbiota and inflammation associated with cognitive decline Suggests potential for early biomarkers based on gut metabolites Calls for larger, longitudinal studies to validate findings.}, }
@article {pmid41164876, year = {2025}, author = {Chen, H and Lu, Z and Xiao, C and Wang, X and Xi, Y and Yan, Y and Zheng, JS and Chen, YM and Deng, K}, title = {Association Between Alternative Complement Pathway and Carotid Plaque and the Underlying Gut Microbial and Inflammatory Biomarkers: A Cohort Study.}, journal = {Arteriosclerosis, thrombosis, and vascular biology}, volume = {}, number = {}, pages = {}, doi = {10.1161/ATVBAHA.125.322968}, pmid = {41164876}, issn = {1524-4636}, abstract = {BACKGROUND: The alternative pathway (AP) plays a crucial role in triggering complement activation and promoting chronic inflammation. This study aims to investigate the longitudinal association between AP and atherosclerosis, and explore the potential role of gut microbiota and inflammatory factors in their association.<br><br>METHOD: This study was based on a 9-year prospective cohort of 3382 participants from Guangzhou, China (mean age&#xb1;SD, 57.75&#xb1;5.85 years; 68.8% female), with data on serum APACPs (AP-associated complement proteins) and carotid plaque (measured by ultrasound) repeatedly measured up to 3&#xd7;. Baseline inflammatory markers were evaluated in 923 participants, and gut shotgun metagenome data were obtained from 1567 participants. Mendelian randomization analysis was performed using genome-wide significant genetic variants as instrumental variables to suggest potential causal associations.<br><br>RESULTS: Both longitudinal and prospective analyses consistently demonstrated positive associations between carotid plaque and 3 complement components: C3 (odds ratios [95% Cl] for the highest versus lowest quartiles, 1.36 [1.07-1.74] in longitudinal analysis and 1.29 [1.06-1.56] in prospective analysis), CFB (complement factor B; 1.36 [1.07-1.72] in longitudinal analysis and 1.39 [1.15-1.69] in prospective analysis), and CFH (complement factor H; 1.39 [1.10-1.76] in longitudinal analysis and 1.31 [1.07-1.61] in prospective analysis). Mendelian randomization analysis suggested a potential causal association between CFB and carotid plaque. Inflammatory factors (CRP [C-reactive protein] and IL-6 [interleukin-6]) and microbial species (Ruminococcus bromii, Roseburia hominis, Rothia mucilaginosa, Collinsella stercoris, Olsenella scatoligenes, and Bacteroides massiliensis) were significantly associated with both APACPs and carotid plaque (P<0.05). For example, butyrate-producing bacterium R bromii was inversely associated with CFB and carotid plaque (odds ratios [95% CI], 0.83 [0.79-0.88]) and may mediate the CFB-carotid plaque association (proportion mediated, 13.5%; P=0.005). Microbial risk score (weighted sum of selected microbial species; proportion mediated, 42.6%; P<0.001) and total immune factors (the sum of all inflammatory factors; proportion mediated, 19.0%; P=0.002) mediated the association between Total-APACPs (sum of standardized carotid plaque-related APACPs [C3, CFB, and CFH]) and carotid plaque.<br><br>CONCLUSIONS: Our study showed a negative association between the AP and carotid plaque in a longitudinal cohort. Gut microbiota and inflammatory biomarkers may provide mechanistic insights into the association between the AP and atherosclerosis. Our findings pave the way for the development of new therapeutic targets for atherosclerosis.}, }
@article {pmid41164228, year = {2025}, author = {Wei, S and Yin, H and Hu, X and Chi, Y and Zhang, L and Zhang, B and Qian, K and Xu, W}, title = {Detection of antimicrobial peptides from fecal samples of FMT donors using deep learning.}, journal = {Frontiers in veterinary science}, volume = {12}, number = {}, pages = {1689589}, pmid = {41164228}, issn = {2297-1769}, abstract = {INTRODUCTION: Antimicrobial peptides (AMPs) represent a class of short peptides that are widely distributed in organisms and are regarded as an effective means to tackle bacterial resistance, potentially functioning as substitutes for onventional antibiotics.<br><br>METHODS: We employed metagenomics in combination with deep learning to mine AMPs from the 120 fecal microbiota transplantation (FMT) donor metagenome. Subsequently, a comprehensive analysis of the candidate AMPs was conducted through metaproteomic cross-validation, solubility analysis, cross-validation with other prediction tools, correlation analysis, and molecular dynamics simulations. Finally, four candidate AMPs were selected for chemical synthesis, and experimental validation identified two with broad-spectrum antimicrobial activity. Furthermore, molecular docking was utilized to further analyze the antimicrobial mechanisms of the candidate AMPs.<br><br>RESULTS: Our approach successfully predicted 2,820,488 potential AMPs. After a comprehensive analysis, four candidate AMPs were selected for synthesis, two of which exhibited broad-spectrum antimicrobial activity. Molecular docking provided further insight into the binding mechanisms of these peptides.<br><br>DISCUSSION: This study demonstrates the feasibility of discovering functional AMPs from the human fecal microbiome using computational and experimental approaches, highlights the potential of mining novel AMPs from the fecal microbiome, and provides new insights into the therapeutic mechanisms of FMT.}, }
@article {pmid41164129, year = {2025}, author = {Zhang, Z and Lin, J and Song, X and Yi, X and Zhou, H and Xu, Z}, title = {Acute intracranial EBV and CMV infections after chemoimmunotherapy for EBV-associated nasopharyngeal carcinoma: a case report and literature review.}, journal = {Frontiers in oncology}, volume = {15}, number = {}, pages = {1608787}, pmid = {41164129}, issn = {2234-943X}, abstract = {A 36-year-old male patient presented to our hospital complaining of epistaxis for 3 months and persistent headaches with facial numbness for 3 days. After a series of exams, he was diagnosed with nasopharyngeal carcinoma (T4N2M1, stage IVB, AJCC 8th), with a biopsy consistent with non-keratinizing squamous cell carcinoma, and received a combination therapy of gemcitabine, cisplatin, and tislelizumab. Following the first dose, headaches and facial numbness were relieved. On the third day, however, he developed recurrent fever, with a peak body temperature of 39.2 °C, and developed severe paroxysmal stabbing pain in the right frontal region suggestive of trigeminal neuralgia, along with numbness on the right face. We considered multiple possibilities and provided symptomatic treatments, but with poor efficacy. Subsequently, given the emergence of prominent neurological symptoms and fever, we proceeded with a lumbar puncture for cerebrospinal fluid (CSF) analysis. Metagenomic next-generation sequencing (mNGS) of CSF detected the presence of Epstein-Barr virus (EBV) and cytomegalovirus (CMV), and acute intracranial viral infections were considered. After treatment with ganciclovir, the patient's body temperature returned to normal, and headaches and facial numbness were alleviated, and no pathogens were detected in a follow-up examination. We report a case of trigeminal neuralgia emerging post-chemoimmunotherapy, accompanied by CSF positivity for EBV and CMV, where antiviral intervention with ganciclovir resulted in significant symptom alleviation.}, }
@article {pmid41164002, year = {2025}, author = {Ferreira, R and Coelho, L and Santos, JD and Sobral, D and Isidro, J and Mixão, V and Pinto, M and Nunes, A and Borrego, MJ and Lopo, S and Oleastro, M and Sousa, R and Palminha, P and Veríssimo, C and Gargaté, MJ and Guiomar, R and Cordeiro, R and Macedo, R and Bajanca-Lavado, P and Paixão, P and Duarte, S and Vieira, L and Borges, V and Gomes, JP}, title = {Probe-based metagenomic pathogen detection: advancing laboratory capacity for complex diagnosis.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1656831}, pmid = {41164002}, issn = {1664-302X}, abstract = {Probe-based pathogen enrichment, followed by NGS, is a promising tool for complex diagnosis, overcoming traditional challenges of shotgun metagenomics, namely small microbial/human genetic material ratio and demanding computational resources. Here, we assessed the combined detection performance of two Illumina probe-based panels, the Respiratory and the Urinary Pathogen ID panels (RPIP and UPIP), using 99 clinical samples of 15 different matrices (e.g., cerebrospinal fluid, plasma, serum, urine, swabs, biopsies, etc.) available from Portuguese National Reference Laboratories. This sample set involved 114 "PCR-positive hits" (Ct values range of 9.7-41.3; median of 28.4) for 52 non-redundant human pathogens. For a more detailed bioinformatics assessment, as a complement of the Illumina turnkey solution (Explify), we applied an extended version of our INSaFLU-TELEVIR(+) metagenomics pipeline. Whereas Explify analyses resulted in an initial detection frequency of 73.7% (84/114), the subsequent application of INSaFLU-TELEVIR(+), including taxonomic classification followed by confirmatory read mapping, enabled an overall detection proportion of 79.8% (91/114) of the PCR-positive hits. This translated into a detection rate increment from 54.3% (19/35) to 65.7% (23/35) for bacteria, and from 85.3% (58/68) to 89.7% (61/68) for viruses. The implemented workflow was also very satisfactory for samples with qPCR Ct values above 30, with an overall detection frequency of 71.8% (28/39) when compared with the 92.0% (46/50) observed for those with Ct ≤ 30. In summary, this study validated and established a pioneering approach at the Portuguese National Institute of Health to support clinicians in complex diagnosis, contributing to advance diagnostic capabilities toward a more informed clinical decision and potential improvement of infectious disease outcomes.}, }
@article {pmid41163852, year = {2025}, author = {Yuan, M and Wang, Q and Lu, Y and Xu, P and Pan, C and Zhang, W and Lu, H}, title = {Comparison of gut viral communities between autism spectrum disorder and healthy children.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1660970}, pmid = {41163852}, issn = {2235-2988}, mesh = {Humans ; *Autism Spectrum Disorder/virology ; Feces/virology ; *Gastrointestinal Microbiome ; Child ; Phylogeny ; *Viruses/classification/genetics/isolation &amp; purification ; Male ; *Virome ; Female ; Metagenomics ; Child, Preschool ; Case-Control Studies ; }, abstract = {INTRODUCTION: Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder, which brings a great burden to the family and society. Gut microbiota is considered to be an important factor in ASD that easily affects function and development of the immune, metabolic, and nervous systems. However, most available studies have mainly focused on the altered gut bacteria, our knowledge of gut viruses in ASD children remains limited.<br><br>METHODS: In this study, we collected fecal samples from ASD children and healthy controls, then analyzed and compared the differences of the gut viral communities between the two groups by viral metagenomic techniques.<br><br>RESULTS: The alpha diversity of the ASD virome was lower than that of the healthy virome, and the beta diversity had a significant difference between ASD and healthy children. Podoviridae accounted for the highest proportion of viruses in ASD patients, while Alphaflexiviridae was dominant in healthy controls. There was a statistical difference in the abundance of Microviridae between the two groups. Additionally, human astrovirus, picobirnavirus, and norovirus were detected by phylogenetic analysis.<br><br>DISCUSSION: This study revealed that alpha diversity was reduced in children with ASD, and different compositions in gut viral communities were observed between ASD patients and healthy controls. Changes in viral diversity and composition deepen our understanding of the differences in the gut viral communities between ASD and healthy children, and also provides a perspective for further exploration of viruses related to ASD children.}, }
@article {pmid41163226, year = {2025}, author = {Huang, S and Chen, Y and Lu, X and Ji, L and Shen, Q and Yang, S and Liu, Y and Wang, X and Wu, P and Yang, H and Shan, T and Zhang, W}, title = {Virome of canine lymph nodes: identification of viruses with zoonotic potential.}, journal = {Virology journal}, volume = {22}, number = {1}, pages = {350}, pmid = {41163226}, issn = {1743-422X}, support = {Nos. 2023YFD1801300 and 2022YFC2603801//National Key Research and Development Programs of China/ ; no. 82341106//National Natural Science Foundation of China/ ; }, mesh = {Dogs ; Animals ; *Lymph Nodes/virology ; Phylogeny ; *Virome ; *Zoonoses/virology ; Genome, Viral ; China ; Humans ; *Viruses/genetics/classification/isolation &amp; purification ; *Dog Diseases/virology ; Metagenomics ; *Viral Zoonoses/virology/transmission ; }, abstract = {BACKGROUND: Zoonotic infectious diseases have significantly impacted global public health, as exemplified by the COVID-19 pandemic that triggered an unprecedented worldwide crisis with millions of infections. Among animals closely associated with humans, canines occupy a prominent position due to their extensive integration into human daily life. Consequently, investigating the virome of canines in close contact with humans holds significant scientific and public health implications.<br><br>RESULTS: This study selected lymph node tissues from 24 dogs in close contact with humans from Shanghai and Henan, specifically collecting submandibular lymph nodes and carefully removing surrounding fat and connective tissues. Through comprehensive metagenomic analysis, we assembled 17 complete viral genomes spanning 6 viral families, including Adenoviridae (n&#x2009;=&#x2009;1), Paramyxoviridae (n&#x2009;=&#x2009;1), Polyomaviridae (n&#x2009;=&#x2009;1), Parvoviridae (n&#x2009;=&#x2009;7), Circoviridae (n&#x2009;=&#x2009;6), and Genomoviridae (n&#x2009;=&#x2009;1). Phylogenetic analysis of these dominant viruses elucidated the evolutionary relationships between the assembled viral sequences in this study and known reference viruses. Notably, we discovered a novel virus belonging to the Genomoviridae family.<br><br>CONCLUSION: This research not only elucidates the remarkable diversity of the virome within canine lymph node tissues but also employs phylogenetic analysis to delineate the evolutionary relationships between these viruses and previously documented strains. Notably, this study represents the first identification of parvoviruses and circoviruses in canine lymph nodes that exhibit high sequence homology with human viral strains, suggesting that these canine-derived and human-associated viruses may have diverged from a common ancestor.}, }
@article {pmid41163171, year = {2025}, author = {Qiu, X and Zhang, M and Zhang, L and Chen, H and Gao, M and Li, W and Yu, Z and Hou, Z}, title = {Peculiarities of vaginal microbiota in perimenopausal and postmenopausal women with type 2 diabetes mellitus.}, journal = {Annals of clinical microbiology and antimicrobials}, volume = {24}, number = {1}, pages = {59}, pmid = {41163171}, issn = {1476-0711}, support = {H2020206490//Natural Science Foundation of Hebei Province,China/ ; 20230095//Medical Science Research Subject Plan of Hebei/ ; PD2023002//Clinical Medicine Postdoctoral Research Support Program of Hebei Medical University/ ; B2024003014//Hebei Province Yanzhao Golden Talent Program/ ; 2024YFC2510600//Key R&amp;D Program of the China Ministry of Science and Technology/ ; }, mesh = {Humans ; Female ; *Vagina/microbiology ; *Diabetes Mellitus, Type 2/microbiology ; Middle Aged ; *Postmenopause ; *Microbiota ; *Perimenopause ; Aged ; *Bacteria/classification/genetics/isolation &amp; purification ; Metagenomics ; Dysbiosis/microbiology ; }, abstract = {BACKGROUND: The changes in the vaginal microbiota and potential dysbiosis adjustment strategies in diabetic patients remain inconclusive. This study was designed to investigate the impact of Type 2 diabetes mellitus (T2DM) on the ecological dynamics of the vaginal microbiota in perimenopausal and postmenopausal women, with a focus on microbial community structure and functional homeostasis.<br><br>METHODS: Vaginal secretion samples from 22 T2DM patients (DM group) and 23 healthy controls (CT group) under perimenopausal and postmenopausal conditions were analyzed via metagenomic sequencing. Alpha diversity (Observe, ACE, Shannon-Weaver, Gini-Simpson indices) and beta diversity (PCoA, NMDS) were assessed. Taxonomic profiling, LEfSe analysis, and co-occurrence network construction were performed to identify differential species and microbial interactions. Neutral community modeling evaluated stochastic vs. deterministic assembly processes.<br><br>RESULTS: No significant differences were observed in age (62.22&#x2009;&#xb1;&#x2009;5.74 vs. 58.23&#x2009;&#xb1;&#x2009;7.55, p&#x2009;=&#x2009;0.052) or perimenopausal/ postmenopausal status (3/19 vs. 5/18, p&#x2009;=&#x2009;0.748) between the DM and CT groups. The DM group exhibited significantly higher alpha diversity (p&#x2009;<&#x2009;0.05) and distinct beta diversity clustering (p&#x2009;<&#x2009;0.05), marked by reduced Lactobacillus relative abundance (28.7% in CT vs. 6.3% in DM) and increased abundance of opportunistic pathogenic genera (Klebsiella, Gardnerella, Staphylococcus). LEfSe identified Firmicutes as CT biomarkers, while the relative abundance of Bacteroidetes and Prevotella increased in DM group. Both fasting blood glucose and HbA1c levels significantly influenced the relative abundance of vaginal Lactobacillus crispatus, Lactobacillus gasseri, and Lactobacillus iners, showing a significant negative correlation. Co-occurrence networks revealed greater complexity and more integrated in the DM group (more triangles, lower modularity, higher node degrees, higher clustering coefficients, p&#x2009;<&#x2009;0.0001). Neutral modeling indicated stochastic assembly (R&#xb2; >0.5), with Lactobacillus species and opportunistic pathogens deviating from neutral predictions in DM.<br><br>CONCLUSION: Under perimenopausal and postmenopausal conditions, T2DM disrupts vaginal microbiota homeostasis by diminishing protective Lactobacillus populations and promoting pathogen proliferation.}, }
@article {pmid41163130, year = {2025}, author = {Cole, J and Raguideau, S and Abbaszadeh-Dahaji, P and Hilton, S and Muscatt, G and Mushinski, RM and Nilsson, RH and Ryan, MH and Quince, C and Bending, GD}, title = {Comparative genomic analysis of a metagenome-assembled genome reveals distinctive symbiotic traits in a Mucoromycotina fine root endophyte arbuscular mycorrhizal fungus.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {967}, pmid = {41163130}, issn = {1471-2164}, support = {BB/T00746X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; DP180103157//Australian Research Council/ ; DP180103157//Australian Research Council/ ; NE/S010270/1//Natural Environment Research Council/ ; NE/S010270/1//Natural Environment Research Council/ ; }, mesh = {*Mycorrhizae/genetics/physiology ; *Symbiosis/genetics ; *Plant Roots/microbiology ; Phylogeny ; *Endophytes/genetics ; *Genomics ; *Metagenome ; *Genome, Fungal ; Glomeromycota/genetics ; }, abstract = {BACKGROUND: Recent evidence shows that arbuscular mycorrhizal (AM) symbiosis, as defined by the presence of arbuscules, is established by two distinct fungal groups, with the distinctive 'fine root endophyte' morphotype formed by fungi from the subphylum Mucoromycotina rather than the sub-phylum Glomeromycotina. While FRE forming fungi are globally distributed, there is currently no understanding of the genomic basis for their symbiosis or how this symbiosis compares to that of other mycorrhizal symbionts.<br><br>RESULTS: We used culture-independent metagenome sequencing to assemble and characterise the metagenome-assembled genome (MAG) of a putative arbuscule forming fine root endophyte, which we show belonged to the family Planticonsortiaceae within the order Densosporales. The MAG shares key traits with Glomeromycotina fungi, which indicate obligate biotrophy, including the absence of fatty acid and thiamine biosynthesis pathways, limited enzymatic abilities to degrade plant cell walls, and a high abundance of calcium transporters. In contrast to Glomeromycotina fungi, it exhibits a higher capacity for degradation of microbial cell walls, a complete cellulose degradation pathway, low abundances of copper, nitrate and ammonium transporters, and a complete pathway for vitamin B6 biosynthesis.<br><br>CONCLUSION: These differences, particularly those typically associated with saprotrophic functions, highlight the potential for contrasting interactions between Mucoromycotina and Glomeromycotina fungi with their host plant and the environment. In turn, this could support niche differentiation in resource acquisition and complementary ecological functions.}, }
@article {pmid41163128, year = {2025}, author = {Xiao, LF and Li, Y and Lian, H and Liu, X and Wen, Y and Chen, X and Huang, W and Li, B and Luo, L and Wang, X and Tutt, C and Zheng, J and Wang, VY and Shao, NY}, title = {Comprehensive metagenomic analysis of the giant panda's oral microbiome reveals distinct taxonomic and functional characteristics.}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {114}, pmid = {41163128}, issn = {2524-4671}, }
@article {pmid41162595, year = {2025}, author = {Wang, C and Yang, S and Liu, Q and Liu, H and Wang, H and Ma, S and Li, J and Cui, L}, title = {Metagenomic next-generation sequencing reveals respiratory flora distribution in COVID-19.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {37813}, pmid = {41162595}, issn = {2045-2322}, support = {61771022, 62071011//National Natural Science Foundation of China/ ; 61771022, 62071011//National Natural Science Foundation of China/ ; 61771022, 62071011//National Natural Science Foundation of China/ ; 61771022, 62071011//National Natural Science Foundation of China/ ; 61771022, 62071011//National Natural Science Foundation of China/ ; 61771022, 62071011//National Natural Science Foundation of China/ ; 61771022, 62071011//National Natural Science Foundation of China/ ; 61771022, 62071011//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *COVID-19/microbiology/virology/diagnosis ; Middle Aged ; Male ; Female ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Retrospective Studies ; Aged ; SARS-CoV-2/isolation &amp; purification ; Adult ; *Respiratory Tract Infections/microbiology ; *Microbiota/genetics ; }, abstract = {This retrospective study compared metagenomic next-generation sequencing (mNGS) and traditional culture for pathogen detection in 43 patients with lower respiratory tract infections (LRTI), including 34 COVID-19 cases (14 critical, 20 non-critical) and 9 non-COVID controls. mNGS demonstrated superior sensitivity (95.35% vs. 81.08%) and broader pathogen coverage, identifying 36.36% of bacteria and 74.07% of fungi detected by cultures. Concordance between methods was observed in 63% of cases. Severe COVID-19 patients exhibited reduced respiratory microbiota abundance, potentially linked to viral dominance or therapeutic interventions. Clinical outcomes correlated positively with inflammatory markers (procalcitonin/PCT, N-terminal pro-B-type natriuretic peptide/N-proBNP, neutrophils, lactate dehydrogenase/LDH, neutrophil-to-lymphocyte ratio/NLR) and negatively with lymphocytes, highlighting systemic inflammation's role in disease progression. While mNGS offers rapid, high-sensitivity pathogen profiling, limitations include small sample sizes, unresolved specificity concerns and unmeasured confounders. The study underscores mNGS as a promising tool for LRTI diagnosis in COVID-19, though larger prospective cohorts and standardized outcome metrics are needed to validate clinical utility, optimize interpretation, and address cost-effectiveness compared to conventional methods.}, }
@article {pmid41162426, year = {2025}, author = {Zhao, Y and Yao, S and Umar, A and Huang, J and Chen, S and Yu, Z}, title = {Comprehensive multi omics explore the microbial function in metabolic pathway flow during altered diet.}, journal = {NPJ science of food}, volume = {9}, number = {1}, pages = {212}, pmid = {41162426}, issn = {2396-8370}, support = {82270564//National Natural Science Foundation of China/ ; 32170071//National Natural Science Foundation of China/ ; 2022JJ30916//Natural Science Foundation of Hunan Province/ ; 2022M713521//China Postdoctoral Science Foundation/ ; 2023CXQD059//Central South University Innovation-Driven Research Programme/ ; }, abstract = {High-protein diet (HPD) and high-fiber diet (HFiD) are two common types of diet, and the transition from HPD to HFiD frequently happens in people who perform diet control. Gut microbiota provide a bridge between diet and health. However, most of the research left out the metabolic landscape change and gut microbial influence under this kind of altered diet. Here, we examined gut microbiome and metabolites change using multi-omics (16S rRNA gene sequencing, shotgun metagenomics, LC-MS/MS metabolomics), and machine-learning methods were introduced to capture the response of gut microbiota to altered diet and associate the variable metabolites and microbial factors. The results suggest that the conversion from HPD to HFiD improves the gut microbial diversity and promotes the pathways of tryptophan, galactose, fructose, and mannose metabolism, which are associated with different gut microbiota and special metabolites. Among them, Faecalibacterium rodentium and Akkermansia muciniphila indicate potential roles in the multi-metabolism. Although these findings are exploratory and hypothesis-generating, they provide a foundation for future mechanistic investigations and emphasize the importance of diverse diets.}, }
@article {pmid41162178, year = {2025}, author = {Zhang, Q and Zhang, Y and Zhu, J and Gao, Y and Zeng, W and Qi, H}, title = {Microbiome Profiling of Pretreated Human Breast Milk Using Shotgun Metagenomic Sequencing.}, journal = {Journal of microbiology and biotechnology}, volume = {35}, number = {}, pages = {e2506012}, doi = {10.4014/jmb.2506.06012}, pmid = {41162178}, issn = {1738-8872}, mesh = {*Milk, Human/microbiology ; Humans ; Female ; *Microbiota/genetics ; *Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; *Bacteria/classification/genetics/isolation &amp; purification ; Adult ; Metagenome ; Sequence Analysis, DNA ; Archaea/genetics/classification/isolation &amp; purification ; Phylogeny ; DNA, Bacterial/genetics ; }, abstract = {This study explored the metagenomic sequencing methodology for analyzing the breast milk microbiome and elucidated its composition. Twenty-two breast milk samples were collected from 11 healthy lactating women. By optimizing microbial cell wall disruption parameters and developing a nucleic acid extraction method, microbial DNA/RNA libraries were constructed and subjected to metagenomic next-generation sequencing (mNGS), microbial standards spiked into breast milk at serial dilutions served to validate the method's reliability. The sequencing data underwent rigorous quality control and classification using the Kraken2 software and a self-generated database. The breast milk microbiome was found to comprise 21 phyla, 234 genera, and 487 species, with Firmicutes and Proteobacteria being the dominant phyla. At the genus level, Staphylococcus and Streptococcus were the most abundant, while at the species level, Staphylococcus aureus, Streptococcus bradystis, and Staphylococcus epidermidis were the most prevalent. The microbial profiles of the left and right breast milk samples were consistent at the phylum, genus, and species levels. Besides common bacteria, diverse viral, eukaryotic, and archaeal sequences were also detected. Functional profiling revealed that the "lactose and galactose degradation I" pathway accumulated the highest read count, whereas the L-valine biosynthesis pathway was detected most frequently. This study provides a comprehensive understanding of the healthy breast milk microbiome, highlighting the presence of specific flora colonization and the distinct yet correlated microbial environments in bilateral breast milk, laying the groundwork for future research into the interactions between breast milk microbiota and maternal and infant health outcomes.}, }
@article {pmid41162143, year = {2025}, author = {Hutchings, P and Rowe, CE and Byrne, M and Przeslawski, R}, title = {Taxonomy is a foundation of marine science, and it is in trouble.}, journal = {Advances in marine biology}, volume = {101}, number = {}, pages = {197-212}, doi = {10.1016/bs.amb.2025.08.003}, pmid = {41162143}, issn = {2162-5875}, mesh = {*Classification/methods ; Animals ; Conservation of Natural Resources ; *Aquatic Organisms/classification ; Biodiversity ; *Marine Biology/education ; Australia ; }, abstract = {This volume of Advances highlights not only the importance of marine benthic diversity in several regions of the world but also the impediments to describing this fauna. Taxonomy is the science of classifying organisms and is the bedrock of marine biodiversity research and conservation, yet it faces significant decline in Australia. Thus, it is critical that the scientific community understand why taxonomy is so important. This paper underscores the foundational role of taxonomy in marine ecology, using case studies that highlight its critical relevance to species management, conservation policy, and international trade regulation. Despite extensive research and funding, unresolved taxonomies continue to affect our management of ecologically and economically important taxa, including crown-of-thorns seastar (Acanthaster spp.), exploited sea cucumbers (Holothuroidea), and invasive Cassiopea jellyfish. These ambiguities hamper accurate species identification, hinder effective conservation strategies, and complicate regulatory listings under frameworks such as CITES and the IUCN Red List. Key challenges include dwindling taxonomic expertise, reduced funding, lack of university training, and limited career pathways, all of which contribute to Australia's inability to adequately explore and manage its vast marine jurisdiction. The paper advocates for immediate systemic reforms through a series of 11 recommendations related to revitalizing taxonomic education, fostering museum-university partnerships, supporting early career researchers, and investing in infrastructure to enable species discovery. Taxonomic rigor is also essential to validate modern tools like eDNA, metagenomics, and image-based analysis. Without it, efforts to safeguard biodiversity and to foster a sustainable blue economy risk failure.}, }
@article {pmid41161821, year = {2025}, author = {Zhou, Z and Lin, JR and Li, J and Huang, X and Yuan, L and Huang, J and Xie, W and Lu, J and Huang, W and He, S and Yu, D and Zhang, H and Ge, X and Li, M and Mao, Y and Yang, F and Cui, ZK and Su, X and Zhan, Y and Liu, L}, title = {Metagenomic next-generation sequencing unraveled the characteristic of lung microbiota in patients with checkpoint inhibitor pneumonitis: results from a prospective cohort study.}, journal = {Journal for immunotherapy of cancer}, volume = {13}, number = {10}, pages = {}, doi = {10.1136/jitc-2025-012444}, pmid = {41161821}, issn = {2051-1426}, mesh = {Humans ; Male ; Female ; Prospective Studies ; *High-Throughput Nucleotide Sequencing/methods ; *Immune Checkpoint Inhibitors/adverse effects/pharmacology ; Middle Aged ; *Metagenomics/methods ; *Microbiota ; *Pneumonia/chemically induced/microbiology/diagnosis ; Aged ; *Lung/microbiology ; Bronchoalveolar Lavage Fluid/microbiology ; }, abstract = {BACKGROUND: Checkpoint inhibitor pneumonitis (CIP) is among the most lethal immune-related adverse events in patients with cancer receiving immunotherapy. This study aims to characterize the lung microbiome in patients with CIP and evaluate its diagnostic potential.<br><br>METHODS: In a prospective clinical trial (NCT06192303), bronchoalveolar lavage fluid samples (BALF) were obtained from 38 patients presenting clinical symptoms and radiographic evidence of pneumonitis following immunotherapy. The cohort included 14 cases of pure-type CIP (PT-CIP), 14 cases of mixed-type CIP, and 10 cases of pulmonary infection (PI). Metagenomic next-generation sequencing (mNGS) of BALF was employed to delineate the lung microbiota profiles. Using linear discriminant analysis effect size, we discerned characteristic microbiota among the three groups and further explored the associations of signature microbiota with host immune-inflammatory markers. Functional enrichment analysis revealed potential metabolic reprogramming and differences in biological functions between patients with CIP and PI. Finally, leveraging four machine-learning models, we ascertained the clinical value of BALF microbiota profiles in diagnosing CIP.<br><br>RESULTS: The composition of lung microbiota differed significantly between patients with CIP and PI. Microbial taxa, such as Porphyromonas, Candida, Peptostreptococcus, Treponema, and Talaromyces, exhibited distinct abundance patterns across the three groups. Correlation analysis revealed a significant positive relationship between Candida abundance and host immune-inflammatory markers, such as neutrophil-lymphocyte ratio, platelet-lymphocyte ratio, monocyte-lymphocyte ratio, and systemic immune inflammation index. In contrast, Porphyromonas demonstrated a significant negative correlation. Compared with the patients with PT-CIP, the lung microbiota of patients with PI exhibited a more diverse biological and metabolic profile. Additionally, machine learning models based on BALF microbiota profiles could accurately diagnose CIP, with the decision tree model showing the best diagnostic performance (area under the curve: 0.88).<br><br>CONCLUSIONS: Our study represents the unique characterization of the lung microbiota profiles across distinct CIP subtypes and establishes a diagnostic model for CIP based on the decision tree. These findings emphasize the value of BALF mNGS in improving the diagnosis of CIP.}, }
@article {pmid41161652, year = {2025}, author = {Li, R and Qiu, C and Chen, X and Liu, N and Zhang, Y and Qi, L and Wang, S}, title = {Effects of thermal alkaline hydrolysis and biochar addition on anaerobic digestion of sewage sludge and fate of antibiotic resistance genes.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {133569}, doi = {10.1016/j.biortech.2025.133569}, pmid = {41161652}, issn = {1873-2976}, abstract = {Anaerobic digestion (AD) has gained wide attention as a potential method to reduce the spread of antibiotic resistance genes (ARGs). This study systematically evaluated the impacts of thermal alkaline hydrolysis (TA), biochar addition (BA), and the combination of these two methods (TA-BA) on the efficiency of AD and the removal of ARGs in the sewage sludge AD process. Metagenomic sequencing and quantitative PCR were used to systematically analyze the dissemination of ARGs in different sludge samples. The results indicated that both TA and TA-BA could enhance the efficiency of sludge AD, and the cumulative biogas production was increased by 68.35 %-258.57 % compared to the control group. In addition, the absolute abundance of ARGs was significantly reduced by 59.31 %-74.67 % in the TA- and BA-treated groups compared to the control group. The combination of TA-BA exhibited a synergistic effect, achieving the most significant reduction in ARGs absolute abundance (up to 74.67 % removal), outperforming individual treatments. Both TA and BA could promote the generation of Anaerolinea and Longilinea. Meanwhile, TA significantly increased the relative abundance of Methanobacteriaceae, while BA enhanced the relative abundance of Methanothrix. The correlation analysis demonstrated a significant negative correlation between TOC and sul1 (P < 0.01), and revealing a significant positive correlation between intI1 and sul1 (P < 0.05). Moreover, a significant correlation was observed between the fate of ARGs and the succession of microbial community structure.}, }
@article {pmid41161648, year = {2025}, author = {Kadam, R and Jo, S and Park, J}, title = {Importance of substrate mixture ratio optimization on efficient anaerobic co-digestion of organic wastes generated in livestock sector: Insights into process performances and metagenomics.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {133561}, doi = {10.1016/j.biortech.2025.133561}, pmid = {41161648}, issn = {1873-2976}, abstract = {Improving the efficiency of anaerobic co-digestion of livestock wastes, particularly through optimizing mixture ratios, is a key research focus. This study identifies an optimal substrate mixture ratio of 23 % cow manure, 22 % pig manure, and 55 % carcass waste, which significantly enhances the degradation of lignocellulose, protein, and lipids compared to equal ratios. In the optimal mixture, the methane (CH4) yield remained stable at 310-360 mL-CH4/g-VS (volatile solids) as the organic loading rate increased to 5 kg-VS/m[3]/d. In contrast, the equal substrate mixture ratio showed lower CH4 yield and less stability under increasing organic loads. Key bacterial genera in the optimal mixture included Cloacamonas, Pseudomonas, Geofilum, and Clostridium, with methanogenic archaea such as Methanosaeta and Methanosarcina. Metagenomic analysis showed enriched pathways for cellulose, hemicellulose, and lipid degradation, alongside enhanced metabolism of volatile fatty acids and ammonia. This study highlights the importance of optimizing substrate ratios for efficient CH4 yield and stability.}, }
@article {pmid41161351, year = {2025}, author = {Rao, H and Gao, L and Zheng, X and Wei, J and Yue, M and Li, B and Wang, Z and Yang, M and Ren, X}, title = {Reducing environmental contamination during reprocessing of highly contaminated flexible bronchoscopes from the intensive care unit.}, journal = {The Journal of hospital infection}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jhin.2025.10.006}, pmid = {41161351}, issn = {1532-2939}, abstract = {BACKGROUND: Flexible bronchoscopes (FBs) used in intensive care units (ICUs) frequently harbour pathogenic micro-organisms, creating early reprocessing risks for environmental contamination and staff exposure.<br><br>METHODS: In a six-month evaluation of 832 ICU FBs sampled immediately post-use with metagenomic next-generation sequencing, 55.4% carried one or more pathogens, including multi-drug-resistant bacteria, fungi and airborne agents. We instituted an enhanced reprocessing protocol centred on sealed transfer using double biohazard bags, a two-person dedicated handling method that separates contaminated-scope contact from support tasks, segregation of sinks and a dedicated automated endoscope reprocessor (AER) for ICU FBs, and rigorous terminal disinfection of equipment and work surfaces.<br><br>FINDINGS: Quality checks showed unchanged cleaning efficacy of FBs, whereas the environmental microbial burden on work surfaces after reprocessing was significantly reduced under the new protocol.<br><br>CONCLUSIONS: These findings identify ICU FBs as a high-load reservoir at the point of receipt and demonstrate that targeted, standardized controls during the earliest reprocessing steps can mitigate environmental contamination and enhance sterile-processing worker protection without compromising device reprocessing outcomes.}, }
@article {pmid41161274, year = {2025}, author = {Cai, X and Yuan, X and Singh, AK and Chen, C and Zhu, X and Liu, W}, title = {Tradeoffs between microbial life-history strategies drive soil carbon cycling during revegetation in karst ecosystems: A metagenomic perspective.}, journal = {Journal of environmental management}, volume = {395}, number = {}, pages = {127802}, doi = {10.1016/j.jenvman.2025.127802}, pmid = {41161274}, issn = {1095-8630}, abstract = {Revegetation strongly influences the dynamics of soil organic carbon (SOC) and microbial communities. While microbial communities are known to drive carbon (C) cycling, the specific traits responsible for C stabilization and mineralization during the revegetation of degraded karst ecosystems are not well understood. This study used a combination of metagenomic and instrumental methods to investigate variations in soil physicochemical properties, organic C fractions, C-cycle microbial community traits (diversity, life strategies, and co-occurrence patterns), and C-cycling (fixation and degradation) genes across four karst ecosystems representing a revegetation chronosequence encompassing cropland, grassland, shrubland, and primary forest. Our findings demonstrated that revegetation increased total SOC and recalcitrant OC (ROC) contents, while it decreased dissolved inorganic nitrogen (DIN) and reduced the ratio of labile OC (LOC) to SOC. This indicates enhanced C pool stabilization and storage, alongside reduced soil nutrient availability. These shifts favored the development of C-cycle microbial communities with low diversity and high proportions of K-strategists, which efficiently utilize recalcitrant C under oligotrophic conditions. Consequently, the increased dominance of K-strategists redirected microbial resource acquisition, manifested in a 29 % decrease in C-fixation gene abundances (rTCA, WL, and DC/4-HB pathways) and a 27 % decrease in genes degrading labile C compounds (starch, hemicellulose, cellulose, and chitin). Conversely, genes involved in degrading recalcitrant C compounds (pectin and lignin) increased by 19 %. Furthermore, the elevated proportion of K-strategists enhanced the complexity and stability of microbial taxonomic and functional networks, potentially strengthening community resilience and nutrient cycling efficiency. These results reveal a causal link between shifts in the soil C pool and nutrient availability during revegetation and the subsequent reshaping of C-cycling microbial communities. Such restructured communities, in turn, drive the expression of genes associated with C stabilization and mineralization, thereby impacting the soil C pool. This study provides mechanistic insights into microbial-mediated biochemical processes governing soil C decomposition and stabilization in karst ecosystems, offering critical guidance for ecological restoration in these degraded and fragile regions.}, }
@article {pmid41161238, year = {2025}, author = {Chi, T and Liu, Z and Zhang, B and Zhu, L and Hu, B}, title = {Risk assessment of the spread of antibiotic resistance genes from hospitals to the receiving environment via wastewater treatment plants.}, journal = {Ecotoxicology and environmental safety}, volume = {306}, number = {}, pages = {119264}, doi = {10.1016/j.ecoenv.2025.119264}, pmid = {41161238}, issn = {1090-2414}, abstract = {Antibiotics and antibiotic resistance genes (ARGs) enter the receiving environment from hospitals through wastewater treatment plants (WWTPs), increasing the presence of exogenous ARGs and conditional pathogens in the receiving environment, thereby elevating the risk of drug resistance. This study, based on metagenomics, investigated changes in risk across each node in the ARG transmission chain, from hospitals through WWTPs to downstream receiving water and sediments. The results showed that the total concentration of antibiotics decreased from 1467.80 ± 215.30 µg/L in hospital wastewater to 111.52 ± 18.70 µg/L in downstream receiving water, achieving a 92.40 % removal rate. However, the types of high ecological risk antibiotics in hospital wastewater were only reduced by 38.46 % after treatment by hospitals and sewage treatment plants. The abundance of Rank I ARGs was reduced by 37.03 % in hospital sewage treatment stations and 28.57 % in WWTPs, but these ARGs accounted for 81.8 % of the Rank I ARGs in receiving water. The potential host bacteria for these ARGs were mainly Proteobacteria, which carried bacitracin and multidrug resistance genes. While WWTPs removed 66.67 % of the conditional pathogens, bacteria such as Acinetobacter and Streptococcus still entered the receiving water. MetaCompare revealed that the potential transmission risk of ARGs decreased by 24.31 % after hospital wastewater treatment and by 20.71 % after WWTPs, with the risk of the receiving water being 7.01 times that in sediments. The potential risk assessment framework developed in this study for antibiotics and ARGs in the environment provides a theoretical guidance for antibiotic treatment and ARGs environmental risk control.}, }
@article {pmid41161021, year = {2025}, author = {Sun, J and Tong, X and Liu, S and Zhang, S and Wang, L and Wang, D and Jia, Q and He, X and Lv, W and Abdo Qasem, MAA and Xiao, Y and Fan, H}, title = {Clinical characteristics and mortality risk factors of Streptococcus constellatus infection: A retrospective cohort study of 390 patients.}, journal = {Journal of infection and public health}, volume = {19}, number = {1}, pages = {103023}, doi = {10.1016/j.jiph.2025.103023}, pmid = {41161021}, issn = {1876-035X}, abstract = {BACKGROUND: Few studies have investigated the clinical characteristics and mortality associated with Streptococcus constellatus (S.constellatus) infection. To identify the clinical features and mortality of patients with S. constellatus infection.<br><br>METHODS: This retrospective cohort study analyzed hospitalized patients with confirmed S.constellatus infection at West China Hospital of Sichuan University from January 2016 to April 2024. S. constellatus was identified using sterile body fluid culture or metagenomic next-generation sequencing (mNGS). Patients were categorized as monomicrobial or polymicrobial infection. Kaplan-Meier curve analysis was performed to compare the 30-day survival rates based on infection type and infection site, while multivariate Cox regression was conducted to identify independent risk factors for 30-day mortality.<br><br>RESULTS: Of the 390 patients, 301 (77.2&#x202f;%) were classified as monomicrobial S. constellatus infection. S. constellatus isolates were highly susceptible to penicillin (98.08&#x202f;%) and levofloxacin (98.90&#x202f;%).Overall 30- and 90-day mortality were 13.08&#x202f;% and 15.13&#x202f;%, higher in polymicrobial than monomicrobial infections (24.72&#x202f;% vs 8.97&#x202f;% at 30 days; 29.21&#x202f;% vs 10.96&#x202f;% at 90 days). Polymicrobial infection (adjusted hazard ratio [aHR] = 2.426, p&#x202f;=&#x202f;0.007) and brain abscess (aHR = 16.689, p&#x202f;<&#x202f;0.001) were identified as independent risk factors for 30-day mortality in patients with S. constellatus infection. In the subgroup of monomicrobial infection, mediastinal abscess (aHR = 6.738, p&#x202f;=&#x202f;0.002) and brain abscess (aHR = 13.933, p&#x202f;<&#x202f;0.001) were significantly associated with an increased risk of 30-day mortality.<br><br>CONCLUSIONS: Although S. constellatus was highly susceptible to antibiotics, short-term mortality remained substantial. Infection site and polymicrobial infection were key prognostic factors in patients with S. constellatus infection.}, }
@article {pmid41161015, year = {2025}, author = {Ekman, M and Mahani, AN and Aralaguppe, SG and Normark, T and Stamouli, S and Andersson-Li, L and Sun, D and Broddesson, S and Wirta, V and Björkström, NK and Albert, J and Allander, T}, title = {Evaluation of a diagnostic metagenomic sequencing assay: Virus detection sensitivity and background nucleic acids in three different sample materials.}, journal = {Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology}, volume = {181}, number = {}, pages = {105882}, doi = {10.1016/j.jcv.2025.105882}, pmid = {41161015}, issn = {1873-5967}, abstract = {BACKGROUND: Metagenomic sequencing has emerged as an attractive, general, and agnostic diagnostic method, in particular for detection of viruses. However, its application faces limitations, including reduced sensitivity due to background nucleic acid content of samples, and the search for an optimized protocol is still ongoing.<br><br>METHODS: We report the development of a metagenomic sequencing protocol for diagnostic use and its performance in detecting DNA and RNA viruses in three different sample materials: serum, cerebrospinal fluid (CSF) and nasopharyngeal swabs (NPS).<br><br>RESULTS: Sensitivity was higher for RNA viruses than for DNA viruses, and also higher in CSF than in serum and lowest in NPS. We characterized the background nucleic acids and found higher DNA than RNA levels in CSF and serum and overall highest nucleic acid levels in NPS, intermediate in serum and lowest in CSF. These differences largely explained the observed variability in sensitivity between sample preparations and sample materials.<br><br>CONCLUSIONS: Our results highlight the need to consider sample-type specific characteristics in efforts to improve the sensitivity of metagenomic assays e.g. via host depletion protocols.}, }
@article {pmid41160250, year = {2025}, author = {Li, Y and Zhu, M and Wang, W and Xu, Q and Cui, J and Liu, L and Liu, Y and Yang, H and Liu, Y}, title = {Comparable tongue coating microbiota profiles from a simplified single-swab versus different sampling approaches: A pilot study.}, journal = {Clinical oral investigations}, volume = {29}, number = {11}, pages = {543}, pmid = {41160250}, issn = {1436-3771}, support = {GZC20233129//the Postdoctoral Fellowship Program of CPSF/ ; 82374290//National Natural Science Foundation of China/ ; Yue Liu//Young Qihuang Scholar of the "Tens of Millions" Talent Project of China/ ; }, mesh = {Humans ; Pilot Projects ; *Tongue/microbiology ; *Microbiota ; Adult ; Male ; Female ; *Specimen Handling/methods ; Reproducibility of Results ; Biofilms ; }, abstract = {OBJECTIVE: The tongue coating microbiota has emerged as a potential biomarker for systemic diseases. However, the absence of a practical and widely applicable sampling protocol hinders cross-study comparability and limits clinical application. This pilot study aimed to evaluate the reliability of different sampling methods.<br><br>MATERIALS AND METHODS: Tongue coating samples were collected from healthy adults using four different methods, including single and multiple scrapes with sterile swabs or scraper. Metagenomic sequencing was performed to assess microbial diversity, taxonomic composition, and predicted functional profiles. DNA extraction quality, alpha- and beta-diversity metrics, taxonomic abundance at the genus and species levels, and KEGG-based functional predictions were analyzed. Spatial and structural features of the tongue biofilm were considered to interpret microbial sampling consistency.<br><br>RESULTS: The single-scrape method yielded comparable microbial profiles to multi-scrape methods, with no significant differences in alpha-diversity or beta-diversity. Taxonomic compositions at both genus and species levels were consistent across groups, with dominant taxa including Streptococcus, Prevotella, and Rothia. Functional prediction via KEGG annotation revealed minimal variation among groups, with only a few metabolic pathways showing statistically significant differences. These findings highlight the spatial stability and representative sampling potential of the tongue coating microbiota.<br><br>CONCLUSIONS: A single scrape using a sterile flocked swab provides a practical, reproducible, and cost-effective approach for tongue coating microbiota sampling. These pilot findings suggest that this simplified method yields representative microbiome data in healthy adults, although validation in larger and more diverse cohorts is required before clinical application.<br><br>CLINICAL RELEVANCE: This study demonstrates that a single-scrape sampling method yields tongue coating microbiota profiles comparable to conventional multi-scrape protocols. The findings support its potential for standardizing sampling in future large-scale studies.<br><br>TRIAL REGISTRATION: ITMCTR2024000616.}, }
@article {pmid41160143, year = {2025}, author = {Begum, M and Barsha, KF and Rahman, MM and Sarkar, MMH and Chowdhury, SF and Bhowmik, S and Shormi, AS and Bari, SM}, title = {Gut microbiome profiling of antibiotic-treated Mystus cavasius using culture-based and shotgun metagenomic approaches.}, journal = {Antonie van Leeuwenhoek}, volume = {118}, number = {12}, pages = {183}, pmid = {41160143}, issn = {1572-9699}, mesh = {*Anti-Bacterial Agents/pharmacology ; Animals ; *Gastrointestinal Microbiome/drug effects ; *Metagenomics/methods ; *Bacteria/classification/genetics/drug effects/isolation &amp; purification ; Phylogeny ; Aquaculture ; *Catfishes/microbiology ; RNA, Ribosomal, 16S/genetics ; Microbial Sensitivity Tests ; }, abstract = {Antibiotic use in aquaculture prevents disease and promotes growth but can disrupt the gut microbiome and drive resistance. The study profiled the gut microbiome of antibiotic-treated Mystus cavasius using both culture-based and shotgun metagenomic approach. Culture-dependent analysis revealed a significant 2-threefold reduction in total viable bacterial count in treated fish. Phylogenetic analysis of 12 cultured isolates revealed treatment-driven enrichment of Bacillus, Enterobacter and Aeromonas. Antibiotic susceptibility testing further revealed increased resistance profiles among isolates from treated fish. Metagenomic profiling identified over 1400 bacterial species and revealed clear taxonomic shifts. Control groups were enriched with beneficial genera such as Lactiplantibacillus and Arthrospira, while treated fish were dominated by opportunistic or resistant taxa including Plesiomonas, Staphylococcus, and Acinetobacter. These shifts were further reflected at the phylum level, with a decline in Proteobacteria and Bacteroidetes, accompanied by an increase in Firmicutes and the enrichment of antibiotic-tolerant lineages. Treated samples exhibited more uniform alpha diversity indices, suggesting a restructuring of the microbial community hierarchy following oxytetracycline exposure, whereas beta diversity analysis showed a moderate separation between control and treated groups. These findings provide critical insights into the ecological and health risks of antibiotic use in aquaculture and underscore the importance of developing sustainable alternatives for disease management in fish farming.}, }
@article {pmid41160089, year = {2025}, author = {Abuzahrah, SS}, title = {The microbiome of marine sponges located on the Saudi Arabia coast of the Red sea using high-throughput 16S amplicon sequencing.}, journal = {AMB Express}, volume = {15}, number = {1}, pages = {160}, pmid = {41160089}, issn = {2191-0855}, support = {PROJECT NO.: CRP/SAU24-02//International Centre for Genetic Engineering and Biotechnology (ICGEB)/ ; }, abstract = {Marine sponges (Porifera) from the Red Sea host diverse microbial communities that are integral to sponge health, nutrient cycling, and ecological resilience. Using high-throughput 16S rRNA amplicon sequencing, we characterized the bacterial diversity and functional potential across several Red Sea sponge species. Our findings revealed that these microbiomes are dominated by Alphaproteobacteria, Gammaproteobacteria, and Roseobacteraceae, with notable contributions from bacterial taxa involved in nitrogen fixation, organic matter degradation, and antimicrobial compound production. Functional predictions indicate that these symbionts support sponge nutrition, defense, and adaptation to the extreme Red Sea environment, including high salinity and temperature. Compared to sponge microbiomes from other marine regions, the Red Sea communities display unique taxonomic compositions and enhanced metabolic and defensive capacities. This highlights the essential ecological roles and potential biotechnological applications of these symbiotic assemblages. Our study underscores the significance of exploring sponge-associated microbiomes in understudied and extreme marine ecosystems. These results provide a foundation for future bioprospecting and work on adaptive mechanisms, emphasizing the value of Red Sea sponges and their microbiota for marine biotechnology and ecosystem resilience.}, }
@article {pmid41159973, year = {2025}, author = {Anani, H and Destras, G and Regue, H and Bulteau, S and Bressollette-Bodin, C and Roquilly, A and Josset, L}, title = {Metagenome-assembled complete genome of Bohxovirus, a virulent bacteriophage involved in the prediction of hospital-acquired pneumonia in intubated critically ill patients.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0059225}, doi = {10.1128/mra.00592-25}, pmid = {41159973}, issn = {2576-098X}, abstract = {We present the complete genome of a Bohxovirus species, a virulent phage targeting Prevotella jejuni, reconstructed from viral metagenomes in respiratory endotracheal aspirates of intubated critically ill patients. The 98-kbp bacteriophage, belonging to the Suoliviridae family, does not contain genes associated with antibiotic resistance or bacterial virulence.CLINICAL TRIALSClinicalTrials.gov numbers: NCT02003196 and NCT04793568.}, }
@article {pmid41159804, year = {2025}, author = {Spottiswoode, N and Neyton, LPA and Calfee, CS and Langelier, CR}, title = {Reply to Liu et al. and Chen et al.}, journal = {American journal of respiratory and critical care medicine}, volume = {}, number = {}, pages = {}, doi = {10.1164/rccm.202509-2218LE}, pmid = {41159804}, issn = {1535-4970}, }
@article {pmid41159664, year = {2025}, author = {Schwab, C and Lang, H and Stegmüller, S and Hosek, J and Marietou, A and Huertas-Díaz, L and Li, Q and Krings, APS and Zander, A and Kræmer Sundekilde, U and Richling, E}, title = {Microbial Transformation of Dietary Glycerol Contributes to Intestinal Acrolein Formation and Urinary Excretion.}, journal = {Molecular nutrition &amp; food research}, volume = {}, number = {}, pages = {e70289}, doi = {10.1002/mnfr.70289}, pmid = {41159664}, issn = {1613-4133}, support = {RI 1176/12-1//Deutsche Forschungsgemeinschaft DFG/ ; RI 1176/13-1//Deutsche Forschungsgemeinschaft DFG/ ; }, abstract = {The aldehyde acrolein has been associated with diabetes, cardiovascular, respiratory, and neurodegenerative diseases, and gut microbiota possesses the potential for acrolein release via the key enzyme glycerol/diol dehydratase (PduCDE). This study aimed at estimating the contribution of gut microbiota to endogenous acrolein production. To minimize confounding sources, we investigated the intestinal acrolein-producing potential of 20 volunteers housed under defined conditions. Glycerol was present in every meal and was detected in feces, suggesting availability to intestinal microbiota. Based on fecal metagenomics and pduC analysis, all volunteers showed potential for intestinal glycerol transformation to acrolein; the genus Anaerobutyricum was the major contributor across donors and time. Levels of urine biomarkers N-acetyl-S-(3-hydroxypropyl)-L-cysteine (3-HPMA) and N-acetyl-S-(carboxyethyl)-L-cysteine (CEMA) were higher after the consumption of meals with high glycerol levels, suggesting immediate microbial transformation to acrolein. Only a small proportion of acrolein metabolites was recovered in urine, possibly due to high compound reactivity. Donors could be separated into 3-HPMA or CEMA phenotypes based on the predominance of urine biomarkers, and phenotypes related to overall fecal microbiota and fermentation metabolite profiles. Our data show that oral fat/glycerol intake together with intestinal microbiota activity might temporarily increase endogenous acrolein formation and that urinary biomarkers link to the intestinal microbiome.}, }
@article {pmid41159034, year = {2025}, author = {Peipert, D and Montgomery, TL and Toppen, LC and Lee, MFJ and Scarborough, MJ and Krementsov, DN}, title = {Colonization by Akkermansia muciniphila modulates central nervous system autoimmunity in an ecological context-dependent manner.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1655428}, pmid = {41159034}, issn = {1664-3224}, mesh = {Animals ; *Encephalomyelitis, Autoimmune, Experimental/immunology/microbiology ; *Gastrointestinal Microbiome/immunology ; *Autoimmunity ; Mice ; Mice, Inbred C57BL ; *Central Nervous System/immunology/microbiology ; *Multiple Sclerosis/immunology/microbiology ; Female ; Akkermansia ; *Verrucomicrobia/immunology ; Disease Models, Animal ; }, abstract = {INTRODUCTION: Multiple sclerosis is autoimmune disease of the central nervous system (CNS) in which myelin-reactive immune attack drives demyelination and subsequent disability. Various studies have documented elevated abundance of the commensal gut bacterium Akkermansia muciniphila (A. muciniphila) in people with multiple sclerosis compared to healthy control subjects, suggesting that its elevated abundance may be a risk factor for the development of CNS autoimmunity. However, A. muciniphila is considered beneficial in various other pathological contexts, and recent studies suggest that A. muciniphila may be paradoxically associated with reduced disability and progression in multiple sclerosis. Moreover, experimental modulation of A. muciniphila levels in experimental autoimmune encephalomyelitis (EAE), an autoimmune model of multiple sclerosis, has generated conflicting results, suggesting that the effects of this microbe on CNS autoimmunity could be context-dependent.<br><br>METHODS: To address this possibility, we generated two distinct microbiome models in C57BL/6J mice, each stably colonized by A. muciniphila or A. muciniphila-free, providing divergent ecological contexts in which A. muciniphila may exert a differential impact. We used EAE, flow cytometry, full-length 16S DNA sequencing, and mass spectrometry to assess the impact of A. muciniphila colonization on neurological outcomes, immune responses, gut microbiome composition, and short-chain fatty acid (SCFA) production, respectively. Dietary intervention was used to assess the functional consequences of differences in gut microbiota metabolic capacity.<br><br>RESULTS: We found that A. muciniphila colonization increased EAE severity only in a specific microbiome context, in conjunction with increased Th17 responses and CNS-infiltrating immune cells. Profiling of gut microbiome composition revealed that A. muciniphila colonization drove a reduction of Clostridia, key producers of SCFAs, specifically in the microbiome model in which A. muciniphila exacerbates EAE. Inferred metagenomic analyses suggested reduced SCFA production in the presence of A. muciniphila, which was confirmed by mass spectrometry. Consistently, provision of high dietary fiber as a substrate for SCFA production suppressed EAE only in the context of the Clostridia-rich microbiome sensitive to A. muciniphila colonization.<br><br>DISCUSSION: Taken together, our data suggest that the effect of A. muciniphila on CNS autoimmunity is highly dependent on the overall composition of the gut microbiome and suggest that this microbe may contribute to decreased gut SCFA metabolism in multiple sclerosis.}, }
@article {pmid41158777, year = {2025}, author = {Skoog, EJ and Cutts, E and Bosak, T}, title = {Linking microbial ecology to the cycling of neutral and acidic polysaccharides in pustular mats from Shark Bay, Western Australia.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1684648}, pmid = {41158777}, issn = {1664-302X}, abstract = {Cyanobacteria and other microbes in peritidal microbial mats have produced extracellular polymeric substances (EPS) for more than two billion years. The production and degradation of EPS contributes to the biogeochemical cycling of carbon and carbonate precipitation within modern microbial mats, but key microbes involved in the cycling of EPS remain unidentified. Here, we investigate the cycling of EPS in the peritidal pustular mats of Shark Bay, Western Australia. We characterize the chemical composition of EPS produced by cyanobacterial enrichment cultures under natural and UV-stress conditions and link these findings to the metabolic potential for EPS production and degradation encoded in 84 metagenome-assembled genomes (MAGs) from the mat community. We further identify the key microbial degraders of specific acidic and neutral polysaccharides in this community by cultivating enrichment cultures on seven commercially available polysaccharides representative of those present in the mats and assessing the dominant taxa. All sequenced Cyanobacteria MAGs have the potential to synthesize mannose, fucose, glucose, arabinose, rhamnose, galactose, xylose, N-acetylglucosamine, galacturonic acid and glucuronic acid. Biochemical analyses confirm the presence of nearly all these monosaccharides in the hydrolysates of EPS extracted from UV- and non-UV exposed cyanobacterial enrichments. Ultraviolet radiation influences the structure and composition of EPS by reducing the hydration, potentially due to cross-linking among polymers in EPS and increasing the relative abundances of uronic acids and xylose in polysaccharides. Analyses of carbohydrate-active enzymes (CAZymes) in the MAGs and of 16S rRNA sequences from experimental polysaccharide enrichments point to major roles for Bacteroidetes, Planctomycetes, and Verrucomicrobia in the cycling of acidic EPS. These experiments reveal a complex interplay among microbial community composition, CAZyme diversity, environmental stressors, and EPS cycling, which together shape carbon flow and biomineralization in pustular mats in Shark Bay.}, }
@article {pmid41158770, year = {2025}, author = {Peng, Y and Huang, D and Li, J and Sun, X and Zhang, Q and Zhang, R and Yang, R and Li, B and Kong, T and Xiong, Z and Huang, Y and Chang, Z and Su, Y and Shang, Y and Ghani, MU and Wang, Y and Sun, W}, title = {Investigation of the role of sulfide oxidation in the gill-associated microbiota of freshwater mussel Limnoperna fortunei.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1671425}, pmid = {41158770}, issn = {1664-302X}, abstract = {INTRODUCTION: Limnoperna fortunei is a notable invasive freshwater species, altering structure and function of natural and engineered aquatic ecosystems. The host-associated microbiomes play a critical role in the survival and thriving of L. fortunei, with the gill-associated microbiomes being particularly significant due to their involvement in filter feeding, nutrient metabolism, and symbiosis. However, research on microbiomes associated with L. fortunei remains limited, and studies specifically focusing on gill-associated microbiota are scarce, leaving a significant gap in our understanding of their ecological roles.<br><br>METHODS: In this study, gill-associated bacterial communities of the L. fortunei were compared with their surrounding water microbial populations in the largest water diversion projects (the Middle Route of the South-to-North Water Diversion Project) to elucidate their environmental adaptations and potential contribution to their hosts. Analyses included assessing bacterial diversity and composition, conducting Neutral Community Model (NCM) analysis to explore community assembly processes, constructing an environmental-microbial co-occurrence network to identify key environmental factors, and performing metagenomic analysis of gill samples to investigate functional genes.<br><br>RESULTS: Significant variations were observed in bacterial diversity and composition between gills and surrounding water. Sulfur oxidizing bacteria Pirellula, SM1A02, and Roseomonas were significantly enriched in gill-associated microbiota. Neutral community model (NCM) analysis unveiled that the assembly of gill microbial communities was primarily governed by stochastic processes, constrained by determined processes. Moreover, environmental-microbial co-occurrence network identified reduced sulfur as the key factor shaping the composition of bacterial communities. Metagenomic binning of gill samples further revealed that metagenome assembled genomes associated with Pirellula within the phylum Planctomycetota contained functional genes related to sulfide oxidation and resistant to oxidative stress.<br><br>DISCUSSION: This study provides systematic insights into the microbial community diversity, assembly patterns, and functional characteristics of L. fortunei gill-asscociated microbiota, contributing to a mechanistic understanding of their ecological roles.}, }
@article {pmid41158352, year = {2025}, author = {Liu, J and Qian, H and Jin, J and Du, M and Wang, C and Yu, J and Pang, P and Shen, M and Mei, Z and Shi, Y and Wang, Z and Jiang, G and Guo, L and Zhong, C and Tang, P and Wang, Y and Shi, C and Ji, C}, title = {Use of metagenomic next-generation sequencing for accurate diagnosis of tuberculous pleurisy: a retrospective cohort study.}, journal = {Journal of thoracic disease}, volume = {17}, number = {9}, pages = {6771-6778}, pmid = {41158352}, issn = {2072-1439}, abstract = {BACKGROUND: Tuberculous pleurisy (TP) presents persistent diagnostic challenges owing to the suboptimal sensitivity of conventional microbiological assays. This study aimed to evaluate the diagnostic performance of metagenomic next-generation sequencing (mNGS) in diagnosing TP using formalin-fixed paraffin-embedded (FFPE) pleural biopsy tissues.<br><br>METHODS: This retrospective study evaluated the diagnostic efficacy of mNGS in FFPE pleural samples of suspected TP patients at The First Affiliated Hospital of Soochow University between April 1, 2018 and February 1, 2023. Those patients with inadequate pleural specimens for mNGS analysis were excluded. Diagnosis of TP was established according to the WS 288-2017 Health Industry Standard of the People's Republic of China.<br><br>RESULTS: A total of 73 patients were enrolled in this study and divided into the TP group and non-tuberculous pleurisy (NTP) group. The TP group comprised 51 patients with a median age of 52 years, including 33 (64.7%) males. The NTP group consisted of 22 patients with a median age of 64 years, including 13 (59.1%) males. Our results showed that mNGS assay on FFPE in pleural biopsies had a sensitivity of 78.43% [95% confidence interval (CI): 0.667-0.901] and a specificity of 100% (95% CI: 1.000-1.000) in diagnosing TP. In the 51 TP cases, mNGS detected Mycobacterium tuberculosis complex (MTBC) in 40 (78.43%) cases and non-tuberculous mycobacteria (NTM) in 31 (60.78%) cases. Of these, 16 cases were MTBC infections alone and 7 cases were NTM infections alone, while 24 were mixed MTBC and NTM infections.<br><br>CONCLUSIONS: mNGS of FFPE of pleural biopsy tissues not only improves the diagnostic efficiency of TP, but also potential accurately distinguishes between MTBC and NTM, providing molecular and microbial basis for the diagnosis of TP, which is helpful for the rapid diagnosis and precise treatment of TP.}, }
@article {pmid41158324, year = {2025}, author = {Fatemi, S and Kriefall, NG and Yogi, D and Weber, D and Hynson, NA and Medeiros, MCI and Sadowski, P and Amend, AS}, title = {Microbial composition and function are nested and shaped by food web topologies.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf175}, pmid = {41158324}, issn = {2730-6151}, abstract = {Food webs govern interactions among organisms and drive energy fluxes within ecosystems. With an increasing appreciation for the role of symbiotic microbes in host metabolism and development, it is imperative to understand the extent to which microbes conform to, and potentially influence, canonical food web efficiencies and structures. Here, we investigate whether bacteria and their taxa and functional genes are compositionally nested within a simple model food web hierarchy, and the extent to which this is predicted by the trophic position of the host. Using shotgun and amplicon sequencing of discrete food web compartments within replicate tank bromeliads, we find that both taxonomy and function are compositionally nested and largely mirror the pyramid-shaped distribution of food webs. Further, nearly the entirety of bacterial taxa and functional genes associated with hosts are contained within host-independent environmental samples. Community composition of bacterial taxa did not significantly correlate with that of functional genes, indicating a high likelihood of functional redundancy. Whereas bacterial taxa were shaped by both location and trophic position of their host, functional genes were not spatially structured. Our work illustrates the advantages of applying food web ecology to predict patterns of overlapping microbiome composition among unrelated hosts and distinct habitats. Because bacterial symbionts are critical components of host metabolic potential, this result raises important questions about whether bacterial consortia are shaped by the same energetic constraints as hosts, and whether they play an active role in food web efficiency.}, }
@article {pmid41157632, year = {2025}, author = {Apanasevich, M and Dubovitskiy, N and Derko, A and Khozyainova, A and Tarasov, A and Kokhanenko, A and Artemov, G and Denisov, E and Shestopalov, A and Sharshov, K}, title = {Genomic Characterization of a Novel Yezo Virus Revealed in Ixodes pavlovskyi Tick Virome in Western Siberia.}, journal = {Viruses}, volume = {17}, number = {10}, pages = {}, doi = {10.3390/v17101362}, pmid = {41157632}, issn = {1999-4915}, support = {23-64-00005//Russian Science Foundation/ ; 225020408196-1//State-funded budget project/ ; }, mesh = {*Ixodes/virology ; Animals ; Phylogeny ; *Genome, Viral ; Siberia ; *Virome/genetics ; Encephalitis Viruses, Tick-Borne/genetics/isolation &amp; purification/classification ; Metagenomics ; Genomics ; Humans ; Encephalitis, Tick-Borne/virology ; }, abstract = {Ixodid ticks are blood-sucking ectoparasites of vertebrates. They constitute an integral part of natural foci and are responsible for the worldwide transmission of infections to humans, which can result in severe symptoms. For instance, the Tomsk region, where three abundant tick species (Dermacentor reticulatus, Ixodes pavlovskyi, I. persulcatus) occur, is an endemic area for tick-borne encephalitis virus (TBEV). An increasing number of novel infectious agents carried by ticks have been identified using metagenomic sequencing. A notable example is the Yezo virus (Orthonairovirus yezoense, YEZV), which was discovered in patients with fever after tick bites in Japan and China between 2014 and 2025. For the first time, we have performed metagenomic sequencing of the virome of ticks collected in the Tomsk region. In a sample obtained from a pool of I. pavlovskyi ticks, all three segments of the YEZV genome were detected. The phylogenetic analysis showed that the newly identified isolate formed a sister group to previously described virus isolates, indicating the presence of a new genetic variant. This study presents the first report of YEZV detection in I. pavlovskyi ticks in the Tomsk region, thereby expanding the geographical range and number of vector species for YEZV and highlighting the importance of monitoring viral agents circulating among ticks in Western Siberia.}, }
@article {pmid41157620, year = {2025}, author = {Weary, TE and Zhou, LH and MacDonald, L and Ibañez Iv, D and Jaramillo, C and Dunn, CD and Wright, TF and Hanley, KA and Goldberg, TL and Orr, TJ}, title = {Novel Bat Adenovirus Closely Related to Canine Adenoviruses Identified via Fecal Virome Surveillance of Bats in New Mexico, USA, 2020-2021.}, journal = {Viruses}, volume = {17}, number = {10}, pages = {}, doi = {10.3390/v17101349}, pmid = {41157620}, issn = {1999-4915}, support = {RAPID Grant 2031816//U.S. National Science Foundation/ ; }, mesh = {Animals ; *Chiroptera/virology ; *Feces/virology ; *Adenoviridae/genetics/classification/isolation &amp; purification ; *Virome ; New Mexico/epidemiology ; Phylogeny ; Dogs ; COVID-19/epidemiology/virology ; Adenoviridae Infections/veterinary/virology/epidemiology ; Metagenomics ; SARS-CoV-2 ; Humans ; }, abstract = {Bats host a wide range of viruses, including several high-profile pathogens of humans and other animals. The COVID-19 pandemic raised the level of concern regarding the risk of spillover of bat-borne viruses to humans and, conversely, human-borne viruses to bats. From August 2020 to July 2021, we conducted viral surveillance on 254 bats from 10 species across urban, periurban, and rural environments in New Mexico, USA. We used a pan-coronavirus RT-PCR to assay rectal swabs and performed metagenomic sequencing on a representative subset of 14 rectal swabs and colon samples. No coronaviruses were detected by either RT-PCR or metagenomic sequencing. However, four novel viruses were identified: an adenovirus (proposed name lacepfus virus, LCPV), an adeno-associated virus (AAV), an astrovirus (AstV), and a genomovirus (GV). LCPV, detected in a big brown bat (Eptesicus fuscus), is more closely related to canine adenoviruses than to other bat adenoviruses, suggesting historical transmission between bats and dogs. All virus-positive bats were either juvenile or adult individuals captured in urban environments; none exhibited obvious clinical signs of disease. Our findings suggest limited or no circulation of enzootic coronaviruses or SARS-CoV-2 in southwestern U.S. bat populations during the study period. The discovery of a genetically distinct adenovirus related to canine adenoviruses highlights the potential for cross-species viral transmission and underscores the value of continued virome surveillance in animals living with and near humans.}, }
@article {pmid41157605, year = {2025}, author = {Zisi, Z and Ruiz Movilla, I and Basler, N and Close, L and Ghijselings, L and Van der Hoeven, R and Papadaki, MI and Rabbinowitsch, E and Van Reeth, F and Swinnen, J and Vogel, E and Vos, C and Hanssen, I and Matthijnssens, J}, title = {Metagenomics Study of the Commercial Tomato Virome Focused on Virus Species of Epidemiological Interest.}, journal = {Viruses}, volume = {17}, number = {10}, pages = {}, doi = {10.3390/v17101334}, pmid = {41157605}, issn = {1999-4915}, support = {Baekeland Mandate number HBC.2020.2306//Flanders Innovation and Entrepreneurship/ ; }, mesh = {*Solanum lycopersicum/virology ; *Virome/genetics ; *Metagenomics ; Phylogeny ; *Plant Diseases/virology ; Genome, Viral ; *Plant Viruses/genetics/classification/isolation &amp; purification ; Genotype ; Genetic Variation ; }, abstract = {Plant viruses have detrimental effects on commercial tomato cultivation leading to severe economic consequences. Viral metagenomics studies provide the opportunity to examine in depth the virome composition of a sample set without any pre-existing knowledge of the viral species that are present. In the present study, 101 plant samples were collected from commercial greenhouses in 13 countries in Europe, Africa, Asia, and North America between 2017 and 2024. All samples were processed with the VLP enrichment protocol NetoVIR and the obtained data were analyzed with the ViPER pipeline. Forty-three eukaryotic viral species were identified, with a median identification of 2 species per sample. The most prevalent viral species were pepino mosaic virus (PepMV), tomato brown rugose fruit virus (ToBRFV), and southern tomato virus (STV). The obtained genome sequences were used to study the diversity and phylogeny of these viruses. The three genotypes identified for PepMV showed low diversity within each genotype (96.2-99.0% nucleotide identity). Low isolate diversity was also found for ToBRFV and STV. No significant association could be found between STV identification and the presence of symptoms, questioning the pathogenic potential of STV. Three other pathogenic viral species of particular interest due to their effects on tomato cultivation or recent emergence, namely tomato torrado virus (ToTV), tomato fruit blotch virus (ToFBV), and cucumber mosaic virus (CMV), were part of the virome with low prevalence. Our study provided a comprehensive overview of the analyzed samples' virome, as well as the possibility to inspect the genetic diversity of the identified viral genomes and to look into their potential role in symptom development.}, }
@article {pmid41157584, year = {2025}, author = {Haisi, A and Nogueira, MF and Possebon, FS and Junior, JPA and Marinho-Prado, JS}, title = {Viral Community and Novel Viral Genomes Associated with the Sugarcane Weevil, Sphenophorus levis (Coleoptera: Curculionidae) in Brazil.}, journal = {Viruses}, volume = {17}, number = {10}, pages = {}, doi = {10.3390/v17101312}, pmid = {41157584}, issn = {1999-4915}, support = {202271250010//Parliamentary Amendment from the S&#xe3;o Paulo State Delegation/ ; 405786/2022-0//National Council for Scientific and Technological Development/ ; 23/2551-0002221-4//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado do Rio Grande do Sul - INCT-One Fapergs/ ; }, mesh = {Animals ; *Weevils/virology ; Brazil ; *Genome, Viral ; Saccharum/parasitology ; *Virome ; Metagenomics ; Phylogeny ; }, abstract = {Sphenophorus levis, commonly known as the sugarcane weevil, is one of the most important pests affecting Brazilian sugarcane crops. It has spread to all sugarcane-producing regions of Brazil, mainly through contaminated stalks. Effective control of this pest is difficult due to the protection conferred by the host plant during the larval stage. As a result, despite current control measures, S. levis populations continue to grow, and reports of new infestations remain frequent. Biotechnological control measures, such as the use of viruses, stands as a promising tool for pest control in agriculture. The aim of this study was to explore the RNA virome associated with S. levis using a viral metagenomic approach. Through the Read Annotation Tool (RAT) pipeline, we characterized, for the first time, the gut-associated viral community in adult weevils, identifying several novel viral genomes. Sphenophorus levis-associated virus (SLAV) had 12,414 nucleotides (nt); Sphenophorus levis tombus-like virus (SLTV) had 4085 nt; and the four genomic segments of Sphenophorus levis reo-like virus (SLRV) ranged from 2021 to 4386 nt. These genomes were assembled from 65,759 reads (SLAV), 114,441 reads (SLTV), and 270,384 reads (SLRV). Among the detected viral families, Partitiviridae was the most abundant. The identification of possible viral pathogens lays the foundation for future research into their potential use as biological control agents against S. levis.}, }
@article {pmid41157271, year = {2025}, author = {Al-Khalaifah, H and Rahman, MH and Al-Surrayai, T and Al-Dhumair, A and Al-Hasan, M}, title = {A One-Health Perspective of Antimicrobial Resistance (AMR): Human, Animals and Environmental Health.}, journal = {Life (Basel, Switzerland)}, volume = {15}, number = {10}, pages = {}, doi = {10.3390/life15101598}, pmid = {41157271}, issn = {2075-1729}, abstract = {Antibiotics are essential for treating bacterial and fungal infections in plants, animals, and humans. Their widespread use in agriculture and the food industry has significantly enhanced animal health and productivity. However, extensive and often inappropriate antibiotic use has driven the emergence and spread of antimicrobial resistance (AMR), a global health crisis marked by the reduced efficacy of antimicrobial treatments. Recognized by the World Health Organization (WHO) as one of the top ten global public health threats, AMR arises when certain bacteria harbor antimicrobial resistance genes (ARGs) that confer resistance that can be horizontally transferred to other bacteria, accelerating resistance spread in the environment. AMR poses a significant global health challenge, affecting humans, animals, and the environment alike. A One-Health perspective highlights the interconnected nature of these domains, emphasizing that resistant microorganisms spread across healthcare, agriculture, and the environment. Recent scientific advances such as metagenomic sequencing for resistance surveillance, innovative wastewater treatment technologies (e.g., ozonation, UV, membrane filtration), and the development of vaccines and probiotics as alternatives to antibiotics in livestock are helping to mitigate resistance. At the policy level, global initiatives including the WHO Global Action Plan on AMR, coordinated efforts by (Food and Agriculture Organization) FAO and World Organisation for Animal Health (WOAH), and recommendations from the O'Neill Report underscore the urgent need for international collaboration and sustainable interventions. By integrating these scientific and policy responses within the One-Health framework, stakeholders can improve antibiotic stewardship, reduce environmental contamination, and safeguard effective treatments for the future.}, }
@article {pmid41156846, year = {2025}, author = {Liu, Y and Shang, Y and Wang, X and Li, X and Yu, Z and Zeng, Z and Chen, Z and Wang, L and Xiang, T and Huang, X}, title = {Metagenomics and In Vitro Growth-Promoting Experiments Revealed the Potential Roles of Mycorrhizal Fungus Humicolopsis cephalosporioides and Helper Bacteria in Cheilotheca humilis Growth.}, journal = {Microorganisms}, volume = {13}, number = {10}, pages = {}, doi = {10.3390/microorganisms13102387}, pmid = {41156846}, issn = {2076-2607}, support = {31872181//National Natural Science Foundation of China/ ; 2021QDL062//Research Start-up Funds from the Hangzhou Normal University/ ; 2025JCXK01//Interdisciplinary Research Project of Hangzhou Normal University/ ; }, abstract = {In mycorrhizal symbiotic relationships, non-photosynthetic myco-heterotrophic plants are unable to supply photosynthates to their associated fungi. On the contrary, they rely on fungal carbon to sustain their own growth. Mycorrhizal fungi can mediate plant interactions with the rhizosphere microbiome, which contributes to the promotion of plant growth and nutrient uptake. However, the microbial community and key microbial species that function during the growth of the myco-heterotrophic plant Cheilotheca humilis remain unclear. In this study, we evaluated the microbial community associated with Cheilotheca humilis, which was confirmed via morphological characteristics typical of this plant species. Metagenomic analysis showed that the Afipia carboxidovorans was dominant at species level. Based on the LDA score, Bradyrhizobium ottawaense exhibited the higher abundance in the CH-B group (related to bud) while Afipia carboxidovorans was identified from the CH-F group (related to flower). Microbial co-occurrence networks showed that the Rhizobium genus, Herbaspirillum genus, and Cyanobacteriota were defined as core functional microbial species. To explore the potential microorganisms, metagenome-assembled genomes (MAGs) of the rhizosphere microbiome identified 14 medium- and high-quality MAGs, mainly involved in carbon fixation, nitrogen transformation, and phosphorus metabolism, possibly providing nutrients for the plant. Furthermore, a total of 67 rhizospheric and 66 endophytic microorganisms were isolated and obtained. In vitro experiments showed that the mycorrhizal helper bacteria (MHBs) Rhizobium genus and Pseudomonas genus possessed the ability of nitrogen fixation, phosphate solubilization, and siderophores production. Most importantly, the mycorrhizal fungus Humicolopsis cephalosporioides was obtained, which could potentially produce cellulase to supply carbohydrates for host. The findings suggest the mycorrhizal fungus Humicolopsis cephalosporioides and helper bacteria have great potential in the growth of the myco-heterotrophic plant Cheilotheca humilis.}, }
@article {pmid41156834, year = {2025}, author = {Kakumyan, P and Yang, L and Liu, S and Saninjuk, K and Dong, Q and Pan, X and Yu, C and Zhao, Y}, title = {Sustainable Recycling of Mushroom Residue as an Effective Substitute for Cotton Hull Waste in Volvariella volvacea Cultivation: Evidence from Physicochemical and Microbiome Analyses.}, journal = {Microorganisms}, volume = {13}, number = {10}, pages = {}, doi = {10.3390/microorganisms13102372}, pmid = {41156834}, issn = {2076-2607}, support = {2024YFD1200204//National Key R&amp;D Program of China/ ; 19390743000//Shanghai Committee of Science and Technology/ ; 2020-02-08-00-12-F01479//Shanghai Agricultural Commission Program/ ; }, abstract = {Mushroom residue (MR) is extensively produced during the industrialized cultivation of mushrooms, and its utilization is environmentally sustainable. Cotton hull waste (CW) serves as a common raw material for the cultivation of Volvariella volvacea in China. This study compared MR- and CW-based cultivation formulas with respect to their physicochemical characteristics, bacterial communities, and functional dynamics during substrate fermentation (composting). Xylanase production was greater in the MR formula than in the CW formula. Conversely, cellulase (CMCase) was generated at higher levels in the CW formula compared to the MR formula. Interestingly, the biological efficiency of MR was found to be comparable to that of CW, but the cost of MR was much lower. The dynamics of bacterial communities and their associated metabolic functions during substrate fermentation were monitored using 16S rRNA metagenomics techniques. Significant alterations in bacterial community structure were observed within both formulas throughout the preparation phase. Indicator species analysis revealed distinct patterns of bacterial diversity development between MR- and CW-based composts during fermentation. Metabolic function analysis indicated that carbohydrate and amino acid metabolism remained relatively active throughout this process. These results suggest that the MR formula is equally effective as conventional CW compost for supporting V. volvacea cultivation, while also offering a lower raw material cost.}, }
@article {pmid41156833, year = {2025}, author = {Xing, L and Niu, S and Wu, D and Zhang, Z and Xu, M}, title = {Sodium Butyrate Supplementation in Whole Milk Modulates the Gastrointestinal Microbiota Without Altering the Resistome and Virulome in Preweaned Calves.}, journal = {Microorganisms}, volume = {13}, number = {10}, pages = {}, doi = {10.3390/microorganisms13102375}, pmid = {41156833}, issn = {2076-2607}, support = {BR221506//Universitiy Basic Research Fund Project of Inner Mongolia Autonomous Region/ ; 2023LHMS03048//Natural Science Foundation of Inner Mongolia Autonomous Region/ ; }, abstract = {This study investigated the effects of supplementing whole milk (WM) with sodium butyrate (SB) on the gastrointestinal microbiota of preweaned calves. Twelve newborn Holstein calves (4 days old, 39.21 ± 1.45 kg) were randomly assigned into one of two dietary treatments: (1) WM without SB (CON) and (2) WM supplemented with SB (8.8 g/d; SB). At 74 days of age, all calves were slaughtered to collect ruminal and cecal digesta. Metagenomic analysis was used to characterize the microbial composition, virulence factor genes (VFGs), and antibiotic resistance genes (ARGs). SB supplementation altered the ruminal microbial composition and increased the abundance of beneficial bacteria, including Actinobacteria, Bifidobacterium, and Olsenella (p < 0.05). Although SB did not significantly affect the overall microbial composition or diversity in the cecum (p > 0.05), it promoted the growth of beneficial genera such as Flavonifractor and Subdoligranulum (p < 0.05). Furthermore, SB supplementation did not significantly alter the composition of VFGs or ARGs in either the rumen or the cecum (p > 0.05). However, significant differences in VFGs and ARGs were observed between the rumen and the cecum, with a greater diversity of both VFGs and ARGs detected in the cecum compared to that in the rumen (p < 0.05). In summary, supplementing whole milk with sodium butyrate modulates gastrointestinal health in preweaned calves by favorably shaping the microbial community without significantly altering the antibiotic resistome or virulome.}, }
@article {pmid41156832, year = {2025}, author = {Tokamani, M and Liakopoulos, P and Tegopoulos, K and Zigkou, AM and Triantaphyllidis, G and Kamidis, N and Grigoriou, ME and Sandaltzopoulos, R and Kolovos, P}, title = {Spatiotemporal Dynamics of Microbial and Fish Communities in the Thracian Sea Revealed by eDNA Metabarcoding.}, journal = {Microorganisms}, volume = {13}, number = {10}, pages = {}, doi = {10.3390/microorganisms13102373}, pmid = {41156832}, issn = {2076-2607}, support = {1671/22-03-2023//Green Fund/ ; }, abstract = {The Thracian Sea, a semi-enclosed coastal basin in the northeastern Aegean Sea, represents a dynamic marine environment influenced by freshwater inputs, stratification, and seasonal variability. Here, we investigated the spatiotemporal dynamics of microbial and ichthyofaunal communities using environmental DNA (eDNA) and high-throughput sequencing across various stations in the vicinity of the Thracian Sea, in consecutive months (through spring and summer). Seawater samples were collected from the surface and thermocline layers, and environmental parameters were recorded to examine their influence on biodiversity patterns. Microbial communities exhibited strong seasonal and depth-related structuring. Alpha diversity was highest in spring and declined during summer, while beta diversity analyses revealed clear clustering by month and depth. Dominant taxa included Alphaproteobacteria (SAR11), Cyanobacteria (Synechococcus, Prochlorococcus), with distinct core microbiomes. Fish communities, identified via CytB metabarcoding, displayed marked temporal turnover but limited spatial segregation. While alpha diversity metrics did not differ significantly, beta diversity analyses showed seasonal shifts with dominant taxa such as Raja spp., Engraulis spp., and Diplodus sargus. Multivariate and co-structure analyses (Mantel, Procrustes) revealed moderate but significant concordance between microbial and fish communities and support the existence of similar biodiversity responses to environmental parameters across temporal and spatial variability. Co-occurrence networks further present depth-specific associations, with surface communities being more cooperative and phototrophic, while thermocline networks showed modularity and potential ecological specialization. This study highlights the value of integrated eDNA-based monitoring in revealing seasonal biodiversity dynamics and ecological interactions in coastal marine ecosystems, supporting future spatial planning and conservation strategies in the Thracian Sea.}, }
@article {pmid41156828, year = {2025}, author = {Stock, EK and Rota, K and Dunn, B and Vasquez, M and Hernandez-Velazquez, D and Lespes, A and Bosmans, S and Smith, JC and Kyndt, JA}, title = {Seasonal Variations of the Nebraska Salt Marsh Microbiome: Environmental Impact, Antibiotic Resistance, and Unique Species.}, journal = {Microorganisms}, volume = {13}, number = {10}, pages = {}, doi = {10.3390/microorganisms13102369}, pmid = {41156828}, issn = {2076-2607}, support = {NSF OIA-2044049//EPSCoR NE/ ; }, abstract = {The Nebraska Salt Marshes are unique inland saltwater ecosystems, and this exploratory study is aimed at understanding the microbial composition and diversity that is providing the underlying support for these ecosystems. The microbiome shows both temporal and spatial variations that are concurrent with seasonal variations in salinity, temperature, and vegetation growth. Whole genome metagenomics analysis showed the predominance of purple non-sulfur bacteria in each season, indicating their importance in the marsh ecosystem. The fall season showed the highest microbial diversity and coincided with the highest levels of antimicrobial resistance markers to a variety of natural and synthetic antibiotics. In addition to the metagenomics approach, we also isolated and sequenced several unique species, most of them belonging to what appear to be new species of purple non-sulfur or purple sulfur bacteria. Both the metagenomics analysis and isolated species indicate that the nitrogen and sulfur cycling is well balanced in these marshes by a high relative abundance of purple bacteria. Noteworthy is the isolation of a new strain of Vibrio cholerae, which is a known human intestinal pathogen, that was predominantly present in the fall samples carrying several antibiotic resistance markers. Overall, the Nebraska salt marsh microbiome showcases both seasonal variations in microbial composition, a concerning prevalence of multiple antibiotic resistance, and the presence of unique bacterial species well-adapted to its distinctive alkaline and saline environment.}, }
@article {pmid41156825, year = {2025}, author = {Lorenzin, G and Carlin, M}, title = {Comparative Meta-Analysis of Long-Read and Short-Read Sequencing for Metagenomic Profiling of the Lower Respiratory Tract Infections.}, journal = {Microorganisms}, volume = {13}, number = {10}, pages = {}, doi = {10.3390/microorganisms13102366}, pmid = {41156825}, issn = {2076-2607}, abstract = {Metagenomic next-generation sequencing (mNGS) is increasingly employed for the diagnosis of lower respiratory tract infections (LRTIs). However, the relative diagnostic performance of long-read versus short-read sequencing platforms remains incompletely defined. For this systematic review, a search was conducted in PubMed, Embase, Scopus, Web of Science, and Google Scholar to identify studies directly comparing long-read (e.g., Oxford Nanopore, PacBio) and short-read (e.g., Illumina, Ion Torrent, BGISEQ) metagenomic sequencing for the diagnosis of LRTI. Eligible studies reported diagnostic accuracy or comparative performance between platforms. Risk of bias was evaluated using the QUADAS-2 tool. Thirteen studies met inclusion criteria. Reported platforms included Illumina, Oxford Nanopore, PacBio, Ion Torrent, and BGISEQ-500. A total of 13 studies met inclusion criteria. Across studies reporting sensitivity, average sensitivity was similar for Illumina (71.8%) and Nanopore (71.9%). Specificity varied substantially, ranging from 42.9 to 95% for Illumina and 28.6 to 100% for Nanopore. Concordance between platforms ranged from 56 to 100%. Illumina consistently produced superior genome coverage (approaching 100% in most reports) and higher per-base accuracy, whereas Nanopore demonstrated faster turnaround times (<24 h), greater flexibility in pathogen detection, and superior sensitivity for Mycobacterium species. Risk of bias was frequently high or unclear, particularly in patient selection (6 studies), index test interpretation (5), and flow and timing (4), limiting the robustness of pooled estimates. Long-read and short-read mNGS platforms exhibit comparable strengths in the diagnosis of LRTIs. Illumina remains optimal for applications requiring maximal accuracy and genome coverage, whereas Nanopore offers rapid, versatile pathogen detection, particularly for difficult-to-detect organisms such as Mycobacterium. However, there are certain limitations of the review, including a lack of comparable outcomes reported in all studies; therefore, further research is warranted to address this.}, }
@article {pmid41156813, year = {2025}, author = {Mollova, D and Baev, V and Iliev, I}, title = {In Vitro Probiotic Modulation of Specific Dietary Complex Sugar Consumption in Fecal Cultures in Infants.}, journal = {Microorganisms}, volume = {13}, number = {10}, pages = {}, doi = {10.3390/microorganisms13102352}, pmid = {41156813}, issn = {2076-2607}, support = {KP-06-M81/6//Bulgarian Science Fund/ ; }, abstract = {Establishing the relative stability of the gastrointestinal microbiome after birth is a long and complex process, and it occurs under various influences. The human gut microbiome plays a crucial role in influencing an individual's health and well-being across all stages of life. Breastfeeding, the introduction of solid food at a certain stage after birth, and the type of food largely determine the composition of the developing microbiome. The influence of probiotics on the early development of the microbiome is gaining increasing interest. The method of in vitro co-cultivation with probiotic strains provides a clearer picture of the influence of these microorganisms on the community and the functional changes that the infant's microbiome undergoes. We used fecal samples to study this influence by conducting metagenomic sequencing to determine the composition of the microbiome and a series of cultivations to determine the absorption of various fibers and prebiotic sugars from breast milk. We found statistically significant differences in the absorption of prebiotic sugars isolated from breast milk, as well as better absorption of several substrates in the presence of a probiotic strain.}, }
@article {pmid41156808, year = {2025}, author = {Mqambalala, A and Maleke, M and Deysel, LM and Osman, JR and Gomez-Arias, A and Valverde, A and Hernandez, JC}, title = {First Insight into the Natural Attenuation of Emerging Contaminants Using a Metagenomics Approach from Drinking Water Sources in the Free State.}, journal = {Microorganisms}, volume = {13}, number = {10}, pages = {}, doi = {10.3390/microorganisms13102349}, pmid = {41156808}, issn = {2076-2607}, support = {PMDS230718136664//National Research Foundation/ ; }, abstract = {Emerging contaminants have gained interest over the years due to their adverse effects on the aquatic environment. Therefore, it is essential to improve the current strategies for their removal. Biodegradation has emerged as an efficient strategy driven by microorganisms through metabolism and co-metabolism pathways. Enzymes encoded by specific genes facilitate these processes. This study aimed to identify and quantify the genes involved in these pathways. The research identified bacterial species belonging to the genera Pseudomonas, Nitrosomonas, Nitrosospira, and Methylotenera, which are associated with the degradation of emerging contaminants. Additionally, it successfully identified genes linked to metabolism and co-metabolism processes within the indigenous bacteria (MAGs). The findings suggest that the native bacteria in the samples may have the natural potential to mitigate emerging contaminants in aquatic environments through the combined actions of metabolism and co-metabolism.}, }
@article {pmid41156764, year = {2025}, author = {Wang, J and Gu, H and Gao, H and Zhang, T and Jiang, F and Song, P and Liu, Y and Fan, Q and Xu, Y and Zhang, R}, title = {Insights into Cold-Season Adaptation of Mongolian Wild Asses Revealed by Gut Microbiome Metagenomics.}, journal = {Microorganisms}, volume = {13}, number = {10}, pages = {}, doi = {10.3390/microorganisms13102304}, pmid = {41156764}, issn = {2076-2607}, support = {32360139//National Natural Science Foundation of China/ ; 2023LHMS03067//Natural Science Foundation of Inner Mongolia Autonomous Region/ ; LHZX-2023-02//Joint Grant from Chinese Academy of Sciences -People's Government of Qinghai Province on San-jiangyuan National Park/ ; }, abstract = {The Mongolian wild ass (Equus hemionus hemionus) is a flagship species of the desert-steppe ecosystem in Asia, and understanding its strategies for coping with cold environments is vital for both revealing its survival mechanisms and informing conservation efforts. In this study, we employed metagenomic sequencing to characterize the composition and functional potential of the gut microbiota, and applied DNA metabarcoding of the chloroplast trnL (UAA) g-h fragment to analyze dietary composition, aiming to reveal seasonal variations and the interplay between dietary plant composition and gut microbial communities. In the cold season, Bacteroidota and Euryarchaeota were significantly enriched, suggesting enhanced fiber degradation and energy extraction from low-quality forage. Moreover, genera such as Bacteroides and Alistipes were also significantly enriched and associated with short-chain fatty acid (SCFA) metabolism, bile acid tolerance, and immune modulation. In the cold season, higher Simpson index values and tighter principal coordinates analysis (PCoA) clustering indicated a more diverse and stable microbiota under harsh environmental conditions, which may represent an important microecological strategy for the host to cope with extreme environments. Functional predictions based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) further indicated upregulation of metabolic and signaling pathways, including ABC transporters, two-component systems, and quorum sensing, suggesting multi-level microbial responses to low temperatures and nutritional stress. trnL-based plant composition analysis indicated seasonal shifts, with Tamaricaceae detected more in the warm season and Poaceae, Chenopodiaceae, and Amaryllidaceae detected more in the cold season. Correlation analyses revealed that dominant microbial phyla were associated with the degradation of fiber, polysaccharides, and plant secondary metabolites, which may help maintain host energy and metabolic homeostasis. Despite the limited sample size and cross-sectional design, our findings highlight that gut microbial composition and structure may be important for host adaptation to cold environments and may also serve as a useful reference for future studies on the adaptive mechanisms and conservation strategies of endangered herbivores, including the Mongolian wild ass.}, }
@article {pmid41156729, year = {2025}, author = {Carnaggio, AA and Barthet, MM}, title = {It's a Question at the 'Root' of the Problem: Fungal Associations of Dionaea muscipula (Venus' Flytrap) Roots in Its Native Habitat.}, journal = {Microorganisms}, volume = {13}, number = {10}, pages = {}, doi = {10.3390/microorganisms13102269}, pmid = {41156729}, issn = {2076-2607}, support = {//US Fish &amp; Wildlife Services; Coastal Carolina University Coastal Marine and Wetlands Science Master's program; the Coastal Carolina University Graduate Student Research Incentive Grant; Savannah Presbytery's M.K. Pentecost Ecology Fund Grant/ ; }, abstract = {Carnivorous plants survive in harsh habitats with limited nutrients and a low pH. Much focus has been placed on carnivorous trap evolution as the primary mechanism to increase nutrient acquisition through insect digestion. Soil microbiome, however, may also play a pertinent role in nutrient acquisition influencing plant vigor and overall success. Dionaea muscipula, commonly known as the Venus' flytrap, is endemic to rims of the Carolina Bays located in southeast North Carolina and northeast South Carolina, where D. muscipula survives in nutrient poor soils with a vestigial root system. We utilized a combination of microscopy, plating, and metagenomics, to investigate the presence/absence of fungal partners that may contribute to success and vigor of D. muscipula in its native habitat in order to further conservation of this carnivorous plant. Results support that D. muscipula forms both mycorrhizal and fungal endophytic associations, most likely to aid nutrient uptake from otherwise nutrient-poor soils, as well as aid in stress defense. Several ectomycorrhizal, endophytic, and saprophytic fungal species were identified from the surrounding rhizosphere of D. muscipula roots presenting a first glimpse into fungal communities that may influence D. muscipula physiology and compose the microbiome of the Carolina Bays ecosystem.}, }
@article {pmid41156696, year = {2025}, author = {Wang, Y and Shi, F and Lang, F and Wang, G and Mao, Y and Xiao, Y and Yin, L and He, G and Liao, Y}, title = {Ecological Imprint of Rare Earth Mining on Microbial Communities and Water Quality Across Depth and Distance Gradients in Ganzhou, China.}, journal = {Microorganisms}, volume = {13}, number = {10}, pages = {}, doi = {10.3390/microorganisms13102236}, pmid = {41156696}, issn = {2076-2607}, support = {42167014//National Natural Science Foundation of China/ ; GJJ2401516//Jiangxi Provincial Department of Education Science and Technology research-youth project/ ; S202510419008//Innovation and Entrepreneurship Project for College Students in Jiangxi Province/ ; JZB1915//the Research Project of Jinggangshan University (Natural Sciences)/ ; }, abstract = {Rare earth element (REE) mining exerts profound impacts on aquatic ecosystems, yet the microbial community responses and water quality under such stress remain underexplored. In this study, the surface (0.2 m) and subsurface (1.0 m) water along a spatial transect from proximal to distal points was investigated in a REE-mining area of Ganzhou, China. Physicochemical analyses revealed pronounced gradients of nitrogen (e.g., NH4[+]-N, NO3[-]-N), heavy metals (e.g., Mn, Zn, Pb), and REEs (e.g., La, Nd, Ce), with higher accumulation near mining sources and partial attenuation downstream. Dissolved oxygen and redox potential indicated mildly reducing conditions at contaminated points, potentially promoting denitrification and altering nitrogen cycling. Metagenomic sequencing showed significant shifts in microbial community composition, with enrichment of metal- and nitrogen-tolerant taxa, and key denitrifiers (e.g., Acidovorax, Bradyrhizobium, Rhodanobacter), particularly at upstream polluted points. KEGG-based gene annotation highlighted dynamic nitrogen transformations mediated by multiple pathways, including nitrification, denitrification, dissimilatory nitrate reduction to ammonium, and nitrogen fixation. Notably, genes associated with nitrite and nitrate reduction (e.g., nir, nar, nrf) were enriched near mining sources, indicating enhanced nitrogen conversion potential, while downstream activation of nitrogen-fixing genes suggested partial ecosystem recovery. Meanwhile, some microbial such as Variovorax carried metal tolerant genes (e.g., ars, chr, cnr). These findings demonstrate that REE and heavy metal contamination restructure microbial networks, modulate nitrogen cycling, and create localized ecological stress gradients. This study provides a comprehensive assessment of mining-related water pollution, microbial responses, and ecological risks, offering valuable insights for monitoring, restoration, and sustainable management of REE-impacted aquatic environments.}, }
@article {pmid41156619, year = {2025}, author = {Sultankulova, KT and Kozhabergenov, NS and Shynybekova, GO and Almezhanova, MD and Zhaksylyk, SB and Abayeva, MR and Chervyakova, OV and Argimbayeva, TO and Orynbayev, MB}, title = {Metagenomic Profile of Bacterial Communities of Hyalomma scupense and Hyalomma asiaticum Ticks in Kazakhstan.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {10}, pages = {}, doi = {10.3390/pathogens14101008}, pmid = {41156619}, issn = {2076-0817}, mesh = {Animals ; Kazakhstan ; *Metagenomics/methods ; *Ixodidae/microbiology ; Male ; Female ; *Bacteria/genetics/classification/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Cattle ; *Microbiota ; *Metagenome ; DNA, Bacterial/genetics ; }, abstract = {Ticks are important vectors of pathogens affecting humans and animals, posing a serious threat to health. For the first time, we studied the metagenomic profile of the microbial composition of Hyalomma scupense and Hyalomma asiaticum ticks in Kazakhstan. A total of 94 adult H. asiaticum and H. scupense ticks collected from randomly selected cattle in Kazakhstan in 2023 were analyzed. 16S rRNA gene sequencing was performed using the Ion Torrent NGS platform. Taxonomic classification was carried out in the BV-BRC platform with the Kraken2 database. Metagenomic analysis revealed 26 bacterial genera, including both pathogenic and symbiotic taxa. In H. scupense, the dominant groups were Francisella (89.0%), Staphylococcus (76.0%) and Candidatus Midichloria (61.0%), while in H. asiaticum, they were Francisella (99.0% and 95.0%) and Helcococcus (65.0%). In male H. scupense, the proportion of Francisella reached 89%, whereas in females, it varied from 2% to 28%. In H. asiaticum, Helcococcus accounted for 65% in males compared to 11% in females. This is the first report on the metagenomic profile of the microbiota of H. scupense and H. asiaticum in Kazakhstan. The detection of pathogens indicates a risk of their transmission to humans and animals and highlights the need to develop new tick control strategies.}, }
@article {pmid41156596, year = {2025}, author = {Dao, TK and Pham, TTN and Nguyen, HD and Dam, QT and Phung, TBT and Nguyen, TVH and Nguyen, TQ and Hoang, KC and Do, TH}, title = {Metagenomic Analysis of the Gastrointestinal Phageome and Incorporated Dysbiosis in Children with Persistent Diarrhea of Unknown Etiology in Vietnam.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {10}, pages = {}, doi = {10.3390/pathogens14100985}, pmid = {41156596}, issn = {2076-0817}, support = {&#x110;T&#x110;LCN.63/22//Ministry of Science and Technology, Vietnam/ ; }, mesh = {Humans ; *Diarrhea/microbiology/virology ; *Dysbiosis/microbiology/virology ; Metagenomics/methods ; Infant ; *Bacteriophages/genetics/classification/isolation &amp; purification ; *Gastrointestinal Microbiome ; Male ; Female ; Vietnam ; Child, Preschool ; *Metagenome ; Bacteria/classification/genetics/virology ; *Virome ; Feces/microbiology/virology ; }, abstract = {Persistent diarrhea of unknown etiology in children under 2 years of age is a common problem and poses a major challenge for the health sector. However, knowledge of the composition and dysbiosis of the intestinal phageome, phage-associated bacteriome in the persistent diarrhea remains limited. In this study, a process for phage enrichment and metagenomic extraction was developed and applied to recover gut phage metagenomes from 30 healthy children and 30 children with persistent diarrhea for high-throughput sequencing. Taxonomic annotation using Kraken2 revealed that, besides Norwalk virus, Primate bocaparvovirus 1 and Human-associated gemykibivirus 2, phage communities in the diarrhea group showed reduced diversity and contained sample-dependent phages targeting Salmonella enterica, Enterobacter, Shigella flexneri, Clostridioides difficile, Pseudomonas aeruginosa, Streptococcus miti, uropathogenic Escherichia coli and functioned balancing bacterial communities. Bacterial fraction in the metagenomic datasets reflected clear patterns of dysbiosis, including a severe deficiency of beneficial bacteria, an increase in Firmicutes, a marked decline in Actinobacteria, Bacteroidetes, Proteobacteria and sample-dependent enrichment of Enterococcus, Escherichia and Acinetobacter in diarrhea cases. This study, for the first time, investigated the dynamics of gut phageome, phage-associated bacteriome in children with persistent diarrhea of unknown causes in Vietnam, providing new insight for complementary treatment.}, }
@article {pmid41156563, year = {2025}, author = {Modrego, J and Pantoja-Arévalo, L and Gómez-Garre, D and Gesteiro, E and González-Gross, M}, title = {Dairy-Gut Microbiome Interactions: Implications for Immunity, Adverse Reactions to Food, Physical Performance and Cardiometabolic Health-A Narrative Review.}, journal = {Nutrients}, volume = {17}, number = {20}, pages = {}, doi = {10.3390/nu17203312}, pmid = {41156563}, issn = {2072-6643}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology/immunology ; *Dairy Products/adverse effects ; Animals ; Milk ; Probiotics ; *Immunity ; Cardiometabolic Risk Factors ; }, abstract = {Background/Objective: Milk and fermented dairy products are widely consumed functional foods and beverages, offering not only essential nutrients but also bioactive compounds with potential to modulate host immunity, metabolism, and the gut microbiome. This narrative review aims to synthesize current knowledge on the relationship between dairy consumption, gut microbiome, immune modulation, adverse reactions to food, physical performance and cardiometabolic health. Methods: An extensive literature analysis was conducted to explore how milk and fermented dairy products modulate the gut microbiome and influence the immune and cardiometabolic health. This study synthesis focused on key dairy bioactive compounds, such as probiotics, miRNAs, milk-derived peptides and exosomes and on evaluating their proposed mechanisms of action in inflammation and metabolic regulation, and their possible influence on physical performance through gut-microbiome interactions. Additionally, advances in metagenomic and metabolomic technologies were reviewed for their potential to uncover host-microbiota interactions relevant to precision nutrition strategies. Results: Fermented dairy products have shown potential in promoting beneficial bacteria growth such as Lactobacillus and Bifidobacterium, short-chain fatty acid synthesis and reduction in proinflammatory biomarkers. Specific dairy-derived peptides and exosomal components may further support gut barrier integrity, immune regulation and improve physical performance and reduce cardiometabolic risk factors. Additionally, emerging evidence links individual gut microbiota profiles to specific metabolic responses, including tolerance to lactose and bovine milk proteins. Conclusions: Integrating microbiome science with traditional nutritional paradigms enhances our understanding of how dairy influences immune and cardiometabolic health. Overall, current evidence suggests that investigating dairy-microbiome interactions, alongside lifestyle factors such as physical activity, may inform future personalized nutrition strategies aimed at supporting metabolic and immune health.}, }
@article {pmid41155945, year = {2025}, author = {Bodnár, K and Fehér, P and Ujhelyi, Z and Haimhoffer, &#xc1; and Papp, B and Sinka, D and Freytag, C and Fidrus, E and Szarka, K and Kardos, G and Nacsa, F and Bácskay, I and Józsa, L}, title = {Formulation and Testing of Alginate Microbeads Containing Salvia officinalis Extract and Prebiotics.}, journal = {Pharmaceutics}, volume = {17}, number = {10}, pages = {}, doi = {10.3390/pharmaceutics17101308}, pmid = {41155945}, issn = {1999-4923}, support = {ek&#xf6;p-24-3-I//university research scholarship program of the ministry for culture and innovation from the source of the national research, development and innovation fund/ ; TKP2021-EGA-18//Ministry of Culture and Innovation of Hungary from the National Research, Development and Innovation Fund/ ; 2022-1.2.2-T&#xc9;T-IPARI-UZ-2022-00006//National Research, Development and Innovation Fund/ ; }, abstract = {Background/Objectives: This study aimed to develop an advanced oral delivery platform for Salvia officinalis (S. officinalis) extract by co-encapsulating it with inulin and pectin in alginate-based microbeads, formulated via ionic gelation. Methods: The microbeads were comprehensively characterized, including the assessment of morphology, particle size, encapsulation efficiency, swelling behavior, in vitro dissolution, and enzymatic stability, and Caco-2 cell-based assays for cytocompatibility, permeability, and transepithelial electrical resistance. Antioxidant capacity and anti-inflammatory effects were also evaluated. Results: The resulting microbeads (~275 µm) achieved > 90% encapsulation efficiency and exhibited pronounced swelling (~90%). The release of S. officinalis constituents displayed pH sensitivity, with sustained release in simulated intestinal fluid, alongside significant enhancement of enzymatic stability. Encapsulation led to markedly improved permeability of bioactive compounds across Caco-2 monolayers, attributable to reversible modulation of tight junctions. Encapsulated extract retained potent antioxidant activity and significantly reduced pro-inflammatory cytokines. The formulation, across various concentrations, further promoted the growth and viability of Lactobacillus strains. Conclusions: Collectively, these findings demonstrate that alginate-inulin-pectin microbeads provide a multifunctional system for stabilizing S. officinalis extract, enabling controlled release, enhanced intestinal absorption, and maintained bioefficacy. Importantly, the formulation also promoted Lactobacillus viability, indicating a prebiotic effect and offering considerable potential for improved oral therapeutic applications.}, }
@article {pmid41155696, year = {2025}, author = {Ji, M and Ma, B and Dong, J and Liu, S and Shi, Y and Bu, M and Wang, L and Liu, L}, title = {Mining Microbial Dark Matter: Advanced Cultivation Techniques for Bioactive Compound Discovery.}, journal = {Pharmaceuticals (Basel, Switzerland)}, volume = {18}, number = {10}, pages = {}, doi = {10.3390/ph18101583}, pmid = {41155696}, issn = {1424-8247}, support = {2022YFC2303100, 32472320, 32022002 and 32270083//National Key Research and Development Program of China, National Natural Science Foundation of China/ ; }, abstract = {The vast majority of microorganisms in the environment remain uncultured using conventional laboratory techniques, representing an immense untapped reservoir of genetic and chemical diversity. Recent innovations in cultivation strategies, combined with advances in metagenomics, single-cell genomics, and synthetic biology, have opened new avenues for accessing and harnessing bioactive natural products from these previously inaccessible microorganisms. This review highlights recent methodological and technological advancements in the cultivation and identification of novel microorganisms, and showcases the resulting discoveries of new natural products, demonstrating their potential for drug development.}, }
@article {pmid41155464, year = {2025}, author = {Usui, M and Miyagi, S and Yamanaka, R and Oka, Y and Kobayashi, K and Sato, T and Sano, K and Onizuka, S and Inoue, M and Fujii, W and Iwasaki, M and Ariyoshi, W and Nakashima, K and Nishihara, T}, title = {Measuring the Invisible: Microbial Diagnostics for Periodontitis-A Narrative Review.}, journal = {International journal of molecular sciences}, volume = {26}, number = {20}, pages = {}, doi = {10.3390/ijms262010172}, pmid = {41155464}, issn = {1422-0067}, mesh = {Humans ; *Periodontitis/diagnosis/microbiology ; *Molecular Diagnostic Techniques/methods ; Nucleic Acid Amplification Techniques/methods ; Porphyromonas gingivalis/isolation &amp; purification/genetics ; }, abstract = {Periodontitis is a biofilm-driven inflammatory disease in which conventional indices (probing depth, clinical attachment level, and radiographs) quantify tissue destruction without capturing the biology of infection. In this review, we synthesized microbiological diagnostics, from chairside tools to omics. We outline sampling strategies and emphasize the quantitative monitoring of bacterial load. Enzymatic assays (e.g., N-benzoyl-DL-arginine-2-naphthylamide hydrolysis assay test) measure functional activity at the point of care. Immunological methods include rapid immunochromatography for Porphyromonas gingivalis and enzyme-linked immunosorbent assay for the high-throughput measurement of bacterial antigens. Molecular platforms encompass quantitative polymerase chain reaction (qPCR) (TaqMan, SYBR, multiplex panels; propidium monoazide quantitative-qPCR for viable cells), checkerboard DNA-DNA hybridization for semi-quantitative community profiling, loop-mediated isothermal amplification (LAMP)/molecular beacon-LAMP for portable isothermal detection, and microarrays. Complementary modalities such as fluorescent in situ hybridization, next-generation sequencing, and Fourier transform infrared spectroscopy provide spatial, ecological, and biochemical resolutions. We discuss the limitations of current approaches, including sampling bias, presence-activity discordance, semi-quantitation, method biases, limited strain/function resolution, low-biomass artifacts, and lack of validated cutoffs. To address these challenges, we propose a pragmatic hybrid strategy: site-specific quantitative panels combined with activity and host-response markers interpreted alongside clinical metrics under standardized quality assurance/quality control. Priorities include outcome-linked thresholds, strain-aware/functional panels, robust point-of-care chemistry, and harmonized protocols to enable personalized periodontal care.}, }
@article {pmid41155136, year = {2025}, author = {Bitter, M and Weigel, M and Mengel, JP and Ott, B and Windhorst, AC and Tello, K and Imirzalioglu, C and Hain, T}, title = {Assessment of Microbiome-Based Pathogen Detection Using Illumina Short-Read and Nanopore Long-Read Sequencing in 144 Patients Undergoing Bronchoalveolar Lavage in a University Hospital in Germany.}, journal = {International journal of molecular sciences}, volume = {26}, number = {20}, pages = {}, doi = {10.3390/ijms26209841}, pmid = {41155136}, issn = {1422-0067}, support = {TRR 84/3 Innate Immunity of the Lung, B08//Deutsche Forschungsgemeinschaft/ ; 519/03/06.001-(0002) LOEWE-Diffusible Signals B03//Hessian Ministry of Science and Research, Arts and Culture (HMWK)/ ; MB2021 JLU TRAINEE//Faculty of Medicine at Justus Liebig University Giessen/ ; }, mesh = {Humans ; *Microbiota/genetics ; *High-Throughput Nucleotide Sequencing/methods ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Male ; Female ; *Bronchoalveolar Lavage Fluid/microbiology ; Aged ; Germany ; *Bacteria/genetics/isolation &amp; purification/classification ; Hospitals, University ; Bronchoalveolar Lavage ; Nanopore Sequencing/methods ; Adult ; *Respiratory Tract Infections/microbiology/diagnosis ; Aged, 80 and over ; }, abstract = {Lower respiratory tract infections (LRTIs) represent a significant global health concern, and the accurate identification of pathogens is crucial for patient care. Culture-based methods are the gold standard, but their detection abilities are limited. Next-generation sequencing (NGS) offers a promising method for comprehensive microbial detection, providing valuable information for clinical practice. In this study, 144 bronchoalveolar lavage fluid samples were collected, culture-based diagnostics were performed, and bacterial microbiome profiles were generated by short-read sequencing of the V4 region of the 16S rRNA gene using Illumina technologies and long-read sequencing with Oxford Nanopore Technologies (ONT) to determine the full-length 16S rRNA gene. The most common genera detected by NGS included Streptococcus, Staphylococcus, Veillonella, Prevotella, Rothia, Enterococcus, and Haemophilus. Short-read sequencing detected cultured bacteria at the genus level in ~85% of cases, while long-read sequencing demonstrated agreement with cultured species in ~62% of cases. In three cases, long-read sequencing identified the uncommon potential lung pathogen Tropheryma whipplei not detected with traditional culturing techniques. The NGS results showed a partial overlap with culture as the current diagnostic gold standard in LRTI. Additionally, NGS detected a broader spectrum of bacteria, revealed fastidious potential pathogens, and offered deeper insights into the complex microbial ecosystem of the lungs.}, }
@article {pmid41154862, year = {2025}, author = {Yin, R and Chen, B and He, X and Cai, C and Zhai, T and Shi, H and Li, N and Ma, X}, title = {Enhanced Phosphorus Removal by Iron-Carbon in Constructed Wetlands Across Salinity Gradients: Mechanisms and Microbial Insights for Aquaculture Tailwater Treatment.}, journal = {Biology}, volume = {14}, number = {10}, pages = {}, doi = {10.3390/biology14101459}, pmid = {41154862}, issn = {2079-7737}, support = {No. BK20220682//Natural Science Foundation of Jiangsu Province/ ; LYG20230005//Postdoctoral Science Foundation of Lianyungang/ ; KYCX24-3671//Postgraduate Research &amp; Practice Innovation Program of Jiangsu Province/ ; PAPD//Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; 2025SNJF008//Zhejiang Province 'San Nong Jiu Fang' Science and Technology Collaboration Project/ ; }, abstract = {Saline aquaculture tailwater challenges conventional constructed wetlands (CWs) with their limited phosphorus (P) removal capacity. To address this, iron-carbon constructed wetlands (IC-CWs) were developed and operated under four salinity gradients (0, 10, 20, and 30) for 155 days to investigate the effects of salinity on P removal and associated microbial mechanisms. The results showed that salinity critically influenced long-term P removal, with the system at salinity 20 (S20) achieving the highest total phosphorus (TP) removal efficiency (78.80 ± 6.01%). Enhanced P removal was primarily attributed to the upregulation of phosphate transport genes (pstS, 14.25-fold increase) and elevated activity of key enzymes (AKP and ACP) in phosphorus-accumulating organisms (PAOs). However, high salinity (30) suppressed microbial metabolic functions. Metagenomic analysis revealed that salinity stress reshaped microbial community structure, with Bacteroidota abundance increasing 10-fold in S20 compared to S0 (control). This phylum harbored the phnE gene, significantly promoting organic phosphorus mineralization. Additionally, iron release increased with rising salinity, and the relative abundance of the phnE gene in Bacteroidota was highest in the S20 group, indicating a close association between iron release and PAOs as well as organic P mineralization genes. The quadratic polynomial model revealed that iron release under high salinity followed nonlinear kinetics, with passivation layer rupture promoting iron-phosphorus precipitate desorption in later stages. These findings provide a theoretical basis for optimizing salinity parameters to enhance chemical-biological P removal synergy, offering a promising strategy for saline aquaculture wastewater treatment.}, }
@article {pmid41154799, year = {2025}, author = {Promariya, A and Treenarat, S and Akrimajirachoote, N and Sricharern, W and Raksajit, W}, title = {Cultivation of Arthrospira platensis in Veterinary Hospital Wastewater Enhances Pigment Production and Reduces Antibiotic Resistance Genes.}, journal = {Biology}, volume = {14}, number = {10}, pages = {}, doi = {10.3390/biology14101396}, pmid = {41154799}, issn = {2079-7737}, support = {FF(KU)18.66 and FF(KU)50.67//Kasetsart University Research and Development (KURDI)/ ; The 80th Anniversary of Kasetsart University's Establishment//Graduate School, Kasetsart University/ ; High Quality Research Graduate Development Cooperation Project//Kasetsart University and the National Science and Technology Development Agency (NSTDA)/ ; }, abstract = {Veterinary hospital wastewater (VHW) is a significant environmental concern due to its high nutrient content, organic pollutants, and antibiotic resistance genes (ARGs). This study evaluated the physicochemical properties of VHW, its potential to support Arthrospira platensis cultivation, and its effects on microbial and resistome profiles. VHW contained high levels of ammonia nitrogen, total Kjeldahl nitrogen, biological oxygen demand (BOD), and chemical oxygen demand (COD), indicating substantial contamination. A. platensis was cultivated for 8 days in Zarrouk medium supplemented with 0-100% VHW. Biomass production peaked in 25% VHW (0.78 ± 0.05 g/L), while growth was strongly suppressed at concentrations ≥75%. Pigment levels in 25% VHW increased significantly compared to the control: 1.3-fold for chlorophyll-a (12.0 μg/mL), 1.5-fold for carotenoids (4.4 μg/mL), 1.7-fold for phycocyanin (120 μg/mL), and 2.3-fold for allophycocyanin (54 μg/mL). Shotgun metagenomic analysis revealed that A. platensis cultivation markedly altered the microbial community and reduced the prevalence of ARGs. In 25% VHW, Proteobacteria dominated the community (97.0%), but their abundance declined to 11.6% when co-cultivated with A. platensis. Likewise, Acinetobacter sp. carrying high levels of the aph gene, along with Methylophaga sp. and Pseudomonas_E sp. harboring oqxB, decreased substantially, suggesting that A. platensis effectively suppressed ARG-rich genera. These findings highlight the dual potential of A. platensis for sustainable pigment-rich biomass production and efficient wastewater treatment.}, }
@article {pmid41154019, year = {2025}, author = {Zhang, S and Wang, Q and Gong, S and Li, M and Zhang, Y and Sun, L and Sun, L}, title = {The Effect of Cucumaria frondosa Tentacles Hydrolysates on Dextran Sulfate Sodium-Induced Colitis: Integrated Metagenomics and Metabolomics Analysis.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {20}, pages = {}, doi = {10.3390/foods14203483}, pmid = {41154019}, issn = {2304-8158}, support = {42106111//National Natural Science Foundation of China/ ; 2023JCYJ088//The Yantai Science and Technology Innovation Development Program/ ; ZR2021QD030//Natural Science Foundation of Shandong Province/ ; QSCDP202304//Fund of Yantai Key Laboratory of Quality and Safety Control and Deep Processing of Marine Food/ ; }, abstract = {Inflammatory bowel disease continues to pose substantial therapeutic challenges in modern gastroenterology. This study systematically evaluated the anti-colitis efficacy of Cucumaria frondosa tentacles hydrolysates (CFTHs) using a dextran sulfate sodium (DSS)-induced murine colitis model. Characterized by enhanced stability and solubility with molecular weights below 1000 Da, administration of CFTHs demonstrated a significant mitigation in colitis pathology. Therapeutic outcomes included an improved splenic index, attenuated colonic mucosal damage, and substantial decreases in serum pro-inflammatory cytokines. Relative to the DSS group, the MPO value in the CFTHs-H group decreased by 27.6%, and the IL-6 value exhibited a reduction of 33%. Metagenomic profiling revealed that CFTHs mediated gut microbiota modulation, particularly the enrichment of beneficial Bacteroidetes and suppression of pro-inflammatory Proteobacteria. Metabolomic analysis identified elevated colonic concentrations of anti-inflammatory metabolites such as gamma-linolenic acid and prostaglandin I2, suggesting a microbiome-metabolome crosstalk in the therapeutic mechanism. These multi-omics findings in a murine model suggest that CFTHs may represent a promising candidate for future studies as a nutraceutical intervention for inflammatory bowel disorder. This intervention may operate through mechanisms that include simultaneous immunomodulation, microbiota restoration, and metabolic reprogramming.}, }
@article {pmid41153961, year = {2025}, author = {Xiang, R and Chen, J and Wang, J and Song, H and Jiang, J and Wu, F and Luo, J and Duan, M and Zhu, G}, title = {Characteristics of the Gut Microbiota in Different Segments of the Gastrointestinal Tract of Big-Eyed Bamboo Snake (Pseudoxenodon macrops).}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {20}, pages = {}, doi = {10.3390/ani15203035}, pmid = {41153961}, issn = {2076-2615}, abstract = {Snakes are model animals to study energy balance, but studies on the gut microbiota of the animals are rather scarce. To fill the gap, we used metagenome sequencing to investigate the microbial community composition and adaptability in the stomach, small intestine, and large intestine of Big-eyed Bamboo Snake. The results showed that there was no significant differences in α-diversity among different gastrointestinal segments. Pseudomonadota, Bacteroidota, and Bacillota were the most abundant phyla. The dominant genera in the stomach and small intestine were similar, while those in the large intestine were distinct. The abundance of Bacteroides, Citrobacter and Clostridium was significantly higher in the large intestine than in the small intestine. The LEfSe analysis revealed that the small intestine had the most characteristic bacteria, with a total of 20 species, while the stomach and large intestine each had two species. Additionally, in the current study, we also focused on the impact of the microbial community structure on functions through functional annotations in the KEGG and CAZy. There were significant differences in the KEGG level 2 between the stomach and the small intestine. The LEfSe analysis revealed the differences in the CAZy level 2 between the large intestine and the small intestine. Overall, our study provided a comparative and contrastive analysis of the gut microbiota in different gastrointestinal segments of Big-eyed Bamboo Snake, offering valuable insights for the co-evolution mechanism of the host and the gut microbiota.}, }
@article {pmid41153865, year = {2025}, author = {Wei, J and Wei, L and Ullah, A and Geng, M and Zhang, X and Wang, C and Khan, MZ and Wang, C and Zhang, Z}, title = {Metagenomic Applications to Herbivore Gut Microbiomes: A Comprehensive Review of Microbial Diversity and Host Interactions.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {20}, pages = {}, doi = {10.3390/ani15202938}, pmid = {41153865}, issn = {2076-2615}, support = {2022YFD1600103; 2023YFD1302004//the National Key R&amp;D Program of China/ ; }, abstract = {Herbivorous animals rely on complex gastrointestinal systems and microbial communities to efficiently digest plant-based diets, extract nutrients, and maintain health. Recent advances in metagenomic technologies have enabled high-resolution, culture-independent analysis of gut microbiota composition, functional potential, and host-microbe interactions, providing insights into microbial diversity across the herbivore digestive tract. This review summarizes key findings on the gastrointestinal microbiota of herbivores, focusing on ruminant foregut and non-ruminant hindgut fermentation. Ruminants like cattle, sheep, and goats host microbiota enriched with fibrolytic and methanogenic microbes that facilitate fiber degradation and volatile fatty acid production, contributing significantly to energy balance. In contrast, non-ruminants such as horses and rabbits rely on hindgut fermentation, with distinct microbial taxa contributing to carbohydrate and protein breakdown. The review further explores how specific microbial taxa, including Prevotella, Fibrobacter, and Ruminococcus, correlate with improved feed efficiency and growth performance, particularly in ruminants. Additionally, the roles of probiotics, prebiotics, and symbiotics in modulating gut microbial composition and enhancing productivity are discussed. Despite significant advances, challenges remain in microbial sampling, functional annotation, and understanding the integration of microbiota with host physiology. The review emphasizes the potential of metagenomic insights in optimizing herbivore gut microbiota to improve feed efficiency, health, and sustainable livestock production.}, }
@article {pmid41153262, year = {2025}, author = {Feng, Y and Feng, H and Yu, X and Zhao, J and Zhou, H and Li, J and Chen, P and Feng, L}, title = {Next-Generation Sequencing for Diagnosis of Fatal Balamuthia Amoebic Encephalitis: A Case Report.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {15}, number = {20}, pages = {}, doi = {10.3390/diagnostics15202590}, pmid = {41153262}, issn = {2075-4418}, support = {Z20200307//The scientific research project of Guangxi Health Commission/ ; }, abstract = {Background:Balamuthia mandrillaris is a free-living amoebic parasite that primarily causes rare opportunistic infections in immunocompromised hosts. Balamuthia amoebic encephalitis (BAE) is a rare yet severe parasitic infection affecting the central nervous system. It has an extremely low incidence in China but can have a mortality rate as high as 98%. The clinical manifestations of amebic infections are similar to those of bacterial and tuberculous meningitis, lacking specificity, which makes accurate diagnosis challenging in the clinical setting. Case Presentation: A 61-year-old immunocompetent woman experienced worsening headache and a moderate fever over the course of five days, initially treated as a common cold. On 25 February 2025, she exhibited behavioral abnormalities, dysphagia, and a high fever of 40.2 °C, which progressed to a coma. On 26 February, her cranial CT scan revealed multifocal hemorrhagic lesions in the right frontotemporoparietal lobes. The MRI revealed similar lesions with slight enhancement and herniation. She underwent an emergency decompressive craniectomy, yet her condition continued to deteriorate following the surgery. On 27 February, serum targeted next-generation sequencing (tNGS) detected B. mandrillaris. Additionally, metagenomic NGS (mNGS) of the cerebrospinal fluid (CSF) sample confirmed the presence on 28 February. Finally, B. mandrillaris was identified through a brain tissue biopsy on 3 March. However, due to the delayed diagnosis and lack of effective drugs, her condition rapidly deteriorated and became irreversible. Her family ultimately chose to withdraw treatment. Conclusions: This study highlights the application of NGS for early diagnosis of patients with severe CNS infection. Both tNGS and mNGS can be considered for the rapid detection of rare or novel pathogens and for facilitating diagnosis.}, }
@article {pmid41152730, year = {2025}, author = {Su, Y and Xiao, Q and Ye, S and Qiu, F and Guo, Q and Chen, Q and Chen, P and You, Y and Huang, S and Wu, Z}, title = {Metagenomic next-generation sequencing (mNGS) guides targeted antibiotic therapy and reduces mortality in sepsis: a propensity-matched retrospective cohort study.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {1430}, pmid = {41152730}, issn = {1471-2334}, support = {A2024130//Guangdong Medical Research Foundation/ ; A2023198//Guangdong Medical Research Foundation/ ; 82374216//National Natural Science Foundation of China/ ; 20251363//Traditional Chinese Medicine Bureau of Guangdong Province/ ; 2320001006680//Foshan Science and Technology Bureau/ ; 2320001006896//Foshan Science and Technology Bureau/ ; 2220001005576//Foshan Science and Technology Bureau/ ; YN2022QN01//Guangdong Hospital of Traditional Chinese Medicine Special Research Project on Traditional Chinese Medicine Science and Technology/ ; SL2025A04J4201//Planned Science Technology Project of Guangzhou/ ; 20210001//Foshan Medical Research Project/ ; }, }
@article {pmid41152727, year = {2025}, author = {Chen, L and Wang, C and Zhang, H and Wu, Y and Li, F and Shi, H and Ren, Z and Chen, Y and Huang, J and Zhao, D and Pan, J and Lu, H and Zheng, S}, title = {Characterization of microbiota dysbiosis in papillary thyroid carcinoma and benign thyroid nodules: low abundance of intestinal butyrate-producing bacteria.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {691}, pmid = {41152727}, issn = {1471-2180}, support = {2022YFC3602000//National Key Research and Development Program of China/ ; 81874038//the National Natural Science Foundation of China/ ; JNL-2022001A//the Research Project of Jinan Microecological Biomedicine Shandong Laboratory/ ; }, mesh = {Humans ; *Dysbiosis/microbiology ; Female ; Male ; *Gastrointestinal Microbiome ; *Thyroid Cancer, Papillary/microbiology ; *Butyrates/metabolism ; Middle Aged ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Feces/microbiology ; *Thyroid Nodule/microbiology ; Adult ; *Thyroid Neoplasms/microbiology ; RNA, Ribosomal, 16S/genetics ; Aged ; DNA, Bacterial/genetics ; }, abstract = {BACKGROUND: The thyroid-gut axis refers to the intricate relationships among the gut, intestinal microbiota, and thyroid gland, and it is speculated to play an important role in the development of thyroid diseases. The aim of this study was to identify the differentiated bacteria in the intestinal microbiota associated with papillary thyroid carcinoma (PTC) and benign thyroid nodules (BTNs) to offer potential avenues for further exploration and therapeutic interventions.<br><br>METHODS: Faecal microbiotas of 197 subjects (73 from subjects with BTNs, 62 from subjects with PTC, and 62 from sex- and age-matched controls) were characterized by sequencing the V3-V4 region of 16&#xa0;S rDNA using the Illumina NovaSeq 6000 platform. Microbiomics and machine learning-assisted approaches were used to identify the PTC-/BTN-associated intestinal microbial indicators.<br><br>RESULTS: Compared with the abundance of coabundant groups (CAGs) in the PTC, BTN, and control groups, the abundance of two Genus-CAGs consisting of butyrate producers, such as Blautia, Lachnoclostridium, Lachnospiraceae_unclassified, Eisenbergiella, Flavonifractor and Hungatella, was lower in the PTC group than in the control group. In particular, both ANCOM-BC2 and Wilcoxon rank-sum test results consistently demonstrated significant enrichment of the butyrate-producing genera Oscillibacter, Coprobacter, and Colidextribacter in both BTN patients and healthy controls. The majority of discriminatory amplicon sequence variants (ASVs) that could discriminate PTCs from controls, as well as from BTNs, were from Prevotella, Streptococcus, Bacteroides, and butyrate-producing groups, such as the Oscillibacter, Lachnospiraceae, and Christensenellaceae (R7) groups. ASV indicators from Prevotella and Streptococcus were most abundant in the PTC group, and those from Bacteroides and the butyrate-producing/-promoting group were least abundant in the PTC group. Additionally, the ASVs that could discriminate the BTN group from the control group, as well as PTC group included other butyrate-producing groups, the Clostridium_sensu_stricto group, and the Eubacterium_siraeum group.<br><br>CONCLUSIONS: This study demonstrates that dysbiosis linked to thyroid nodules is marked by a substantial decline in intestinal butyrate-producing and butyrate-promoting taxa. Future work to confirm these results should include shotgun metagenomic sequencing paired with quantitative analyses of gene abundance and expression to fully ascertain the functional implications.}, }
@article {pmid41152726, year = {2025}, author = {Zou, Y and Zou, Q and Wang, Y and Han, C}, title = {Metagenomics reveals seasonal changes of intestinal microbes in Eospalax rothschildi.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {693}, pmid = {41152726}, issn = {1471-2180}, support = {62402344//Youth Found of the National Natural Science Foundation of China/ ; 62373080//National Natural Science Foundation of China/ ; }, mesh = {*Gastrointestinal Microbiome/genetics ; *Seasons ; *Metagenomics/methods ; Animals ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; China ; Feces/microbiology ; }, abstract = {BACKGROUND: Seasonal behavioral divergence in zokors, driven primarily by their reproductive cycle, results in distinct ecological strategies between breeding and non-breeding periods. To elucidate how intestinal microbes adapt to these behavioral shifts, we used metagenomics to characterize the seasonal variations in the intestinal microbes of Eospalax rothschildi, a subterranean zokor endemic to China.<br><br>RESULTS: Metagenomics revealed that summer samples showed an increased proportion of carbohydrate-degrading bacteria. Moreover, a significant difference in taxonomic composition was observed between the samples collected in the two seasons. Functional analysis based on the KEGG and CAZy databases revealed stronger carbohydrate degradation capacities in summer samples, notably through enhanced galactose metabolism capabilities. The enhanced galactose metabolism capabilities observed in summer were predominantly driven by increased abundance of &#x3b1;-galactosidase and &#x3b2;-galactosidase genes from enriched microbial populations, particularly Bacteroides, unclassified_f_Lachnospiraceae, Roseburia, and Faecalibacterium. Furthermore, iCAMP analysis revealed that deterministic and stochastic processes jointly governed intestinal microbial assembly in E. rothschildi during summer, as elevated nutritional demands potentially intensified host selection in the breeding season. Conversely, stochastic dominance in autumn may align with relaxed host selection.<br><br>CONCLUSIONS: Collectively, these results demonstrated that season played a crucial role in modulating the composition, function, and assembly process of the intestinal microbes of E. rothschildi.}, }
@article {pmid41152332, year = {2025}, author = {Ciuchcinski, K and Bluszcz, A and Dziewit, L}, title = {Taxonomy, function and plasmids of microbial soil communities of Polish salt graduation towers.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1702}, pmid = {41152332}, issn = {2052-4463}, support = {BOB-IDUB-622-105/2024//Uniwersytet Warszawski (University of Warsaw)/ ; }, mesh = {*Soil Microbiology ; RNA, Ribosomal, 16S/genetics ; Poland ; Salinity ; *Plasmids ; *Microbiota ; Metagenomics ; }, abstract = {Salt graduation towers create hypersaline environments that host specialized microbial communities, offering unique opportunities to study their adaptations to salinity. In this study, we present a comprehensive catalogue of data recovered from soil samples collected across three salt graduation towers in Poland (Ciechocinek, Konstancin-Jeziorna and Busko-Zdrój). Our investigation includes total metagenomic and 16S rRNA amplicon sequencing of nine collected soil samples, as well as metaplasmidome sequencing from most saline samples at each location. We established both solid and liquid enrichment cultures for these high-salinity samples, followed by hybrid long- and short-read sequencing. We also used multiple state-of-the-art tools to fully describe and characterize the recovered sequences. Overall, this comprehensive dataset integrates metagenomic, enrichment culture, 16S rRNA amplicon, and (meta)plasmidome sequencing data with corresponding physicochemical soil parameters, providing a valuable resource for comparative analyses, method development, and studies of microbial diversity and adaptation across saline environments.}, }
@article {pmid41152293, year = {2025}, author = {Pold, G and Saghaï, A and Jones, CM and Hallin, S}, title = {Denitrification is a community trait with partial pathways dominating across microbial genomes and biomes.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {9495}, pmid = {41152293}, issn = {2041-1723}, support = {2016-03551//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; 2023-03627//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; Senior Career Grant 2019//Sveriges Lantbruksuniversitet (Swedish University of Agricultural Sciences)/ ; }, mesh = {*Denitrification/genetics ; *Bacteria/genetics/metabolism/classification ; Nitrates/metabolism ; *Genome, Bacterial ; *Genome, Microbial ; Metagenome ; Nitrites/metabolism ; Metabolic Networks and Pathways/genetics ; }, abstract = {Diverse microorganisms can execute one or more steps in denitrification, during which nitrate or nitrite is successively reduced into nitric oxide, nitrous oxide, and ultimately dinitrogen. Many of the best-characterized denitrifiers are complete denitrifiers capable of executing all steps in the pathway, but their dominance in natural communities and what metabolic traits and environmental factors drive the global distribution of complete vs. partial denitrifiers are unclear. To address this, we conducted a comparative analysis of denitrification genes in 61,293 genomes, 3991 metagenomes, and 413 terrestrial and aquatic metatranscriptomes. We show that partial denitrifiers outnumber complete denitrifiers and the potential to initiate denitrification is more common than the potential to terminate it, particularly in nutrient rich environments. Our results further indicate that complete denitrifiers tend to be fast-growing organisms, favoring organic acid over sugar metabolism, and encoding the ability to oxidize and reduce a broader range of organic and inorganic compounds compared to partial denitrifiers. This suggests complete denitrifiers are metabolically flexible opportunists. Together, our results indicate an environmental footprint on the presence of denitrification genes which favors the genomic potential for partial over complete denitrification in most biomes and highlight that completion of the denitrification pathway is a community effort.}, }
@article {pmid41152000, year = {2025}, author = {Saguti, F and Wang, H and Churqui, MP and Tunovic, T and Holmer, L and Pettersson, &#xc4; and Schleich, C and Pott, BM and Bergstedt, O and Nyström, K and Norder, H}, title = {Variations of the Virome in Raw and Treated Water: A One-Year Follow-Up at Six Different Drinking Water Treatment Plants.}, journal = {Environmental microbiology reports}, volume = {17}, number = {6}, pages = {e70222}, doi = {10.1111/1758-2229.70222}, pmid = {41152000}, issn = {1758-2229}, support = {2020-02710//Svenska Forskningsr&#xe5;det Formas/ ; 20-102//Svenskt Vatten/ ; }, mesh = {*Drinking Water/virology ; *Virome ; *Water Purification/methods ; *Viruses/genetics/classification/isolation &amp; purification ; Sweden ; Metagenomics ; *Water Microbiology ; Genome, Viral ; Bacteriophages/genetics/isolation &amp; purification/classification ; High-Throughput Nucleotide Sequencing ; }, abstract = {Little is known about virome changes in raw and drinking water over time, and differences between raw water sources and treatment technologies. This study used metagenomics to assess viruses prevalent in raw and drinking water samples over 1 year from six Swedish drinking water treatment plants (DWTPs) with varying treatment barriers and with different raw water sources. Sequences homologous to known viruses in the raw water samples were detected by amplification and next-generation sequencing and classified into 152 different virus species belonging to 76 virus families/orders. The majority were small bacteriophages. Other viral genomes were homologous to viruses infecting plants, invertebrates, vertebrates, mammals and giant viruses infecting amoeba or algae. Several virus species were simultaneously found in both raw and drinking water, indicating passage through the purification barriers, although reduced by 1-3 log10 after treatment. Most viruses detected in water samples after ultrafiltration were small viruses, and other barriers appeared more effective at removing smaller viruses. To avoid detecting viruses possibly replicating within DWTPs, viruses were separated according to the possibility that the host could be found in the water sources or not. These results underscore the importance of monitoring both raw and drinking water for small viruses, especially when viral contamination of the source water is at risk, to ensure drinking water quality.}, }
@article {pmid41151807, year = {2025}, author = {Bontemps, Z and Abrouk, D and Moënne-Loccoz, Y and Hugoni, M}, title = {Functional Characterisation of Microbial Communities Related to Black Stain Formation in Lascaux Cave.}, journal = {Environmental microbiology reports}, volume = {17}, number = {6}, pages = {e70112}, doi = {10.1111/1758-2229.70112}, pmid = {41151807}, issn = {1758-2229}, support = {//DRAC Nouvelle Aquitaine (Bordeaux, France)/ ; }, mesh = {*Caves/microbiology ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; *Microbiota/genetics ; *Fungi/genetics/metabolism/classification/isolation &amp; purification ; Metagenomics ; Melanins/biosynthesis/genetics ; Carotenoids/metabolism ; Phylogeny ; }, abstract = {Anthropization of Palaeolithic caves may cause cave microbiota dysbiosis and promote the development of microbial stains on cave walls. In certain cases, chemical biocides have been used to mitigate rock alterations, but this may exacerbate microbiota unbalance. Here, we tested this model by metagenomics, using black stains that threaten art conservation in Lascaux Cave. Thus, we evidenced a wide range of microbial taxa differing between black stains and neighbouring unmarked surfaces. Genes for synthesis of melanin and carotenoid pigments were more prevalent in black stains and were identified in reconstructed genomes for fungi (as expected) and bacteria. The presence of genes for degradation of aromatic compounds supports the hypothesis that recycling of chemical biocides favoured melanin-producing microorganisms. These findings extend previous predictions by revealing a wider range of microorganisms, potential biotransformations favouring pigment synthesis, as well as microbial interactions influencing microbial dynamics during cave wall alterations.}, }
@article {pmid41151605, year = {2025}, author = {Burillo, A and Serrano-Lobo, J and Bouza, E and Muñoz, P}, title = {Is it possible to identify genotypes underlying resistant phenotypes in Gram-negative pathogens?.}, journal = {Current opinion in infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1097/QCO.0000000000001158}, pmid = {41151605}, issn = {1473-6527}, abstract = {PURPOSE OF REVIEW: This review explores the relationship between genotypes and resistant phenotypes in Gram-negative pathogens. We analyse to what extent conventional phenotypic methods predict genetic mechanisms of resistance, the reliability of genotypic approaches, and how integrated strategies may improve diagnostic accuracy and clinical utility.<br><br>RECENT FINDINGS: Traditional AST remains the clinical reference standard due to its correlation with therapeutic outcomes, yet it often fails to identify the molecular basis of resistance. Molecular methods such as PCR, microarrays, and targeted sequencing allow rapid detection of known genes but cannot reliably predict expression or functionality. Whole-genome sequencing provides the most comprehensive overview, capturing both known and novel resistance determinants as well as mobile genetic elements. Nevertheless, genotype-phenotype discordance persists, driven by regulatory mutations, inducible expression, or synergistic mechanisms. Emerging technologies - including real-time sequencing, metagenomics, and machine learning-based predictive models - are enhancing our ability to infer phenotypes from genomic data. Still, these approaches face challenges of standardization, validation, and integration into clinical workflows.<br><br>SUMMARY: Linking genotypes to resistant phenotypes in Gram-negative pathogens remains complex. While phenotypic AST ensures reliability for therapy, genotypic methods provide unprecedented insight into resistance mechanisms and epidemiology. Discrepancies between the two highlight the need for integrated diagnostic platforms that combine functional and genomic perspectives. Artificial intelligence-driven predictive models and curated resistance databases hold promise for improving accuracy, but widespread adoption requires robust datasets, clinical validation, and harmonized interpretative frameworks. Ultimately, integrating phenotypic and genotypic data represents the most effective strategy to provide mechanism-informed, clinically actionable diagnostics for antimicrobial resistance management.}, }
@article {pmid41151513, year = {2025}, author = {Qin, C and Xie, X and Wang, H and Ma, L and Lu, X}, title = {Metagenomic investigation of antibiotic resistance genes and assessment of their health risk in antimony-mining area.}, journal = {Journal of hazardous materials}, volume = {499}, number = {}, pages = {140278}, doi = {10.1016/j.jhazmat.2025.140278}, pmid = {41151513}, issn = {1873-3336}, abstract = {Here, we conducted a metagenomic investigation of antibiotic resistance genes (ARGs) from soil, surface water, and groundwater samples collected in Xikuangshan antimony (Sb)-mine area in China. Overall, 1737 subtypes of ARGs were detected which collectively conferred resistance to 27 classes of antibiotics. The health risk of the ARGs to humans were quantitatively evaluated by integrating human accessibility, mobility, pathogenicity, and clinical availability. A total of 6706 ARGs were identified within metagenome-assembled genomes (MAGs), with 44 of these ARGs posing a health risk, particularly those that confer multidrug resistance. Soil served as a potential reservoir of ARGs, harboring a greater variety of ARGs. In contrast, aquatic environments were hotspots for high-risk ARGs, with groundwater containing the most numerous risk-associated ARGs but surface waters posing the greatest health risks. Remediated soils showed significantly reduced ARG abundance and health risk, indicating that ecological restoration effectively mitigates ARG-related health risks. Pseudomonadota persisted as the dominant functional phylum in Sb mining area, exhibiting significant positive correlations with ARGs abundance. Acinetobacter, Achromobacter, and Stenotrophomonas, were identified as opportunistic pathogens carrying high-risk ARGs. Our analysis suggested that mining activities may amplify public health risks of ARGs, highlighting the importance for ecological remediation of mining areas.}, }
@article {pmid41151484, year = {2025}, author = {Wang, Y and Zhang, Q and Luo, Q and Li, H and Li, F and Huang, D and Wu, B and Huang, D and Zhao, X and Zhang, J and Wu, D and Hao, H and Huang, R and Lai, J}, title = {Melatonin ameliorates bronchopulmonary dysplasia by modulating the NF-κB pathway via the gut microbiota-short-chain fatty acid axis.}, journal = {International immunopharmacology}, volume = {167}, number = {}, pages = {115730}, doi = {10.1016/j.intimp.2025.115730}, pmid = {41151484}, issn = {1878-1705}, abstract = {OBJECTIVE: To elucidate the mechanism by which melatonin ameliorates bronchopulmonary dysplasia (BPD) via modulation of gut microbiota and its metabolite, short-chain fatty acids (SCFAs).<br><br>METHODS: A bleomycin-induced BPD mouse model was developed. Post-melatonin intervention, a comprehensive multi-omics approach, including metagenomics, 16S rRNA sequencing, untargeted metabolomics, and RNA transcriptomics, was employed alongside butyrate supplementation experiments to assess changes in alveolar architecture, oxidative stress, inflammatory cytokine levels, and the NF-&#x3ba;B signaling pathway. In vitro experiments utilizing human bronchial epithelial cells (BEAS-2B) and analyses of publicly available single-cell RNA sequencing data from infant lung tissues were conducted to further substantiate the underlying mechanisms.<br><br>RESULTS: The administration of melatonin led to a significant increase in the abundance of Ligilactobacillus murinus within the gut microbiota and enhanced the production of SCFAs. Notably, butyrate metabolites were found to be enriched in both serum and lung tissues, which was associated with the suppression of NF-&#x3ba;B pathway activation. Intervention with butyrate mirrored the therapeutic effects observed with melatonin, resulting in the alleviation of alveolar simplification, a reduction in oxidative damage and inflammatory cytokines, and the inhibition of both NF-&#x3ba;B pathway activation and pyroptosis in lung tissues. Additionally, in vitro experiments demonstrated that both melatonin and butyric acid directly inhibited NF-&#x3ba;B activation and pyroptosis in BEAS-2B cells injured by bleomycin. Analysis of single-cell data from human infant lungs revealed differential enrichment of genes related to NF-&#x3ba;B and pyroptosis in the bronchial and alveolar epithelial cells of patients with BPD, thereby underscoring the clinical significance of these pathways.<br><br>CONCLUSION: Melatonin ameliorates BPD by modulating the gut microbiota-SCFA metabolic axis, which in turn suppresses NF-&#x3ba;B pathway activation and pyroptosis in lung tissues via systemic circulation. This finding suggests a novel therapeutic strategy for the treatment of BPD.}, }
@article {pmid41151425, year = {2025}, author = {Lv, J and Zhao, Q and Jiang, J and Ding, J and Wei, L and Liang, J}, title = {Electron transfer performance and mechanism in twin microbial fuel cell powered electro-Fenton system with waste activated sludge as substrate.}, journal = {Bioelectrochemistry (Amsterdam, Netherlands)}, volume = {168}, number = {}, pages = {109154}, doi = {10.1016/j.bioelechem.2025.109154}, pmid = {41151425}, issn = {1878-562X}, abstract = {The twin microbial fuel cell powered electro-Fenton system (twin-MFCⓅEFs), combining active oxygen component and microbial metabolism, was constructed to improve the treatment process of waste activated sludge (WAS). Nevertheless, the performance and mechanism of electron transfer underlying this enhancement remain poorly understood. This study investigated the performance and mechanism of electron generation and utilization in twin-MFCⓅEFs with WAS as substrate. The higher electron generation and recovery efficiency (8.25 % of coulombic efficiency) was attributed to the higher content of amino acids (such as tryptophan), humic substances and their aromatic groups and unsaturated conjugated double bonds in the soluble organic matter, which facilitated biodegradation and electron transfer. The higher electron utilization performance (52.76 % of faraday efficiency) relied on the superior electron supply system that exhibited greater free radical oxidation. Metagenomic analysis indicated that an increased secretory capacity of glycosyltransferases (including glucosyltransferases and β-glucosidases) and a reduced activity of acetate kinase and methyl-coenzyme M reductase alpha subunit in cellular metabolic processes favored signaling and electricity production. The study focused on electron flow in twin-MFCⓅEFs and offered a promising strategy for improving the sludge treatment process.}, }
@article {pmid41151197, year = {2025}, author = {Ortiz-López, G and Sánchez-Reyes, A and Téllez-Galván, A and Bustamante, VH and Breton-Deval, L}, title = {Influence of anthropogenic inputs on microbial risks and resistance genes in a riverine environment.}, journal = {International journal of hygiene and environmental health}, volume = {271}, number = {}, pages = {114699}, doi = {10.1016/j.ijheh.2025.114699}, pmid = {41151197}, issn = {1618-131X}, abstract = {Rivers face significant anthropogenic pressures due to diverse water discharges, which alter microbial community structures and may facilitate the dissemination of potentially pathogenic microorganisms and antibiotic-resistance genes (ARGs). This study used metagenomic analysis to characterize microbial and viral communities, determine antibiotic resistance profiles, and evaluate potential public health risks associated with different discharges sources. Water samples were collected from agricultural, hospital, untreated domestic wastewater, treated wastewater, and environmental inputs. Results revealed that hospital wastewater (HW) had microbial genera associated with the wastewater treatment plant; however, we were able to isolate a multidrug-resistant Klebsiella aerogenes, Enterobacter spp. and Staphylococcus spp. Untreated domestic wastewater (UW) was dominated by species such as Arcobacter cryaerophilus, Acinetobacter johnsonii, Escherichia coli, and Acinetobacter lwoffii, while treated wastewater (TW) showed the presence of Arcobacter cryaerophilus, Aeromonas caviae, Prevotella copri, Arcobacter butzleri, Acinetobacter johnsonii, Escherichia coli, and Pseudomonas stutzeri. Regarding ARGs, HW contributed significantly to ARGs diversity, particularly genes conferring resistance to critical antibiotics such as meropenem and vancomycin. TW exhibits the highest ARG diversity, including genes for broad-spectrum resistance to aminoglycosides, penicillins, and cephalosporins, suggesting cumulative contamination from multiple sources. These findings emphasize the importance of advancing efforts to tackle this challenge in wastewater treatment practices and stricter regulations to mitigate the spread of antibiotic resistance and pathogenic microorganisms in aquatic environments.}, }
@article {pmid41150814, year = {2025}, author = {Jiang, L and Qing, Y and Huang, K and Huang, H and Li, C and Mei, Q and Wu, Q}, title = {Comparison of Gut Microbial Structure and Function Changes in Sichuan-Tibetan Black Pigs at Different Growth Stages Based on Metagenomic Analysis.}, journal = {Current issues in molecular biology}, volume = {47}, number = {10}, pages = {}, doi = {10.3390/cimb47100866}, pmid = {41150814}, issn = {1467-3045}, support = {2023NSFSC0206//the Natural Science Foundation Project of Science and Technology Department of Sichuan Province/ ; }, abstract = {The gut microbiota plays a crucial role in maintaining swine health and understanding its stage-specific variations provides a scientific basis for health assessment. This study investigated the structural changes in intestinal microbiota during the development of Sichuan-Tibetan black pigs (n = 15) by collecting fecal samples at three growth stages: the nursery period (1 month), growing period (3 months), and finishing period (10 months). Microbial profiling was performed using 16S rRNA sequencing. Results showed no significant difference in the Shannon index between the nursery and growing periods, while the finishing period exhibited distinct ACE and Chao 1 indices compared to other stages. PCoA and NMDS analyses revealed significant structural divergence in the finishing period microbiota, with greater intra-group variability observed in the nursery and growing periods. At the phylum level, Firmicutes abundance increased progressively with growth, becoming the absolute dominant phylum, whereas Bacteroidota showed a declining trend. These characteristics are particularly prominent during the finishing period. At the family level, Lactobacillaceae abundance increased continuously. Oscillospiraceae remained stable during the early stages but decreased significantly in the finishing period. Genus-level analysis shows that Lactobacillus, especially L. amylovorus and L. reuteri, become dominant bacterial species during the finishing period. A total of 84 differentially abundant core microbiota were identified, with the finishing period containing the highest number. Functional annotation revealed 19 significantly different metabolic pathways across the three stages. The most significant is the enhanced activity of microorganisms during the finishing period in pathogen-related metabolism and exogenous degradation, reflecting their adaptability to complex feed. These findings demonstrate stage-dependent variations in the gut microbiota of Sichuan-Tibetan black pigs, providing valuable references for nutritional regulation and feeding management practices.}, }
@article {pmid41150726, year = {2025}, author = {Ma, M and Li, Q and Wu, F and Zhu, B and Lu, H and Zhang, D and Łukasik, P and Hu, Y}, title = {Symbiotic solutions for colony nutrition: Conserved nitrogen recycling within the bacterial pouch of Tetraponera ants.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {44}, pages = {e2514882122}, doi = {10.1073/pnas.2514882122}, pmid = {41150726}, issn = {1091-6490}, support = {32370448//MOST | National Natural Science Foundation of China (NSFC)/ ; 2243200009//MOE | Fundamental Research Funds for the Central Universities (Fundamental Research Fund for the Central Universities)/ ; }, mesh = {*Ants/microbiology/physiology/metabolism ; Animals ; *Symbiosis/physiology ; *Nitrogen/metabolism ; Microbiota/physiology ; Larva/microbiology/growth &amp; development ; Amino Acids/metabolism ; *Bacteria/metabolism/genetics ; Urea/metabolism ; }, abstract = {While microbial symbioses are fundamental to the nutrition of many animal groups, current paradigms focus on symbiont functions at the host individual level. It remains unclear whether microbial symbioses can sustain colony-level fitness in social insects, whose ecological success depends on nutrient coordination across castes. Here, we investigate the specialized bacterial pouch, a symbiont-containing organ present exclusively in adult workers of Tetraponera nigra-group ants, revealing its crucial role in colony-wide nutrient provisioning. Using a combination of microscopy, amplicon and metagenomic sequencing, and [15]N-urea feeding experiments on four species in the group, we show that its adult-specific pouch-associated microbiota, primarily Tokpelaia, recycle nitrogen from urea and convert it into amino acids which are provisioned to adult workers and developing larvae. Disruption of this nitrogen-recycling symbiosis severely impairs larval growth and overall colony fitness. Our results show how caste-restricted microbial organs can centralize metabolic functions at the colony level, challenging individual-centric paradigms of host-microbe mutualism and providing insights into the pivotal role of microbial symbionts in superorganismal adaptation to nutritional constraints.}, }
@article {pmid41150505, year = {2025}, author = {Zong, C and Gao, S and Wei, Q and Yin, Y and Shi, Y}, title = {Impact of Chromium Exposure on Potato Farming Systems and Plant Responses.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.5c09289}, pmid = {41150505}, issn = {1520-5118}, abstract = {Chromium (Cr) is a major source of heavy metal pollution, posing a significant threat to agricultural production. This study investigated the impact of chromium on potato farmland and explored integrated control strategies using the potato cultivar Dongnong 310 as the research subject. Transcriptomic and rhizosphere microbial metagenomic sequencing methods were employed. The main findings were as follows: (1) chromium stress downregulated genes encoding photosystem II, thereby inhibiting photosynthesis in potatoes. (2) Chromium stress altered the diversity of rhizosphere soil microorganisms, reduced the abundance of nitrous oxide reductase, and increased emissions of the greenhouse gas N2O. (3) The rhizosphere microorganism Bacillus strain C5 and potato gene LOC102599109 exhibited chromium resistance. This study provides theoretical guidance for the integrated management of chromium pollution in potato farmland.}, }
@article {pmid41149776, year = {2025}, author = {Tana, C and Moffa, S and Tana, M and Ucciferri, C and Moffa, L}, title = {Gut Microbiota, Mild Cognitive Impairment and Dementia: A Systematic Review.}, journal = {Neurology international}, volume = {17}, number = {10}, pages = {}, doi = {10.3390/neurolint17100155}, pmid = {41149776}, issn = {2035-8385}, abstract = {BACKGROUND: Alterations of the gut microbiota have been increasingly implicated in the pathogenesis of dementia through mechanisms involving systemic inflammation, immune dysregulation, and gut-brain axis disruption. Clinical evidence, however, remains fragmented.<br><br>OBJECTIVES: This systematic review aimed to characterize gut microbiota profiles in individuals with mild cognitive impairment (MCI) or Alzheimer's dementia (AD), explore mechanistic associations with neurodegeneration, and evaluate the impact of microbiota-targeted interventions on cognitive outcomes.<br><br>METHODS: Following PRISMA 2020 guidelines and a registered protocol (PROSPERO CRD420251074832), PubMed/Medline was searched through May 2025. Eligible studies included randomized controlled trials (RCTs) and cohort and case-control studies assessing microbiota composition or interventions in participants with MCI or AD.<br><br>RESULTS: Twenty-one studies were included (1 RCT, 20 observational; sample size 22-302). Most used 16S rRNA sequencing; one used shotgun metagenomics. Across cohorts, MCI and AD patients consistently showed reduced short-chain fatty acid-producing bacteria (Faecalibacterium, Ruminococcaceae, Lachnospiraceae) and increased pro-inflammatory taxa (Escherichia/Shigella, Enterobacteriaceae, Bacteroides). Several studies reported reduced microbial diversity. Specific taxa, including Akkermansia muciniphila and Faecalibacterium, were associated with amyloid burden, hippocampal atrophy, and cognitive decline. Environmental and dietary factors influenced microbial composition and cognition. The RCT reported that probiotic supplementation improved inflammatory markers and BDNF levels, although changes in microbiota composition were inconsistent.<br><br>CONCLUSIONS: Gut dysbiosis is strongly associated with cognitive impairment and markers of neurodegeneration. Modulation of the microbiota through diet and probiotics emerges as a promising avenue for dementia prevention and management, though robust longitudinal and interventional studies are needed to confirm causality and therapeutic efficacy.}, }
@article {pmid41149107, year = {2025}, author = {Matsumoto, R and Takahashi, M and Hosomichi, K and Okuwaki, S and Koizumi, S and Hikita, Y and Hatanaka, R and Yamaguchi, T}, title = {Comparison of Long-Term Oral Bacterial Flora Before and After Orthognathic Surgery in Surgical Orthodontic Treatment.}, journal = {Dentistry journal}, volume = {13}, number = {10}, pages = {}, doi = {10.3390/dj13100458}, pmid = {41149107}, issn = {2304-6767}, support = {24K20091//Yu Hikita/ ; 24K13185//Tetsutaro Yamaguchi/ ; }, abstract = {Background/Objectives: Multi-bracket appliances are essential in surgical orthodontic treatment, and perioperative oral management during orthognathic surgery is critical. Thorough plaque control, appropriate use of antibiotics, and shortening of operative time have been reported to be effective in preventing postoperative infections and ensuring surgical success. As highly invasive orthognathic surgery involving osteotomy may influence the postoperative oral microbiota, this study aimed to investigate the characteristics of and clarify the changes occurring in the salivary oral microbiota after orthognathic surgery. Methods: The study included 14 patients (Group S; mean age 29.3 ± 9.8 years) who underwent surgical orthodontic treatment and 15 control patients (Group C; mean age 27.1 ± 8.7 years) who received orthodontic treatment alone. Salivary samples were analyzed via 16S rRNA gene sequencing, and the relative abundances of bacteria were evaluated using the Linear Discriminant Analysis Effect Size. Results: The prevalence of Neisseria, which is associated with early biofilm formation, decreased over time in both groups. In contrast, Streptococcus exhibited an increase in prevalence. In Group S, members of Pseudomonas, the family Saccharimonadaceae, and the order Rhizobiales showed increases at 5-8 months post-surgery. Conclusions: Surgical orthodontic treatment may influence the oral microbiota and promote colonization by opportunistic pathogens. Instructions regarding oral hygiene and appropriately timed professional cleaning interventions are critical in preventing such colonization. Longitudinal monitoring of the microbiota using metagenomic analysis may be useful for future perioperative management and guidance of oral hygiene.}, }
@article {pmid41149072, year = {2025}, author = {Amorim Filho, AG and Martins, RCR and Franco, LAM and Marinelli, JVC and Peres, SV and Francisco, RPV and Carvalho, MHB}, title = {Vaginal Microbiota in Short Cervix Pregnancy: Secondary Analysis of Pessary vs. Progesterone Trial.}, journal = {Diseases (Basel, Switzerland)}, volume = {13}, number = {10}, pages = {}, doi = {10.3390/diseases13100338}, pmid = {41149072}, issn = {2079-9721}, abstract = {BACKGROUND/OBJECTIVES: Preterm birth (PTB) is a leading cause of neonatal mortality, particularly in women with a short cervix. Vaginal dysbiosis has been associated with increased PTB risk. Progesterone (PR) and Arabin pessary (PE) are commonly used for PTB prevention, but their impact on vaginal microbiome composition is unclear. This study aimed to compare the effects of these interventions on the vaginal microbiome in women at risk of PTB.<br><br>METHODS: In a secondary analysis of a randomized trial at Hospital das Cl&#xed;nicas, Universidade de S&#xe3;o Paulo, 203 women with singleton pregnancies and cervical length &#x2264; 25 mm at the second trimester were assigned to daily vaginal PR (200 mg) or PE. Vaginal swabs from 44 participants (n = 22 per group) were collected at baseline and 4 weeks post-treatment and analyzed via 16S rRNA gene sequencing.<br><br>RESULTS: From 88 samples analyzed, 80 showed a low-diversity, Lactobacillus-dominated microbiota, 42 classified into Lactobacillus iners-dominated community state type (CST-III), and 38 presented other Lactobacillus species dominance (termed CST-I/II/V). The remaining eight samples presented non-Lactobacillus dominance (CST-IV). Comparing the two groups, no significant changes in CST were observed between sampling timepoints (PE group, p = 0.368; PR group, p = 0.223). Similarly, Shannon alpha diversity did not change (PE group, p = 0.62; PR group, p = 0.30), and Bray-Curtis dissimilarity also did not change after treatment (p = 0.96, before; p = 0.87, after treatment).<br><br>CONCLUSIONS: Arabin pessary and vaginal progesterone maintain vaginal microbiome stability in women at high PTB risk, supporting the microbiological safety of both interventions.}, }
@article {pmid41148745, year = {2025}, author = {Tewolde, R and Thombre, R and Farley, C and Nadarajah, S and Khan, I and Sewell, M and Spiller, OB and Afshar, B}, title = {Comparison of Phenotypic and Whole-Genome Sequencing-Derived Antimicrobial Resistance Profiles of Legionella pneumophila Isolated in England and Wales from 2020 to 2023.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {14}, number = {10}, pages = {}, doi = {10.3390/antibiotics14101053}, pmid = {41148745}, issn = {2079-6382}, abstract = {Background: Antimicrobial resistance (AMR) in Legionella pneumophila is emerging as a concern, particularly with resistance to macrolides and fluoroquinolones. Although clinically significant resistance in Legionella pneumophila remains uncommon, systematic genomic surveillance using whole-genome sequencing (WGS) is needed to anticipate treatment failure as metagenomic diagnostics move toward routine use. Objectives: We assessed the UK Health Security Agency AMR pipeline for predicting resistance in L. pneumophila by analysing 522 L. pneumophila isolates from England and Wales (2020-2023) together with nine database sequences that carry confirmed 23S rRNA mutations conferring high-level azithromycin resistance. The objective of the present study was to examine the presence of antimicrobial resistance genes (ARGs) in L. pneumophila isolates and to determine whether they exhibited phenotypic resistance through minimum inhibitory concentration (MIC) testing. Methods: Serogroups (sgs) were determined using an in-house qPCR assay, and L. pneumophila non-sg1 isolates were serogrouped using the Dresden monoclonal antibody (mAb) typing method. Sequence types were determined using the standard sequence-based typing method by Sanger sequencing. WGS reads were screened against standard AMR databases to identify resistance genes and resistance-mediating mutations. Agar dilution measured MICs for azithromycin, erythromycin, ampicillin, levofloxacin, tetracycline and spectinomycin in isolates possessing the blaOXA-29, lpeAB or aph(9)-Ia gene. Results: AMR screening detected lpeAB, two allelic β-lactamase variants (blaOXA-29 and blaLoxA) and aph(9)-Ia in 165 of the 522 L. pneumophila isolates, while all high-azithromycin MIC reference sequences contained the expected 23S mutation. Only lpeAB was associated with a significant twofold elevation in macrolide MICs. Neither β-lactamase variant increased ampicillin MICs, and aph(9)-Ia carriage did not correlate with higher spectinomycin MICs. Conclusions: Advanced genomic analytics can now deliver timely therapeutic guidance, yet database-flagged genes may not translate into phenotypic resistance. Continuous pairing of curated mutation catalogues with confirmatory testing remains essential for distinguishing clinically actionable determinants such as 23S mutations and lpeAB from silent markers like blaOXA-29 and aph (9)-Ia.}, }
@article {pmid41148714, year = {2025}, author = {Lertcanawanichakul, M and Bhoopong, P and Horpet, P}, title = {Mangrove Ecosystems as Reservoirs of Antibiotic Resistance Genes: A Narrative Review.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {14}, number = {10}, pages = {}, doi = {10.3390/antibiotics14101022}, pmid = {41148714}, issn = {2079-6382}, support = {The official grant number has not yet been assigned.//Plant Genetic Conservation Project Unde&#xe1e; the Royal Initiative of Her Royal Highness Princess Maha Chakri Sirindhorn - RSPG/ ; }, abstract = {Background: Mangrove ecosystems are critical coastal environments providing ecological services and acting as buffers between terrestrial and marine systems. Rising antibiotic use in aquaculture and coastal agriculture has led to the dissemination of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in these habitats. Aim: This narrative review aims to synthesize current knowledge on the prevalence, diversity, and environmental drivers of ARGs in mangrove ecosystems, highlighting their role as reservoirs and the potential for horizontal gene transfer. Methods: Studies published up to September 2024 were identified through PubMed, Scopus, Web of Science, and Google Scholar. Inclusion criteria focused on ARGs and ARB in mangrove sediments, water, and associated biota. Data on ARG prevalence, microbial community composition, detection methods, and environmental factors were extracted and narratively synthesized. Results: Seventeen studies from Asia, South America, and Africa were included. ARGs conferring resistance to tetracyclines, sulfonamides, β-lactams, and multidrug resistance were found to be widespread, particularly near aquaculture and urban-influenced areas. Metagenomic analyses revealed diverse resistomes with frequent mobile genetic elements, indicating high potential for horizontal gene transfer. Environmental factors, including sediment type, organic matter, and salinity, influenced ARG abundance and distribution. Conclusions: Mangrove ecosystems act as both reservoirs and natural buffers for ARGs. Sustainable aquaculture practices, continuous environmental monitoring, and integrated One Health approaches are essential to mitigate ARG dissemination in these sensitive coastal habitats.}, }
@article {pmid41148708, year = {2025}, author = {Lynch, S and Thomson, P and Santibañez, R and Avendaño-Herrera, R}, title = {Influence of Florfenicol Treatments on Marine-Sediment Microbiomes: A Metagenomic Study of Bacterial Communities in Proximity to Salmon Aquaculture in Southern Chile.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {14}, number = {10}, pages = {}, doi = {10.3390/antibiotics14101016}, pmid = {41148708}, issn = {2079-6382}, support = {FONDAP No. 1523A0007//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; }, abstract = {Background/Objectives: Metagenomic analyses are an important tool for understanding ecological effects, particularly in sites exposed to antimicrobial treatments. Marine sediments host diverse microbial communities and may serve as reservoirs for microbial resistance. Although it is known that antimicrobials can alter microbial composition, specific impacts on sediments surrounding salmon farms remain poorly understood. This study analyzed bacterial community structure in marine sediments subjected to florfenicol treatment from salmon farms in the Los Lagos Region of southern Chile. Methods: Sediment samples were collected and examined through DNA extraction and PCR amplification of the 16S rRNA gene (V3-V4 region). Sequences were analyzed using a bioinformatics pipeline, and amplicon sequence variants (ASVs) were taxonomically classified with a Naïve Bayesian classifier. The resulting ASV abundance were then used to predict metabolic functions and pathways via PICRUSt2, referencing the MetaCyc database. Results: Significant differences in bacterial phyla were observed between the control farm and two farms treated with florfenicol (17 mg kg[-1] body weight per day) for 33 and 20 days, respectively. Farm 1 showed notable differences in phyla such as Bacteroidota, Bdellovibrionota, Crenarchaeota, Deferrisomatota, Desulfobacterota, Fibrobacterota, Firmicutes, and Fusobacteriota, while Farm 2 exhibited differences in the phyla Bdellovibrionota, Calditrichota, Crenarchaeota, Deferrisomatota, Desulfobacterota, Fusobacteriota, Nanoarchaeota, and Nitrospirota. Shannon Index analysis revealed a reduction in alpha diversity in the treated farms. Comparative analysis between the control and the treated farms showed pronounced shifts in the relative abundance of several bacterial phyla, including statistically significant differences in Chloroflexi and Firmicutes. Predicted functional pathways revealed a notable enrichment of L-methionine biosynthesis III in Farm 2, suggesting a shift in sulfur metabolism potentially driven by antimicrobial treatment. Additionally, increased activity in fatty acid oxidation pathways indicates a higher microbial potential for lipid degradation at this site. Conclusions: These findings highlight the considerable influence of florfenicol on sediment microbial communities and reinforce the need for sustainable management strategies to minimize ecological disruption and the spread of antimicrobial resistance.}, }
@article {pmid41148701, year = {2025}, author = {Ramsay, DE and McDonald, W and Gow, SP and McLeod, L and Otto, SJG and Osgood, ND and Waldner, CL}, title = {The Potential for Sample Testing at the Pen Level to Inform Prudent Antimicrobial Selection for Bovine Respiratory Disease Treatment: Investigations Using a Feedlot Simulation Tool.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {14}, number = {10}, pages = {}, doi = {10.3390/antibiotics14101009}, pmid = {41148701}, issn = {2079-6382}, support = {N/A//Genome Canada/ ; N/A//Saskatchewan Agriculture Development Fund/ ; N/A//Beef Cattle Research Council (BCRC)/ ; N/A//National Sciences and Engineering Research Council (NSERC)/ ; N/A//University of Saskatchewan/ ; N/A//University of Alberta/ ; }, abstract = {Background: Antimicrobial drugs are used to treat bacterial diseases in livestock production systems, including bovine respiratory disease (BRD) in feedlot cattle. It is recommended that therapeutic antimicrobial use (AMU) in food animals be informed by diagnostic tests to limit the emergence of antimicrobial resistance (AMR) and preserve the effectiveness of available drugs. Recent evidence demonstrates preliminary support for the pen as a prospective target for AMR testing-based interventions in higher-risk cattle. Methods: A previously reported agent-based model (ABM) was modified and then used in this study to investigate the potential for different pen-level sampling and laboratory testing-informed BRD treatment strategies to favorably impact selected antimicrobial stewardship and management outcomes in the western Canadian context. The incorporation of sample testing to guide treatment choice was hypothesized to reduce BRD relapses, subsequent AMU treatments and resultant AMR in sentinel pathogen Mannheimia haemolytica. The ABM was extended to include a discrete event simulation (DES) workflow that models the testing process, including the time at sample collection (0 or 13 days on feed) and the type of AMR diagnostic test (antimicrobial susceptibility testing or long-read metagenomic sequencing). Candidate testing scenarios were simulated for both a test-only control and testing-informed treatment (TI) setting (n = 52 total experiments). Key model outputs were generated for both the pen and feedlot levels and extracted to data repositories. Results: There was no effect of the TI strategy on the stewardship or economic outcomes of interest under baseline ecological and treatment conditions. Changes in the type and number of uses by antimicrobial class were observed when baseline AMR in M. haemolytica was assumed to be higher at feedlot arrival, but there was no corresponding impact on subsequent resistance or morbidity measures. The impacts of sample timing and diagnostic test accuracy on AMR test positivity and other outputs were subsequently explored with a theoretical "extreme" BRD treatment protocol that maximized selection pressure for AMR. Conclusions: The successful implementation of a pen-level sampling and diagnostic strategy would be critically dependent on many interrelated factors, including the BRD treatment protocol, the prevalences of resistance to the treatment classes, the accuracy of available AMR diagnostic tests, and the selected "treatment change" thresholds. This study demonstrates how the hybrid ABM-DES model can be used for future experimentation with interventions proposed to limit AMR risk in the context of BRD management.}, }
@article {pmid41148456, year = {2025}, author = {Loera, MY and de Figueras, CG and Sánchez-Costa, M and Martínez-Rodríguez, P and Mirete, S and Lamprecht-Grandío, M and Díaz, S and González-Pastor, JE and Díaz-Rullo, J}, title = {Co-expression of environmental extremophilic genes strongly enhances Escherichia coli cross-protection to abiotic stress.}, journal = {Extremophiles : life under extreme conditions}, volume = {29}, number = {3}, pages = {39}, pmid = {41148456}, issn = {1433-4909}, support = {PID2021-126114NB-C43//Ministerio de Ciencia e Innovaci&#xf3;n/ ; }, mesh = {*Escherichia coli/genetics/physiology/metabolism/radiation effects ; *Extremophiles/genetics ; *Stress, Physiological ; Oxidative Stress ; Escherichia coli Proteins/genetics/metabolism ; }, abstract = {Nature is home to a wide range of species that thrive in extreme conditions. Despite the identification and study of many extremophilic organisms, significant questions remain regarding the limits of life and the potential for enhancing, combining, or transferring extreme characteristics to other organisms. In previous works of our group, several genes retrieved from environmental extremophiles using functional metagenomics were shown to increase the tolerance of the model bacterium Escherichia coli towards different stress conditions. Here, we proposed to evaluate whether the rational combination of those resistance genes isolated from environmental extremophiles and involved in different molecular mechanisms enhanced the cross-protection of E. coli to extreme conditions. Data revealed that the simultaneous introduction in E. coli of environmental extremophilic resistance genes involved in protein degradation, biofilm formation, oxidative stress, and DNA protection resulted in strongly enhanced, non-additive effects, significantly increasing survival rate under perchlorate exposure, UV radiation, and low pH compared to the individual introduction of these genes. Our findings supports that the introduction of multiple resistance genes isolated from environmental extremophiles that belong to diverse biological processes of stress adaptation may be crucial for engineering of multi-resistant species of interest in biomanufacturing and astrobiology.}, }
@article {pmid41148396, year = {2025}, author = {Xie, X and Ren, W and Zhou, W and Wang, Y and Zhu, H and Wu, Y and Lu, Q}, title = {Genetic prediction of the effect of gut microbiota on retinal vein occlusion via blood metabolites.}, journal = {International ophthalmology}, volume = {45}, number = {1}, pages = {447}, pmid = {41148396}, issn = {1573-2630}, support = {2024KY376//Medical Science and Technology Program of Zhejiang Province/ ; 2022L003//Ningbo Clinical Research Center for Ophthalmology/ ; 2016-370 S05//Ningbo Clinical Research Center for Ophthalmology and the Project of NINGBO Leading Medical &amp; Health Disipline/ ; 2021Z054//Technology Innovation 2025 Major Project of Ningbo/ ; 2024Z233//Ningbo"Innovation Yongjiang 2035" Key Technology Breakthrough program/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Retinal Vein Occlusion/genetics/blood/microbiology ; Mendelian Randomization Analysis ; Genome-Wide Association Study ; Male ; Female ; *Polymorphism, Single Nucleotide ; Biomarkers/blood ; }, abstract = {PURPOSE: Given the unclear causal relationship between gut microbiota (GM) and retinal vein occlusion (RVO) and the potential mediating role of blood metabolites, this study aims to investigate this causal link and the mediating effects of blood metabolites.<br><br>METHODS: Our Mendelian randomization (MR) study used data from genome-wide association studies pooled data, including 473 microbiota taxa (n&#x2009;=&#x2009;5959), 233 blood metabolites (n&#x2009;=&#x2009;136,016), and RVO cases and controls from the FinnGen consortium (cases, n&#x2009;=&#x2009;775; controls, n&#x2009;=&#x2009;308,633). We used bidirectional two-sample MR, multivariate MR, and mediation analysis to assess the causal association between GM and RVO.<br><br>RESULTS: By analyzing gut microbial metagenomic data with adjustment for confounding factors, we identified 1 taxon with significant causal association and 14 taxa with potential causal links to RVO, where Halomonadaceae remained after Bonferroni correction. Parallel analysis of blood metabolites revealed 18 causal associations (2 significant, 16 potential), with apolipoprotein A-I and creatinine retaining significance post-correction. Three GM taxa affected RVO through three blood metabolites. Caloranaerobacteraceae, Rhodococcus, and Citrobacter A affected RVO through Total cholesterol in HDL2, Apolipoprotein A-I, and phenylalanine, respectively. Apolipoprotein A-1 possessed the greatest mediated effect (5.6%) between Rhodococcus and RVO.<br><br>CONCLUSION: These findings provide new insights into the pathogenesis of RVO and may contribute to the development of new strategies for preventing the onset of RVO.}, }
@article {pmid41148302, year = {2025}, author = {Hirayama, M and Maeda, T and Kashihara, K and Tsuboi, Y and Ito, M and Nishiwaki, H and Ohno, K and Ueyama, J}, title = {Linking diet, gut microbiota, and metabolites to Parkinson's disease risk: a shotgun metagenomic comparison of Japanese and Taiwanese cohorts.}, journal = {Journal of neural transmission (Vienna, Austria : 1996)}, volume = {}, number = {}, pages = {}, pmid = {41148302}, issn = {1435-1463}, support = {24K10657//Japan Society for the Promotion of Science/ ; 23H02794//Japan Society for the Promotion of Science/ ; 2022G025//Smoking Research Foundation/ ; }, abstract = {Emerging evidence suggests that gut microbiota and its metabolites play pivotal roles in the pathogenesis of Parkinson's disease (PD). However, cross-national differences in diet and microbial composition may account for the striking variability in PD prevalence worldwide. To address this, we performed a comparative shotgun metagenomic analysis between Japanese and Taiwanese individuals, two genetically similar East Asian populations with distinct dietary habits and differing PD incidence rates. Our analysis revealed marked differences in dietary intake: Taiwanese individuals consumed higher amounts of animal fats and tropical fruits, whereas the Japanese diet was characterized by greater intake of seafood, root vegetables, and traditional fermented foods such as natto. These dietary patterns were reflected in gut microbiota profiles. Japanese individuals exhibited a higher abundance of Blautia, Faecalibacterium, and Bifidobacterium, while Taiwanese samples were enriched in Bacteroides and Alistipes. Functionally, genes involved in short-chain fatty acid (SCFA), vitamin, and polyamine biosynthesis were significantly reduced in PD patients and in the Taiwanese cohort. Metabolomic analyses corroborated these findings, showing decreased levels of SCFAs, polyamines, and key vitamins such as nicotinate and pantothenate in PD patients. Notably, Blautia abundance correlated positively with a broad range of beneficial metabolites, highlighting its potential role as a central modulator of host-microbe metabolic interactions. Our findings suggest that traditional Japanese dietary practices may shape a gut microbial environment that confers resistance to PD, underscoring the need for future interventional studies targeting diet-microbiota interactions in PD prevention and treatment.}, }
@article {pmid41148242, year = {2025}, author = {Kumar, R and Nagraik, R and Lakhanpal, S and Abomughaid, MM and Jha, NK and Gupta, R}, title = {Artificial intelligence in gut microbiome research: Toward predictive diagnostics for neurodegenerative disorders.}, journal = {Acta microbiologica et immunologica Hungarica}, volume = {}, number = {}, pages = {}, doi = {10.1556/030.2025.02725}, pmid = {41148242}, issn = {1588-2640}, abstract = {The human gut microbiota plays a pivotal role in maintaining host immunity, regulating metabolism, and sustaining neurophysiological homeostasis. Increasing evidence implicates gut dysbiosis in the onset and progression of neurodegenerative disorders (NDDs), including Alzheimer's and Parkinson's disease, primarily through the gut-brain axis. Recent advances in high-throughput sequencing and multi-omics technologies, such as metagenomics, metabolomics, and metaproteomics have generated vast datasets, yet their clinical translation remains hindered by data heterogeneity, analytical complexity, and the absence of standardized workflows. Disjointed findings across studies underscore the urgent need for reproducible pipelines and integrative computational strategies. This review presents a comprehensive framework that leverages artificial intelligence (AI) and machine learning (ML) for systematic microbiome investigation in NDDs. We highlight how multi-omics integration with AI improves the resolution of host-microbiome interactions, while standardized preprocessing workflows ensure reproducibility and comparability across datasets. The role of explainable AI is emphasized in enhancing interpretability, improving biomarker discovery, and fostering trust in predictive models. We further examine the emerging field of pharmacomicrobiomics, where ML-driven approaches support the development of precision therapies tailored to microbiome-drug interactions in neurodegeneration. Sophisticated models, including random forests (RF), neural networks, and transfer learning, are critically assessed for predictive diagnostics, therapeutic target identification, and cross-cohort generalizability. Finally, the review proposes a roadmap to address current barriers, particularly challenges of heterogeneity and reproducibility, and advocates for validated pipelines and interdisciplinary collaboration. Collectively, AI-driven multi-omics strategies hold transformative potential for advancing microbiome-based precision medicine in NDDs.}, }
@article {pmid41147939, year = {2025}, author = {Zhang, T and Xing, M and Zhang, H and Song, X and Song, Z and Yuan, C and Zhang, J and Ai, L and Zhang, Z and Xie, F}, title = {Docynia delavayi (Franch.) Schneid polyphenols alleviate dextran sulfate sodium-induced colitis by regulating the gut microbiota.}, journal = {Food &amp; function}, volume = {}, number = {}, pages = {}, doi = {10.1039/d5fo03604f}, pmid = {41147939}, issn = {2042-650X}, abstract = {Docynia delavayi (Franch.) Schneid is rich in polyphenols; however, its functions remain unclear. In this study, we identified and characterized the key constituents of D. delavayi fruit polyphenols (DDP), validated their anti-inflammatory effects, and provided insights into their underlying mechanisms of action. UPLC-MS/MS was used to quantify the major phenolic compounds in DDP, including glycitin, procyanidin B2, vitexin, myricitrin, astilbin, chlorogenic acid, phlorizin, (-)-epicatechin, naringenin-7-O-glucoside, taxifolin-7-O-rhamnoside, rhoifolin, methylnissolin-3-O-glucoside, and scutellarein. In the dextran sulfate sodium-induced colitis mouse model, DDP significantly improved colon length and the disease activity index. It also reduced the expression of inflammatory cytokines, including interleukin (IL)-1β, IL-6, and tumor necrosis factor-α. Metagenomic analysis revealed that DDP increased gut microbiota diversity, particularly enriching species capable of producing short-chain fatty acids (SCFAs), such as Lawsonibacter and Ruminiclostridium. Metabolomic data further demonstrated the upregulation of SCFA-associated pathways, such as glycolysis and pyruvate metabolism, with elevated colonic acetate, propionate, and butyrate levels corroborating these findings. Multi-omics analysis linked SCFAs to reduced inflammation. Collectively, these findings suggest that SCFAs play a pivotal role in the anti-inflammatory effects of DDP by modulating the gut microbiota to enhance SCFA biosynthesis. These findings demonstrate that SCFAs serve as critical mediators of the anti-inflammatory properties of DDP, highlighting their considerable potential as natural therapeutic agents for intestinal inflammation.}, }
@article {pmid41147782, year = {2025}, author = {Zhang, L and Yang, G and Zhang, C and Ji, B and Wu, D}, title = {Symbiotic nitrogen fixation and recycling in xylophagous insects: insights from gut microbiota of Apriona swainsoni larvae.}, journal = {Pest management science}, volume = {}, number = {}, pages = {}, doi = {10.1002/ps.70323}, pmid = {41147782}, issn = {1526-4998}, support = {81503115//National Natural Science Foundation of China/ ; JNFX2025192//Domestic Visiting Program for Young Key Teachers of Anhui Province/ ; BK2012816//Natural Science Foundation of Jiangsu Province/ ; 201409/WT_/Wellcome Trust/United Kingdom ; CX (16)1005//Jiangsu Agricultural Science and Technology Independent Innovation Project/ ; 2023AH050727//Natural Science Foundation (Key project) of the University in Anhui Province/ ; 2024AH050921//Natural Science Foundation (Key project) of the University in Anhui Province/ ; HZR2436//Hefei Municipal Natural Science Foundation/ ; 2024A755//Anhui Postdoctoral Scientific Research Program Foundation/ ; }, abstract = {BACKGROUND: Xylophagous insects, as nitrogen-limited organisms, face severe nutritional constraints due to the inherently low nitrogen content of lignocellulosic substrates-insufficient for growth. To alleviate this limitation, they rely on gut microbiota-mediated symbiotic nitrogen fixation and nitrogenous waste recycling. Apriona swainsoni, a model wood-boring cerambycid, exemplifies this adaptation: under extreme nitrogen scarcity in its xylem diet. While gut symbionts are hypothesized to overcome nitrogen limitation, the underlying mechanisms remain unclear.<br><br>RESULTS: First, metagenomic sequencing and functional gene analysis revealed enrichment of nitrogenase and urease genes in the posterior hindgut (PHG). Metaproteomics detected the nitrogenase gene nifU but no urease proteins, identifying nitrogen fixation as the primary nitrogen limitation mitigation strategy in A. swainsoni larvae. Subsequently, in vivo/in vitro [15]N isotope tracing showed peak [15]N in the PHG (105.02% higher than the natural environment) and&#x2009;~&#x2009;25-fold greater [15]N incorporation in cultured Klebsiella oxytoca versus controls. Targeted amino acid profiling further demonstrated [15]N enrichment in both essential and non-essential amino acids, with a spatial gradient (intestinal tissues > extra-intestinal tissues > frass)-indicating efficient microbial conversion of nitrogen into host-utilizable amino acids. Importantly, we identified that intestinal microbiota primarily mediate ammonia-to-amino acid conversion via the glutamine synthetase-glutamate synthase (GS/GOGAT) pathway in the PHG. This is the first reported GS/GOGAT-mediated nitrogen fixation pathway in cerambycids.<br><br>CONCLUSIONS: Our comprehensive analysis of gut microbial nitrogen metabolism might elucidate a set of mechanisms by which some xylophagous insects may overcome nutritional constraints in nitrogen-deficient niches, via evolutionarily optimized host-microbe metabolic interactions. &#xa9; 2025 Society of Chemical Industry.}, }
@article {pmid41147731, year = {2025}, author = {Jones, JA and Moczek, AP and Newton, ILG}, title = {The dung beetle microbiome complements host metabolism and nutrition.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0117225}, doi = {10.1128/msystems.01172-25}, pmid = {41147731}, issn = {2379-5077}, abstract = {Many multicellular organisms rely on communities of microbial organisms to properly benefit from their diets, for instance, by assisting in the breakdown of complex polysaccharides, the synthesis of essential resources, detoxification, or even preventing putrefaction. Dung beetles commonly rely on herbivore dung as their main source of nutrition, a diet rich in recalcitrant, hard-to-digest plant polysaccharides yet poor in essential amino acids, which animals typically cannot synthesize on their own. The work presented here investigates the potential role of the host-associated microbial community in allowing these insects to thrive on their nutrient-poor diet. Specifically, we investigated whether the microbiota of the bull-headed dung beetle, Onthophagus taurus, may be capable of synthesizing amino acids and breaking down complex plant polysaccharides. To do so, we functionally annotated genes within metagenomically assembled genomes (MAGs) obtained via shotgun-metagenomic sequencing. The annotation of these MAGs revealed that bacteria found in association with O. taurus possess the metabolic potential necessary to bridge the gap between host metabolic needs and the limitations imposed by their diet. Specifically, O. taurus microbiota contain amino acid biosynthesis pathways and genes encoding cellulases and xylanases, both of which are absent in the beetle genome. Further, multiple functionally relevant bacterial taxa identified here have also been observed in other studies across diverse dung beetle species, possibly suggesting a conserved pool of dung beetle symbionts and metabolic functions.IMPORTANCEHost-symbiont interactions allow animals to take advantage of incomplete and/or challenging diets and niches. The work presented here aims to identify the physiological and metabolic means by which host-associated microbial species shape the ecology of one of the most speciose genera in the animal kingdom: dung beetles in the genus Onthophagus. Both larva and adult stages of most Onthophagus rely on herbivore dung, a diet rich in recalcitrant, hard-to-digest plant polysaccharides yet poor in essential amino acids, which animals typically cannot synthesize on their own. To utilize such a challenging diet, Onthophagus vertically transmits a maternally derived microbial community which supports normative development in immature individuals and maintenance and reproduction in adults. Taken together, Onthophagus' extraordinary diversity, complex ecology, and varied relationship with their microbial associates make them an ideal system to investigate mechanisms and diversification of host-diet-microbiome interactions.}, }
@article {pmid41147494, year = {2025}, author = {Naureckas Li, C and Jhaveri, R and Huston, S}, title = {Results of a local modified Delphi consensus on use of plasma metagenomic next-generation sequencing.}, journal = {Infection control and hospital epidemiology}, volume = {}, number = {}, pages = {1-3}, doi = {10.1017/ice.2025.10334}, pmid = {41147494}, issn = {1559-6834}, abstract = {Molecular tests without well-defined test performance characteristics are increasingly available for diagnosis of infectious diseases. These tests present a diagnostic stewardship challenge for institutions. We share the results of a local modified Delphi consensus undertaken to define appropriate scenarios for use of plasma metagenomic next-generation sequencing.}, }
@article {pmid41147490, year = {2025}, author = {Qin, X and Liu, P and Lu, D and Lu, T and Li, C and Deng, Z and Liu, Z}, title = {The clinical value of metagenomic next-generation sequencing for diagnosing pulmonary infections in kidney transplant recipients.}, journal = {Laboratory medicine}, volume = {}, number = {}, pages = {}, doi = {10.1093/labmed/lmaf035}, pmid = {41147490}, issn = {1943-7730}, abstract = {INTRODUCTION: Rapid and accurate identification of pathogens is essential for managing lung infections in patients following kidney transplantation. This study aimed to compare the diagnostic performance and clinical utility of conventional detection methods and metagenomic next-generation sequencing (NGS) in kidney transplant recipients with respiratory infections.<br><br>METHODS: We conducted a retrospective analysis of metagenomic NGS and conventional detection method results in 71 patients, examining the spectrum of pathogen detection characteristics between the 2 methods.<br><br>RESULTS: The overall positivity rate of conventional detection methods was statistically significantly lower than that of metagenomic NGS (61.97% vs 84.51%, P&#x2005;=&#x2005;.004). Among the 38 participants who tested positive by both methods, metagenomic NGS identified a greater number of pathogens than conventional detection methods. Following metagenomic NGS results, antibiotic therapy was modified in 71.83% of participants, leading to improved prognoses in 33.33% of patients. In additionally, metagenomic NGS demonstrated a shorter turnaround time than conventional detection methods. The most prevalent bacteria identified in pulmonary infections among kidney transplant recipients were Klebsiella pneumoniae, while cytomegalovirus was the most common virus and Pneumocystis jirovecii was the predominant fungus.<br><br>DISCUSSION: This study offers preliminary insights into the spectrum of pathogens responsible for pulmonary infections following kidney transplantation, laying the foundation for better understanding their clinical characteristics. In patients with post-transplant pulmonary infections, metagenomic NGS outperforms conventional detection methods in terms of pathogen detection, speed, positivity rate, sensitivity, and ability to diagnose mixed infections.}, }
@article {pmid41147138, year = {2025}, author = {Lee, YL and Hsueh, PR}, title = {An update on antimicrobial selection and duration for intra-abdominal infections.}, journal = {Expert review of anti-infective therapy}, volume = {}, number = {}, pages = {}, doi = {10.1080/14787210.2025.2580451}, pmid = {41147138}, issn = {1744-8336}, abstract = {INTRODUCTION: Intra-abdominal infections (IAIs) pose significant challenges to clinicians. The increasing prevalence of multidrug-resistant (MDR) organisms with evolving resistance patterns adds to the difficulty in managing IAIs.<br><br>AREAS COVERED: This review synthesizes the latest evidence and recommendations from major global guidelines. Key topics include novel antimicrobial agents, empirical and targeted therapy strategies, and the role of antimicrobial stewardship in optimizing antibiotic use. Furthermore, advances in diagnostic tools, such as metagenomic next-generation sequencing and rapid resistance detection assays, are highlighted. Updates in therapy duration, emphasizing shorter courses guided by biomarkers and source control, are critically analyzed.<br><br>EXPERT OPINION: The management of IAIs has advanced significantly, with updated guidelines highlighting the importance of early and appropriate antimicrobial therapy tailored to the infection's severity and resistance patterns, along with effective source control. Novel antibiotics such as ceftolozane-tazobactam, ceftazidime-avibactam, imipenem-relebactam, eravacycline, and cefiderocol have broadened treatment options for MDR pathogens. Shorter antibiotic courses, guided by source control and biomarkers, have shown to be as effective as traditional longer regimens. Future research should focus on understanding of global resistance patterns, expanding real-world evidence for novel antibiotics, refining biomarker-guided strategies, enhancing rapid diagnostics, and applying artificial intelligence for more personalized and precise management of IAIs.}, }
@article {pmid41146816, year = {2025}, author = {Wang, N and Wu, J and Xiang, X and Zhao, Q and Yao, L}, title = {Endogenous Fungal Endophthalmitis Following Eyebrow Tattooing: A Case Report.}, journal = {Cureus}, volume = {17}, number = {9}, pages = {e93246}, pmid = {41146816}, issn = {2168-8184}, abstract = {This case report describes a rare instance of bilateral endogenous fungal endophthalmitis in a 50-year-old healthy female patient, following a facial tattooing procedure. Initially misdiagnosed as iritis in the right eye due to presenting symptoms of blurred vision and ocular pain, the patient's condition worsened following treatment with corticosteroids. Ophthalmic examination revealed severe vitreous opacity in the right eye and a yellowish-white lesion in the inferonasal retina of the left eye. Metagenomic sequencing of the vitreous fluid confirmed infection with Aspergillus fumigatus. The patient underwent pars plana vitrectomy with silicone oil tamponade, retinal laser photocoagulation, and intravitreal voriconazole injection in the right eye. Both eyes received multiple intravitreal voriconazole injections, supplemented with systemic antifungal therapy. Postoperatively, the visual acuity in the right eye improved, and the left eye gradually recovered to 20/35. Serial optical coherence tomography follow-up of the left eye documented the progressive detachment of the fungal embolus from the retinal lesion into the vitreous cavity. This case highlights that traumatic cosmetic procedures, such as eyebrow tattooing, can be a potential risk factor for endogenous fungal infection. In cases of atypical uveitis, early etiological investigation is crucial to avoid misdiagnosis and inappropriate treatment. Dynamic imaging provides valuable evidence for assessing the efficacy of antifungal therapy and determining prognosis.}, }
@article {pmid41146290, year = {2025}, author = {Kraft, L and Söding, J and Steinegger, M and Jochheim, A and Wad Sackett, P and Fernandez-Guerra, A and Renaud, G}, title = {CarpeDeam: a de novo metagenome assembler for heavily damaged ancient datasets.}, journal = {Genome biology}, volume = {26}, number = {1}, pages = {372}, pmid = {41146290}, issn = {1474-760X}, support = {NNF20OC0062491//Novo Nordisk Fonden/ ; NNF20OC0062491//Novo Nordisk Fonden/ ; 031A537B, 031A533A, 031A538A, 031A533B, 031A535A, 031A537C, 031A534A, 031A532B//German Network for Bioinformatics Infrastructure (de.NBI)/ ; }, mesh = {*Metagenome ; *Metagenomics/methods ; *Software ; *DNA, Ancient/analysis ; Sequence Analysis, DNA/methods ; Humans ; }, abstract = {De novo assembly of ancient metagenomic datasets is a challenging task. Ultra-short fragment size and characteristic postmortem damage patterns of sequenced ancient DNA molecules leave current tools ill-equipped for ideal assembly. We present CarpeDeam, a novel damage-aware de novo assembler designed specifically for ancient metagenomic samples. Utilizing maximum-likelihood frameworks that integrate sample-specific damage patterns, CarpeDeam demonstrates improved recovery of longer continuous sequences and protein sequences in many simulated and empirical datasets compared to existing assemblers. As a pioneering ancient metagenome assembler, CarpeDeam opens the door for new opportunities in functional and taxonomic analyses of ancient microbial communities.}, }
@article {pmid41145643, year = {2025}, author = {Karpęcka-Gałka, E and Zielińska, K and Frączek, B and Łabaj, PP and Kościółek, T and Humińska-Lisowska, K}, title = {High-altitude mountaineering induces adaptive gut microbiome shifts associated with dietary intake and performance markers.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {37529}, pmid = {41145643}, issn = {2045-2322}, support = {39/PB/RID/2022//Ministerstwo Edukacji i Nauki/ ; 2020/38/E/NZ2/00598//Narodowe Centrum Nauki/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Male ; *Altitude ; Adult ; *Mountaineering/physiology ; Biomarkers/blood ; *Diet ; Young Adult ; }, abstract = {This study examined how high-altitude exposure and expedition-specific dietary changes influence gut microbiome composition, functional pathways, and their relationships with performance and health markers in alpinists. Seventeen male mountaineers (age 30.29 ± 5.8 years) participating in multi-week expeditions (> 3,000 MASL) were assessed before and after their climbs. Assessments included dietary intake analysis, blood and urine biomarkers, aerobic and anaerobic performance tests, and metagenomic sequencing of the gut microbiome. Bioinformatic and statistical analyses evaluated changes in microbiome composition and function and their correlations with physiological and dietary parameters. High-altitude exposure was associated with significant shifts in gut microbial composition and functional capacity. While the total number of bacterial species and functions remained stable, the glucose degradation pathway increased post-expedition. Participants with greater microbiome shifts showed improved performance and had richer baseline microbiomes. Pre-expedition, certain microbial functions were associated with vitamin B6 and C intake, while post-expedition correlations involved specific macronutrients and micronutrients. Additionally, some microbiome changes correlated with blood markers, indicating links to nutrient metabolism and electrolyte balance. The gut microbiome of alpinists adapts to extreme environmental stress and dietary changes, influencing metabolic, immune, and performance-related processes. Optimizing dietary strategies to support a beneficial microbiome profile may enhance resilience and performance in challenging high-altitude environments.}, }
@article {pmid41145216, year = {2025}, author = {Peel, N and Martin, S and Heavens, D and Yu, DW and Clark, MD and Leggett, RM}, title = {Real-time analysis and visualization of nanopore metagenomic samples with MARTi.}, journal = {Genome research}, volume = {}, number = {}, pages = {}, doi = {10.1101/gr.280550.125}, pmid = {41145216}, issn = {1549-5469}, abstract = {The emergence of nanopore sequencing technology has the potential to transform metagenomics by offering low-cost, portable, and long-read sequencing capabilities. Furthermore, these platforms enable real-time data generation, which could significantly reduce the time from sample collection to result, a crucial factor for point-of-care diagnostics and biosurveillance. However, the full potential of real-time metagenomics remains largely unfulfilled due to a lack of accessible, open-source bioinformatic tools. We present Metagenomic Analysis in Real-Time (MARTi), an innovative open-source software designed for the real-time analysis, visualization, and exploration of metagenomic data. MARTi supports various classification methods, including BLAST, Centrifuge, and Kraken2, letting users customize parameters and utilize their own databases for taxonomic classification and antimicrobial resistance analysis. With a user-friendly, browser-based graphical interface, MARTi provides dynamic, real-time updates on community composition and AMR gene identification. MARTi's architecture and operational flexibility make it suitable for diverse research applications, ranging from in-field analysis to large-scale metagenomic studies. Using both simulated and real-world data, we demonstrate MARTi's performance in read classification, taxon detection, and relative abundance estimation. By bridging the gap between sequencing and actionable insights, MARTi marks a significant advance in the accessibility and functionality of real-time metagenomic analysis.}, }
@article {pmid41145088, year = {2025}, author = {Dan Guan,  and Chen, C and Zheng, Y and Shen, W and Huang, Y and Ge, M and Jiang, T and Zhang, J and Liu, R and Xiong, L}, title = {Chlorination-driven selection of resistant pathogens and mobile genetic elements exacerbates antibiotic resistance risks in drinking water treatment.}, journal = {Ecotoxicology and environmental safety}, volume = {305}, number = {}, pages = {119281}, doi = {10.1016/j.ecoenv.2025.119281}, pmid = {41145088}, issn = {1090-2414}, abstract = {The dissemination of Antibiotic resistance genes (ARGs) in drinking water systems poses public health risks; treatment impacts on pathogen dynamics remain unclear. In this study, two treatment trains-PK (sand filtration, ozonation-activated carbon, 5 % NaClO)and CX(ozonation-activated carbon, ultrafiltration, and 10 % NaClO) were compared through metagenomics analysis. Chlorination reduced microbial α-diversity but selected for divergent pathogens: CX-Treated Water (TW) was enriched with Salmonella enterica, Escherichia coli, and Erwinia amylovora, while PK retained Xanthomonas oryzae and Mycobacterium tuberculosis. Virulence gene tufA persisted, with 43 human-associated virulence factors being differentially expressed after disinfection. ARG analysis revealed high abundances of bacitracin and multidrug resistance gene (MRG) in early treatment stages for both lines. Chlorination paradoxically enriched these ARGs in TW, particularly MRG, which increased by 5.99 and 126.12 times in PK and CX, respectively. Mobile genetic elements (MGEs), particularly IS91, rebounded after disinfection and strongly correlated with the dissemination of ARGs (R > 0.9, p < 0.05). Higher concentrations of hypochlorite doses in CX-DWTP amplified plasmid associated Rep7/IS91 abundances, increasing ARG transmission risks. These findings revealed that aggressive disinfection selected resistant pathogens, enriches virulence determinants, and facilitated the dissemination of ARGs via MGEs, highlighting the need for optimized disinfection strategies to safeguard water biosafety.}, }
@article {pmid41145028, year = {2025}, author = {Zhu, F and Penha, FM and Cetecioglu, Z}, title = {Functional microbial enrichment and chelation-enhanced phosphorus release from marine sediments: Toward sustainable phosphorus management.}, journal = {Water research}, volume = {289}, number = {Pt A}, pages = {124842}, doi = {10.1016/j.watres.2025.124842}, pmid = {41145028}, issn = {1879-2448}, abstract = {To improve the efficiency of phosphorus (P) release from marine sediments and contribute to P loop closure, this study proposed a novel strategy combining bio-inoculation with polyphosphate-accumulating organisms (PAOs) and chemical enhancement via chelating agents. Based on prior findings, two-stage experiments were conducted. In Stage 1, anaerobic batch tests assessed the effect of different chelating agents for P release. While citrate showed no promoting effect, the addition of ethylenediaminetetraacetic acid (EDTA) significantly enhanced total P release, reaching 48.5 % within 15 days. In Stage 2, PAO-acclimated sediments were introduced into the system, followed by alternating anaerobic-aerobic fed-batch operation for 7 days, and subsequent EDTA addition with anaerobic incubation for another 6 days. This combined approach achieved a total P release efficiency 83.4 %, with final soluble P concentrations reaching 145.9 mg/L. During this process, PAOs were rapidly enriched, with their relative abundance increasing from 12.9 % to 65.0 %. Metagenomic analysis revealed that EDTA promoted environmental filtering, selectively enriching PAOs (Candidatus Accumulibacter) and thereby reinforcing their specific contributions to P functional genes. The resulting P-rich supernatant was then subjected to precipitation. PHREEQC simulations guided the prediction of optimal precipitation conditions, and laboratory experiments confirmed that most soluble P, especially Fe-bound forms, could be efficiently recovered, with maximum precipitation efficiencies of 98.8 %.}, }
@article {pmid41144667, year = {2025}, author = {Xu, JY and Yu, YT and Du, S and Shen, LQ and Zhang, Q and Qian, H and Cai, TG and Wang, YF and Zhao, J and Li, HZ and Zhang, C and Zhu, D}, title = {Discarded cigarette butts as overlooked reservoirs and amplifiers of antibiotic resistance genes and pathogens in urban green spaces.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {44}, pages = {e2525377122}, doi = {10.1073/pnas.2525377122}, pmid = {41144667}, issn = {1091-6490}, support = {42222701//MOST | National Natural Science Foundation of China (NSFC)/ ; 22193062//MOST | National Natural Science Foundation of China (NSFC)/ ; 22193062//MOST | National Natural Science Foundation of China (NSFC)/ ; 22125601//MOST | NSFC | National Science Fund for Distinguished Young Scholars (NSF for Distinguished Young Scholars)/ ; 2023321//Youth Innovation Promotion Association of the Chinese Academy of Sciences (CAS YIPA)/ ; 2022A-163-G//Ningbo Yongjiang Talent Project/ ; }, mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; *Drug Resistance, Microbial/genetics ; China ; *Tobacco Products/microbiology ; Gene Transfer, Horizontal ; *Bacteria/genetics/drug effects ; Genes, Bacterial ; *Drug Resistance, Bacterial/genetics ; Biofilms/growth &amp; development ; }, abstract = {Cigarette butts are widely discarded in urban green spaces, yet their microbial health risks remain poorly understood. In a nationwide survey across China, we investigated the presence, sources, health risks, and drivers of antibiotic resistance genes (ARGs) and potential pathogens in discarded cigarette butts. Shotgun metagenomic and full-length 16S ribosomal rRNA (rRNA) sequencing revealed that cigarette butts harbored significantly higher abundances of ARGs and bacterial pathogens than plant litter or soil. Health risk assessment further showed that cigarette butts carried ARGs with greater mobility, clinical relevance, and pathogenic potential. Genomic analyses highlighted enrichment of ARG-carrying pathogens, particularly Enterobacteriaceae and Pseudomonas, with mobile genetic elements and oxidative stress responses as key contributors. Functional assays, including plasmid transfer, transcriptomic profiling, and single-cell Raman spectroscopy, demonstrated that cigarette butts promoted horizontal gene transfer and upregulated key ARGs (e.g., mexE, mexF, cfrC) under stress conditions. Scanning electron microscopy confirmed biofilm formation on cigarette fibers, supporting enhanced bacterial persistence. Source-tracking analyses identified both human oral and environmental sources of the enriched ARGs and pathogens in cigarette butts. Finally, socioeconomic factors such as lower gross domestic product (GDP), reduced education, and poor sanitation were strongly associated with elevated ARG and pathogen risks. Collectively, our findings identify cigarette butts as overlooked yet potent vectors of ARG and pathogen dissemination in urban green spaces, underscoring the need for targeted interventions within a One Health framework.}, }
@article {pmid41144656, year = {2025}, author = {Myburgh, DA and da Silva, NA and Haller-Caskie, M and Colominas, L and Castanyer, P and Frigola, J and Tremoleda, J and Hölzel, C and Unterweger, D and Nebel, A and Krause-Kyora, B}, title = {Detection of Clostridium sporogenes in a Roman-era cattle mass grave at Vilauba.}, journal = {Virulence}, volume = {}, number = {}, pages = {2580731}, doi = {10.1080/21505594.2025.2580731}, pmid = {41144656}, issn = {2150-5608}, abstract = {In the ancient Roman world, cattle played an integral role in daily agricultural tasks, providing the means necessary to plow fields, mill grains, and transport goods. The research presented here deals with the remains of 14 cattle discovered in a mass grave at the Roman villa of Vilauba in Catalonia, Spain. According to the archeological record, it can be ruled out that the animals were slaughtered for consumption, banqueting, or sacrificial purposes. By investigating the metagenomic sequences generated from the bovine remains, we identified in three individuals a group I Clostridium strain, phylogenetically related to known producers of botulinum neurotoxins - suggesting that the Vilauba strain may have had toxigenic potential. Moreover, we discovered a Mycolicibacterium species phylogenetically related to known opportunistic pathogens. While no definitive conclusions can be drawn about disease, the phylogenetic placement of these taxa and the detection of Clostridium virulence-associated genes suggest a possible role beyond postmortem contamination. Collectively, these findings draw attention to atypical bacterial species, such as C. sporogenes, which are often overlooked in palaeogenomic studies due to their ambiguous status as environmental microbes, commensals, or potential pathogens. Their detection in animal remains highlights that they may represent a blind spot in our current understanding of livestock health. More broadly, this study underscores the current complexity of investigating such taxa and emphasizes the need for novel methods to disentangle the roles of these bacterial species.}, }
@article {pmid41144256, year = {2025}, author = {Dziegiel, AH and Duong, VT and Bloomfield, SJ and Thomson, NR and Maskell, DJ and Wain, J and Janecko, N and Baker, S and Mather, AE}, title = {Metagenomic identification of disease-causing Salmonella enterica serovars and antimicrobial resistance genes from paediatric faecal samples.}, journal = {Microbial genomics}, volume = {11}, number = {10}, pages = {}, doi = {10.1099/mgen.0.001547}, pmid = {41144256}, issn = {2057-5858}, mesh = {Humans ; *Feces/microbiology ; *Salmonella enterica/genetics/isolation &amp; purification/drug effects/classification ; *Metagenomics/methods ; *Salmonella Infections/microbiology ; Child, Preschool ; *Drug Resistance, Bacterial/genetics ; Infant ; Child ; Serogroup ; Metagenome ; Vietnam ; Anti-Bacterial Agents/pharmacology ; Male ; Female ; }, abstract = {Background. Nontyphoidal Salmonella (NTS) is a common cause of enterocolitis and a major cause of death in children in low- and middle-income countries (LMICs). High antimicrobial resistance (AMR) prevalence in LMICs reduces treatment options for individuals at risk of severe infections.Methods. We investigated the use of metagenomics to identify NTS and associated AMR genes in 28 faecal metagenomes from children with culture-confirmed salmonellosis in Vietnam, using accompanying NTS genomes from isolated serovars (one per metagenome). Read-based and assembly-based methods were utilised for NTS and AMR detection. Case metagenomes were compared to healthy control metagenomes (n=21) with respect to the microbiome composition, NTS relative abundances, number of unique AMR genes and antimicrobial classes to which the genes confer resistance, including classes used in Salmonella treatment.Results. Salmonellosis cases displayed significantly higher relative abundances of Enterobacteriaceae than controls. Bracken and Centrifuge analysis facilitated the identification of Salmonella enterica sequences in case metagenomes at varying relative abundances (0.00259-27.7 % of total reads), which were significantly higher than controls. MetaPhlAn4 did not detect S. enterica in any control metagenomes, though 12 case metagenomes were also negative. The isolated serovars were identified in 78.6% of the associated case metagenomes with Centrifuge, suggesting this method is the most sensitive; however, the isolated genome serovar was the most abundant in only six case metagenomes, and serovar sequences were also identified in control metagenomes. Alignment to a Salmonella reference database, followed by local assembly and realignment, predicted the isolated serovar as the most likely serovar present in 35.7% of metagenomes, whereas Salmonella in silico typing resource classification of the local assembly was concordant with the isolate genome in 28.6% of cases. Metagenome-assembled genomes produced using two tools following de novo assembly identified the isolated serovar in 17.8-21.4% of cases. The percentage of NTS AMR genes identified in each case metagenome ranged between 0.00 and 100%. There was no significant difference in the number of unique AMR genes or antimicrobial classes between cases and controls, indicating comparable resistomes between cohorts.Conclusions. This study highlights the potential of metagenomics for NTS identification in faecal samples, although overlap in S. enterica relative abundance between cohorts calls for further work to identify a diagnostic cutoff. Reliable characterisation of the organism to the serovar and AMR genotype level is affected by the complexity of the microbiome, sequencing and analysis approaches. Increased sequencing depth, for example through improved host DNA depletion, may facilitate enhanced characterisation. Detection of multiple serovars within individual samples with the Centrifuge suggests inaccurate classification or the presence of multiple serovars, making characterisation difficult.}, }
@article {pmid41143690, year = {2025}, author = {Kim, KJ and Garcia, M and Romero, AS and Jin, Y and Chi, J and Campen, MJ and Gu, H and Richardson, JR and Castillo, EF and Cui, JY}, title = {In vivo exposure of mixed microplastic particles in mice and its impacts on the murine gut microbiome and metabolome.}, journal = {Toxicological sciences : an official journal of the Society of Toxicology}, volume = {}, number = {}, pages = {}, doi = {10.1093/toxsci/kfaf145}, pmid = {41143690}, issn = {1096-0929}, abstract = {Microplastics (MPs) are emerging environmental contaminants due to increasing global plastic production and waste. Microplastics, defined as plastic particles less than 5 mm in diameter, are formed through degradation of larger plastics via sunlight, weathering, and microbes. These plastic compounds are widely detected in water, soil, food, as well as human stool and blood. The gut microbiome, often referred to as our second genome, is important in human health and is the primary point of contact for orally ingested microplastics. To investigate the impact of ingested MPs on the gut microbiome and the metabolome, 8-week-old male and female C57BL/6 mice were orally gavaged mixed plastic (5 µm) exposure consisting of polystyrene, polyethylene, and the biodegradable/biocompatible plastic, poly(lactic-co-glycolic acid), twice a week for 4 weeks at 0, 2, or 4 mg/week (n = 8/group). Fecal pellets were collected for bacterial DNA extraction and metagenomic shotgun sequencing, and serum was subjected to targeted and untargeted metabolomics. A total of 1162 bacterial species and 1437 metabolites were evaluated for downstream analysis. MPs exposure resulted in significant sex-specific and dose-dependent changes to the gut microbiome composition along with substantial regulation of predicted metabolic pathways. Untargeted metabolomics in serum showed that a low MPs dose displayed a more prominent effect on key metabolic pathways such as amino acid metabolism, sugar metabolism, and inflammation. Additionally, SCFA-targeted metabolomics showed significant changes in neuroprotective SCFAs levels in both sexes. Our study demonstrates that microplastics dysregulate the gut microbiome and serum metabolome, highlighting potential human disease risks.}, }
@article {pmid41143557, year = {2025}, author = {Shi, Z and Liu, Q and Zhou, M and Xu, W and Luo, G}, title = {Persistent Risks in the Effluents of Wastewater Treatment Plants: Mobile Genetic Elements and Viral-Mediated Dissemination of Pathogenic Antibiotic-Resistant Bacteria.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c08352}, pmid = {41143557}, issn = {1520-5851}, abstract = {Wastewater treatment plants (WWTPs) are recognized as reservoirs of pathogenic antibiotic-resistant bacteria (PARB), yet their genomic risk dynamics remain unclear. This study recovered PARB genomes from 102 influent and effluent metagenomes from six countries; their activity and risk potential were then experimentally validated with metatranscriptomics on samples from a Shanghai WWTP. A total of 44 PARB genomes were reconstructed, which carried both antibiotic resistance genes (ARGs) and virulence factor genes (VFGs), and they persisted in the effluent. Mobile genetic elements might mediate ARG transfer in 13 PARB genomes. Moreover, bacteriophages infecting PARB harbored and were transcribing ARGs/VFGs, and antiviral defense systems of PARB correlated with horizontal gene transfer (HGT). Evolutionary analyses indicated that influent PARB maintained high microdiversity via homologous recombination, while effluent populations underwent purifying selection, suggesting that wastewater treatment reduced the genetic diversity of PARB through purifying selection. However, the persistent accumulation of PARB as well as HGT might maintain the dissemination of ARGs. This study emphasized the necessity of selecting the PARB genomes for wastewater monitoring, thereby optimizing treatment strategies and mitigating the potential health risks posed by pathogenic bacteria.}, }
@article {pmid41143534, year = {2025}, author = {Conrad, R and Gerhardt, K and Konstantinidis, KT and Williams-Newkirk, AJ and Huang, AD}, title = {ROCker models for reliable detection and typing of short-read sequences carrying mcr, erm, mph, and lnu antibiotic resistance genes.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0241325}, doi = {10.1128/spectrum.02413-25}, pmid = {41143534}, issn = {2165-0497}, abstract = {Quantitative monitoring of emerging antimicrobial resistance genes (ARGs) using short-read sequences remains challenging due to the high frequency of amino acid functional domains and motifs shared with related but functionally distinct (non-target) proteins. To facilitate ARG monitoring efforts using unassembled short reads, we present novel ROCker models for mcr, mph, erm, and lnu ARG families, as well as models for variants of special public health concern within these families, including mcr-1, mphA, ermB, lnuF, lnuB, and lnuG genes. For this, we curated target gene sequence sets for model training and built these models using the recently updated ROCker V2 pipeline (Gerhardt et al., in review). To validate our models, we simulated reads from the whole genome of ARG-carrying isolates spanning a range of common read lengths and used them to challenge the filtering efficacy of ROCker versus common static filtering approaches, such as similarity searches using BLASTx with various e-value thresholds or hidden Markov models. ROCker models consistently showed F1 scores up to 10× higher (31% higher on average) and lower false-positive (by 30%, on average) and false-negative (by 16%, on average) rates based on 250 bp reads compared to alternative methods. The ROCker models and all related reference materials and data are freely available through http://enve-omics.ce.gatech.edu/rocker/models, further expanding the available model collection previously developed for other genes. Their application to short-read metagenomes, metatranscriptomes, and PCR amplicon data should facilitate more accurate classification and quantification of unassembled short-read sequences for these ARG families and specific genes.IMPORTANCEAntimicrobial resistance gene families encoding erm and mph genes confer resistance to the macrolide class of antimicrobials, which are used to treat a wide range of infections. Similarly, the mcr gene family confers resistance to polymyxin E (colistin), a drug of last resort for many serious drug-resistant bacterial infections, and the lnu gene family confers resistance to lincomycin, which is reserved for patients allergic to penicillin or where bacteria have developed resistance to other antimicrobials. Assessing the prevalence of these genes in clinical or environmental samples and monitoring their spread to new pathogens are thus important for quantifying the associated public health risk. However, detecting these and other resistance genes in short-read sequence data is technically challenging. Our ROCker bioinformatic pipeline achieves reliable detection and typing of broad-range target gene sequences in complex data sets, thus contributing toward solving an important problem in ongoing surveillance efforts of antimicrobial resistance.}, }
@article {pmid41143528, year = {2025}, author = {Mukherjee, SD and Adler, A and Dang, T and Taylor, EN and Curhan, G and Miller, AW}, title = {Evaluating the use of biobanked urine specimens for human urobiome studies.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0216424}, doi = {10.1128/spectrum.02164-24}, pmid = {41143528}, issn = {2165-0497}, abstract = {Case-control studies focused on the urinary tract microbiome, or urobiome, have consistently reported significant associations with disease. However, clinical urobiome studies have typically been small, averaging ~50 patients per study. While these sample sizes are sufficient to detect large effect sizes, they have not been able to differentiate disease phenotypes within a larger disease complex (e.g., different types of kidney stones), which have unique etiological origins. Biobanked urine specimens can help fill this void. However, since these specimens were not collected specifically for urobiome studies, they must be validated before drawing any strong conclusions. The objective of this study was to evaluate microbiome data derived from metagenomic analysis of biobanked urine specimens against the following criteria: (i) level of contaminants; (ii) retention of high-quality DNA; (iii) overgrowth of a few dominant bacteria; and (iv) preservation of sex-specific taxa. A total of 174 samples were assessed from biobanked or freshly collected specimens (N = 118 patients total), in addition to multiple positive and negative controls. While there were significant differences in diversity (alpha/beta; P < 0.001) based on whether or not samples were biobanked, these differences can largely be explained by study-specific variation. With these criteria, we find that biobanked urine specimens provide similar data to fresh specimens collected using standardized protocols and can be used for clinical urobiome studies.IMPORTANCEThe urinary tract microbiome, or urobiome, is an emerging field of study that has shown promise as an important contributor to urologic health and disease. However, since this field is relatively new, clinical studies to evaluate the urobiome in the context of urologic disease have been relatively small. The use of biobanked urine specimens would allow for much larger studies to be conducted in a relatively short period of time. However, the use of biobanked urine specimens must first be validated. In this study, we sought to evaluate the use of biobanked urine specimens through multiple metrics, compared to previous studies conducted specifically to assess the impact of the urobiome. Results of our study suggest that biobanked urine specimens produce similar data to urine samples collected under rigorously controlled conditions and can be used in casecontrol studies of urologic conditions.}, }
@article {pmid41143408, year = {2025}, author = {Liao, Y and Cheng, J and Xiong, S and Liu, Y and Qian, J and Shi, M and Guo, Y and Kang, Y-J}, title = {Dynamics of the respiratory infectome in children with community-acquired pneumonia: insights from large and short time-scale analyses.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0145025}, doi = {10.1128/spectrum.01450-25}, pmid = {41143408}, issn = {2165-0497}, abstract = {UNLABELLED: Community-acquired pneumonia (CAP) has emerged as a significant health challenge for young children, especially after the relaxation of COVID-19 restrictions, which coincided with a sharp increase in CAP cases. While pathogen profiling is commonly performed, comprehensive studies examining the total infectome and its dynamic changes during disease progression and in relation to the pandemic remain scarce. To address this gap, we conducted a prospective cohort study involving 58 children hospitalized with CAP in Wuxi, China, during and after COVID-19 control measures. Sputum samples were analyzed using metagenomic and metatranscriptomic sequencing to characterize the total infectome. Results showed that RNA sequencing offers a more comprehensive view of the infectome, while DNA sequencing excels in detecting DNA viruses with greater sensitivity. Notable increases in Mycoplasma pneumoniae, human respiratory syncytial virus (RSV), and Haemophilus influenzae were observed after COVID-19 restrictions were lifted. During disease progression, some patients exhibited a decline in pathogen abundance, while others developed secondary infections, frequently involving co-infections, which might contribute to prolonged pneumonia or complicated disease course. Viral-bacterial co-infections were common, with M. pneumoniae and RSV being the most prevalent combination. In summary, this study highlights the shifting respiratory infectome in children with CAP, both after the relaxation of COVID-19 control measures and throughout hospitalization. It emphasizes the need for comprehensive infectome monitoring to track dynamic changes across broader timeframes and during disease progression, offering insights for improved clinical management and future research.<br><br>IMPORTANCE: Community-acquired pneumonia (CAP) remains a leading threat to children's health globally, with shifting pathogen dynamics post-COVID-19 posing new challenges. This study reveals how pandemic control measures and their relaxation influenced the respiratory "infectome"-the full spectrum of pathogens-in children with CAP. By integrating multi-sequencing technologies, we uncovered critical trends: a resurgence of virulent pathogens like Mycoplasma pneumoniae and respiratory syncytial virus after restrictions eased, frequent viral-bacterial co-infections linked to prolonged pneumonia, and distinct infection patterns during hospitalization that predict recovery or complications. These findings highlight the need for dynamic, multi-pathogen surveillance to guide clinical decisions, particularly in managing co-infections and preventing secondary infections. Our work provides actionable insights for pediatricians and public health experts to anticipate post-pandemic pathogen behavior, tailor treatments, and mitigate risks during future outbreaks, ultimately improving care for vulnerable young patients.}, }
@article {pmid41142817, year = {2025}, author = {Lee, JY and Mahurkar-Joshi, S and Young, A and Labus, JS and He, B and Aja, E and Jacobs, JP and Volkmann, ER}, title = {Ultra-processed food intake is associated with increased gastrointestinal tract symptoms and alterations in gut microbiota in patients with systemic sclerosis.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1610360}, pmid = {41142817}, issn = {1664-3224}, mesh = {Humans ; *Scleroderma, Systemic/microbiology/complications ; Female ; *Gastrointestinal Microbiome ; Male ; Middle Aged ; Adult ; Aged ; *Gastrointestinal Diseases/etiology/microbiology ; *Dysbiosis ; Feces/microbiology ; Food Handling ; Food, Processed ; }, abstract = {BACKGROUND: Alterations in the gastrointestinal (GI) microbiome (i.e., dysbiosis) are a feature of systemic sclerosis (SSc). Diet is a known modifier of the GI microbiome, and ultra-processed food (UPF) consumption has been associated with adverse changes in GI microbial composition. This study aimed to determine whether UPF consumption affects the GI microbiota and GI symptoms in patients with SSc.<br><br>METHODS: Adult SSc patients provided stool samples and completed both the Diet History Questionnaire II (DHQ-2) and the UCLA Scleroderma Clinical Trial Consortium Gastrointestinal Tract Instrument (GIT 2.0). Shotgun metagenomics were performed using the Illumina NovaSeq 6000 with a target depth of 10 million 150x2 sequences per sample. UPF items (N=54) on the DHQ-2 were identified using the NOVA scale of food classification, and UPF intake was calculated as gram-per-week consumption according to patient reported frequency. General linear models were created to identify differentially abundant species based on UPF consumption and to evaluate the relationship between UPF consumption and GI symptoms as measured by the GIT 2.0. These models adjusted for body mass index (BMI), current proton pump inhibitor (PPI) use, current probiotic use, current or prior immunomodulatory therapy, and presence of small intestinal bacterial overgrowth (SIBO).<br><br>RESULTS: Of the 65 total SSc patients included, 84.6% were female. The mean age was 53.83 &#xb1; 13.19 years, and the mean BMI was 25.25 &#xb1; 4.75. The median UPF consumption was 2395.82 g/week. Increased UPF consumption was significantly associated with increased GI symptoms in our multivariate model (&#x3b2;=0.34; p<0.01). Among 257 species analyzed, 5 bacterial species were significantly associated with UPF consumption in the multivariate models, including Limosilactobacillus fermentum (&#x3b2;=0.32; p<0.01) and Faecalicatena fissicatena (&#x3b2;= -0.36; p-value<0.01), while the abundance of 6 bacterial species was significantly associated with GI symptom severity after adjusting for the aforementioned covariates.<br><br>CONCLUSIONS: SSc patients reporting a higher UPF consumption demonstrated alterations in GI microbial composition as well as increased GI symptoms, even after adjusting for factors known to affect the microbiota of patients with SSc. Future studies are needed to determine whether interventions aimed at lowering UPF consumption may improve GI outcomes for patients with SSc.}, }
@article {pmid41142066, year = {2025}, author = {Kyrychenko, A}, title = {Molecular architecture of giant viruses infecting microbial eukaryotes (protists).}, journal = {Biotechnologia}, volume = {106}, number = {3}, pages = {361-376}, pmid = {41142066}, issn = {2353-9461}, abstract = {In this review, I describe recent findings on the molecular architecture and genomic characterization of giant viruses that infect microbial eukaryotes (protists) across diverse ecosystems and ecological niches. Giant viruses are distinguished by their large and complex genomes, which encode a wide range of functions, including protein translation, carbohydrate and lipid metabolism, nitrogen cycling, light assimilation, and key metabolic pathways such as glycolysis and the tricarboxylic acid cycle. Additionally, these genomes feature unique genes, often acquired through horizontal gene transfer, that are not found in other viruses and contribute to the viruses' ability to manipulate host metabolism and evade host defenses. A core set of genes conserved across different families of giant viruses is highlighted, serving as essential components for key life-cycle processes and providing valuable phylogenetic markers. The review also discusses the role of ORFans and virophages in contributing to the genetic diversity and evolutionary adaptation of these viruses. These findings are crucial for understanding the diversity, evolutionary mechanisms, and complex virus-host interactions of giant viruses, as well as for developing more advanced classification systems. Furthermore, the potential biotechnological applications of unique viral genes and pathways are explored, underscoring the importance of ongoing research in this field.}, }
@article {pmid41140871, year = {2025}, author = {Talamantes-Becerra, B and Chang, WS and Michie, M and Hodda, M and Hopper, M and Caron, V}, title = {RNA-seq dataset of land snails collected in Australia.}, journal = {Data in brief}, volume = {63}, number = {}, pages = {112122}, pmid = {41140871}, issn = {2352-3409}, abstract = {Snails are known to be host of pathogens and parasites and they can play an important role in the transmission of some parasites and pathogens, including nematodes and trematodes of medical and veterinary importance. They have a diverse diet, and can be classified as detritivores, plant feeders, or carnivores. The datasets presented here include raw RNA-seq data of 10 terrestrial land snails collected in three locations in Australia, including Northern Territory, Queensland and South Australia. The snails were identified morphologically, and RNA was extracted from whole organisms using a modified version of the Maxwell ® RSC simplyRNA Tissue Kit. The sequencing was performed in all samples and generated an average of at least 56 million paired-end reads per sample. RNA-seq raw reads and assembled transcripts including both host-derived and non-host sequences were deposited into a DRYAD repository. Assembled transcripts including only host data are also provided in this project. The dataset has reuse potential for environmental studies related to conservation biology, invasive species surveillance, disease research, educational purposes, development of bioinformatic tools for environmental transcriptomics or host-pathogen interactions. Moreover, the dataset can be used for benchmarking metatranscriptomic classification tools in non-model invertebrates.}, }
@article {pmid41140851, year = {2025}, author = {Tran, SH and Restrepo-Ortiz, CX and Vu, DQ and Troussellier, M and Bettarel, Y and Bouvier, T and Bui, VN and Minh, NH and Hoang, TD and Nguyen, QH and Auguet, JC}, title = {NEMESISdb: A full length 16S rRNA gene dataset for the detection of human, fish, and crustacean potentially pathogenic bacteria.}, journal = {Data in brief}, volume = {63}, number = {}, pages = {112135}, pmid = {41140851}, issn = {2352-3409}, abstract = {NEMESISdb is a 16S rRNA full length sequence curated dataset designed to enable the identification and tracking of potentially pathogenic bacteria (PPB) for human, fish, and crustacean hosts. It addresses the limited focus on marine and coastal environments as key reservoirs for PPB, where bacteria from diverse sources-terrestrial, marine, and animal-can coexist. Leveraging recent advances in high-throughput sequencing, NEMESISdb provides a robust resource for the detection of PPB in 16S rRNA gene metabarcoding or metagenomic data. The database comprises three datasets corresponding to human, fish, and crustacean hosts, containing 1703, 222, and 64 PPB species, respectively, with a total of over 150,000 16S rRNA full length sequences curated for accuracy. This resource was constructed by extracting sequences from the SILVA 138.2 SSU Ref NR99 database, refining them through a rigorous curation pipeline to ensure taxonomic consistency and eliminate misclassifications. The resulting datasets are optimized for use with popular tools such as BLAST and classifier software, enabling rapid and accurate detection of PPB in metabarcoding and metagenomic data. NEMESISdb supports diverse applications, including pathogen surveillance in aquatic ecosystems, studies on environmental factors influencing PPB dynamics, and the development of targeted strategies for mitigating pathogen impacts in aquaculture. Additionally, it facilitates research within the One Health framework by linking the circulation of PPB across environmental, animal, and human compartments.}, }
@article {pmid41140834, year = {2025}, author = {Van Uffelen, A and Posadas, A and Fraiture, MA and Roosens, NHC and De Keersmaecker, SCJ and Marchal, K and Vanneste, K}, title = {Detection of Bacillus production strains and contaminants in food enzyme products.}, journal = {Food chemistry. Molecular sciences}, volume = {11}, number = {}, pages = {100309}, pmid = {41140834}, issn = {2666-5662}, abstract = {Shotgun metagenomics enables taxonomic analysis of microbial communities by aligning sequencing reads to reference genomes, for which interpretation of alignment results often lacks standardization and relies on arbitrary abundance thresholds. This can bias species detection, especially for low-abundance or taxonomically complex genera like Bacillus, where closely related species may differ in safety and function, and their co-occurrence increases misclassification risk. This study presents a bioinformatics framework for defining detection thresholds of biological contaminations in samples using nanopore shotgun metagenomics data, demonstrated through a case study on Bacillus subtilis sensu lato (s.l.) and Bacillus cereus s.l. contaminations in food enzyme (FE) products. The framework was developed by employing in silico mixes of isolate sequencing data of different B. subtilis and B. cereus species, and uses the tool KMA for taxonomic classification with post-processing steps based on template identity to differentiate true positives from false positives, coupled with curation of the underlying reference genomic database. The performance of the developed framework was afterwards validated with five in vitro mixes mimicking potential FE contaminations. Finally, the applicability of the validated framework was evaluated with six real and well-characterized commercial contaminated FE samples, confirming its ability to accurately detect B. subtilis and B. cereus contaminants, even at low abundances up to a relative abundance of 1 %. In conclusion, we present a bioinformatics framework allowing reliable species-level detection of challenging low-level contaminants in samples using nanopore shotgun metagenomics sequencing, which was successfully applied to identify B. subtilis and B. cereus contaminations in FE products.}, }
@article {pmid41140673, year = {2025}, author = {Ao, D and Li, X and Zhang, G and Ma, H and Yang, L and Tian, H and Ao, S and Feng, J and Geng, W}, title = {Diagnostic value of metagenomic next-generation sequencing in atypical brucellosis: a case report.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1652671}, pmid = {41140673}, issn = {2296-858X}, abstract = {BACKGROUND: Brucellosis with atypical presentations, such as submandibular abscess without fever, is frequently misdiagnosed.<br><br>METHODS: Metagenomic next-generation sequencing (mNGS) was applied to pus samples from a 47-year-old female with a treatment-refractory submandibular abscess and a history of livestock exposure; results were confirmed serologically.<br><br>RESULTS: Within 48&#x202f;h, mNGS identified Brucella suis-representing, to our knowledge, the first reported afebrile submandibular infection caused by this pathogen. Targeted therapy with doxycycline and rifamycin led to symptom resolution within 6&#x202f;days.<br><br>CONCLUSION: This case highlights that mNGS, combined with a thorough epidemiological history, can resolve diagnostic dilemmas in atypical brucellosis, guide precise treatment, and mitigate antibiotic misuse.}, }
@article {pmid41140651, year = {2025}, author = {Wang, X and Chen, S and Yang, C}, title = {Coexistence of cat scratch disease lymphadenitis and active pulmonary tuberculosis in an immunocompetent host - a case report with metagenomic diagnosis and literature review.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1667171}, pmid = {41140651}, issn = {2296-858X}, abstract = {Cat scratch disease (CSD), caused by Bartonella henselae (B. henselae), typically presents as localized swelling of lymph nodes following a scratch or bite from a cat. It is crucial to differentiate CSD from tuberculosis (TB), particularly in regions where TB is prevalent. This report describes a 56-year-old man who exhibited bilateral swelling of the cervical lymph nodes. Initially, he was suspected to have tuberculous lymphadenitis due to the granulomatous changes observed in a biopsy of the lymph nodes, typical signs of TB on a chest CT scan, and a positive result from an interferon-gamma release assay (IGRA). He was subsequently referred to our hospital for TB treatment. Testing of bronchoalveolar lavage fluid confirmed the presence of TB-DNA, indicating active pulmonary tuberculosis (PTB). However, further investigation revealed recent cat contact. This led to the identification of a B. henselae infection using metagenomic pathogen detection workflow (MetaPath™) on formalin-fixed paraffin-embedded (FFPE) histopathological sections from a cervical lymph node specimen obtained at an external hospital, which confirmed the diagnosis of CSD and ruled out TB. Through a review of the literature, we found that this represents the first documented case of concurrent active PTB and CSD-related lymphadenitis in an immunocompetent individual. It highlights the diagnostic challenges in distinguishing CSD from TB in cases of granulomatous lymphadenitis and emphasizes the need to consider CSD in patients with a history of cat exposure, showcasing the pivotal role of advanced metagenomic diagnostics in accurately diagnosing CSD.}, }
@article {pmid41140474, year = {2025}, author = {Chen, Y and Li, X and Bi, C and Yang, Y and Xiong, S and Tian, X and Zhong, D and Gan, Y and Gao, A}, title = {Cutaneous Talaromyces marneffei Infection in an Immunocompetent Adolescent: A Case Report.}, journal = {Clinical, cosmetic and investigational dermatology}, volume = {18}, number = {}, pages = {2701-2706}, pmid = {41140474}, issn = {1178-7015}, abstract = {Talaromyces marneffei (TM) infection is a rare but potentially fatal deep fungal disease that typically affects immunocompromised individuals in endemic regions. However, an increasing number of cases have been reported in HIV-negative, immunocompetent patients without classical risk factors. We report the case of a 15-year-old girl residing in urban southern China who presented with chronic cutaneous plaques and cervical lymphadenopathy, initially misdiagnosed as tuberculous lymphadenitis. Despite one year of anti-tuberculosis therapy, her condition worsened and liver dysfunction developed. Subsequent skin biopsy, fungal culture, and metagenomic next-generation sequencing (mNGS) confirmed localized cutaneous TM infection. The patient responded well to oral itraconazole, and lesions resolved after four months of treatment, with no recurrence during an 18-month follow-up. This case highlights the importance of considering deep fungal infections in the differential diagnosis of chronic granulomatous skin lesions, even in immunocompetent hosts, and emphasizes the diagnostic utility of mNGS in atypical presentations.}, }
@article {pmid41140407, year = {2025}, author = {Li, D and Li, Z and Liu, W}, title = {The gut-kidney axis in urolithiasis: roles of gut microbiota, metabolites, and therapeutic implications.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1655808}, pmid = {41140407}, issn = {1664-302X}, abstract = {Urolithiasis affects 2-20% of the global population and recurs frequently. Emerging evidence positions the gut-kidney axis as a central driver of stone formation. This review synthesizes epidemiological data, comparative metagenomic analyzes, and mechanistic studies to demonstrate that stone formers exhibit reduced α-diversity, depletion of oxalate-degrading taxa (e.g., Oxalobacter, Lactobacillus, Bifidobacterium), and enrichment of pro-inflammatory genera (Escherichia, Bacteroides). Microbial metabolites-oxalate, short-chain fatty acids, p-cresol, and secondary bile acids-modulate intestinal oxalate transport, systemic inflammation, and renal crystal nucleation. Therapeutic modulation via targeted probiotics, prebiotics, engineered Lactobacillus, or fecal microbiota transplantation restores oxalate homeostasis and attenuates nephrolithiasis in rodent models; however, human efficacy remains preliminary. Large-scale multi-omics cohorts and randomized controlled intervention trials are imperative to translate gut-centric strategies into precision urology.}, }
@article {pmid41140401, year = {2025}, author = {Rozmiarek, KS and Yang, J and Schambach, J and Bennett, H and Caro, TA and Sammon, J and Whiting, JJ and Miller, PR and Ricken, B and Bigler, L and Jayne, RS and Fukuyama, D and Jones, TR and Smallwood, CR}, title = {Microbial and chemical predictors of methane release from a stratified thermokarst permafrost hotspot.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1657143}, pmid = {41140401}, issn = {1664-302X}, abstract = {Soils are dynamic interfaces that can act as both sources and sinks of methane (CH4), yet the microbial processes underlying these fluxes remain poorly constrained in current Earth system models-particularly in thawing permafrost regions. Accurately quantifying subsurface microbial activity and its response to environmental variation is essential for improving predictions of CH4 emissions under shifting temperature regimes. Here, we explore the potential of volatile organic compounds (VOCs) as early chemical indicators of microbial processes driving CH4 production within a thermokarst-associated CH4 hotspot. Field surveys at Big Trail Lake, a young thermokarst feature in central Alaska, identified localized CH4 emission zones. Anaerobic soil laboratory microcosms from 50, 200, and 400 cm depths were incubated at -4 °C, 5 °C, and 12 °C to simulate freeze-thaw transitions. Methane flux increased markedly with temperature, and microbial community shifts revealed Methanosarcina spp. as the dominant methanogen, particularly at 200 cm. VOC profiling showed strong depth- and temperature-dependent patterns, with the 50 cm layer exhibiting the greatest chemical diversity. Notably, 200 cm soils produced VOC signatures overlapping with those from pure Methanosarcina acetivorans C2A cultures, supporting the identification of shared metabolites linked to active methanogenesis. Extended 60-day incubations confirmed temperature-sensitive CH4 production. Carbon isotopic enrichment in CH4 was unexpectedly strong with warming, and metagenomic detection of ANME-associated markers-including multiheme cytochromes and formate dehydrogenases-supports temperature-sensitive anaerobic oxidation of methane as a significant control on isotopic signatures. Calculated Q10 values for methanogenesis exceeded typical values for boreal soils, highlighting an underappreciated temperature responsiveness of Arctic methanogens. Together, these results demonstrate that VOCs can serve as informative biomarkers of subsurface microbial activation and offer a novel diagnostic tool for detecting early-stage CH4 hotspot formation. Incorporating such chemically and biologically resolved metrics into process-based models will be critical for improving forecasts of CH4 release from thawing permafrost landscapes.}, }
@article {pmid41140397, year = {2025}, author = {Mudoor Sooresh, M and Jayawickrama, A and Silva, A and Nguyen, S and Schmidt, S and Sebastian, J and Carey, S and Harynuk, J and Willing, BP and Bourrie, BCT}, title = {Fermentation of kefir with traditional freeze-dried starter cultures successfully recreates fresh culture fermented kefir.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1655390}, pmid = {41140397}, issn = {1664-302X}, abstract = {INTRODUCTION: Interest in fermented foods and their purported health benefits has led to increased scientific research investigating the development of starter cultures which maintain the characteristics of traditional products while allowing for industrial scale production. One such fermented food that is gaining steady attention for industrial production is kefir. To improve the ease of use and maintenance of starter cultures without compromising desirable fermentation characteristics and potential health benefits, this study investigated the impact of freeze-drying a previously described reconstituted kefir consortia with two lyoprotectants trehalose and milk.<br><br>METHODS: 5 bacterial species (Lentilactobacillus kefiri, Lactobacillus kefiranofaciens, Lactococcus cremoris, Leuconostoc mesenteroides, and Acetobacter pasteurianus) and 4 yeast species (Saccharomyces cerevisiae, Pichia fermentans, Monosporozyma unispora, and Kluyveromyces marxianus) underwent freeze-drying prior to viability testing and use as starter cultures in kefir fermentations. Completed kefir fermentations were analyzed for pH, microbial composition, volatile compounds, organic acids, and sugar consumption. Freeze-dried starter culture fermentations were compared to kefir made with fresh starter cultures of the same species and pitching rate.<br><br>RESULTS: All starter cultures were able to ferment milk to a similar pH, however the freeze-dried cultures prepared with milk took a longer time to complete fermentation. The total bacterial and yeast counts were comparable across the fermentations performed as was the composition of bacteria and yeast present as determined by shotgun metagenomic sequencing. High performance liquid chromatography (HPLC) analysis showed no difference in the levels of lactic acid, acetic acid, ethanol, glucose, and galactose. Additionally, solid-phase microextraction followed by two-dimensional gas chromatography-time-of-flight mass spectrometry (SPME-GC &#xd7; GC-TOFMS) showed that kefir fermented with freeze-dried starter cultures did not change the volatile profile compared to fresh cultures.<br><br>CONCLUSION: These findings indicate that freeze-dried starter cultures consisting of traditional kefir microorganisms are able to recreate the fresh starter culture version of this product. This provides encouraging evidence for the development of commercially viable starter cultures that are capable of recreating traditional functional fermented foods.}, }
@article {pmid41140395, year = {2025}, author = {Li, G and Lao, J and Jiang, Y and Tang, P and Huang, H and He, L and Yuan, K and Lai, X}, title = {Exploring drug resistance genes in Acinetobacter baumannii using metagenomic next-generation sequencing.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1669208}, pmid = {41140395}, issn = {1664-302X}, abstract = {INTRODUCTION: With the rising incidence of infectious diseases, the overuse of antibiotics has become a serious problem in clinical practice. In recent years, metagenomic next-generation sequencing (mNGS) has emerged as a promising alternative, offering advantages such as rapid turnaround, broad-spectrum detection, and comprehensive coverage. However, its clinical utility for antimicrobial resistance testing remains to be fully established.<br><br>METHODS: In this study, we evaluated the effectiveness of mNGS in detecting antimicrobial resistance in Acinetobacter baumannii using 53 clinical samples. The performance of mNGS was compared with conventional culture-based methods. In addition, clinical judgment of drug resistance was used as a reference to assess concordance between sequencing results and patient treatment.<br><br>RESULTS: Metagenomic sequencing produced an average of 8.4 &#xd7; 10&#x2077; reads per sample and identified 61 resistance loci-20 of which appeared in at least five isolates. Among the A. baumannii-positive samples, class-specific accuracy of mNGS exceeded 80% for &#x3b2;-lactams, aminoglycosides, quinolones, and minocycline, underscoring its strong performance in comprehensive resistome profiling. We further investigated resistance-associated genes in A. baumannii that appeared with high frequency, including enzymatic inactivation mechanisms (ADC-type cephalosporinases and OXA-type oxacillinases), efflux systems (AbaQ, AbeM), and RND-type efflux pumps (adeIJK/adeN and adeFGH/adeL).<br><br>DISCUSSION: Our findings demonstrate a high concordance between mNGS results, culture-based methods, and clinical evaluations, highlighting the potential of mNGS as a reliable tool for assessing antimicrobial resistance in A. baumannii.}, }
@article {pmid41140172, year = {2025}, author = {Negri, T and Vitale, GA and Adamek, M and Bağcı, C and Hegemann, JD and Petras, D and Hughes, CC and Ziemert, N}, title = {Discovery and Heterologous Expression of the Soil Metagenome-Derived Lasso Peptide Metanodin with an Unprecedented Ring Structure.}, journal = {Journal of natural products}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jnatprod.5c00970}, pmid = {41140172}, issn = {1520-6025}, abstract = {Culture-independent metagenomic approaches have proven to be effective tools for identifying previously hidden biosynthetic gene clusters (BGCs) encoding novel natural products with potential medical relevance. However, producing these compounds remains challenging as metagenomic BGCs often originate from organisms phylogenetically distant from available heterologous hosts. Lasso peptides, a subclass of ribosomally synthesized and post-translationally modified peptide (RiPP) natural products, exhibit diverse bioactivities, yet no lasso peptide has previously been discovered directly from a metagenome. Here, we report the discovery and heterologous expression of the first soil metagenome-derived lasso peptide. Expression of its biosynthetic gene cluster in Escherichia coli, followed by mass spectrometry analysis, strongly supported the predicted amino acid sequence and lasso structure of the peptide. Notably, this lasso peptide is the first to feature asparagine as the ring-forming residue at position one. Taxonomic analysis of the corresponding BGC identified an uncultivated member of the Steroidobacterales family (Gammaproteobacteria) as the closest known relative of the potential native host. These findings underscore the potential of metagenomic genome mining to reveal structurally novel RiPPs and to expand our understanding of the natural diversity of lasso peptides.}, }
@article {pmid41140047, year = {2025}, author = {Wang, Y and Zhang, B and Han, G and Bartlam, M and Wang, Y}, title = {Chiral Pesticides Stereoselectively Stimulate N2O Emissions: An Overlooked Environmental Risk in Agricultural Soils.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c09622}, pmid = {41140047}, issn = {1520-5851}, abstract = {Agricultural soil is a major source of N2O emissions due to soil denitrification. However, the influence of pesticides, particularly chiral pesticides, on soil denitrification has often been overlooked. In this study, we investigated the effects and regulatory mechanisms of the widely used chiral pesticide cis-epoxiconazole on denitrification and N2O emissions. The 2R, 3S-(+)-cis-epoxiconazole ((+)-EPO) enantiomer reduced nitrate removal efficiency by 15.04%-54.49% after 3 days and increased N2O emissions by 109.27%-163.68% after 35 days of exposure in a microcosm system, whereas the 2S, 3R-(-)-cis-epoxiconazole ((-)-EPO) enantiomer had minimal impact. At a concentration of 0.5 mg/kg, (+)-EPO inhibited β-glucosidase activity by 34.80% and decreased electron transport system activity by 43.70%, thereby impairing electron generation and transfer during denitrification. Expression of the nosZ gene was suppressed by 53.34%, while nitric oxide reductase and nitrous oxide reductase activities were upregulated by 118.89% and downregulated by 46.70%, respectively. These key regulatory changes directly contribute to the increased N2O emissions observed with (+)-EPO treatment. Additionally, although (+)-EPO caused only minor changes in denitrifying microbial taxa, it increased the relative abundance of Nitrososphaerota and Euryarchaeota by 0.08%-0.10% and 0.40%-0.45%, respectively, after 35 days, enhancing nitrification and indirectly stimulating N2O emissions. Overall, this study deepens our understanding of how cis-epoxiconazole disrupts denitrification in agricultural soils through microbial, genetic, electronic, and enzymatic pathways.}, }
@article {pmid41139867, year = {2025}, author = {Cao, X and Yan, Z and Ma, X and Yang, X and Liu, Z and Yang, L and Cui, Z and Xu, L and Jiang, X and Xiao, M}, title = {Discovery of Sialidases with Transglycosylation Activity and Rational Engineering of Their Catalytic Pockets for Efficient Synthesis of 6'-Sialyllactose.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.5c10966}, pmid = {41139867}, issn = {1520-5118}, abstract = {Sialyloligosaccharides are essential components of human milk oligosaccharides. Sialidases with transglycosylation activity have shown great potential for industrial production of sialyloligosaccharides using cheaper glycosyl donors. Herein, five novel sialidases with transglycosylation activity were identified from human gut metagenomic DNA, among which BiS47 synthesized 6'-sialyllactose with the highest yield of 1.32 g/L. Molecular dynamics simulations revealed that BiS47 possessed an open conformation of the catalytic pocket which was then remodeled to narrow, a more favorable near-attack conformation, by site-directed mutagenesis and combinatorial mutations based on the design of entrance loops flexibility and bottom residues side chains. Two mutants G185C and G398H were obtained with 6'-sialyllactose yields increased 2.43-fold and 2.45-fold, respectively. "Property grafting" of G185C and G398H onto other four sialidases improved their transglycosylation activities, and eight mutants generated also exhibited narrowed catalytic pockets. This work provides efficient enzymatic tools for sialyloligosaccharide synthesis and important guidance for rational design of glycosidases.}, }
@article {pmid41139486, year = {2025}, author = {Tran, T and Duong, DV and Le, TD and Bui, XT}, title = {Metagenomic Characterization of Biofilm and Suspended Microbial Communities in a Hybrid Algal Turf Scrubber-Based Wastewater Treatment System.}, journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica}, volume = {133}, number = {10}, pages = {e70072}, doi = {10.1111/apm.70072}, pmid = {41139486}, issn = {1600-0463}, mesh = {*Biofilms/growth &amp; development ; *Wastewater/microbiology ; Metagenomics ; *Water Purification/methods ; Aquaculture ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation &amp; purification ; Drug Resistance, Microbial/genetics ; Animals ; Nitrogen/metabolism ; Metagenome ; }, abstract = {This study investigates a hybrid wastewater treatment system combining a biofilm-based Algal Turf Scrubber (ATS) with a membrane-coupled High Rate Algal Pond (ATS-MHRAP) for shrimp aquaculture effluents. Shotgun metagenomic sequencing was used to compare microbial composition, functional pathways, and antibiotic resistance genes (ARGs) across attached biofilm (ATS1) and suspended biomass (ATS2, HRAP1) under three nutrient loading stages. Biofilm samples (ATS1) exhibited higher microbial richness and evenness, with Shannon index values up to 9.25, compared to 6.93 in suspended cultures. Functional pathways enriched in ATS1 included nitrogen cycling, amino acid metabolism, and terpenoid biosynthesis, with elevated expression of amoA, nirK, and nirS genes under moderate loading. These traits coincided with higher removal efficiency of COD (up to 88.6%), phosphate (82.1%), and total nitrogen (73.4%). ARGs were more diverse in ATS1, with up to 11 resistance classes detected, including β-lactam and sulfonamide genes co-occurring with intI1, indicating possible horizontal gene transfer. The ATS-MHRAP system offers a robust and biologically enriched platform for nature-based aquaculture wastewater treatment. Our findings reveal microbial and functional differentiation between attached and suspended communities, with implications for optimizing dissolved oxygen, nutrient ratios, and retention time.}, }
@article {pmid41139468, year = {2025}, author = {Yang, Q and Kang, KL and Zhao, B and Feng, K and Feng, YS and Ye, J and Deng, Y and Wang, L}, title = {Geographical inference of dust from typical Chinese cities based on metagenomic shotgun sequencing.}, journal = {Yi chuan = Hereditas}, volume = {47}, number = {10}, pages = {1156-1168}, doi = {10.16288/j.yczz.25-009}, pmid = {41139468}, issn = {0253-9772}, mesh = {*Dust/analysis ; *Metagenomics/methods ; China ; Cities ; Bacteria/genetics/classification/isolation &amp; purification ; Archaea/genetics/classification/isolation &amp; purification ; Metagenome ; Shotgun Sequencing ; }, abstract = {Microbial profiles in dust are closely correlated with geographical locations and provide valuable clues for criminal investigation, demonstrating significant potential in forensic use. However, the feasibility of using microbial profiles from metagenomics datasets to infer the geographical locations remains underexplored. In this study, we collect 170 dust samples from resident communities in four cities across northern, eastern, southwestern, and northwestern China. All samples are subjected to shotgun metagenomic sequencing to reveal variations in microbial composition. In total, 41,029 species are annotated, including 93.39% bacteria, 6.37% eukaryotes, 0.21% viruses, and 0.03% archaea. Clear clustering patterns are observed among the four cities (R[2]=0.870, P<0.001). Further filtering of species with detection rates below 10% across all samples strengthens city-level clustering (R[2]=0.948, P<0.001). Additionally, 127 biomarkers are identified using linear discriminant analysis effect size (LEfSe) to distinguish between the cities. Each city harbors a distinct microbial community, with unique species and relatively abundant taxa that contribute to its differentiated microbial profile. All samples are randomly split into training and testing sets in a 7:3 ratio. Five machine learning models including SourceTracker, FEAST, LightGBM, Random Forest and Support Vector Machine are applied to 51 randomly sample data and achieve average accuracies of 88.89%, 92.16%, 98.04%, 99.35% and 69.28%, respectively. These results constitute a microbial genetic map of four cities in China that highlights distinct microbial taxonomic signatures and provides an approach for city-scale source tracking of dust samples.}, }
@article {pmid41139156, year = {2025}, author = {Habot-Wilner, Z and Ostrovsky, M and Zur, D and Schwartz, S and Hagin, D and Gadoth, A and Ben-Ami, R and Paran, Y and Goldshmidt, H and Slutzkin, M and Adler, A and Levytskyi, K}, title = {Metagenomic next-generation sequencing: a game-changer in the diagnosis of unique intraocular infections.}, journal = {Eye (London, England)}, volume = {}, number = {}, pages = {}, pmid = {41139156}, issn = {1476-5454}, abstract = {OBJECTIVE: To thoroughly describe unique intraocular infections diagnosed by metagenomic next-generation sequencing (mNGS).<br><br>METHODS: A retrospective case series of patients presenting with challenging atypical intraocular infections at Tel Aviv Sourasky Medical Center during 2024. Clinical and demographic data, as well as mNGS results were extracted from patient records. mNGS was performed on the Illumina NextSeq500 platform using a custom bioinformatics pipeline. The following parameters were examined: Reads Per Million, Reads Per Million-ratio to negative control and E-index (K-mers*coverage/reads).<br><br>RESULTS: The study included three patients with novel presentations of intraocular infections, manifesting with atypical clinical manifestations and negative routine diagnostic workups. mNGS allowed the identification of Cytomegalovirus in a 43-year-old male with a history of autosomal dominant hyper-IgE syndrome, Bartonella henselae infection manifesting with photoreceptoritis, retinal vasculitis and global retinal dysfunction in a healthy 28-year-old female, and polymicrobial endophthalmitis with Rothia mucilaginosa and Pantoea agglomerans following intravitreal faricimab injection for neovascular age-related macular degeneration in an 81-year-old male. Treatment regimens were adjusted based on mNGS results.<br><br>CONCLUSIONS: Metagenomic next-generation sequencing has an important role in the diagnosis of challenging intraocular infections. It enables comprehensive pathogen identification and enhances the precision of treatment strategies.}, }
@article {pmid41139029, year = {2025}, author = {Guo, Z and Li, YG and Liu, XL and Teng, ZJ and Qin, QL and Cha, QQ and Wang, ZB and Ni, SQ}, title = {Bulk metagenomics and machine learning unravels nitrogen metabolism patterns in extreme-temperature marine environments.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {133551}, doi = {10.1016/j.biortech.2025.133551}, pmid = {41139029}, issn = {1873-2976}, abstract = {The nitrogen metabolism genes and associated microorganisms in polar oceans and hydrothermal vents remain insufficiently studied. In this study, metagenomic data were analyzed to characterize the geographical and biological features of 16 key nitrogen-cycling genes. NasA/B, narG, and nxrB were consistently abundant in both environments. Polar oceans were dominated by common nitrogen-cycling taxa, whereas hydrothermal vents hosted species linked to sulfur and methane metabolism. Environmental extremes exerted a stronger influence on nitrogen cycling than depth. Distinct co-occurrence networks (centralized vs. redundant) and accurate habitat classification (>95 %) highlighted strong environmental shaping. Differences in amino acid preferences and enzyme thermal stability reflected evolutionary divergence and adaptation to extreme temperatures. Overall, depth and environmental conditions structured community networks, while genetic variation supported ecological adaptation. These findings reveal contrasting nitrogen-cycling strategies and adaptations, with potential implications for biotechnological applications.}, }
@article {pmid41138869, year = {2025}, author = {Bamigbade, GB and Subhash, A and Jarusheh, H and Liu, SQ and Palmisano, G and Ayyash, M}, title = {Selenium nanoparticles stabilized by date pulp polysaccharides: Bioactivities, gut microbiota modulation and short chain fatty acids production.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {148387}, doi = {10.1016/j.ijbiomac.2025.148387}, pmid = {41138869}, issn = {1879-0003}, abstract = {Natural polysaccharides confer various physiological functions, including prebiotic qualities, modulation of gut microbiota, and regulation of gut health. This study investigated the green synthesis and characterization of bioactive selenium nanoparticles synthesized from complexation of date pulp residues polysaccharides and sodium selenite (UP-SeNPs). UP-SeNPs were evaluated for in vitro bioactivities, digestion, prebiotic properties, and gut microbiota modulation. Structural analysis indicated UP-SeNPs were crystalline, spherical, evenly distributed (size 91.1 ± 2.34 nm, polydispersity index 0.071, zeta potential -25.24 mV). Compared to controls, UP-SeNPs showed significant dose-dependent radical scavenging activities: 66.8 ± 10.49 % (DPPH), 82.8 ± 1.92 % (ABTS), 495.2 ± 8.94 μg/mL (FRAP), and 981.8 ± 9.09 μg/mL (TAC) at 100 mg/L. Inhibition rates of 82.54 %, 52.97 %, and 39.84 % against α-amylase, α-glucosidase, and ACE, respectively, were noted at 100 mg/L. UP-SeNPs (50 mg/L) showed antiproliferative activities of 34.72 % against Caco-2 and 15.16 % against MCF-7. At 100 mg/L, UP-SeNPs exhibited antibacterial properties against four foodborne pathogens. UP-SeNPs supported the proliferation of standard probiotic strains, evidenced by the high Vmax, reduced lag, and extended exponential phases. Metagenomic analysis indicated that Bifidobacterium adolescentis and other species were abundant. In contrast, metabolomic analysis confirmed pathways for the synthesis of short-chain fatty acids (SCFAs), lipids, carbohydrates, amino acids, and vitamins. These findings may offer a basis for the nanobiotechnological and nanomedical applications of UP-SeNPs.}, }
@article {pmid41138860, year = {2025}, author = {Mishra, S and Vadakkethil, AA and Iquebal, MA and Jaiswal, S and Kumar, D and Singh, BP and Ajlouni, S and Ranadheera, CS and Chakkaravarthi, S}, title = {Deciphering microbial diversity and predicting metabolic functionalities in fermented pigmented rice water using culture-independent characterization.}, journal = {Journal of microbiological methods}, volume = {}, number = {}, pages = {107295}, doi = {10.1016/j.mimet.2025.107295}, pmid = {41138860}, issn = {1872-8359}, abstract = {Fermented rice water is gaining importance lately due to its traditional food culture and potential beneficial effects. Flavored fermented rice water (FFRW) produced from pigmented rice varieties, viz., black, brown, and red, is shown to have rich nutritional and functional profiles. However, the microbiota in this spontaneously fermented beverage is scantly known. Hence, this study aimed to explore the total bacterial and fungal diversity using 16S rRNA and Internal Transcribed Spacer (ITS) sequencing, respectively, along with the phytochemicals and their metabolites produced/utilized during storage. The bacterial diversity showed significant differences (p < 0.05) in black FFRW while depicting stability for brown- and red-FFRW on the 0th day and 30th day of refrigerated storage. Lactic acid bacteria (LAB) like Weissella were abundantly recorded; similarly, fungal diversity showed dominance of various yeasts. Predictive functional/metabolic pathways suggested 23 pathways of which the predominant were metabolism amino acids like branched-chain amino acids (BCAAs) viz., leucine, valine, and isoleucine, aromatic amino acids such as tryptophan, and metabolites of glycan biosynthesis, polyphenols, lipids, cofactors and vitamins. KEGG pathways revealed a shift in microbial metabolism from amino acid degradation pathways dominating on day 0 to carbohydrate and fatty acid metabolism by day 30. Enzymes like lactate dehydrogenase showed increased abundance by the 30th day, particularly in red and black-FFRW. The untargeted profiling showed that brown FFRW had more polyphenol-related compounds, followed by black and red FFRW. Decrements in the compounds were detected on the 30th day of storage compared to the 0th day. The findings provide insights into the microbial diversity, metabolic potential, and phytochemical composition of FFRW, supporting its potential as a functional beverage.}, }
@article {pmid41138814, year = {2025}, author = {Matsumoto, A and Yoshimura, Y and Wakabayashi, H and Nagano, F and Shimazu, S and Kido, Y and Shiraishi, A and Hamada, T and Yoneda, K and Maeda, K}, title = {Polypharmacy is associated with altered gut microbiota diversity in older post-stroke inpatients.}, journal = {Clinical nutrition ESPEN}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.clnesp.2025.10.015}, pmid = {41138814}, issn = {2405-4577}, abstract = {RATIONALE: Gut microbiota diversity plays a crucial role in various health outcomes, including metabolic regulation and nutritional status. Polypharmacy, common among older adults, has been linked to adverse clinical outcomes, yet its impact on gut microbiota diversity remains poorly understood. This study aimed to investigate the association between polypharmacy and gut microbiota diversity in older post-stroke patients.<br><br>METHODS: This cross-sectional study included post-stroke inpatients aged 65 years or older undergoing rehabilitation. Polypharmacy was defined as the prescription of five or more drugs. Metagenomic analysis of DNA from patient fecal samples was conducted, calculating three alpha diversity indices: the Shannon Diversity Index, Operational Taxonomic Unit (OTU) richness, and Faith's Phylogenetic Diversity (PD). Multiple linear regression analysis was used to determine whether polypharmacy was independently associated with the gut microbiota diversity upon admission, adjusting for potential confounders.<br><br>RESULTS: A total of 156 patients (mean age 78.4 years; 55.8% male) were analyzed. The median number of medications taken on admission was 6 (4-8), and 69.9% of patients had polypharmacy. Polypharmacy was independently associated with decreased Shannon Diversity Index (&#x3b2; = -0.202, p = 0.019). No statistically significant association was found with Observed OTUs (&#x3b2; = -0.159, p = 0.067) and Faith's PD (&#x3b2; = -0.38, p = 0.111).<br><br>CONCLUSIONS: Polypharmacy is associated with qualitative alterations in the gut microbiota of older post-stroke patients, with a potential negative trend in quantitative alterations and phylogenetic classification. The findings underscore the need to consider the impact of polypharmacy on the gut microbiome in stroke management.}, }
@article {pmid41138407, year = {2025}, author = {Zhao, Q and Zhao, Y and Liu, W and Wang, J and Xie, H and Wu, H and Hu, Z}, title = {Nitrogen-transforming bacteria as key hosts and disseminators of antibiotic resistance genes in constructed wetlands: Metagenomic and metatranscriptomic evidence.}, journal = {Journal of hazardous materials}, volume = {499}, number = {}, pages = {140220}, doi = {10.1016/j.jhazmat.2025.140220}, pmid = {41138407}, issn = {1873-3336}, abstract = {Given global concerns over antibiotic resistance genes (ARGs), constructed wetlands (CWs) have emerged as a cost-effective strategy to remove nitrogen (N) and mitigate ARG-related ecological risks. The occurrence and dissemination of ARGs are mainly driven by microorganisms. Although nitrogen transformation is a key process in CWs, the relationship between nitrogen-transforming bacteria (NTB) and ARG dynamics remains unclear. In this study, metagenomic and metatranscriptomic analyses were employed to comprehensively examine the associations between N transformation and the abundance, hosts, and ecological risks of ARGs in full-scale CWs. NTB, particularly dissimilatory nitrate reducers and bacteria involved in N organic degradation and synthesis, were identified as the primary hosts of ARGs. Furthermore, CWs substantially reduced ARG-related ecological risks, achieving decreases of 79.5 % in ARG expression, 94.9 % in mobile genetic elements, and 88.0 % in antibiotic-resistant pathogens, and identified NTB as key contributors to these risks. Both the decline in NTB abundance and adaptive fitness costs were identified as key mechanisms driving ARG reduction and mitigating ecological risk. This study highlights the critical role of N transformation in shaping ARG dynamics from a microbial perspective, providing a theoretical foundation for engineering practice in the co-control of ARGs and nitrogen removal in CWs.}, }
@article {pmid41138387, year = {2025}, author = {Ochoa-Bernal, TG and Huber, DH and Espinosa-Solares, T}, title = {The progressive shift in anaerobic digestion communities under extreme propionate levels led to a redundant microbiome capable of producing methane.}, journal = {Journal of environmental management}, volume = {395}, number = {}, pages = {127698}, doi = {10.1016/j.jenvman.2025.127698}, pmid = {41138387}, issn = {1095-8630}, abstract = {Propionate accumulation exerts a significant inhibitory effect on anaerobic digestion, which may result in the cessation of methane production. It has been reported that propionate can be degraded solely by a limited group of syntrophic propionate-oxidizing bacteria belonging to the following genera: Syntrophobacter, Smithella, and Pelotomaculum. Chicken litter is a substrate rich in protein and nitrogen, which makes it more susceptible by total ammonia nitrogen toxicity. This study aimed to elucidate the alterations and responses of microbial communities to extreme concentrations of propionate in co-digestion with chicken litter, thereby providing an extensive overview of community composition and functional potential through shotgun metagenomics sequencing. An enrichment process was conducted over 1220 days in co-digestion with chicken litter, utilizing a 10 L digester operating in semi-continuous mode and progressively increasing sodium propionate concentrations to create a selection pressure. The feed had 12 propionate concentration levels, varying from 0 to 24 g L[-1]; chicken litter was kept at 3 %. At the end of the enrichment process, it was surprisingly observed that the well known syntrophic bacteria were not present; instead, bacteria from the Proteiniphilum, Petrimonas, Vibrio, Corynebacterium, Coprobacter, Brachymacterium, Cloacimonas, and Treponema genera were found. Propionate degradation was mainly attributed to Corynebacterium stationis and Corynebacterium casei, through the ackA and pta enzymes. The putative lactate pathway was also detected by the pct enzyme. Methanogenic archaea increased relative abundance, particularly the genera Methanoculleus, Methanospirillum, Methanococcus, and Methanocella, synthesizing methane in several pathways, mainly hydrogenotrophic in the range from 0.189 to 0.320 mL CH4 kgvsadded[-1]. The enrichment using extreme propionate concentrations in co-digestion with chicken litter resulted in a microbial consortium that stabilized propionate degradation and methane production, which can be attributed to an adaptive functional redundancy.}, }
@article {pmid41138382, year = {2025}, author = {Chen, C and Zhang, L and Tong, C and Ding, B and Li, A and Ji, B}, title = {Intermittent nighttime lighting enhances microalgal-bacterial granular sludge in synthetic wastewater treatment.}, journal = {Journal of environmental management}, volume = {395}, number = {}, pages = {127689}, doi = {10.1016/j.jenvman.2025.127689}, pmid = {41138382}, issn = {1095-8630}, abstract = {The microalgal-bacterial granular sludge (MBGS) system is a promising technology due to its low energy demand and high treatment efficiency under illumination. However, its performance declines at night owing to the absence of light, reducing dissolved oxygen and microbial activity. This study proposes and evaluates an intermittent nighttime lighting strategy (12 h-light/3 h-dark/6 h-light/3 h-dark using LEDs) to enhance MBGS performance for treating synthetic wastewater. Supplemental lighting improved removal efficiencies of chemical oxygen demand, ammonia nitrogen, and phosphate by 7.5 %, 27.7 %, and 27.1 %, respectively. Metagenomic analysis revealed an increased genetic potential for pollutant degradation, evidenced by a higher abundance of genes involved in key metabolic pathways (e.g., GLU, ppa). Microbial community structure shifted, with increased abundances of Cyanobacteria and Verrucomicrobia and a decreased abundance of Proteobacteria. Genetic potential analysis suggested enhanced nitrogen assimilation, ATP cycling, and glycogen synthesis, alongside reduced lactate metabolism, indicating a shift toward aerobic pathways. These results demonstrate that intermittent nighttime lighting enables sustainable round-the-clock wastewater treatment.}, }
@article {pmid41138328, year = {2025}, author = {Bai, X and Bi, J and Li, A and Deng, X and Zhao, Z and Hu, H and Pan, H}, title = {Walnut cake meal improves amino acids, fatty acid composition and flavor of egg yolk via the microbiota-yolk metabolites crosstalk in Jingfen-1 laying hens.}, journal = {Poultry science}, volume = {104}, number = {12}, pages = {105981}, doi = {10.1016/j.psj.2025.105981}, pmid = {41138328}, issn = {1525-3171}, abstract = {Egg production is important for both human nutrition and its economic contribution. However, regions with a shortage of soybean meal (SM) may not meet the nutritional needs of the laying hen industry. Walnut cake meal (WM), a by-product of walnut processing, can be reused in laying hen production. In this study, we evaluated the feasibility of using WM to reduce the demand for SM in the laying hen industry. A total of 144 47-week laying hens (with similar performance) were randomly assigned to two groups (12 hens in each replicate and six replicates for each group). One group was fed a maize-SM diet (SM group), and the other was fad a maize-WM diet (WM group). The diets of both groups had similar crude protein and ME contents. After replacing SM with WM, the laying rate, egg weight, and feed efficiency did not significantly change (P > 0.05). WM increased (P < 0.05) the polyunsaturated fatty acids content, particularly linoleic acid, as well as umami and essential amino acids, in the eggs. WM diet also enhanced the flavor of eggs by enriching multiple volatile organic compounds that smell of sweet and herb-like foods. In addition, probiotic bacteria such as Cyanobacteriota and Prevotella, were enriched in the cecal microbiota of laying hens fed WM. Moreover, targeted metabolomics revealed the enrichment of butyric acid, 4-methylvaleric acid, isoleucine, and valine in the cecal digesta of laying hens fed with WM. Metagenomic sequencing revealed genes in the cecal microbiota associated with the synthesis of these enriched metabolites. Increased isoleucine and 4-methylvaleric acid in the digestive system contributed to the enrichment of fatty acids and amino acids in the yolks, whereas elevated flavor substances in the yolk could be associated with more amino acids in the intestine of laying hens. In conclusion, WM can reduce the need for soybean meal, improve cecal metabolism and egg quality, and ultimately achieve sustainable agriculture.}, }
@article {pmid41138271, year = {2025}, author = {Mishra, R and Singh, R and Goel, R and Hasmi, RR and Malik, M and Gaur, PK and Lata, K}, title = {Biologically Active Molecules from Marine Brown Algae: A Review of Their Potential and Applications.}, journal = {Chemistry &amp; biodiversity}, volume = {}, number = {}, pages = {e01813}, doi = {10.1002/cbdv.202501813}, pmid = {41138271}, issn = {1612-1880}, abstract = {The highly bioactive secondary metabolites present in marine flora may prove to be abundant sources for producing innovative pharmaceuticals. Numerous brown algae species are being researched extensively because of their commercial relevance in nutraceuticals and medication discovery. The difficult environments that these creatures live in aid in the synthesis of special and powerful bioactive substances such as fucoidans, polysaccharides, hentriacontane, sterols like fucosterol, 24-ketocholesterol, and so forth. Despite its promising characteristics, additional in vivo studies are needed to validate algae's efficacy in a variety of applications. Effective extraction techniques must also be known to inexpensively isolate these chemicals, permit industrial application, and facilitate large-scale manufacturing. A comprehensive study of the genomes, metagenomics, transcriptomics metagenomics, transcriptomics, and metabolomics of marine algae is also necessary to elaborate on the underlying genetic and metabolic pathways involved in the manufacture of algal chemicals; these topics are covered in detail in this review. Brown algae are a major source of numerous secondary metabolites as evidenced by their phytoconstituents. This review elucidates the bioactive substance found in marine brown algae and their major pharmacological role so as to pave the way for maximum utilization of these underused resources.}, }
@article {pmid41138185, year = {2025}, author = {Waschina, S and Pagel, J and Seeger, K and Pasderski, E and Rühlemann, M and Froitzheim, S and Künzel, S and Sommer, F and Franzenburg, S and Fortmann, I and Sugihara, F and Faust, K and Marissen, J and Demmert, M and Baines, JF and Göpel, W and Herting, E and Kaleta, C and Rupp, J and Härtel, C}, title = {Bacterial metabolite patterns of infants receiving multi-strain probiotics and risk of late-onset sepsis.}, journal = {Cell reports}, volume = {44}, number = {11}, pages = {116431}, doi = {10.1016/j.celrep.2025.116431}, pmid = {41138185}, issn = {2211-1247}, abstract = {The effect of multi-strain probiotics containing Bifidobacterium longum (B. longum) on late-onset sepsis (LOS) risk in very-low-birth-weight infants (VLBWIs; birth weight < 1,500 g) remains uncertain. In a single-center study, we analyzed intestinal metagenome and metabolome data in VLBWIs during the period of highest vulnerability of LOS. Using a unit's policy change to routinely administer B. longum subspecies infantis plus Lactobacillus acidophilus as natural experiment, we compared 97 infants (including 38 LOS cases) after change with 78 infants (including 32 LOS cases) before. Probiotic supplementation was associated with more beneficial bacteria and reduced abundance of nosocomial pathobionts, such as Klebsiella spp. Infants in the probiotic group had significantly lower concentrations of B. longum fermentation products prior to sepsis diagnosis than matched non-LOS cases (acetate: padj = 0.0049; lactate: padj = 0.048). Modulation of the gut metabolic milieu is an interesting target for LOS prevention.}, }
@article {pmid41138182, year = {2025}, author = {Gao, SM and Lan, LY and Yang, L and Chen, T and Fan, PF}, title = {Health-associated key gut microbiota drives the variation in community metabolic interactions in non-human primates.}, journal = {Cell reports}, volume = {44}, number = {11}, pages = {116477}, doi = {10.1016/j.celrep.2025.116477}, pmid = {41138182}, issn = {2211-1247}, abstract = {Gut microbiota often undergo metabolic cross-feeding and resource competition. However, our understanding of global variations in these interactions and their implications for host health remain elusive. By analyzing a microbial genome catalog from 841 fecal metagenomes across 53 primate species worldwide, we identified key microbiota assigned to two taxa, i.e., Bacillota_A and Pseudomonadota, which well predicted the trade-off of community-level interaction types between metabolic competition and cooperation. Specifically, Bacillota_A species were inherently competitive and amino acid auxotrophic and typically found in anaerobic habitats. In contrast, members of Pseudomonadota were inherently cooperative, siderophore producers, and more abundant in aerobic conditions. Random forest models successfully distinguished unhealthy gut samples from healthy samples through the key competitive and cooperative microbiota, suggesting potential links between community metabolic interactions and host health. Together, this study enhances our mechanistic understanding of microbial interaction dynamism within complex gut ecosystems, offering new targets for understanding host health.}, }
@article {pmid41138002, year = {2025}, author = {Yarahmadi, A and Emrahoglu, S and Afkhami, H and Mehdipour, A and Aghaali, M}, title = {Integrative insights into the oral microbiome's role in systemic diseases: novel therapeutic strategies and future directions.}, journal = {Antonie van Leeuwenhoek}, volume = {118}, number = {12}, pages = {178}, pmid = {41138002}, issn = {1572-9699}, mesh = {Humans ; *Microbiota ; *Mouth/microbiology ; Periodontal Diseases/microbiology/therapy ; Dental Caries/microbiology/therapy ; Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The oral microbiome, which is known as the diverse and abundant microbial community within the human oral cavity, is an integral part of the human body. The investigation of its composition and functions in both wellness and illness has received notable attention from researchers in recent times. The presence of oral bacteria directly impacts the disease condition of dental caries and periodontal diseases. The oral microbiota interacts dynamically with the host to influence immune regulation and metabolic processes. Advances in sequencing technologies, including whole-metagenome shotgun sequencing, the examination of 16S ribosomal RNA, and meta-transcriptomes, we now possess the capability to comprehensively explore the diversity and functionalities of oral microorganisms, encompassing those that are not amenable to cultivation. As research advances, there is a growing body of evidence suggesting the notable contribution of the oral microbiome to various health conditions, extending beyond ailments solely associated with the oral cavity. This review advances current understanding by presenting a systemic, integrative perspective on the oral microbiome's role in chronic diseases, offering novel hypotheses and therapeutic directions beyond those explored in prior literature.}, }
@article {pmid41137523, year = {2025}, author = {Tegegne, HA and Savidge, TC}, title = {Gut microbiome metagenomics in clinical practice: bridging the gap between research and precision medicine.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2569739}, doi = {10.1080/19490976.2025.2569739}, pmid = {41137523}, issn = {1949-0984}, mesh = {Humans ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; *Precision Medicine/methods ; }, abstract = {Gut microbiome metagenomics is emerging as a cornerstone of precision medicine, offering exceptional opportunities for improved diagnostics, risk stratification, and therapeutic development. Advances in high-throughput sequencing have uncovered robust microbial signatures linked to infectious, inflammatory, metabolic, and neoplastic diseases. Clinical applications now include pathogen detection, antimicrobial resistance profiling, microbiota-based therapies, and enterotype-guided patient stratification. However, translation into routine care is hindered by significant barriers including methodological variability, limited functional annotation, lack of bioinformatics standardization, and underrepresentation of global populations. This review synthesizes current translational strategies, emphasizing the need for hypothesis-driven designs, multi-omic integration, longitudinal and multi-center cohorts, and mechanistic validation. We also examine critical ethical, regulatory, and equity considerations shaping the clinical landscape. Realizing the full potential of microbiome-informed care will require globally harmonized standards, cross-sector collaboration, and inclusive frameworks that ensure scientific rigor and equitable benefit.}, }
@article {pmid41137517, year = {2025}, author = {Bayne, J and Charavaryamath, C and Hu, Y and Yousefi, F and Murphy, M and Law, A and Michael, A and Muyyarikkandy, MS and Nibbering, B and Smits, WK and Kuijper, E and Opriessnig, T and Sauer, M and Scaria, J and Sponseller, B and Ramirez, A and Mooyottu, S}, title = {The swine IsoLoop model of the gut host-microbiota interface enables intra-animal treatment comparisons to advance 3R principles.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2568706}, doi = {10.1080/19490976.2025.2568706}, pmid = {41137517}, issn = {1949-0984}, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Swine ; Ileum/microbiology/surgery ; *Host Microbial Interactions ; Humans ; Feces/microbiology ; Clostridioides difficile/physiology ; Fecal Microbiota Transplantation ; Bacteria/classification/genetics/isolation &amp; purification ; Models, Animal ; Disease Models, Animal ; }, abstract = {Understanding gut-host microbiota interactions requires models that replicate human physiology while providing region-specific resolution, translational precision, and minimal animal use. To this end, we developed the IsoLoop model, a swine gut loop platform enabling intra-animal, multi-treatment comparisons. Microbiota-depleted ileal loops were surgically created in pigs, maintaining neurovascular integrity while isolating them from the anastomosed digestive tract. In Experiment 1, loops were inoculated with human fecal microbiota (HFM) or HFM combined with Peptacetobacter hiranonis. In Experiment 2, they were inoculated with Clostridioides difficile. Host-microbiota interactions were compared with respective controls in each experiment. The IsoLoop model reduced animal use by 75% compared to conventional whole-animal designs. Following antibiotic-induced depletion, loops re-established microbial diversity by day 5, despite reduced richness and loss of taxa, including Lactobacillus. HFM transplantation in microbiota-depleted loops induced robust transcriptomic recovery, enriched Akkermansia and Bifidobacterium, and restored specific metabolic pathways, although taxonomic and metabolic restoration remained incomplete and divergent. P. hiranonis promoted normal ileum-like metagenomic functional convergence, activated epithelial repair pathways, and increased specific secondary bile acids. C. difficile challenge recapitulated early infection pathology in IsoLoops. The IsoLoop model offers an ethical and precise platform for investigating host-microbiota crosstalk, localized enteric pathologies, and therapeutic interventions.}, }
@article {pmid41137451, year = {2025}, author = {Liu, Y and Wu, X and Wegner, CE and Ma, K and Xu, G and Cui, Z and Zhang, F and Liesack, W and Peng, J}, title = {Temperature Increase in Paddy Soils Remodels the Relationship Between the Anaerobic Food Web and the Q10 of CH4 Production.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {e70156}, doi = {10.1111/mec.70156}, pmid = {41137451}, issn = {1365-294X}, support = {2021YFD1900100//National Key Research and Development Program of China/ ; 42277307 and 41977038//National Natural Science Foundation of China/ ; }, abstract = {Rice paddies are a major source of anthropogenic CH4 emissions globally, with the temperature sensitivity (Q10) of CH4 production playing a key role in forecasting emissions under future climate scenarios. However, the mechanistic links among Q10, the soil microbiome and mean annual temperature (MAT) in paddy soils remain poorly understood. To address this gap, we employed quantitative PCR, amplicon sequencing, genome-resolved metagenomics and metatranscriptomics to investigate CH4 production dynamics and the response of the methanogenic food web to warming in low MAT (LMAT, 4°C-9°C) and high MAT (HMAT, 14°C-16°C) soils. Our results indicate that CH4 production exhibits a higher Q10 in LMAT soils, while warming exerts a more pronounced impact on the methanogenic food web in HMAT soils. Notably, we identified negative correlations between the Q10 and the metagenomic abundance of genes encoding glycoside hydrolases, carbohydrate-binding modules, polysaccharide lyases-related carbohydrate-active enzymes (CAZymes), hydrogenotrophic methanogenesis, and the average genome size (AGS) of the microbiome. Conversely, genes encoding auxiliary activity CAZymes and those associated with acetate metabolism and fermentation were positively correlated with Q10. Genes linked to acetoclastic and hydrogenotrophic methanogenesis exhibited lower responsiveness to warming in LMAT soils compared to HMAT soils. Additionally, warming led to a significant reduction in both gene and transcript abundances associated with methylotrophic methanogenesis across both MAT regimes. These findings provide novel insights into the temperature-dependent restructuring of methanogenic pathways and resource utilisation strategies in paddy soils, with important implications for predicting CH4 emissions under climate change.}, }
@article {pmid41137177, year = {2025}, author = {Correa, F and Luise, D and Palladino, G and Estellé, J and Turroni, S and Scicchitano, D and Babbi, G and Rampelli, S and Candela, M and Martelli, PL and Stefanelli, C and Perez-Calvo, E and Trevisi, P}, title = {Early antimicrobial regimen shapes gut microbiota and health trajectories in pigs: a longitudinal study from weaning to finishing.}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {110}, pmid = {41137177}, issn = {2524-4671}, support = {818290//Horizon 2020 Framework Programme/ ; }, }
@article {pmid41137068, year = {2025}, author = {Asin, ICA and Egana, JMC and Paul, RE and Bautista, MAM}, title = {Virome sequencing and analysis of Aedes aegypti and Aedes albopictus from ecologically different sites in the Philippines.}, journal = {Parasites &amp; vectors}, volume = {18}, number = {1}, pages = {426}, pmid = {41137068}, issn = {1756-3305}, mesh = {Animals ; *Aedes/virology ; Philippines ; *Virome/genetics ; *Mosquito Vectors/virology ; Metagenomics ; Phylogeny ; *Insect Viruses/genetics/classification/isolation &amp; purification ; }, abstract = {BACKGROUND: Aedes aegypti and Aedes albopictus are important vectors of arthropod-borne viruses (arboviruses) such as dengue, chikungunya, and Zika. Changes in land use have long been considered a factor in the emergence of infectious diseases; thus, it is imperative to look at how the diversity of viruses is also affected by land use.<br><br>METHODS: Viral metagenomics was used to determine the virome compositions of 260 Ae. aegypti and 75 Ae. albopictus collected from the three study sites in Los Ba&#xf1;os, Laguna, Philippines, that differ in topography and land use transformations.<br><br>RESULTS: The virome of Ae. aegypti and Ae. albopictus revealed virus sequences belonging to 12 different taxon groups, dominated by insect-specific viruses (ISVs) such as Phasi Charoen-like phasivirus (PCLV), Humaita Tubiacanga virus (HTV), and Wenzhou sobemo-like virus 4 (WSLV4). Both species were found to share the majority of identified viruses. Moreover, a relatively higher number of viral families were observed in sites that had undergone transformation from agriculture to bare and built-up areas, compared with a forest site.<br><br>CONCLUSIONS: The findings of this study underscore the vast diversity of Ae. aegypti and Ae. albopictus viruses from the selected sites in the Philippines generated by viromics. Results also impact the understanding that land use may contribute to virus diversity. The prevalence of ISVs and nondetection of arboviruses in the virome composition of Ae. aegypti and Ae. albopictus were notable, suggesting further examination of the roles of ISVs in arbovirus transmission.}, }
@article {pmid41136898, year = {2025}, author = {Junier, T and Palmieri, F and Ubags, ND and Trompette, A and Koutsokera, A and Junier, P and Pagni, M and Neuenschwander, S}, title = {Prevalence of oxalotrophy in the human microbiome.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {954}, pmid = {41136898}, issn = {1471-2164}, support = {40B2-0_194701//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; GRS-064/18//Gebert R&#xfc;f Stiftung/ ; }, mesh = {Humans ; *Oxalates/metabolism ; *Microbiota/genetics ; Metagenome ; Gene Transfer, Horizontal ; *Bacteria/genetics/metabolism ; }, abstract = {BACKGROUND: Incomplete degradation of oxalate, a compound commonly found in the diet, can lead to disease in humans, particularly affecting the kidneys. The concentration of oxalate in the body depends on several factors, one of which is intestinal absorption-an aspect influenced by oxalotrophy among enteric bacteria. Despite its potential significance, oxalotrophy in the human microbiome remains poorly understood.<br><br>RESULTS: In this study, we conducted a systematic search for the co-occurrence of three key oxalotrophy genes-frc, oxc, and oxlT. We developed and validated specific conservation models for each gene and applied them to genomes and metagenomes associated with the human digestive tract, oral cavity, and lungs. Our analysis revealed that oxalotrophy, defined as the capacity to use oxalate as an energy source, is a rare metabolic trait predominantly confined to the gut. We also found evidence that this capacity can be acquired via horizontal gene transfer.<br><br>CONCLUSIONS: While oxalotrophy is relatively uncommon, the broader capacity for oxalate degradation is more widespread. Notably, the genes frc and oxc are frequently found in close proximity within genomes, suggesting a selective advantage for organisms possessing this capability. Incomplete degradation of oxalate, a compound commonly found in the diet, can cause disease in humans, particularly affecting the kidney. Its concentration in the body depends on several factors, one of which is intestinal absorption, which is itself affected by oxalotrophy among enteric bacteria. Oxalotrophy in the human microbiome is poorly known. In this study, we perform a systematic search for the simultaneous presence of the three oxalotrophy genes, namely frc, oxc and oxlT. Thanks to the construction and validation of specific conservation models for all three genes, we were able to search for oxalotrophy in genomes and metagenomes associated with the human digestive tract, oral cavity, and lungs. We report that oxalotrophy-the capacity to use oxalate as an energy source-is a rare metabolic trait, mostly confined to the gut, and also find evidence that it can be acquired by horizontal gene transfer. By contrast, the capacity for oxalate degradation is more widespread, and two genes responsible for it (frc and oxc) are almost always close together in the genome, suggesting selection pressure.}, }
@article {pmid41136619, year = {2025}, author = {Fujikawa, K and Saito, T and Kawashima, A and Jingushi, K and Motooka, D and Nakai, S and Hagi, T and Momose, K and Yamashita, K and Tanaka, K and Makino, T and Takahashi, T and Kurokawa, Y and Tsujikawa, K and Wada, H and Eguchi, H and Doki, Y}, title = {Bacteria-derived DNA in serum extracellular vesicles as a biomarker for gastric cancer.}, journal = {Cancer immunology, immunotherapy : CII}, volume = {74}, number = {11}, pages = {346}, pmid = {41136619}, issn = {1432-0851}, mesh = {Humans ; *Stomach Neoplasms/blood/microbiology/diagnosis ; *Extracellular Vesicles/genetics/microbiology ; *Biomarkers, Tumor/blood/genetics ; Male ; *DNA, Bacterial/genetics/blood ; Middle Aged ; Female ; RNA, Ribosomal, 16S/genetics ; Prognosis ; Aged ; Adult ; Case-Control Studies ; Tumor Microenvironment/immunology ; }, abstract = {Bacterial flora is present in various parts of the human body, and bacterial 16S rRNA genes have been detected in the bloodstream. Distinct blood microbiomes have been identified in various diseases, including cancer, and are thought to play a role in disease pathogenesis. In this study, we conducted a 16S rRNA metagenomic analysis of serum extracellular vesicles from 89 patients with gastric cancer (GC) and 25 healthy donors. We identified lower levels of Bacteroidetes and Actinobacteria and higher levels of Firmicutes in patients with GC than in healthy donors. By integrating this characteristic bacterial DNA profile, we developed a BAF index, defined as the ratio of Bacteroidetes and Actinobacteria to Firmicutes, which exhibited high sensitivity for detecting GC in both the discovery and validation cohorts, suggesting its potential utility as a screening tool. A high BAF index was significantly associated with an advanced tumor stage and poor prognosis. Moreover, a high BAF index was linked to an immunosuppressive tumor microenvironment, which may contribute to the unfavorable outcomes observed in these patients. These findings indicate that circulating bacterial signatures may serve as promising biomarkers for GC.}, }
@article {pmid41136439, year = {2025}, author = {Xue, W and Liu, Z and Zhang, Y and Raza, W and Li, Y and Jiang, L and Tao, Y and Qian, J and Alexandre, J and Zhao, FJ and Xu, Y and Sedlazeck, F and Shen, Q and Jiang, G and Wei, Z}, title = {LorBin: efficient binning of long-read metagenomes by multiscale adaptive clustering and evaluation.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {9353}, pmid = {41136439}, issn = {2041-1723}, mesh = {*Metagenome/genetics ; *Metagenomics/methods ; *Microbiota/genetics ; Humans ; Cluster Analysis ; Gastrointestinal Microbiome/genetics ; *Software ; Algorithms ; }, abstract = {Long-read sequencing has transformed metagenomics and improved the quality of metagenome-assembled genomes (MAGs). However, current binning methods struggle with identifying unknown species and managing imbalanced species distributions. Here, we present LorBin, an unsupervised binner specially designed to reconstruct MAGs in natural microbiomes. LorBin deploys a two-stage multiscale adaptive DBSCAN and BIRCH clustering with evaluation decision models using single-copy genes to maximize MAG recovery. LorBin outperforms six competing binners in both simulated and real microbiomes, including oral, gut, and marine samples. LorBin generated 15-189% more high-quality MAGs with high serendipity and identified 2.4-17 times more novel taxa than state-of-the-art binning methods. Together, LorBin is a promising long-read metagenomic binner for accessing species-rich samples containing unknown taxa and is efficient at retrieving more complete genomes from imbalanced natural microbiomes.}, }
@article {pmid41136135, year = {2026}, author = {Du, R and Li, X and Xu, Y and Jing, K and Ao, L and Deng, B and Xu, Q and Song, P and Yu, J}, title = {Metagenomics reveals potential antimicrobial peptides in Chinese baijiu fermentation.}, journal = {Food microbiology}, volume = {134}, number = {}, pages = {104918}, doi = {10.1016/j.fm.2025.104918}, pmid = {41136135}, issn = {1095-9998}, mesh = {Humans ; Fermentation ; Metagenomics ; *Antimicrobial Peptides/pharmacology/chemistry/metabolism ; Bacteria/genetics/drug effects/metabolism/classification/isolation &amp; purification ; Molecular Docking Simulation ; Microbial Sensitivity Tests ; Anti-Bacterial Agents/pharmacology ; *Fermented Foods/microbiology ; Escherichia coli/drug effects ; A549 Cells ; China ; Hep G2 Cells ; Food Microbiology ; }, abstract = {Antimicrobial peptides (AMPs) from food fermentation microbiota hold promise for food preservation and as potential antimicrobial agents. However, the biosynthetic potential of AMPs in food fermentations remains largely unclear. Here, using Chinese baijiu fermentation as a model, we provided a workflow for AMP mining by combining metagenomics and machine learning. We recovered 389 metagenome-assembled genomes (MAGs) spanning both bacteria and archaea from 18 fermented samples. In total, 414 AMPs, including 290 novel AMPs, were predicted in 59.38 % of these MAGs using a machine learning model. Correlation network analysis showed that AMP-producing microorganisms potentially mediated negative microbial interactions. We selected ten AMPs for experimental validation, and eight AMPs exhibited antimicrobial activity against five human pathogens and two food spoilage microorganisms. One peptide, AMP_22, showed a broad-spectrum activity (all seven test strains) with high potency (MIC = 3.06-200 μg/mL) and cytotoxicity was not observed below 25 μg/mL using HepG2 and A549 cell lines. We further investigated the antimicrobial mechanism of AMP_22 using Escherichia coli as a model. Treatment with AMP_22 caused severe damage to the bacterial cell membrane, inhibited intracellular protein synthesis, and led to a significant accumulation of reactive oxygen species (ROS). Furthermore, molecular docking analysis indicated that AMP_22 can bind to DNA gyrase and dihydrofolate reductase via hydrogen bonding. This study highlights the potential of food-derived AMPs for application as preservatives and antimicrobial agents.}, }
@article {pmid41135804, year = {2025}, author = {Dang, H and Zhang, Y and Zhang, L and Liu, Y}, title = {Transitional role of granular activated carbon for potentially promoting the expression of conductive pili and quorum sensing during anaerobic digestion.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {133544}, doi = {10.1016/j.biortech.2025.133544}, pmid = {41135804}, issn = {1873-2976}, abstract = {Granular activated carbon (GAC) amendment mediated the microorganisms to significantly enhances methane production in anaerobic digestion. To elucidate the underlying microbial mechanisms, a genome-centric metagenomic analysis was conducted on DNA extracted from lab-scale anaerobic digesters treated with GAC. A total of 431 non-redundant metagenome-assembled genomes (MAGs) were recovered. Co-occurrence network analysis demonstrated that methanogens exhibit a distinct preference for associating with syntrophic partners that harboring potential pilA (e-pilA) producing conductive pili. Analysis revealed a potential temporal succession of key enhancement mechanisms: in the less developed community, QS facilitates biofilm formation and granulation, particularly for that of methanogens and MAGs with e-pilA. As the community became more developed, this QS-mediated influence weakens, concurrently e-pilA enrichment signifying established conductive pili connections. These connections optimize interspecies electron transfer for sustained methane yield enhancement. These results realved GAC sequentially promoting biofilm assembly via QS and optimizing electron flux for enhanced AD performance.}, }
@article {pmid41135729, year = {2025}, author = {Li, M and Wang, H and Chu, H and Wang, Y and Lu, J}, title = {Deciphering Microbial Dynamics in Coastal Ecosystems Under Polycyclic Aromatic Hydrocarbon Stress: Community Assembly, Interaction Networks, and Metabolic Adaptations.}, journal = {Environmental research}, volume = {}, number = {}, pages = {123179}, doi = {10.1016/j.envres.2025.123179}, pmid = {41135729}, issn = {1096-0953}, abstract = {The significant toxicity and carcinogenicity of polycyclic aromatic hydrocarbons (PAHs) have raised increasing concern about their contamination, particularly in coastal regions with intensive human activities and urbanization. However, limited information exists on microbial response mechanisms across varying levels of PAHs contamination. In this study, sediment samples at 18 locations along the Yantai inland river and estuary were collected in October 2024 to examine the partitioning and spatial dispersal of PAHs, while microbial community assembly, interaction networks, and metabolic adaptations were analysed using metagenomics. Results showed that the average ∑PAHs concentration in the estuary (27.95 ± 2.91 ng/g) was significantly lower than that in the river (77.54 ± 43.39 ng/g), with a correspondingly higher ecological risk in the river. High-molecular-weight (HMW) PAHs dominated in both estuary and river sediments due to their high hydrophobicity and stability. Microbial community analysis revealed increased microbial diversity and a higher abundance of PAHs-degrading microbes (e.g., Ruegeria, known for degrading low-molecular-weight PAHs) under higher PAHs contamination. Co-occurrence network and topological analyses demonstrated dual regulatory effects of PAHs stress on microbial interactions, where elevated PAHs contamination intensified interspecies connectivity while simultaneously inducing destabilizing negative covariance patterns that weakened microbial network integrity. Additionally, neutral community model analysis indicated that stochastic processes dominated community assembly, with higher proportions of stochasticity observed in rivers under high PAHs stress. Notably, elevated PAHs concentrations significantly impaired energy metabolism and nitrogen metabolic pathways (p < 0.05), suggesting altered nitrogen biogeochemistry under PAHs contamination. This study advances the understanding of microbial population responses to different PAHs contamination levels in coastal regions.}, }
@article {pmid41135463, year = {2025}, author = {Zhang, A and Pan, P and Zhou, NY and Li, T}, title = {Synergistic mineralization of the UV filter benzophenone-3 by a cross-feeding consortium from wastewater treatment plants: Insights into novel pathway and bioremediation strategy.}, journal = {Journal of hazardous materials}, volume = {499}, number = {}, pages = {140176}, doi = {10.1016/j.jhazmat.2025.140176}, pmid = {41135463}, issn = {1873-3336}, abstract = {Benzophenone-3 (BP-3), used as an organic UV filter in diverse consumer products including cosmetics, has been frequently detected in wastewater treatment plants (WWTPs) and aquatic environments. BP-3 and its transformation products are regarded as emerging micropollutants due to their low biodegradability. Here, we investigate the synergistic degradation of BP-3 by a bacterial consortium seeded from aerobic sludge WWTPs. BP-3 is found to be initially degraded through a novel pathway involving a C-C bond cleavage step, producing intermediates 3-methoxyphenol (3MOP) and benzoate, two naturally occurring compounds which can be readily degraded in the environment. Metagenome-guided pure culture isolation and pathway analysis reveal that bacterial strains from genera Pigmentiphaga and Brucella synergistically contribute to the BP-3 mineralization. Specifically, the Pigmentiphaga strain degrades BP-3 into benzoate and 3MOP, with the former being utilized by itself and the latter utilized by the Brucella strain. A reconstructed consortium, consisting of two isolated strains from Pigmentiphaga and Brucella, exhibits similar degradation performance to that of the natural consortium, indicating their crucial roles in environmental BP-3 degradation. These findings provide new insights into BP-3 biodegradation at the microbial community level, offering potential strategies for wastewater treatment applications by manipulating synthetic microbial consortia.}, }
@article {pmid41135184, year = {2025}, author = {Meng, J and Yang, C and Jing, M and Huang, J and Wang, W and Li, X and Zhao, P}, title = {Metagenomic sequencing of bronchoalveolar lavage fluid in pediatric pneumonia: A single-center study in Gansu province.}, journal = {Diagnostic microbiology and infectious disease}, volume = {114}, number = {2}, pages = {117153}, doi = {10.1016/j.diagmicrobio.2025.117153}, pmid = {41135184}, issn = {1879-0070}, abstract = {BACKGROUND: Pneumonia is one of the important causes of death in children. Conventional detection methods such as bacterial culture and polymerase chain reaction (PCR) are very limited for the detection of pathogens. Metagenomic next generation sequencing (mNGS) has shown strong coverage in nucleic acid detection, but its research in lower respiratory tract samples of children with pneumonia is still quite limited, especially in northwest China.<br><br>AIM: To characterize the pathogenic microbial spectrum in bronchoalveolar lavage fluid (BALF) of pediatric pneumonia patients in Gansu Province, China, using mNGS, and to demonstrate the advantages of mNGS in pediatric pneumonia diagnostics.<br><br>METHODS: A total of 128 pediatric pneumonia patients admitted to Gansu Provincial Maternal and Child Health Hospital (Gansu Central Hospital) between March 1, 2023 and February 5, 2025 were enrolled. BALF data, including bacterial culture, Polymerase chain reaction (PCR), and mNGS results, were collected from each patient for comprehensive analysis.<br><br>RESULTS: A total of 128 patients were enrolled in this retrospective study. Out of all patients, 68(53 %) were male and the median age was 3 years. A total of 31 patients had underlying diseases. mNGS demonstrated a significantly higher pathogen detection rate compared to conventional testing. Through mNGS analysis, viruses were identified as the predominant pathogenic microorganisms in children with pneumonia, and the most common infection pattern was a combination of viral and bacterial infections. Additionally, mNGS detected three types of difficult-to-culture bacteria, namely Tropheryma whipplei, Legionella pneumophila, and Mycobacterium tuberculosis complex, in the BALF from pediatric pneumonia patients in this study.<br><br>CONCLUSIONS: mNGS has shown obvious advantages in the detection of pathogenic microorganisms in children with pneumonia. Its universality helps to identify the pathogen as soon as possible and make up for the shortcomings of conventional testing, which is particularly important for the accurate treatment of patients with unclear infection or no obvious curative effect.}, }
@article {pmid41134432, year = {2025}, author = {Kumar, A and Kumar, T and Batra, K and Dhania, NK and Jangir, BL and Budania, S and Maan, S}, title = {Detection, isolation, and complete genome sequencing of pigeon torque teno virus in Indian racing pigeons with pock-like lesions.}, journal = {Virus genes}, volume = {}, number = {}, pages = {}, pmid = {41134432}, issn = {1572-994X}, support = {State scheme//LUVAS, Hisar/ ; }, abstract = {This study investigates the potential pathogens associated with joint swelling, yellow exudates, and scab formation near the joints and eyelids in adult white racing pigeons.Pooled samples of scab and swab were collected and subjected to molecular, microbiological, and histopathological analyses. Initial screening focused on the detection of poxvirus using polymerase chain reaction (PCR). Subsequently, next-generation sequencing (metagenomic sequencing) using the Illumina MiSeq platform was performed, followed by virus isolation in embryonated specific pathogen-free chicken eggs and Vero cells, along with histopathological examination.Polymerase chain reaction (PCR) analysis for pigeon pox virus did not produce the expected amplicons, indicating a negative result for this virus. However, metagenomic sequencing identified the complete genome of Pigeon Torque Teno Virus (PTTV), with a genome size of 1574 nucleotides. Comparative sequence analysis revealed a nucleotide sequence similarity of 96.47%-97.7%, with the highest identity to a Canadian PTTV genome previously detected in the Bursa of Fabricius of a dead pigeon. Genome annotation identified two open reading frames (ORFs): encoding replication-associated protein and viral capsid protein. The presence of PTTV was further confirmed through real-time PCR and virus isolation in embryonated SPF chicken eggs and Vero cell cultures.The present study marks the first identification of PTTV in white racing pigeons with joint, ocular, and pock-like lesions. Although pigeon pox virus (PPV) was not detected, the findings suggest that PTTV could be an emerging avian pathogen necessitating further investigation into its pathogenicity, transmission dynamics, and clinical significance in pigeons.}, }
@article {pmid41134295, year = {2025}, author = {Muralidhar, M and Naseem, MN and Mesa, JRB and Omaleki, L and Turni, C}, title = {Optimization of DNA extraction methods from pig farm wastewater for pathogen detection using metagenomic sequencing.}, journal = {Microbial genomics}, volume = {11}, number = {10}, pages = {}, doi = {10.1099/mgen.0.001532}, pmid = {41134295}, issn = {2057-5858}, mesh = {Animals ; Swine ; *Wastewater/microbiology/virology ; *Metagenomics/methods ; Farms ; DNA, Bacterial/isolation &amp; purification/genetics ; SARS-CoV-2/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {Wastewater can be a useful sample to monitor disease outbreaks in the community, as it was demonstrated during the recent Severe acute respiratory syndrome coronavirus 2 pandemic. Due to housing conditions, diseases can rapidly spread within pig herds, resulting in high mortalities and significant economic losses. Monitoring piggery wastewater using Oxford Nanopore Technology's (ONT) sequencing platform combined with metagenomic analysis can provide early disease detection to deploy preventative measures. Nevertheless, obtaining DNA of the required purity and integrity from piggery wastewater is a major challenge. This study aims to identify and optimize the most effective method for obtaining high-quality and quantity DNA, which can be used in downstream applications for pathogen detection. Six DNA extraction protocols were tested on piggery wastewater samples and evaluated based on yield and overall DNA quality. The three best-performing methods, using commercially available kits (QIAGEN QIAamp® PowerFecal® Pro, QIAGEN DNeasy® PowerLyzer® PowerSoil® and Macherey-Nagel NucleoSpin® Soil), were then used to extract DNA from piggery wastewater samples spiked with a mock community composed of known pig pathogens. The extracted DNA samples were then sequenced on the ONT platform, and the effectiveness of the methods was evaluated using kraken2 taxonomic classifier and an in-house database. Results demonstrated that the optimized QIAGEN PowerFecal® Pro protocol was the most suitable and reliable extraction method. Overall, this study highlights the importance of determining the optimal DNA extraction method in effective disease surveillance using a complex environmental sample and takes an important step in making metagenomic disease surveillance a practical reality.}, }
@article {pmid41133998, year = {2025}, author = {Bağci, C and Negri, T and Atienza, EB and Gross, C and Ossowski, S and Ziemert, N}, title = {Ultra-deep long-read metagenomics captures diverse taxonomic and biosynthetic potential of soil microbes.}, journal = {GigaScience}, volume = {}, number = {}, pages = {}, doi = {10.1093/gigascience/giaf135}, pmid = {41133998}, issn = {2047-217X}, abstract = {BACKGROUND: Soil ecosystems have long been recognised as hotspots of microbial diversity, but most estimates of their microbial and functional complexity remain speculative despite decades of study, in part because conventional sequencing campaigns lack the depth and contiguity required to recover low-abundance and repetitive genomes. Here, we revisit this question using one of the deepest metagenomic sequencing efforts to date, applying 148 billion base pairs of Nanopore long-read and 122 billion base pairs of Illumina short-read data to a single forest soil sample.<br><br>RESULTS: Our hybrid assembly reconstructed 837 metagenome-assembled genomes, including 466 that meet high- and medium-quality standards, nearly all lacking close relatives among cultivated taxa. Rarefaction and k-mer analyses reveal that, even at this depth, we capture only a fraction of the extant diversity: non-parametric models project that more than ten trillion base pairs of sequencing data would be required to approach saturation. These findings offer a quantitative, technology-enabled update to long-standing diversity estimates and demonstrate that conventional metagenomic sequencing efforts likely miss the majority of microbial and biosynthetic potential in soil. We further identify more than 11&#xa0;000 biosynthetic gene clusters, over 99% of which have no match in current databases, underscoring the breadth of unexplored metabolic capacity.<br><br>CONCLUSIONS: Taken together, our results emphasise both the power and the present limitations of metagenomics in resolving natural microbial complexity, and they provide a new baseline for evaluating future advances in microbial genome recovery, taxonomic classification, and natural product discovery.}, }
@article {pmid41133101, year = {2025}, author = {Li, Q and Zhou, D and Cao, L and Li, Y and Li, J and Ye, J and Chen, H and Zhao, J and Cao, S and Peng, Z}, title = {Profiling the composition of resistome and bacteriome in the upper respiratory tract of domestic cats with respiratory signs in China.}, journal = {Microbiome research reports}, volume = {4}, number = {3}, pages = {27}, pmid = {41133101}, issn = {2771-5965}, abstract = {Aim: Domestic cats, among the most popular pets globally, may harbor antimicrobial resistance genes (ARGs) and zoonotic pathogens that impact human health. This study aims to investigate the resistome and bacteriome composition in the upper respiratory tract of domestic cats with respiratory signs in China. Methods: We performed metagenomic sequencing on 1,454 oropharyngeal-nasal swabs from cats with respiratory signs across diverse living conditions in 22 Chinese provinces. Resistome and bacteriome profiles were analyzed using these sequencing data. Results: We characterized the resistome and bacteriome in the upper respiratory tract of cats, identifying a wide range of ARGs - including those conferring resistance to last-resort antibiotics {e.g., carbapenems (bla NDM, bla OXA-244, bla VIM-13, bla VIM-33), colistin (mcr), and high-level tigecycline [MIC ≥ 4 µg/mL; tet(X3), tet(X4), tet(X5), tet(X6)]}. Additionally, we detected numerous bacterial species of public health concerns, including the six leading antimicrobial resistance-associated pathogens (Escherichia coli, Staphylococcus aureus, Klebsiella pneumoniae, Streptococcus pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa) and other high-burden pathogens linked to global morbidity, mortality, and therapeutic challenges. Conclusion: The findings highlight the potential zoonotic risks posed by cats. Including monitoring of this companion species within the One Health approach to address public health concerns is necessary.}, }
@article {pmid41132634, year = {2025}, author = {Liu, Y and Xia, F and Cai, W and Zhang, Y and Zhu, J and Shen, Z and Li, J and Yang, Q and Qu, Q and Chen, J}, title = {Blinatumomab Along With Combined Antifungal Agents for Refractory Adult Acute Lymphoblastic Leukemia With Invasive Aspergillosis: A Case Report.}, journal = {Clinical case reports}, volume = {13}, number = {10}, pages = {e71342}, pmid = {41132634}, issn = {2050-0904}, abstract = {There is an increased risk of invasive aspergillosis (IA) during the induction of acute lymphoblastic leukemia (ALL) because of the use of cytoreductive chemotherapy and high-dose steroids. This case demonstrates the utility of metagenomic next-generation sequencing and repeat sampling in clarifying complex infections and highlights blinatumomab as an effective antileukemic option when conventional chemotherapy is limited by active infection. Together, these strategies enabled the successful management of refractory ALL in a patient with pulmonary IA and fungal DNAemia.}, }
@article {pmid41132583, year = {2025}, author = {Zou, Z and Lei, D and Wang, X and Yin, Y and Li, H and Di, X and Li, X}, title = {Crocin Ameliorates Cognitive Impairment and Pathological Changes in Alzheimer's Disease Model Mice by Regulating Gut Microbiota.}, journal = {Food science &amp; nutrition}, volume = {13}, number = {10}, pages = {e71117}, pmid = {41132583}, issn = {2048-7177}, abstract = {Alzheimer's disease (AD), a primary cause of dementia, places a significant strain on both patients and society due to the absence of effective treatments. Recent research suggests that the gut microbiota may play a role in the development of AD. Crocin, a compound derived from traditional medicine, has demonstrated potential in alleviating neurological disorders and influencing gut microbiota, yet its specific mechanisms in AD remain unclear. In this study, we administered Crocin or saline to 5xFAD mice and wild-type controls. We discovered that Crocin treatment led to notable improvements in cognitive function, as measured by the Morris water maze test, reduced beta-amyloid (Aβ) accumulation, and decreased neuroinflammation, as indicated by reduced microglial and astrocyte activation. Metagenomic sequencing revealed a significant increase in the gut microbiota diversity, specifically the abundance of Firmicutes, Verrucomicrobiota, and Akkermansia. Additionally, Crocin enhanced intestinal barrier function by upregulating tight junction proteins and Secretory immunoglobulin A, while improving the structure of the jejunal mucosa. These results suggest that Crocin may alleviate cognitive deficits and neuropathological changes in 5xFAD mice, possibly through modulation of the gut microbiota and strengthening the gut barrier, presenting it as a promising therapeutic approach for AD.}, }
@article {pmid41132557, year = {2025}, author = {Chen, J and Luo, Y and Hao, Y and Wang, Q and Wang, Q}, title = {Structural and functional characterization of gut microbiota in dyslipidemic patients from high-altitude Tibetan pastoral areas.}, journal = {Frontiers in nutrition}, volume = {12}, number = {}, pages = {1676238}, pmid = {41132557}, issn = {2296-861X}, abstract = {INTRODUCTION: Approximately 49.3% of individuals living at high altitudes suffer from dyslipidemia. Emerging evidence indicates that gut microbiota can regulate lipid metabolism and cholesterol homeostasis, but the composition and function of gut microbiota in dyslipidemic patients from Tibetan pastoral regions remain unclear.<br><br>METHODS: To address this, we enrolled a cohort consisting of 22 dyslipidemic patients and 33 healthy controls (HCs) from the Gannan Tibetan pastoral region (average altitude: 3,600&#x202f;m). Phenotypic data, blood, and fecal samples were collected from all the participants for a metagenome-wide association study based on shotgun metagenomic sequencing.<br><br>RESULTS: Compared with HCs, dyslipidemic patients showed a significant reduction in gut microbial diversity. Specifically, the abundance of beneficial species-including Faecalibacterium prausnitzii, Bifidobacterium adolescentis, Bifidobacterium longum, Bifidobacterium bifidum, and Parabacteroides distasonis-was significantly decreased, while opportunistic pathogens such as Veillonella parvula, V. tobetsuensis, Streptococcus oralis, and Streptococcus mitis were notably enriched. Functional prediction revealed that pathways involved in glycolysis, starch degradation, and biosynthesis of L-methionine, L-arginine, L-lysine, L-citrulline, and L-threonine were significantly downregulated in dyslipidemic patients, whereas pathways for the biosynthesis of lipopolysaccharides, fatty acids, polyamines, and (Kdo)&#x2082;-lipid A were enriched. Correlation analysis showed that the enriched taxa in dyslipidemic patients were significantly positively associated with total cholesterol (TC), total triglycerides (TG), and low-density lipoprotein cholesterol (LDL-C). In contrast, the enriched functional pathways were significantly negatively correlated with TC but positively correlated with high-density lipoprotein cholesterol (HDL-C).<br><br>DISCUSSION: These findings clarify the alterations in gut microbiota composition and function in plateau-dwelling dyslipidemic populations and their associations with blood lipid levels, suggesting potential microbial biomarkers for hyperlipidemia in plateau environments.}, }
@article {pmid41132537, year = {2025}, author = {Liu, X and Wang, L and Huang, B and Jiao, Y and Guan, Y and Nuli, R}, title = {Barnesiella intestinihominis improves gut microbiota disruption and intestinal barrier integrity in mice with impaired glucose regulation.}, journal = {Frontiers in pharmacology}, volume = {16}, number = {}, pages = {1635579}, pmid = {41132537}, issn = {1663-9812}, abstract = {INTRODUCTION: Impaired glucose regulation (IGR) is a prediabetic state closely associated with gut microbiota dysbiosis. Our previous metagenomic analysis identified a significant deficiency of Barnesiella intestinihominis (B. intestinihominis) in IGR patients (p < 0.01). The present study was therefore designed to investigate the therapeutic potential of B. intestinihominis supplementation in a high-fat diet (HFD)-induced IGR mouse model and to explore its potential mechanisms of action.<br><br>METHODS: A mouse model of IGR was established by HFD. The treatment group received a daily supplementation of live B. intestinihominis (1&#xd7;10[8] CFU) for 5 weeks. Gut microbiota composition was analyzed. Colonic expression levels of tight junction proteins (ZO-1 and occludin) and cytokines (IL-10, TNF-&#x3b1;, IL-6) were measured. In vitro experiments using Caco-2 human intestinal epithelial cells were conducted to assess the direct effects of B. intestinihominis. B. intestinihominis fermentation broth, heat-inactivated bacterial solution, and bacterial solution were co-cultured with Caco-2 cells. Cell viability was assessed using the CCK-8 assay, and the expression levels of tight junction proteins were evaluated. Trans-epithelial electrical resistance (TEER) and alkaline phosphatase activity were also assessed in the Caco-2 model.<br><br>RESULTS: Daily supplementation with B.intestinihominis significantly attenuated HFD-induced hyperglycemia in mice. It also modulated the gut microbiota, evidenced by an increased abundance of beneficial Ligilactobacillus and a reduction in pathogenic Lachnoclostridium. Furthermore, B. intestinihominis administration upregulated the expression of colonic tight junction proteins (ZO-1 and occludin) and the anti-inflammatory cytokine IL-10, while simultaneously inhibiting the pro-inflammatory mediators TNF-&#x3b1; and IL-6. In vitro, the fermentation broth of B.intestinihominis (10%) increased Caco-2 cell viability, and heat-inactivated bacteria (1&#xd7;10[7] CFU) enhanced ZO-1 expression. However, neither treatment significantly affected trans-epithelial electrical resistance (TEER) nor alkaline phosphatase activity in Caco-2 cells.<br><br>DISCUSSION: These findings suggest that intestinal probiotics B. intestinihominis may ameliorate IGR by modulating the gut microbiota, enhancing intestinal barrier integrity, and attenuating inflammation, thus supporting their potential as a therapeutic intervention for metabolic disorders.}, }
@article {pmid41132377, year = {2025}, author = {Han, Z and Jia, L and Zhu, R and Fu, H and Lin, C and Huang, H and Deng, L and Zhang, J and Zhao, L}, title = {The genetic and proliferation characterization analysis of novel coxsackievirus A12 in Beijing, China.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1665461}, pmid = {41132377}, issn = {1664-302X}, abstract = {INTRODUCTION: Coxsackievirus A12 (CVA12) is a serotype of Enterovirus A. Its evolutionary and molecular characteristics remain poorly understood.<br><br>METHODS: The metagenomic Next-Generation Sequencing (mNGS) strategy were used to investigate the viral diversity. The viral isolation, proliferation assays, phylogenetic relationships and recombination events were analyzed.<br><br>RESULTS: In this study, nine clinical specimens collected in Beijing, China, during March 2010 to October 2019 were identified as CVA12 positive, among which five were confirmed by mNGS. Then five CVA12 strains were isolated, and the proliferation assays demonstrated the preferential replication of CVA12 in rhabdomyosarcoma (RD) cells, with rapid intracellular replication before being released extracellularly, over Hep-2 cells. Transcriptomic profiling of infected RD cells revealed that the significant up-regulated genes were involved in inflammatory responses and transcriptional regulation (e.g., JUN, FOS), suggesting robust host immune activation. Phylogenetic analysis identified that four strains were clustered into genogroup E, indicating a lineage undergoing active transmission in Beijing, China, the other one into genogroups B. Recombination analysis revealed that strain s7275 exhibited recombination with CVA5 (strain 3,490, GenBank access number OK334538) at the breakpoint position 3,373-6,634, while the others showed recombination with EV-A71 (strain EV71/P1034/2013/China, GenBank access number KP289419) at breakpoint position 3,370-6,645.<br><br>DISCUSSION: These findings underscored the genetic diversity and recombination dynamics which provided insights into the evolutionary implications of CVA12, and its proliferation features in RD cells of CVA12. Further research is needed to elucidate the functional mechanisms of CVA12 infection and its role for disease.}, }
@article {pmid41132089, year = {2025}, author = {Zhao, Y and Wang, H and Lin, W and Wang, H and Cao, LL}, title = {Gut microbiota and bile acids changes in MASLD mice model with hepatic PLD1 knockout.}, journal = {Acta biochimica et biophysica Sinica}, volume = {}, number = {}, pages = {}, doi = {10.3724/abbs.2025183}, pmid = {41132089}, issn = {1745-7270}, abstract = {Hepatocyte phospholipase D1 (PLD1) knockout alleviates metabolic dysfunction-associated steatotic liver disease (MASLD) in mice, but the underlying mechanism is largely unknown. In this study, the mice were divided into four groups: Con (wild-type mice with normal control diet), HFHC (wild-type mice with high-fat diet), Con_KO (hepatocyte PLD1-knockout mice with normal control diet), and HFHC_KO (hepatocyte PLD1-knockout mice with high-fat diet). Intestinal contents of mice are analyzed via metagenomics and metabolomics, and the liver bile acids are assessed by mass spectrometry imaging. The results show that at the phylum level the abundance of Bacillota in the intestines of MASLD model mice is significantly increased, whereas that of Bacteroidota significantly is decreased. However, after the deletion of hepatocyte PLD1, Pseudomonadota and Candidatus Bathyarchaeota are significantly decreased in the MASLD model mice. At the species level, compared with that in the Con group, the abundance of Faecalibaculum rodentium is significantly increased in the HFHC group, whereas hepatocyte PLD1 knockout causes the abundances of Desulfovibrionaceae bacterium LT0009 and Lachnospiraceae bacterium 10-1 to be significantly decreased. In terms of intestinal bile acids, the levels of two bile acids (hyodeoxycholic acid and glycolithocholic acid) differ between the HFHC_KO group and the HFHC group. Association analysis shows that Faecalibaculum co-occurs with DCA, βMCA, ΩMCA and αMCA, while probiotic Bacteroides uniformis is significantly correlated with UDCA, 12-KetoLCA, and 7-KetoLCA. Finally, mass spectrometry imaging reveals that the TCA and TDCA contents in the liver are significantly decreased after PLD1 knockout in hepatocytes. These findings demonstrate that hepatocyte PLD1 knockout alters the gut microbiota and bile acids profiles, suggesting that PLD1 deficiency may modulate MASLD progression by changing intestinal microbiota-bile acid homeostasis.}, }
@article {pmid41131686, year = {2025}, author = {Ramchandar, N and Farnaes, L and Coufal, N}, title = {Host Transcriptomic Analysis of Operative Samples From Children With Suspected Osteoarticular Infections.}, journal = {The Pediatric infectious disease journal}, volume = {}, number = {}, pages = {}, doi = {10.1097/INF.0000000000004969}, pmid = {41131686}, issn = {1532-0987}, }
@article {pmid41131658, year = {2025}, author = {Li, Z and Luo, W and Xie, H and Mo, C and Qin, B and Zhao, Y and Chen, X and Zhang, S and Zhao, Y and Wang, M and Yang, Y and Cai, J and Wang, B and Liu, X and Shi, Y}, title = {Reovirus infection results in rice rhizosphere microbial community reassembly through metabolite-mediated recruitment and exclusion.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {214}, pmid = {41131658}, issn = {2049-2618}, mesh = {*Oryza/virology/microbiology ; *Rhizosphere ; *Reoviridae/physiology/pathogenicity ; Soil Microbiology ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Microbiota ; Metagenomics/methods ; *Plant Diseases/virology/microbiology ; Metabolomics/methods ; }, abstract = {BACKGROUND: Microbial assembly plays a critical role in ecosystem function and biodiversity. While numerous studies have explored the effect of abiotic factors on the belowground community assembly, much less is known about the role of biotic interactions, particularly viral infections, in shaping microbial communities. Southern rice black-streaked dwarf virus (SRBSDV), a member of the Fijivirus genus in the Reoviridae family, has caused severe yield losses in rice due to its rapid transmission. However, its specific effects on rhizosphere microbiota and the dynamics of microbial community changes have not been fully elucidated.<br><br>RESULTS: By leveraging metabolomics with amplicon and metagenomics, this study provided a comprehensive understanding of the effect of SRBSDV infection on the rhizosphere microbial community and their functions. The results revealed that SRBSDV invasion led to significant changes in rhizosphere metabolites and microbial assembly processes. Specifically, the estimated overdispersion of cations sharply decreased following viral infection, while anion levels decreased markedly during early infection and then increased rapidly after 15&#xa0;days. Key taxa, such as methanotrophs (e.g., Methylomicrobium), nitrifiers (e.g., Nitrospira), and iron-cycling bacteria (e.g., Sideroxydans), not only increased in abundance but also showed strong involvement in the microbial assembly processes. These key microbes were closely linked to specific metabolites and organized into two distinct network modules. Both modules predominantly recruited beneficial microbes, but one module also actively excluded potentially harmful taxa (e.g., Salmonella), which could disrupt community stability. Further experiments with exogenous metabolites confirmed the vital role of quercetin in attracting beneficial microbes while repelling harmful ones.<br><br>CONCLUSION: The findings indicate that arboviruses can strongly influence the belowground rhizosphere microbial assembly processes by modulating metabolite profiles to selectively recruit or exclude key microbial species. These taxa, in turn, play fundamental roles in rhizosphere functions. These insights lay the groundwork for strategies to enhance rice immunity against viral infections by managing the rhizosphere microbial community. Video Abstract.}, }
@article {pmid41131656, year = {2025}, author = {Chen, X and Xu, J and Zhang, L and Xie, B and Ren, J and He, J and Liu, T and Liu, Q and Dong, Y and He, X and Yao, J and Wu, S}, title = {Altered ruminal microbiome tryptophan metabolism and their derived 3-indoleacetic acid inhibit ruminal inflammation in subacute ruminal acidosis goats.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {215}, pmid = {41131656}, issn = {2049-2618}, support = {2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 32272829//National Natural Science Foundation of China/ ; 32272829//National Natural Science Foundation of China/ ; 32272829//National Natural Science Foundation of China/ ; 32272829//National Natural Science Foundation of China/ ; 32272829//National Natural Science Foundation of China/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; }, mesh = {Animals ; Goats/microbiology ; *Rumen/microbiology/metabolism ; *Acidosis/veterinary/microbiology/metabolism ; Animal Feed/analysis ; *Tryptophan/metabolism ; *Indoleacetic Acids/metabolism ; *Gastrointestinal Microbiome ; *Inflammation ; *Goat Diseases/microbiology/metabolism ; Diet ; Female ; Metagenomics ; Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Fermentation ; Metagenome ; }, abstract = {BACKGROUND: Subacute ruminal acidosis (SARA) is a digestive disorder that often severely jeopardizes the health and lactation performance of ruminants fed a high-energy diet. Different dairy ruminants exhibit varying degrees of inflammation accompanied by variations in the rumen microbiota when SARA occurs. Our understanding of the occurrence of SARA and varying degrees of rumen epithelial inflammation is lacking. Hence, we performed rumen metagenomic, metagenome-assembled genome and metabolomic analyses, with transcriptome and single-nucleus RNA sequence analyses, to explore the microbial mechanism of SARA occurrence and different degrees of inflammation.<br><br>RESULTS: A total of 36 goats fed two diets with gradually increasing levels of rumen-degradable starch (RDS) were included in this study, and SARA goats fed 70% concentrate diets supplemented with whole corn (HGW-SARA) and SARA goats fed 70% concentrate diets supplemented with crushed corn (HGC-SARA) were identified. Moreover, 11 goats fed a control basal diet, named LGW-CON, were also included. Compared with those in the LGW-CON group, the rumen fermentation capacity was enhanced, accompanied by ruminal epithelial and systemic inflammation, in goats from HGW-SARA and HGC-SARA. Between them, HGC-SARA goats presented less inflammation. Notably, the ruminal inflammation-related pathways were increased only in the HGW-SARA group but not in the HGC-SARA group. Metagenomic analysis revealed that the &#x3b2; diversity of SARA goats was significantly different from that of LGW-CON goats. Ruminococcus significantly increased in both SARA groups, whereas Prevotella and Bacteroidales significantly decreased, which was accompanied by a decrease in cellulose and hemicellulose enzymes and an increase in lysozymes and lipopolysaccharide synthesis enzymes. Multi-omics analysis of the ruminal contents and tissues suggested that epithelial inflammation was caused by disturbed ruminal microbiome-induced Th17 cell differentiation and IL-17 signalling pathway activation. Comparative analyses between the HGW-SARA and HGC-SARA groups highlighted the importance of Selenomonas and Bifidobacterium, as well as bacterial tryptophan metabolism, in the production of 3-indoleacetic acid, which mitigated ruminal epithelial inflammation by modulating Th17 cells and inhibiting IL-17 signalling. Ruminal microbiota transplantation from HGW-SARA goats to healthy dairy goats and mice revealed the role of microbes in epithelial inflammation. Additionally, 3-indoleacetic acid supplementation reduced rumen inflammation and the IL-17 concentration in the serum, improved VFAs absorption, and enhanced milk production.<br><br>CONCLUSIONS: This study unveiled that after SARA was induced by high-concentrate feeding, the rumen homeostasis was disrupted, and rumen fiber degradation capacity of dairy goats decreased, but the LPS synthesis capacity increased, and inflammation of the rumen epithelium was observed. However, the ruminal microbial species from the Bifidobacterium and Selenomonas genera and bacterial 3-indole acetic acid are pivotal in mitigating ruminal epithelial inflammation during SARA in dairy goats. This could potentially be attributed to the modulation of ruminal Th17 cell proportions and the inhibition of IL-17 signalling pathways. Video Abstract.}, }
@article {pmid41131583, year = {2025}, author = {Lou, Y and Lv, Y and Wang, X and Luo, Y and Lou, J and Yu, Y and Gu, W and Yu, J and Fang, Y and Zhao, H and Peng, K and Chen, J and Ni, Y}, title = {Ruminococcus torques ameliorates the inflammation bowel disease and gut barrier dysfunction by modulating gut microbiota and bile acid metabolism.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {1162}, pmid = {41131583}, issn = {1479-5876}, support = {No. CCCF-QF-2022B04-4//the China Crohn's &amp; Colitis Foundation/ ; 2024KY1171//Medical Science and Technology Project of Zhejiang Province/ ; 82170583//National Natural Science Foundation of China/ ; U23A20167//National Natural Science Foundation of China/ ; 82400595//National Natural Science Foundation of China/ ; 2025C02085//the Key R&amp;D Program of Zhejiang/ ; 2021YFC2701900//the National Key Research and Development Program of China/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Animals ; Male ; *Bile Acids and Salts/metabolism ; *Inflammatory Bowel Diseases/microbiology ; *Ruminococcus/physiology ; *Intestinal Mucosa/pathology/microbiology ; Child ; Colitis/pathology/microbiology ; Mice ; Female ; Mice, Inbred C57BL ; Crohn Disease/microbiology ; Adolescent ; }, abstract = {BACKGROUND: Recent advances in microbiome-targeted therapies have uncovered immunomodulatory bacterial taxa with strain-specific therapeutic potential; however, the microbial signatures driving exclusive enteral nutrition (EEN) efficacy, particularly protective microbiota, and their mechanistic links to therapeutic outcomes remain uncharacterized in pediatric inflammatory bowel disease (IBD). Elucidating these microbial determinants and their functional pathways is critical for advancing targeted probiotic strategies in children.<br><br>METHODS: A cohort of treatment-na&#xef;ve pediatric Crohn's disease (CD) patients and age-matched healthy controls (HC) were enrolled. Fecal samples were collected from both HC and CD patients during active phase and remission following EEN therapy. Metagenomic sequencing, qPCR validation, and targeted bile acid (BA) analysis were conducted to identify candidate protective strains and potential impacts on BA homeostasis. Mechanistic investigations were conducted using dextran sulfate sodium (DSS)- and trinitrobenzene sulfonic acid (TNBS)-induced colitis model in male mice.<br><br>RESULTS: The relative abundance of Ruminococcus torques (R. torques) demonstrated significant depletion in active CD cases (p&#x2009;=&#x2009;0.02) compared to HC, which was restored after EEN treatment at remission status (p&#x2009;<&#x2009;0.001). Its level was negatively correlated with the disease severity index (PCDAI r=-0.64; CDEIS r=-0.70) and positively correlated with the secondary to primary BA ratio (r&#x2009;=&#x2009;0.27). In murine models, R. torques supplementation attenuated colitis severity through enhancing epithelial integrity (claudin-3, 3.3-fold; occludin, 7.5-fold), suppressing pro-inflammatory mediators (TNF-&#x3b1;, -44%; IL-6, -71%), regulating BA metabolism (secondary/unconjugated BAs, 29%) and autophagy pathway (LC3-II/LC3-I ratio, -1.8-fold).<br><br>CONCLUSIONS: Our findings demonstrated R. torques as a novel microbial therapeutic candidate for IBD management. The anti-colitis mechanisms involve the modulation of BA metabolic homeostasis, epithelial barrier reinforcement, and inflammation resolution.}, }
@article {pmid41131579, year = {2025}, author = {Niemann, J and Huang, Y and Lanigan, LT and Willingham Grijalba, AL and Dunn, RR and Sikora, M and Schroeder, H}, title = {ParaRef: a decontaminated reference database for parasite detection in ancient and modern metagenomic datasets.}, journal = {Genome biology}, volume = {26}, number = {1}, pages = {365}, pmid = {41131579}, issn = {1474-760X}, support = {101045643//HORIZON EUROPE European Research Council/ ; }, mesh = {*Metagenomics/methods ; *Parasites/genetics ; *Databases, Genetic ; DNA Contamination ; Animals ; Humans ; }, abstract = {Shotgun metagenomics holds great potential for identifying parasite DNA in biological samples, but its effectiveness is limited by widespread contamination in publicly available reference genomes, which hinders accurate detection. In this study, we systematically quantify and remove contamination from 831 published endoparasite genomes to create ParaRef, a curated reference database for species-level parasite detection. We show that decontamination significantly reduces false detection rates and improves overall detection accuracy. Our study highlights the pervasive issue of contamination in public databases and offers a resource that will enhance the reliability of parasite detection using metagenomics.}, }
@article {pmid41131543, year = {2025}, author = {Lin, P and Xu, Y and Sun, Z and Li, J and Ban, Y and Zhang, M and Wang, Y and Zhang, C}, title = {Investigating the relationship between intestinal microbiota and Th1/Th2/Th17 imbalance in subclinical hypothyroidism during the first half of pregnancy: a multi-omics approach.}, journal = {Gut pathogens}, volume = {17}, number = {1}, pages = {83}, pmid = {41131543}, issn = {1757-4749}, abstract = {BACKGROUND: Gestational subclinical hypothyroidism (SCH), marked by elevated Thyroid-stimulating hormone (TSH) with normal free thyroxine (FT4), links to adverse perinatal outcomes. During early pregnancy (< 20 weeks), maternal thyroid hormones are crucial for fetal neurodevelopment, with deficiencies risking irreversible deficits. SCH pregnancies show gut microbiota alterations and metabolic dysregulation. Emerging evidence suggests these changes may drive Th(helper T cells)1/Th2/Th17 immune imbalance, though mechanisms remain unclear. This study combines metagenomics and lipidomics to investigate gut microbiota-Th1/Th2/Th17 interactions in patients with SCH in the first 20 weeks during pregnancy.<br><br>METHODS: This study included 20 pregnant women with SCH (SCH group) in the first half of pregnancy (&#x2264;&#x2009;20 gestational weeks) and 20 normal pregnant women (CON group) in the same period. Collect fecal and blood samples from both groups. Metagenomic sequencing was used to determine the differences in the composition of the intestinal microbiota between the two groups, and non-targeted lipidomics was used to compare the lipid differences between the two groups. Flow cytometry was used to assess Th1, Th2 and Th17 cells in peripheral blood, and a cell microbead array was used to determine cytokine levels.<br><br>RESULTS: (1) Metagenomic sequencing showed an increased abundance of Faecalibacterium prausnitzii and a decreased abundance of Bacteroides uniformis in the SCH group. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated significant enrichment in lipid and polysaccharide biosynthesis and mucopolysaccharide biodegradation pathways in the SCH group. (2) Lipidomics identified 692 different lipids, with Triglyceride (TG) being the most significant. KEGG pathway analysis revealed that TG was mainly concentrated in the Th1, Th2, and Th17 cell differentiation pathways. (3) Additionally, serological indicators of the two groups showed that TSH, Interleukin (IL)-2,IL-10, Tumor necrosis factor (TNF)-&#x3b1;, TG, Th1, and Th17 in the SCH group were higher than those in the CON group, while Th2 was significantly lower (P&#x2009;<&#x2009;0.05).<br><br>CONCLUSION: In the first half of pregnancy, patients with SCH may experience intestinal microbiota disorder, characterized by increased levels of Faecalibacterium prausnitzii and decreased levels of Bacteroides uniformis, at the same time, it was accompanied by an increase in TG synthesis and a Th1/Th2/Th17 imbalance, these factors may be involved in the occurrence of SCH during pregnancy.}, }
@article {pmid41131518, year = {2025}, author = {Zhang, Y and Zhang, Q and Wang, L and Hu, Y}, title = {The value of second-generation gene sequencing in lung cancer immunotherapy with concurrent infections.}, journal = {BMC cancer}, volume = {25}, number = {1}, pages = {1636}, pmid = {41131518}, issn = {1471-2407}, support = {023YZ09//Medical and Health Talent Training Program/ ; 023YZ09//Medical and Health Talent Training Program/ ; 023YZ09//Medical and Health Talent Training Program/ ; 023YZ09//Medical and Health Talent Training Program/ ; }, }
@article {pmid41052877, year = {2025}, author = {Tran, LN and Castellano, D and Gutenkunst, RN}, title = {Interpreting Supervised Machine Learning Inferences in Population Genomics Using Haplotype Matrix Permutations.}, journal = {Molecular biology and evolution}, volume = {42}, number = {10}, pages = {}, pmid = {41052877}, issn = {1537-1719}, support = {R01GM127348/GM/NIGMS NIH HHS/United States ; R35GM149235/GM/NIGMS NIH HHS/United States ; }, mesh = {*Haplotypes ; *Supervised Machine Learning ; *Genetics, Population/methods ; *Metagenomics/methods ; Linkage Disequilibrium ; Gene Frequency ; Humans ; Neural Networks, Computer ; }, abstract = {Supervised machine learning methods, such as convolutional neural networks (CNNs), that use haplotype matrices as input data have become powerful tools for population genomics inference. However, these methods often lack interpretability, making it difficult to understand which population genetics features drive their predictions-a critical limitation for method development and biological interpretation. Here, we introduce a systematic permutation approach that progressively disrupts population genetics features within input test haplotype matrices, including linkage disequilibrium, haplotype structure, and allele frequencies. By measuring performance degradation after each permutation, the importance of each feature can be assessed. We applied our approach to three published CNNs for positive selection and demographic history inference. We found that the positive selection inference CNN ImaGene critically depends on haplotype structure and linkage disequilibrium patterns, while the demographic inference CNN relies primarily on allele frequency information. Surprisingly, another positive selection inference CNN, disc-pg-gan, achieved high accuracy using only simple allele count information, suggesting its training regime may not adequately challenge the model to learn complex population genetic signatures. Our approach provides a straightforward, model-agnostic, and biologically-motivated framework for interpreting any haplotype matrix-based method, offering insights that can guide both method development and application in population genomics.}, }
@article {pmid40755398, year = {2025}, author = {Johnson, BJ and Graham, MC and Panahi, E and Vieira, CJSP and Nath, NS and Mason, P and Gleadhill, J and Thomas, D and Onn, MB and Shivas, MA and Shearman, D and Darbro, JM and Devine, GJ}, title = {An All-in-One Metabarcoding Approach to Mosquito and Arbovirus Xenosurveillance.}, journal = {Molecular ecology resources}, volume = {25}, number = {8}, pages = {e70022}, doi = {10.1111/1755-0998.70022}, pmid = {40755398}, issn = {1755-0998}, support = {//Mosquito and Arbovirus Research Committee Inc./ ; }, mesh = {Animals ; *Arboviruses/genetics/isolation &amp; purification/classification ; *Culicidae/virology/classification/genetics ; *DNA Barcoding, Taxonomic/methods ; *Mosquito Vectors/virology/classification ; High-Throughput Nucleotide Sequencing ; *Biosurveillance/methods ; *Metagenomics/methods ; Vertebrates/virology/classification ; Arbovirus Infections ; }, abstract = {Next-generation sequencing (NGS) has the potential to transform mosquito-borne disease surveillance but remains under-utilised. This study introduces a comprehensive multi-loci metabarcoding-based MX (molecular xenomonitoring) approach to mosquito and arbovirus surveillance, enabling parallel identification of mosquito vectors, circulating arboviruses, and vertebrate hosts from bulk mosquito collections. The feasibility of this approach was demonstrated through its application to a large set (n = 110) of bulk field collections. This set was complemented by a number (n = 28) of single-species mosquito pools that had previously been screened for viruses using quantitative reverse transcription PCR (RT-qPCR) and metatranscriptomics. Universal alphavirus and flavivirus primer sets were used to screen for arboviruses in the resulting metabarcoding library. Viral amplicons were then indexed and combined with mosquito-specific (ITS2), universal invertebrate (COI), and vertebrate (Cyt b) barcode amplicons prior to sequencing. This approach confirmed the presence of all previously identified mosquito species, as well as those commonly misidentified morphologically, and enabled a degree of quantification regarding their relative physical abundance in each collection. Additionally, the developed approach identified a diverse vertebrate host community (18 species), demonstrating its potential for defining host preferences and, in tandem with the viral screens and associated vector data, understanding disease transmission pathways. Importantly, metabarcoding detected a diversity of regionally prevalent arboviruses and insect-specific viruses, with all three viral diagnostics demonstrating a similar sensitivity and specificity in detecting Ross River virus and Barmah Forest virus, Australia's most common arboviruses. In summary, multi-loci metabarcoding is an affordable and efficient MX tool that enables complete mosquito-borne disease surveillance.}, }
@article {pmid40755083, year = {2025}, author = {Koseki, Y and Takeshima, H and Yoneda, R and Katayanagi, K and Ito, G and Yamanaka, H}, title = {gmmDenoise: A New Method and R Package for High-Confidence Sequence Variant Filtering in Environmental DNA Amplicon Analysis.}, journal = {Molecular ecology resources}, volume = {25}, number = {8}, pages = {e70023}, doi = {10.1111/1755-0998.70023}, pmid = {40755083}, issn = {1755-0998}, support = {JP21K12329//Japan Society for the Promotion of Science/ ; JP22K14908//Japan Society for the Promotion of Science/ ; JP25K02038//Japan Society for the Promotion of Science/ ; }, mesh = {*DNA, Environmental/genetics ; *DNA Barcoding, Taxonomic/methods ; *Computational Biology/methods ; *Genetic Variation ; *Metagenomics/methods ; *Software ; Sequence Analysis, DNA/methods ; }, abstract = {Assessing and monitoring genetic diversity is vital for understanding the ecology and evolution of natural populations but is often challenging in animal and plant species due to technically and physically demanding tissue sampling. Although environmental DNA (eDNA) metabarcoding is a promising alternative to the traditional population genetic monitoring based on biological samples, its practical application remains challenging due to spurious sequences present in the amplicon data, even after data processing with the existing sequence filtering and denoising (error correction) methods. Here we developed a novel amplicon filtering approach that can effectively eliminate such spurious amplicon sequence variants (ASVs) in eDNA metabarcoding data. A simple simulation of eDNA metabarcoding processes was performed to understand the patterns of read count (abundance) distributions of true ASVs and their polymerase chain reaction (PCR)-generated artefacts (i.e., false-positive ASVs). Based on the simulation results, the approach was developed to estimate the abundance distributions of true and false-positive ASVs using Gaussian mixture models and to determine a statistically based threshold between them. The developed approach was implemented as an R package, gmmDenoise and evaluated using single-species metabarcoding datasets in which all or some true ASVs (i.e., haplotypes) were known. Example analyses using community (multi-species) metabarcoding datasets were also performed to demonstrate how gmmDenoise can be used to derive reliable intraspecific diversity estimates and population genetic inferences from noisy amplicon sequencing data. The gmmDenoise package is freely available in the GitHub repository (https://github.com/YSKoseki/gmmDenoise).}, }
@article {pmid41131465, year = {2025}, author = {Hamdene, I and Bez, C and Bertani, I and López-Menchero, JR and Yahyaoui, A and Venturi, V and Sadfi-Zouaoui, N}, title = {Endophytic bacterial communities associated with halophytic plants in kebili and Gabes regions of Southern Tunisia.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {683}, pmid = {41131465}, issn = {1471-2180}, abstract = {In the arid regions of southern Tunisia, soil and irrigation water salinity represent major challenges to agricultural sustainability. Despite the increasing interest in plant-associated microbes, the role of endophytic bacteria in conferring salt tolerance remains largely unexplored in this context. To address this gap, twenty-two halophytic plants and their associated soils were sampled from five distinct sites across the Kebili and Gabes governorates. Significant differences in soil physicochemical properties were observed between sampling sites. The soils are generally poorly developed, non-fertile (with very low organic matter and high CaCO3 levels), and highly saline, leading to limited cultivation potential. Molecular identification of plants revealed nine different families and 14 genera, with the Amaranthaceae family being the most prominent, including Atriplex spp. (2), Bassia spp. (2), Suaeda spp. (4), and Halocnemum spp. (1). Bacterial community studies were conducted of both culturable and non-culturable endophyte communities inhabiting the green and root compartments of different halotolerant plants. Endophytic microbiome compositions differed between above-ground and below-ground tissues within the same plant family. A higher prevalence of three phyla Proteobacteria (67.80%), Firmicutes (14.06%), and Actinobacteria (6.57%) was detected across all samples. At the genus level, Acinetobacter, Halomonas, Kushneria, Pseudomonas, Psychrobacter, Stenotrophomonas, and Streptomyces formed the common core microbiome. Functional predictions of endophytic bacteria in halophytes highlighted multiple KEGG functional pathways, indicating recruitment of beneficial bacterial taxa to adapt to extreme hypersaline conditions, including plant growth-promoting, biocontrol, and halophilic bacteria.}, }
@article {pmid41131367, year = {2025}, author = {Welsh, C and Cabotaje, PR and Marcelino, VR and Watts, TD and Kountz, DJ and Jespersen, M and Gould, JA and Doan, NQ and Lingford, JP and Koralegedara, T and Solari, J and D'Adamo, GL and Huang, P and Bong, N and Gulliver, EL and Young, RB and Land, H and Walter, K and Cann, I and Pereira, GV and Martens, EC and Wolf, PG and Ridlon, JM and Gaskins, HR and Giles, EM and Lyras, D and Lappan, R and Berggren, G and Forster, SC and Greening, C}, title = {A widespread hydrogenase supports fermentative growth of gut bacteria in healthy people.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {41131367}, issn = {2058-5276}, support = {FT240100502//Department of Education and Training | Australian Research Council (ARC)/ ; DE220100965//Department of Education and Training | Australian Research Council (ARC)/ ; FL210100258//Department of Education and Training | Australian Research Council (ARC)/ ; DE230100542//Department of Education and Training | Australian Research Council (ARC)/ ; APP1178715//Department of Health | National Health and Medical Research Council (NHMRC)/ ; NNF21OC0066716//Novo Nordisk/ ; "STEM" 48574-1//Energimyndigheten (Swedish Energy Agency)/ ; }, abstract = {Disruption of hydrogen (H2) cycling in the gut is linked to gastrointestinal disorders, infections and cancers. However, the mechanisms and microorganisms controlling H2 production in the gut remain unresolved. Here we show that gut H2 production is primarily driven by the microbial group B [FeFe]-hydrogenase. Metagenomics and metatranscriptomics of stool and tissue biopsy samples show that hydrogenase-encoding genes are widely present and transcribed in gut bacteria. Assessment of 19 taxonomically diverse gut isolates revealed that the group B [FeFe]-hydrogenases produce large amounts of H2 gas and support fermentative growth of Bacteroidetes and Firmicutes. Further biochemical and spectroscopic characterization of purified enzymes show that they are catalytically active, bind a di-iron active site and reoxidize ferredoxin derived from the pyruvate:ferredoxin oxidoreductase reaction. Group B hydrogenase-encoding genes are significantly depleted in favour of other fermentative hydrogenases in patients with Crohn's disease. Finally, metabolically flexible respiratory bacteria may be the dominant hydrogenotrophs in the gut, rather than acetogens, methanogens and sulfate reducers. These results uncover the enzymes and microorganisms controlling H2 cycling in the healthy human gut.}, }
@article {pmid41131151, year = {2025}, author = {Buffington, JD and Kuo, HC and Hu, K and Chang, YC and Javanmardi, K and Voigt, B and Li, YR and Little, ME and Devanathan, SK and Xhemalçe, B and Gray, RS and Finkelstein, IJ}, title = {Discovery and engineering of retrons for precise genome editing.}, journal = {Nature biotechnology}, volume = {}, number = {}, pages = {}, pmid = {41131151}, issn = {1546-1696}, support = {F-1808//Welch Foundation/ ; F-1808//Welch Foundation/ ; F-1808//Welch Foundation/ ; F-1808//Welch Foundation/ ; F-1808//Welch Foundation/ ; F-1808//Welch Foundation/ ; F-1808//Welch Foundation/ ; }, abstract = {Retrons can produce multicopy single-stranded DNA in cells through self-primed reverse transcription. However, their potential for inserting genetic cargos in eukaryotes remains largely unexplored. Here we report the discovery and engineering of highly efficient retron-based gene editors for mammalian cells and vertebrates. Through bioinformatic analysis of metagenomic data and functional screening, we identify retron reverse transcriptases that are highly active in mammalian cells. Rational design further improves the editing efficiency to levels comparable with conventional single-stranded oligodeoxynucleotide donors but from a genetically encoded cassette. Retron editors exhibit robust activity with Cas12a nuclease and Cas9 nickase, expanding the genomic target scope and bypassing the need for a DNA double-stranded break. Using a rationally engineered retron editor, we incorporate a split GFP epitope tag for live-cell imaging. Lastly, we develop an all-RNA delivery strategy to enable DNA-free gene editing in cells and vertebrate embryos. This work establishes retron editors as a versatile and efficient tool for precise gene editing.}, }
@article {pmid41131078, year = {2025}, author = {Chen, R and Guo, X and Wu, M and Zheng, T and Chen, S and He, B}, title = {Bacillus velezensis ES2-4 modulates root exudation and microbiome remodeling to enhance soybean resistance against gray mold.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {37098}, pmid = {41131078}, issn = {2045-2322}, support = {32100240//National Natural Science Foundation of China/ ; 32100240//National Natural Science Foundation of China/ ; 32100240//National Natural Science Foundation of China/ ; 32100240//National Natural Science Foundation of China/ ; 32100240//National Natural Science Foundation of China/ ; 32100240//National Natural Science Foundation of China/ ; }, mesh = {*Bacillus/physiology ; *Glycine max/microbiology/metabolism/immunology ; *Plant Roots/microbiology/metabolism ; *Botrytis/pathogenicity ; *Microbiota ; *Plant Diseases/microbiology/prevention &amp; control ; Rhizosphere ; *Disease Resistance ; Soil Microbiology ; }, abstract = {Gray mold, caused by Botrytis cinerea, represents a significant threat to soybean productivity, while conventional chemical control strategies raise concerns regarding long-term sustainability. Plant-associated beneficial microbes, such as Bacillus velezensis, have been proposed as environmentally sustainable alternatives; however, their specific roles in modulating root-microbe interactions remain insufficiently characterized. This study investigated the mechanisms by which B. velezensis ES2-4 enhances soybean resistance by modulating root exudate composition and restructuring rhizosphere microbial communities. Metabolomic and metagenomic analyses indicated that ES2-4 inoculation led to the upregulation of antifungal metabolites (e.g., oxalic acid, eicosane) in root exudates, which facilitated the recruitment of beneficial bacteria while inhibiting B. cinerea proliferation. Pathogen infection was associated with disruptions in rhizosphere microbial diversity; however, ES2-4 application restored bacterial richness, particularly within the Alphaproteobacteria and Streptomyces lineages, while reducing the relative abundance of fungal pathogens. Co-occurrence network analysis further demonstrated that ES2-4 inoculation promoted microbial interactions associated with stress-responsive pathways, including two-component signaling systems and fatty acid metabolism, while downregulating pathogen-associated metabolic functions. These findings elucidate a dual mechanism through which ES2-4 enhances plant immunity via metabolite-mediated microbiome modulation, highlighting its potential as a sustainable biocontrol agent against soybean gray mold.}, }
@article {pmid41130610, year = {2025}, author = {Karim, DM and Papp, M and Fehérvári, P and Turan, C and Hegyi, P and Molnar, Z and Madách, K}, title = {No difference in microbial diversity between bronchoalveolar lavage and tracheal sampling: a systematic review and meta-analysis.}, journal = {BMJ open respiratory research}, volume = {12}, number = {1}, pages = {}, doi = {10.1136/bmjresp-2025-003456}, pmid = {41130610}, issn = {2052-4439}, mesh = {Humans ; *Trachea/microbiology ; *Microbiota ; *Bronchoalveolar Lavage Fluid/microbiology ; *Bronchoalveolar Lavage/methods ; *Specimen Handling/methods ; }, abstract = {INTRODUCTION: The respiratory microbiome has a vital role in maintaining respiratory health and preventing pathogen colonisation, but traditional diagnostic methods fail to capture a complete picture of it. Metagenomic sequencing has improved our understanding of microbial ecosystems in both acute and chronic pathologies. However, its results have not been systematically compared between different respiratory sampling techniques, as has been done with traditional methods. Our study aims to compare the microbial diversity in bronchoalveolar lavage (BAL) and tracheal samples using microbiome sequencing.<br><br>METHODS: A systematic search was conducted in Medline, Embase and CENTRAL databases to identify studies where lower respiratory tract microbiome specimens were collected simultaneously using BAL and tracheal sampling and diversity was analysed postsequencing. Risk of bias was assessed with our specifically tailored tool. A random-effects model was used for data synthesis, analysing pooled Shannon, Chao1 and Simpson indices.<br><br>RESULTS: We screened 1050 potentially relevant publications, 10 of which were included. No significant difference was found in microbial alpha diversity between BAL and tracheal samples. The subgroup analysis of tracheal sample types, including sputum and endotracheal aspirate, revealed no significant differences compared with BAL.<br><br>CONCLUSIONS: Tracheal sampling methods offer a viable and less invasive alternative to BAL for characterising microbiome alpha diversity in clinical or research settings where segmental sampling is not required. However, further high-quality comparative studies are needed to confirm these findings.<br><br>PROSPERO REGISTRATION NUMBER: CRD42023436934.}, }
@article {pmid41130504, year = {2025}, author = {Song, Y and Zhang, J and Shen, X and Yang, L and Jia, Y and Song, F and Huang, Y and Han, B and Zhang, N and Ma, G}, title = {Study on the association between microplastic exposure and gut microbiota based on metagenomics: A pilot study on 66 young college students in China.}, journal = {Environmental research}, volume = {}, number = {}, pages = {122995}, doi = {10.1016/j.envres.2025.122995}, pmid = {41130504}, issn = {1096-0953}, abstract = {OBJECTIVE: This study aimed to evaluate the types and mass concentrations of microplastics found in the stools of young college students. The underlying connections between microplastic exposure and gut microbiota were revealed.<br><br>METHODS: The study involved 66 participants, from whom stool samples were collected. Pyrolysis gas chromatography/mass spectrometry(Py-GCMS) was used to identify the types and mass concentrations of microplastics. Metagenomic sequencing was performed on the gut microbiota using high-throughput sequencing and metagenomic analysis techniques. Participants were divided into low group (LG) and high group (HG) based on the median mass concentration of microplastics in their stools. The differences in microbial diversity and species with significant differences between the two groups were analyzed. Spearman's correlation analysis was conducted to assess the associations between microbial characteristics and gene functions.<br><br>RESULTS: The detection rate of microplastics in the stool samples was 98.5%, with a median mass concentration of 54.7 &#x3bc;g/g. Significant differences were observed in gut microbiota between the two groups in terms of alpha and beta diversities. The relative abundance of Segatella copri was higher in the LG, while the relative abundance of Escherichia coli was higher in the HG. Compared with the LG, the gut microbiota in the HG exhibited an increase in the relative abundance of harmful bacteria, such as Dialister invisus, Clostridium fessum, and Evtepia gabavorous. The ADONIS analysis revealed that PS microplastics had a significant impact on the structure of the gut microbiota. However, no significant differences were observed among the metabolic pathways annotated in the Kyoto Encyclopedia of Genes and Genomes database between the two groups at either level I or II.<br><br>CONCLUSION: Participants with higher mass concentrations of microplastics in their stools exhibited an increase in the abundance of harmful intestinal bacteria. PS microplastics had the most profound impact on the gut microbiota structure.}, }
@article {pmid41130083, year = {2025}, author = {Tripathy, B and Singh, S and Behera, ID and Mishra, S and Das, AP}, title = {Metagenomic profiling of diversified marine microbiome across microplastic-contaminated niches of Bay of Bengal, India.}, journal = {Marine pollution bulletin}, volume = {222}, number = {Pt 3}, pages = {118872}, doi = {10.1016/j.marpolbul.2025.118872}, pmid = {41130083}, issn = {1879-3363}, abstract = {Diverse microorganisms in the marine sediment share a significant section of the global marine ecosystem and play a dominant role in marine biogeochemistry. The present study is the first to report an evaluation of shotgun metagenomic sequencing of microplastic-contaminated marine water and sediment samples from the coastal shores of the Bay of Bengal, India, across a stretch of 25 km, which houses a plethora of ubiquitous and uncultured microbial biodiversity coexisting with multitudinous human interventions. Illumina Nova sequencing 6000 suggested the presence of 88,539 scaffolds of data containing 132,568 identified genes of marine microorganisms. Taxonomic identification with the assistance of curated global databases ensued in the presence of Proteobacteria (53.12 %), Bacteroidetes (7.13 %), Actinobacteria (5.87 %), and miscellaneous (33.86 %) in abundance. Azonexus hydrophillus, Mycobacteroides abscessus, and Acidaminobacter hydrogenoformans were identified in profusion from the sequenced samples of the study area. The adaptation, sustenance, and survivability in the presence of plastic pollutants confirm the presence of microplastic-degrading enzymes in the microorganisms. The functional annotations revealed 54.32 % and 58.34 % similarities in genes with KEGG and COG databases, revealing the heavy presence of inorganic and amino acid transport channels. Further metabolic profiling of the identified novel microorganisms will assist in engineering the enhancement of microbial enzymes, such as cutinases, lipases, and esterases, leading to microplastic degradation activity. The present research work signifies the analysis and documentation of native microbiota of the marine shores of the Bay of Bengal and their interactive potentialities with microplastic-contaminated anthropogenic environments.}, }
@article {pmid41130000, year = {2025}, author = {Jin, G and Wang, M and Wang, X and Yuan, S and Peng, A and Chen, Z}, title = {Effects of sub-inhibitory antibiotic exposure on elemental cycling genes in an aquatic microbial community.}, journal = {Journal of hazardous materials}, volume = {499}, number = {}, pages = {140201}, doi = {10.1016/j.jhazmat.2025.140201}, pmid = {41130000}, issn = {1873-3336}, abstract = {Understanding how low concentrations of antibiotics influence biogeochemical cycling mediated by aquatic microbes is essential for assessing the ecological risks of antibiotic pollution. Here we examined the responses of carbon, nitrogen, and sulfur cycling genes in an aquatic microbial community to trimethoprim, lincomycin, and their combined exposure across seven sub-inhibitory concentrations spanning three orders of magnitude. We found that while the diversity of elemental cycling genes remained largely unchanged, the abundance of associated metabolic pathways declined significantly under high antibiotic levels,particularly after seven days of exposure to 10 mg/L lincomycin or ≥ 1 mg/L trimethoprim-lincomycin combinations. Some elemental cycling genes increased in abundance under elevated antibiotic exposure, accompanied by concentration-dependent enrichment of antibiotic resistance genes (ARGs). Metagenomic assembly further revealed that enriched ARGs and cycling genes co-localized on the same contigs. In addition, antibiotic exposure reshaped the topological structure of molecular ecological networks among cycling genes, indicating altered microbial interactions and ecological processes. Together, these findings show that antibiotics not only enrich resistance determinants but also modulate the abundance of carbon, nitrogen, and sulfur cycling genes, underscoring the complex impacts of anthropogenic antibiotic pollution on microbially mediated biogeochemical cycles.}, }
@article {pmid41129998, year = {2025}, author = {Hu, K and Wang, Z and Xu, Q and Chu, Y and Qian, Y and Zhang, X and Li, W and Han, Y and Wang, B and Zhang, H}, title = {Metagenomic insights into the effects of ecological water replenishment on resistome and pathogens in urban wetland.}, journal = {Journal of hazardous materials}, volume = {499}, number = {}, pages = {140117}, doi = {10.1016/j.jhazmat.2025.140117}, pmid = {41129998}, issn = {1873-3336}, abstract = {Urban wetland restoration increasingly relies on water replenishment, yet its impacts on resistome dissemination remain critically understudied. Here, we performed a comprehensive metagenomic survey of water and sediment from the Xixi National Wetland Park to investigate how water diversion from the surrounding Qiantang River affects the distribution and composition of antibiotic-resistant genes (ARGs), mobile genetic elements (MGEs), virulence factors (VFs), and pathogens. Among the detected ARGs, multidrug, macrolide-lincosamide-streptogramin, and bacitracin resistance genes were predominant. MGEs such as tnpA, IS91, and istA, and VFs involved in adherence and immune modulation were also abundant. Pathogens including Fusobacterium varium and Leptospira noguchii were frequently observed. RDA and MRM analysis revealed certain antibiotics emerged as influent factors of resistome composition. Notably, the vast majority of resistome types were shared between the wetland park and the external riverine environment, with a decline in resistome richness as distance from the water diversion source increased. This phenomenon indicates that river-to-wetland water diversion acts as a conduit, facilitating the broad dissemination of resistome components and pathogens into the wetland, while the wetland's self-purification capacity also plays a role. Nevertheless, a small subset of ARGs and MGEs was significantly enriched within the wetland interior. Collectively, these results highlight the ecological risks of water replenishment in urban wetlands and underscores the need for mitigation strategies, such as source-water pretreatment and wetland sediment remediation.}, }
@article {pmid41129997, year = {2025}, author = {Lu, W and Sun, S and Wang, Q and Wang, Z and Lu, YZ and Guo, J and Zhao, HP and Lai, CY}, title = {Acesulfame degradation within a methane-fed biofilm: a novel and efficient biodegradation route.}, journal = {Journal of hazardous materials}, volume = {499}, number = {}, pages = {140152}, doi = {10.1016/j.jhazmat.2025.140152}, pmid = {41129997}, issn = {1873-3336}, abstract = {Acesulfame (ACE), a persistent organic pollutant, is frequently detected across diverse aquatic environments, yet its environmental remediation remains challenging due to the inherently slow biodegradation. Here, we unveil a highly efficient ACE removal strategy using a methane-fed biofilm, achieving a degradation rate of 59.6 mg ACE/g VSS/h. Comprehensive analyses of transformation products (TPs) and toxicity profiles revealed that the biofilm mediated important and effective biodegradation pathways, promoting deep ACE degradation. Microbial community analysis, methane interruption experiments and pure culture studies implicated aerobic methanotrophs Methylococcus sp. and Methylomonas sp. as key players in ACE degradation. Metagenomic and metatranscriptomic analyses demonstrated that these methanotrophs exhibited high expression levels of particulate methane monooxygenase (pMMO) and cytochrome P450 monooxygenase (CYP450) genes within the biofilm community. Enzyme inhibition assays, combined with TP profiling, suggested that pMMO and CYP450 initiated the degradation of ACE. Scavenging experiments further suggested that hydroxyl radicals (•OH) generated through the catalytic activity of pMMO and CYP450 are crucial mediators in the ACE hydroxylation pathway. These findings provide the first evidence of ACE degradation in a methane-fed biofilm system, offering a promising and sustainable approach for the removal of recalcitrant organic contaminants from wastewater.}, }
@article {pmid41128819, year = {2025}, author = {Zhao, Y and Chen, J and Zhu, S and Xu, Y and Zhu, J and Yang, J and Zhou, W and Yang, Y and Lin, M and Chen, Q and Xia, M and Chen, Y and Liu, Y}, title = {Olsenella scatoligenes-derived Skatole Promotes Smooth Muscle Cell Proliferation and Migration to Aggravate Atherosclerosis.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf238}, pmid = {41128819}, issn = {1751-7370}, abstract = {Coronary artery disease remains the leading cause of mortality and morbidity globally. The gut microbiota has been implicated in the development of coronary artery disease through unclear mechanisms. Here, we demonstrate that the abundance and inter-species interactions of Olsenella scatoligenes are 4.7-fold and 1.6-fold higher in patients with coronary artery disease, respectively, and positively associated with disease severity. Furthermore, integrative metagenomic and metabolomic analyses identify skatole as the key microbial effector mediating the pro-atherogenic effect of Olsenella scatoligenes. Consistently, supplementation with Olsenella scatoligenes or skatole results in 1.26- and 1.23-fold increases in aortic plaque area, respectively, by promoting vascular smooth muscle cell proliferation and migration to the intima. Mechanistically, Olsenella scatoligenes -derived skatole facilitates nuclear translocation of the aryl hydrocarbon receptor, and enhances its binding to the promoter region of calponin 1. Silencing either aryl hydrocarbon receptor or calponin 1 attenuates approximately 40% of the vascular smooth muscle cell proliferation and migration induced by skatole. Collectively, our study identifies increased skatole production as the principal microbial effector linking Olsenella scatoligenes to aggravated atherosclerosis through activation of aryl hydrocarbon receptor -calponin 1 axis and underscores the therapeutic potential of targeting skatole production for the management of coronary artery disease.}, }
@article {pmid41128801, year = {2025}, author = {Blomström, AL and Hansen, S and Riihimäki, M}, title = {Identification and whole-genome characterization of a novel equine papillomavirus.}, journal = {Virus genes}, volume = {}, number = {}, pages = {}, pmid = {41128801}, issn = {1572-994X}, support = {H-20-47-555//The Swedish-Norwegian Foundation for Equine Research/ ; }, abstract = {Papillomaviruses (PVs) are small, non-enveloped viruses with double-stranded circular DNA genomes that infect a wide range of hosts, including mammals, birds, reptiles, and fish. While human papillomaviruses are extensively studied, recent advancements in high-throughput sequencing techniques have increased the detection and genetic characterization of PVs from various animal species. Here, we describe the identification and whole-genome characterization of a divergent equine papillomavirus (EcPV) detected through a viral metagenomic investigation of a horse in Denmark exhibiting neurological signs. Using Nanopore sequencing and Sanger sequencing, we assembled a complete viral genome of 7767 nucleotides. Phylogenetic analysis, based on concatenated E1, E2, L2, and L1 gene sequences, showed that the identified virus clustered within the same clade as EcPV3 (genus Dyoiotapapillomavirus) and EcPV6 (genus Dyorhopapillomavirus) but was situated on a distinct separate branch. Comparative genome analysis revealed approximately 52% nucleotide sequence similarity to EcPV3 and EcPV6, which share 66% similarity with each other. The L1 gene, commonly used for papillomavirus classification, exhibited a sequence identity to EcPV3 (58.4%) and EcPV6 (60.0%). The other viral genes displayed a 39-62% identity to the respective genes from EcPV3 and 6 further supporting the divergence of this newly identified PV. The combination of the phylogenetic analysis and the genetic divergence suggests that this newly identified papillomavirus may constitute a novel species or genus within the Papillomaviridae family. Our findings expand the known diversity of equine papillomaviruses and contribute valuable insights into their evolutionary relationships.}, }
@article {pmid41128541, year = {2025}, author = {Liu, C and He, Y and Zhang, H and Zhang, D and Ai, C and Tang, X and Yang, Q and Yu, Z and Tan, S and Friman, V-P and Liao, H and Zhou, S}, title = {Metabolic activity and survival strategies of thermophilic microbiomes during hyperthermophilic composting.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0095625}, doi = {10.1128/msystems.00956-25}, pmid = {41128541}, issn = {2379-5077}, abstract = {UNLABELLED: Hyperthermophilic composting (HTC) is a promising strategy for the treatment of organic solid waste, leveraging extreme thermophilic conditions (up to 90°C) driven by specialized microbial communities. While microbial community composition and succession have been previously described during HTC, the metabolic activity and adaptation of thermophilic microbiomes remain largely unexplored. In this study, we conducted time-series metagenomic and metatranscriptomic analyses on samples from a full-scale HTC system to characterize the composition, functional potential, and metabolic activity of thermophilic bacteria. A total of 227 non-redundant metagenome-assembled genomes (MAGs) were recovered, including 45 thermophilic MAGs (optimal growth temperatures > 45°C). Metatranscriptomic profiling revealed that thermophilic taxa-such as Thermus thermophilus, Planifilum fulgidum, and Thermaerobacter spp.-were highly transcriptionally active and played vital roles in heat generation through the upregulation of energy production and carbohydrate metabolism pathways. Additionally, these thermophiles exhibited survival and adaptation strategies involving physiological changes (e.g., spore formation, enhanced motility, and genome streamlining) and the induction of thermal resistance mechanisms (e.g., DNA repair systems, heat-shock proteins, and synthesis of compatible solutes). Overall, this study provides novel insights into the diverse survival strategies of thermophilic microbiomes in HTC and suggests potential avenues for optimizing thermophilic biotreatment processes for solid waste management.<br><br>IMPORTANCE: Despite increasing interest in hyperthermophilic composting as a sustainable waste treatment strategy, the mechanisms by which microbial communities both tolerate and drive extreme thermal conditions remain unclear. This study fills a critical knowledge gap by identifying a small group of highly active thermophilic bacteria that dominate during peak composting temperatures and orchestrate endogenous heat production. Using genome-resolved multi-omics, we demonstrate that these thermophiles couple high metabolic output with specialized survival strategies-such as genome streamlining, thermotolerance systems, and adaptive motility systems. These findings advance our understanding of microbial function under extreme conditions and provide a framework for optimizing thermophilic microbiome performance in engineered ecosystems.}, }
@article {pmid41128412, year = {2025}, author = {Peng, L and Song, H and Shi, H and Wu, L and Ma, Y and Fan, X and Wu, M and Duan, L and Li, Z and Yuan, H}, title = {Oral Multi-Enzymatic Manganese-Carbon Dots Alleviate Sepsis-Associated Lung Injury via the Gut-Lung Axis.}, journal = {ACS nano}, volume = {}, number = {}, pages = {}, doi = {10.1021/acsnano.5c10625}, pmid = {41128412}, issn = {1936-086X}, abstract = {Sepsis-induced pulmonary injury represents a life-threatening global health challenge due to poorly defined pathological mechanisms. The gut-lung axis has been proven to be widely involved in sepsis-induced lung injury, yet effective interventions targeting gut microbiota homeostasis remain unknown. Single-cell sequencing revealed increased alveolar apoptosis and impaired macrophage efferocytosis during sepsis pathogenesis. Thus, we designed oral manganese-doped carbon dots (Mn-CDs) to alleviate septic lung injury by remodeling gut microbiota homeostasis and targeting the gut-lung axis. Biochemical characterization demonstrated Mn-CDs possess multienzyme mimetic activities (SOD-, CAT-, POD-, GPx-like) and potent ROS scavenging capacity. In murine sepsis models, Mn-CDs significantly improved systemic indices and were associated with macrophage anti-inflammatory states with enhanced efferocytosis, as evidenced by transcriptomic profiling. Integrated metagenomic/metabolomic analyses identified Mn-CDs-mediated enrichment of g_Clostridium and g_Bacteroides, concomitant with elevated indole-3-propionic acid (IPA) production. Subsequent in vitro studies demonstrate that IPA likely binds primarily to the aryl hydrocarbon receptor (AHR), promoting both efferocytosis and anti-inflammatory polarization in macrophages, thereby mitigating septic lung injury. Notably, the fecal microbiota transplantation (FMT) from Mn-CDs-treated mice not only alleviated systemic symptoms but also effectively promoted efferocytic polarization of pulmonary macrophages in septic mice. Depletion of the gut microbiota resulted in a significant loss of the protective efficacy of Mn-CDs in a murine model of septic lung injury. Collectively, the gut-lung axis mediated by microbiota-derived IPA and macrophage efferocytosis contributes to the remediation of septic lung injury, highlighting the potential of Mn-CDs in microbiome-directed critical care.}, }
@article {pmid41127841, year = {2025}, author = {Turner, Z and Drabovich, AP}, title = {Opportunities and Challenges of Multiomics for Discovery and Monitoring of Human Pathogens.}, journal = {Environment &amp; health (Washington, D.C.)}, volume = {3}, number = {10}, pages = {1139-1153}, pmid = {41127841}, issn = {2833-8278}, abstract = {Detection and monitoring of pathogens is a central aspect of maintaining public health. Rare and neglected zoonotic viruses have the potential to evolve and expand exponentially, leading to unforeseen outbreaks, epidemics, and pandemics. The emerging multiomics and meta-omics techniques and workflows, such as proteogenomics and meta-genomics, offer the potential for the detection of harmful pathogens, as well as opportunities for the discovery of previously unknown bacterial, parasitic, or viral pathogens. Multiomics and meta-omics workflows provide molecular information for tracking pathogens and understanding the effectiveness of spread mitigation strategies. In addition to environmental monitoring, multiomics and meta-omics approaches have the potential for clinical applications and in-depth characterization of novel pathogens. In this review, we discuss recent applications of multiomics and meta-omics techniques, their advantages over traditional methods, and their potential implementations in biomedical research, environmental studies, and healthcare. We critically assess the benefits and challenges of multiomics and meta-omics studies and discuss their future perspectives.}, }
@article {pmid41127630, year = {2025}, author = {Kamau, M and Ergunay, K and Bourke, BP and Mutura, J and Lebunge, R and Ochieng, G and Gathii, K and Waitumbi, J and Mutai, B and Hassell, J and von Fricken, ME and Zimmerman, D and Murray, S and Jiang, L and Liao, HM and Grieco, JP and McDermott, EG and Achee, NL and Linton, YM}, title = {Potential spillover investigated by metagenome sequencing in Laikipia, Kenya reveals tick-borne pathogens and a novel bunyavirus.}, journal = {One health (Amsterdam, Netherlands)}, volume = {21}, number = {}, pages = {101226}, pmid = {41127630}, issn = {2352-7714}, abstract = {Tick-borne infections continue to present a global public health threat, and require a One Health approach for successful mitigation. We conducted cross-sectional tick screening utilizing an agnostic metagenomic screening strategy based on nanopore sequencing (NS), in an area spanning a range of habitats with intensified human-livestock-wildlife interactions in central Kenya. We further used targeted amplification by polymerase chain reaction (PCR) and sequence independent single primer amplification (SISPA) for confirmation and genome characterization, as necessary. We initially screened 44 ticks across pooled and individual samples belonging to seven species. Tick-associated bacteria-including spotted fever Rickettsia (13.3 %) and Coxiella-like endosymbionts, Francisella turcica and Francisella opportunistica, and tick-associated Borrelia-were detected in 86.6 % of samples. Viruses were detected in 93.3 % of samples, where Jingmen tick virus (JMTV) was observed as the most prevalent virus, detectable in 80 % of samples. A follow-up specific PCR confirmed JMTV virus detection in 75 %, associated with viral read abundance in NS. A complete JMTV genome was assembled from an Amblyomma sparsum tick, that displayed conserved motifs of putative structural and replication proteins. Maximum likelihood analyses placed the virus genome within a distinct clade in the proposed East African-Asian JMTV lineage. We further investigated a virus contig generated during the initial screening, with limited identities to Volzhskoe tick virus (VSTV). Subsequent NS and targeted PCR screening in an additional collection of 650 ticks from 11 species revealed a JMTV prevalence of 12.3 % in Amblyomma, Hyalomma and Rhipicephalus species. Follow-up NS and SISPA generated viral genomic segments, encoding a putative replicase and glycoprotein precursor. Pairwise comparisons and phylogeny indicated a novel virus-herein named as the Mpala tick virus-which is related to but distinct from VSTV and placed among unclassified members of Bunyaviricetes. In conclusion, our approach provides an effective strategy to detect a wide range of tick-borne bacteria and viruses, facilitating identification of opportunistic or endosymbiotic bacteria as well as novel viruses.}, }
@article {pmid41126918, year = {2025}, author = {Li, W and Zhou, D and Ji, Y and Tian, H and Meng, N and Li, J and Guo, N and He, X and Dao, M and Jin, X}, title = {Exploring the molecular intersection for hypertension, hyperlipidemia and their comorbid conditions through multi-omics approaches.}, journal = {Frontiers in cardiovascular medicine}, volume = {12}, number = {}, pages = {1593688}, pmid = {41126918}, issn = {2297-055X}, abstract = {BACKGROUND: Hypertension and hyperlipidemia are interconnected conditions that heighten cardiovascular risk, yet their intricate multi-scale molecular signatures remain inadequately mapped. This study aimed to conduct an integrated multi-omics investigation to unravel the key pathways and biomarkers underlying hypertension, hyperlipidemia, and both conditions.<br><br>METHODS: Metabolomic analysis was performed on serum samples and metagenomic analysis on fecal samples collected from individuals with hypertension (n&#x2009;=&#x2009;16), hyperlipidemia (n&#x2009;=&#x2009;19), or both conditions concurrently (n&#x2009;=&#x2009;20). In addition, 20 healthy individuals were recruited as controls.<br><br>RESULTS: Metabolomics uncovered altered levels of sphingolipids, phosphatidylcholines, glycylprolines, and nucleic acid metabolites, which may be associated with changes in vascular tone, lipid and protein homeostasis, and thyroid signaling. Metagenomics showed depletion in the abundance of the Fibrobacteres phylum. Altered abundances of Escherichia coli and Bacteroides vulgatus were also observed, which were correlated with deviations in lipid and carbohydrate metabolism. Sphingomyelin d18:1/16:0 and sphingomyelin d18:1/24:1(15Z) were the key metabolites that were identified as potential diagnostic biomarkers across conditions. Microbial taxa such as Enterococcus cecorum, Lachnospiraceae bacterium, Prevotella histicola, and Flavobacterium discriminated these diseases. Pathway analysis revealed glycoxylate, amino acid, purine, and sphingolipid metabolism alterations intersecting hypertension and hyperlipidemia.<br><br>CONCLUSIONS: This multi-omics landscape of comorbid disease pathways and biomarkers lays the foundation for precision diagnosis and treatment of prevalent cardiovascular conditions.}, }
@article {pmid41126179, year = {2025}, author = {Heuberger, M and Wehrkamp, CM and Pfammatter, A and Poretti, M and Graf, JP and Herger, A and Isaksson, J and Schlagenhauf, E and Honegger, R and Wicker, T and Sotiropoulos, AG}, title = {A reference metagenome sequence of the lichen Cladonia rangiformis.}, journal = {BMC biology}, volume = {23}, number = {1}, pages = {319}, pmid = {41126179}, issn = {1741-7007}, support = {310030_212428//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; }, mesh = {*Lichens/genetics/microbiology ; *Metagenome ; Symbiosis/genetics ; *Genome, Fungal ; *Ascomycota/genetics ; Chlorophyta/genetics ; }, abstract = {BACKGROUND: Lichens are an ancient symbiosis comprising the thalli of lichen-forming fungi, their photoautotrophic partners, and their microbiome. So far, they were poorly studied at the genome sequence level. Here, we present a reference metagenome for the holobiont of Cladonia rangiformis, aiming to illuminate the genomic complexity and evolutionary interactions within lichen symbioses.<br><br>RESULTS: Using long-read sequences from an entire symbiotic complex, plus short-read libraries from 28 additional diverse European lichen samples, we were able to separate genome sequences of 20 individual species. We constructed chromosome-scale assemblies of the C. rangiformis fungus and its trebouxioid green algal photobiont Asterochloris mediterranea. The genome of the fungus comprises&#x2009;~&#x2009;22% transposable elements and is highly compartmentalized into genic regions and large TE-derived segments which show extensive signatures of repeat-induced point mutations (RIP). We found that A. mediterranea centromeres are predominantly derived from two interacting retrotransposon families. We also identified strong candidates for genes that were horizontally transferred from bacteria to both alga and fungus. Furthermore, we isolated 18 near-complete bacterial genomes, of which 13 are enriched in the lichen compared to surrounding soil. Analysis of gene content in fungus, algae, and bacteria identified 22 distinct biosynthetic gene cluster categories for known secondary metabolites.<br><br>CONCLUSIONS: Our findings revealed that the thalli of C. rangiformis have a highly complex microbiome, comprising a mix of species that may include opportunists, ecologically obligate symbionts and possibly even lichen-beneficial bacteria. This study provides the first chromosome-scale genomic framework for a lichen holobiont, offering a foundational resource for future research into metagenomics, symbiosis, and microbial ecology in lichens.}, }
@article {pmid41125958, year = {2025}, author = {Fan, Y and Ni, M and Aggarwala, V and Mead, EA and Ksiezarek, M and Cao, L and Kamm, MA and Borody, TJ and Paramsothy, S and Kaakoush, NO and Grinspan, A and Faith, JJ and Fang, G}, title = {Long-read metagenomics for strain tracking after faecal microbiota transplant.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {41125958}, issn = {2058-5276}, support = {R35 GM139655/GM/NIGMS NIH HHS/United States ; }, abstract = {Accurate tracking of bacterial strains that stably engraft in faecal microbiota transplant (FMT) recipients is critical for understanding the determinants of strain engraftment, evaluating correlations with clinical outcomes and guiding the development of therapeutic consortia. While short-read sequencing has advanced FMT research, it faces challenges in strain-level de novo metagenomic assembly. Here we describe LongTrack, a method that uses long-read metagenomic assemblies for FMT strain tracking. LongTrack shows higher precision and specificity than short-read approaches, especially when multiple strains co-exist in the same sample. We uncovered 648 engrafted strains across six FMT cases involving patients with recurrent Clostridioides difficile infection and inflammatory bowel disease. Furthermore, long reads enabled assessment of the genomic and epigenomic stability of engrafted strains at the 5-year follow-up timepoint, revealing structural variations that may be associated with strain adaptation in a new host environment. Our findings support the use of long-read metagenomics to track microbial strains and their adaptations.}, }
@article {pmid41125530, year = {2025}, author = {Wang, X and Zhang, P and Suo, JS and Li, QJ and Wang, LZ and Zhang, Y and Wang, ZL}, title = {Clinical and microbiological insights into endogenous endophthalmitis: A ten-year study highlighting mNGS efficacy.}, journal = {Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jmii.2025.10.002}, pmid = {41125530}, issn = {1995-9133}, abstract = {BACKGROUND: Endophthalmitis is an ophthalmic emergency. In recent years, the incidence of endogenous endophthalmitis (EE) has increased. This study aims to elucidate the clinical characteristics and risk factors associated with the visual prognosis of EE.<br><br>METHODS: This study included 111 patients (121 eyes) diagnosed with EE who received intraocular and systemic treatment at Huashan Hospital, Fudan University, between January 2014 to December 2023. We conducted a comprehensive review of the demographic and clinical characteristics of the cohort and analyzed the risk factors linked to poor visual prognosis.<br><br>RESULTS: A total of 111 patients (121 eyes) were included in this study, of whom 101 eyes (83.5&#xa0;%) had identifiable pathogenic microorganisms, with Klebsiella pneumoniae (KP) was the most common pathogen. Compared to conventional culture methods (sensitivity 47.6&#xa0;%), metagenomic next-generation sequencing (mNGS) demonstrated significantly higher sensitivity (97.6&#xa0;%) in vitreous samples. Outcome analysis indicated that mNGS played a critical role in guiding clinical antibiotic adjustments, and patients receiving targeted therapy showed significant visual improvement (P&#xa0;=&#xa0;0.002), with stable systemic recovery. Furthermore, vitreous surgery had a positive effect on visual prognosis (P&#xa0;<&#xa0;0.001). Regression analysis revealed that poor initial visual acuity (VA) (OR: 20.622, 95&#xa0;% CI: 3.894-109.2) and KP infection (OR: 3.398, 95&#xa0;% CI: 1.096-10.538) were independent risk factors for poor final VA.<br><br>CONCLUSION: Our findings identify KP as the most common causative pathogen of EE. Infections caused by KP and poor initial VA are significant risk factors for poor visual outcomes. Looking ahead, mNGS holds promise as a crucial tool for the clinical diagnosis of EE.}, }
@article {pmid41124971, year = {2025}, author = {Gao, Y and Liu, Z and Sun, Y and Wang, J and Wu, X and Lu, X and Zhen, G}, title = {Mitigating perfluorooctanoic acid inhibition in electrochemically-assisted spiral upflow anaerobic membrane reactor for wastewater treatment: EPS interaction-desorption dynamics and metabolic pathway reconstruction.}, journal = {Water research}, volume = {289}, number = {Pt A}, pages = {124761}, doi = {10.1016/j.watres.2025.124761}, pmid = {41124971}, issn = {1879-2448}, abstract = {The widespread occurrence of perfluorooctanoic acid (PFOA) in industrial wastewater poses a major challenge to anaerobic treatment systems due to its chemical stability and persistence. Here, an electrochemical spiral upflow anaerobic membrane reactor (EC-SU-AnMBR) was developed by integrating a Ru-Ir/Ti-mesh-wrapped hollow-fiber membrane anode and a spiral Ti-mesh cathode to facilitate PFOA desorption and detoxification. PFOA readily accumulated in tightly bound extracellular polymeric substances (EPS) under open-circuit mode via hydrophobic interactions and electrostatic adsorption, disrupting anaerobic granular sludge (AnGS) structure and impairing microbial functionality. Electrochemical regulation (closed-circuit) effectively alleviated PFOA inhibition, achieving COD removal of 80.7 % (vs. 66.7 %) and a 1.5-fold higher CH4 recovery (227.7 vs. 140.8 mL/g COD/d). Electric field-migration and bioanode-membrane interception/oxidation together weakened PFOA-AnGS binding capability by altering EPS structural stability and interaction-desorption dynamics, decreasing PFOA retention rate in the bioreactor from initial 60.4 % to 2.1 % (p < 0.01) and reinforcing sludge regranulation. Further analysis demonstrated that the bioelectrocatalysis upregulated the relative abundance of functional genes involved in glucose metabolism (pfk, por, and ackA) and methanogenesis (fwd, mtr, and mcr) by selectively enriching hydrolytic/acidogenic bacteria and syntrophic-methanogenic consortia (Smithellaceae, Kosmotogaceae, and Methanotrichaceae) at both bioelectrodes. This study proposes a promising EC-SU-AnMBR system for the sustainable treatment of PFOA-contaminated wastewater and elucidates the metagenome-informed metabolic adaptation mechanisms under PFOA stress.}, }
@article {pmid41124778, year = {2025}, author = {Ohlsson, C and Li, L and Horkeby, K and Lawenius, L and Colldén, H and Sjögren, K and Baldanzi, G and Engström, G and Ärnlöv, J and Orho-Melander, M and Fall, T and Grahnemo, L}, title = {The circulating dihydrotestosterone/testosterone ratio is increased by gut microbial 5α-reductase activity in females.}, journal = {EBioMedicine}, volume = {121}, number = {}, pages = {105978}, doi = {10.1016/j.ebiom.2025.105978}, pmid = {41124778}, issn = {2352-3964}, abstract = {BACKGROUND: Dihydrotestosterone (DHT), the most potent ligand to the androgen receptor, is synthesised from testosterone (T) by 5α-reductase type 1 and 2. While type 1 is expressed in several non-reproductive tissues in both sexes, men also express high levels of the high-affinity type 2 isoform in reproductive tissues; yet women have a higher circulating DHT to T (DHT/T) ratio than men. We hypothesised that the high DHT/T ratio in women is caused by high gut microbiota (GM) 5α-reductase activity or altered β-glucuronidase-induced androgen reabsorption from the gut.<br><br>METHODS: We used a large cross-sectional subsample of the Swedish CArdioPulmonary bioImage Study (2897 women and 4338 men, 50-65 years of age) with GM composition and functionality determined by metagenome sequencing and circulating androgens determined by liquid chromatography-tandem mass spectrometry.<br><br>FINDINGS: We confirmed that women had higher (+194%) circulating DHT/T ratio than men. The relative abundance of microbial genes for 5&#x3b1;-reductase type 1 (P = 3 &#xd7; 10[-4]), but not &#x3b2;-glucuronidase, was positively associated with the DHT/T ratio in women. In women, the GM relative abundances of Odoribacter splanchnicus and Parabacteroides distasonis were positively associated with the relative abundance of microbial genes for 5&#x3b1;-reductase type 1 (P < 2 &#xd7; 10[-149]) and the circulating DHT/T ratio (O. splanchnicus P = 3 &#xd7; 10[-6]; P. distasonis P = 5 &#xd7; 10[-5]). In mechanistic studies, we observed very high DHT/T ratio in intestinal content of female conventionally-raised but not germ-free mice. In female mice, the DHT/T ratio was 86.9% higher in serum from the portal vein than in inferior vena cava (P = 0.007).<br><br>INTERPRETATION: These findings demonstrate that the circulating DHT/T ratio is increased by GM 5&#x3b1;-reductase activity in females. We propose that the GM acts as an endocrine organ influencing the androgenic status in females.<br><br>FUNDING: See Acknowledgements.}, }
@article {pmid41124743, year = {2025}, author = {Chu, S and Chen, Y and Xu, Z and Zhou, J and Li, K and Zhang, Q and Qian, M and Han, J and Qu, D}, title = {Metagenomic analysis of bacterial fitness and plasmids carrying blaTEM-1 and virulence genes before and after cleaning and disinfection in pig slaughterhouses.}, journal = {Journal of hazardous materials}, volume = {499}, number = {}, pages = {140168}, doi = {10.1016/j.jhazmat.2025.140168}, pmid = {41124743}, issn = {1873-3336}, abstract = {The identification of antibiotic resistance genes (ARGs), virulence genes, and pathogens in animal slaughterhouses poses a major threat to human health. However, limited data is available about the contamination and dissemination of ARGs in commercial pig slaughterhouses before and after disinfectant application. In this study, we used metagenomics and plasmid profiling to analys ethe effect of quaternary-ammonium-based cleaning and disinfection (C&amp;D) on the microbiota, antibiotic resistance genes (ARGs), and virulence genes (VFs) in a pig slaughterhouse. According to results C&amp;D effectively reduced the total microbial population and abundance of ARGs. However, the prevalence of disinfectant-resistant bacteria, particularly Escherichia coli, increased dramatically from 5.9 % to 14.9 %. Additionally, the clinically significant β-lactamase gene blaTEM-1 remained intact throughout C&amp;D process. The persistence of blaTEM-1 is primarily facilitated by low-fitness-cost IncR-type plasmids (pTZ17 and pSB24), which are characterised by their simplified structures that have no effect on bacterialgrowth or motility and exhibit stability in the absence of antibiotics. On the other hand, the high-virulence IncFIB plasmid (pYA21) harbors numerous ARGs and VFs. Despite their low survival rate after C&amp;D, the remaining bacteria may pose an even greater risk. The results suggest that current disinfection protocols may unintentionally promote the persistence and dissemination of resistance plasmids with potential fitness or economic advantages. Our findings highlight the need of integrating plasmid ecology and virulence profiling into standard surveillance practices, which will enhance disinfection strategies and help to mitigate the spread of antimicrobial resistance.}, }
@article {pmid41124226, year = {2025}, author = {Barcytė, D and Žihala, D and Eliáš, M}, title = {Expanded diversity of pedinophytes provides a window into the evolution of the genetic code in organelles.}, journal = {PLoS genetics}, volume = {21}, number = {10}, pages = {e1011901}, doi = {10.1371/journal.pgen.1011901}, pmid = {41124226}, issn = {1553-7404}, abstract = {Mitochondria and plastids of various lineages exhibit genetic code alterations. However, the knowledge of the diversity and occurrence, mechanistic underpinnings, and evolutionary origins of codon reassignments in organelles remains incomplete. To address this gap, we focused on organelles of the neglected green algal class Pedinophyceae, as well as pedinophyte-derived secondary plastids of green-coloured dinoflagellates (peDinoflagellates). We isolated and characterized a novel pedinophyte, herein formally described as Oistococcus okinawensis gen. et sp. nov., and phenotypically documented the previously sequenced but morphologically uncharacterized strain YPF-701, herein described as Akinorimonas japonica gen. et sp. nov. Based on phylogenetic analyses, both new taxa were classified into the expanded family Resultomonadaceae. We sequenced the organellar genomes of O. okinawensis, and utilizing existing raw (meta)genomic data we assembled organellar genome sequences from other previously unexplored pedinophyte lineages. Bioinformatic analyses of the expanded set of pedinophyte organellar genomes painted a complex picture of their genetic code landscape. Concerning mitochondria, the stop-to-Trp reassignment of the UGA codon turned out to have evolved multiple times in pedinophytes, and the Arg-to-Ala reassignment of AGA/AGG codons was shown to be apomorphic for the whole order Marsupiomonadales. The latter has additionally converted UUA and UUG into termination codons, relying on specific mutations in the mtRF1a protein. All pedinophyte mitochondria seem to decode AUA as methionine rather than the standard isoleucine, and an analogous reassignment seems to be evolving also in plastids of two separate pedinophyte lineages. Finally, apart from the previously reported Ile-to-Met AUA reassignment, peDinoflagellate plastids have switched the meaning of the AGA/AGG codons from arginine to another amino acid (most likely alanine), and have modified their pRF2 protein to mediate translation termination at UUA/UCA codons. Pedinophyte(-derived) organelles present a broad spectrum of codon reassignments and provide important insights into the emergence and mechanisms of non-standard codon translation.}, }
@article {pmid41123794, year = {2025}, author = {Xiong, L and Liu, X and Zhang, L and Chen, W and Mo, Q and Sun, C}, title = {Q fever sternum osteomyelitis in a patient with history of cardiovascular surgery: A case report from China.}, journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {}, number = {}, pages = {}, pmid = {41123794}, issn = {1435-4373}, abstract = {This article reports a rare case of sternal osteomyelitis caused by Coxiella burnetii. The patient, a 59-year-old male with a history of aortic dissection and hypertension, had undergone ascending aorta replacement and aortic valvuloplasty. He was admitted in May 2022 due to a chest mass that had been enlarging since its discovery in October 2021. Despite antibiotic treatment, the symptoms did not improve, and he experienced recurrent low-grade fevers. Upon admission, CT imaging revealed multiple mediastinal lymph node enlargements and a cystic shadow anterior to the sternum handle. The infection was confirmed as Coxiella burnetii through surgical debridement and metagenomic next-generation sequencing (mNGS). The treatment was subsequently changed to doxycycline and hydroxychloroquine. Positron emission computed tomography with 18 F-fluorodeoxyglucose ([18 F] FDG PET/CT) imaging showed that the infection was localized to the sternum, excluding vascular and implant infections. The patient completed an 18-month course of antibiotics, leading to controlled infection and normalized renal function. This case highlights the complexities of diagnosing and managing Q fever osteomyelitis in patients post-cardiovascular surgery, demonstrating the crucial roles of mNGS and [18 F] FDG PET/CT in rapid diagnosis and effective treatment. These findings provide valuable insights and guidance for managing similar cases in the future.}, }
@article {pmid41123363, year = {2025}, author = {Yue, Z and Zhang, J and Xu, W and Peng, L and Liu, T and Sheng, S and Tao, Y and Zeng, L and Zhao, Z and Alberoni, D and Baffoni, L and Zhang, Q and Liu, B and Li, Q and Zhang, J and Zou, Y}, title = {CNPS.cycle: streamlining shotgun metagenomic data analysis for biogeochemical cycles.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0102125}, doi = {10.1128/msystems.01021-25}, pmid = {41123363}, issn = {2379-5077}, abstract = {UNLABELLED: Shotgun metagenomic data analysis for investigating biogeochemical cycles in the environment remains challenging, primarily due to the steep learning curve, intensive time investment, and high computational demands, all of which pose significant barriers for many researchers. We present a new R package called "CNPS.cycle," designed to streamline the interpretation of shotgun metagenomic data related to biogeochemical processes, complete with visually informative outputs. This comprehensive package comprises four distinct analysis modules, focused on carbon, nitrogen, phosphorus, and sulfur cycling. Users can easily utilize the package by uploading annotation result files derived from shotgun metagenomic data, specifically those based on the Kyoto Encyclopedia of Genes and Genomes and the NCBI non-redundant protein sequence database. The package then automates essential steps, including data preprocessing, curation, and differential analysis of biogeochemical cycle-related genes; analysis of microorganisms possessing biogeochemical cycle-related genes at the contig level; β-diversity analysis; and, finally, data visualization. The outcome is a comprehensive analysis revealing differentially abundant genes and functionally significant microbial entities associated with the carbon, nitrogen, phosphorus, and sulfur cycles, presented in the form of tables and high-quality images. This tool will provide profound insights into the relationship between soil microorganisms and elemental chemical cycles, thereby advancing our comprehension of soil ecosystems. For accessibility, the CNPS.cycle package is available on GitHub (https://github.com/yuezhengfu/CNPS.cycle), where detailed instructions on its usage can be found in the project's GitHub page (https://github.com/yuezhengfu/CNPS.cycle/wiki).<br><br>IMPORTANCE: The "CNPS.cycle" R package offers significant environmental implications by simplifying the analysis of shotgun metagenomic data related to biogeochemical cycles. Its automated workflow identifies key genes and microbes involved in carbon, nitrogen, phosphorus, and sulfur cycling, enhancing our understanding of microbial contributions to ecosystem functions. This tool enables researchers to explore microbial-mediated nutrient cycling more efficiently, supporting informed decisions in environmental management and climate change mitigation. By providing accessible, high-quality outputs, "CNPS.cycle" facilitates data-driven insights into the interplay between microbes and global biogeochemical processes.}, }
@article {pmid41123352, year = {2025}, author = {Akinsola, OA and Dahunsi, SO and Odekanle, EL}, title = {Metagenomic study of food waste anaerobic digestion.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0208725}, doi = {10.1128/spectrum.02087-25}, pmid = {41123352}, issn = {2165-0497}, abstract = {This study explores anaerobic digestion of food waste to understand the microbial community dynamics and metabolic pathways that drive the conversion of organic waste into biogas. Sampling was done at multiple time points during those 4 weeks (weekly) to capture microbial succession/changes over time. The microbial profile was evaluated using QIIME2 and BV-BRC, while functional annotation tools (PICRUSt2) were used to identify dominant pathways. The results reveal a temporal shift in microbial communities, with fermentative bacteria, such as Lactobacillus and Clostridia, dominating the early stages of digestion, followed by methanogenic archaea like Methanomicrobia in the later stages. Pathway analysis showed that fermentation, aromatic compound degradation, and methanogenesis were the primary metabolic processes, with methanogenesis becoming more prominent by week 3 (FW3_S162_R1). The study highlights the critical role of microbial community adaptation in maximizing methane production and offers new insights into optimizing anaerobic digestion for more efficient food waste biogas generation. By combining metagenomic and metabolomic approaches, this research provides a comprehensive understanding of the microbial and metabolic factors that shape the anaerobic digestion process, contributing to the development of sustainable waste management practices.IMPORTANCEThis study employs a metagenomic approach to elucidate the intricate microbial communities and metabolic processes involved in the anaerobic digestion of food waste. It highlights microbial interactions that influence biogas production, offering insights for optimizing waste-to-energy conversion. Understanding these dynamics is key to improving digestion efficiency, reducing environmental impacts, and advancing sustainable waste management and circular economy strategies. The findings provide a valuable foundation for future innovations addressing global waste and energy challenges.}, }
@article {pmid41122951, year = {2025}, author = {Vilonen, L and Thompson, A and Adams, B and Ayres, E and Franco, ALC and Wall, DH}, title = {Characterising Soil Eukaryotic Diversity From NEON Metagenomics Datasets.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e70062}, doi = {10.1111/1755-0998.70062}, pmid = {41122951}, issn = {1755-0998}, support = {//U.S. National Science Foundation/ ; }, abstract = {Belowground eukaryotic diversity serves a vital role in soil ecosystem functioning, yet the composition, structure, and macroecology of these communities are significantly under-characterized. The National Ecological Observatory Network (NEON) provides publicly available datasets from long-term surveillance of numerous taxa and ecosystem properties. However, this dataset is not routinely evaluated for its eukaryotic component, likely because analyzing metagenomes for eukaryotic sequences is hampered by low relative sequence abundance, large genomes, poorer eukaryote representation in public reference databases, and is not yet mainstream. We mined the NEON soil metagenome datasets for 18S rRNA sequences using a custom-built pipeline and produced a preliminary assessment of biodiversity trends in North American soil eukaryotes. We extracted ~800 18S rRNA reads per sample (~22,000 reads per site) from 1455 samples from 495 plots across 45 NEON sites in 11 biomes, which corresponded to 5183 genera in 35 phyla. To our knowledge, this represents the first large-scale soil eukaryote analysis of NEON data. We asked whether taxonomic richness paralleled patterns previously established ecological trends and found that eukaryotic richness was negatively correlated with pH, managed sites lowered eukaryotic richness by 47%, most biomes had a distinct eukaryotic community, and fire decreased eukaryotic richness. These findings parallel generally accepted ecological trends and support the notion that NEON soil metagenome datasets can and should be used to explore spatiotemporal patterns in soil eukaryote diversity, its association with ecosystem functioning, and its response to environmental changes in North America.}, }
@article {pmid41122237, year = {2025}, author = {Terra Machado, D and Bernardes Brustolini, OJ and Dos Santos Corrêa, E and Ribeiro Vasconcelos, AT}, title = {Prediction of sporulating Firmicutes from uncultured gut microbiota using SpoMAG, an ensemble learning tool.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e20232}, pmid = {41122237}, issn = {2167-8359}, mesh = {*Gastrointestinal Microbiome/genetics ; *Machine Learning ; *Spores, Bacterial/genetics ; Animals ; Humans ; *Firmicutes/genetics/physiology ; Cattle ; Feces/microbiology ; Metagenome ; Swine ; Phylogeny ; Ensemble Learning ; }, abstract = {Sporulation represents a key adaptive strategy among Firmicutes, facilitating bacterial persistence under environmental stress while mediating host colonization, transmission dynamics, and microbiome stability. Despite the recognized ecological and biomedical significance of spore-forming Bacilli and Clostridia, most taxa remain uncultivated, limiting phenotypic characterization of their sporulation capacity. To bridge this knowledge gap, we developed SpoMAG, an ensemble machine learning framework that predicts sporulation potential of metagenome-assembled genomes (MAGs) through supervised classification models trained on the presence/absence of 160 sporulation-associated genes. This R-based tool integrates Random Forest and support vector machine algorithms, achieving probabilistic predictions with high performance (AUC = 92.2%, F1-score = 88.2%). Application to fecal metagenomes from humans, cattle, poultry, and swine identified 63 putatively spore-forming MAGs exhibiting distinct host- and order-specific patterns. Bacilli MAGs from Bacillales and Paenibacillales orders showed high sporulation probabilities and gene richness, while Clostridia MAGs exhibited more heterogeneous profiles. Predictions included undercharacterized families in the spore-forming perspective, such as Acetivibrionaceae, Christensenellaceae, and UBA1381, expanding the known phylogenetic breadth of sporulation capacity. Nine genes were consistently present across all predicted spore-formers (namely pth, yaaT, spoIIAB, spoIIIAE, spoIIIAD, ctpB, ftsW, spoVD, and lgt), suggesting conserved genetic elements across uncultivated Firmicutes for future research. Average nucleotide identity (ANI) analysis revealed seven cases of species-level sharing (ANI value > 95%) among hosts, including a putative novel Acetivibrionaceae species, suggesting possible cross-host transmission facilitated by sporulation. In all 63 genomes predicted to sporulate, we identified nine genes across sporulation steps. In addition, SHapley Additive exPlanations (SHAP) analysis indicated 16 consensus genes consistently contributing to predictions (namely lytH, cotP, spoIIIAG, spoIIR, spoVAD, gerC, yabP, yqfD, gerD, spoVAA, gpr, ytaF, gdh, ypeB, spoVID, and ymfJ), bringing biologically meaningful features across sporulation stages. By combining gene annotation with interpretable machine learning, SpoMAG provides a reproducible and accessible framework to infer sporulation potential in uncultured microbial taxa. This tool enhances targeted investigations into microbial survival strategies and supports research in microbiome ecology, probiotic discovery, food safety, and public health surveillance. SpoMAG is freely available as an R package and expands current capabilities for functional inference in metagenomic datasets.}, }
@article {pmid41121668, year = {2025}, author = {Enagbonma, BJ and Modise, DM and Babalola, OO}, title = {Effects of Legume‒Cereal Rotation on Sorghum Rhizosphere Microbial Community Structure and Nitrogen-Cycling Functions.}, journal = {MicrobiologyOpen}, volume = {14}, number = {5}, pages = {e70085}, doi = {10.1002/mbo3.70085}, pmid = {41121668}, issn = {2045-8827}, support = {//This study was supported by the ICGEB Research Project (CRP/ZAF22-03) awarded to O.O.B./ ; }, mesh = {*Sorghum/microbiology/growth &amp; development ; *Rhizosphere ; *Soil Microbiology ; *Microbiota ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Fabaceae/growth &amp; development/microbiology ; Nitrogen/metabolism ; *Nitrogen Cycle ; Soil/chemistry ; Zea mays/microbiology/growth &amp; development ; *Edible Grain/growth &amp; development/microbiology ; Agriculture/methods ; }, abstract = {Legumes form mutualistic interactions with specific soil microbiomes that fix atmospheric nitrogen and improve soil fertility. However, legume-based rotations influence on soil microorganisms and their correlations with soil physicochemical parameters during subsequent crop development are not yet clear. We examined the shifts in microbial community structure and nitrogen genes via shotgun sequencing across cowpea-sorghum, soybean-sorghum, maize-sorghum rotations, and sorghum without precrops. Precropping in rotation significantly affected N-NO3, clay, and silt, and caused a shift in the rhizosphere microbiome. Actinomycetota was the most predominant bacteria across all the cropping systems, followed by Pseudomonadota, whose composition differed across the cropping systems. Legume in rotation increased the relative abundance of Streptomyces and reduced the relative abundances of Pyxidicoccus, Microbacterium, and Microvirga. Nocardioides and Solirubrobacter predominated in the soil after the maize crops. Shannon index, non-metric multidimensional scaling, and permutational multivariate analysis of variance revealed that crop rotation caused significant differences in both the alpha and beta diversity of the microbial community and the nitrogen-cycling functional genes. The relative abundances of amoC, narH, gltB, glnA, ureC, napA, and napA significantly increased in legume monocrops in rotation. The relative abundances of glnA, gltB, narZ, and narH increased in the soil after maize cropping, whereas sorghum without precrops significantly increased the relative abundances of glnA, narZ, and ureC. Several soil physicochemical parameters drive microbial communities. *S, Na, N-NH4, N-NH3, and P were the most significant environmental variables regulating microbiome and nitrogen-cycling genes by crop rotation. This study supports sustainable agricultural practices and promotes sorghum development through rhizosphere microbiome optimization.}, }
@article {pmid41121143, year = {2025}, author = {Zhou, H and Li, X and Mao, Y and Chen, Q and Zhu, D and Liu, C and Yao, Y and Yao, Y and Yu, Y and Feng, Y}, title = {Strain-level characterization of bacterial pathogens using metagenomic sequencing for patients with pneumonia.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {1149}, pmid = {41121143}, issn = {1479-5876}, support = {82072241//National Natural Science Foundation of China/ ; 82272338//National Natural Science Foundation of China/ ; 2022YFC2504502//Key R&amp;D Plan of the Ministry of Science and Technology of China/ ; 2023C03068//Research and Development Program of Zhejiang Province/ ; 2024C03187//Research and Development Program of Zhejiang Province/ ; }, mesh = {Humans ; *Metagenomics/methods ; Bronchoalveolar Lavage Fluid/microbiology ; High-Throughput Nucleotide Sequencing ; Acinetobacter baumannii/genetics/pathogenicity ; *Pneumonia/microbiology ; Klebsiella pneumoniae/genetics/pathogenicity ; Male ; Female ; Middle Aged ; Aged ; *Bacteria/genetics/pathogenicity ; Whole Genome Sequencing ; }, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) has emerged as an indispensable diagnostic tool for infectious diseases. The disparity in virulence and antimicrobial resistance among strains of the same species requires mNGS to reach strain-level resolution.<br><br>METHODS: To compare the subtyping performance between mNGS and culture, thirty bronchoalveolar lavage fluid (BALF) or blood specimens positive by culture were sequenced using the Illumina NextSeq platform, while whole genome sequencing (WGS) was conducted on the corresponding cultured colonies. Additionally, thirty BALF specimens underwent both mNGS and Oxford&#xa0;nanopore technology (ONT)-based metagenomic third-generation sequencing (mTGS) to compare the subtyping efficacy of the two platforms. To characterize the strain-level composition of pneumonia pathogen Acinetobacter baumannii and Klebsiella pneumoniae, 185 BALF specimens from three hospitals were analyzed by mNGS.<br><br>RESULTS: WGS of the cultured colonies yielded identical subtyping results to mNGS at the level of clonal complex (CC). Although mNGS and mTGS predicted largely consistent primary CCs, mTGS demonstrated less accuracy and precision in CC identification. Co-infections at the CC level were detected in 5.40% of&#xa0;A. baumannii-positive and 19.55% of&#xa0;K. pneumoniae-positive BALF specimens. CC composition differed markedly according to bacterial load and between primary and secondary CCs in co-infection specimens. Antimicrobial resistance profiles remained constant for patients with single-infection but varied for those with co-infection. Spatial and temporal consistency of CC composition was observed within individual patients.<br><br>CONCLUSIONS: The heterogeneity in virulence and antimicrobial resistance among CCs, together with the prevalence of strain-level co-infections, highlights the need to extend pathogen identification to the strain level. Under current technical conditions, mNGS is a more suitable subtyping tool compared to culture and mTGS.}, }
@article {pmid41121093, year = {2025}, author = {Jia, Y and He, M and Wang, F and Zhan, Y and Deng, Q and Shen, J and Wang, X and Ran, Q and Huang, W and Ling, Y and Wen, S}, title = {Indole-3-lactic acid protects the gut vascular barrier following intestinal ischemia injury through AhR/Nrf2/STAT3 mediated claudin 2 downregulation.}, journal = {Cell communication and signaling : CCS}, volume = {23}, number = {1}, pages = {447}, pmid = {41121093}, issn = {1478-811X}, support = {82302457//National Natural Science Foundation of China/ ; 82372187//National Natural Science Foundation of China/ ; 82272223//National Natural Science Foundation of China/ ; 23qnpy134//Fundamental Research Funds for the Central Universities/ ; }, mesh = {Animals ; *Receptors, Aryl Hydrocarbon/metabolism ; *NF-E2-Related Factor 2/metabolism ; Mice ; *Reperfusion Injury/metabolism/pathology/drug therapy ; *Down-Regulation/drug effects ; *STAT3 Transcription Factor/metabolism ; *Indoles/pharmacology ; *Intestinal Mucosa/metabolism/drug effects/pathology ; Male ; Mice, Inbred C57BL ; Gastrointestinal Microbiome/drug effects ; *Basic Helix-Loop-Helix Transcription Factors/metabolism ; Tryptophan ; *Intestines/pathology/blood supply/drug effects ; *Protective Agents/pharmacology ; Signal Transduction/drug effects ; }, abstract = {BACKGROUND &amp; AIMS: Dysfunction of the intestinal epithelial barrier (IEB) and gut vascular barrier (GVB) contributes to the development of intestinal ischemia/reperfusion (IR) injury. Tryptophan (TRP), an essential amino acid, plays a crucial role in maintaining intestinal homeostasis, yet its regulatory effects on the GVB following IR remain unexplored. We aimed to better define the role of TRP in intestinal IR in vivo and in vitro.<br><br>METHODS: Mice underwent intestinal ischemia/reperfusion (IR) and were fed control, TRP-recommended (TRP-r), or TRP-sufficient (TRP-s) diets. Fecal metagenomic sequencing analyzed microbial composition, and targeted metabolomics quantified tryptophan and its metabolites in intestinal and serum samples. ILA's effects on barrier integrity were assessed via tight junction protein expression and FITC-dextran permeability assays. RNA sequencing of intestinal endothelial cells elucidated mechanisms by which ILA modulated GVB function. The STAT3-claudin 2 relationship was validated in vitro by ChIP-qPCR.<br><br>RESULTS: TRP supplementation significantly reshaped the gut microbiota, mitigated tissue damage and enhanced the integrity of both the IEB and GVB. Indole-3-lactic acid (ILA), a key tryptophan metabolite, was identified as an important factor in preserving GVB function. Mechanistically, our results show that the aryl hydrocarbon receptor (AhR)/Nrf2/signal transducer and activator of transcription 3 (STAT3) pathway is essential for ILA-mediated improvement of GVB integrity and downregulation of the pore-forming protein claudin 2.<br><br>CONCLUSIONS: Our findings highlight the dual role of ILA in reinforcing both IEB and GVB functions and shed light on the molecular mechanisms underlying ILA's GVB-protective effects. This study implicates that ILA or other AhR-activating metabolites may serve as promising pharmacological agents for alleviating IR-induced intestinal damage.}, }
@article {pmid41120531, year = {2025}, author = {Brito, B and DeMaere, M and Lean, I and Hazelton, M and O'Rourke, BA and Holmes, EC and House, JK and Rowe, S and Myers, GSA and Roy Chowdhury, P}, title = {Leveraging metatranscriptomics for the characterisation of bovine blood viromes.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {36670}, pmid = {41120531}, issn = {2045-2322}, mesh = {Animals ; Cattle ; *Virome/genetics ; *Transcriptome ; *Cattle Diseases/virology/blood/genetics ; Kenya ; *Viruses/genetics/classification ; Gene Expression Profiling ; }, abstract = {Understanding the diversity of the bovine virome is essential for assessing their potential impact on cattle health and transmission risks. Viruses present in the blood comprise both those that establish persistent infections in blood cells and those present during transient viremia. Farm management practices, such as the reuse of syringes for treatments, vaccinations, and supplements, may inadvertently contribute to the spread of blood-borne pathogens, emphasizing the need for improved biosecurity measures. Herein, we used a metatranscriptomic approach to analyse 20 bovine blood transcriptomes from dairy cows in New South Wales, Australia, along with 577 publicly available blood transcriptomes from studies in Australia and Kenya. Our analysis identified several viruses that are known to infect blood cells, transmitted either by direct contact or by vectors, including bovine viral diarrhea virus, bovine gammaherpesvirus 6, hepacivirus, foamy virus, ephemeroviruses and a new species of a coltivirus. Our findings highlight the complexity of the bovine blood virome and underscore the importance of sustained surveillance to identify emerging pathogens and assess their potential role in cattle health. This study provides a framework for integrating transcriptomic data into disease monitoring efforts, ultimately contributing to improved cattle management and biosecurity practices.}, }
@article {pmid41120014, year = {2025}, author = {Zhang, L and Zhang, Y and Li, YY and Dou, Q and Peng, Y}, title = {Sequential oxygen intervention drives novel AOB-DGAOs interaction network enabling advanced nitrogen removal in simultaneous partial nitrification and endogenous denitrification (SPNED) process.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {133529}, doi = {10.1016/j.biortech.2025.133529}, pmid = {41120014}, issn = {1873-2976}, abstract = {The simultaneous partial nitrification and endogenous denitrification (SPNED) process, driven by ammonia-oxidizing bacteria (AOB) and denitrifying glycogen-accumulating organisms (DGAOs), shows significant potential for low-carbon wastewater treatment. However, rapid startup and efficiency are challenged by persistent nitrite-oxidizing bacteria (NOB) proliferation under low NH4[+]-N conditions and dissolved oxygen depletion of intracellular polyhydroxyalkanoates (PHA) in DGAOs. Here, a sequential oxygen intervention strategy is innovatively proposed: DGAOs population dominance was first established through anaerobic/anoxic mode, followed by a mid-position aerobic phase to construct a DGAOs-dominated AOB-DGAOs interaction network. SPNED startup was achieved within 46 days with > 99 % nitrogen removal efficiency. Co-occurrence networks and metagenomics revealed functional bacterial cooperation enabling carbon-efficient nitrogen removal. Results demonstrated that enriched DGAOs (abundance increased from 9.22 % to 28.25 %) preferentially consumed NO2[-]-N over oxygen under microaerobic conditions, starving NOB and creating a low-competition niche for AOB. Consequently, AOB abundance surged 22.69-fold within 16 days. Correspondingly, AOB-generated low-electron-demand NO2[-]-N reduced endogenous electron (NADH from PHA degradation) requirements for DGAOs denitrification. Furthermore, Candidatus Contendobacter (NO2[-]-N → NO) and Candidatus Competibacter (NO → N2) within DGAOs potentially executed stepwise denitrification, avoiding NADH loss through intra-community substrate competition. Coupled with subsequent oxygen intervention, activation of β-oxidation (151.4 % up-regulation in key enzyme) and TCA cycle (96.0 % increase in α-ketoglutarate dehydrogenase) in DGAOs boosted intracellular NADH levels 1.76-fold. This NADH-rich environment enhanced DGAOs functionality and sustained enrichment, stabilizing the AOB-DGAOs network for advanced nitrogen removal. This study proposes a previously underappreciated NOB-inhibition function of DGAOs, offering a novel strategy for efficient endogenous carbon utilization, advanced nitrogen removal, and operational stability.}, }
@article {pmid41118772, year = {2025}, author = {Jacoby, C and Scorza, K and Ecker, L and Nol Bernardino, P and Little, AS and McMillin, M and Ramaswamy, R and Sundararajan, A and Sidebottom, AM and Lin, H and Dufault-Thompson, K and Hall, B and Jiang, X and Light, SH}, title = {Gut bacteria metabolize natural and synthetic steroid hormones via the reductive OsrABC pathway.}, journal = {Cell host &amp; microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2025.09.014}, pmid = {41118772}, issn = {1934-6069}, abstract = {Steroid hormone metabolism by the gut microbiome affects host physiology, however, the underlying microbial pathways remain incompletely understood. Here, we isolate a gut bacterial species, which we designate Clostridium steroidoreducens, that reduces cortisol and related steroid hormones to 3β,5β-tetrahydrosteroid products. Through transcriptomics and enzymatic discovery, we establish the C. steroidoreducens OsrABC steroid hormone pathway. OsrA is a 3-oxo-Δ[1]-steroid hormone reductase that targets synthetic glucocorticoids, including prednisolone-a frontline Crohn's disease therapy. OsrB is a 3-oxo-Δ[4]-steroid reductase that converts steroid hormones to 5β-dihydrosteroid intermediates, which OsrC subsequently reduces to 3β,5β-tetrahydro products. Homologs of osrA and osrB predict steroid-reducing activity across gut bacteria and are enriched in metagenomes of Crohn's disease patients. Consistent with a role in modulating drug efficacy, C. steroidoreducens colonization decreases prednisolone bioavailability in gnotobiotic mice. These findings thus define a previously unrecognized pathway for microbial steroid hormone inactivation and establish a mechanistic basis for bacterial interference with anti-inflammatory therapies.}, }
@article {pmid41118252, year = {2025}, author = {Qi, X and Li, Y and Zhu, Y and Shen, R and Xie, Z}, title = {Rebuilding the gut ecosystem: Emerging strategies targeting the microbiota in antibiotic-associated diarrhea.}, journal = {Acta microbiologica et immunologica Hungarica}, volume = {}, number = {}, pages = {}, doi = {10.1556/030.2025.02690}, pmid = {41118252}, issn = {1588-2640}, abstract = {Antibiotic-associated diarrhea (AAD) is a prevalent iatrogenic complication of antibiotic therapy, primarily triggered by dysbiosis and loss of intestinal homeostasis. The traditional interventions, such as empirical probiotic use, have shown a modest and a heterogeneous efficacy. This review integrates the current mechanistic understanding of AAD through the lens of the microbiota-mucosal-immune axis and provides a comprehensive overview of emerging therapeutic strategies. By integrating evidence from metagenomics, metabolomics, and immunology, we highlight next-generation approaches, including rationally engineered probiotics, standardized fecal microbiota transplantation (FMT), and synthetic-biology-derived interventions. Recent progress in multi-omics technologies and machine learning has enabled patient-stratified modulation of the gut microbiota, moving beyond empirical supplementation toward precision ecological reprogramming. These advanced therapies demonstrate superior outcomes in restoring microbial diversity, strengthening epithelial barrier function, and re-establishing immunological homeostasis. Ultimately, the management of AAD requires a systems-biology strategy that leverages real-time microbiome analytics for targeted, accurate, and sustainable restoration of gut health.}, }
@article {pmid41117817, year = {2025}, author = {Gogoi, R and Bora, SS and Gogoi, B and Naorem, RS and Barooah, M}, title = {Insights into the microbial diversity and functionalities of potential hydrocarbon-degrading bioremediation agents in oil spill sludge of Assam, India.}, journal = {Archives of microbiology}, volume = {207}, number = {12}, pages = {325}, pmid = {41117817}, issn = {1432-072X}, mesh = {India ; Biodegradation, Environmental ; *Hydrocarbons/metabolism ; *Petroleum Pollution/analysis ; *Sewage/microbiology ; *Bacteria/metabolism/classification/genetics/isolation &amp; purification ; Surface-Active Agents/metabolism ; RNA, Ribosomal, 16S/genetics ; Petroleum/metabolism ; Phylogeny ; Biodiversity ; }, abstract = {Oil spill contamination poses a significant threat to environmental and ecological health, particularly in crude oil-rich regions such as Assam, a north-eastern state of India. This study explores the microbial diversity and functional potential of hydrocarbon-degrading bacteria in crude oil-contaminated sludge. Sludge samples were collected from three contaminated sites in Assam and analyzed for microbial diversity by culture dependent and independent (using 16 S rRNA amplicon sequencing) approaches. Metagenomic analysis revealed a diverse microbial community, with Proteobacteria and Planctomycetes dominating the metagenomes. Seven bacterial isolates, including Diaphorobacter nitroreducens, Lysinibacillus capsici, and Pseudomonas otitidis, were isolated and identified as potential hydrocarbon degraders. The isolates were screened and evaluated for biosurfactant production, hydrocarbon adhesion, and key enzymatic activities involved in degradation. These isolates exhibited significant biosurfactant-producing abilities, with Diaphorobacter nitroreducens MBRG1 showing the highest emulsification index (79%) and strong adherence to hydrocarbons. The enzymatic activities of alkane hydroxylase and alcohol dehydrogenase confirmed the metabolic capabilities of the isolates in hydrocarbon degradation. Optimal growth conditions for biosurfactant production were determined to be pH 7, 30 °C, 2% sucrose as the carbon source, and 3% yeast extract as the nitrogen source. The study highlights the potential of these indigenous bacterial isolates in bioremediation strategies to mitigate oil contamination. Future studies should focus on large-scale bioreactor studies, field trials, and strain improvement of these bacteria to enhance their degradation efficiency and adaptability to varied environmental conditions.}, }
@article {pmid41117699, year = {2025}, author = {Xie, H and Zhang, X and Liu, X}, title = {The Co-Metabolic Bioremediation of Benzo[a]pyrene Contaminated Soil by Achromobacter xylosoxidans B-2 and Its Effect on Indigenous Microbial Community.}, journal = {Environmental toxicology}, volume = {}, number = {}, pages = {}, doi = {10.1002/tox.24576}, pmid = {41117699}, issn = {1522-7278}, support = {2023YFC3709000//National Key Research and Development Program of China/ ; 2018YFC1800600//National Key Research and Development Program of China/ ; 21677093//National Natural Science Foundation of China/ ; 21806100//National Natural Science Foundation of China/ ; }, abstract = {Benzo[a]pyrene (BaP) is a persistent polycyclic aromatic hydrocarbon (PAH) that poses significant environmental and health risks. Co-metabolic bioremediation, which uses additional carbon sources to enhance microbial degradation, offers a promising approach for BaP removal. This study investigated the effects of different co-metabolic carbon sources on the growth of Achromobacter xylosoxidans B-2 and its efficiency in degrading BaP in both mineral salt medium (MSM) and BaP-contaminated soil. The addition of supplementary carbon sources, particularly starch and salicylic acid, significantly enhanced strain B-2 growth and BaP removal in MSM (p < 0.05), with the highest degradation rate reaching 46.35% in the starch-supplemented group. In soil, salicylic acid and starch also markedly improved BaP degradation, achieving 47.99% and 23.53% removal (both p < 0.01) after 30 days, respectively, compared to only 9.78% in the BaP-only group. Metagenomic analysis revealed that co-substrate amendments significantly altered soil microbiota, enriching PAH-degrading genera such as Achromobacter, especially the introduced A. xylosoxidans. This enrichment was accompanied by reduced overall microbial diversity, indicating strong selective pressure from the amendments. Functional gene profiling based on metagenomic data indicated an increased abundance of key PAH-degrading enzymes, including dioxygenases and dehydrogenases, in response to co-substrate addition. Redundancy analysis further indicated that environmental factors such as pH, organic matter, and phosphorus were significantly correlated with microbial community composition and BaP degradation efficiency. These findings demonstrate that co-metabolism not only enhances BaP removal but also drives functional and ecological changes in soil microbiota, providing mechanistic insight and practical guidance for improved bioremediation strategies.}, }
@article {pmid41117680, year = {2025}, author = {Karakayalı, EM and Tuğlu, M&#x130;}, title = {The contribution of probiotics to combined cellular therapy in skin wound healing in diabetic rats.}, journal = {Ulusal travma ve acil cerrahi dergisi = Turkish journal of trauma &amp; emergency surgery : TJTES}, volume = {31}, number = {10}, pages = {925-936}, doi = {10.14744/tjtes.2025.37711}, pmid = {41117680}, issn = {1307-7945}, mesh = {Animals ; *Probiotics/therapeutic use/pharmacology ; *Wound Healing/drug effects ; Rats ; *Diabetes Mellitus, Experimental/complications ; Male ; Skin/injuries ; *Cell- and Tissue-Based Therapy/methods ; }, abstract = {BACKGROUND: Diabetes-related wound care is still a major issue due to chronic and non-healing ulcers that are prone to infection and ultimately amputation. In recent years, cellular therapy (CT) products such as mesenchymal stem cells (MSC), platelet-rich plasma (PRP), and stromal vascular fraction (SVF) have been widely used. A combined cellular therapy (CCT) has not yet been tested as a triple combination, although its use alone and in dual combinations has been investigated. Probiotics (PB) accelerate healing by altering the intestinal microbiota. This study aims to examine the role of PB in enhancing the effects of CCT on diabetic wound healing.<br><br>METHODS: A 1&#xd7;1 cm2 full-thickness cutaneous wound was created after administering 40 mg/kg streptozotocin intraperitoneally (STZ i.p.) to induce a diabetic (DB) animal model. Animals were divided into four groups: DB, DB+PB, DB+CCT, and DB+CCT+PB, each with six adult Albino rats. The wound edges were treated with a total of 300 &#xb5;L of solution, consisting of 30 &#xb5;L each of 100 &#xb5;L 1&#xd7;106 MSC, 100 &#xb5;L SVF, and 100 &#xb5;L PRP as CCT. PB was administered orally at a dose of approximately 200 mg daily. Histochemical analyses were performed using hematoxylin and eosin (HE) and Masson's trichrome (MT). Immunohistochemical analyses were conducted for endothelial nitric oxide synthase (eNOS), Caspase-3, interleukin-10 (IL-10), vascular endothelial growth factor (VEGF), and Collagen I. The intestinal microbiome was examined through metagenomic analyses of taxonomic structure.<br><br>RESULTS: Combined cellular therapy provided more effective and faster healing in DB animals. It was discovered that PB further accelerated this process, leading to greater improvement. CCT was observed to reverse high eNOS, Caspase-3, and IL-10 expression, as well as low VEGF and Collagen I levels. Moreover, PB therapy significantly enhanced the positive effects of CCT. CCT in combination with PB significantly improved wound healing by preventing oxidative stress, apoptosis, and inflammation, while promoting vascularization and collagen organization.<br><br>CONCLUSION: Probiotic support was considered important for diabetic wound healing and was suggested to improve patients' quality of life.}, }
@article {pmid41117333, year = {2025}, author = {Naureckas Li, C and Jordan, N and Haymond, S and Koscinski, D and Jhaveri, R}, title = {Direct cost savings associated with reduction in plasma metagenomic sequencing.}, journal = {Infection control and hospital epidemiology}, volume = {}, number = {}, pages = {1-3}, doi = {10.1017/ice.2025.10329}, pmid = {41117333}, issn = {1559-6834}, abstract = {Following recognition that our hospital had higher use of plasma metagenomic next-generation sequencing than our peers, we implemented a process for approval by infectious diseases before test collection. This intervention is calculated to result in a direct cost savings of $79,505-$84,057/year, driven mainly by reduced laboratory costs.}, }
@article {pmid41115930, year = {2025}, author = {Fitzjerrells, RL and Meza, LA and Yadav, M and Olalde, H and Hoang, J and Paullus, M and Cherwin, C and Cho, TA and Brown, G and Ganesan, SM and Mangalam, AK}, title = {Multiple sclerosis patients exhibit oral dysbiosis with decreased early colonizers and lower hypotaurine level.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {199}, pmid = {41115930}, issn = {2055-5008}, support = {F31DE033564/DE/NIDCR NIH HHS/United States ; T90DE023520/DE/NIDCR NIH HHS/United States ; R03DE030527/DE/NIDCR NIH HHS/United States ; 1P20NR018081-01/NR/NINR NIH HHS/United States ; 1RO1AI137075//National Institute of Allergy and Infectious Diseases/ ; 1I01CX002212//U.S. Department of Veterans Affairs/ ; P30 ES005605/ES/NIEHS NIH HHS/United States ; }, mesh = {Humans ; *Dysbiosis/microbiology ; Female ; Male ; Adult ; *Taurine/analogs &amp; derivatives/analysis/metabolism ; Middle Aged ; Metagenomics ; *Mouth/microbiology ; *Multiple Sclerosis, Relapsing-Remitting/microbiology ; Metabolomics ; *Bacteria/classification/genetics/isolation &amp; purification ; Microbiota ; Fusobacterium nucleatum/isolation &amp; purification ; Metabolome ; *Multiple Sclerosis/microbiology ; Actinomyces/isolation &amp; purification ; Porphyromonas gingivalis/isolation &amp; purification ; }, abstract = {Although gut microbiome dysbiosis is implicated in the pathobiology of multiple sclerosis (MS), the role of the oral microbiome (OM), the second largest microbiome, remains poorly understood. Additionally, while the salivary metabolome has been linked to other neurodegenerative diseases; its role in people with Relapsing-Remitting MS (pwRRMS), the most prevalent form of MS, is unknown. Combining shotgun metagenomics with untargeted metabolomics, we identified a reduced abundance of several early colonizing species including Streptococcus and Actinomyces in pwRRMS and an enrichment of bacteria with pathogenic potential including Fusobacterium nucleatum, Porphyromonas gingivalis, and several Prevotella species. pwRRMS had an altered metabolite profile including a decreased hypotaurine compared to healthy controls. Thus we report altered oral microbiome and metabolome in pwRRMS which might contribute to MS pathobiology. These findings offer potential microbiome-metabolome based diagnostic biomarkers for MS and pave the way for novel therapeutic interventions to improve disease management and patient outcomes.}, }
@article {pmid41115834, year = {2025}, author = {Facey, FSB and Maharjan, R and Dinh, H and Buchanan, JS and Connal, LA and Tay, AP and Paulsen, IT and Cain, AK}, title = {Characterising the Multiple-Plastic Degrading Strain of Bacillus subtilis GM_03 From the Galleria mellonella Microbiome.}, journal = {Environmental microbiology reports}, volume = {17}, number = {5}, pages = {e70216}, doi = {10.1111/1758-2229.70216}, pmid = {41115834}, issn = {1758-2229}, support = {W911NF2320155//US Department of Defense/ ; FT220100152//Australian Research Council Future Fellowship/ ; 20235185//FSBF was supported by Macquarie University Research Excellence Scholarship Programme/ ; }, mesh = {Animals ; *Bacillus subtilis/metabolism/genetics/isolation &amp; purification/classification ; Larva/microbiology ; *Moths/microbiology ; Biodegradation, Environmental ; *Plastics/metabolism ; *Microbiota ; Polyethylene/metabolism ; Polyurethanes/metabolism ; Phylogeny ; Bacterial Proteins/genetics/metabolism ; Gastrointestinal Microbiome ; }, abstract = {Plastic waste is a mounting global problem with over 400 million tons of plastic produced annually and over 50% ending up in landfill after its intended use. Two types of plastics are particularly problematic and are difficult to recycle: low-density polyethylene (LDPE) and polyurethane (PU). Fortuitously, nature may offer a potential solution; Galleria mellonella larvae can digest various plastics, including LDPE, which is believed to be driven by microbes in their gut microbiome. Although some studies have examined their gut microbiota on a metagenomic level, little is known about their ability to degrade plastics. Here, we isolated six bacterial strains from G. mellonella larvae feeding on LDPE. One of them, identified as Bacillus subtilis GM_03, has the capacity to break down commercial PU (Impranil), in addition to LDPE. This bacterium encodes a suite of genes required for plastic degradation. Directed evolution was used to enhance this strain's plastic degrading rate by over six-fold. Sequencing of the evolved culture revealed four genes, srfAB, fadD, appA and citS, associated with this increased PU degradation rate. This is the first time that B. subtilis isolated from G. mellonella larvae has been shown to be capable of degrading multiple types of plastics.}, }
@article {pmid41115830, year = {2025}, author = {Yang, F and Xu, W and Zhu, L and Tian, X and Duan, Y and Xu, Y and Huang, Q and Zhao, F}, title = {Multiple Roles of Extracellular Vesicles in Promoting Microbial-Driven Manganese Reduction.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c05310}, pmid = {41115830}, issn = {1520-5851}, abstract = {Microbial-driven manganese (Mn) reduction influences the geochemical cycling of Mn and the environmental fate of various organic and inorganic substances. Extracellular vesicles (EVs) are known to impact microbial metabolic activities, but their specific role in Mn reduction remains arcane. Here, we explored the potential involvement of environmental EVs in this process through metagenomic analysis and validated their function using representative functional strains. There are 8.05 and 12.89% of EVs originating from electroactive microorganisms in soil and wastewater, respectively. The addition of EVs increases the birnessite reduction rate of Shewanella oneidensis MR-1 from 2.31 μmol/(L·h) to 20.86 μmol/(L·h). Microbial physiological assays and in situ electrochemical analyses revealed that EVs enhanced cellular metabolism, promoted biofilm formation, and facilitated extracellular electron transfer (EET). The presence of diverse redox enzymes and metabolites in EVs contributed to more efficient substrate utilization and energy conservation, which promoted biomass accumulation and increased substrate consumption by 45.33%. The inner and outer membrane c-type cytochromes, along with flavins contained in the EVs, are essential for promoting microbial EET. These findings highlight the multifaceted role of EVs in microbial-driven Mn reduction, which might also participate in other element cycles in the same way.}, }
@article {pmid41114585, year = {2025}, author = {Aries Marchington, M and Gasvoda, H and Michelotti, M and Rodriguez-Caro, F and Gooman, A and Perez, A and Hensley-McBain, T}, title = {APOE genotype and sex drive microbiome divergence after microbiome standardization in APOE-humanized mice.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0042925}, doi = {10.1128/msphere.00429-25}, pmid = {41114585}, issn = {2379-5042}, abstract = {The APOE4 allele is the greatest known genetic factor for sporadic or late-onset Alzheimer's Disease (LOAD). Gut microbiome (GMB) dysbiosis can lead to poorer outcomes in disease. The intersection of sex, APOE genotype, inflammation, and gut microbiota is incompletely understood. Previous studies in humans and humanized APOE mice have demonstrated APOE-genotype-specific differences in the GMB. However, most of these studies were unable to resolve bacteria to the species level. It remains unclear how GMB changes with age and sex in the context of APOE genotype. In this study, humanized male mice with either APOE 2, 3, or 4 genotype were bred with the same two C57BL/6J sisters to standardize microbiomes across lines and monitor divergence based on APOE allele. Stool samples were collected at breeder set up and from the heterozygous (F1) and homozygous (F2) generations at wean and 6 months old. Stool was assessed via shallow shotgun sequencing to enable species and strain-level taxonomic resolution. The heterozygous pups' microbiome resembled each other at wean across all genotypes. However, the heterozygous pups and their homozygous offspring continued to diverge, particularly the APOE2 females. In homozygous mice, the GMB demonstrated significant divergence at 6 months of age based on sex and APOE genotype. In comparison to their APOE3 and APOE4 counterparts, APOE2 females and males demonstrated an increased quantity of bacteria associated with anti-inflammatory profiles, including in the Lachnospiraceae family (Lachnospiraceae bacterium UBA3401) and decreased quantities in the Turicibacteraceae family (higher levels are associated with LOAD).IMPORTANCEThe APOE4 allele is implicated as a significant risk factor for many diseases, including cardiovascular disease (responsible for more deaths than any other disease) and sporadic or late-onset Alzheimer's Disease (accounts for an estimated 60%-80% of all dementia cases). It is known that the gut microbiome (GMB) is affected by different genotypes and disease states. Mouse model studies have environmental and genetic controls, allowing a specific gene to be studied. This study aims at discovering key GMB species differences allowing for future therapeutic targets. The GMB of the experimental mice was standardized, and genotype and sex-specific divergence was observed with species and even strain level taxonomic resolution. Reported here are the first data demonstrating GMB divergence over time driven by APOE genotype from an inherited source and the first data to identify APOE genotype-specific bacteria species that may serve as therapeutic targets in APOE-driven disease.}, }
@article {pmid41114582, year = {2025}, author = {Zhang, Z and Wang, Z and Teng, P and Yu, T and Zhang, Y}, title = {Oxygen-tolerant nitrogen fixation in a marine alga-colonizing Planctomycetota.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0131625}, doi = {10.1128/aem.01316-25}, pmid = {41114582}, issn = {1098-5336}, abstract = {UNLABELLED: The microbiomes colonizing macroalgal surfaces orchestrate nutrient fluxes and symbiotic interactions within the algal environment. Among these communities, Planctomycetota are often dominant taxa. Although nitrogenase (nif) gene clusters have been identified in Planctomycetota isolates and metagenome-assembled genomes, functional validation of nitrogen fixation in pure culture has remained elusive. Moreover, the mechanisms enabling these bacteria to overcome oxygen sensitivity and fix nitrogen in algal-associated oxic niches remain unexplored. Here, we isolated Crateriforma sp. HD03, a Planctomycetota strain from the surface of Saccharina japonica (kelp), and provided the first experimental evidence of nitrogen-fixing activity in pure-cultured Planctomycetota. Strain HD03 harbors a complete nifHDKBEN gene cluster and exhibits a remarkable nitrogen fixation rate of 14.2 ± 1.5 nmol C2H4/(10[7] cells)/h under aerobic conditions. Genomic and physiological analysis reveals a suite of adaptations that likely mitigate oxygen stress, including genes associated with biofilm formation, hopanoid lipid synthesis, FeSII protein, hydrogenase, and bacterial microcompartments. Notably, while strain HD03 demonstrates oxygen-tolerant nitrogen fixation in pure culture, co-culture experiments with kelp under a photoperiod revealed that nifH (nitrogenase reductase gene) expression peaks during the low-oxygen dark phase, indicating that HD03 utilizes diurnal rhythms to temporally separate nitrogen fixation from photosynthetic oxygen production. A genomic survey of 142 Planctomycetota strains from NCBI GenBank database and HD03 identified two distinct clades harboring complete nifHDK gene clusters, suggesting a nitrogen-fixing potential across the phylum. By bridging the gap between genomic potential and functional validation, this study establishes Planctomycetota as important but underappreciated contributors to marine nitrogen input.<br><br>IMPORTANCE: Planctomycetota are abundant colonizers of macroalgal surfaces, yet their role in nitrogen fixation has remained unresolved despite genomic evidence of nitrogenase (nif) genes. Until now, no functional validation of nitrogen fixation in pure-cultured Planctomycetota has been reported. Here, we isolated Crateriforma sp. HD03 from kelp and for the first time demonstrated its ability to fix nitrogen in pure culture, confirming this key metabolic potential in marine Planctomycetota. Strain HD03 overcomes oxygen stress through a combination of biofilm formation and diurnal regulation of nifH expression, allowing nitrogen fixation under aerobic conditions to cope with the algal environment's oxic nature. Furthermore, genomic surveys revealed nitrogen fixation gene clusters across multiple Planctomycetota clades, suggesting widespread nitrogen-fixing capability in this phylum. Collectively, these findings identify Planctomycetota as important nitrogen providers in the ocean.}, }
@article {pmid41114530, year = {2025}, author = {Xiao, Y and Zhang, X and Shao, B and Wu, Z and Li, X and Yi, D and Li, T and Yang, T and Zhu, J and Huang, T and Deng, Y and Qiu, T and Yang, G and Sun, X and Wang, N}, title = {Hydroxytyrosol Improves Metabolic Dysfunction-Associated Fatty Liver Disease Dependent on the Modulation of Gut Microbiota.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.5c07003}, pmid = {41114530}, issn = {1520-5118}, abstract = {The global threat of metabolic dysfunction-associated fatty liver disease (MAFLD) is significant, but effective measures are still lacking. To explore the potential impact of hydroxytyrosol (HT), a plant polyphenol, in the metabolic outcomes of MAFLD and the mediating role of the gut microbiota, we performed an 8-week randomized placebo-controlled clinical trial in MAFLD patients and collected fecal bacteria for metagenomics analysis and targeted metabolomics. In this population-based trial, we have revealed that HT mitigates liver injury and steatosis in patients with MAFLD, as well as systemic glucolipid metabolism disorder. Through analysis of the differences in bacterial taxon and functional profiles, as well as correlation analysis between species and metabolic indicators, it was found that Fusicatenibacter saccharivorans (F. saccharivorans), the microbial species with the greatest difference after HT intervention, was also the most significantly correlated with metabolic parameters of MAFLD and showed a significant positive correlation with the content of fecal butanoic acid. Butanoic acid was further associated with MAFLD-related metabolic indexes. To confirm the potential causal relationship between alterations in gut microbiota induced by HT intervention and improved MAFLD metabolic phenotypes, fecal microbiota transplantation (FMT) was conducted using a model of pseudogerm-free mice. We have further demonstrated that the fecal microbiota from donors of MAFLD patients receiving HT supplementation can ameliorate liver and systemic phenotypes in western-diet-induced MAFLD mice, interpreting the robust action of gut microbiota remodeled by HT in improving MAFLD. Consequently, HT supplementation may represent a tactic for improving MAFLD by modulating the composition and functionality of the gut microbiota.}, }
@article {pmid41114048, year = {2025}, author = {Andermann, TM and Zeng, K and Guirales-Medrano, S and Groth, A and Ramachandran, BC and Sun, S and Sorgen, AA and Hill, L and Bush, AT and Liu, H and Jones, C and Roach, J and Conlon, BP and Rao, G and Chao, NJ and Fodor, AA and Sung, AD}, title = {Duration of Hospitalization is Associated with the Gut Microbiome in Patients Undergoing Hematopoietic Stem Cell Transplantation: Early Results from a Randomized Trial of Home Versus Hospital Transplantation.}, journal = {OBM transplantation}, volume = {9}, number = {3}, pages = {}, pmid = {41114048}, issn = {2577-5820}, abstract = {Home-based hematopoietic stem cell transplantation (HCT) is an innovative care model with growing interest, but its impact on the gut microbiome remains unexplored in a randomized setting. We present interim results from the first randomized controlled trials (RCT) evaluating the effect of HCT location-home versus hospital-on gut microbial diversity and antimicrobial resistance (AMR) gene carriage. We hypothesize that patients randomized to undergo home HCT would have higher gut taxonomic diversity and lower AMR gene abundance compared to those undergoing standard hospital HCT. We analyzed stool samples from the first 28 patients enrolled in ongoing Phase II RCTs comparing home (n = 16) and hospital (n = 12) HCT at Duke University using shotgun metagenomic sequencing to compare taxa and AMR gene composition between groups. We also performed a secondary analysis comparing patients who received transplants at outpatient infusion clinics versus inpatient standard HCT to evaluate the influence of hospitalization duration. In the primary RCT analysis, taxonomic and AMR gene α- and β-diversity were comparable between home and hospital groups, reflecting similar durations of hospitalization despite group allocation. In contrast, secondary analyses demonstrated that patients transplanted in outpatient infusion clinics who experienced significantly reduced hospitalization had higher gut taxonomic α-diversity and differential β-diversity, although AMR gene diversity remained unchanged. In summary, randomization by transplant location did not impact the gut microbiota to the same extent as the duration of hospitalization, although secondary analyses were heavily confounded. Even when taxonomic differences were observed, AMR genes were similar between groups. This RCT represents a novel investigation into how care setting influences the gut microbiome during HCT. Our findings suggest that hospital duration, rather than randomization allocation alone, is the primary driver of microbial disruption. These results underscore the potential for reducing hospital duration to mitigate microbiome injury, thereby informing future interventions to reduce infection risk and improve patient outcomes.}, }
@article {pmid41114028, year = {2025}, author = {Huang, H and Tong, Y and Hu, X and Liao, FK and Chen, R}, title = {The application value and challenges of metagenomic next-generation sequencing in the diagnosis of periprosthetic joint infection after arthroplasty.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1686503}, pmid = {41114028}, issn = {2296-858X}, abstract = {Metagenomic next-generation sequencing (mNGS) demonstrates high sensitivity, rapid diagnostic capabilities, and the potential to identify complex pathogens in periprosthetic joint infection (PJI) following arthroplasty, particularly when conventional culture methods are limited. mNGS enables the detection of polymicrobial infections and rare/fastidious pathogens, along with the ability to predict antimicrobial resistance (AMR) genes; however, the concordance between genotypic predictions and phenotypic resistance profiles requires further validation. In clinical practice, mNGS overcomes biofilm-related diagnostic barriers, facilitating early targeted antibiotic therapy and potentially reducing unnecessary revision surgeries, thereby lowering overall healthcare costs and improving patient outcomes. Nevertheless, its widespread adoption is hindered by high costs, lack of standardization, and risks of false-positive/false-negative results. Future research priorities include optimizing sample processing protocols, host DNA depletion, establishing diagnostic thresholds, and validating mNGS through integration with conventional methods. This review synthesizes recent advances in the diagnostic accuracy and clinical utility of mNGS for PJI, aiming to provide evidence-based insights for therapeutic decision-making and enhance the prevention and management of PJI.}, }
@article {pmid41114012, year = {2025}, author = {Wang, H and Li, J and Huang, W}, title = {Case Report: Fever of unknown origin with hemophagocytic lymphohistiocytosis and intestinal hemorrhage-a successfully treated case of severe visceral leishmaniasis.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1663551}, pmid = {41114012}, issn = {2296-858X}, abstract = {In recent years, some cases of severe visceral leishmaniasis (VL) in immunocompetent adults have gradually been reported. Hemophagocytic lymphohistiocytosis (HLH) and intestinal hemorrhage are two rare complications in patients with VL. Without treatment, the mortality rate of such patients is extremely high. We report a case of a 31-year-old immunocompetent male who initially presented with fever of unknown origin (FUO), later developed HLH and experienced multiple episodes of life-threatening intestinal hemorrhage. The diagnosis of visceral leishmaniasis was confirmed through metagenomic next-generation sequencing (mNGS). The patient was successfully treated with amphotericin B deoxycholate (AmB-D) and supportive care. During the two-year follow-up period, no new complications were found. This case highlights the value of mNGS in the diagnosis of complex infectious diseases and emphasizes the clinical significance of the multidisciplinary collaborative model for patients with VL and complex complications. It can provide a reference for the early diagnosis and comprehensive treatment of severe VL.}, }
@article {pmid41114005, year = {2025}, author = {Sun, R and Xu, W and Xu, Y and Xu, Z and Tan, Y and Li, J and Liu, H and Yung, CCM}, title = {Environmental gradients shape viral-host dynamics in the Pearl River estuary.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf164}, pmid = {41114005}, issn = {2730-6151}, abstract = {Marine viruses play critical roles in shaping microbial communities and driving biogeochemical cycles, yet their dynamics in estuarine systems are not well characterized. Here, we conducted a comprehensive metagenomic analysis of viral communities and virus-host interactions across the Pearl River estuary, a dynamic subtropical estuary in southern China. Using 24 metagenomic libraries from eight sampling sites, we identified 29,952 viral populations, with Uroviricota and potential Uroviricota accounted for 80.48% of taxa, underscoring their ecological importance. A key finding of our integrated analysis is the unexpectedly high abundance of nucleocytoplasmic large DNA viruses in offshore waters, which suggests a more significant role for eukaryotic viruses in coastal ecosystems than previously acknowledged and correlates with elevated levels of their eukaryotic hosts. Environmental variables, particularly salinity and nutrient availability, emerged as key drivers of viral and host distribution patterns. By linking environmental gradients to distinct community "envirotypes" and their underlying genomic features, we revealed novel virus-host interactions and highlighted the impact of environmental gradients on microbial ecology. Additionally, viral auxiliary metabolic genes linked to phosphorus and nitrogen metabolism suggest critical roles in modulating host metabolic pathways and influencing nutrient cycling. Our findings demonstrate how spatial heterogeneity and environmental gradients shape viral and microbial ecology in estuarine ecosystems. Our findings provide a holistic, multi-domain view of microbial and viral ecology, demonstrating how integrating prokaryotic, eukaryotic, and viral community analyses offers a more complete understanding of ecosystem function in these critical transition zones.}, }
@article {pmid41113669, year = {2025}, author = {Onohuean, H and Naik Bukke, SP and Thalluri, C and Abass, KS and Choonara, YE}, title = {Exosome engineering for targeted therapy of brain-infecting pathogens: molecular tools, delivery platforms, and translational advances.}, journal = {Frontiers in medical technology}, volume = {7}, number = {}, pages = {1655471}, pmid = {41113669}, issn = {2673-3129}, abstract = {Central nervous system (CNS) infections caused by pathogens such as HIV, Herpes simplex virus, Cryptococcus neoformans, and Toxoplasma gondii remain among the most difficult to treat due to the physiological barrier posed by the blood-brain barrier (BBB), pathogen latency, and systemic toxicity associated with conventional therapies. Exosome-based delivery systems are becoming a game-changing platform that can solve these therapeutic problems using their natural biocompatibility, minimal immunogenicity, and capacity to cross the BBB. This review current developments in exosome engineering that aim to make brain-targeted therapy for neuroinfectious illnesses more selective and effective. Much focus is on new molecular methods like pathogen-specific ligand display, aptamer conjugation, lipid modification, and click-chemistry-based surface functionalisation. These methods make it possible to target diseased areas of the brain precisely. Exosomes can also carry therapeutic payloads, such as anti-viral and antifungal drugs, gene editing tools like CRISPR/Cas9 and siRNA, and more. This makes them helpful in changing pathogens' persistence and the host's immunological responses. The paper tackle problems with translation, such as biodistribution, immunogenicity, GMP production, and regulatory issues. Future possibilities like synthetic exosomes, combinatory medicines, and delivery design that uses AI. The combination of nanotechnology, molecular biology, and infectious disease therapies shows that exosome engineering offers a new way to meet the clinical needs that are not satisfied in treating CNS infections.}, }
@article {pmid41113648, year = {2025}, author = {Dong, L and Du, Y and Qiu, F and Zhang, M and Wang, X and Zhu, X and Yao, Y and Li, J and Ji, X and Zhu, X}, title = {Metagenomic insights reveal the differences in the community composition and functional characteristics of the sea turtle microbiomes based on host species and tissue region.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1652229}, pmid = {41113648}, issn = {1664-302X}, abstract = {INTRODUCTION AND METHODS: Sea turtles have been proposed as health indicators of marine ecosystems for their characteristic of longevity and migratory, but they are facing serious threats due to various factors. The microbial communities within animals play an important role in health and disease. Our study aims to explore a thorough evaluation of the sea turtle microbiome by examining the oral, nasal, and cloacal microbial communities of three species: green turtles, hawksbills, and loggerheads, through metagenomic sequencing.<br><br>RESULTS: Utilizing approximately 705.81&#x202f;GB of metagenomic sequencing data from 63 samples collected from different turtle species and tissue regions, we created a nonredundant sea turtle microbial gene catalog (STMGC) containing 10,733,232 unique genes through the de-redundancy of open reading frames (ORFs). Our findings revealed that the sea turtle microbiomes were primarily composed of Pseudomonadota (formerly Proteobacteria) and Bacteroidota (formerly Bacteroidetes). The tissue region was a key factor affecting the variability in the sea turtle microbiome, with green turtles showing notable differences among the three turtle species. Pseudomonadota was significantly more abundant in oral samples, while Bacteroidota was more prevalent in nasal samples. Campylobacterota was identified as significantly more abundant in cloacal samples. Importantly, we discovered 389 genera and 1,445 species of potential pathogens within the sea turtle microbiome, indicating potential pathogenic risks that warrant further investigation alongside culturomics. Additionally, our study highlighted significant functional differences among the three turtles and tissue regions. It is worth noting that among the three sea turtles, antibiotic resistance genes are more prevalent in hawksbills, while virulence genes are more abundant in loggerheads. Moreover, within the three tissue regions, antibiotic resistance genes are higher in oral samples, while virulence genes are more extensive in cloacal samples.<br><br>CONCLUSION: The findings in our study demonstrate that the microbial composition and function in these sea turtles exhibit both species-specific and region-specific variations. The implications of these associations and the underlying mechanisms not only provide valuable insights for future studies on the microbial communities of turtles, but also lay the foundation for further research on the health interrelationships among sea turtles, marine and terrestrial animals, humans and the environment, and for defining "One Health" factors.}, }
@article {pmid41113647, year = {2025}, author = {Meng, Y and Xu, Y and Hu, D and Pan, Q and Weng, L and Huang, W and Zhao, J and Lan, W and Shi, Q and Yu, Y and Jiang, Y}, title = {Evaluating the effects of hospital wastewater treatment on bacterial composition and antimicrobial resistome.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1620677}, pmid = {41113647}, issn = {1664-302X}, abstract = {Hospital wastewater treatment systems (HWTS) are crucial in reducing the spread of antimicrobial resistance genes (ARGs) and antibiotic-resistant bacterial pathogens in hospital wastewater. This study aims to evaluate the impact of HWTS on the changes of bacterial composition and the relative abundance of ARGs. We collected wastewater samples from influent and effluent in a university hospital, and performed metagenomic sequencing. The results showed that HWTS altered the bacterial composition, with a decrease in the proportion of Gammaproteobacteria. However, phylogenetic analysis of metagenome-assembled genomes showed that Mycobacterium and Zoogloea from influent and effluent had a close relationship. A total of 140 non-redundant ARGs were identified based on open reading fragments analysis, with beta-lactam and aminoglycoside resistance genes being the most prevalent. The relative abundance of ARGs generally decreased after wastewater treatment (p < 0.0001), with 70.0% of genes that conferring resistance to "last-resort" antibiotics being undetectable in the effluent. However, the relative abundance of quaternary ammonium compounds resistance genes increased in the effluent. We identified that 66.4% of ARGs were located on plasmids, and 17.9% of ARGs were adjacent to mobile gene elements (MGEs), suggesting their potential for mobility. Subsequent analysis showed that ARGs originating from plasmids and adjacent to MGEs were negatively associated with their relative abundance reduction. In conclusion, this study provides a comprehensive evaluation of the impact of HWTS on composition of bacteria and the relative abundance of ARGs, highlighting the importance of effective wastewater treatment in combating the spread of antimicrobial resistance.}, }
@article {pmid41113646, year = {2025}, author = {Chen, X and Wu, J and Fan, D and Zhang, P and Li, Y and Cao, Y and Cao, M}, title = {Gut viral metagenomics identifies viral signatures and their role in depression.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1573851}, pmid = {41113646}, issn = {1664-302X}, abstract = {BACKGROUND: The gut microbiome has been implicated in the onset and progression of depression. Yet, the role of the gut virome in depression remains unexplored, and a diagnostic model has not been satisfactorily constructed.<br><br>METHODS: Herein, we analysed the gut virome profiles of 29 patients with depression and 33 healthy controls using bulk metagenome sequencing.<br><br>RESULTS: A total of 45 differentially abundant viral taxa were identified, among which four, s_Stenotrophomonas_virus_Pokken, g_Pokkenvirus, s_Dickeya_virus_AD1, and g_Alexandravirus, demonstrated strong diagnostic potential (AUCs > 0.8). These four viruses also exhibited strong correlations, suggesting they may constitute a synergistic ecological cluster. Function annotation revealed seven metabolic pathways with significant differences, including alanine, aspartate, and glutamate metabolism, branched-chain amino acid (BCAA) biosynthesis, and energy metabolism in patients with depression.<br><br>CONCLUSION: This study identified four distinct viral signatures for depression and proposes novel viral biomarkers for the diagnosis of depression, offering a robust diagnostic approach and new insights into the pathological mechanisms of depression.}, }
@article {pmid41113645, year = {2025}, author = {Durán-González, E and Ramírez-Tejero, JA and Pérez-Sánchez, M and Morales-Torres, C and Gómez-Morano, R and Díaz-López, C and Martínez-Lara, A and Cotán, D}, title = {Fibromyalgia diagnosis from a multi-omics approach: a gut feeling.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1641185}, pmid = {41113645}, issn = {1664-302X}, abstract = {BACKGROUND: Fibromyalgia is a complex disorder whose main symptoms are chronic widespread pain and fatigue and affects between 0.2 and 6.6% of the world population. Nowadays, there are no molecular biomarkers that could facilitate diagnosis. The latest efforts by researchers have focused on studying problems at the level of central nervous system sensitivity, inflammation, and oxidative disorders.<br><br>METHODS: A total of 892 women were initially enrolled in the study. For individuals who met the inclusion criteria, a plasma proteome analysis was conducted using blood samples. Briefly, blood was collected, centrifuged, and analyzed by liquid nano-chromatography coupled to tandem mass spectrometry. After the raw data analysis, proteins with statistically significant differential abundance and a fold change over 1.2 (20% increase in fibromyalgia compared with control samples) or under 0.8 (20% decrease in fibromyalgia compared with control samples) in fibromyalgia were selected. For fecal metagenome analysis, fecal samples were collected and processed for DNA extraction. Amplicon sequencing of V3-V4 regions from the 16S ribosomal RNA gene was performed using the Illumina MiSeq platform. The statistical analysis was conducted using R v4.3.2 base packages.<br><br>RESULTS: After applying exclusion criteria, 242 women (199 patients and 43 age- and environmentally paired controls) provided plasma and feces samples, as well as properly filled health questionnaires. A total of 30 proteins and 19 taxa were differentially expressed in fibromyalgia patients, and their integration into an algorithm allows for discrimination between cases and controls. The multi-omic approach for biomarker discovery in this study proposes a multifactorial connection between gut microbiota and mitochondria-derived oxidative stress and inflammation.<br><br>CONCLUSIONS: Plasma and fecal multi-omics analysis suggest an intricate and multifactorial connection between gut microbiota and mitochondria-derived oxidative stress and inflammation in FM patients, with glyceraldehyde-3-phosphate dehydrogenase and Streptococcus salivarius as leading actors.<br><br>TRIAL REGISTRATION: NCT05921409.}, }
@article {pmid41113638, year = {2025}, author = {Verma, D and Zhang, Z and Liu, J}, title = {Editorial: Tobacco disease and biological control.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1694523}, pmid = {41113638}, issn = {1664-302X}, }
@article {pmid41113400, year = {2025}, author = {Ning, H and Feng, R and Wu, H and Sun, C}, title = {[Innovative Practices of Precision Nutrition in Obesity Intervention: From Theory to Application].}, journal = {Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition}, volume = {56}, number = {4}, pages = {893-899}, pmid = {41113400}, issn = {1672-173X}, mesh = {Humans ; *Obesity/prevention &amp; control ; *Precision Medicine/methods ; Metabolomics ; Genomics ; Diet ; }, abstract = {Obesity has emerged as a critical global public health challenge, with an urgent need for effective prevention and control strategies. Traditional nutritional intervention approaches often overlook individual variability and dietary complexity, which limits their effectiveness in achieving precision-based prevention and control. In this context, nutritional intervention strategies are gradually shifting from population-based models to individualized precision nutrition models, which integrate and analyze multidimensional data to open new pathways for obesity prevention and control. The theoretical framework of precision nutrition is based on the recognition that individual heterogeneity in biological mechanisms underlies individual variations in nutritional needs. The research approaches in precision nutrition include genomics, epigenetics, metagenomics, metabolomics, and integrated multi-omics analyses. In terms of application, precision nutrition combines advanced external dietary exposure assessment tools-such as Internet-based dietary assessment systems and AI-driven image recognition-with omics-derived internal biomarkers to enable accurate quantification of dietary intake. Principles such as holistic dietary integrity, full coverage of dietary restrictions, optimized cooking methods, and chrononutrition are emphasized in intervention strategies. Future efforts in precision nutrition should focus on overcoming technical challenges, including thorough integration of multi-omics data and the development of intelligent decision-making systems. The goal is to move beyond generalized, "one-size-fits-all" model toward tailored, precision-based intervention. Precision nutrition will provide essential scientific and technological support for the Healthy China 2030 initiative and help usher in a new era of scientific and individualized obesity prevention and control.}, }
@article {pmid41112778, year = {2025}, author = {Dong, Y and Fan, S and He, S and Zhao, W and Lancuo, Z and Sharshov, K and Li, Y and Wang, W}, title = {Comparative analysis of fecal DNA viromes in Large-billed crows and Northern ravens reveals diverse viral profiles.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e20170}, pmid = {41112778}, issn = {2167-8359}, mesh = {Animals ; *Crows/virology ; *Feces/virology ; *Virome/genetics ; *DNA, Viral/genetics ; *DNA Viruses/genetics/isolation &amp; purification/classification ; Metagenomics ; }, abstract = {As facultative scavenger birds, crows carry various parasites, viruses, and bacteria, making them significant infection hosts and transmission vectors. In this study, we employed viral metagenomics to enrich viral particles from three fecal samples of the Northern ravens (Corvus corax) and four fecal samples of the Large-billed crows (Corvus macrorhynchos). Viral DNA was then extracted, and seven sequencing libraries were constructed. The composition and characteristics of the DNA viromes in the feces of these two facultative scavenging bird species were analyzed using the Illumina NovaSeq platform (PE150 mode). The results showed that the fecal DNA viruses carried by Northern ravens mainly belonged to Parvoviridae (31.49%), Caudoviricetes_Unclassified (21.91%), Microviridae (21.57%), and Genomoviridae (18.2%), while those carried by Large-billed crows were predominantly Genomoviridae (29.7%), Parvoviridae (26.15%), and Caudoviricetes_Unclassified (22.15%). Diversity analysis using Richness, Shannon, and Simpson indices showed no significant differences in viral composition between the two crow species. Additionally, principal coordinate analysis (PCoA) (F = 1.079, P = 0.155) and non-metric multidimensional scaling (NMDS) (F = 1.079, P = 0.154) analyses demonstrated no distinct separation between the two groups. Moreover, the KEGG-enriched pathways in both crow species were primarily associated with metabolic and genetic information processing functions. The selection of the Large-billed crows and Northern ravens in this study was based on their widespread distribution, close association with human settlements, and distinctive scavenging behavior. Comparative analysis of the diversity and composition of their DNA viral communities offers a basis for evaluating the zoonotic risks associated with these scavenger birds.}, }
@article {pmid41112578, year = {2025}, author = {Chen, J and Xu, Q and Zhang, L and Zhang, D and Wu, X}, title = {Enrichment of prevotella melaninogenica in the lower respiratory tract links to checkpoint inhibitor pneumonitis and radiation pneumonitis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1594460}, pmid = {41112578}, issn = {2235-2988}, mesh = {Humans ; Male ; Female ; Middle Aged ; Aged ; Bronchoalveolar Lavage Fluid/microbiology ; *Radiation Pneumonitis/microbiology ; *Prevotella/isolation &amp; purification/genetics/classification ; Microbiota ; Lung Neoplasms/drug therapy ; *Immune Checkpoint Inhibitors/adverse effects ; High-Throughput Nucleotide Sequencing ; Metagenomics ; *Pneumonia/microbiology ; Lung/microbiology ; }, abstract = {BACKGROUND: Checkpoint inhibitor pneumonitis (CIP) and radiation pneumonitis (RP) lead to anti-cancer therapy discontinuation and poor diagnosis. The human microbiome is related to various respiratory diseases. However, the role of the lung microbiome in CIP and RP remains unknown. Our study aimed to explore the lower respiratory tract (LRT) microbiome in CIP/RP patients.<br><br>METHODS: The study enrolled 61 patients with pneumonitis or pneumonia, including 23 with CIP/RP, and 38 with lung cancer with pneumonia (LC-P). Metagenomic next-generation sequencing (mNGS) was performed to identify the microbiota in bronchoalveolar lavage fluid (BALF), and bioinformatics methods were used to compare the microbial differences between CIP/RP and LC-P groups. Correlation analysis was conducted to explore the relationship between LRT microbiota and clinical features.<br><br>RESULTS: The Prevotella was the dominant genus in both groups. The Prevotella melaninogenica, which belongs to the Prevotella genus, was the dominant species in the CIP/RP group and the second most abundant species in the LC-P group. Compared to the LC-P group, the CIP/RP group had significantly high levels of Prevotella melaninogenica species and lymphocyte percentage in BALF but significantly low levels of lymphocytes, eosinophils and albumin in peripheral blood. In addition, the Prevotella melaninogenica species had a negative correlation with peripheral blood lymphocytes.<br><br>CONCLUSION: The enrichment of Prevotella melaninogenica species in LRT and a decreased level of peripheral blood lymphocytes are associated with CIP/RP.}, }
@article {pmid41112491, year = {2025}, author = {Kumari V S, S and Potdar, V and Shinde, M and Parashar, D and Alagarasu, K and Cherian, S and Lavania, M}, title = {Dysbiosis of the oropharyngeal microbiota in COVID-19: distinct profiles in patients with severe respiratory symptoms.}, journal = {Journal of oral microbiology}, volume = {17}, number = {1}, pages = {2569523}, pmid = {41112491}, issn = {2000-2297}, abstract = {BACKGROUND: COVID-19 has been strongly associated with alterations in the oropharyngeal microbiota, yet the microbial features linked to disease severity remain unclear.<br><br>OBJECTIVE: This study aimed to elucidate the microbial signatures associated with COVID-19 disease severity.<br><br>DESIGN: 16S rRNA gene sequencing was employed to profile the oropharyngeal microbiota of patients with varying degrees of COVID-19 severity.<br><br>RESULTS: A significant reduction in alpha diversity suggests a major microbial dysbiosis in critically ill patients compared to less severe cases and healthy individuals, whereas beta diversity analysis revealed a broadly conserved community structure across different groups. Comparative analysis showed significant depletion of the phylum Fusobacteriota and enrichment of bacterial families, including Corynebacteriaceae, Methylobacteriaceae, Acetobacteraceae, Bradyrhizobiaceae, Lactobacillaceae, Staphylococcaceae, Propionibacteriaceae, and Moraxellaceae. Rothia mucilaginosa was notably enriched in patients with severe respiratory symptoms, and many of the enriched taxa are known opportunistic pathogens associated with respiratory infections.<br><br>CONCLUSION: The marked dysbiosis and enrichment of opportunistic pathogens in the oropharyngeal microbiota of critically ill patients indicate their possible role in respiratory complications. The identified microbial patterns highlight the potential of microbiome profiling as a tool for disease prognosis and guide further research into the role of microbes in COVID-19 pathogenesis and implications for treatment protocols.}, }
@article {pmid41112258, year = {2025}, author = {Filippi Xavier, L and Gacesa, R and da Rocha, GHO and Broering, MF and Scharf, P and Lima, FDS and Faber, KN and Harmsen, H and Hoffmann, C and Farsky, SHP}, title = {Annexin A1 levels affect microbiota in health and DSS-induced colitis/inflammatory bowel disease development.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1679071}, pmid = {41112258}, issn = {1664-3224}, mesh = {Animals ; *Annexin A1/genetics/metabolism ; *Gastrointestinal Microbiome ; Humans ; Mice ; Mice, Knockout ; *Colitis/chemically induced/microbiology/metabolism ; Mice, Inbred C57BL ; Dextran Sulfate ; Male ; *Inflammatory Bowel Diseases/microbiology/metabolism ; Female ; Disease Models, Animal ; Dysbiosis ; Feces/microbiology ; Adult ; Middle Aged ; }, abstract = {BACKGROUND: Inflammatory Bowel Diseases (IBDs) are characterized by intestinal dysbiosis and immune dysregulation. Annexin A1 (AnxA1) promotes epithelial repair and inhibits immune responses during IBD. However, AnxA1's impact on gut microbiota during IBD remains unclear. Here, we experimentally investigated the microbiota profile during colitis in wild-type (WT) and AnxA1-deficient mice (AnxA1[-/-]), and evaluated an observational cohort in IBD patients with high or low AnxA1 expression.<br><br>METHODS: Colitis was induced in C57BL/6 WT and AnxA1 [[-]/[-]] mice via oral administration of 2% DSS for six days. Fecal samples were collected at baseline, peak inflammation (day 6), and during the recovery phase (day 10) for 16S rRNA sequencing. Human microbiota data from the Lifelines Dutch Microbiome Project cohort, including IBD and healthy subjects, were analyzed for AnxA1 expression using R software.<br><br>RESULTS: Healthy AnxA1[-/-] mice exhibited reduced microbial richness and a distinct gut microbiota composition, marked by increased Proteobacteria and Parasutterella, and reduced Deferribacterota, Campylobacterota, and Verrucomicrobiota. During DSS-induced colitis, AnxA1[-/-] mice showed greater weight loss and heightened inflammation, displaying earlier and more pronounced microbial shifts, including increased Proteobacteria, Cyanobacteria, Parabacteroides, Bacteroides, and Escherichia-Shigella. In contrast, WT mice exhibited delayed changes, with expansion of Alloprevotella, Akkermansia, and Faecalibaculum after day 6. In human IBD samples, Crohn's disease (CD) patients with low AnxA1 expression and active inflammation presented an altered microbiota enriched in Lachnoclostridium and Parabacteroides, while ulcerative colitis (UC) patients showed phylum-level shifts modulated by AnxA1 levels. Notably, non-inflamed CD and UC patients with low AnxA1 differed significantly in microbiota composition. Moreover, inflamed CD patients with high AnxA1 expression showed microbial profiles resembling those of healthy controls, while low AnxA1 expression was associated with a more pronounced dysbiotic state.<br><br>CONCLUSION: AnxA1 is implicated in microbiota control under healthy and IBD conditions. Accordingly, the microbiota of healthy AnxA1[-/-] mice, colitic AnxA1[-/-] mice, and IBD patients with low AnxA1 expression exhibit dysbiosis compared to their respective controls. Together, these unprecedented findings reveal AnxA1 as a potential regulatory protein in the immune-microbiota axis involved in IBD pathogenesis.}, }
@article {pmid41112053, year = {2025}, author = {Li, P and Xie, L and Zheng, H and Feng, Y and Mai, F and Tang, W and Wang, J and Lan, Z and Lv, S and Jayawardana, T and Koentgen, S and Xu, S and Wan, Z and Chen, Y and Xu, H and Shen, S and Zhang, F and Yang, Y and Hold, G and He, F and El-Omar, EM and Yu, G and Chen, X}, title = {Gut microbial-derived 3,4-dihydroxyphenylacetic acid ameliorates reproductive phenotype of polycystic ovary syndrome.}, journal = {iMeta}, volume = {4}, number = {5}, pages = {e70065}, pmid = {41112053}, issn = {2770-596X}, abstract = {Polycystic ovary syndrome (PCOS) is a prevalent endocrine and reproductive disorder affecting women of reproductive age. While the gut microbiota has been implicated in PCOS pathophysiology, the role of microbial-derived metabolites as mediators of host-microbe interactions remains poorly defined. Here, we integrated untargeted gut metabolomics with metagenomic profiling in patients with PCOS and identified a marked depletion of 3,4-dihydroxyphenylacetic acid (DHPAA), a flavonoid-derived microbial catabolite. Oral administration of DHPAA ameliorated PCOS-like phenotypes in two mouse models by suppressing bone morphogenetic protein signaling and reducing anti-Müllerian hormone (AMH) levels. We found that DHPAA production depends on gut microbial degradation of dietary flavonoids. We further identified a bacterial species, Streptococcus thermophilus, consistently depleted in PCOS across two human cohorts and a mouse model, restored DHPAA levels and improved reproductive outcomes in mice. Conversely, a β-galactosidase-deficient mutant of S. thermophilus failed to confer these benefits, highlighting β-galactosidase as a critical enzyme in DHPAA biosynthesis. Our findings establish DHPAA as a key microbial metabolite linking diet, microbiota, and reproductive health, and propose its potential as a novel therapeutic candidate for PCOS.}, }
@article {pmid41112047, year = {2025}, author = {Xu, M and Guan, S and Zhong, C and Ma, M and Tao, L and Huang, G}, title = {Characterizing the microbiome of "sterile" organs in experimental mice and evidence of translocation of bacteria from the gut to other internal organs.}, journal = {iMeta}, volume = {4}, number = {5}, pages = {e70081}, pmid = {41112047}, issn = {2770-596X}, abstract = {Using culturomics and metagenomics, we demonstrate the existence of non-pathogenic microbiota in the internal organs of healthy experimental mice, challenging the traditional dogma of organ sterility. Based on the analysis of 104 commercially sourced mice (C57BL/6J, BALB/c, ICR), the study reveals that over 20% of the analyzed mice harbored a high microbial burden in the internal organs and identified a total of 463 microbial species. Several species, including Ligilactobacillus murinus, Alcaligenes faecalis, Micrococcus luteus, Pseudochrobactrum asaccharolyticum, Escherichia coli, and Microbacterium sp., were frequently identified and were abundant in the mouse tissues. Further investigation implies that microorganisms in the "sterile" tissues could be associated with the gut microbiota. Given the wide use of experimental mice in medical and biological research, these findings of resident microorganisms in the animal's internal organs raise concerns about potential variability in experimental outcomes.}, }
@article {pmid41112045, year = {2025}, author = {Zhang, Y and Gilbert, JA and Liu, X and Nie, L and Xu, X and Gao, G and Lyu, L and Ma, Y and Fan, K and Yang, T and Zhang, Y and Zhang, J and Chu, H}, title = {SynCom-mediated herbicide degradation activates microbial carbon metabolism in soils.}, journal = {iMeta}, volume = {4}, number = {5}, pages = {e70058}, pmid = {41112045}, issn = {2770-596X}, abstract = {Extensive herbicide residues in the black soil of northeastern China are considered a significant agricultural pollution threat, yet effective bioremediation of this complex and persistent mixture remains a challenge. We identified 16 bacterial species that associated with these herbicide residues in situ, nine of which were culturable and could degrade multiple herbicides. From these strains, we constructed a four-member synthetic microbial community (SynCom) that degrades multiple herbicides, stabilizes colonization, increases soil bacterial biodiversity, and alters soil enzyme activity. Under laboratory conditions, the SynCom degraded eight herbicides within 48 h with >60% efficiency, and accumulated carbon on the cell surface of the constituent species. In black soil microcosm trials, the SynCom achieved 60%-99% degradation efficiency of the endogenous herbicides over 35 days and was able to consistently maintain biomass above 10[4] cfu/g soil. Additionally, SynCom application resulted in an accumulation of carbohydrate-active enzymes and microbial necromass-associated carbon, which suggests activation of soil microbial carbon metabolism. In support of this, metagenomic analyses identified a significant increase in the abundance of genes involved in the tricarboxylic acid cycle, pyruvate metabolism, and glycolysis. This SynCom represents a compelling bioremediation solution that simultaneously improves soil microbial carbon metabolism activity in polluted soils.}, }
@article {pmid41112040, year = {2025}, author = {Johansen, PL and Chatzigiannidou, I and Berzina, L and Kristiansen, K and Brix, S}, title = {Unveiling soil microbial diversity through ultra-deep short-read metagenomic sequencing and co-assembly.}, journal = {iMeta}, volume = {4}, number = {5}, pages = {e70075}, pmid = {41112040}, issn = {2770-596X}, abstract = {By combining ultra-deep short-read shotgun metagenomic sequencing with 5-sample co-assembly across 600 agricultural soil samples, we significantly enhanced the representation and recovery of microbial communities in both clay and sandy soils. Despite an average of 107 Gb clean reads per sample, projections indicated that 1-4 Tb per sample would be required to capture 95% of the microbial community. Co-assembly of five biological replicates markedly improved metagenomic recovery, yielding up to 3.7× more metagenome-assembled genomes, up to 95% more unique genes, and broader recovery of prokaryotic phyla compared to single-sample assemblies.}, }
@article {pmid41110780, year = {2025}, author = {Sreekutti, S and Ndomondo, S and Sharma, P and Patel, R and Mevada, V}, title = {Forensic application of metagenomics: Methods and future directions.}, journal = {Journal of microbiological methods}, volume = {239}, number = {}, pages = {107300}, doi = {10.1016/j.mimet.2025.107300}, pmid = {41110780}, issn = {1872-8359}, abstract = {The microbial communities are found commonly in our environment, making it impossible to touch any surface without interfering with them. The human microbiome, primarily bacteria in the saliva, skin, and gut, can be used for forensic purposes. Human-associated and environmental samples, such as soil, water, etc., carry the microbiome, which can be used for geolocation inference. These microbiomes have considerable potential for use in forensic investigations, including many instances of sexual violence, post-mortem examinations, individual identification, and location identification. Recent developments in metagenomic sequencing have greatly contributed to microbial analysis. Yet, because of certain issues and challenges, the forensic application of microbiomes is still in its infancy. This article reviewed the use of metagenomics in forensic science and some of the main obstacles that are faced by experts in this area. The first and foremost issues noted were the lack of standardization protocols and a poor reference database for research studies. Some limitations, such as storage sensitivity and limited samples, are also indicated. Future research studies should concentrate on more standardized investigations to overcome these difficulties and explore the enormous potential of microbiomes for beneficial applications in forensic contexts.}, }
@article {pmid41110713, year = {2025}, author = {Wang, T and Zhang, Q and Li, J and Dan, Q and Peng, Y}, title = {Unlocking the potential of anaerobic ammonia oxidation: Enhancing nitrogen removal in municipal wastewater through strategic nitrate introduction and microbial synergy.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {133523}, doi = {10.1016/j.biortech.2025.133523}, pmid = {41110713}, issn = {1873-2976}, abstract = {Coordinating the utilization of raw carbon sources with anammox nitrogen removal is pivotal in mainstream wastewater treatment. A novel strategy was developed to enhance nitrogen removal and anammox performance by introducing nitrate into the anoxic stage of an anaerobic/aerobic/anoxic anammox process treating municipal wastewater. This strategy achieved a nitrogen removal efficiency of 97.6 ± 0.9 %, reducing effluent total inorganic nitrogen to 1.8 ± 0.9 mg/L at a high N loading rate (87.7 ± 1.4 g N/m[3]/d) and a low C/N (2.8). After nitrate introduction, anammox contribution increased to 58.9 % and the relative abundance of the anammox genus Candidatus Brocadia increased by 250 %. Metagenomic analysis revealed upregulation of key genes ackA and acs, supporting endogenous carbon storage and utilization by denitrifying glycogen-accumulating organisms (DGAOs). This cooperation between anammox bacteria and DGAOs provided potential for integrating anammox into the mainstream and nitrate wastewater treatment, paving the way for sustainable nutrient management.}, }
@article {pmid41110566, year = {2025}, author = {Wu, Z and He, Z and Dou, P and Wang, K and Zhang, Y}, title = {Study on the intestinal metabolism and absorption of polysaccharides from Dendrobium officinale.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {148390}, doi = {10.1016/j.ijbiomac.2025.148390}, pmid = {41110566}, issn = {1879-0003}, abstract = {Dendrobium officinale polysaccharide (DOP) is widely recognized for its excellent pharmacological activities, however, the in-depth pharmacokinetic characteristic remains unrevealed, significantly hindering its further development. It was hypothesized that Bacteroides predominantly mediates the in vivo metabolism of DOP via polysaccharide utilization loci (PULs), and the resulting oligosaccharides can be directly absorbed by the intestine. To verify this hypothesis, metagenomic sequencing analysis was first employed, confirming that DOP stimulates an upregulation of PULs associated with carbohydrate metabolism within the gut microbiota dominated by Bacteroides. The metabolized oligosaccharides were correlated with highly expressed endo-β-1,4-mannanase from Bacteroides. Further utilizing fluorescent labeling techniques, it was demonstrated that oligosaccharides derived from DOP metabolism are directly absorbed by intestinal tissues. Unabsorbed metabolites subsequently undergo disordered metabolism by gut microbiota into small molecules such as short-chain fatty acids. Collectively, these findings provide novel evidence for elucidating the pharmacological activities of DOP and offer new insights into pharmacokinetic research for other polysaccharides.}, }
@article {pmid41110291, year = {2025}, author = {Liu, C and Liu, Y and Li, Y and Liu, M and Lu, H and Liu, X and Lu, M}, title = {Host-dominated oxidative cascades and transgenerational Cu transfer drive population collapse in Spodoptera frugiperda under chronic CuO nanoparticle exposure: Implications for nano-pesticide environmental risk assessment.}, journal = {Environment international}, volume = {205}, number = {}, pages = {109874}, doi = {10.1016/j.envint.2025.109874}, pmid = {41110291}, issn = {1873-6750}, abstract = {The increasing use of CuO nanoparticles (NPs) in agriculture raises urgent concerns about their long-term ecological risks, particularly regarding transgenerational reproduction and gut microbiota in pest species. Here, we chronically exposed Spodoptera frugiperda to a sublethal concentration of CuO NPs (25 mg/kg). Population collapse occurred in the F4 generation (0 % survival), driven by pronounced oxidative stress (CAT and MDA activities increased up to 2.0-fold), substantial Cu accumulation in eggs (12 → 30 ng/mg) and gut tissue (25 → 750 ng/mg), and impaired reproductive output (33 % reduction in egg production with only 30 % hatching in F3). Although gut microbial diversity remained structurally stable (Shannon index, P > 0.05), metagenomic analysis revealed functional reprogramming, particularly in energy metabolism. Sterile larva inoculation assays confirmed that microbiota exacerbated toxicity, though direct NPs effects dominated. These findings highlight that current risk assessment frameworks, which are primarily focused on acute toxicity and microbial composition, severely underestimate the hazards of nanopesticides. We advocate for integrating multigenerational toxicity testing and metagenomic profiling into nano-pesticide risk evaluations to better capture population-level outcomes.}, }
@article {pmid41109936, year = {2025}, author = {Ali, A and Khattak, AI and Chawla, D and Hasan, F and Khan, H and Ali, MA and Moeez, A and Tanveer, S and Ubaidullah,  and Afridi, MJ and Ikram, J and Hayat, S and Shah, FZ and Nadeem, A and Nadeem, MA and Mushtaq, A and Haroon, W and Bharadwaj, HR and Dahiya, DS and Mansoor, E}, title = {Diagnostic Performance of Metagenomic Next-Generation Sequencing (mNGS) and Culture in Infected Pancreatic Necrosis: A Systematic Review and Meta-Analysis.}, journal = {Digestive diseases and sciences}, volume = {}, number = {}, pages = {}, pmid = {41109936}, issn = {1573-2568}, abstract = {BACKGROUND: Infected pancreatic necrosis (IPN) is a severe complication of acute pancreatitis, requiring prompt diagnosis. Conventional microbial culture, the current gold standard, has limitations in sensitivity and turnaround time. Metagenomic next-generation sequencing (mNGS) offers rapid, comprehensive pathogen detection, but its diagnostic performance for IPN remains unclear.<br><br>METHODS: We conducted a systematic review and meta-analysis following PRISMA-DTA guidelines, prospectively registered in PROSPERO (CRD420251008574). PubMed, Embase, and Web of Science databases were searched from inception to March 2025. Seven studies (313 patients) evaluating mNGS for IPN diagnosis were included, with four providing direct comparisons to culture. Pooled sensitivity, specificity, and area under the curve (AUC) were calculated using a random-effects model. Heterogeneity was assessed using I[2] statistics.<br><br>RESULTS: In double-arm analysis, mNGS showed significantly higher sensitivity (0.87, 95% CI: 0.72-0.95) than culture (0.36, 95% CI: 0.23-0.51), with comparable specificity (0.83 for both). The AUC for mNGS (0.92, 95% CI: 0.79-0.94) surpassed that of culture (0.52, 95% CI: 0.27-0.86). Single-arm analysis confirmed mNGS as a reliable standalone test (sensitivity: 0.86; specificity: 0.85; AUC: 0.89). A threshold effect (r&#x2009;= -&#xa0;0.991) indicated variability in diagnostic criteria across studies.<br><br>CONCLUSIONS: mNGS outperforms culture in diagnosing IPN, offering higher sensitivity and faster results. Its ability to detect diverse pathogens, including fastidious and polymicrobial infections, makes it a valuable tool for early intervention. However, challenges like cost, standardization, and interpretation persist. Future studies should focus on prospective validation and cost-effectiveness to integrate mNGS into routine clinical practice.}, }
@article {pmid41109511, year = {2025}, author = {Wang, W and Wang, H and Zhang, Q and Li, L and Lian, X and Yin, C and Lin, Y and Li, Z and Wang, Y and Han, Z and Shen, F and Chen, X and Sun, R and Wang, T}, title = {Diagnosis of spinal infections caused by fastidious bacteria: a multicenter, retrospective observational study.}, journal = {The spine journal : official journal of the North American Spine Society}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.spinee.2025.10.019}, pmid = {41109511}, issn = {1878-1632}, abstract = {BACKGROUND CONTEXT: Identifying pathogens in pyogenic spinal infections is essential for guiding clinical treatment. However, the fastidious characteristics of certain bacteria often make traditional microbial culture methods ineffective, resulting in diagnostic delays and postponed intervention. In recent years, metagenomic next-generation sequencing (mNGS) has shown strong potential in analyzing complex microbial communities, offering a more advanced strategy for pathogen detection.<br><br>PURPOSE: Evaluating mNGS versus microbial culture for diagnosing fastidious bacteria in pyogenic spinal infections.<br><br>STUDY DESIGN: A multicenter, retrospective observational study.<br><br>PATIENT SAMPLE: We retrospectively reviewed clinical data from 553 patients diagnosed with spinal infections across four medical centers between December 2019 and December 2024.<br><br>OUTCOME MEASURES: Identification of fastidious bacteria in patients.<br><br>METHODS: All patients underwent imaging and standard laboratory testing. Specimens from infected sites obtained through puncture or surgery were analyzed using both microbial culture and mNGS. According to predefined diagnostic, inclusion, and exclusion criteria for fastidious bacteria, 49 patients (8.86%, 49/553) were identified with pyogenic spinal infections caused by fastidious organisms. We compared the diagnostic outcomes of mNGS with those of culture-based methods for detecting fastidious bacterial pathogens in spinal infections.<br><br>RESULTS: Among the 49 patients, mNGS yielded a positive detection rate of 87.76% (43/49), which was significantly higher than that of conventional culture methods at 16.33% (8/49) (&#x3c7;&#xb2;=12.683, p < 0.001). Among the 41 culture-negative cases, mNGS successfully identified fastidious bacteria in 37, corresponding to an effective supplementary detection rate of 90.24% (37/41). While culture identified 5 species of fastidious bacteria, mNGS detected 15, giving an effective pathogen supplementation rate of 66.7% (10/15). These 15 bacteria fell into two groups: the first included those that cannot be cultured using routine clinical media (26/43, 60.47%), and the second included those that may sporadically grow in standard cultures but tend to show low positivity (17/43, 39.53%). Out of the total 553 cases, 382 were culture-negative. Among these, 37 (37/382, 9.69%) were identified as fastidious bacteria via mNGS. mNGS yielded results within 48 hours, significantly faster than the 3-7 days typically required by culture methods.<br><br>CONCLUSIONS: In cases of pyogenic spinal infections caused by fastidious bacteria, mNGS demonstrated a higher detection rate, wider pathogen range, and significantly shorter turnaround compared to traditional microbial culture. The culture-independent approach of mNGS presents a distinct advantage in identifying fastidious pathogens.}, }
@article {pmid41109083, year = {2025}, author = {Wu, W and Song, J and Wu, Q and Wu, X and Sun, N and Xia, X}, title = {Development and evaluation of CD45-conjugated magnetic particles-based host cell depletion for enhanced metagenomic next-generation sequencing in bloodstream infection.}, journal = {Journal of chromatography. B, Analytical technologies in the biomedical and life sciences}, volume = {1267}, number = {}, pages = {124823}, doi = {10.1016/j.jchromb.2025.124823}, pmid = {41109083}, issn = {1873-376X}, abstract = {Metagenomic next-generation sequencing (mNGS) enables unbiased detection of human pathogens without prior assumptions. However, the direct detection of bloodstream infection pathogens is limited by host DNA interference, leading to the clinical adoption of microbial cell-free DNA mNGS (plasma cfDNA mNGS). This study developed a host cell depletion method based on immunomagnetic separation using CD45-conjugated magnetic particles (CD45-MPs, termed the IP method) to reduce host DNA interference and enhance mNGS performance for bloodstream pathogen detection. In simulated samples, known concentrations of pathogens (intact Escherichia coli and Candida albicans cells, fragmented Staphylococcus aureus genomic DNA) were spiked into whole blood samples, serially diluted 10-fold, and divided into whole blood, plasma, and IP-treated groups. These groups were analyzed using hematological analysis, microscopic smear, DNA concentration measurement, relative quantification of GAPDH using qPCR, and mNGS. Results showed that CD45-conjugated magnetic particles effectively removed host cells from whole blood (reducing cell count by 99.9%). The results of nucleic acid measurement and qPCR indicated that the supernatant from IP-treated samples contained significantly lower host DNA compared to whole blood and plasma groups. mNGS detection of simulated samples demonstrated that the IP method enabled detection of pathogens at concentrations as low as 100 CFU/mL for E. coli and S. aureus, and 50 CFU/mL for C. albicans. In clinical testing of 77 samples from patients with suspected bloodstream infections, mNGS combined with the IP method showed significantly higher positivity rates than plasma cfDNA mNGS. In conclusion, CD45-conjugated magnetic particles effectively deplete human cells and enhance the clinical performance of mNGS on the detection of bloodstream infections.}, }
@article {pmid41108980, year = {2025}, author = {Liu, C and Li, C and Guo, X and Wang, L and Wang, N}, title = {Swine farming emissions drive deterministic assembly of antibiotic resistance genes in receiving River: A new ecological perspective.}, journal = {Water research}, volume = {289}, number = {Pt A}, pages = {124803}, doi = {10.1016/j.watres.2025.124803}, pmid = {41108980}, issn = {1879-2448}, abstract = {Livestock farming constitutes a critical reservoir of antibiotic resistance genes (ARGs). Following the fertilization of manure, ARGs enter agricultural soils and subsequently migrate into riverine ecosystem via paddy water (PW), posing potential environmental and public health risks. Understanding the ecological processes behind the assembly of ARG profiles is crucial for predicting the dynamics of ARGs and guiding effective mitigation strategies, while research gaps persist regarding how exogenous inputs affect ARG assembly in receiving environments. This study integrated source fingerprinting via metagenomic sequencing with analytical frameworks from community ecology processes to determine the specific influence of livestock farming emissions on ARG assembly in receiving river. The research targeted intensive swine farming regions in the lower Yangtze River Basin in China, and systematically collected manure-impacted PW as pollution source, alongside receiving river water (RW) and sediment (RS) matrices. In the ecosystem, 946 ARGs belonging to 24 types were identified. Despite the elevated abundance of ARGs in RW relative to RS, the composition in RS closely resembled that in PW and was enriched in high-risk genes (e.g., acrE and acrF), resulting in a higher risk score for RS compared to RW (p < 0.01). Network topology analysis revealed characteristics indicative of exogenous-driven ARG transmission, including high modularity and intra-type clustering of ARGs within modules. Variance partitioning analysis (VPA) collectively revealed that ARGs in RW exhibited a greater potential for horizontal transfer, whereas host communities exerted a predominant influence on ARG distribution in RS. Neutral model yielded fits of R[2] = 0.197 and 0.175 for RW and RS, respectively. Meanwhile, a null model-based stochasticity ratio ranged 30.3 %∼42.7 %, jointly demonstrating that deterministic processes, particularly heterogeneous selection, dominated ARG assembly in the river ecosystem, with a more pronounced effect in sediments. Crucially, removal of PW-specific ARGs led to a marked increase in the contribution of neutral processes, confirming livestock emissions as the core driver shifting assembly towards determinism. Fast expectation-maximization microbial source tracking (FEAST) quantified the contribution of swine farming to ARGs in RW and RS at 12.35 % and 31.09 %, respectively. This study provided novel insights into the deterministic role of exogenous inputs in governing ARG assembly within receiving environments, thus offering theoretical support for developing targeted strategies to control ARG dissemination.}, }
@article {pmid41108960, year = {2025}, author = {Han, C and Zhang, H and Guan, W and Li, L and Zhao, Y and Gao, C and Zhao, Z and Xing, Q and Yuan, A and Guo, D and Gao, Y and Qiao, J and Peng, Y and Zhong, C and He, J and Li, Z and Xiong, X}, title = {From flagellar assembly to DNA replication: CJSe's role in mitigating microbial antibiotic resistance genes.}, journal = {Ecotoxicology and environmental safety}, volume = {305}, number = {}, pages = {119205}, doi = {10.1016/j.ecoenv.2025.119205}, pmid = {41108960}, issn = {1090-2414}, abstract = {The emergence of Antibiotic Resistance Genes (ARGs) in Campylobacter jejuni (CJ) poses a severe threat to food safety and human health. However, the specific impact of CJ and its variants on ARGs and other related factors remains to be further elucidated. Herein, integrated metagenomic sequencing and co-occurrence network analysis approach were employed to investigate the impact of CJ and CJ incorporated with biogenic selenium (CJSe) on ARGs, flagellar assembly pathways, microbial communities, and DNA replication pathways in chicken manure. Compared to the Control (CON) and CJ groups, the CJSe group exhibited 2.4-fold increase selenium levels (P < 0.01) in chicken manure. Notable differences were also observed between the CJ and CJSe groups, with sequence results showing a CJ > CJSe > CON trend in total ARG copy numbers. Furthermore, the CJSe group showed 31.6 % fewer flagellar assembly genes compared to the CJ group. Additionally, compared to the CJ group, CJSe inhibited pathways such as basal body/hook (e.g., FliH, FliO, FliQ reduced by 25-52 %) and stator (MotB downregulated by 42.3 %), suppressing flagellar assembly. We also found that both CJ and CJSe influenced bacterial DNA replication pathways, with the former increasing ARG-carrying bacteria and the latter, under selenium-induced selective pressure, reducing ARG-carrying bacteria. Moreover, compared to the CJ group, the CJSe group showed a significantly lower 9.72 % copy number of total archaeal DNA replication genes. Furthermore, through intricate co-occurrence network analysis, we discovered the complex interplay between changes in ARGs and bacterial and archaeal DNA replication dynamics within the microbial community. These findings indicate that CJSe mitigates the threat posed by CJ and reduces ARG prevalence, while its dual functionality enables applications in biofortified crop production and soil remediation in selenium-deficient regions, thereby advancing circular economy systems. While the current study demonstrates CJSe's dual functionality under controlled conditions, future work will implement a dedicated ecological risk assessment framework encompassing Se speciation/leaching tests and non-target organism assays to confirm environmental safety under field-relevant scenarios. This approach aligns with sustainable strategies for food security and public health safeguarding.}, }
@article {pmid41108937, year = {2025}, author = {Yang, MT and Xie, LH and Wang, L and Gao, YQ and Liu, R and Ma, H and Lei, CC and Jiang, J and Su, JW and Zhang, XX and Ni, HB and Nan, FL}, title = {Metagenomic analysis of bile acid biotransformation by gut microbiota in wild birds.}, journal = {Poultry science}, volume = {104}, number = {12}, pages = {105956}, doi = {10.1016/j.psj.2025.105956}, pmid = {41108937}, issn = {1525-3171}, abstract = {Although gut microbiota-mediated bile acid (BA) metabolism is well characterized in mammals, its mechanisms in wild birds remain largely unknown, hindering our understanding of their ecological adaptation and health. In this study, metagenomic analysis was performed on 10,455 metagenome-assembled genomes (MAGs) derived from 718 wild bird gut samples, from which 1,034 high-quality non-redundant MAGs were selected for further analysis. Functional annotation analysis identified 755 MAGs encoding genes associated with BA biotransformation pathways, primarily derived from the phyla Bacillota_A, Bacteroidota, and Bacillota, with dominant genera including Helicobacter_G and Ligilactobacillus. Subsequent genomic analysis identified 379 MAGs encoding bile salt hydrolase (BSH), with phylogenetic classification demonstrating predominant affiliation to the Bacteroidota and Bacillota_A phyla. Compared to the BSH-producing microbiota in the human and chicken gut, the phylum Bacillota exhibited a notably higher relative abundance in wild birds. Within the wild bird gut microbiome, Helicobacter_G was identified as the predominant BSH-encoding genus, whereas its relative abundance was substantially lower in both humans and chickens. Moreover, migratory birds (MB) displayed significantly higher diversity of BA biotransformation genes than resident birds (RB), with Helicobacter_G being notably enriched at the genus level in MB, potentially associated with their heightened energy and nutritional demands during migration. Notably, in addition to residency status, host species emerged as the most influential factor shaping the compositional variation of BA biotransformation genes, followed by environmental factors and dietary habits. In summary, this study systematically elucidates the potential functions of gut microbiota in BA metabolism and their close associations with host ecological traits in wild birds, not only advancing our understanding of host-microbe interactions and metabolic adaptation mechanisms but also providing a theoretical foundation for future interventions targeting gut microbiota to improve wildlife health.}, }
@article {pmid41108646, year = {2025}, author = {Jeon, JY and Allen, NM and Black, AN and DeWoody, JA}, title = {Short-Read Pangenomes and Their Potential Utility in Population and Conservation Genomics.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e70060}, doi = {10.1111/1755-0998.70060}, pmid = {41108646}, issn = {1755-0998}, abstract = {As a collection of all the genetic variants in the gene pool, the pangenome is a concept that will become fundamental to conservation genomic studies. Unfortunately, most pangenomic approaches developed for humans and model organisms are financially impractical for conservation genomic studies of threatened or endangered species due to the high costs associated with deep sequencing multiple individuals using long-read platforms. Here, by integrating metagenomic and iterative map-then-assemble approaches, we (1) propose novel workflows to construct graph pangenomes from multiple low-coverage short-read datasets; (2) benchmark these short-read pangenomes (both linear and graph) against a previously published long-read graph pangenome of the barn swallow; and (3) evaluate the utility of our workflows in population and conservation genomics. Our results indicate that economical short-read graph pangenomes can recover the vast majority of the variants identified through expensive long-read graph approaches, and that these variants accurately detect important biological signals (e.g., spatial structure and independent taxonomic delineations). These results mean that researchers can utilize their limited, conservation-oriented funding to more fully characterize all the variants in a particular gene pool for population-level analyses.}, }
@article {pmid41108124, year = {2025}, author = {Manzoor, M and Putaala, J and Zaric, S and Leskelä, J and Dong, A and Könönen, E and Lahti, L and Paju, S and Pussinen, PJ}, title = {Oral Microbial Determinants of Saliva and Serum Lipopolysaccharide Activity.}, journal = {Journal of dental research}, volume = {}, number = {}, pages = {220345251370995}, doi = {10.1177/00220345251370995}, pmid = {41108124}, issn = {1544-0591}, abstract = {Lipopolysaccharide (LPS) is a virulence factor of gram-negative bacteria, and endotoxemia or translocation of LPS in serum plays a significant role in oral and systemic pathologies. The contribution of the oral microbiome composition to saliva LPS activity and endotoxemia remains unclear. We investigated whether salivary and serum LPS levels are associated with oral microbiome diversity, taxonomic profiles, and functional characteristics. The oral microbiome was analyzed using metagenomic sequencing of saliva from 298 individuals enrolled in a multicenter case-control study, SECRETO (NCT01934725). Serum and salivary LPS activities were measured, and multiple linear regression models were fitted to identify the microbial taxa that predicted LPS levels. MaAsLin2 (Microbiome Multivariable Associations with Linear Models) was used to determine the associations of microbial functional features and LPS levels. Salivary alpha diversity was positively associated with serum LPS but negatively associated with salivary LPS, smoking, and antibiotic use in the preceding 1 to 6 mo. Community composition (beta diversity) differed between the salivary LPS tertiles (P = 0.001) but not between serum LPS tertiles. In total, 10 oral taxa associated with serum LPS tertiles and 59 with salivary LPS tertiles were identified. Prevotella, Neisseria, Leptotrichia, and Porphyromonas had significant positive associations with salivary LPS, whereas Fusobacterium had a negative association. Among these genera, Prevotella sp. E13_17, P. gingivalis, L. wadei, and F. nucleatum were the species with the strongest associations. Among the 1,016 oral microbiome metabolic features, several were linked to the biosynthesis of LPS, lipid A, and O-antigen pathways. The oral microbiome composition was strongly associated with salivary LPS activity in addition to weaker links to serum LPS. Oral microbiota-derived LPS activity in saliva was associated with microbial metabolism characterized by the predominance of proliferation and biosynthesis pathways. Our study indicates that dysbiosis of the oral microbiome is a source of increased salivary and serum LPS activity.}, }
@article {pmid41107843, year = {2025}, author = {Meki, IK and Ahn, KB and Dundon, WG and Settypalli, TBK and Leth, C and Steinrigl, A and Revilla-Fernández, S and Schmoll, F and Ceglie, L and Berete, K and Metlin, A and Dhingra, M and Nowotny, N and Cattoli, G and Lamien, CE}, title = {Novel multiplex family-wide PCR and Nanopore sequencing of amplicons (FP-NSA) approach for surveillance of influenza- and coronaviruses in humans and animals.}, journal = {Genome medicine}, volume = {17}, number = {1}, pages = {123}, pmid = {41107843}, issn = {1756-994X}, mesh = {Humans ; Animals ; *Nanopore Sequencing/methods ; *Coronavirus/genetics/isolation &amp; purification/classification ; *Multiplex Polymerase Chain Reaction/methods ; *Influenza, Human/virology/diagnosis/epidemiology ; SARS-CoV-2 ; *Coronavirus Infections/virology/diagnosis ; *Orthomyxoviridae/genetics/isolation &amp; purification ; }, abstract = {BACKGROUND: Recent outbreaks of zoonotic diseases like Ebola, Mpox, dengue fever, and COVID-19 highlight gaps in surveillance and early detection at disease hotspots. Virus family-wide diagnostic assays offer a cost-effective and sensitive alternative to metagenomics for initial virus identification. This study introduces a multiplex family-wide PCR coupled with Nanopore sequencing of amplicons (FP-NSA) for surveillance of novel and known zoonotic respiratory viruses, including influenza A and D viruses (IAV and IDV), alpha (α-), beta (β-), and gamma (γ-) coronaviruses (CoVs).<br><br>METHODS: This assay utilized primers in conserved regions of each virus group for multiplex reverse transcription (RT)-PCR coupled with the portable MinION device for rapid Nanopore sequencing. The FP-NSA was optimized using seven IAV subtypes, IDVs, and &#x3b1;- and &#x3b2;-CoVs. The analytical sensitivity of the FP-NSA was assessed using positive controls of known concentrations from each targeted viral family and validated using clinical samples and cell culture isolates from various host species and geographical origins. Potential novel viruses detected in the clinical samples, based on the FP-NSA, were further analyzed using metagenomics sequencing with the Sequence-Independent Single Primer Amplification (SISPA) approach.<br><br>RESULTS: The optimized FP-NSA assay efficiently detected all the targeted viruses singly as well as in co-infection scenarios of multiple respiratory viruses. Evaluation of the assay on 78 selected clinical and cell culture samples (from 184 initially screened) successfully detected IAVs; &#x3b1;-CoVs: porcine epidemic diarrhea virus (PEDV), human coronavirus (HCoV) NL63, and HCoV-229E; &#x3b2;-CoVs: HCoV-OC43, severe acute respiratory syndrome (SARS)-CoV-(1), SARS-CoV-2, and MERS-CoV; and &#x3b3;-CoV infectious bronchitis virus (&#x3b3;-CoV_IBV) infections. Additionally, the FP-NSA assay discovered a novel &#x3b3;-CoV_IBV from Guinea that is phylogenetically distant from known genotypes using a SISPA metagenomics approach.<br><br>CONCLUSIONS: The assay's short PCR amplicons enable screening of samples within 4&#xa0;h, from PCR to sequencing and bioinformatics analysis, providing an adequate number of pathogens' reads. The portable MinION device makes the assay suitable for pathogen surveillance in disease hotspots and resource-limited regions such as low- and middle-income countries. Thus, the FP-NSA assay is a valuable tool for detecting potential novel and known zoonotic respiratory viruses in the targeted families across various host species.}, }
@article {pmid41106786, year = {2025}, author = {Guo, M and Zhao, H and Song, N and Huang, P and Li, M and Han, L and Zeng, KW and Lu, Z}, title = {Shenmai injection attenuates sepsis-associated acute lung injury by remodeling gut microbiota and restoring steroid hormone biosynthesis.}, journal = {Fitoterapia}, volume = {187}, number = {}, pages = {106935}, doi = {10.1016/j.fitote.2025.106935}, pmid = {41106786}, issn = {1873-6971}, abstract = {Sepsis-associated acute lung injury (SA-ALI), a critical complication of sepsis, is characterized by immune dysregulation-induced pulmonary dysfunction. Shenmai Injection (SMI) is a standardized herbal preparation consisting of Panax ginseng C.A.Mey (Hongshen) and Ophiopogon japonicus (Thunb.) Ker Gawl (Maidong), traditionally used for qi-replenishing, collapse-stabilizing, and lung-moistening therapy. Although clinically utilized in the management of SA-ALI, the specific mechanisms by which it acts against SA-ALI necessitate further investigation. The present study endeavors to comprehensively determine the therapeutic efficacy of SMI against SA-ALI through an integrated approach combining network pharmacology, metabolomics, metagenomic sequencing, and experimental validation. In this study, murine SA-ALI was established using lipopolysaccharide (LPS) and Poly(I:C). Results indicated that SMI administration significantly attenuated pulmonary inflammation, restored blood-gas barrier integrity, reduced serum pro-inflammatory cytokines and suppressed NF-κB pathway activation in SA-ALI mice. Network pharmacology elucidated the multi-targeted mechanism of SMI in modulating steroid hormone biosynthesis. Integrated metabolomics and target analysis revealed that ophiopogonin A/B and luteolin in SMI alleviates metabolic dysregulation by targeting key enzymes, including AKR1C3, HSD17B1/2, and SULT1E1. Metagenomic profiling demonstrated SMI-mediated gut microbiota remodeling, marked by suppression of pathogenic Chlamydiaceae (particularly Chlamydia abortus) and enrichment of commensal Lactobacillaceae. Correlation analysis showed that intestinal androstenedione and androsterone levels during SMI treatment recovery were negatively correlated with Chlamydia abortus abundance. In conclusion, SMI enhances the recovery from sepsis-associated SA-ALI by dual modulation of gut microbial ecology and host metabolic homeostasis, thereby establishing its potential as a multi-mechanistic therapeutic candidate for sepsis-related organ injury.}, }
@article {pmid41106415, year = {2025}, author = {Grimm, SL and Kaufman, JT and Rice, DP and Whittaker, C and Bradshaw, WJ and McLaren, MR}, title = {Inferring the sensitivity of wastewater metagenomic sequencing for early detection of viruses: a statistical modelling study.}, journal = {The Lancet. Microbe}, volume = {}, number = {}, pages = {101187}, doi = {10.1016/j.lanmic.2025.101187}, pmid = {41106415}, issn = {2666-5247}, abstract = {BACKGROUND: Metagenomic sequencing of wastewater (W-MGS) can in principle detect any known or novel pathogen in a population. We aimed to quantify the sensitivity and cost of W-MGS for viral pathogen detection by jointly analysing W-MGS and epidemiological data for a range of human-infecting viruses.<br><br>METHODS: In this statistical modelling study, we analysed sequencing data from four studies of untargeted W-MGS to estimate the relative abundance of 11 human-infecting viruses. Corresponding prevalence and incidence estimates were obtained or calculated from academic and public health reports. We combined these estimates using a hierarchical Bayesian model to predict relative abundance at set prevalence or incidence values, allowing comparison across studies and viruses. These predictions were then used to estimate the sequencing depth and concomitant cost required for pathogen detection using W-MGS with or without use of a hybridisation capture enrichment panel.<br><br>FINDINGS: After controlling for variation in local infection rates, relative abundance varied by orders of magnitude across studies for a given virus. For instance, a local SARS-CoV-2 weekly incidence of 1% corresponded to a predicted SARS-CoV-2 relative abundance ranging from 3&#xb7;8&#x2009;&#xd7;&#x2009;10[-10] to 2&#xb7;4&#x2009;&#xd7;&#x2009;10[-7] across studies, translating to orders-of-magnitude variation in the cost of operating a system able to detect a SARS-CoV-2-like pathogen at a given sensitivity. Use of a respiratory virus enrichment panel in two studies greatly increased predicted relative abundance of SARS-CoV-2, lowering yearly costs by 27-fold (from US$7&#xb7;87 million to $287&#x2009;000) and 29-fold (from $1&#xb7;98 million to $69&#x2009;100) for a system able to detect a SARS-CoV-2-like pathogen before reaching 0&#xb7;01% cumulative incidence.<br><br>INTERPRETATION: The large variation in viral relative abundance after controlling for epidemiological factors indicates that other sources of inter-study variation, such as differences in sewershed hydrology and laboratory protocols, have a substantial impact on the sensitivity and cost of W-MGS. Well chosen hybridisation capture panels can greatly increase sensitivity and reduce cost for viruses in the panel, but might reduce sensitivity to unknown or unexpected pathogens.<br><br>FUNDING: The Wellcome Trust, Open Philanthropy, and Musk Foundation.}, }
@article {pmid41106267, year = {2025}, author = {Cai, F and Wang, Y and Xie, M and Li, G and Wang, S and Daygon, VD and Tian, D and Ni, G and Liu, X and Zhang, R and Lei, L and Yuan, Z and Guo, J and Zhang, X and Hu, S}, title = {Pyrogenic carbon-stimulated nitrate-dependent anaerobic methane oxidation: insights into redox activity and conductivity in anaerobic methanotrophic archaea metabolism and microbial dynamics.}, journal = {Water research}, volume = {289}, number = {Pt A}, pages = {124798}, doi = {10.1016/j.watres.2025.124798}, pmid = {41106267}, issn = {1879-2448}, abstract = {Pyrogenic carbon (PC) plays a critical role in regulating greenhouse gas emissions by influencing methanogenesis and methane oxidation in aquatic environments. However, its impact on nitrate-dependent anaerobic oxidation of methane (AOM), associated methane emissions, and the underlying mechanisms remain poorly understood. Here, we demonstrated that in nitrate-dependent AOM consortia amended with HNO3-treated biochar and graphite (representing redox-active and conductive forms of PC, respectively), AOM rates were significantly elevated by 2.7- and 4.4-fold, respectively, compared to unamended biotic controls. This enhancement was accompanied by a pronounced proliferation of anaerobic methanotrophic archaea, specifically "Candidatus Methanoperedens nitroreducens", along with elevated metabolic activity driven by enhanced electron transport and energy conservation, as indicated by significantly increased electron transfer system activity, total adenine nucleotide levels, and concentrations of key redox carrier F420. Metagenomic analysis revealed that PC addition reshaped microbial interactions. Notably, graphite facilitated the potential establishment of direct interspecies electron transfer between "Ca. M. nitroreducens" and coexisting denitrifying populations (Bacteroidota sp. and Ignavibacteriaceae sp.), while also fostering the formation of new interspecies networks that enabled division of labor within the denitrification pathway. These findings not only advance the mechanistic understanding of PC-facilitated methane mitigation in aquatic ecosystems but also suggest strategies for engineering AOM-based systems to optimize methane removal and nitrogen cycling in environmental applications.}, }
@article {pmid41105996, year = {2025}, author = {Chen, ZY and Gao, FZ and Bai, H and He, LY and Liu, YS and Ying, GG}, title = {Airborne free DNA in chicken farms: The overlooked traits in microbial diversity, viral composition, and antimicrobial resistance risk.}, journal = {Journal of hazardous materials}, volume = {499}, number = {}, pages = {140144}, doi = {10.1016/j.jhazmat.2025.140144}, pmid = {41105996}, issn = {1873-3336}, abstract = {The enrichment of DNA from total suspended particulates (TSP) onto 0.22 µm pore size filters (intracellular DNA, iDNA) is a critical step in characterizing the airborne microbiome. However, free DNA (< 0.22 µm, fDNA) may harbor unrecognized microbial and genetic components. In this study, metagenomic analysis was employed to compare airborne fDNA and iDNA from eight chicken houses. Overall, the average concentration of fDNA was 5.6-fold higher than that of iDNA. A total of 587 genera spanning 28 phyla were identified in fDNA, including 162 genera absent from iDNA. Notably, 39.7 % of open reading frames were unique to fDNA, involving key metabolic and regulatory pathways. A total of 50.2 % viral contigs were only detected in fDNA, carrying mobile genetic elements, virulence factor genes, and resistance genes against antibiotics, biocides, and metals. The total absolute abundance of the antibiotic resistome was higher in fDNA, with 79.2 % of significantly varied genes enriched therein, including 16 high-risk genes. Metagenomic binning further supported that fDNA harbors broader microbial diversity and functional traits. These findings underscore airborne fDNA as an underexplored reservoir of microbial and genetic diversity, meriting further investigation for its ecological and public health implications.}, }
@article {pmid41104935, year = {2025}, author = {Feijão, E and Duarte, IA and Pereira, M and Pascoal, P and Nunes, M and Tanner, SE and Dias, R and Duarte, B and Matos, AR and Figueiredo, A and Fonseca, VF}, title = {Gilthead sea bream gut bacteriome as a valuable tool for seafood provenance analysis.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0150825}, doi = {10.1128/aem.01508-25}, pmid = {41104935}, issn = {1098-5336}, abstract = {The increasing demand for high-quality seafood underscores the significant challenges posed by rampant seafood fraud. This study aimed to identify regional capture biomarkers by using the gut bacteriome of Sparus aurata specimens through state-of-the-art long-read sequencing allied to machine learning tools. The gut bacteriomes of animals from four different fishing areas on the Portuguese coast were sequenced. The alpha and beta diversity analyses were shown to enable Center-South gut bacteriome differentiation from other fishing areas due to higher abundance of species of the phyla Pseudomonadota, Bacteroidota, and Bacillota and classes such as Alphaproteobacteria, Betaproteobacteria, and Bacilli. The gradient boosting machine (GBM) model selected by the H2O automatic machine learning pipeline presented a high global accuracy during training and validation phases, identifying Center-South and South sample provenance with 100% and 71.1% accuracy, respectively. By integrating the most important OTUs to the GBM model with the regional biomarkers identified through point biserial correlation analysis (indicspecies packages), a reduced set of five provenance biomarkers was identified, belonging to Gammaproteobacteria, Betaproteobacteria, and Bacilli classes, possibly highlighting the anthropogenic activities surrounding the fishing areas and local environmental abiotic factors. This study highlights the extensive and valuable information obtained by long-read sequencing and couples it with the potential of machine learning algorithms to ultimately demonstrate its efficiency in providing efficient and highly accurate seafood provenance biomarkers. This study also reports the likely influence of industrial and recreational activities, population density, and water management facilities on the gut bacteriome of S. aurata.IMPORTANCEThis study significantly contributes to a topic of utmost importance-seafood provenance analysis and seafood fraud-by leveraging gut bacteriome profiling. Through the application of long-read sequencing and machine learning, it identifies reliable biomarkers that distinguish gilthead sea bream from different fishing areas. These findings enhance traceability methods by providing a robust tool to combat seafood fraud and ensure food authenticity, thereby protecting the supply chain, the consumer, and the environment. Additionally, this study explores the possible interactions between the gut bacteriome and the industrial, recreational, and environmental factors that could influence the identified biomarkers of regional provenance while also offering insights into the composition of the marine ecosystems surrounding the fishing areas. This approach has broader implications for fishery management, sustainable sourcing, and regulatory enforcement.}, }
@article {pmid41104113, year = {2025}, author = {Kulaš, A and Lemonnier, C and Alric, B and Kahlert, M and Trobajo, R and Udovič, MG and Rimet, F}, title = {Can genetic diversity in microalgae species be explained by climate: an overview of metabarcoding with diatoms.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf171}, pmid = {41104113}, issn = {2730-6151}, abstract = {Diatoms, a diverse and abundant group of microalgae, play a crucial role in the functioning of rivers, and are widely used as indicators of ecological quality. This microalgae group has an intraspecific genetic diversity that is poorly understood on a global scale. We examined their genetic diversity using metabarcoding data from Nordic to Equatorial rivers (n = 1103 samples). Notably, 61% of genetic variants were endemic to a single climate zone, including 33% from the Equatorial zone. Looking at the genetic diversity within species, one third of the species showed geographic pattern between climate zones and the phylogenetic structure of their communities indicated that they were shaped by environmental filtering. Another third showed no geographic pattern, and their communities were in majority shaped by neutral processes. A final group was between these two situations. Interestingly, no geographic pattern was observed within the same climate zones, even in regions over 10 000 km apart. We conclude that the numerous species showing allopatric diversification between climate zones, would deserve to be separated into new species to improve diatom-based biomonitoring tools. For future studies, expanding geographical sampling coverage, together with using multi-markers or metagenomes approaches would enable to go beyond these results.}, }
@article {pmid41104112, year = {2025}, author = {Hayes, A and Zhang, L and Snape, J and Feil, E and Kasprzyk-Hordern, B and Gaze, WH and Murray, AK}, title = {Common non-antibiotic drugs enhance selection for antimicrobial resistance in mixture with ciprofloxacin.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf169}, pmid = {41104112}, issn = {2730-6151}, abstract = {Antimicrobial resistance (AMR) is a major health concern, and a range of antibiotic and non-antibiotic agents can select for AMR across a range of concentrations. Selection for AMR is often investigated using single compounds, however, in the natural environment and the human body, pharmaceuticals will be present as mixtures, including both non-antibiotic drugs (NADs), and antibiotics. Here, we assessed the effects of one of three NADs in combination with ciprofloxacin, a commonly used antibiotic that is often found at concentrations in global freshwaters sufficiently high to select for AMR. We used a combination of growth assays and qPCR to determine selective concentrations of mixtures and used metagenome sequencing to identify changes to the resistome and community composition. The addition of the three NADs to ciprofloxacin altered the selection dynamics for intI1 compared to the ciprofloxacin alone treatments, and sequencing indicated that mixtures showed a stronger selection for some AMR genes such as qnrB. The communities exposed to the mixtures also showed changed community compositions. These results demonstrate that NADs and ciprofloxacin are more selective than ciprofloxacin alone, and these mixtures can cause distinct changes to the community composition. This indicates that future work should consider combinations of antibiotics and NADs as drivers of AMR when considering its maintenance and acquisition.}, }
@article {pmid41103765, year = {2025}, author = {Li, M and Bi, J and Wang, X and Li, H}, title = {The hidden nitrogen nexus: stochastic assembly and linear gene synergies drive urban park microbial networks.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1652652}, pmid = {41103765}, issn = {1664-302X}, abstract = {Urban parks play a significant role in environmental greening, cultural heritage, and recreational activities. The diversity and distribution of park environmental microbiota have become a hot focus of microbial ecology. However, there has been limited attention on the functional attributes of microbial communities, highlighting the importance of studying the distribution and diversity of functional genes in urban parks. Here, we employed metagenomic sequencing and binning to explore the diversity, assembly, and functional synergy of nitrogen cycling genes from the grassland soil and water in urban parks. Our results showed that glutamate metabolism and assimilatory nitrate reduction are the predominant nitrogen cycling pathways in both the soil and water. The diversity of nitrogen cycling genes in water was more abundant than in soil. The assembly of nitrogen cycling genes in both the soil and water was primarily driven by stochastic processes. Nutrient factors (such as total sulfur) were the most significant influencers of nitrogen cycling genes in park soil, while bacterial communities were the most critical determinants in water. The gene narH, involved in multiple nitrogen cycling metabolic pathways, was identified as an important marker of nitrogen storage in both soil and water. Through metagenomic binning, we discovered linear arrangements of multiple nitrogen cycling genes, such as narG-narH-narJ-narI, which collectively participate in the reduction of nitrate to nitrite, demonstrating the synergy, functional redundancy, and complementarity among nitrogen cycling genes. Our study holds significant implications for the biochemical cycling and the management of nitrogen pollution in urban parks.}, }
@article {pmid41103762, year = {2025}, author = {Sheng, X and Zhu, J and Li, W and Wan, J and Wu, K and Yang, P and Duan, R and Yang, Z and Bai, J and Zheng, Y}, title = {Antimony-resistant PGPR mitigates Sb toxicity and accumulation in peppers by restructuring rhizosphere microorganisms.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1658223}, pmid = {41103762}, issn = {1664-302X}, abstract = {Plant growth-promoting rhizobacteria (PGPR) provide a sustainable biofertilizer strategy for remediating heavy metal-contaminated soils by enhancing plant stress resistance through rhizosphere microbiota interactions. However, the mechanisms by which PGPR modulate rhizosphere communities and plant growth under antimony (Sb) stress remain poorly understood. This study investigated the effects of inoculating Sb-tolerant Cupriavidus sp. S-8-2 in pepper (Capsicum annuum L.) cultivated under varying levels of Sb contamination (0, 500, 1,000 mg/kg), employing a combination of metagenomic profiling and physicochemical analyses. Pot experiments demonstrated that inoculation significantly enhanced plant growth and nutrient acquisition while alleviating oxidative stress in Sb-stressed plants. Crucially, it reduced Sb translocation, resulting in a 54.75% decrease in shoot Sb content, along with a 33.33% increase in leaf biomass and a 38.98% increase in root biomass under 1,000 mg/kg Sb treatment. In parallel, rhizosphere properties such as total nitrogen (TN), total phosphorus (TP), and soil organic matter (SOM) were improved, as evidenced by an 81.35% increase in acid phosphatase activity under the same Sb concentration. Microbiota analysis revealed that inoculation enriched stress-responsive bacterial phyla, such as Proteobacteria and Actinobacteria, as well as key functional genera associated with Sb tolerance (e.g., Ramlibacter) and nutrient cycling (e.g., Nitrospira), despite a decrease in alpha-diversity. Co-occurrence networks analysis indicated that inoculation significantly enhance node connectivity and mean degree in rhizosphere bacterial networks, reflecting an increase in structural complexity, especially under severe Sb stress (1,000 mg/kg). These findings demonstrate that Cupriavidus sp. S-8-2 enhances plant resistance to Sb by restructuring the rhizobacterial community and improving soil health, with reducing Sb accumulation in edible parts, thereby highlighting its potential as a biofertilizer for safe crop production in Sb-contaminated soils. For the first time, our study explored the potential of Sb-tolerant PGPR to alleviate Sb stress in pepper plants cultivated in Sb-polluted soils.}, }
@article {pmid41103722, year = {2025}, author = {Menozzi, E and Geiger, M and Meslier, V and Fierli, F and Gilles, M and Chau, KY and David, A and Shahar Golan, R and Famechon, A and Koletsi, S and Morabito, C and Quinquis, B and Pons, N and Ehrlich, SD and Macnaughtan, J and Almeida, M and Schapira, AH}, title = {Exploring the relationship between GBA1 host genotype and gut microbiome in the GBA1 [L444P/WT] mouse model: implications for Parkinson's disease pathogenesis.}, journal = {Frontiers in neuroscience}, volume = {19}, number = {}, pages = {1546203}, pmid = {41103722}, issn = {1662-4548}, abstract = {BACKGROUND: Heterozygous variants in GBA1 are the commonest genetic risk factor for Parkinson's disease (PD), but penetrance is incomplete. GBA1 dysfunction can cause gastrointestinal disturbances and microbiome changes in preclinical models. Mounting evidence suggests that the microbiota-gut-brain axis is potentially implicated in PD pathogenesis. Whether the gut microbiome composition is influenced by host GBA1 genetics in heterozygosis has never been explored.<br><br>OBJECTIVES: This study aimed to evaluate whether heterozygosity for the GBA1 pathogenic L444P variant can cause perturbations in gut microbiome composition.<br><br>METHODS: Faecal samples collected from GBA1 [L444P/WT] and GBA1 [WT/WT] mice at 3 and 6&#x202f;months of age were analysed through shotgun metagenomic sequencing.<br><br>RESULTS: No differences in &#x3b1;- and &#x3b2;-diversities were detected between genotyped groups, at either time point. Overall, we found a little variation in the gut microbiome composition and functional potential between GBA1 [L444P/WT] and GBA1 [WT/WT] mice over time.<br><br>CONCLUSION: Host GBA1 genotype does not impact gut microbiome structure and composition in the presented GBA1 [L444P/WT] mouse model. Studies investigating the effect of a second hit on gut physiology and microbiome composition could explain the partial penetrance of GBA1 variants in PD.}, }
@article {pmid41103389, year = {2025}, author = {Shi, G and Yan, P and Shen, S and Tang, P and Chen, P and Sun, L and Xing, S and Fang, C and Li, C and Lin, L and Zhang, C}, title = {The insight into instability mechanism of Jiangxiangxing Baijiu fermentation and the key functional regulation of Schizosaccharomyces pombe.}, journal = {Food chemistry: X}, volume = {31}, number = {}, pages = {103085}, pmid = {41103389}, issn = {2590-1575}, abstract = {Jiangxiangxing Baijiu (JXXB) suffers from quality instability due to its complex spontaneous fermentation. This study compared fermented grains from excellent (Group-E) and normal (Group-N) workshops, identifying 28 volatiles as distinguished substances for quality. The core functional species were revealed by integrated meta-genomic and meta-transcriptomic sequencing analysis. Moreover, Schizosaccharomyces pombe and Acetilactobacillus jinshanensis were demonstrated as key functional contributors, while only Schi. pombe was highlighted active participation in both heap fermentation and pit fermentation. Notably, the proportions and doses of the functional yeasts, particularly Schi. pombe, were higher in Group-E, resulting in the higher quality. Furthermore, the industrial-scale bioaugmentation with Schi. pombe enhanced substrate utilization, elevated the production of flavor substances by 13.61 %, and improved the yield and excellent-quality proportion of base Baijiu by 32.18 % and 37.16 %, respectively. This study provided insights into the quality instability mechanism of JXXB, and fostered a foundation for ensuring consistent quality in solid-state fermentation.}, }
@article {pmid41102833, year = {2025}, author = {Rodriguez, K and Ricci, F and Ni, G and Iram, N and Palfreyman, R and Gonzalez-Garcia, RA and Heffernan, J and Greening, C and Adame, MF and Marcellin, E}, title = {Abundant and active acetogens enhance the carbon dioxide sink of Blue Carbon ecosystems.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {207}, pmid = {41102833}, issn = {2049-2618}, support = {CE 200100029//Australian Research Council Centre of Excellence in Synthetic Biology/ ; }, mesh = {*Carbon Dioxide/metabolism ; Wetlands ; Soil Microbiology ; Carbon Cycle ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; Metagenomics/methods ; Hydrogen/metabolism ; *Carbon Sequestration ; Bioreactors/microbiology ; *Archaea/metabolism/genetics/classification/isolation &amp; purification ; Photosynthesis ; Carbon/metabolism ; Ecosystem ; }, abstract = {BACKGROUND: Blue Carbon ecosystems, which include all tidal wetlands, mitigate climate change by capturing and storing carbon dioxide (CO2) from the atmosphere. Most carbon fixation in these systems is thought to be driven by plant and microbial photosynthesis, whereas chemosynthetic processes are assumed to play a minor role. However, these ecosystems often contain anoxic environments ideal for chemosynthetic microbes such as acetogens.<br><br>RESULTS: In this study, we show that acetogens are abundant and active mediators of carbon sequestration in tidal wetland soils. We combined metagenomic analysis of CO2 fixation genes and reconstruction of microbial genomes with enrichment and analysis of gas-fermenting acetogens in bioreactors. Genome-resolved metagenomics revealed that diverse microbes can mediate carbon fixation, primarily through the Calvin-Benson-Bassham (CBB) cycle and Wood-Ljungdahl pathway (WLP). These include various bacteria and archaea capable of reductive acetogenesis. Based on these findings, we established bacterial enrichment cultures from tidal wetland soils using hydrogen (H2) and CO2 as the sole energy and carbon sources. Bioreactor analysis revealed that these enrichments are dominated by clostridial acetogens that grow rapidly by converting CO2 into acetate and other products.<br><br>CONCLUSIONS: Collectively, these results reveal Blue Carbon ecosystems harbor microbial communities that can exclusively subsist by using CO2 as their sole electron acceptor and carbon source. This provides evidence for a novel carbon sink pathway within these ecosystems beyond the well-known mechanisms of photosynthetic carbon fixation and soil sequestration. Additionally, the discovery and enrichment of these chemosynthetic communities provide opportunities for developing further mechanisms of CO2 removal through industrial gas fermentation. Video Abstract.}, }
@article {pmid41102734, year = {2025}, author = {Lv, Y and Zhang, L and Zhang, Y}, title = {Clear niche partitioning of nitrite-oxidizing bacteria from the bottom and the slope of Mariana Trench.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {208}, pmid = {41102734}, issn = {2049-2618}, support = {42306104//National Natural Science Foundation of China/ ; 42122043//National Natural Science Foundation of China/ ; 2023M742237//China Postdoctoral Science Foundation/ ; HRSJ-ZSZX-008//Project of Hainan Research Institute/ ; 21TQ1400201//Shanghai Jiao Tong University, Shanghai Pilot Program for Basic Research-Shanghai Jiao Tong University/ ; 2023YFC2812800//National Key Research and Development Program of China/ ; }, mesh = {*Nitrites/metabolism ; Oxidation-Reduction ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; *Geologic Sediments/microbiology ; Metagenome ; Ecosystem ; Microbiota ; Metagenomics/methods ; Phylogeny ; Nitrogen Cycle ; }, abstract = {BACKGROUND: The hadal zone, characterized by extreme hydrostatic pressure and geographic isolation, hosts microbial communities uniquely adapted to these harsh conditions. While niche partitioning has been observed in other deep-sea environments, its existence within hadal trench ecosystems remains controversial. Focusing on the Mariana Trench, we investigated whether nitrite-oxidizing bacteria (NOB) exhibit depth-stratified ecological specialization between slope (6000-10,000 m) and bottom (> 10,000 m) sediments. By analysing the genomic features and ecological interactions of NOB, we aimed to resolve their functional roles in nitrogen cycling under distinct hadal microniches.<br><br>RESULTS: We reconstructed 8 high-quality NOB metagenome-assembled genomes (MAGs) from 58 sediment metagenomes, revealing stark niche differentiation between depth zones. Slope-dominant NOB harboured expanded genetic arsenals for antioxidation (e.g. superoxide dismutase) and osmoprotection (compatible solute transporters), Suggesting enhanced adaptive capacity to pressure-adjacent stresses. Metatranscriptomics revealed 1.48&#x2009;&#xd7;&#x2009;(nxrA) and 1.28&#x2009;&#xd7;&#x2009;(aclA) greater expression of nitrite oxidation and carbon fixation genes in slope communities than in their bottom counterparts. Network analysis identified slope NOB as keystone taxa with elevated among-module connectivity and intramodule linkages, in contrast with bottom NOB, which exhibited localized nitrate-production gene networks. Functional profiling revealed complementary biogeochemical roles: slope NOB primarily consumed nitrite, whereas bottom populations dominated nitrate synthesis.<br><br>CONCLUSION: Our multiomics analysis revealed depth-dependent niche partitioning among hadal NOB, with transcriptional and network evidence supporting distinct pressure adaptation strategies and biogeochemical functions. The slope-bottom differentiation in stress response systems and nitrogen transformation pathways highlights how micron-scale environmental gradients drive microbial specialization in Earth's deepest ecosystems. These findings establish NOB as critical mediators of hadal biogeochemical cycles and provide a framework for understanding microbial resilience in extreme biospheres. Video Abstract.}, }
@article {pmid41102233, year = {2025}, author = {Kwak, MJ and Park, J and Park, H and Yoon, J and Lee, J and Hahnke, RL and Lee, SW and Kwon, SK and Song, JY and Kim, JF}, title = {Polyphasic and comparative genomic characterization of a novel Mariniflexile species in the rhizosphere microbiome of tomato resistant to bacterial wilt.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {36158}, pmid = {41102233}, issn = {2045-2322}, support = {918011-4//Ministry of Agriculture, Food and Rural Affairs/ ; NRF-2023R1A2C3004496//Ministry of Science and ICT, South Korea/ ; NRF-2018R1A6A1A03025607//Ministry of Education, South Korea/ ; }, mesh = {*Solanum lycopersicum/microbiology ; *Rhizosphere ; Phylogeny ; *Plant Diseases/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Genome, Bacterial ; Ralstonia solanacearum ; Soil Microbiology ; Genomics ; Disease Resistance ; }, abstract = {A plethora of microbes resides in the plant rhizosphere, and some play roles in host health and disease. We previously isolated a Gram-negative, aerobic, rod-shaped rhizobacterium, TRM1-10, that contributes to bacterial wilt resistance of tomato caused by Ralstonia solanacearum. In this study, we characterized TRM1-10 through physiological and biochemical analyses, complemented by whole genome sequencing and comparative genomic analyses. Phylogenetic analysis using the 16S rRNA gene and genome sequences revealed that TRM1-10 belongs to the genus Mariniflexile and represents a new lineage. TRM1-10 also exhibits noticeable differences in physiological and biochemical characteristics compared to other Mariniflexile species. Thus, based on phylogenetic affiliation and chemotaxonomic characteristics, we propose this bacterium as a novel species in the genus, Mariniflexile rhizosphaerae sp. nov. (type strain TRM1-10[T] = KCTC 18646P[T] = DSM 33122[T]). Comparative genome analyses revealed that TRM1-10 harbors more genes linked to soil adaptation compared to other phylogenetically related Mariniflexile species, most of which are associated with marine habitats. The genomic features of TRM1-10 and other strains in the species may allow the taxon to adapt to the soil and rhizosphere, compete effectively with the resident soil microbiota, and contribute to plant health.}, }
@article {pmid41102171, year = {2025}, author = {Leu, AO and Woodcroft, BJ and McIlroy, SJ and Tyson, GW}, title = {Potential for aerobic hydrocarbon oxidation in archaea.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {9188}, pmid = {41102171}, issn = {2041-1723}, mesh = {Oxidation-Reduction ; *Hydrocarbons/metabolism ; *Archaea/metabolism/genetics/classification ; Aerobiosis ; Phylogeny ; Genome, Archaeal ; Metagenome ; Gene Transfer, Horizontal ; Mixed Function Oxygenases/genetics/metabolism ; }, abstract = {Over the last decade, there have been significant advances in our understanding of anaerobic hydrocarbon oxidation in archaea. However, the ability to oxidise hydrocarbons aerobically has been described in bacteria but not yet in archaea. Here, we provide evidence supporting potential aerobic hydrocarbon oxidation ability in archaea belonging to a novel order within the class Syntropharchaeia, which we propose to name Candidatus 'Aerarchaeales'. This order is represented by six metagenome-assembled genomes (MAGs) spanning three genera that are found in terrestrial and marine ecosystems. In particular, MAGs belonging to a newly defined genus, Ca. 'Aerovita', encode a copper monooxygenase complex with homology to bacterial hydrocarbon monooxygenases. The presence of genes encoding other oxygen-dependent enzymes, such as haem-copper oxygen reductase, indicates that Ca. 'Aerovita' may be capable of aerobic respiration. Our findings suggest that horizontal gene transfer between archaeal and bacterial domains facilitated the evolution of aerobic hydrocarbon-oxidizing archaea.}, }
@article {pmid41101270, year = {2025}, author = {Wang, H and Wu, Y and Zhang, Q and Li, X and Weng, H and Zhang, L and Peng, Y}, title = {Dynamic redox regimes drive metabolic versatility of a Candidatus Brocadia in municipal wastewater treatment.}, journal = {Water research}, volume = {288}, number = {Pt B}, pages = {124781}, doi = {10.1016/j.watres.2025.124781}, pmid = {41101270}, issn = {1879-2448}, abstract = {Deciphering the adaptive mechanisms of anaerobic ammonium-oxidizing (anammox) bacteria to redox dynamics is pivotal for overcoming critical bottlenecks in achieving carbon-neutral wastewater treatment. This study uncovers the survival strategy and response mechanisms of a Candidatus Brocadia strain (B. SW5) thriving in municipal wastewater treatment system with continuous anaerobic-aerobic-anoxic cycling. Isotopic labeling and metagenomic analyses confirmed that the B. SW5 adapts to fluctuating environmental stresses. Comparative genomic and transcriptomic analyses demonstrated that B. SW5 exhibits more comprehensive metabolic pathways than conspecific strains in single environments. Beyond fatty acid metabolism/transport, B. SW5 alleviates organics inhibition by upregulating enzymes for aromatic compound and antibiotic efflux/catabolism in anaerobic stage. In addition to the classical superoxide dismutase-catalase antioxidant system, B. SW5 employs a complete aerobic respiratory chain containing cbb3-type cytochrome c oxidase to directly scavenge intracellular oxygen during aerobic stage. Furthermore, B. SW5 encodes and expresses multiple functionally redundant nitrate reductase genes. These phylogenetically distinct duplicate genes enable survival in substrate-deprived anoxic conditions by constructing complete assimilatory/dissimitative nitrate reduction pathways. These findings elucidate the molecular mechanisms underlying B. SW5 adaptability to redox-fluctuating systems through metabolic versatility, providing a theoretical foundation and novel paradigm for developing energy-efficient wastewater treatment technologies.}, }
@article {pmid41101029, year = {2025}, author = {Ma, L and Liu, F and Zhou, M and Zhang, M and Zheng, J and Wang, Z and He, Z and Yan, Q and Wu, B and Wang, C and Shu, L}, title = {Amoebae contribute to the diversity and fate of antibiotic resistance genes in drinking water system.}, journal = {Environment international}, volume = {204}, number = {}, pages = {109867}, doi = {10.1016/j.envint.2025.109867}, pmid = {41101029}, issn = {1873-6750}, abstract = {Free-living amoebae represent a significant eukaryotic group that thrives in drinking water systems, posing considerable risks to water quality due to their inherent pathogenicity and associations with various microorganisms. However, the symbiotic microbial profiles of different amoeba species and the impact of amoeba-bacteria interactions on the antibiotic resistome within drinking water systems remain poorly understood. In this study, we obtained 24 amoeba isolates from tap water, encompassing diverse phyla within the amoeba lineage. Through metagenome sequencing, we uncovered variations in symbiotic microbiome composition across different amoeba species and strains. Notably, amoebae acted as vectors for human pathogens, including bacteria and viruses. The majority of symbionts carried multiple antibiotic-resistance genes and virulence factors. Furthermore, dominant symbiotic species could be cultured independently, underscoring the critical role of amoebae in preserving and transmitting antibiotic-resistant opportunistic pathogens in drinking water systems. Disinfection experiments demonstrated highly diverse viability of amoebae and their protective capabilities for symbionts against chlorine disinfection. Our findings expand the germplasm bank for amoebae and symbiotic bacteria derived from tap water and emphasize the necessity for further research on amoeba-bacteria symbiosis to ensure drinking water quality and public health safety.}, }
@article {pmid41100443, year = {2025}, author = {Shi, F and Zou, D and Zhang, L and Guo, N and Yu, J and Degen, AA and Tang, X and Ren, S and Ru, Y and Zheng, S and Zhang, Y and Wang, D}, title = {Increased urea nitrogen salvaging by a remodeled gut microbiota helps nonhibernating pikas maintain protein homeostasis during winter.}, journal = {PLoS biology}, volume = {23}, number = {10}, pages = {e3003436}, doi = {10.1371/journal.pbio.3003436}, pmid = {41100443}, issn = {1545-7885}, mesh = {*Gastrointestinal Microbiome/physiology ; Animals ; *Nitrogen/metabolism ; *Urea/metabolism ; Seasons ; *Lagomorpha/metabolism/microbiology/physiology ; Homeostasis ; *Proteostasis/physiology ; Feces/microbiology ; Diet, Protein-Restricted ; Male ; Liver/metabolism ; Herbivory ; Fecal Microbiota Transplantation ; }, abstract = {Nitrogen balance is a major challenge for herbivores when consuming a low-nitrogen diet. Gut microbiota-mediated urea nitrogen recycling facilitates protein homeostasis during times of nitrogen deficiency, yet its relevance to wild nonhibernating small mammals remains unclear. Here, through a combination of isotope tracing, metagenomics, targeted short-chain fatty acid analysis, and fecal microbiota transplantation, we investigated the effects of protein restriction in winter on urea nitrogen recycling in plateau pikas (Ochotona curzoniae) of the Qinghai-Tibetan Plateau. Hepatic urea-cycle metabolism was downregulated during winter protein restriction, accompanied by increases in beneficial bacteria with ureolytic capacity (such as the genus Alistipes), gut urease activity, and urea transporters, and acetate production, with a consequent increase in nitrogen reincorporation into the pika's protein pool. Critically, supplementing a low-protein diet with yak fecal microbiota enhanced the ureolytic capacity by increasing Alistipes abundance, revealing a critical mechanism whereby interspecies horizontal microbial transfer between sympatric species enhances host protein homeostasis. Our results reveal a functional role for the gut microbiota in urea nitrogen recycling to maintain protein balance in winter-active herbivorous small mammals and contribute to our understanding of species coexistence and mammalian adaptation to high-altitude environments. Our findings establish that microbiota-driven urea nitrogen recycling is a key adaptive strategy for protein homeostasis in winter-active herbivores. This work provides new insights into the mechanisms of mammalian adaptation to high-altitude environments and the dynamics of interspecies coexistence.}, }
@article {pmid41099560, year = {2025}, author = {Patel, RR and Triplett, LR and Taerum, SJ and Nason, SL and Wilson, CO and Steven, B}, title = {Diverse soil protists show auxin regulated growth in partnership with auxin-producing bacteria.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf234}, pmid = {41099560}, issn = {1751-7370}, abstract = {Predatory protists are single-cell eukaryotic organisms capable of hunting and ingesting bacteria and other microorganisms, which are thought to enrich populations of beneficial bacteria in the rhizosphere, potentially influencing plant health. However, the mechanisms underpinning protist interactions with plant growth promoting bacteria are not well understood. We examined the conservation of plant beneficial traits in bacteria associated with ten protists of diverse lineages that were isolated from the maize rhizosphere. Metagenomics, whole-genome sequence analysis, and functional assays of 61 groups of protist-associated bacteria identified tryptophan-dependent biosynthesis of the auxin hormone indole-3-acetic acid (IAA) as the most prevalent predicted trait. Mass spectrometry confirmed that all the protist cultures accumulated IAA after tryptophan supplementation, and that IAA production was bacterial-dependent. Hypothesizing that IAA affects protist function, we observed that exogenous IAA significantly increased the culture density and cell size of all ten protists. Examination of four partial protist genome assemblies identified 13 candidate auxin metabolic gene homologs conserved across plants and protists, and transcriptomic analysis of a Colpoda sp. protist revealed differential expression of thousands of genes in the presence of IAA, further supporting auxin regulation of protist function. These findings demonstrate that soil microeukaryotes can widely host auxin-producing bacteria and that much broader range of eukaryotic lineages perceive and respond to auxin signals than previously recognized. This significantly expands the known breadth of auxin perception as an interkingdom signal, with important implications for soil nutrient cycling and rhizosphere ecology.}, }
@article {pmid41099535, year = {2025}, author = {Rusanova, A and Mamontov, V and Ri, M and Meleshko, D and Trofimova, A and Fedorchuk, V and Ezhova, M and Finoshin, A and Lyupina, Y and Isaev, A and Sutormin, D}, title = {Taxonomically different symbiotic communities of sympatric Arctic sponge species show functional similarity with specialization at species level.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0114725}, doi = {10.1128/msystems.01147-25}, pmid = {41099535}, issn = {2379-5077}, abstract = {UNLABELLED: Marine sponges harbor diverse communities of associated organisms, including eukaryotes, viruses, and bacteria. Sponge-associated microbiomes contribute to the health of host organisms by defending them against invading bacteria and providing them with essential metabolites. Here, we describe the microbiomes of three sympatric species of cold-water marine sponges-Halichondria panicea, Halichondria sitiens, and Isodictya palmata-sampled at three time points over a period of 6 years in the White Sea. We identified the sponges as low microbial abundance species and detected stably associated bacteria that represent new taxa of sponge symbionts within Alpha- and Gammaproteobacteria. The sponges carried unique sets of unrelated species of symbiotic bacteria, illustrating the varying complexity of their microbiomes. At the community level, sponge-associated microbiomes shared common symbiotic features: they encoded multiple eukaryotic-like proteins, biosynthetic pathways and transporters of amino acids and vitamins essential for sponges. At the species level, however, different classes of eukaryotic-like proteins and pathways were distributed between dominant and minor symbionts, indicating specialization within microbiomes. Particularly, the taurine and sulfoacetate import and degradation pathways were associated exclusively with dominant symbionts in all three sponge species, suggesting that these pathways may represent symbiotic features. Our study indicates convergent evolution in the microbiomes of sympatric cold-water sponge species, as reflected by strong functional similarity despite the presence of distinct, taxonomically unrelated symbiotic communities.<br><br>IMPORTANCE: Sponges are regarded among the earliest multicellular organisms and the most ancient examples of animal-bacterial symbiosis. The study of host-microbe interactions in sponges has advanced rapidly due to the application of next-generation sequencing (NGS) technologies that help overcome the challenges of investigating their communities. However, many sponge species, particularly those from polar ecosystems, remain poorly characterized. Here, we demonstrate that three sympatric cold-water sponge species, including two analyzed for the first time, harbor distinct sets of bacterial symbionts, stably associated over 6 years. Using CORe contigs ITerative Expansion and Scaffolding, an algorithm developed in this study, we reconstructed high-quality symbiont genomes and revealed shared features indicative of convergent evolution toward symbiosis. Notably, we identified a potentially novel symbiotic feature-a gene cluster likely involved in sulfoacetate uptake and dissimilation. We also observed shifts in microbiome composition, associated with increasing water temperatures, raising concerns about the impact of global warming on cold-water ecosystems.}, }
@article {pmid41099512, year = {2025}, author = {Elkassas, SM and Fortunato, CS and Grim, SL and Butterfield, DA and Holden, JF and Vallino, JJ and Algar, CK and Zeigler Allen, L and Larson, BT and Proskurowski, G and Reddington, E and Stewart, LC and Topçuoğlu, B and Huber, JA}, title = {Metabolic and population profiles of active subseafloor autotrophs in young oceanic crust at deep-sea hydrothermal vents.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0186825}, doi = {10.1128/aem.01868-25}, pmid = {41099512}, issn = {1098-5336}, abstract = {UNLABELLED: At deep-sea hydrothermal vents, magmatically driven rock-water reactions in the crust generate gases and other reduced compounds that subseafloor microorganisms use for chemolithoautotrophy. In this study, microbial autotrophs from three diffuse flow hydrothermal vents at Axial Seamount in 2013 and 2014 were isotopically labeled using RNA stable isotope probing, targeting subseafloor autotrophic mesophiles (30°C), thermophiles (55°C), and hyperthermophiles (80°C). We constructed taxonomic and functional profiles of active chemolithoautotrophs, examined population distributions across sites, and linked primary producers to their specific metabolic strategies within the subseafloor community. Dominant autotrophs exhibited hydrogen-dependent dissimilatory metabolisms, such as sulfur and nitrate reduction and methanogenesis, as well as microaerophilic sulfide oxidation even at 80°C, consistent with fluid chemistries at each site. While hydrogenotrophic methanogenic archaea (Methanothermococcus) were restricted in their distribution and activity, hydrogenotrophic sulfur and nitrate reducers from the Aquificota (Thermovibrio) and Campylobacterota (Nautiliaceae, Hydrogenimonas, and Desulfurobacteriaceae) were consistently active and present at all sites and years at both the population and community levels. Hydrogenase transcripts were significantly differentially expressed, and diverse hydrogenases were found in metagenome-assembled genomes of Aquificota members, highlighting the importance and versatility of their hydrogen utilization strategies, which likely contribute to their cosmopolitan distribution across geochemically disparate subseafloor sites. Together, this study provides new insights into the functional dynamics and distribution of key subseafloor autotrophic microbial communities in young oceanic crust at deep-sea hydrothermal vents.<br><br>IMPORTANCE: Deep-sea hydrothermal vents are hotspots for life in the dark ocean, where rich animal ecosystems are supported by microbial primary producers utilizing the abundant chemical energy supplied by high-temperature water-rock reactions. Despite increasing knowledge about the geochemistry and microbiology of deep-sea hydrothermal vents, there is still a gap in our understanding of the key microbial players who fix much of the carbon at these sites, especially in the productive subseafloor. In this study, stable isotope probing was used to label active microbial autotrophs in diffuse flow venting fluids from three sites over 2 years and was combined with metatranscriptomic sequencing to identify their specific metabolic strategies. This research highlights the microbial community composition, function, gene regulation, and population dynamics that enable hydrothermal ecosystems to persist.}, }
@article {pmid41099510, year = {2025}, author = {Wallace, BA and Varona, NS and Stiffler, AK and Vermeij, MJA and Silveira, C}, title = {High microbial diversity, functional redundancy, and prophage enrichment support the success of the yellow pencil coral, Madracis mirabilis, in Curaçao's coral reefs.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0120825}, doi = {10.1128/msystems.01208-25}, pmid = {41099510}, issn = {2379-5077}, abstract = {UNLABELLED: Coral reefs have undergone extensive coral loss and shifts in community composition worldwide. Despite this, some coral species appear naturally more resistant, such as Madracis mirabilis (herein Madracis). Madracis has emerged as the dominant hard coral in Curaçao, comprising 26% of coral cover in reefs that declined by 78% between 1973 and 2015. Although life history traits and competitive mechanisms contribute to Madracis's success, these factors alone may not fully explain it, as other species with similar traits have not shown comparable success. Here, we investigated the potential role of microbial communities in the success of Madracis on Curaçao reefs by leveraging a low-bias bacterial and viral enrichment method for metagenomic sequencing of coral samples, resulting in 77 unique bacterial metagenome-assembled genomes and 2,820 viral genomic sequences. Our analyses showed that Madracis-associated bacterial and viral communities are 12% and 20% richer than the communities of five sympatric coral species combined. The Madracis-associated bacterial community was dominated by Ruegeria and Sphingomonas, genera that have previously been associated with coral health, defense against pathogens, and bioremediation. These communities also displayed higher functional redundancy, which is often associated with ecological resilience. The viral community exhibited a 50% enrichment of proviruses relative to other corals. These proviruses had the genomic capacity to laterally transfer genes involved in antibiotic resistance, central metabolism, and oxidative stress responses, potentially enhancing the adaptive capacity of the Madracis microbiome and contributing to Madracis's success on Curaçao's reefs.<br><br>IMPORTANCE: Understanding why some coral species persist and thrive while most are in fast decline is critical. Madracis mirabilis is increasingly dominant on degraded reefs in Cura&#xe7;ao, yet the role of microbial communities in its success remains underexplored. This study highlights the potential role of Madracis-associated bacterial and viral communities in supporting coral resilience and competitive success. By identifying key microbial partners and viral genes that may enhance host stress tolerance and defense against pathogens, we broaden the understanding of how the coral holobiont contributes to species persistence under environmental stress. These insights are valuable for predicting key microbial community players in reef interactions and may inform microbiome-based strategies to support coral conservation and restoration.}, }
@article {pmid41099501, year = {2025}, author = {Feeser, K and Longley, R and Gallegos-Graves, LV and Albright, M and Shakya, M}, title = {Recovering new viruses from New Mexico soils.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0090825}, doi = {10.1128/mra.00908-25}, pmid = {41099501}, issn = {2576-098X}, abstract = {Here, we utilized metagenomic and size-filtered virome sequencing to recover 4,157 medium, high, or complete quality viral genomes from soils taken from three high elevation sites in New Mexico, USA. Among recovered viral genomes, 90% were from size-filtered samples, indicating the importance of this enrichment in assessments of complex viromes.}, }
@article {pmid41098988, year = {2025}, author = {Bautista, J and Fuentes-Yépez, MP and Adatty-Molina, J and López-Cortés, A}, title = {Microbial signatures in metastatic cancer.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1654792}, pmid = {41098988}, issn = {2296-858X}, abstract = {Metastasis remains the leading cause of cancer-related death, yet the biological determinants that enable tumor cells to disseminate and colonize distant organs are incompletely understood. Emerging evidence identifies the microbiome, not merely as a bystander, but as an active architect of the metastatic cascade. Microbial communities residing in the gut, mucosal barriers, and within tumors shape metastatic progression by modulating immune surveillance, stromal remodeling, oncogenic signaling, and therapy response. Intratumoral and even intracellular microbes regulate epithelial-mesenchymal transition, angiogenesis, and immune escape, while gut-derived metabolites condition pre-metastatic niches and alter systemic immunity. Technological advances in spatial transcriptomics, single-cell multi-omics, and metagenomics have revealed a spatially organized, functionally integrated microbial ecosystem within tumors, challenging long-held assumptions of sterility in cancer biology. This review synthesizes five converging dimensions of this paradigm: microbial interactions in the metastatic tumor microenvironment; microbiome-mediated immunoediting and metastatic escape; the role of intratumoral and intracellular bacteria in dissemination; spatial-multi-omic approaches to map microbial niches; and microbial biomarkers predictive of metastasis and therapy outcomes. Collectively, these findings recast the microbiome as a critical and targetable determinant of metastasis. Deciphering the tumor-microbe-host triad holds transformative potential for biomarker development, therapeutic innovation, and precision oncology.}, }
@article {pmid41098928, year = {2025}, author = {Kimbell, LK and Ali, N and Adelgren, M and Kohls, S and Folvarska, V and Marshall, CW and Newton, RJ and Wang, Y and McNamara, P}, title = {Antibiotic Resistome Changes Associated with Different Types of Corrosion Inhibitors When Chlorine is Used as a Disinfectant.}, journal = {ACS ES&amp;T engineering}, volume = {5}, number = {10}, pages = {2474-2485}, pmid = {41098928}, issn = {2690-0645}, abstract = {Drinking water distribution systems contain chlorine and metals that can promote antibiotic resistance. Corrosion inhibitors are required to prevent the leaching of metals into drinking water. While utilities have a choice of which corrosion inhibitor they employ, the impact of corrosion inhibitor type when combined with chlorine on antibiotic resistance is unknown. The objective of this research was to understand the impacts of zinc orthophosphate, sodium orthophosphate, and sodium silicate, three commonly used corrosion inhibitors, on antibiotic resistance when mixed with chlorine. Culture-based plating was paired with metagenomics analysis on lab-scale microcosms. The addition of all three corrosion inhibitors resulted in a significantly higher absolute abundance of antibiotic resistant bacteria with resistance to rifampicin, sulfamethoxazole, and vancomycin, while the addition of phosphate-based inhibitors (sodium orthophosphate and zinc orthophosphate) at 1 mg/L also resulted in significantly higher absolute abundance of ampicillin-resistant bacteria. Exposure to all three types of corrosion inhibitors and free chlorine led to significantly higher abundances of ARGs conferring resistance to the target antibiotics used in the phenotypic assessment. Observed changes in the resistomes compared to the controls were influenced by an enrichment in ARGs responsible for multidrug resistance and resistance to peptide antibiotics. In general, most of the ARGs were associated with chromosomes, but a significant increase in the number of ARGs colocated with plasmid and integron sequences was observed. In contrast, the abundance of viral-associated ARGs decreased in the treatments compared to the controls. These results highlight the importance of corrosion inhibitor selection and the potential impacts on antibiotic resistance in potable water systems.}, }
@article {pmid41098901, year = {2025}, author = {Gong, W and Ma, X and Wang, G and Guo, Y and Zhuo, Z and Han, C and Wu, Y}, title = {Analysis of co-infection in severe and critical patients with influenza A (H1N1) pneumonia using metagenomic next-generation sequencing on bronchoalveolar lavage samples.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1669328}, pmid = {41098901}, issn = {2235-2988}, mesh = {Humans ; *Coinfection/microbiology/epidemiology/virology ; Male ; Female ; *Influenza, Human/virology/complications/epidemiology ; Middle Aged ; *Influenza A Virus, H1N1 Subtype/genetics/isolation &amp; purification ; Retrospective Studies ; High-Throughput Nucleotide Sequencing ; *Bronchoalveolar Lavage Fluid/microbiology/virology ; Adult ; Metagenomics/methods ; Aged ; Bacteria/classification/genetics/isolation &amp; purification ; Critical Illness ; *Pneumonia, Viral/virology ; Prevalence ; }, abstract = {OBJECTIVES: The study aimed to clarify the co-infection patterns in adult patients with severe influenza A (H1N1) pneumonia using Metagenomic Next-Generation Sequencing (mNGS) and to examine their impact on clinical outcomes, particularly focusing on the differences between severe and critical patient groups.<br><br>METHODS: This retrospective analysis evaluated bronchoalveolar lavage fluid (BALF) from 53 adult patients diagnosed with severe influenza A (H1N1) pneumonia. Patients were categorized into severe and critical groups depending on the need for invasive ventilation. mNGS was utilized to detect and analyze co-infections, which included fungal, bacterial and viral pathogens. Statistical analysis was conducted to assess the prevalence of these co-infections and their association with clinical outcomes, such as 28-day mortality.<br><br>RESULTS: In the cohort, 48 patients (90.6%) experienced co-infections. In the severe group, fungal infections were noted in 14 patients (66.7%), bacterial in 4 patients (19.0%), and viral in 11 patients (52.4%). Among the critical group, 22 patients (68.8%) had fungal, 23 patients (71.9%) had bacterial, and 10 patients (31.3%) had viral co-infections. There was a significantly higher incidence of co-infections in critical patients (P =&#xa0;0.0002), with notable differences in Acinetobacter baumannii prevalence between the groups (P =&#xa0;0.0339). Aspergillus emerged as the predominant fungal genus across the study. Septic shock (odds ratio [OR] 33.63[4.29-538.3]; P =&#xa0;0.003) and fungal co-infection (OR 24.42[1.98-810.6]; P =&#xa0;0.029) were identified as independent risk factors for 28-day mortality.<br><br>CONCLUSION: The study revealed a high rate of co-infections in both severe and critical patients suffering from influenza A (H1N1) pneumonia, with a higher frequency of bacterial infections in critical patients. Importantly, septic shock and fungal co-infections were independently associated with increased 28-day mortality, highlighting the need for monitoring and management of co-infections in these patients.}, }
@article {pmid41098899, year = {2025}, author = {Li, W and Di, X and Lv, X and Zhang, L and Yu, J}, title = {Characteristics of adults with influenza A virus pneumonia and co-infections identified by mNGS in Jilin, China during 2024-2025.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1662422}, pmid = {41098899}, issn = {2235-2988}, mesh = {Humans ; *Coinfection/epidemiology/virology/microbiology/diagnosis ; Male ; China/epidemiology ; Female ; *Influenza, Human/epidemiology/virology/diagnosis ; Middle Aged ; Retrospective Studies ; Adult ; Aged ; High-Throughput Nucleotide Sequencing ; *Influenza A virus/genetics/isolation &amp; purification/classification ; *Pneumonia, Viral/epidemiology/virology/diagnosis ; Metagenomics/methods ; Severity of Illness Index ; Influenza A Virus, H3N2 Subtype/genetics/isolation &amp; purification ; Bronchoalveolar Lavage Fluid/virology ; Influenza A Virus, H1N1 Subtype/genetics/isolation &amp; purification ; }, abstract = {INTRODUCTION: Influenza A virus (IAV) was included in the World Health Organization priority pathogen list for 2024 owing to its pandemic potential. We aimed to investigate the characteristics of IAV pneumonia and co-infection identified using metagenomic next-generation sequencing (mNGS) in hospitalized patients in Jilin, China, during 2024-2025.<br><br>METHODS: This retrospective study included patients hospitalized for IAV pneumonia. All patients underwent mNGS testing using sputum or bronchoalveolar lavage fluid. Patients were categorized into mild-to-moderate (MM) and severe-to-critical (SC) groups, depending on their disease severity. We analyzed demographic data, clinical manifestations, laboratory findings, and imaging results, and compared the two groups.<br><br>RESULTS: Of the 73 patients included, 45 were in the MM group and 28 were in the SC group. Compared with nucleic acid tests of throat swabs, mNGS has higher sensitivity for detecting IAV (60% vs 100%). H1N1 and H3N2 were the predominant IAV subtypes. Underlying conditions, especially asthma and chronic obstructive pulmonary disease, were associated with an increased risk of severe illness. The D-dimer levels were higher, and lymphocyte counts were lower in patients in the SC group than in those in the MM group. Of the 73 patients, 63 (86.3%) had secondary infections, with bacterial infections being more prevalent (mild/moderate: 26 [58%] and severe/critical: 24 [86%]) than fungal infections (23 [51%] and 23 [82%], respectively).<br><br>CONCLUSIONS: mNGS is a sensitive method for detecting IAV co-infections, effectively identifying co-infection with pathogenic bacterial strains. Hospitalized patients with IAV pneumonia, especially those with H3N2 infection and chronic airway disease, showed a high prevalence of severe and critical illness [total: 8 [11%], severe/critical: 7 [25%]). Fungal infections were frequent regardless of the presence of underlying comorbidities, and patients with SC disease were more likely to develop gram-negative bacterial and fungal infections. These findings may assist clinicians in the early identification of critically ill patients and the provision of appropriate empirical treatment.}, }
@article {pmid41098770, year = {2025}, author = {Zhou, F and Wu, Y and Ren, B and Liu, Y and Luo, K and Li, Q and Huang, F and Peng, X and Li, Y and Su, Z and Li, J}, title = {Meta-omics reveals subgingival plaque reconstruction dynamics.}, journal = {Journal of oral microbiology}, volume = {17}, number = {1}, pages = {2569528}, pmid = {41098770}, issn = {2000-2297}, abstract = {BACKGROUND: The homeostasis of the subgingival microbiome is crucial for periodontal health, although the dynamics governing its community variation remain insufficiently studied. This study aims to investigate the dynamics of subgingival microbiota reassembly after disruption, focusing on core taxa, functions, and driving forces.<br><br>METHODS: 339 subgingival plaques in periodontally healthy states were collected before and after ultrasonic cleaning across 12 timepoints for 1 year. All samples underwent full-length 16S rRNA sequencing; 30 were selected for metagenomic sequencing.<br><br>RESULTS: Our findings revealed that disturbed subgingival microbiota underwent short-term disruptions but subsequently reverted to baseline, maintaining stability within a year. Homogeneous selection dominated assembly, driving convergent structure under consistent pressure. Such a recovery process was accompanied by key taxa increased sequentially: Pseudomonas fluorescens early, Haemophilus parainfluenzae mid-stage, and Capnocytophaga spp. late. Functionally, reconstruction began with energy metabolism, expanded via biofilm formation and LPS biosynthesis mid-stage, and involved late apoptosis and complex amino acid metabolism. Microbial interactions, including positive regulation from Veillonella HMT 780 to Fusobacterium HMT 248, internally drove community assembly.<br><br>CONCLUSION: Our study clarifies species and functional dynamics during subgingival microbiota reconstruction and maps time-directed networks among stage-specific bacteria, offering a theoretical basis for targeted microbiome regulation.}, }
@article {pmid41098739, year = {2025}, author = {Fan, Y and Tan, Z and Wang, Z and Pan, H and Zhou, J and Yang, J and Zhang, G}, title = {Evaluation of non-invasive diagnostic tests for Mycoplasma pneumoniae pneumonia.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1656192}, pmid = {41098739}, issn = {1664-3224}, mesh = {Humans ; *Pneumonia, Mycoplasma/diagnosis/microbiology/immunology/blood ; Male ; Female ; *Mycoplasma pneumoniae/immunology/genetics ; Middle Aged ; Immunoglobulin M/blood ; Retrospective Studies ; Adult ; Aged ; Sensitivity and Specificity ; Antibodies, Bacterial/blood ; Community-Acquired Infections/diagnosis/microbiology ; Bronchoalveolar Lavage Fluid/microbiology ; *Diagnostic Tests, Routine/methods ; High-Throughput Nucleotide Sequencing ; Young Adult ; }, abstract = {BACKGROUND: Accurate and timely identification of Mycoplasma pneumoniae pneumonia (MPP) remains a clinical challenge. Although nasopharyngeal swab nucleic acid testing (NAAT) and serum IgM antibody assays are widely used, their diagnostic performance varies across studies. This study aimed to retrospectively evaluate the sensitivity and specificity of the two non-invasive methods (NAAT and serum IgM antibody assays) for MPP in real-world clinical settings.<br><br>METHODS: We conducted a retrospective study of adult patients hospitalized for community-acquired pneumonia (CAP) from January 2024 to October 2024. All enrolled patients underwent bronchoalveolar lavage fluid metagenomic next-generation sequencing (BALF-mNGS) and had received at least one of two non-invasive tests (NAAT or serum IgM antibody assays). The sensitivity and specificity of NAAT and serum IgM antibody assays were calculated against the final diagnosis. A non-inferiority test was used to determine whether the sensitivity of NAAT or serum IgM antibody assays was not inferior to that of mNGS.<br><br>RESULTS: Among 594 patients included in the analysis, 60 were diagnosed with MPP based on a composite reference standard that included laboratory testing results and adjudication by two senior clinicians in accordance with clinical and radiological findings. The sensitivity and specificity of NAAT were 74.1% and 99.3%, respectively, while those of serum IgM antibody assays were 23.6% and 98.0%. McNemar's test revealed a statistically significant difference in sensitivity between mNGS and the two non-invasive tests (NAAT and serum IgM antibody assays) (P<0.05). The non-inferiority analysis revealed that both NAAT (sensitivity difference: -24.2%, 95% CI: -36.1 to -12.1%; P<0.01) and serum IgM antibody assays (-76.5%, 95% CI: -96.6 to -56.3%; P<0.01) failed to meet the 10% non-inferiority margin compared to mNGS.<br><br>CONCLUSION: In clinical practice, a positive result from either NAAT or serum IgM antibody assays can serve as reliable adjunct evidence for diagnosing MPP. However, in cases with a high clinical suspicion of MPP, negative results from both methods are not sufficient to rule out the diagnosis. For MPP, mNGS remains the most effective diagnostic method compared to non-invasive testing alternatives.}, }
@article {pmid41098538, year = {2025}, author = {He, X and Zhao, Q and Zhang, J and Shi, J and Wan, N and Tang, B and Tian, B and Li, P}, title = {Potential and application of Fusobacterium nucleatum in the diagnosis and treatment of colorectal cancer.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1652702}, pmid = {41098538}, issn = {1664-302X}, abstract = {Colorectal cancer (CRC), as a globally prevalent malignant tumor, relies on in-depth analysis of tumor microenvironment regulation mechanisms for precision diagnosis and treatment. Fusobacterium nucleatum (F. nucleatum), a key carcinogenic bacterium, has been revealed in recent studies to play multidimensional roles in CRC initiation, progression, and metastasis. This review systematically summarizes the progress of Fn applications in CRC full-cycle management: (1) In the diagnostic field, Fn detection technology based on fecal samples has developed into a new non-invasive screening strategy. Cohort studies show its diagnostic performance (AUC 0.82-0.89), with significant correlations to tumor stage (III/IV stage OR = 2.87), lymph node metastasis (HR = 1.94), and reduced 5-year survival rate (35% vs. 62%); (2) For therapeutic monitoring, dynamic Fn load changes can predict chemotherapy (OR = 0.63) and immunotherapy responses (PFS extended by 2.1 months); (3) In prognostic evaluation, metagenomic analysis shows that high Fn abundance is closely related to TNM staging (C-index 0.81 vs. 0.69) and recurrence risk (AUC = 0.88). Notably, a nomogram model integrating Fn biomarkers can improve the predictive accuracy of the traditional TNM staging system by 17.3%. Although existing evidence supports the clinical translational value of Fn, its standardized detection protocols, threshold setting, and targeted intervention strategies (such as antibiotic therapy and phage therapy) still require validation through multi-center prospective studies. This review provides evidence-based medical evidence for the application of Fn in CRC precision medicine by integrating multi-omics data.}, }
@article {pmid41098531, year = {2025}, author = {Juárez-Aragón, MC and Pantoja-Irys, JR and de la Rosa-Manzano, E and Garrido-Olvera, L and Mujica-Sánchez, H and Trejo-De León, CR and Vázquez-Lobo, A}, title = {Microbiome diversity across physicochemical gradient in low-medium enthalpy springs at the Sierra Madre Oriental eastern flank, northeastern Mexico.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1663000}, pmid = {41098531}, issn = {1664-302X}, abstract = {INTRODUCTION: Bacterial communities are fundamental to the functionality of thermal springs where they engage in essential processes such as the oxidation of sulfur, reduction of nitrates, carbon fixation, production of unique metabolites, and stabilization of microbial trophic networks. Northeastern Mexico presents a diverse array of thermal springs located within tropical karst systems situated among folded mountains and ancient inactive karstic regions. The geological complexity of these environments indicates a substantial potential for microbiome diversity; however, the composition and functional dynamics of microbial communities in these springs have not been thoroughly investigated.<br><br>METHODS: This study involved the collection of water samples from six hot springs, to characterize the planktonic microbiome using advanced metagenomic sequencing techniques. Additionally, we examined the relationship between microbial composition and physicochemical parameters.<br><br>RESULTS: Our analysis identified a total of 425 microbial species, which included 409 bacterial species, 13 eukaryotic organisms, and 3 archaeal taxa. The Ojo Caliente and Mainero Azufroso springs displayed the highest microbial diversity, whereas the Balneario El Ba&#xf1;ito and Taninul springs exhibited the lowest. The Phyum Pseudomonadota was the predominant across the majority of springs, while Campylobacterota and Chlorobiota were specifically identified in the less diverse Balneario El Ba&#xf1;ito and Taninul springs, respectively. A total of 30 indicator species were identified, predominantly in El Ba&#xf1;ito and Potrero Prieto springs, emphasizing the distinctiveness of their microbial environments. Moreover, we found that electrical conductivity and bicarbonate concentration had a significant impact on the structure of this microbial communities.<br><br>DISCUSSION: This study highlights the ecological importance of these unique ecosystems in northeastern Mexico, with the Mainero Azufroso and Ojo Caliente springs identified as reservoirs of high microbial diversity.}, }
@article {pmid41098344, year = {2025}, author = {Li, H and Wei, J and Zhou, S and Zhan, Z and Tang, J and Wang, W and Tang, H}, title = {Metagenomic Next-Generation Sequencing Unmasks Atypical Rabies - Guangxi Zhuang Autonomous Region, China, 2024.}, journal = {China CDC weekly}, volume = {7}, number = {39}, pages = {1251-1257}, pmid = {41098344}, issn = {2096-7071}, abstract = {Human rabies remains nearly universally fatal despite medical advances. Diagnosis is frequently delayed when patients present with atypical symptoms, and the failure to receive postexposure prophylaxis (PEP) continues to be a major contributor to mortality worldwide.<br><br>WHAT IS ADDED BY THIS REPORT?: This represents the first confirmed human rabies case in Guangxi caused by the JSTZ190314 strain, successfully identified through metagenomic next-generation sequencing (mNGS). The patient initially presented with urinary symptoms that led to a misdiagnosis before characteristic neurological manifestations developed, ultimately progressing to brain death 28 days after neurological onset (34 days from initial urinary symptoms).<br><br>This case demonstrates the critical importance of mNGS in diagnosing atypical rabies presentations and emphasizes the urgent need for enhanced early clinical recognition, standardized PEP administration protocols, and strengthened regional viral surveillance systems.}, }
@article {pmid41098206, year = {2025}, author = {Chen, Y and Li, M and Gan, X and Wang, Y and Tang, X and Zhou, Y and Niu, T}, title = {Metagenomic Next-Generation Sequencing Unveils Prognostic Microbial Synergism and Guides Precision Therapy in Candidemia: A Retrospective Cohort Study.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {5263-5275}, pmid = {41098206}, issn = {1178-6973}, abstract = {PURPOSE: Candidemia remains a life-threatening infection, compounded by diagnostic delays and limited prognostic tools. While metagenomic next-generation sequencing (mNGS) offers rapid pathogen detection, its prognostic utility and therapeutic impact in candidemia remain unestablished.<br><br>PATIENTS AND METHODS: This retrospective cohort study analyzed 97 candidemia patients with positive blood mNGS at West China Hospital (2020-2024). Multivariable logistic regression and survival analyses identified mortality predictors, while therapeutic impacts were assessed through antifungal regimen modifications.<br><br>RESULTS: The 28-day mortality was 44.3% (43/97). Blood mNGS outperformed cultures in species identification (5 vs 4 species) and co-infection detection. Bacterial co-detections (HR=2.00, 95% CI:1.15-3.48; p<0.05) doubled mortality risk. SOFA score was the strongest mortality predictor (adjusted OR=1.29 per point; p<0.001). mNGS-guided antifungal initiation reduced mortality by 52.4% in treatment-na&#xef;ve patients (22.6% vs 75.0%; p<0.05), though regimen adjustments in pretreated cases showed no benefit (p>0.05). Notably, Candida species exhibited equivalent virulence (log-rank p>0.05), and mNGS read counts lacked prognostic value (p>0.05).<br><br>CONCLUSION: mNGS transforms candidemia management by enabling early risk stratification (via SOFA scores and co-infection profiles) and precision therapy initiation. Its capacity to unmask high-risk bacterial synergists and guide time-sensitive interventions supports integration into diagnostic algorithms, particularly for culture-negative cases. Further validation of standardized mNGS protocols is warranted to maximize clinical impact.}, }
@article {pmid41097911, year = {2025}, author = {Verhoeven, JTP and Malwe, AS and Roussel, N and Nielsen, IB and Mak, SST and Nielsen, TK and Barnes, CJ}, title = {Adaptive sampling with Oxford Nanopore offers a simple way to improve the efficiency of plant metagenomic studies.}, journal = {The New phytologist}, volume = {248}, number = {4}, pages = {1620-1624}, doi = {10.1111/nph.70450}, pmid = {41097911}, issn = {1469-8137}, support = {60770//Villum Fonden/ ; AUFF-E-2024-9-14//Aarhus Universitets Forskningsfond/ ; }, }
@article {pmid41097662, year = {2025}, author = {He, J and Shu, X and Pan, H and Wang, M and Song, Y and Zhou, F and Lian, L and Chen, L and Ma, G and Zhao, Y and Li, R and Liu, L}, title = {Ginseng Polysaccharides Inhibit Aspergillus sydowii-Driven Lung Adenocarcinoma via Modulating Gut Microbiota-Bile Acid Metabolism Axis.}, journal = {Cancers}, volume = {17}, number = {19}, pages = {}, doi = {10.3390/cancers17193134}, pmid = {41097662}, issn = {2072-6694}, support = {(82204677, 82474267//National Natural Science Foundation of China/ ; 2024ZD0521405//National Science and Technology Major Project of China/ ; GZNL2023A02009//Major Project of Guangzhou National Laboratory/ ; 20241112//Traditional Chinese Medicine Bureau of Guangdong Province Project/ ; QZ2023ZZ11//State Key Laboratory of Traditional Chinese Medicine Syndrome/ ; HQL2024PZ005//Chinese Medicine Guangdong Laboratory/ ; 2025M773868//China Postdoctoral Science Foundation/ ; }, abstract = {BACKGROUND: Lung cancer is the leading cause of cancer-related mortality globally, with lung adenocarcinoma (LUAD) as the most common subtype. Dysbiotic intratumoral mycobiomes drive LUAD pathogenesis, and Aspergillus sydowii (A. sydowii) acts as a key oncogenic fungal species. Ginseng polysaccharides (GPs), bioactive phytochemicals with immunomodulatory and oncostatic properties, counteract fungal infections and restore immunosurveillance in LUAD.<br><br>METHODS: Subcutaneous and orthotopic LUAD murine models were established by implanting Lewis lung carcinoma (LLC) cells. Subcutaneous tumors were infected intratumorally and orthotopic models via nasal inoculation. GPs (200 mg/kg/day) were orally administered to evaluate tumor growth. Metagenomic and targeted bile acid metabolomic profiling of fecal and tumor tissues was performed, with Spearman correlations analyzed using R packages.<br><br>RESULTS: GPs significantly inhibited A. sydowii-induced tumor growth in both models. In subcutaneous tumors; GPs reduced volume (p < 0.05) and weight vs. infected controls. In orthotopic models, GPs decreased pathological nodules and lung weight, with micro-CT/H&amp;E confirming attenuated hyperplasia. Metagenomics showed GPs restored gut homeostasis by enriching Lactobacillus/Muribaculum intestinale and suppressing pro-inflammatory Alistipes. Targeted metabolomics revealed reduced &#x3b2;-Hyodeoxycholic Acid (3&#x3b2;-HDCA), Chenodeoxycholic acid 24-acyl-b-D-glucuronide (CDCA-24G) and 3&#x3b2;-hydroxychol-5-en-24-oic acid (5-isoLCA) after GP treatment. Network analysis confirmed significant microbe-bile acid interactions.<br><br>CONCLUSIONS: GPs exert antitumor effects against A. sydowii-induced LUAD by modulating gut microbiota and bile acid metabolism. This identifies GPs as a promising therapy for mycobiome-influenced cancers, with dual targeting of fungal infection and metabolic reprogramming.}, }
@article {pmid41097145, year = {2025}, author = {Tuigunov, D and Sinyavskiy, Y and Nurgozhin, T and Zholdassova, Z and Smagul, G and Omarov, Y and Dolmatova, O and Yeshmanova, A and Omarova, I}, title = {Precision Nutrition and Gut-Brain Axis Modulation in the Prevention of Neurodegenerative Diseases.}, journal = {Nutrients}, volume = {17}, number = {19}, pages = {}, doi = {10.3390/nu17193068}, pmid = {41097145}, issn = {2072-6643}, support = {Grant No. AP23489983//This research is funded by the Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; }, mesh = {Humans ; *Neurodegenerative Diseases/prevention &amp; control/microbiology ; *Gastrointestinal Microbiome/physiology ; *Brain ; *Precision Medicine/methods ; *Brain-Gut Axis/physiology ; Prebiotics/administration &amp; dosage ; Probiotics/administration &amp; dosage ; }, abstract = {In the recent years, the accelerating global demographic shift toward population aging has been accompanied by a marked increase in the prevalence of neurodegenerative disorders, notably Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, and multiple sclerosis. Among emerging approaches, dietary interventions targeting the gut-brain axis have garnered considerable attention, owing to their potential to modulate key pathogenic pathways underlying neurodegenerative processes. This review synthesizes current concepts in precision nutrition and elucidates neurohumoral, immune, and metabolic regulatory mechanisms mediated by the gut microbiota, including the roles of the vagus nerve, cytokines, short-chain fatty acids, vitamins, polyphenols, and microbial metabolites. Emerging evidence underscores that dysbiotic alterations contribute to compromised barrier integrity, the initiation and perpetuation of neuroinflammatory responses, pathological protein aggregations, and the progressive course of neurodegenerative diseases. Collectively, these insights highlight the gut microbiota as a pivotal target for the development of precision-based dietary strategies in the prevention and mitigation of neurodegenerative disorders. Particular attention is devoted to key bioactive components such as prebiotics, probiotics, psychobiotics, dietary fiber, omega-3 fatty acids, and polyphenols that critically participate in regulating the gut-brain axis. Contemporary evidence on the contribution of the gut microbiota to the pathogenesis of Alzheimer's disease, Parkinson's disease, and multiple sclerosis is systematically summarized. The review further discusses the prospects of applying nutrigenomics, chrononutrition, and metagenomic analysis to the development of personalized dietary strategies. The presented findings underscore the potential of integrating precision nutrition with targeted modulation of the gut-brain axis as a multifaceted approach to reducing the risk of neurodegenerative diseases and preserving cognitive health.}, }
@article {pmid41097095, year = {2025}, author = {Russell, T and Formiconi, E and Casey, M and McElroy, M and Mallon, PWG and Gautier, VW}, title = {Viral Metagenomic Next-Generation Sequencing for One Health Discovery and Surveillance of (Re)Emerging Viruses: A Deep Review.}, journal = {International journal of molecular sciences}, volume = {26}, number = {19}, pages = {}, doi = {10.3390/ijms26199831}, pmid = {41097095}, issn = {1422-0067}, support = {101132970//European Commission/ ; }, mesh = {Humans ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Animals ; One Health ; *Communicable Diseases, Emerging/virology/epidemiology ; *Viruses/genetics ; SARS-CoV-2/genetics ; Genome, Viral ; Zoonoses/virology ; }, abstract = {Viral metagenomic next-generation sequencing (vmNGS) has transformed our capacity for the untargeted detection and characterisation of (re)emerging zoonotic viruses, surpassing the limitations of traditional targeted diagnostics. In this review, we critically evaluate the current landscape of vmNGS, highlighting its integration within the One Health paradigm and its application to the surveillance and discovery of (re)emerging viruses at the human-animal-environment interface. We provide a detailed overview of vmNGS workflows including sample selection, nucleic acid extraction, host depletion, virus enrichment, sequencing platforms, and bioinformatic pipelines, all tailored to maximise sensitivity and specificity for diverse sample types. Through selected case studies, including SARS-CoV-2, mpox, Zika virus, and a novel henipavirus, we illustrate the impact of vmNGS in outbreak detection, genomic surveillance, molecular epidemiology, and the development of diagnostics and vaccines. The review further examines the relative strengths and limitations of vmNGS in both passive and active surveillance, addressing barriers such as cost, infrastructure requirements, and the need for interdisciplinary collaboration. By integrating molecular, ecological, and public health perspectives, vmNGS stands as a central tool for early warning, comprehensive monitoring, and informed intervention against (re)emerging viral threats, underscoring its critical role in global pandemic preparedness and zoonotic disease control.}, }
@article {pmid41095773, year = {2025}, author = {Suárez-Cortés, M and Juan-Pérez, A and Molina-Rodríguez, A and Araújo de Castro, J and Castaño-Molina, M&#xc1; and Fernández-Ruiz, VE and Jiménez-Méndez, A and Martínez Pérez-Munar, P and Rico-Chazarra, S and Ramos-Molina, B and Sánchez-Solís, M and Blanco-Carnero, JE and Ruiz-Alcaraz, AJ and Núñez-Sánchez, M&#xc1;}, title = {Dynamics of the Epigenome, Microbiome, and Metabolome in Relation to Early Adiposity in the Maternal-Infant Axis: Protocol for a Prospective, Observational Pilot Study in the Spanish NEMO Cohort.}, journal = {Journal of clinical medicine}, volume = {14}, number = {19}, pages = {}, doi = {10.3390/jcm14196694}, pmid = {41095773}, issn = {2077-0383}, support = {22080/JLI/22//Fundaci&#xf3;n S&#xe9;neca - Agencia de Ciencia y Tecnolog&#xed;a de la Regi&#xf3;n de Murcia/ ; CP23/00051//Instituto de Salud Carlos III/ ; }, abstract = {Background: Childhood obesity has reached epidemic levels in developed countries and is an emerging concern in developing regions. Children with excess weight are more likely to maintain this condition over time into adulthood and face a higher risk of developing metabolic disorders such as type 2 diabetes, hypertension, metabolic dysfunction-associated liver disease, and dyslipidemia. Early identification of obesity risk is, therefore, a key public health challenge. Methods: This is an observational, prospective, single-center cohort pilot study in 66 mother-infant dyads recruited at the Gynecology and Obstetrics Service of the Virgen de la Arrixaca University Hospital (Murcia, Spain). The primary objective is to identify early-life, non-invasive biomarkers associated with increased adiposity by integrating multi-omics approaches and analyzing maternal-infant interactions. Pregnant women will be enrolled during the third trimester and will undergo a baseline visit at 38 weeks of gestation for clinical and anthropometric assessment. Buccal swabs and fecal samples will be collected at baseline and in the peripartum period for epigenetic (DNA methylation), metagenomic, and metabolomic analyses. Infants will be evaluated at birth and followed at 6 months, 1 year, 2 years, and 3 years. Each visit will include detailed anthropometric measurements, along with collection of buccal swabs and fecal samples for multi-omics profiling. Conclusions: This multidisciplinary study aims to assess how maternal factors influence infant epigenetic and microbial patterns, and their relation to adiposity development. Early identification of such biomarkers may guide personalized prevention strategies and reduce the long-term burden of obesity-related comorbidities.}, }
@article {pmid41095699, year = {2025}, author = {Ziad, GA and Jalal, D and Hashem, M and Sayed, AA and Mahfouz, S and Bayoumi, A and Lotfi, M and Hassanain, O and Tolba, M and Madney, Y and Shalaby, L and Elanany, M}, title = {Rapid Identification of Carbapenemase Genes Directly from Blood Culture Samples.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {15}, number = {19}, pages = {}, doi = {10.3390/diagnostics15192480}, pmid = {41095699}, issn = {2075-4418}, support = {#54699605//Pfizer Global Medical Grants/ ; }, abstract = {Background/Objectives: The rapid identification of carbapenemase genes directly from positive blood culture (BC) samples shortens the time needed to initiate optimal antimicrobial therapy for Carbapenemase-Producing Enterobacterales (CPE) infections. Several commercial automated PCR systems are available for detecting CPE resistance genes but are expensive. The Xpert[®] Carba-R assay (Cepheid GeneXpert System) has high sensitivity and specificity for the detection of carbapenamase genes from bacterial colonies or rectal swabs, with an affordable price. This assay was not used for positive BC testing of CPE resistance genes. Whole-Genome Sequencing (WGS) for resistance genes can be used as the gold standard at a research level. In this study, we evaluated the performance of the Xpert[®] Carba-R assay for the early detection of carbapenamase genes directly from positive BCs, using WGS as the gold standard. Methods: A prospective observational study was conducted at Children's Cancer Hospital-Egypt (CCHE-57357). All positive BCs underwent direct gram staining and conventional cultures. A total of 590 positive BCs containing Gram-negative rods (GNRs) were identified. The Xpert[®] Carba-R assay was used to detect carbapenemase genes directly from the positive BC bottle compared with WGS results. Results: Among the 590 GNR specimens, 178 were found to carry carbapenemase genes using the Xpert[®] Carba-R assay, with results obtained in approximately one hour. The main genotypes detected were blaNDM, blaOXA-48-like, and dual blaNDM/blaOXA-48-like at 27%, 29%, and 33%, respectively. The agreement between Xpert[®] Carba-R assay and WGS results was almost perfect for the genotype resistance pattern of isolates and individual gene detection. Conclusions: The use of the Xpert[®] Carba-R assay directly from BC bottles was an easy-to-use, time-saving, affordable tool with high accuracy in identifying carbapenemase genes and, thus, shortens the time needed to initiate optimal antimicrobial therapy for CPE infections.}, }
@article {pmid41094699, year = {2025}, author = {Serrana, JM and Dessirier, B and Nascimento, FJA and Broman, E and Posselt, M}, title = {Microbial hydrocarbon degradation potential of the Baltic Sea ecosystem.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {204}, pmid = {41094699}, issn = {2049-2618}, support = {Project No. 30002687//Stockholm University Center for Circular and Sustainable Systems (SUCCeSS) Postdoc Funding/ ; Project No. 30002687//Stockholm University Center for Circular and Sustainable Systems (SUCCeSS) Postdoc Funding/ ; Project No. 30002687//Stockholm University Center for Circular and Sustainable Systems (SUCCeSS) Postdoc Funding/ ; Project No. 30002687//Stockholm University Center for Circular and Sustainable Systems (SUCCeSS) Postdoc Funding/ ; }, mesh = {*Hydrocarbons/metabolism ; Biodegradation, Environmental ; *Seawater/microbiology ; *Bacteria/metabolism/classification/genetics/isolation &amp; purification ; Ecosystem ; Metagenome ; Petroleum/metabolism ; Microbiota ; Metagenomics/methods ; *Water Pollutants, Chemical/metabolism ; Oceans and Seas ; }, abstract = {BACKGROUND: The Baltic Sea receives petroleum hydrocarbons from various point sources. The degradation of these contaminants in the environment is typically facilitated by a variety of microorganisms that possess a range of genes and metabolic functions related to the degradation of various hydrocarbon substrates. However, our understanding of natural attenuation and the microbial capacity to degrade these contaminants within the Baltic Sea ecosystem remains limited. In this study, we compiled metagenomes from the benthic and pelagic ecosystems across the Baltic Sea to identify microorganisms and characterize their genes and metabolic functions involved in the degradation of hydrocarbon compounds.<br><br>RESULTS: Known hydrocarbon-degrading phyla, i.e., Pseudomonadota, Myxococcota A, Actinomycetota, and Desulfobacterota, were identified within the Baltic Sea metagenome-assembled genomes (MAGs). Notably, 80% of the MAGs exhibited multiple hydrocarbon degradation gene annotations (>&#x2009;10 reads per kilobase million). Aerobic degradation was the predominant pathway for hydrocarbon degradation across environmental samples. Hydrocarbon degradation gene abundances varied among samples and Baltic Sea subbasins, with long-chain alkanes and dibenzothiophene compounds being the preferred substrates. Species richness and diversity of both benthic and pelagic microorganisms positively correlated with hydrocarbon degradation gene diversity, with the pelagic ecosystem exhibiting significantly higher richness and diversity compared to the benthic ecosystem. Additionally, the composition of the hydrocarbon degradation genes across the Baltic Sea subbasins was influenced by oil spill history, with areas that experienced higher spill volumes showing lower microbial diversity, suggesting potential enrichment of specific hydrocarbon degraders. Among the environmental factors assessed, depth played a significant role in shaping the composition of genes involved in hydrocarbon degradation within the Baltic Sea.<br><br>CONCLUSIONS: Using metagenomics, we profiled the native microorganisms associated with hydrocarbon degradation in the Baltic Sea. This knowledge will aid in understanding the natural capacities of microbial communities, potentially linked to the natural attenuation of hydrocarbon pollutants in the area. Insights into microbial degradation potential can enhance predictions of petroleum pollutant persistence and accumulation, support mitigation strategies for marine pollution, and reveal the ecological resilience of native microbial communities in marine ecosystems. Video Abstract.}, }
@article {pmid41094674, year = {2025}, author = {Yuan, M and Lv, X and Yuan, Y and Kang, M and He, F}, title = {Disseminated Listeria monocytogenes and human pegivirus-1 coinfection.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {1335}, pmid = {41094674}, issn = {1471-2334}, mesh = {Humans ; Middle Aged ; *Listeria monocytogenes/isolation &amp; purification/genetics ; *Coinfection/virology/microbiology/diagnosis ; Male ; *Listeriosis/complications/drug therapy ; *Flaviviridae Infections/complications/virology/diagnosis ; *Flaviviridae/isolation &amp; purification/genetics ; Anti-Bacterial Agents/therapeutic use ; *Meningitis, Listeria/drug therapy/diagnosis/complications/microbiology ; }, abstract = {BACKGROUND: Listeria monocytogenes is one of the major bacteria responsible for meningitis. Controversy exists regarding the neuropathological effect of human pegivirus-1 (HPgV-1). Whether HPgV-1 interacts with L. monocytogenes is unknown. Herein, we describe a multiple myeloma patient with disseminated L. monocytogenes and HPgV-1 coinfection.<br><br>CASE PRESENTATION: The case of a 57-year-old patient with fever accompanied by headache, dizziness, nausea, vomiting of stomach contents, and urinary and faecal incontinence is presented. Through metagenomic next-generation sequencing and the detection of L. monocytogenes and HPgV-1 in cerebrospinal fluid, along with blood culture of L. monocytogenes and PCR of HPgV-1 in the blood, a diagnosis of HPgV-1 and L. monocytogenes meningitis, HPgV-1 viremia, and L. monocytogenes sepsis was made, enabling timely and proper treatment with meropenem. After treatment, the patient recovered and was discharged from the hospital.<br><br>CONCLUSIONS: To our knowledge, this is the first reported case of disseminated L. monocytogenes and HPgV-1 coinfection. Determining whether HPgV-1 was responsible for meningitis will require further research, including histopathological analysis.}, }
@article {pmid41094150, year = {2025}, author = {Zhang, Y and Bhosle, A and Bae, S and Eckenrode, K and Huang, X and Tang, J and Lavrentovich, D and Awad, L and Hua, J and Wang, Y and Morgan, XC and Li, B and Krueger, A and Garrett, WS and Franzosa, EA and Huttenhower, C}, title = {Predicting functions of uncharacterized gene products from microbial communities.}, journal = {Nature biotechnology}, volume = {}, number = {}, pages = {}, pmid = {41094150}, issn = {1546-1696}, support = {R24DK110499//U.S. Department of Health &amp; Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes &amp; Digestive &amp; Kidney Diseases)/ ; U19AI110820//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; }, abstract = {The majority of genes in microbial communities remain uncharacterized. Here we develop a method to infer putative function for microbial proteins at scale by assessing community-wide multiomics data. We predict high-confidence functions for >443,000 protein families (~82.3% previously uncharacterized), including >27,000 protein families with weak homology to known proteins and >6,000 protein families without homology. These were drawn from 1,595 gut metagenomes and 800 metatranscriptomes from the Integrative Human Microbiome Project (HMP2/iHMP). Integrating additional information such as sequence similarity, genomic proximity and domain-domain interactions improves performance of the method. Our method's implementation, FUGAsseM, is generalizable and predicts protein function in both well-studied and undercharacterized communities. FUGAsseM achieves similar levels of accuracy in the context of microbial communities when compared to state-of-the-art approaches designed for application to single organisms while simultaneously providing much greater breadth of coverage. This initial study expands the functional landscape of the human gut microbiome and allows for exploration of microbial proteins in undercharacterized communities.}, }
@article {pmid41094135, year = {2025}, author = {Dahlman, S and Avellaneda-Franco, L and Rutten, EL and Gulliver, EL and Solari, S and Chonwerawong, M and Kett, C and Subedi, D and Young, RB and Campbell, N and Gould, JA and Bell, JD and Docherty, CAH and Turkington, CJR and Nezam-Abadi, N and Grasis, JA and Lyras, D and Edwards, RA and Forster, SC and Barr, JJ}, title = {Isolation, engineering and ecology of temperate phages from the human gut.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {41094135}, issn = {1476-4687}, abstract = {Large-scale metagenomic and data-mining efforts have revealed an expansive diversity of bacteriophages (phages) within the human gut[1-3]. However, functional understanding of phage-host interactions within this complex environment is limited, largely due to a lack of cultured isolates available for experimental validation. Here we characterize 134 inducible prophages originating from 252 human gut bacterial isolates using 10 different induction conditions to expand the experimentally validated temperate phage-host pairs originating from the human gut. Importantly, only 18% of computationally predicted prophages could be induced in pure cultures. Moreover, we construct a 78-member synthetic microbiome that, when co-cultured in the presence of human colonic cells (Caco2), led to the induction of 35% phage species. Using cultured isolates, we demonstrate that human host-associated cellular products may act as induction agents, providing a possible link between gastrointestinal cell lysis and temperate phage populations[4,5]. We provide key insights into prophage diversity and genetics, including a genetic pathway for domestication, finding that polylysogeny was common and resulted in coordinated prophage induction, and that differential induction can be influenced by divergent prophage integration sites. More broadly, our study highlights the importance of culture-based techniques, alongside experimental validation, genomics and computational prediction, to understand the biology and function of temperate phages in the human gut microbiome. These culture-based approaches will enable applications across synthetic biology, biotechnology and microbiome fields.}, }
@article {pmid41093983, year = {2025}, author = {Zhang, J and Sekela, JJ and Hutchinson, LE and Yang, J and Sellers, RS and Bhatt, AP and Redinbo, MR}, title = {Sex-dependent responses in mice to indomethacin-induced organ injury and gut microbiome-targeted alleviation.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {36025}, pmid = {41093983}, issn = {2045-2322}, support = {NIH R35 award GM152079/NH/NIH HHS/United States ; }, mesh = {Animals ; *Indomethacin/adverse effects/toxicity ; Female ; Male ; *Gastrointestinal Microbiome/drug effects ; Mice ; Mice, Inbred C57BL ; *Anti-Inflammatory Agents, Non-Steroidal/adverse effects/toxicity ; Sex Factors ; Spleen/drug effects/pathology ; Liver/drug effects/pathology ; Colon/drug effects/pathology ; RNA, Ribosomal, 16S/genetics ; Glucuronidase/antagonists &amp; inhibitors/metabolism ; Sex Characteristics ; }, abstract = {Nonsteroidal anti-inflammatory drugs (NSAIDs) are used widely but produce gastrointestinal (GI) toxicities in both short- and long-term users. Previous studies have shown that the intestinal microbiota play an important role in gut damage and that gut microbial β-glucuronidase (GUS) inhibitors can alleviate NSAID-induced injury in male mice by blocking the GI reactivation of NSAID-glucuronides. Here, in both male and female C57BL/6 mice, we examine the effects of indomethacin alone and with the GUS inhibitor UNC10201652. Oral delivery of 5 mg/kg body weight indomethacin over 5 days decreased body weight, induced colonic and hepatic inflammatory cytokine gene expression, and enlarged the spleens of both male and female mice. However, sex-specific inflammatory responses to indomethacin were observed, with males demonstrating more colonic injury while females presented greater splenic and hepatic toxic responses. Females also showed a unique indomethacin-induced bloom of fecal Verrucomicrobia as measured by 16S rRNA metagenomic sequencing. UNC10201652 alleviated aspects of these indomethacin-induced toxicities, including features of the male-specific colonic damage and the female-specific compositional changes and spleen and liver toxicities. Thus, GI and non-GI tissues in male and female mice respond distinctly to indomethacin-induced damage. These findings advance our understanding of how sex impacts systemic responses to xenobiotic exposure and may lead to improved therapeutic outcomes with these widely used drugs.}, }
@article {pmid41093555, year = {2025}, author = {Suto, Y and Horiba, K and Masuda, Y and Tanaka, K and Hashino, M and Kuroda, M and Fukuda, H}, title = {Candida tropicalis Brain Abscess Diagnosed by Metagenomic Next-Generation Sequencing: A Case Report.}, journal = {Internal medicine (Tokyo, Japan)}, volume = {}, number = {}, pages = {}, doi = {10.2169/internalmedicine.5937-25}, pmid = {41093555}, issn = {1349-7235}, abstract = {We report the case of a 59-year-old HIV-negative male diagnosed with a brain abscess following vasculitis-associated stroke. The causative pathogen remains unidentified using conventional methods including culture and rapid multiplex PCR. Craniotomy and biopsy were performed to establish a definitive diagnosis, and metagenomic next-generation sequencing (mNGS) of the abscess tissue identified Candida tropicalis as the causative pathogen. This case highlights the utility of mNGS in identifying pathogens in culture-negative CNS infections, even when conventional methods fail to detect the causative agent, particularly when evaluating abscess pus.}, }
@article {pmid41093108, year = {2025}, author = {Chandel, N and Patel, P and Somvanshi, PR and Verma, AK and Thakur, V}, title = {Inverse association between serum vitamin B12 level and abundance of potential B12-producing gut microbes in Indian children.}, journal = {The Journal of nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tjnut.2025.10.021}, pmid = {41093108}, issn = {1541-6100}, abstract = {BACKGROUND: The human gut microbiome is a natural source of essential micronutrients like B-vitamins, which are utilized by both the host and other community members. The prevalence and abundance of known B-vitamin producers and B-vitamin biosynthesis pathways have already been reported in gut microbiome cohorts of a few countries including India.<br><br>OBJECTIVE: To test whether the presence of B-vitamin producers/biosynthetic pathways associates with serum B-vitamin levels, taking B12 as a case example.<br><br>METHODS: Fecal samples were collected from non-deficient (serum B12 level > 210 pg/mL, n=29) and B12 deficient (serum B12 level < 210 pg/mL, n=30) children from a tribal region of central India. Whole metagenomic DNA was extracted, sequenced, and analyzed for taxonomic profiling and diversity comparisons. Differentially abundant taxa between two groups were identified. The prevalence and abundance of potential B12 producers were compared, and their association with serum B12 level was established.<br><br>RESULTS: A comparison of within-sample diversity between the two groups didn't show any difference; however, between-sample diversity was significantly less in the B12 deficient group. Differential abundance testing also showed different microbiome structure in the B12 deficient group, where a higher abundance of B12 transporter-carrying Bacteroides thetaiotaomicron, a few pathogenic species, and ten known B12 producers was observed. Potential B12 producers were also significantly prevalent and abundant in the deficient group. Their cumulative abundance was also significantly higher in the deficient group and showed a negative association with serum B12 levels.<br><br>CONCLUSION: A higher abundance of potential B12 producers in the deficient group suggested an adaptive mechanism by the gut microbiome to meet the community's B12 requirements, by selectively promoting the growth of B12 producers, but causality remains to be proved.}, }
@article {pmid41093042, year = {2025}, author = {Noordzij, HT and Wortel, MT and Heintz-Buschart, A and Petrikonyte, P and de Muinck, EJ and Trosvik, P}, title = {Assembly-based analysis of the infant gut microbiome reveals novel ubiquitous plasmids.}, journal = {Plasmid}, volume = {134}, number = {}, pages = {102761}, doi = {10.1016/j.plasmid.2025.102761}, pmid = {41093042}, issn = {1095-9890}, abstract = {Little is known about the role of mobile genetic elements in natural ecosystems such as the infant gut microbiome. Here, we conduct the most comprehensive longitudinal study of the infant plasmidome to date by analyzing monthly fecal samples from 12 infants from birth to one year of age. We employ an assembly-based bioinformatic pipeline for the reconstruction and identification of full-length plasmids, including a novel approach for assigning putative plasmid hosts. We then investigated plasmid content and dynamics in the infant gut microbiome. After assembly and identification, we identified 620 unique circular plasmids in the infant cohort, including a number of novel sequences. Independent assembly of the same plasmids in several samples and infants helped corroborate the authenticity of the plasmids. Among the observed plasmids was the recently described ubiquitous and abundant Bacteroides plasmid pBI143. Overall, the genus Bacteroides had the highest plasmid carriage, while the highest plasmid diversity was observed in Clostridium, including 5 previously unknown widespread plasmids. Lastly, we leveraged the longitudinal nature of our dataset to investigate contemporaneous correlations between temporal variations in plasmid abundances and species dynamics. This enabled us to link co-residing plasmids and tightly linked plasmid-taxon pairs within each infant. These insights into plasmid ecology help us understand determinants driving plasmid distribution in complex microbial communities.}, }
@article {pmid41093027, year = {2025}, author = {Li, KY and Zhou, JL and Tian, ZH and Gao, F}, title = {N-acyl-homoserine lactone regulation of nutrient removal, microbial community assembly, and process efficacy in dialysis membrane-algal-bacterial photobioreactors.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {133502}, doi = {10.1016/j.biortech.2025.133502}, pmid = {41093027}, issn = {1873-2976}, abstract = {Quorum sensing is a central mechanism by which signal bacteria sense and integrate signaling molecules to coordinate gene expression and physiological activities at the community level. To investigate how exogenous signal molecules regulate the maintenance of algal-bacterial symbiosis, this study constructed a dialysis membrane-coupled algal-bacterial photobioreactor and separately amended it with N-butyryl-l-homoserine lactone (C4-HSL), N-hexanoyl-l-homoserine lactone (C6-HSL), and N-(3-oxodecanoyl)-l-homoserine lactone (3-oxo-C10-HSL), systematically investigated their effects on nutrient removal, microbial community composition, and functional characteristics within the system. Compared with the control, all three N-acyl-homoserine lactones (AHLs) enhanced total nitrogen and total phosphorus removal and stimulated biomass (sludge) growth, while redirecting microalgal carbon allocation toward lipid accumulation; notably, the C6-HSL treatment achieved the highest nitrogen (80.39 %) and phosphorus (53.01 %) removal efficiencies. Metagenomic analyses revealed that exogenous AHLs exerted selective effects on the microbial assemblage, enriching dominant signal-responsive bacteria whose relative abundance was positively correlated with nitrogen and phosphorus removal performance. Furthermore, genes associated with nitrogen metabolism, the tricarboxylic acid cycle, and glycolysis were more abundant in the 3-oxo-C10-HSL and C6-HSL groups, indicating that strengthened metabolic coupling likely underpins the observed biomass increase and enhanced nutrient removal. Collectively, these findings demonstrate that AHL-mediated signaling is a key driver shaping algal-bacterial interactions, community assembly, and functional expression.}, }
@article {pmid41092906, year = {2025}, author = {Wu, L and Li, Y and Wang, W and Deng, L and Ge, H and Cui, M and Bi, N}, title = {Gut microbiota predictive of the efficacy of consolidation immunotherapy and chemoradiotherapy toxicity in lung cancer.}, journal = {Med (New York, N.Y.)}, volume = {}, number = {}, pages = {100877}, doi = {10.1016/j.medj.2025.100877}, pmid = {41092906}, issn = {2666-6340}, abstract = {BACKGROUND: Gut microbiota (GM) predict responses to immune checkpoint inhibitors (ICIs) in patients with advanced lung cancer. However, its role in patients with locally advanced lung cancer undergoing chemoradiotherapy (CRT) combined with consolidation ICIs remains unclear.<br><br>METHODS: A total of 177 fecal samples were collected pre- and post-CRT. Using 16S ribosomal RNA (16S rRNA) sequencing and metagenomic data from an internal cohort and published studies, the kinetics of microbiota were analyzed using the Wilcoxon signed-rank test, while prognostic factors for progression-free survival (PFS) were identified using Cox regression modeling and machine learning algorithms.<br><br>FINDINGS: The GM configuration was unaffected by traditional CRT. However, in cases of CRT with consolidation ICIs, patients with long-PFS showed a higher alpha diversity at baseline, followed by a reduction during treatment, contrasting with the stable diversity observed in the short-PFS group. Enrichment of the symbiotic microbe Akkermansia muciniphila (Akk) after CRT was observed, with its increased abundance correlating with extended distant metastasis-free survival in patients undergoing CRT with consolidation ICIs. Notably, the trend in Akk variation was a prognostic indicator of survival outcomes in patients undergoing CRT combined with ICIs. GM was also involved in the development of treatment-related pneumonia and was a promising predictive marker for severe pneumonia.<br><br>CONCLUSIONS: CRT with consolidation ICIs has more pronounced effects on the GM than CRT alone in patients with locally advanced lung cancer. The dynamic variation in Akk has predictive potential for patient survival in this context.<br><br>FUNDING: This study was supported by the National Science and Technology Major Project.}, }
@article {pmid41092847, year = {2025}, author = {Zhang, Y and Su, K and Munir, F and Wang, W and Liang, X and Wang, J and Hua, J and Ma, W}, title = {Gut microbiome metagenomics in diarrheic and healthy Simmental cattle from Ningxia Province, China.}, journal = {Research in veterinary science}, volume = {197}, number = {}, pages = {105922}, doi = {10.1016/j.rvsc.2025.105922}, pmid = {41092847}, issn = {1532-2661}, abstract = {INTRODUCTION: The gut microbiome plays a crucial role in health and disease. This study aims to investigate the composition, characteristics, and functional diversity of the intestinal microbiome by performing metagenomic sequencing on fecal samples from diarrheic and healthy Simmental cattle.<br><br>RESULTS: This study compared the gut microbiome differences between two groups of Simmental cattle (5 diarrheic and 20 healthy) in Ningxia province, China. Metagenomic analysis revealed higher microbial heterogeneity in the diarrheic group, likely reflecting pathogen-driven ecological disruption, whereas the healthy group was dominated by butyrate-producing and fiber-degrading bacteria, maintaining intestinal homeostasis. Antibiotic resistance gene analysis detected glycopeptide resistance genes in both groups, but the healthy group also carried aminoglycoside/tetracycline resistance genes and poxtA. KEGG pathway analysis showed that the diarrheic group was enriched in purine synthesis-related pathways, while the healthy group exhibited dominant metabolic pathways such as glutamine synthase. Virulence factor analysis indicated that the diarrheic group had higher abundances of capsular polysaccharides and type IV secretion systems, potentially promoting bacterial colonization and immune evasion. In summary, diarrheic cattle harbored a gut microbiome dominated by opportunistic pathogens, accompanied by metabolic dysregulation and antimicrobial resistance risks, whereas healthy cattle maintained a microbial community rich in short-chain fatty acid producers. This study provides a theoretical foundation for gut microbiome modulation and antimicrobial resistance control in ruminants.<br><br>CONCLUSION: This study revealed distinct gut microbiome composition and function between diarrheic and healthy cattle through sequencing analysis. The findings offer insights for ruminant diarrhea management and provide a basis for developing more scientific antibiotic management strategies in animal husbandry.}, }
@article {pmid41092755, year = {2025}, author = {Hu, X and Gu, H and Wang, Y and Xu, Y and Li, Y and Yu, Z and Liu, J and Jin, J and Liu, X and Wang, G}, title = {Biodegradable microplastics show greater potential than conventional types in facilitating antibiotic resistance gene enrichment and transfer through viral communities.}, journal = {Environment international}, volume = {204}, number = {}, pages = {109855}, doi = {10.1016/j.envint.2025.109855}, pmid = {41092755}, issn = {1873-6750}, abstract = {Whether and how conventional (CP) and biodegradable microplastics (BP) affect viral communities and virus-carried antibiotic resistance genes (ARGs) in agricultural soils remains largely unknown. Here, we established a soil microcosm incubation with addition of 1 % (w/w) microplastics (MPs) in maize-cultivated soil that had been treated with different fertilizers for over 10 years, and the dynamic variations of viral communities and ARG profiles were investigated using a combination of metagenomic and metatranscriptomic methods. Our results revealed that BP, but not CP, significantly decreased viral α-diversity, changed viral community structure, community resistance and taxonomic turnover in all fertilized treatments. Caudoviricetes was the most dominate viral class and BP significantly increased the abundances of viral families (i.e. Phycodnaviridae) in all fertilized treatments, while CP altered the viral family abundance mainly observed in manure-amended soils. Also, BP was associated with increased ARG α-diversity, altered ARG community structure and community resistance, especially at the transcriptional level. Particularly, BP significantly enriched high-risk ARGs and mobile genetic elements (MGEs) in soils regardless of fertilization regimes. Correlation analysis revealed the important role of lytic viruses in shaping the abundance of high-risk ARGs and MGEs. Furthermore, BP induced more variations in reconstructed metagenome-assembled genome (MAGs), and significantly enriched high-risk ARGs carried by phage genomes. Co-occurrence patterns revealed three Actinobacteriota MAGs as primary viral hosts sharing high-risk ARGs with phages and containing multiple MGEs. Notably, we identified four viral genomes carrying ARG transcripts identical to their hosts. Both CP and BP differentially stimulated ARG expression in these virus-host systems, withmarkedlystronger effects observed in manure-amended soils. In conclusion, this study revealed a high risk of ARG dissemination induced by biodegradable MP residues regardless of fertilization regimes, while conventional MPs strengthen the ARG health risks mainly in manure-amended soils.}, }
@article {pmid41092742, year = {2025}, author = {Norgan, AP and Sadiq, Q and Fedyshyn, B and Wolf, MJ and Enninga, EAL}, title = {Pan-viral metagenomic sequencing demonstrates that cryptic viral infection is rarely observed in villitis of unknown etiology.}, journal = {Placenta}, volume = {171}, number = {}, pages = {205-209}, doi = {10.1016/j.placenta.2025.10.009}, pmid = {41092742}, issn = {1532-3102}, abstract = {INTRODUCTION: Aberrant maternal immune responses are implicated in villitis of unknown etiology (VUE), but the underlying cause of this loss of tolerance, including cryptic causative or precipitating infections, has been difficult to define. Herein, we performed pan-viral metagenomic sequencing of placentas with VUE to investigate the possibility of cryptic viral infection as a contributing factor in this inflammatory pathology.<br><br>METHODS: Placentas evaluated at a single tertiary medical center between 2010 and 2024 were included in this study. Overall, the cohort included infectious villitis due to cytomegalovirus (CMV; n&#xa0;=&#xa0;4), VUE (n&#xa0;=&#xa0;25), and a reference group composed of pathologically unremarkable placentas (n&#xa0;=&#xa0;17). Total nucleic acid was extracted from formalin-fixed paraffin embedded (FFPE) placental tissues and subjected to pan-viral metagenomic sequencing (PVMS) to identify viral-associated reads.<br><br>RESULTS: PVMS detected reads mapping to CMV in 4 (of 4) of CMV cases. For VUE cases, 22 (of 25) had no identifiable viral reads, while 1 case demonstrated CMV reads and two had papillomavirus reads. The control samples demonstrated no identifiable reads in 13 (of 17) samples, while 3 cases had reads mapping to human papillomavirus 16 and one case had reads mapping to human Herpesvirus 6.<br><br>DISCUSSION: Utilizing PVMS, we did not identify cryptic viral sequences in 88&#xa0;% of morphologic VUE cases. In one clinical VUE case, CMV sequences were identified, suggesting a misclassification of infectious villitis. Both papillomavirus and herpesvirus sequences have previously been identified in the placenta, with unknown clinical significance. Overall, these findings exclude active viral infection as a potential etiology of VUE.}, }
@article {pmid41092730, year = {2025}, author = {Wang, Y and Wen, S and Yu, Q and Huang, H and Tang, Y and Miao, C and Xia, Y and Guan, F}, title = {Microbiologically influenced corrosion of oil-water pipeline steel from local field failure case to specific Shewanella &amp; Desulfovibrio corrosion highlights the significance of hydrocarbon-degrading bacteria.}, journal = {Bioelectrochemistry (Amsterdam, Netherlands)}, volume = {168}, number = {}, pages = {109129}, doi = {10.1016/j.bioelechem.2025.109129}, pmid = {41092730}, issn = {1878-562X}, abstract = {Unconventional natural gas pipeline corrosion is associated with microbes, especially sulfate-reducing bacteria (SRB), though it is uncertain if SRB's role is overemphasized. Using metagenomics, corrosion immersion, and microbial cultivation, diverse hydrocarbon-degrading microorganisms, such as Shewanella, in corroded pipeline rust layers, oil-water mixtures, and produced water from unconventional natural gas fields are identified. These bacteria use crude oil as a carbon source, accelerating pitting corrosion of carbon steel and forming corrosion product films (Pitmax = 28.96 μm). The 16S rRNA sequencing results show that Shewanella, prevalent in various steel service environments, is a potential key microorganism in pipeline corrosion. X70 steel exhibits lower electron transfer resistance than Desulfovibrio in the Shewanella medium. Shewanella's aerobic respiration degrades crude oil and oxidizes iron, speeding up iron oxide formation and magnesium phosphate precipitation. Microbial acidification of the oil-water medium also contributes to severe pitting corrosion beneath the oil film. Crude oil accelerates microbial growth. Thus, studying carbon steel corrosion in oil-water environments must consider the impact of hydrocarbon-degrading microorganisms.}, }
@article {pmid41092706, year = {2025}, author = {Zhang, X and Yang, B and Zhang, H and Guo, X and Zhang, Y}, title = {Nicosulfuron-driven antibiotic resistance in corn silage: Effect and its mitigation by zinc oxide nanoparticles.}, journal = {Journal of hazardous materials}, volume = {499}, number = {}, pages = {140119}, doi = {10.1016/j.jhazmat.2025.140119}, pmid = {41092706}, issn = {1873-3336}, abstract = {Antibiotic resistance genes (ARGs) present in animal feed represent a significant threat to human health via the food chain, and pesticide application in crop production may further accelerate the ARGs dissemination. Corn silage, a primary forage for herbivorous livestock, has been shown to harbor diverse ARGs; however, the impact of pesticide-induced stress and potential mitigation strategies on ARG proliferation remains poorly understood. This study investigated the mechanistic link between nicosulfuron exposure and ARG dynamics in corn silage, as well as the mitigating effects of zinc oxide nanoparticles (ZnO NPs) on ARG under nicosulfuron exposure using metagenomic sequencing and high-throughput quantitative PCR. Nicosulfuron exposure increased (P < 0.05) ARG diversity and abundance, enriched (P < 0.05) ARG-hosting genera such as Pantoea, Escherichia, and Klebsiella, and intensified (P < 0.05) the correlation between ARGs and mobile genetic elements (MGEs). Additionally, it disrupted microbial metabolic pathways and elevated (P < 0.05) the ARG-associated risk index in corn silage. Conversely, ZnO NPs alleviated (P < 0.05) these effects by reducing the abundance of key ARGs-bacA, tetM, and ermB, enhancing microbial diversity, promoting beneficial genera such as Levilactobacillus and Companilactobacillus, and decreasing the complexity of ARG-MGE-microbe co-occurrence networks in corn silage under nicosulfuron exposure. Structural equation modeling indicated that there was a significant association between bacterial community and ARGs proliferation, and it had the strongest explanatory power for the variation in ARGs abundance, followed by MGEs. These findings underscore the ecological risks associated with nicosulfuron and demonstrate that ZnO NPs have the potential to mitigate ARGs dissemination in pesticide-contaminated silage. However, this potential does not qualify ZnO NPs as an effective strategy, and their role in promoting safer forage production still requires further evaluation.}, }
@article {pmid41092232, year = {2025}, author = {Meneguzzi, M and Bravo, J and Gaire, TN and Ferm, PM and Torremorell, M and Boucher, C and Noyes, NR}, title = {Enriched Long-Read Sequencing of Co-circulating Viruses in Complex Samples.}, journal = {Molecular biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/molbev/msaf261}, pmid = {41092232}, issn = {1537-1719}, abstract = {At present, no single workflow is available for quick and accurate identification and analysis of genomes of various viruses present together in a field or clinical sample, particularly when followed by long-read sequencing. Our work addressed this limitation by combining targeted enrichment with long-read, real-time sequencing. Using a panel of probes targeting 16,069 complete viral genomes, we validated this workflow (termed TELSVirus) on complex sample matrices collected from pigs, and compared its performance to traditional methods including rRT-PCR and shotgun metagenomics. Using serial dilutions of samples with known viral status, we observed that TELSVirus generated viral reads for dilutions up to 10-9. TELSVirus was able to detect viral targets when shotgun metagenomic long- and short-read datasets did not, and when rRT-PCR results were undetermined. Finally, we performed TELSVirus on 144 oral fluid samples collected in the field, which are highly complex and diverse samples used for viral surveillance in swine. We identified a high prevalence of relatively understudied viruses, often found co-circulating with better-characterized viruses. In many cases, TELSVirus generated ultra-deep genome coverage, allowing for further genomic epidemiological investigations, although bioinformatic methods need further development to work robustly with TELSVirus data. Our results support using TELSVirus for rapid detection and genomic characterization of multiple low-abundance viruses from single samples using long-read sequencing.}, }
@article {pmid41091222, year = {2025}, author = {Tajdozian, H and Seo, H and Kim, S and Rahim, MA and Park, HA and Sarafraz, F and Yoon, Y and Kim, H and Barman, I and Park, CE and Ghorbanian, F and Lee, S and Jeong, HR and Song, HY}, title = {Microbiome therapeutic PMC101 inhibits the translocation of carbapenem-resistant Klebsiella while enhancing eubiosis in antibiotic-induced dysbiosis mice.}, journal = {Medical microbiology and immunology}, volume = {214}, number = {1}, pages = {49}, pmid = {41091222}, issn = {1432-1831}, support = {No. RS-2023-00219563//Ministry of Science and ICT, South Korea/ ; P248400003//Korea Institute for Advancement of Technology/ ; }, mesh = {Animals ; *Dysbiosis/chemically induced/microbiology/therapy ; *Carbapenem-Resistant Enterobacteriaceae/drug effects/physiology ; *Anti-Bacterial Agents/adverse effects/pharmacology ; Mice ; *Gastrointestinal Microbiome/drug effects ; Disease Models, Animal ; *Klebsiella Infections/microbiology/therapy ; *Bacterial Translocation/drug effects ; Carbapenems/pharmacology ; Humans ; Mice, Inbred C57BL ; Feces/microbiology ; }, abstract = {Carbapenem-resistant Enterobacteriaceae (CRE), known for their extensive antibiotic resistance, pose a severe global medical threat. Therefore, developing novel therapeutics beyond conventional antibiotics is urgently needed, and the importance of microbiome therapeutics is increasingly being recognized. This study explores the expanded systemic efficacy of PMC101, a microbiome therapeutic, beyond intestinal CRE infections and investigates its mechanism of action from a microbiome perspective. First, the genetic characteristics of the novel strain were identified through whole-genome analysis, and a scalable cultivation process was established as part of the overall development of this microbiome therapeutic. PMC101 increased the survival rate to 100%, significantly reduced disease severity scores, and prevented weight loss in CRE-infected mice treated with antibiotics. These effects are attributed to the inhibition of CRE growth in stool and the reduced detection of CRE in the lungs and kidneys, indicating suppression of systemic translocation. Metagenomic analysis revealed that PMC101 prevented the reduction in microbial population caused by antibiotics and CRE infection, restored species diversity indices, and mitigated dysbiosis while promoting eubiosis. This CRE translocation suppression was closely associated with increased CRE translocation-microbiome index, defined as the ratio of Bacteroidetes to Proteobacteria. This relationship was further confirmed through simulations using a human intestinal microbial ecosystem model. Additionally, increases in short-chain fatty acids, reductions in excessive inflammatory responses, and decreases in tissue damage were observed, all of which contribute to preventing CRE translocation. Finally, pathogen inhibition effects and safety tests were conducted, confirming the prophylactic potential of PMC101 as a microbiome therapeutic. These findings strongly support PMC101 as a promising candidate for future microbiome-based therapies against CRE infections.}, }
@article {pmid41089932, year = {2025}, author = {Zhang, W and Guo, H and Xu, W and Chen, W and Hu, Y and Wang, Z}, title = {Di-(2-ethylhexyl) phthalate-degrading functional microorganisms were identified in black soil based on high throughput analysis.}, journal = {Current research in microbial sciences}, volume = {9}, number = {}, pages = {100479}, pmid = {41089932}, issn = {2666-5174}, abstract = {Di-(2-ethylhexyl) phthalate (DEHP) has become an increasingly serious pollutant in soils. Microbial degradation represents a highly promising approach for its remediation. In this study, four black soils were used to simulate the natural degradation of DEHP over a 75-day microenvironmental experiment. High-throughput analysis was conducted to investigate the distribution and abundance of functional genes in soil microorganisms, aiming to explore functional microbial information. The degradation efficiency of DEHP in black soils was 76.37 %, 74.16 %, 92.21 %, and 75.35 %. The α-diversity of microbial community was positively correlated with the degradation rate. Actinobacteria and Proteobacteria exhibited sensitivity to DEHP contamination. Xanthomonaceae, Sphingomonadaceae, Hypomicrobiaceae, and Comamonadaceae contributed to the upstream metabolism of DEHP. The abundances of Rhodococcus, Sphingomonas, Nocardioides, and Arthrobacter were positively correlated with the abundance of functional genes enriched in the black soil for benzoate degradation. Concurrently, 10 DEHP-degrading bacterial communities were identified, and the taxonomic and functional profiles of certain members within these communities were consistent with the metagenomic data. Bacterial communities JQ104, JQ52, and JQ129 degraded >98 % of DEHP (400 mg/L) in 48 h, demonstrating remarkable degradation efficiency. This study demonstrated the dynamic impact of the indigenous microbiome on DEHP contamination and verified the degradation capabilities of key functional microorganisms.}, }
@article {pmid41089718, year = {2025}, author = {Takahashi, Y and Fujitani, H and Taniguchi, I and Gotoh, Y and Shimada, Y and Ikeda, S and Hayashi, T and Tago, K and Hayatsu, M and Tsuneda, S}, title = {Acid tolerance and metabolic potential of comammox and nitrite-oxidizing Nitrospira enriched from soil.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf167}, pmid = {41089718}, issn = {2730-6151}, abstract = {Nitrification is the two-step microbial oxidation of ammonia to nitrate via nitrite, and it can contribute to environmental problems in soils. Some nitrifiers have been cultivated from acidic soils at pH <5.5, allowing their metabolic potential and phylogeny to be investigated through genomic analyses. However, the genomic features of the genus Nitrospira remain poorly understood in the context of acid tolerance, despite its wide distribution in acidic environments. This study aimed to characterize the physiology and genomics of acid-tolerant Nitrospira enriched from an acidic soil. Using a metagenomic approach, two closed genomes of Nitrospira were reconstructed: a complete ammonia-oxidizing (comammox) bacterium and a nitrite-oxidizing bacterium (NOB). Both enriched Nitrospira survived at pH <5.5 in physiological tests, and the enriched comammox Nitrospira was phylogenetically close to clones derived from acidic soils. The active-site residues of hydroxylamine oxidase, a key nitrification enzyme, were conserved between the comammox Nitrospira characterized in this study and the previously reported betaproteobacterial ammonia oxidizers. This conservation suggests that existing nitrification inhibitors targeting this enzyme may also inhibit ammonia oxidation by comammox Nitrospira in acidic soils. Although the comammox and NOB Nitrospira in this study shared nearly all key metabolic pathways with Nitrospira species identified from neutral pH environments, both possessed passive urea transporters homologous to those found in acid-tolerant bacteria. These results revealed the acid tolerance of the enriched Nitrospira at pH <5.5, as well as their genomic features shared with acid-tolerant bacteria, rather than with previously reported Nitrospira species.}, }
@article {pmid41089454, year = {2025}, author = {Hu, X and He, Z and Liu, C and Zhang, Y and Mu, D and Guskov, VY and Wang, K and Yao, Y and Jin, D and Lu, J and Ning, Y and Jiang, G}, title = {Revealing Amur tiger family pedigrees based on age identification using fecal microbiome and kinship analysis.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1666201}, pmid = {41089454}, issn = {1664-302X}, abstract = {INTRODUCTION: The construction of a species' family pedigree is crucial for understanding population structure, assessing genetic diversity, and conserving the genetic resources of endangered species. However, developing non-invasive and reliable methods for age identification in wild individuals remains a significant challenge in family pedigree establishments.<br><br>METHODS: In this study, we employed 16S rRNA sequencing and metagenomic analysis to examine 30 fecal samples collected from captive Amur tigers across three distinct age groups, aiming to identify the age-specific biomarker, which could subsequently facilitate age determination of wild individuals and support the construction of species pedigree.<br><br>RESULTS: Our results demonstrate that, through 16S rRNA high-throughput sequencing, 16 potential microbial age biomarkers were identified in fecal samples from captive Amur tigers, and the ages of 17 captive individuals were distinguished. Notably, f_Erysipelotrichaceae_Unclassified and Paraclostridium, identified as potential age-associated bacterial markers in captive Amur tigers, were also detected in fecal samples from wild individuals of this species. To explore their potential application in age inference for Amur tigers, we integrated genetic relationship analysis with these potential age-specific biomarkers to construct a comprehensive pedigree of wild Amur tigers.<br><br>DISCUSSION: This study established a comprehensive scientific framework for pedigree reconstruction based on age determination in Amur tigers and developed a scalable, non-invasive methodology offering opportunities for population structure and promoting the precision of conservation for wild tigers.}, }
@article {pmid41089363, year = {2025}, author = {Park, T and Praisler, G and Wenner, BA}, title = {Treatment of dual-flow continuous culture fermenters with an organic essential oil product minimally influenced prokaryotic microbiome.}, journal = {Journal of animal science and technology}, volume = {67}, number = {5}, pages = {1018-1032}, pmid = {41089363}, issn = {2055-0391}, abstract = {Previous research reported an essential oil (EO) product decreasing methane (CH4) production by dual-flow continuous culture (DFCC); this product could assist organic dairy producers in decreasing emissions. Our objective was to assess the effect of this EO product on the microbial populations within DFCC. Here, we hypothesized that the EO either decreased protozoal population or induced shifts in the bacterial relative abundance to decrease CH4 production. Metagenomic DNA was extracted from previous effluent samples taken from a DFCC system (n = 2) across four experimental periods, after which samples were sequenced the 16S rRNA gene and microbial taxonomy was assigned using the SILVA v138 database. The treatments included a control (CON) diet (60:40 concentrate:orchardgrass pellet mix, 17.1% crude protein, 33.0% neutral detergent fiber, 20.1% acid detergent fiber, and 27.1% starch) fed twice daily for a total of 80 g/d dry matter, or the same CON diet with the addition of EO at 3 mg/d. Protozoa were also quantified in both fermenter contents and unpooled daily effluent samples. The statistical model included fixed effects of treatment and fermenter, and random effect of period, using either MaAsLin2 or the adonis2 function in the vegan package of R for microbial features, or SAS mixed model for protozoal counts. The results were deemed significant at Q < 0.05 and p < 0.05 for the MaAsLin2 and adonis2/SAS analyses, respectively. For the protozoal populations, the treatments had no significant effect (p > 0.10) on the total counts, differentiated groups, or cell outflow. The addition of EO increased the relative abundance of Methanobrevibacter and decreased that of uncultured Methanomethylophilaceae (Q < 0.05). In contrast, EO addition had no significant effect on archaeal α- or β-diversity (p > 0.05). Despite not having a significant effect on the β-diversity of archaeal and bacterial communities, EO decreased (p < 0.05) α-diversity indices in prokaryotic communities. Moreover, EO decreased (Q < 0.01) the relative abundance of Clostridia UCG-014, Rikenellaceae RC9 gut group, and Christenellaceae R7 group, and increased (Q < 0.01) others including Treponema, Succinivibrionaceae UCG-002, and Ruminococcus. Offsetting shifts in the relative abundance of fiber-degrading bacteria and detailed methanogen communities deserves further investigation including predicted metabolic pathways impacted by population shifts induced by this EO combination.}, }
@article {pmid41089014, year = {2025}, author = {Li, B and Xu, F and Xia, M and Li, X and Hou, X and Lyu, X and Guo, X}, title = {[Retrospective clinical analysis of 31 cases of necrotizing fasciitis of the neck with or without descending necrotizing mediastinitis].}, journal = {Lin chuang er bi yan hou tou jing wai ke za zhi = Journal of clinical otorhinolaryngology head and neck surgery}, volume = {39}, number = {10}, pages = {971-975}, doi = {10.13201/j.issn.2096-7993.2025.10.014}, pmid = {41089014}, issn = {2096-7993}, mesh = {Humans ; Retrospective Studies ; *Fasciitis, Necrotizing/complications/therapy ; *Mediastinitis/complications ; *Neck/pathology ; Male ; Female ; Middle Aged ; Adult ; Aged ; Prognosis ; }, abstract = {Objective:To summarize the clinical characteristics and management experience of complications in patients with cervical necrotizing fasciitis （CNF） with or without descending necrotizing mediastinitis （DNM）, in order to provide a basis for optimizing diagnosis and treatment strategies. Methods:A retrospective analysis was conducted on the clinical data of 31 patients diagnosed with CNF and DNM at Shandong Provincial Hospital Affiliated to Shandong First Medical University between October 2019 and March 2024. A comprehensive evaluation was performed based on the patients' clinical characteristics, metagenomic next-generation sequencing （mNGS） pathogen detection results, imaging assessments, surgical interventions, management approaches for specific complications, and prognostic outcomes. Results:Among the 31 patients, 10 had severe diabetes mellitus. Etiological analysis was summarized as follows: 5 cases were odontogenic, 3 were of tonsillar origin, 3 were due to endogenous esophageal injury, 2 were due to exogenous cervical trauma, 2 originated from a congenital branchial cleft fistula, and 16 cases had an unknown etiology. Among them, 29 patients underwent surgery via an external cervical approach, 1 patient underwent surgery via an intraoral approach, and 1 patient received ultrasound-guided puncture and drainage therapy. Ultimately, 29 patients were cured and discharged （including 1 patient who experienced two instances of major neck vessel rupture and successfully underwent two interventional embolization procedures for hemostasis）; 2 patients died after failed rescue efforts due to concurrent sepsis and multiple organ dysfunction. The treatment success rate was 93%, and the mortality rate was 7%. In this cohort of CNF and DNM cases, only a minority had a clearly identified odontogenic cause; although the etiology was unknown in most cases, imaging consistently showed oropharyngeal lymph node necrosis, suggesting a possible pharyngeal origin of infection in adults. The mNGS pathogen profile was predominantly Gram-positive bacteria, accompanied by anaerobic bacilli and fungi. Conclusion:CNF and DNM are severe and rapidly progressive conditions that can lead to life-threatening complications within hours. Timely recognition can reduce unnecessary examinations and expedite treatment.}, }
@article {pmid41088813, year = {2025}, author = {Guo, YN and De, R and Wang, FM and Han, ZZ and Liu, LY and Sun, Y and Yao, Y and Ma, XL and Liu, S and Zhu, C and Qu, D and Zhao, LQ}, title = {Molecular Characterization of New Recombinant Human Adenoviruses Detected in Children with Acute Respiratory Tract Infections in Beijing, China, 2022-2023.}, journal = {Biomedical and environmental sciences : BES}, volume = {38}, number = {9}, pages = {1071-1081}, doi = {10.3967/bes2025.105}, pmid = {41088813}, issn = {2214-0190}, mesh = {Humans ; *Adenoviruses, Human/genetics/classification/isolation &amp; purification ; *Respiratory Tract Infections/virology/epidemiology ; Child, Preschool ; Child ; *Recombination, Genetic ; Male ; Beijing/epidemiology ; Infant ; Female ; Phylogeny ; *Adenovirus Infections, Human/virology/epidemiology ; Acute Disease ; Genome, Viral ; }, abstract = {OBJECTIVE: Recombination events are common and serve as the primary driving force of diverse human adenovirus (HAdV), particularly in children with acute respiratory tract infections (ARIs). Therefore, continual monitoring of these events is essential for effective viral surveillance and control.<br><br>METHODS: Respiratory specimens were collected from children with ARIs between January 2022 and December 2023. The penton base, hexon, and fiber genes were amplified from HAdV-positive specimens and sequenced to determine the virus type. In cases with inconsistent typing results, genes were cloned into the pGEM-T vector to detect recombination events. Metagenomic next-generation sequencing (mNGS) was performed to characterize the recombinant HAdV genomes.<br><br>RESULTS: Among 6,771 specimens, 277 (4.09%, 277/6,771) were positvie for HAdV, of which 157 (56.68%, 157/277) were successfully typed, with HAdV-B3 being the dominant type (91.08%, 143/157), and 14 (5.05%, 14/277) exhibited inconsistent typing results, six of which belonged to species B. The penton base genes of these six specimens were classified as HAdV-B7, whereas their hexon and fiber genes were classified as HAdV-B3, resulting in a recombinant genotype designated P7H3F3, which closely resembled HAdV-B114. Additionally, a partial gene encoding L1 52/55 kD was identified, which originated from HAdV-B16.<br><br>CONCLUSION: A novel recombinant, P7H3F3, was identified, containing sequences derived from HAdV-B3 and HAdV-B7, which is similar to HAdV-B114, along with additional sequences from HAdV-B16.}, }
@article {pmid41088467, year = {2025}, author = {Osburn, ED and Weissman, JL and Strickland, MS and Bahram, M and Stone, BW and McBride, SG}, title = {Relative abundances of bacterial phyla are strong indicators of community-scale microbial growth rates in soil.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {131}, pmid = {41088467}, issn = {2524-6372}, support = {2131837//National Science Foundation/ ; 2020-67034-41310//National Institute of Food and Agriculture/ ; }, abstract = {BACKGROUND: To improve our understanding of microbial systems, it is essential to refine the conceptual frameworks that connect microorganisms to their ecological functions. While trait-based approaches can provide nuanced perspectives on how microorganisms influence ecosystem processes, there is ongoing debate over the link between microbial taxonomic classifications and life history traits. Here, we integrate genomic, metagenomic, amplicon sequencing, and experimental (stable isotope probing) data to investigate the scaling of bacterial growth traits from individual taxa to complex assemblages and to identify specific taxonomic groups of soil bacteria that can be used as indicators of community-scale microbial growth.<br><br>RESULTS: Our results revealed broadly different distributions of growth rates among bacterial phyla, including significantly different mean and median rates. This, in turn, manifested in strong relationships between relative abundances of some phyla and community-scale growth rates in soil. Specifically, we calculated community weighted mean growth rates using measured growth rates of constituent taxa and found that the fast-growing taxa that had sufficient abundance and ubiquity across samples to contribute to variation in community-average growth were mostly lineages of Proteobacteria (e.g., Sphingomonas). As a result, the relative abundance of phylum Proteobacteria was the single strongest taxonomic predictor of community-average growth, explaining up to ~&#x2009;60% of the variation in growth rates across communities. In contrast, Verrucomicrobia were consistent indicators of slower community-average growth. These patterns were especially strong when using taxon-level growth rates measured following carbon and nitrogen additions to soil.<br><br>CONCLUSIONS: Our results demonstrate that phylum relative abundances can be strong indicators of community-level bacterial growth despite the wide variation in growth rates observed within phyla. The stronger phylum-growth relationships for whole assemblages than are apparent for individual taxa are due to relative abundance-weighted trait averaging in complex assemblages, i.e., at the community scale, broad differences in growth traits among phyla become more important than variation within phyla. Overall, our results provide clarity regarding the use of bacterial taxonomic information for inferring traits, demonstrating that high taxonomic ranks can be valid indicators of microbial traits in soil provided that inferences are drawn at the appropriate scale.}, }
@article {pmid41088378, year = {2025}, author = {Chen, Z and Jia, Y and Li, H and Fan, R and Cao, Y and Ni, L and Yang, L and Yuan, Z and Zhu, K and Gao, Y and Lin, Y}, title = {Effects of zacopride and multidimensional impacts of cross-kingdom symbiosis: gut microbiota modulates coronary microvascular dysfunction via the chlorophyll/heme-tryptophan metabolic axis.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {1097}, pmid = {41088378}, issn = {1479-5876}, support = {20210302123485//Fundamental Research Program of Shanxi Province/ ; BYJL065//Shanxi Province Higher Education "Billion Project" Science and Technology Guidance Project/ ; NSFC-82102104//National Natural Science Foundation of China/ ; 2021M702054//China Postdoctoral Science Foundation/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Rats, Sprague-Dawley ; *Tryptophan/metabolism ; Male ; *Symbiosis/drug effects ; *Benzamides/pharmacology/therapeutic use ; *Coronary Vessels/drug effects/physiopathology ; *Microvessels/drug effects/physiopathology ; Rats ; *Microcirculation/drug effects ; }, abstract = {BACKGROUND: Coronary Microvascular Dysfunction (CMD) represents a critical pathological substrate for ischemic heart disease and is strongly associated with major adverse cardiovascular events. Zacopride, known for its dual cardiovascular regulatory properties targeting the 5-HT4 receptor and Kir2.1 channel, lacks evidence regarding its systemic impact on the gut microbiota-metabolism axis. Therefore, this study aims to elucidate the structural and metabolic characteristics of gut bacteria and fungi in CMD, and to explore the multidimensional therapeutic mechanisms of Zacopride through "microbial remodeling-metabolic regulation-microcirculation repair."<br><br>METHODS: Sixty Sprague-Dawley rats were randomized into three groups: coronary microvascular dysfunction (CMD), healthy control (NC), and Zacopride intervention (ZAC). CMD and ZAC groups received high-fat diet plus streptozotocin (STZ, 35&#xa0;mg/kg) for modeling. ZAC rats were orally administered 5&#xa0;mg/kg Zacopride daily for 7&#xa0;days. Transthoracic Doppler echocardiography measured left anterior descending coronary artery resting/stress peak flow velocity and coronary flow reserve (CFR). Ileocecal contents underwent bacterial-fungal metagenomic sequencing to identify differential metabolic pathways. Spearman's correlation assessed cross-kingdom ecological interactions. Nine machine learning algorithms constructed classification models, with Random Forest (RF) and an optimal model identifying key genera. Linear Discriminant Analysis Effect Size validated microbial biomarkers.<br><br>RESULTS: Zacopride partially restored the CFR in CMD rats, demonstrating a therapeutic effect, and exerted a beneficial influence on the structure and diversity of the gut microbiota. The CMD state significantly reduced the expression levels of the Chlorophyll a and tryptophan metabolic pathways in the gut microbiota. Zacopride specifically restored the Chlorophyll a pathway but did not significantly recover the tryptophan metabolic pathway. RF and Elastic Net (ENET) identified JC017, Chromelosporium, and Barnesiella as biomarker microbiota for CMD. Notably, JC017 primarily mediate the therapeutic effects of Zacopride via direct or indirect modulation of the Chlorophyll a metabolic pathway. Chromelosporium, acting as an interactive hub between fungi and bacteria, formed a cross-kingdom symbiotic relationship with Bradyrhizobium. Additionally, the reduction in Barnesiella abundance constitutes a distinctive feature of gut microbial dysbiosis in CMD.<br><br>CONCLUSION: This study provides the first evidence that the gut microbiota modulates the pathogenesis of CMD through the "chlorophyll/heme-tryptophan metabolic axis." Furthermore, we demonstrate that Zacopride exerts therapeutic effects by remodeling microbiota-host interactions and regulating this metabolic axis, revealing a novel mechanistic link between microbial metabolism and CMD progression.}, }
@article {pmid41088296, year = {2025}, author = {Tang, A and Chen, Y and Ding, J and Li, Z and Xu, C and Hu, S and Lai, J}, title = {Gut microbiota remodeling and sensory-emotional functional disruption in adolescents with bipolar depression.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {1083}, pmid = {41088296}, issn = {1479-5876}, support = {82201676//National Natural Science Foundation of China/ ; 82471542//National Natural Science Foundation of China/ ; No. JNL-2023001B//Research Project of Jinan Microecological Biomedicine Shandong Laboratory/ ; 2023YFC2506200//National Key Research and Development Program of China/ ; 2023ZFJH01-01//Fundamental Research Funds for the Central Universities/ ; 2024ZFJH01-01//Fundamental Research Funds for the Central Universities/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/physiology ; Adolescent ; *Bipolar Disorder/microbiology/physiopathology/drug therapy/psychology ; Male ; Female ; *Emotions ; Quetiapine Fumarate/therapeutic use/pharmacology ; Magnetic Resonance Imaging ; Case-Control Studies ; Brain/physiopathology/diagnostic imaging ; Neuroimaging ; }, abstract = {BACKGROUND: Adolescence is the peak period of newly-onset bipolar disorder (BD). Accumulating studies have revealed disturbed gut microbiota can interfere with neurodevelopment in adolescents. In this study, we aimed to characterize the gut microbiota in adolescents with BD and its correlation with brain dysfunction.<br><br>METHODS: Thirty unmedicated BD adolescents within depressive episode were recruited and underwent four-week quetiapine treatment. Twenty-five age-, gender-, and BMI-matched healthy controls (HCs) were recruited. Fecal samples were collected from HCs and all BD adolescents before and after treatment and analyzed by metagenomic sequencing. Resting-state cranial functional magnetic images were collected from 21 BD adolescents before treatment. Random forest models were used to evaluate the discriminative power of gut microbiota and neuroimaging data for BD and the predictive power of treatment effect.<br><br>RESULTS: Although no significant difference was found in alpha-diversity, intra- and inter-group differences in beta-diversity were observed among HCs, pre- and post-treatment patients. Compared to HCs, unmedicated BD adolescents presented a differentiated gut microbial communities, which correlated to the short-chain fatty acids, choline, lipids, vitamins, polyamines, aromatic amino acids metabolic pathways. Four-week quetiapine treatment improved the abundance of specific genus, such as Odoribacter splanchnicus, Oribacterium sinus, Hafnia alvei, Fusobacterium periodonticum, Acidaminococcus interstini and Veillonella rogosae. Neuroimaging analysis revealed sensor-emotional brain regions were associated with BD severity. Finally, random forest models based on gut microbial biomarkers can well distinguish unmedicated BD from HCs (AUC&#x2009;=&#x2009;91.12%) and predict the treatment effect (AUC&#x2009;=&#x2009;91.84%). The random forest model integrating gut microbiota and neuroimaging data exhibited a better predictive efficacy than using microbiota data alone.<br><br>CONCLUSION: This study first characterized the gut microbiota architecture in adolescent BD. Combining gut microbiota and brain function biomarkers may benefit disease diagnosis and predict treatment outcome. Nonetheless, these findings should be carefully interpreted considering the limitations of a modest sample size and the absence of detailed mechanistic explorations. Trial registration NCT05480150. Registered 29 July 2022-Retrospectively registered, https://clinicaltrials.gov/study/NCT05480150 .}, }
@article {pmid41088250, year = {2025}, author = {Koehler, AV and Wang, T and Stevens, MA and Haydon, SR and Gasser, RB}, title = {Long-term molecular surveillance of Cryptosporidium and Giardia in wildlife in protected drinking water catchments.}, journal = {Parasites &amp; vectors}, volume = {18}, number = {1}, pages = {413}, pmid = {41088250}, issn = {1756-3305}, support = {LP160101299//Australian Research Council/ ; }, mesh = {*Cryptosporidium/genetics/isolation &amp; purification/classification ; Animals ; *Giardia/genetics/isolation &amp; purification/classification ; *Cryptosporidiosis/epidemiology/parasitology ; Feces/parasitology ; *Giardiasis/epidemiology/veterinary/parasitology ; *Animals, Wild/parasitology ; *Drinking Water/parasitology ; Victoria/epidemiology ; Genotype ; Longitudinal Studies ; Prevalence ; Epidemiological Monitoring ; }, abstract = {BACKGROUND: This study presents findings from a 15-year longitudinal surveillance program (2009-2024) monitoring Cryptosporidium and Giardia in protected drinking water catchments in Melbourne and environs in the State of Victoria, Australia. As one of the few major cities worldwide sourcing largely unfiltered water from forested catchments, Melbourne presents a unique opportunity to assess the occurrence and prevalence of protozoan parasites in a minimally disturbed ecosystem.<br><br>METHODS: A total of 14,960 animal faecal samples were analysed using polymerase chain reaction (PCR)-based sequencing, including 8695 samples collected over the past 9&#xa0;years.<br><br>RESULTS: Cryptosporidium was detected in 3.15% of samples and Giardia in 0.16%. A total of 12 recognised Cryptosporidium species and genotypes were identified, nine of which have known zoonotic potential, as well as two sub-assemblages (AI and AIII) of Giardia duodenalis, including four novel assemblage AI variants. Parasite diversity was the highest in eastern grey kangaroos, which hosted at least 18 Cryptosporidium variants. Temporal analyses revealed significant inter-annual variation, with peak prevalence during the 2023 La Ni&#xf1;a year and seasonal differences by host group. Notably, C. ubiquitum, C. muris and C. occultus were recorded for the first time in these catchments. In spite of the low prevalence of high-risk species such as C. parvum and the absence of C. hominis, the detection of emerging and previously uncharacterised genotypes emphasises the importance of sustained surveillance.<br><br>CONCLUSIONS: These findings have broad implications for managing zoonotic risk in unfiltered water systems worldwide. Advances in metagenomics and high-throughput sequencing platforms will be critical for enhancing future pathogen monitoring and catchment management strategies in the context of increasing climate and environmental pressures.}, }
@article {pmid41087996, year = {2025}, author = {Kruasuwan, W and Pathomchareansukchai, D and Tangsawad, W and Wankaew, N and Arigul, T and Nitayanon, P and Nimsamer, P and Duangjanchot, R and Arayamethakorn, S and Chancharussin, N and Jenjaroenpun, P and Kamolvit, W and Suputtamongkol, Y and Wongsurawat, T and Tansirichaiya, S}, title = {Clinical long-read metagenomic sequencing of culture-negative infective endocarditis reveals genomic features and antimicrobial resistance.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {1299}, pmid = {41087996}, issn = {1471-2334}, }
@article {pmid41087940, year = {2025}, author = {Li, C and Liu, M and Ji, Y and Pang, S and Tian, J and Li, X and Zhang, M and Gu, Y and Chen, H and He, L and Wu, Y}, title = {Clinical characteristics and prognostic indicators in Listeria monocytogenes meningoencephalitis: A retrospective case series and literature review.}, journal = {BMC neurology}, volume = {25}, number = {1}, pages = {420}, pmid = {41087940}, issn = {1471-2377}, support = {YKD2022LH060//Inner Mongolia Medical University Joint Project/ ; YKD2022LH060//Inner Mongolia Medical University Joint Project/ ; YKD2022LH060//Inner Mongolia Medical University Joint Project/ ; YKD2022LH060//Inner Mongolia Medical University Joint Project/ ; YKD2022LH060//Inner Mongolia Medical University Joint Project/ ; YKD2022LH060//Inner Mongolia Medical University Joint Project/ ; YKD2022LH060//Inner Mongolia Medical University Joint Project/ ; YKD2022LH060//Inner Mongolia Medical University Joint Project/ ; YKD2022LH060//Inner Mongolia Medical University Joint Project/ ; YKD2022LH060//Inner Mongolia Medical University Joint Project/ ; YKD2022LH060//Inner Mongolia Medical University Joint Project/ ; 2023GLLH0034//Inner Mongolia Academy of Medical Sciences Scientific Research Joint Fund key Project/ ; 2023GLLH0034//Inner Mongolia Academy of Medical Sciences Scientific Research Joint Fund key Project/ ; 2023GLLH0034//Inner Mongolia Academy of Medical Sciences Scientific Research Joint Fund key Project/ ; 2023GLLH0034//Inner Mongolia Academy of Medical Sciences Scientific Research Joint Fund key Project/ ; 2023GLLH0034//Inner Mongolia Academy of Medical Sciences Scientific Research Joint Fund key Project/ ; 2023GLLH0034//Inner Mongolia Academy of Medical Sciences Scientific Research Joint Fund key Project/ ; 2023GLLH0034//Inner Mongolia Academy of Medical Sciences Scientific Research Joint Fund key Project/ ; 2023GLLH0034//Inner Mongolia Academy of Medical Sciences Scientific Research Joint Fund key Project/ ; 2023GLLH0034//Inner Mongolia Academy of Medical Sciences Scientific Research Joint Fund key Project/ ; 2023GLLH0034//Inner Mongolia Academy of Medical Sciences Scientific Research Joint Fund key Project/ ; 2023GLLH0034//Inner Mongolia Academy of Medical Sciences Scientific Research Joint Fund key Project/ ; 202202019//Inner Mongolia Region Health Science and Technology Plan Project/ ; 202202019//Inner Mongolia Region Health Science and Technology Plan Project/ ; 202202019//Inner Mongolia Region Health Science and Technology Plan Project/ ; 202202019//Inner Mongolia Region Health Science and Technology Plan Project/ ; 202202019//Inner Mongolia Region Health Science and Technology Plan Project/ ; 202202019//Inner Mongolia Region Health Science and Technology Plan Project/ ; 202202019//Inner Mongolia Region Health Science and Technology Plan Project/ ; 202202019//Inner Mongolia Region Health Science and Technology Plan Project/ ; 202202019//Inner Mongolia Region Health Science and Technology Plan Project/ ; 202202019//Inner Mongolia Region Health Science and Technology Plan Project/ ; 202202019//Inner Mongolia Region Health Science and Technology Plan Project/ ; KC23262//The project of Xuzhou Science and Technology Bureau in 2023/ ; KC23262//The project of Xuzhou Science and Technology Bureau in 2023/ ; KC23262//The project of Xuzhou Science and Technology Bureau in 2023/ ; KC23262//The project of Xuzhou Science and Technology Bureau in 2023/ ; KC23262//The project of Xuzhou Science and Technology Bureau in 2023/ ; KC23262//The project of Xuzhou Science and Technology Bureau in 2023/ ; KC23262//The project of Xuzhou Science and Technology Bureau in 2023/ ; KC23262//The project of Xuzhou Science and Technology Bureau in 2023/ ; KC23262//The project of Xuzhou Science and Technology Bureau in 2023/ ; KC23262//The project of Xuzhou Science and Technology Bureau in 2023/ ; KC23262//The project of Xuzhou Science and Technology Bureau in 2023/ ; XZSYSKF2020010//The opening project of key laboratories of colleges and universities in Jiangsu Province in 2020/ ; XZSYSKF2020010//The opening project of key laboratories of colleges and universities in Jiangsu Province in 2020/ ; XZSYSKF2020010//The opening project of key laboratories of colleges and universities in Jiangsu Province in 2020/ ; XZSYSKF2020010//The opening project of key laboratories of colleges and universities in Jiangsu Province in 2020/ ; XZSYSKF2020010//The opening project of key laboratories of colleges and universities in Jiangsu Province in 2020/ ; XZSYSKF2020010//The opening project of key laboratories of colleges and universities in Jiangsu Province in 2020/ ; XZSYSKF2020010//The opening project of key laboratories of colleges and universities in Jiangsu Province in 2020/ ; XZSYSKF2020010//The opening project of key laboratories of colleges and universities in Jiangsu Province in 2020/ ; XZSYSKF2020010//The opening project of key laboratories of colleges and universities in Jiangsu Province in 2020/ ; XZSYSKF2020010//The opening project of key laboratories of colleges and universities in Jiangsu Province in 2020/ ; XZSYSKF2020010//The opening project of key laboratories of colleges and universities in Jiangsu Province in 2020/ ; XWKYHT20200001//The Youth Medical Science and Technology Innovation Project of Xuzhou Municipal Health Commission in 2020/ ; XWKYHT20200001//The Youth Medical Science and Technology Innovation Project of Xuzhou Municipal Health Commission in 2020/ ; XWKYHT20200001//The Youth Medical Science and Technology Innovation Project of Xuzhou Municipal Health Commission in 2020/ ; XWKYHT20200001//The Youth Medical Science and Technology Innovation Project of Xuzhou Municipal Health Commission in 2020/ ; XWKYHT20200001//The Youth Medical Science and Technology Innovation Project of Xuzhou Municipal Health Commission in 2020/ ; XWKYHT20200001//The Youth Medical Science and Technology Innovation Project of Xuzhou Municipal Health Commission in 2020/ ; XWKYHT20200001//The Youth Medical Science and Technology Innovation Project of Xuzhou Municipal Health Commission in 2020/ ; XWKYHT20200001//The Youth Medical Science and Technology Innovation Project of Xuzhou Municipal Health Commission in 2020/ ; XWKYHT20200001//The Youth Medical Science and Technology Innovation Project of Xuzhou Municipal Health Commission in 2020/ ; XWKYHT20200001//The Youth Medical Science and Technology Innovation Project of Xuzhou Municipal Health Commission in 2020/ ; XWKYHT20200001//The Youth Medical Science and Technology Innovation Project of Xuzhou Municipal Health Commission in 2020/ ; }, mesh = {Humans ; Middle Aged ; Male ; Retrospective Studies ; Female ; Prognosis ; Adult ; *Listeria monocytogenes ; Aged ; *Meningitis, Listeria/diagnosis/cerebrospinal fluid ; *Meningoencephalitis/diagnosis/cerebrospinal fluid ; *Listeriosis/diagnosis/cerebrospinal fluid ; }, abstract = {BACKGROUND: Listeria monocytogenes meningoencephalitis (LMM) is a rare but severe central nervous system (CNS) infection. This study aimed to characterize the clinical manifestations, diagnostic findings, treatment responses, and prognostic factors associated with LMM.<br><br>METHODS: We retrospectively analyzed the clinical data of 13 patients diagnosed with LMM at Xuzhou Medical University Affiliated Hospital between 2018 and 2023. An additional five cases were identified through a literature search in the China National Knowledge Infrastructure (CNKI) and Wanfang databases from 2019 to 2022. Clinical features, cerebrospinal fluid (CSF) and blood test results, imaging findings, treatments, and outcomes were summarized.<br><br>RESULTS: Among 18 patients (11 males, 7 females; mean age 51.6&#x2009;&#xb1;&#x2009;17.2 years), all had acute onset with fever (100%), headache (83.3%), and altered consciousness (77.8%). CSF analysis showed elevated pressure in 83.3%, increased leukocytes and protein in all cases, and variable glucose levels. LM was cultured from CSF in 10 patients and detected via metagenomic next-generation sequencing (mNGS) in 12. Imaging findings included hydrocephalus in 4 cases and meningeal enhancement in 2 cases. Full recovery was observed in 2 cases, improvement in 9, palliative care in 3, and death in 4. Early seizures and hydrocephalus were linked to worse outcomes.<br><br>CONCLUSION: Listeria monocytogenes meningoencephalitis is a rapidly progressive CNS infection with variable presentations and significant risk of poor outcomes. Early recognition, appropriate antimicrobial coverage, and timely diagnostic testing are essential to improving prognosis.<br><br>TRIAL REGISTRATION: Not applicable.}, }
@article {pmid41040331, year = {2025}, author = {Li, S and Zhu, D and Saha, K and Kundu, BB and Sonkusale, S and Britton, RA and Ajo-Franklin, CM}, title = {Synthetic microbial co-cultures for modular bioelectronic sensing in diverse environments.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41040331}, issn = {2692-8205}, abstract = {Human disruption of ecosystems poses a significant threat to global health, driving the need for low-cost, low-power, and easily deployable sensors for environmental and health monitoring. Microbial bioelectronic sensors are particularly well-suited as they generate electrical signals and can be integrated into compact electronic devices for field deployment over extended periods. However, current engineering strategies for bioelectronic sensors lack modularity, are limited to a few microbial chassis, and depend on specialized instruments for signal detection. Here, we present the electroactive co-culture sensing system (e[-]COSENS), a plug-and-play platform for bioelectronic sensor development. This system comprises a "sender" bacterium that produces electron mediators in response to analytes and a "receiver" bacterium that utilizes the electron mediators to generate electrical signals via extracellular electron transfer (EET). By modularly swapping the sender bacterium and its associated genetic sensing elements, we achieved bioelectronic sensing of metals, small molecules, and peptides in distinct environmental, food, and human-relevant settings. Moreover, we designed a centimetre-sized bioelectronic device that enables low-cost, portable signal readout from e[-]COSENS using a household digital multimeter. The e[-]COSENS platform greatly simplifies the bioelectronic sensor design and opens unprecedented potential for bioelectronic sensor applications.}, }
@article {pmid40889483, year = {2025}, author = {Bertrans-Tubau, L and Martínez-Campos, S and López-Doval, JC and Abril, M and Pladelasala-Rocafiguera, G and Ponsá, S and Suñer, AC and Salvadó, V and Hidalgo, M and Doménech-Pascual, A and Romaní, AM and Pico-Tomàs, A and Balcázar, JL and Proia, L}, title = {Improving small urban wastewater treatment plants with a nature-based reactor for tertiary treatment.}, journal = {Journal of environmental management}, volume = {393}, number = {}, pages = {126983}, doi = {10.1016/j.jenvman.2025.126983}, pmid = {40889483}, issn = {1095-8630}, mesh = {*Wastewater ; Nitrogen ; Phosphorus ; *Bioreactors ; *Water Purification/methods ; *Waste Disposal, Fluid/methods ; Sewage ; Biofilms ; }, abstract = {Urban wastewater treatment has significantly improved in recent decades, reducing the environmental impacts of their effluents and improving the chemical and ecological status of receiving water bodies. However, specific treatments, focused on nitrogen and phosphorus removal, have been implemented principally in large urban wastewater treatment plants (UWWTPs) serving over 10,000 population equivalents (P.E). In contrast, small UWWTPs (<10,000 P.E.) are generally not required to meet nutrient discharge limits despite the revised Urban Wastewater Treatment Directive. Nature-Based Solutions (NBS) offer cost-effective alternatives for small facilities as potential tertiary treatments. This research evaluated a pond-stream system, based on the biological activity of benthic (biofilms) and planktonic microbial communities (biofilm-plankton reactor, BPR), as an additional treatment step for activated sludge UWWTPs. The BPR achieved removal efficiencies for nitrogen (67.4 ± 11.1 %) and Escherichia coli (75.4 ± 37.3 %), while phosphorus, carbon, and targeted contaminants of emerging concern were highly variable and were not consistently removed. Microbial communities' structure and functions were assessed through algal biomass, stoichiometry, and extracellular enzymatic activities, providing a distinctive perspective into the BPR's microbial ecological dynamics related to removal efficiencies. Shotgun metagenomics identified a broad range of nitrogen functional genes, mainly involved in biodegradation and biosynthesis processes. This next-generation sequencing approach complemented conventional E. coli count methods, offering a deeper understanding of potential pathogen hotspots in treated effluents. Overall, the BPR system demonstrated a promising NBS for nitrogen and microbiological contaminant removal in small UWWTPs, whereas further investigation is needed to optimise the removal of other important water quality parameters.}, }
@article {pmid41087922, year = {2025}, author = {Wang, Y and Liang, M and Hu, M and Mao, G}, title = {Disseminated Talaromyces marneffei infection in a patient with Ankylosing Spondylitis: a case report and review of the literature.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {1316}, pmid = {41087922}, issn = {1471-2334}, abstract = {BACKGROUND: Ankylosing Spondylitis (AS) is a prevalent autoimmune disorder that necessitates the prolonged use of corticosteroids, non-steroidal anti-inflammatory drugs (NSAIDs), and disease-modifying antirheumatic drugs (DMARDs). Immunosuppressive medications are now commonly incorporated into treatment plans; however, this may increase patients' risk of severe infections. Infections caused by Talaromyces marneffei (TM) are rarely seen in patients with AS, yet if left untreated, they could result in severe morbidity and even death.<br><br>CASE REPORT: This report presents a comprehensive case study of a 44-year-old Human Immunodeficiency Virus (HIV)-negative male with Ankylosing Spondylitis (AS) complicated by diabetes mellitus, who developed both soft tissue and pulmonary infections. Initial diagnosis suggested a bacterial etiology; however, clinical response to broad-spectrum antibiotics was suboptimal. Subsequent diagnostic procedures, including biopsy and culture of axillary lymph nodes and pulmonary tissue, coupled with Metagenomic Next-Generation Sequencing (mNGS), confirmed the diagnosis of disseminated TM infection. The patient achieved favorable outcomes following targeted antifungal therapy.<br><br>CONCLUSION: Patients with compromised immune function due to chronic immunosuppressive treatments require vigilant monitoring for uncommon opportunistic pathogens, particularly fungal infections. Advanced diagnostic techniques for early identification of pathogens, prompt and accurate prescription of antimicrobial agents, tailored dosing schedules, and stringent monitoring for potential complications are crucial for optimizing patient outcomes.}, }
@article {pmid41087898, year = {2025}, author = {Zheng, N and Wang, D and Xing, G and Gao, Y and Li, S and Liu, J and Kang, J and Sha, S and Cheng, L and Fan, S and Yu, J and Yan, Q and Jiang, C}, title = {Characterization of the gut mycobiome in patients with non-alcoholic fatty liver disease and correlations with serum metabolome.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {660}, pmid = {41087898}, issn = {1471-2180}, abstract = {BACKGROUND: Emerging evidence suggests that the gut microbiome plays a key role in metabolic diseases such as non-alcoholic fatty liver disease, yet the contribution of the gut mycobiome remains largely overlooked.<br><br>METHODS: We performed a comprehensive analysis of publicly available fecal metagenomic sequencing data and matched serum metabolomic profiles from 90 non-alcoholic fatty liver disease patients and 90 healthy controls. A curated fungal genome database was constructed for taxonomic profiling. We integrated fungal, bacterial, and metabolomic data to assess taxon-specific associations, cross-kingdom interactions, and predictive potential.<br><br>RESULTS: Although overall fungal diversity showed no significant differences between groups, four fungal species-Pseudopithomyces sp. c174, Mucor sp. c176, Aspergillus sp. c25, and Ascochyta c213-were significantly enriched in non-alcoholic fatty liver disease patients. The gut mycobiome explained 38.2% of the variance in serum metabolomic profiles, with several species displaying strong correlations with non-alcoholic fatty liver disease relevant metabolites. For instance, Pseudopithomyces sp. c174 was positively associated with protective metabolites such as glycoursodeoxycholic acid and alpha-linolenic acid, while Aureobasidium c170 and Basipetospora c193 were linked to phenylacetic acid, a metabolite implicated in hepatic lipid accumulation. Network analysis revealed altered fungal-bacterial co-abundance patterns in non-alcoholic fatty liver disease, with fungal taxa such as Alternaria alternata c42 and Malassezia c303 emerging as key hubs. A random forest classifier integrating 42 bacterial and fungal features achieved an AUC of 0.772 for distinguishing non-alcoholic fatty liver disease from controls, highlighting the predictive value of the mycobiome.<br><br>CONCLUSIONS: Our findings reveal that gut fungal communities are functionally and ecologically altered in non-alcoholic fatty liver disease and contribute to shaping the host metabolic environment. These results underscore the need to incorporate the gut mycobiome into future microbiome-based strategies for non-alcoholic fatty liver disease diagnosis and treatment.}, }
@article {pmid41087864, year = {2025}, author = {Chen, H and Wang, Z and Su, W and Li, S and Ye, Q and Zhang, G and Zhou, X}, title = {Helicobacter pylori infection impairs glucose homeostasis through gut microbiota dysbiosis.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {663}, pmid = {41087864}, issn = {1471-2180}, support = {82100594//National Natural Science Foundation of China,China/ ; }, abstract = {BACKGROUND: Epidemiological data show that Helicobacter pylori (H. pylori) infection is not only the most important risk factor for gastric cancer, but is also associated with poor glycemic control in patients with diabetes. However, the direct causal and functional relationship between H. pylori infection and dysglycemia is unclear.<br><br>METHOD: A retrospective cohort study was conducted to examine the association between H. pylori infection and glycemic levels in individuals with Type 2 diabetes. C57BL/6 diabetic mice were infected with H. pylori, and the resulting changes in colonic inflammation and intestinal Glucagon-like peptide-1 (GLP-1) secretion were thoroughly examined using immunohistochemistry, RNA sequencing, metagenomic sequencing, and targeted metabolomics. The microbial and metabolomics profiles were analyzed and compared in antibiotic-treated mice through fecal transfer experiments.<br><br>RESULTS: H. pylori infection aggravated insulin resistance in diabetic individuals and mice. We identified a unique H. pylori-induced epithelial inflammation and reduced intestinal GLP-1 secretion in the colon. H. pylori infection also interrupts the normal microbial composition in the colon, leading to a decrease in SCFA-producing bacteria and a reduction in acetic and propionate acids. Similar changes were observed in antibiotic-treated mice after receiving fecal transplants from H. pylori-infected diabetic mice. In vitro studies revealed that the intestinal flora of H. pylori-positive diabetic mice inhibited proglucagon transcription, cAMP levels, and GLP-1 secretion in colonic endocrine cells, with SCFA supplementation reversing this effect on GLP-1 production. These microbial, metabolic, and GLP-1 alterations were also seen in antibiotic-treated mice after receiving fecal transplants from H. pylori-infected diabetic mice. H. pylori eradication with antibiotics improved glucose metabolism and GLP-1 secretion to levels comparable to uninfected controls.<br><br>CONCLUSION: Our studies offer evidence that H. pylori infection significantly contributes to the progression of glucose impairment and insulin resistance. Therefore, incorporating H. pylori status into preventive strategies for diabetes should be taken into account. (Chinese Clinical Trial Registry Center, ChiCTR2200063489, Registered 08 September 2022, https://www.chictr.org.cn/showproj.html?proj=178102).}, }
@article {pmid41087617, year = {2025}, author = {Liu, M and Yang, L and Nan, D and Ma, L and Zhang, J and Liang, F and Yang, J and Liu, X}, title = {Hyperbaric oxygen treatment mitigates gut dysbiosis of mice with spinal cord injury.}, journal = {Journal of molecular medicine (Berlin, Germany)}, volume = {}, number = {}, pages = {}, pmid = {41087617}, issn = {1432-1440}, support = {No. 82101964//National Natural Science Foundation of China/ ; No. 7202055//Natural Science Foundation of Beijing Municipality/ ; CYDXK 202208//Beijing Chao-Yang Hospital Multi-disciplinary Team Program/ ; }, abstract = {Gut dysbiosis impacts the recovery of neurological function after spinal cord injury (SCI). Hyperbaric oxygen (HBO) can alleviate SCI, but its effects on the gut microbiota post-SCI remain unclear. This study aimed to clarify the impact of HBO on SCI-induced gut dysbiosis and to explore the mechanisms of locomotor recovery in HBO-treated SCI mice. After establishing different groups of mouse models, bacterial cultures and Basso Mouse Scale (BMS) scores were performed at various time points post-SCI. Intestinal tissues were collected for intestinal permeability assay, histological analysis, immunofluorescence, and qPCR analysis. Flow cytometry and ELISA were used to detect immune-inflammatory cells and cytokines in intestinal tissue. The composition of gut microbiota in fecal samples from each group was also analyzed. Spinal cord tissues were collected for immunofluorescence and untargeted metabolomics analysis. Spearman correlation analysis was used to correlate differential microbiota with differential metabolites. Our results showed that the expression of tight junction proteins was increased after HBO treatment in SCI mice. Metagenomic analysis of the fecal DNA revealed that HBO altered intestinal bacterial composition. Differential metabolites were mainly enriched in pathways, such as glycerophospholipid metabolism, steroid biosynthesis, and glycolysis/gluconeogenesis. Moreover, differential microbiota showed a strong correlation with differential metabolites related to glycerophospholipids. HBO treatment significantly inhibited immune cells and inflammatory cytokines in the gut after SCI. In addition, HBO treatment significantly increased BMS scores and body weight, and repaired damaged cholinergic neurons. Antibiotic-induced gut dysbiosis impaired the recovery of locomotor function and exacerbated intraspinal pathology. However, these effects could be mitigated by HBO treatment. Overall, HBO treatment may improve neurological recovery through multiple regulatory mechanisms including alleviating gut dysbiosis, reducing intestinal inflammation, and rectifying glycerophospholipid metabolic disorders after SCI. These findings highlight HBO as a promising therapeutic strategy for SCI treatment and support its clinical application. KEY MESSAGES: The intestinal microbiota composition of mice changed after SCI. HBO treatment could preserve intestinal barrier integrity, modulate the composition of intestinal microbiota, rectify glycerophospholipid metabolic disorders, and reduce intestinal immune inflammatory responses. Intestinal microbiota identified as the target for HBO therapeutic in SCI recovery. Alleviating SCI-induced gut dysbiosis may be one of the mechanisms underlying the beneficial effect of HBO on neurological functions.}, }
@article {pmid41087549, year = {2025}, author = {Chauhan, M and Maniya, H and Mori, P and Nagpal, R and Tirgar, P and Kumar, V}, title = {Assessment of multi-strain probiotics in regulating diet-induced obesity in Balb/c mice model.}, journal = {International journal of obesity (2005)}, volume = {}, number = {}, pages = {}, pmid = {41087549}, issn = {1476-5497}, abstract = {BACKGROUND/OBJECTIVES: This study investigated the efficacy of a novel multi-strain probiotic (MSP), composed of Limosilactobacillus fermentum BAB 7912, Bacillus rugosus PIC5CR, and Bacillus rugosus PIB9CR, in preventing and reverting diet-induced obesity in Balb/c male mice.<br><br>SUBJECTS/METHODS: This study used 8-week-old Balb/c mice. A total of 40 mice were divided into five groups namely control negative (CN), control with obesity (CO), and three treatment groups: microbial consortium treated (MCT), Healthy control 1 (HC1), and Healthy control 2 (HC2). Obesity was induced using a high-fat diet. MSP formulation developed indigenously as part of previous study, was fed to Balb/c mice at different time intervals to study its preventive and ameliorative potential. Animals were dissected for the collection of blood as well as various organs to study the effect of MSP feeding on obesity status. Results were validated using histopathological and metagenomic data.<br><br>RESULTS: The CN and other treatment groups gained significant weight at the end of 6 weeks, while no significant weight gain was observed among HC1 group animals that were fed with HFD and MSP together. This highlights the preventive effect of continuous MSP feeding in the HC1 animal group. Initial liver histopathology in the HC1 group revealed enlarged hepatocytes and fat droplets. By week 9, the MCT group, which received MSP with a basal diet, showed liver recovery towards normal, accompanied by body weight improvement from 28.02&#x2009;&#xb1;&#x2009;0.7&#x2009;g to 26.18&#x2009;&#xb1;&#x2009;0.96&#x2009;g. Metagenomic analysis revealed that MSP treatment increased the relative abundance of health-promoting bacteria, notably Lactobacillaceae (specifically Lactobacillus).<br><br>CONCLUSIONS: Findings indicated that continuous consumption of MSP contributes significantly in prevention of obesity and associated metabolic disorders. Future studies are needed to explore the mechanisms underlying these effects and to evaluate the potential of MSP for human health.}, }
@article {pmid41087370, year = {2025}, author = {Balachandran, KRS and Mani, G and Sidharthan, AT and Mary Leema, JT and Senthilkumar, R and Gopal, D}, title = {Unearthing the genetic resources of Arabian sea seamount and metagenomic insights into phosphate cycling genes for next generation plant biostimulants.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {35782}, pmid = {41087370}, issn = {2045-2322}, mesh = {*Metagenomics/methods ; *Metagenome ; *Phosphates/metabolism ; *Geologic Sediments/microbiology ; Bacteria/genetics ; Microbiota/genetics ; Phosphoric Monoester Hydrolases/genetics/metabolism ; }, abstract = {Deep-sea encompasses a wide diversity of microbiomes including bacteria, fungi and viruses which play crucial significant roles in nutrient biogeochemical cycling thereby imparting majorly to functional biodiversity of these hotspots. Sea mounts harboring microbes with extremophilic properties found in deep oceans could be conserved as living repository by functional metagenomics approach which is a potent source to screen bioactive compounds and novel enzymes thereby could address biological question on developing next generation plant biostimulants. This study outlines construction of fosmid metagenome library and adapted combined strategy of functional and nanopore sequence-based metagenomic screening to unveil phosphatase enzymes from Arabian Sea seamount sediment. About 9068 metagenomic clones were generated with an average insert size of 38 kb and stored in pools of 1024 clones, out of which 42 were found to be positive for phosphatase. Five clones with high phosphatase activity were further characterized and NIOT F41 showed the greatest specific activity for phosphatase (41.2 U/mg). Gluconic (1041 mg/L), oxalic (327 mg/L), and succinic acids (610 mg/L) were the predominant organic acids produced by recombinant clones. Fosmid DNA were extracted from five potential clones for nanopore-based metagenomics sequencing which generated an average of 6,00,786 reads. Taxonomic analysis revealed an abundance of Proteobacteria and Firmicutes phyla harboring phosphate-solubilising bacteria Pseudomonas aeruginosa, Bacillus subtilis and Staphylococcus warneri. Furthermore, functional annotation using phosphorus cycling database (PCycDB) predicted variation in relative abundance of phosphatase gene clusters encoding alkaline phosphatase (PhoD, PhoX and PhoA) and acid phosphatase (OlpA, PhoNand PhoC) produced by recombinant clones. In the pot assay, potential metagenomic clones exhibited positive impacts on shoot length (9.1 ± 1.1 cm, p < 0.05), root length (2.05 ± 0.05 cm, p < 0.05), wet biomass (39.3 ± 0.65 mg, p < 0.05), and dry biomass (5.1 ± 1.15 mg, p < 0.05) compared to the negative control indicating significant effect on promoting plant growth. The advanced nanopore sequencing and functional metagenomics methods employed in this study could serve as a marine biodiversity conservation approach for deep-sea microbes hidden in sea mount sediments towards harnessing potential next generation plant biostimulants with promising biotechnological application for sustainable agriculture.}, }
@article {pmid41087364, year = {2025}, author = {Boulay, A and Leprince, A and Enault, F and Rousseau, E and Galiez, C}, title = {Empathi: embedding-based phage protein annotation tool by hierarchical assignment.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {9114}, pmid = {41087364}, issn = {2041-1723}, support = {325947//Fonds de Recherche du Qu&#xe9;bec - Nature et Technologies (Quebec Fund for Research in Nature and Technology)/ ; }, mesh = {*Bacteriophages/genetics/metabolism ; *Viral Proteins/genetics/metabolism/classification ; *Molecular Sequence Annotation/methods ; Machine Learning ; Genome, Viral ; Databases, Protein ; *Software ; Bacteria/virology ; *Computational Biology/methods ; }, abstract = {Bacteriophages, viruses infecting bacteria, are estimated to outnumber their cellular hosts by 10-fold, acting as key players in all microbial ecosystems. Under evolutionary pressure by their host, they evolve rapidly and encode a large diversity of protein sequences. Consequently, the majority of functions carried by phage proteins remain elusive. Current tools to comprehensively identify phage protein functions from their sequence either lack sensitivity (those relying on homology for instance) or specificity (assigning a single coarse grain function to a protein). Here, we introduce Empathi, a protein-embedding-based classifier that assigns functions in a hierarchical manner. New categories were specifically elaborated for phage protein functions and organized such that molecular-level functions are respected in each category, making them well suited for training machine learning classifiers based on protein embeddings. Empathi outperforms homology-based methods on a dataset of cultured phage genomes, tripling the number of annotated homologous groups. On the EnVhogDB database, the most recent and extensive database of metagenomically-sourced phage proteins, Empathi doubled the annotated fraction of protein families from 16% to 33%. Having a more global view of the repertoire of functions a phage possesses will assuredly help to understand them and their interactions with bacteria better.}, }
@article {pmid41086989, year = {2025}, author = {Zheng, L and Yao, L and Zhu, B and Chen, S and JinQian,  and Liu, S and JinZhao,  and Chen, Z and ShuaiXiang,  and Xie, Z and Zhu, J and Wang, S and KaiWu,  and Chen, J and Zhang, S and Lu, X}, title = {Cross-kingdom gut microbiota signatures and their associations with clinical phenotypes in adolescents with bipolar depression.}, journal = {Journal of affective disorders}, volume = {}, number = {}, pages = {120399}, doi = {10.1016/j.jad.2025.120399}, pmid = {41086989}, issn = {1573-2517}, abstract = {Emerging evidence highlights the pivotal role of the gut microbiota (GM) in mental health; however, investigations into its cross-kingdom composition in adolescent bipolar disorder remain critically limited. Most studies have focused solely on bacteria, overlooking the complex interactions involving archaea, viruses, and fungi. This study aimed to comprehensively characterize the taxonomic and functional alterations in the cross-kingdom gut microbiota of adolescents with bipolar depression and examine their associations with clinical parameters. We enrolled 60 adolescents aged 12-18 years, including 30 diagnosed with bipolar depression and 30 age- and sex-matched healthy controls. Fecal samples were collected alongside detailed clinical data, including psychiatric symptomatology, cognitive assessments, and dietary habits. Metagenomic sequencing was conducted to profile microbial taxa and functional gene pathways across domains. Statistical analyses assessed differences in alpha and beta diversity, differential abundance, and correlations with clinical phenotypes. Alpha diversity was significantly reduced in the viral and fungal domains among patients, while archaeal and bacterial diversity showed no significant differences. Beta diversity analysis did not reveal global community structural shifts across domains. Taxonomic profiling identified Methanohalobium evestigatum as significantly enriched in archaea, alongside increased abundance of several Firmicutes and Actinobacteria species in the bacterial domain. Viral analysis revealed elevated levels of Brussowvirus AlQ132, Orpheovirus IHUMI LCC2, Afonbuvirus coli, Carjivirus hominis, and Carjivirus communis in the patient group. LEfSe analysis uncovered 15 significantly altered metabolic pathways, including those involved in DNA repair, energy metabolism, and immune signaling. Notably, several taxa and pathways were significantly associated with clinical parameters such as symptom severity, cognitive flexibility, sleep quality, and dietary intake. Adolescents with bipolar depression exhibit distinct alterations in cross-kingdom gut microbiota composition and function, with specific microbial taxa and metabolic pathways correlating with key clinical phenotypes. These findings underscore the potential of gut microbiome signatures as biomarkers and therapeutic targets in early-onset mood disorders and highlight the importance of including archaea, fungi, and viruses in future microbiome-based mental health research.}, }
@article {pmid41086964, year = {2025}, author = {Zhang, X and Qaisar, M and Xu, F and Sun, J and Li, J and Cai, J}, title = {Bio-induced hydroxylated magnesium ammonium phosphate precipitation drives non-biological ammonium removal in sulfide-based denitrification.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {133492}, doi = {10.1016/j.biortech.2025.133492}, pmid = {41086964}, issn = {1873-2976}, abstract = {The sulfide-based autotrophic denitrification (SAD) process showed remarkable efficiency in nitrate (98.18 ± 2.13 %) and sulfide (97.4 ± 2.75 %) removal, while also resulting in unintentional ammonium elimination (18.92 ± 9.79 %) through a 138-day continuous-flow experiment. Batch tests demonstrated kinetic decoupling between ammonium removal and SAD activity, with ammonium elimination exhibiting a substantial dependence on pH (p < 0.01), indicating a chemically driven process. XRD and SEM-EDS analysis suggested biologically induced precipitation of magnesium ammonium phosphate-like compounds (Mg3(NH4)2H4(PO4)4·8H2O). Metagenomic analysis further confirmed the absence of biological ammonium conversion pathways, as dominant functional genes were linked to sulfur-oxidizing denitrification (napAB and nosZ), driven by genus Sulfurovum (42.89 % relative abundance). No genes (hdh and hzsA) associated with ammonium oxidation were detected which ruled out the biological nitrogen transformation. These findings definitively confirm that magnesium ammonium phosphate precipitation was the principal mechanism for ammonium removal in SAD systems, offering essential insights for enhancing energy-efficient nitrogen removal in wastewater treatment.}, }
@article {pmid41086845, year = {2025}, author = {White, AE and Koch, TJ and Jensen, TZT and Niemann, J and Pedersen, MW and Søtofte, MB and Binder, D and Lepère, C and Harb, C and Huber, R and Kramer, L and Mauvilly, M and Ebersbach, R and Wahl, J and Little, A and Wales, N and Regert, M and Schroeder, H}, title = {Ancient DNA and biomarkers from artefacts: insights into technology and cultural practices in Neolithic Europe.}, journal = {Proceedings. Biological sciences}, volume = {292}, number = {2057}, pages = {20250092}, doi = {10.1098/rspb.2025.0092}, pmid = {41086845}, issn = {1471-2954}, support = {//HORIZON EUROPE European Research Council/ ; //Carlsbergfondet/ ; //HORIZON EUROPE Marie Sklodowska-Curie Actions/ ; }, mesh = {*DNA, Ancient/analysis ; Archaeology ; Humans ; Europe ; History, Ancient ; Biomarkers/analysis ; Plant Bark/chemistry ; Animals ; }, abstract = {Birch bark tar was widely used throughout prehistoric Europe for hafting stone tools as well as various other purposes. While previous research has mainly focused on the identification and production of birch bark tar, its diverse uses remain to be fully explored. In this study, we combined ancient DNA with organic residue analysis to analyse 30 birch tar artefacts from nine Neolithic sites in and around the Alps. We identified birch tar as the main component, with some samples also containing conifer resin or tar, possibly added to modify its properties. Degradation markers indicate that tar used for ceramic repair was heated repeatedly, probably during cooking. Additionally, the presence of human and oral microbial DNA in some of the samples suggests the tar was chewed, in some cases by multiple individuals. The human DNA also enables us to determine the sex of those who chewed the tar, offering insights into gendered practices in the past, while plant and animal DNA shed light on past diets and the possible use of additives. This study underscores the value of integrating organic residue and ancient DNA analysis of archaeological artefacts to deepen our understanding of past cultural practices.}, }
@article {pmid41086610, year = {2025}, author = {Li, H and Gao, H and Chen, S and Li, X and Zhou, J}, title = {Intensive mariculture shifts microbial communities and life-history strategies in the semi-enclosed bay: Case study in Sansha Bay, China.}, journal = {Marine environmental research}, volume = {213}, number = {}, pages = {107607}, doi = {10.1016/j.marenvres.2025.107607}, pmid = {41086610}, issn = {1879-0291}, abstract = {Coastal bays often experience significant disturbances from various mariculture activities, frequently leading to severe eutrophication. Yet, the ecological consequences of nutrient inputs derived from mariculture on bay-associated microbial communities remain insufficiently understood. Sansha Bay, known as the world's largest cage mariculture site for Larimichthys crocea, represents a characteristic semi-enclosed bay commonly utilized for studying the environmental impacts of intensive mariculture. In this study, we compared the highly eutrophic Sansha Bay with the relatively undisturbed natural East China Sea to investigate how intensive mariculture influences the bay microbial biosphere, focusing on community composition, assembly mechanisms, functional profiles, and life-history strategies. Amplicon sequencing and metagenomic analyses showed that Sansha Bay had a greater proportion of fast-growing microorganisms, nitrogen and carbon cycling microbes, and antibiotic-resistant bacteria. Null model analysis indicated that while natural coastal microbial assemblages were predominantly shaped by stochastic processes, deterministic selection became increasingly prominent as mariculture activities intensified. Correspondingly, microbial life-history traits, including 16S rRNA gene copy number, codon usage bias, predicted maximum growth rates, genome size, guanine-cytosine content, transposase abundance, and niche breadth, were consistently elevated in the eutrophic bay. These results suggest that eutrophication associated with mariculture drives a shift in life-history strategies from oligotrophs (K-strategists) to copiotrophs (r-strategists). Collectively, this study yields novel mechanistic understanding of how intensive mariculture reshapes microbial community structures, laying the groundwork for forecasting changes in coastal ecosystems subjected to ongoing human disturbances.}, }
@article {pmid41086517, year = {2025}, author = {Obeten, AU and Avellán-Llaguno, RD and Huang, H and Yin, YH and Zhu, Y and Xu, XL and Chen, JY and Wang, Y and Ye, G and Pan, Z and Zhu, LT and Huang, Q}, title = {Decoding extracellular vesicles-mediated encapsulation of enveloped and nonenveloped gut viruses through phosphatidylserine affinity profiling.}, journal = {Virology}, volume = {613}, number = {}, pages = {110712}, doi = {10.1016/j.virol.2025.110712}, pmid = {41086517}, issn = {1096-0341}, abstract = {Viruses are generally classified as enveloped viruses (EnVs) or nonenveloped viruses (non-EnVs), based on the presence of a lipid membrane, with membrane-mediated transmission traditionally attributed to EnVs. However, the composition and characteristics of viral populations encapsulated within extracellular vesicles (EVs) which are phospholipid bilayer nanoparticles released by all living organisms remain poorly understood. Here, we applied a phosphatidylserine (PS)-affinity enrichment strategy to isolate EV-encapsulated viral populations from human stool-derived extracellular viral-like particles (VLPs). Quantitative particle analysis revealed that EnVs exhibited an 11-fold higher PS affinity compared to free non-EnVs (fold change 2.79 vs 0.25). Metagenomic analysis revealed significant enrichment of non-EnVs within PS-positive fractions, including DNA viruses Salasmaviridae (3.84 ± 6.44 %) and RNA bacteriophage Fiersviridae (44.99 ± 32.80 %). Predicted Host-virus correlation analysis highlighted strong correlations between viral families Autographiviridae, Microviridae and host family Enterobacteriaceae. Functional annotation further showed enrichment of structural and replication-related genes in the EV-associated virome. These findings provide evidence for EVs-mediated encapsulation of non-EnVs, challenging the traditional dichotomy of viral classification. This noteworthy observation positions EVs encapsulation as a critical determinant in viral life cycles and underscores the need to revisit current viral taxonomy systems.}, }
@article {pmid41086499, year = {2025}, author = {Li, Y and Zheng, X and He, H and Hu, R and Han, Z and Tao, J and Lin, T and Chen, W}, title = {Microalgal-bacterial granular sludge enhances oxytetracycline removal: Microbial responses, degradation pathways, and adaptive mechanisms.}, journal = {Journal of hazardous materials}, volume = {499}, number = {}, pages = {140103}, doi = {10.1016/j.jhazmat.2025.140103}, pmid = {41086499}, issn = {1873-3336}, abstract = {Oxytetracycline (OTC), an emerging "low-concentration, high-toxicity" contaminant, presents considerable hurdles to wastewater treatment processes. This study systematically evaluated for the first time the impacts of OTC on the operational performance, sludge characteristics, and microbial metabolic activity across three treatment systems: microalgal-bacterial granular sludge (MBGS), aerobic granular sludge (AGS), and activated sludge (AS). Results demonstrated that MBGS exhibited superior treatment efficiency, maintaining stable removal of 500 μg/L OTC at 88.06 ± 1.45 % (p < 0.05). MBGS adapted to OTC exposure by increasing ATP content and reducing lactate dehydrogenase release. Acclimated MBGS primarily removed OTC through biodegradation. Moreover, multiple OTC transformation products with reduced toxic potential were detected, signifying that MBGS systems achieve efficient microbial degradation. Metagenomic analyses revealed that Pseudomonadota in MBGS displayed high adaptability under OTC exposure. Additionally, OTC exposure upregulated carbohydrate and energy metabolism in MBGS, thereby enhancing overall microbial metabolic activity. Alphaproteobacteria contributed most significantly to key functional genes, underscoring their critical role in contaminant removal in the MBGS. Redundancy analysis highlights a robust association between Alphaproteobacteria and the abundance of antibiotic resistance genes. This study confirms the MBGS's resilience to OTC-contaminated wastewater, highlighting its potential for efficient antibiotic wastewater treatment.}, }
@article {pmid41086488, year = {2025}, author = {Chen, L and Lin, Y and Jia, X and Zheng, X and Zhuo, Y and Chen, Q and Fan, H and Fang, Y and Zhang, H and Lin, C}, title = {Dual-Path valorization of organic waste via black soldier fly: Synergistic enhancement of feed efficiency, crop quality, and climate mitigation in closed-loop aquaculture.}, journal = {Waste management (New York, N.Y.)}, volume = {209}, number = {}, pages = {115186}, doi = {10.1016/j.wasman.2025.115186}, pmid = {41086488}, issn = {1879-2456}, abstract = {The rapid expansion of aquaculture generates vast quantities of hyperhydrated organic waste (e.g., eel feces), posing a severe waste management challenge due to its recalcitrance and high disposal costs. This study presents a circular bio-strategy using black soldier fly (BSF, Hermetia illucens) larvae to synergistically convert aquaculture waste and agro-industrial residue (Flammulina velutipes substrate) within a closed-loop system. The process achieved 92.6 % waste utilization efficiency, yielding two valuable co-products: First, BSF larvae accumulated nutrient-rich biomass (17.9 % crude protein, 8.03 % lauric acid). As a 1.0 % supplement in broiler diets, it significantly enhanced feed efficiency by 2.6 % and increased 42-day body weight by 7.5 % (P < 0.01), demonstrating a viable fishmeal alternative. Second, BSF frass was composted into a superior organic fertilizer, which outperformed conventional composting by reducing NH3 emissions by 34 % (P < 0.001) and increasing total nitrogen retention by 15.3 %, attributed to pH modulation and chitin-NH4[+] complexation. The frass also enhanced phosphorus (7.05 %) and potassium (2.76 %) bioavailability. Metagenomics analysis revealed that frass inoculation enriched functional microbes (Azoarcus, LDA > 2.5; Roseisolibacter) driving synchronized nitrogen fixation and phosphate solubilization. Field application of the compost boosted tomato yields by 12.1 % (P < 0.05) and improved fruit quality (vitamin C + 18.6 %, soluble sugars + 20 %). This work establishes a scalable waste-to-resource paradigm that concurrently addresses waste management, livestock feed security, and sustainable crop intensification.}, }
@article {pmid41085836, year = {2025}, author = {Vidal-Silva, IM and Loza, A and Gutierrez-Rios, RM}, title = {Unlocking microbial potential: advances in omics and bioinformatics for aromatic hydrocarbon degradation.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {41}, number = {10}, pages = {384}, pmid = {41085836}, issn = {1573-0972}, support = {IN202524//PAPIIT-DGAPA/ ; 319234//Ciencia B&#xe1;sica y/o Ciencia de Frontera. Modalidad: Paradigmas y Controversias de la Ciencia 2022/ ; }, }
@article {pmid41085703, year = {2025}, author = {Sharma, N and Verma, A and Ambardar, S and Raj, S and Vakhlu, J}, title = {Comparative evaluation of MG-RAST, MEGAN6 and Kraken2 for whole metagenome analysis of saffron corms for bacterial community structure and function.}, journal = {Molecular genetics and genomics : MGG}, volume = {300}, number = {1}, pages = {97}, pmid = {41085703}, issn = {1617-4623}, support = {Rashtriya Uchchatar Shiksha Abhiyan//Rashtriya Uchchatar Shiksha Abhiyan/ ; JKST&amp;IC/J/14/2022/160//JKST&amp;IC-JKDST/ ; DST-INSPIRE/03/2022/004594//DST-INSPIRE/ ; BT/AIR01624/PACE-28/22//BIRAC-PACE/ ; }, mesh = {*Crocus/microbiology/genetics ; *Software ; *Metagenome/genetics ; *Metagenomics/methods ; *Bacteria/genetics/classification ; *Microbiota/genetics ; Algorithms ; }, abstract = {Taxonomic and functional analysis outcomes are greatly influenced by the algorithms and databases used by different software. The present study evaluated three widely used software; MG-RAST, MEGAN6 and Kraken2 for the analysis of the shotgun metagenomic data of saffron cormosphere. Kraken2 outperformed other two for taxonomy. It gave significantly higher alpha diversity values, indicating greater taxonomic diversity and evenness compared to MG-RAST and MEGAN6. The limitation of the Kraken2 is that it does not support functional analysis which both MG-RAST and MEGAN6 can do in addition to taxonomical analysis. Additionally, they can analyse sequence data generated by different sequencing methods such as Sanger, Illumina and PacBio. MG-RAST is comparatively easy to use and integrates large number of databases than MEGAN6, however data processing is relatively slow. Additionally, MEGAN6 has a feature of extraction of genes automatically, that allows user to study sub set of specific genes, though in MG-RAST, it can be done manually and the process is cumbersome. The difference in the outcome of these three software can be attributed to differences in the databases, algorithms, and parameters used by the three software. A combined approach using the results from more than one software can be considered to create a more comprehensive taxonomy and functional profile until a factotum software is developed.}, }
@article {pmid41085588, year = {2025}, author = {Purohit, HV and Chakraborty, J}, title = {Metagenomic approaches for studying ubiquitous yet diverse nucleoid associated proteins in microbial communities: challenges and advances.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {41}, number = {10}, pages = {383}, pmid = {41085588}, issn = {1573-0972}, }
@article {pmid41085530, year = {2025}, author = {Fan, M and Wang, Z and Yao, M and Li, X and van der Meer, W and Tao, Y and Rose, JB and Liu, G}, title = {Unveiling Chemical-Microbial Cascade Risk Factors from Plastic Pipe Leaching in Drinking Water.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c10244}, pmid = {41085530}, issn = {1520-5851}, abstract = {Plastic pipes are increasingly used in drinking water distribution systems, yet their impact on water quality remains insufficiently understood. Here, we systematically investigate the dual outcomes posed by plastic pipes─chemical leaching and cascaded microbial exposure risks─by integrating Fourier Transform Ion Cyclotron Resonance Mass Spectrometry and metagenomic analysis. Our results reveal that plastic pipes continuously release dissolved organic matter (DOM), including organic additives such as bisphenols (BPs) and organophosphate esters (OPEs), which profoundly reshape microbial communities. Under chlorinated conditions, leached DOM alters microbial diversity, promoting chlorine-resistant bacteria and opportunistic pathogens (OPs), while under nonchlorinated conditions, it accelerates microbial growth and enriches antibiotic resistance genes (ARGs), OPs, and virulence factors (VFs). Among plastic materials, polyethylene (PE) exhibited the highest chemical risk, releasing high concentrations of TCPP (700 ng/L) and BPF (200 ng/L) along with 207-227 unique DOM molecules. In contrast, polyvinyl chloride (PVC) supported the highest OP abundance, while polypropylene random copolymer (PPR) fostered the greatest OP diversity. These findings challenge conventional drinking water safety assessments that separate chemical contamination from microbial risk, underscoring the urgent need for an integrated risk assessment framework. Furthermore, they highlight the necessity of paying greater attention to the chemical and cascading microbial issues arising from the leaching of plastic pipes into drinking water, and of conducting a more comprehensive assessment of the associated potential health risks.}, }
@article {pmid41084448, year = {2025}, author = {Han, Z and Jin, LX and Wang, ZT and Yang, LQ and Li, L and Ruan, Y and Chen, QW and Yao, SH and Heng, XP}, title = {[Regulatory effects of Dangua Humai Oral Liquid on gut microbiota and mucosal barrier in mice with glucolipid metabolism disorder].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {50}, number = {15}, pages = {4315-4324}, doi = {10.19540/j.cnki.cjcmm.20250421.401}, pmid = {41084448}, issn = {1001-5302}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Intestinal Mucosa/drug effects/metabolism/microbiology ; Male ; *Drugs, Chinese Herbal/administration &amp; dosage ; Mice, Inbred C57BL ; Humans ; *Glycolipids/metabolism ; Lipid Metabolism/drug effects ; Administration, Oral ; Disease Models, Animal ; }, abstract = {The gut microbiota regulates intestinal nutrient absorption, participates in modulating host glucolipid metabolism, and contributes to ameliorating glucolipid metabolism disorder. Dysbiosis of the gut microbiota can compromise the integrity of the intestinal mucosal barrier, induce inflammatory responses, and exacerbate insulin resistance and abnormal lipid metabolism in the host. Dangua Humai Oral Liquid, a hospital-developed formulation for regulating glucolipid metabolism, has been granted a national invention patent and demonstrates significant clinical efficacy. This study aimed to investigate the effects of Dangua Humai Oral Liquid on gut microbiota and the intestinal mucosal barrier in a mouse model with glucolipid metabolism disorder. A glucolipid metabolism disorder model was established by feeding mice a high-glucose and high-fat diet. The mice were divided into a normal group, a model group, and a treatment group, with eight mice in each group. The treatment group received a daily gavage of Dangua Humai Oral Liquid(20 g·kg~(-1)), while the normal group and model group were given an equivalent volume of sterile water. After 15 weeks of intervention, glucolipid metabolism, intestinal mucosal barrier function, and inflammatory responses were evaluated. Metagenomics and untargeted metabolomics were employed to analyze changes in gut microbiota and associated metabolic pathways. Significant differences were observed between the indicators of the normal group and the model group. Compared with the model group, the treatment group exhibited marked improvements in glucolipid metabolism disorder, alleviated pathological damage in the liver and small intestine tissue, elevated expression of recombinant claudin 1(CLDN1), occluding(OCLN), and zonula occludens 1(ZO-1) in the small intestine tissue, and reduced serum levels of inflammatory factors lipopolysaccharides(LPS), lipopolysaccharide-binding protein(LBP), interleukin-6(IL-6), and tumor necrosis factor-α(TNF-α). At the phylum level, the relative abundance of Bacteroidota decreased, while that of Firmicutes increased. Lipid-related metabolic pathways were significantly altered. In conclusion, based on the successful establishment of the mouse model of glucolipid metabolism disorder, this study confirmed that Dangua Humai Oral Liquid effectively modulates gut microbiota and mucosal barrier function, reduces serum inflammatory factor levels, and regulates lipid-related metabolic pathways, thereby ameliorating glucolipid metabolism disorder.}, }
@article {pmid41083999, year = {2025}, author = {Holst, BS and Bonnevie, A and Spens, J and Lindahl, JF and Huupponen, A and Syrjä, P and Blomström, AL}, title = {Tick-borne encephalitis virus associated with foetal death in a bitch, a case report.}, journal = {Virology journal}, volume = {22}, number = {1}, pages = {326}, pmid = {41083999}, issn = {1743-422X}, mesh = {Animals ; Dogs ; Female ; Pregnancy ; *Dog Diseases/virology/pathology/diagnosis/transmission ; *Encephalitis Viruses, Tick-Borne/isolation &amp; purification/genetics ; *Infectious Disease Transmission, Vertical/veterinary ; *Fetal Death/etiology ; *Encephalitis, Tick-Borne/veterinary/virology/transmission/pathology/diagnosis ; *Pregnancy Complications, Infectious/veterinary/virology ; Placenta/virology/pathology ; }, abstract = {BACKGROUND: For the first time, a case of vertical transmission of TBEV in a dog associated with foetal death is described.<br><br>CASE PRESENTATION: A six-year-old beagle bitch experienced foetal death from day 49 in pregnancy. A caesarean section was performed on day 56, and one live and three dead pups in different stages of resorption were delivered. Black mucoid, non-smelling foetal membranes surrounded the dead foetuses. The live-born foetus died despite efforts to save it and was sent for autopsy together with the placenta. Autopsy demonstrated lung atelectasis and no malformations. A mild acute necrotizing placentitis was diagnosed on histopathology. Selective bacteriological cultures for Brucella canis from blood, vagina and the foetus were all negative, as was PCR for canine herpes virus (CHV). Viral metagenomics analysis identified the presence of tick-borne encephalitis virus (TBEV) in the placental tissue and in situ hybridization revealed TBEV in the trophoblasts. The bitch had antibodies to TBEV. One year later, the bitch had a normal pregnancy and whelping.<br><br>CONCLUSION: With the spread of both ticks and TBEV, infection with TBEV should be given further consideration as a potential differential diagnosis in cases of foetal death in dogs.}, }
@article {pmid41083440, year = {2025}, author = {Prasad, A and Pallujam, AD and Siddaganga, R and Suryanarayanan, A and Mazel, F and Brockmann, A and Yek, SH and Engel, P}, title = {Evolution of gut microbiota across honeybee species revealed by comparative metagenomics.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {9069}, pmid = {41083440}, issn = {2041-1723}, support = {225148//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 180575//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; }, mesh = {Animals ; Bees/microbiology ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation &amp; purification ; Symbiosis ; Phylogeny ; Metagenome/genetics ; *Evolution, Molecular ; Biological Evolution ; }, abstract = {Studying gut microbiota evolution across animals is crucial for understanding symbiotic interactions but is hampered by the lack of high-resolution genomic data. Honeybees, with their specialized gut microbiota and well-known ecology, offer an ideal system to study this evolution. Using shotgun metagenomics on 200 worker bees from five honeybee species, we recover thousands of metagenome-assembled genomes and identify several novel bacterial species. While microbial communities were mostly host-specific, we found both specialists and generalists, even among closely related bacterial species, with notable variation between honeybee hosts. Some bacterial generalists emerged host-specific only at the strain level, suggesting recent host switches. While we found some signal of co-diversification between hosts and symbionts, this was not more than expected by chance and was much less pronounced than what has been observed for gut bacteria of hominids and small mammals. Instead, symbiont gains, losses, and replacements emerged as important factors for honeybees. This highly dynamic evolution of the specialized honey bee gut microbiota has led to taxonomic and functional differences across hosts, such as the ability to degrade pollen-derived pectin. Our results provide new insights into the evolutionary processes that govern gut microbiota diversity across closely related hosts and uncover the functional potential of the previously underexplored gut microbiota of these important pollinators.}, }
@article {pmid41082849, year = {2025}, author = {Su, R and Zhu, L and He, X and Zhang, H and Huang, R and Zeng, J and Zhao, D}, title = {Denitrifying anaerobic methane oxidation reduces greenhouse gas emissions in floodplain sediments of the largest freshwater lake in China under flash drought.}, journal = {Journal of environmental management}, volume = {394}, number = {}, pages = {127532}, doi = {10.1016/j.jenvman.2025.127532}, pmid = {41082849}, issn = {1095-8630}, abstract = {Climate change-induced extreme heat, flooding and drought events influence the carbon and nitrogen cycling, including the denitrifying anaerobic methane oxidation (DAMO) process which couples the nitrogen removal and methane (CH4) mitigation. To assess the impacts of 2022 record-breaking flash drought (summer FD) on the DAMO process, we collected bulk soils and Carex cinerascens-associated soils in the littoral wetlands of Poyang Lake during summer FD and winter drought. The in situ CH4 fluxes and potential DAMO rates were determined using static-chamber technique and [13]C stable isotope method. The abundance, composition and metabolic pathways of DAMO archaeal and bacterial communities were investigated using quantitative PCR, high-throughput and metagenomic sequencing techniques. Higher DAMO rates (8.73 ± 3.79 and 16.03 ± 7.45 nmol [13]CO2 g[-1] d[-1] for nitrate-DAMO and nitrite-DAMO respectively) were observed during summer FD compared to winter drought, and nitrite-DAMO (52%∼74%) dominated the DAMO processes. DAMO bacterial pmoA genes (4.7 × 10[4]∼1.1 × 10[6] copies g[-1] dry soil) were more abundant than DAMO archaeal mcrA genes (1.4 × 10[3]∼1.3 × 10[4] copies g[-1] dry soil). Nitrate- and nitrite-DAMO rates were mainly driven by temperature, available nitrogen substrate and the abundance of DAMO archaea and bacteria, possibly contributing to CH4 consumption in the littoral wetlands of Poyang Lake. Several reconstructed metagenome-assembled genomes possessing genes involved in anaerobic methane oxidation and nitrate/nitrite reduction could potentially participate in cooperative DAMO process. This study elucidates the DAMO process and microbial mechanisms under flash droughts, providing a novel insight for the carbon-nitrogen coupling and mitigation of greenhouse gases in aquatic ecosystems.}, }
@article {pmid41082619, year = {2025}, author = {Huang, PH and Liao, YC and Chen, FJ and Wu, HC and Liu, PY}, title = {Metagenomic Sequencing of Blood Culture Broth for Diagnosing Fastidious Endocarditis.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {}, number = {}, pages = {}, doi = {10.1093/cid/ciaf554}, pmid = {41082619}, issn = {1537-6591}, }
@article {pmid41082531, year = {2025}, author = {Mwasi, L and Khamadi, S and Bulimo, W and Kinyua, J and Yalwala, S and Sang, LP and Robert, H and Kellar, GG and Eads, J and Eyase, F}, title = {Identification and genetic characterization of Jingmen tick virus from ticks sampled in select regions of Kenya; 2022-2024.}, journal = {PloS one}, volume = {20}, number = {10}, pages = {e0329878}, doi = {10.1371/journal.pone.0329878}, pmid = {41082531}, issn = {1932-6203}, mesh = {Animals ; Kenya/epidemiology ; Phylogeny ; *Ticks/virology ; *Flavivirus/genetics/isolation &amp; purification/classification ; Genome, Viral ; High-Throughput Nucleotide Sequencing ; Cattle ; }, abstract = {Jingmen tick virus (JMTV), an emerging segmented RNA virus classified as an ungrouped flavivirus, poses a growing public health concern globally. Known for its association with febrile illnesses and wide host range, JMTV has been detected in Rhipicephalus, Hyalomma, and Amblyomma ticks collected from cattle, goats, sheep, camels, and chickens in pastoral regions of Kenya, including Baringo, Mandera, Malindi, Lamu, Mombasa, Wajir, Isiolo, and West Pokot. Using viral metagenomics next-generation sequencing, this study analysed adult ticks (n = 1629, 72 pools). A total of 53% (38/72) pools were positive for at least one viral pathogen, with JMTV detected in 87% (33/38) of these pools across all study sites. Phylogenetic analyses revealed evidence of distinct Kenyan JMTV strains, with sequence segments from Malindi and Wajir clustering uniquely in their own clade; suggesting potential localised evolutionary pressures. Time calibrated phylogeny for the segment 1(RdRp) suggested varied ancestral origins and evolutionary relationships for the JMTV strains. MEME, BUSTED and FUBAR methods implemented in the Data-Monkey, unanimously identified codon 290 in segment 1 and 30 in segment 4 to be undergoing episodic positive selection. Recombination analysis performed using the RDP4 recombination detection tool indicated a recombination event in segment 2 of the Lamu JMTV strain that was confirmed by seven detection methods of the RDP4 tool and visualised in BootScan. These findings suggest that Kenyan JMTV strains are undergoing positive selection, potentially driven by unique ecological and host factors. Segmented genome evidence of recombination highlights the increasing virus's potential for antigenic diversity. Host diversity and virus phylogenetic patterns underscore the zoonotic potential and its capacity for regional spread, emphasizing the critical need for enhanced vector surveillance. Temporal and ecological drivers like seasonal tick activity and livestock movement warrant investigation to elucidate JMTV transmission dynamics. Prioritizing tick-borne virus surveillance in Kenya will strengthen public health strategies and mitigates emerging viral risks.}, }
@article {pmid41082485, year = {2025}, author = {Zhou, W and Zhang, D and Alhaskawi, A and Ezzi, SHA and Kota, VG and Abdulla, MHAH and Abdulla, AHAH and Abdalbary, SA and Lu, H and Liang, J}, title = {Rare Pathogen in Diabetic Foot Gangrene: A Case of Wohlfahrtiimonas chitiniclastica Infection.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {223}, pages = {}, doi = {10.3791/68877}, pmid = {41082485}, issn = {1940-087X}, mesh = {Humans ; Male ; Aged ; *Diabetic Foot/microbiology ; *Gangrene/microbiology ; *Gram-Negative Bacterial Infections/microbiology/diagnosis ; }, abstract = {Wohlfahrtiimonas chitiniclastica is a rare Gram-negative bacterium typically associated with wound infections, particularly in immunocompromised patients or individuals exposed to unsanitary conditions. Although clinical cases are infrequent, the infection can lead to severe complications such as bacteremia, septic shock, and even death if unrecognized or inadequately treated. We present the case of a 76-year-old diabetic male who developed chronic, non-healing foot ulcers complicated by gangrene and maggot infestation. Diagnostic challenges were addressed using metagenomic next-generation sequencing, which identified W. chitiniclastica alongside Proteus mirabilis and Corynebacterium striatum. Management included aggressive surgical debridement to remove necrotic tissue, local application of gentamicin-impregnated bone cement, systemic antibiotic therapy with ertapenem, and wound reconstruction using a dorsally based fascial flap. This combined approach resulted in significant clinical improvement, progressive wound healing, and marked reductions in infection markers. The case highlights the decisive role of advanced sequencing technologies in identifying rare pathogens within polymicrobial infections, where conventional methods such as MALDI-TOF mass spectrometry may fail. It also emphasizes the importance of integrating precision diagnostics with surgical intervention, targeted antimicrobial therapy, and rigorous postoperative care to achieve successful outcomes. By documenting this unusual presentation, we aim to expand clinical awareness of W. chitiniclastica infections and provide a practical framework for managing similarly complex diabetic foot infections.}, }
@article {pmid41082055, year = {2025}, author = {Aderolu, AZ and Salam, LB and Lawal, MO and Kabiawu-Mutiu, LF and Bassey, ME and Shobande, MA}, title = {Microbial ecology and functional landscape of black soldier fly larval bioconversion of orange waste: A metataxonomic perspective.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {41}, number = {10}, pages = {377}, pmid = {41082055}, issn = {1573-0972}, mesh = {Animals ; Larva/microbiology/metabolism ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Gastrointestinal Microbiome/genetics ; *Simuliidae/microbiology ; *Citrus sinensis/metabolism ; *Diptera/microbiology ; Nigeria ; Metagenome ; Metagenomics ; Phylogeny ; }, abstract = {The accumulation of citrus waste, particularly orange waste (OW), presents significant environmental and economic challenges in Nigeria and worldwide. This study presents the first high-resolution, species-level metataxonomic analysis of OW bioconversion mediated by black soldier fly larvae (BSFL) in a West African context, addressing a critical gap in region-specific microbial ecology. Using long-read PacBio 16S rRNA sequencing and PICRUSt2-based functional prediction, microbial communities were profiled across three ecologically distinct substrates: untreated OW, BSFL gut microbiota (OW-BSFL), and post-digestion frass (OWF). Results revealed a dramatic microbial shift driven by host filtering: the OW-BSFL metagenome was overwhelmingly dominated (> 96%) by Lysinibacillus and Cytobacillus, while OWF exhibited markedly higher diversity (263 species), including Mycolatisynbacter and Sphingobacterium. Functional analysis revealed a significant enrichment of genes associated with carbohydrate (e.g., COG2814, COG0726) and amino acid metabolism (e.g., COG1173, COG0444) in the BSFL gut, indicating an elevated enzymatic processing capacity during waste digestion. In contrast, OWF displayed unique enrichment in genes associated with residual carbohydrate turnover and environmental colonization. This microbial succession highlights the selective enrichment and functional specialization that occur across the substrate-gut-frass continuum. By elucidating keystone taxa and metabolic signatures, the study not only advances understanding of insect-microbiome symbiosis but also provides a microbial blueprint for optimizing waste-to-value strategies. The findings support the deployment of BSFL bioconversion as a scalable, sustainable solution for organic waste valorization and biofertilizer production in sub-Saharan Africa's circular bioeconomy.}, }
@article {pmid41081627, year = {2025}, author = {Yuan, Q and Yang, Y and Shen, Y and Sun, B and Chen, S and Zheng, C and Lou, Y and Zheng, M}, title = {Exploring the ocular microecology and its role in pterygium based on metagenomics.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0173025}, doi = {10.1128/spectrum.01730-25}, pmid = {41081627}, issn = {2165-0497}, abstract = {Pterygium is a chronic ocular surface condition marked by fibrovascular growth extending from the conjunctiva to the cornea. Emerging evidence suggests that microbial dysbiosis may play a role in its pathogenesis. To elucidate the microbial landscape associated with pterygium, we conducted metagenomic shotgun sequencing on conjunctival sac secretions from 24 patients with pterygium and 23 healthy controls, along with 19 pterygium tissue samples. We observed significantly higher microbial richness in the disease group, with distinct taxonomic profiles compared with healthy and tissue groups. Key species enriched in the disease group included Microbacterium proteolyticum and Bacillus cereus. Functional analyses revealed elevated bacterial motility, chemotaxis, and virulence genes, alongside a notable increase in antibiotic resistance genes such as tetB and AcrAB-TolC. In contrast, pterygium tissue samples showed limited microbial diversity and no detectable virulence or resistance genes. Importantly, the predominance of Vibrio phages in tissue samples, together with the frequent detection of their bacterial host Vibrio diabolicus, suggests a potential region-specific microbial risk factor, particularly relevant in coastal populations. These findings highlight distinct microbiome and functional profiles associated with pterygium, providing new insights into its pathogenesis and possible microbiome-based therapeutic targets.IMPORTANCEUnderstanding how microbial communities contribute to ocular diseases is crucial for advancing both diagnostics and therapy. This study provides the first integrated comparison of healthy ocular surfaces, diseased ocular surfaces, and pterygium tissues, revealing distinct microbial signatures and functional disruptions. The enrichment of specific bacterial taxa, virulence factors, and antibiotic resistance genes in diseased eyes underscores their potential role in shaping local immunity and driving disease progression. Meanwhile, the discovery of distinct viral elements in pterygium tissue expands current understanding of its microecological complexity. These findings lay a theoretical foundation for the development of microbiome-informed diagnostic tools and novel therapeutic interventions for pterygium.}, }
@article {pmid41081605, year = {2025}, author = {Lee, S and Kim, J and Mirdita, M and Gilchrist, CLM and Steinegger, M}, title = {Easy and interactive taxonomic profiling with Metabuli App.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btaf557}, pmid = {41081605}, issn = {1367-4811}, abstract = {SUMMARY: Accurate metagenomic taxonomic profiling is critical for understanding microbial communities. However, computational analysis often requires command-line proficiency and high-performance computing resources. To lower these barriers, we developed Metabuli App, an all-in-one desktop application that efficiently runs taxonomic profiling locally on a consumer-grade computer. It features user-friendly graphical interfaces for custom database curation, raw read quality control (QC), taxonomic profiling, and interactive result visualization.<br><br>GPLv3-licensed source code and prebuilt apps for Windows, macOS, and Linux are available at https://github.com/steineggerlab/Metabuli-App and are archived at https://doi.org/10.5281/zenodo.15876171. Analysis scripts are available at https://github.com/jaebeom-kim/metabuli-app-analysis. The Sankey-based taxonomy visualization component is available at https://github.com/steineggerlab/taxoview for easy integration into other web projects.}, }
@article {pmid41081506, year = {2025}, author = {Jiang, C and Wu, Y and Qiu, C and Zhu, S and Zhang, Y and Shui, W}, title = {Metagenomic insights into soil microbial diversity and antibiotic resistance genes in pristine karst tiankeng ecosystems.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0034825}, doi = {10.1128/msphere.00348-25}, pmid = {41081506}, issn = {2379-5042}, abstract = {Surveys of microorganisms and antibiotic resistance genes (ARGs) in edaphic systems have centered on those in human-impacted environments, with relatively little information from primitive environments. The karst tiankeng (also known as sinkholes) is the largest negative terrain on the earth's surface, and the trapped terrain keeps the interior relatively pristine. In this study, three of the most representative tiankeng types (severely, moderately, and non-degraded tiankengs) were selected, and microbial composition, function, and their association with ARGs were determined using metagenetic techniques. The dominant phyla in karst tiankengs were Proteobacteria, Actinobacteria, and Acidobacteria; the dominant archaea were Crenarchaeota; and the dominant fungi were Ascomycota. The non-degrade tiankeng maintains a complex and stable microbial network. The major functional profiles of the microorganisms are involved in amino acid metabolism and carbohydrate metabolism. A total of 145 ARGs were annotated, and the dominant ARGs in karst tiankeng were CeoB, AcrB, and MexF. Paraburkholderia, Rhodococcus, Bradyrhizobium, and Agromyces were the main hosts of ARGs in karst tiankengs. Compared with ARGs, microorganisms were more influenced by soil factors. These results provide a novel insight into microbes and ARGs in unexplored karst tiankeng ecosystems.IMPORTANCECurrently, knowledge regarding the origin of antibiotic resistance genes (ARGs) in pristine soil environments remains limited, with some potentially linked to ancestral genetic diversity. In this study, metagenomics was employed to investigate the distribution of ARGs across nine relatively pristine karst tiankengs. We identified the predominant microbial communities and prevalent types of ARGs within these tiankengs. Soil factors primarily influenced the microbial community structure but had little effect on ARGs. This study offers insights for in-depth research on the microbial composition and risk assessment of antibiotic resistance genes within pristine karst tiankeng ecosystems.}, }
@article {pmid41081392, year = {2025}, author = {Rasmussen, AN and Langenfeld, K and Tolar, BB and Perzan, Z and Maher, K and Cardarelli, EL and Bargar, JR and Boye, K and Francis, CA}, title = {Floodplain nitrifiers harbor the genetic potential for utilizing a wide range of organic nitrogen compounds.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0082925}, doi = {10.1128/msystems.00829-25}, pmid = {41081392}, issn = {2379-5077}, abstract = {UNLABELLED: Organic compounds such as urea and cyanate can serve as nitrogen (N) sources for nitrifying microorganisms, including ammonia-oxidizing archaea (AOA) and bacteria (AOB), complete ammonia-oxidizing (comammox) bacteria, and nitrite-oxidizing bacteria (NOB). Here we investigated metagenome-assembled genomes (MAGs) for all four nitrifier guilds generated from hydrologically variable floodplain sediments of the Wind River Basin (WRB; Riverton, WY, USA) for their genetic potential to utilize organic N compounds. A vast majority of WRB nitrifier MAGs harbored urease (ure) and at least one urea transporter (utp, urt, dur3). AOA were the most abundant and phylogenetically diverse nitrifiers in WRB floodplain sediments. Several AOA MAGs encoded cyanase (cynS), nitrilase (nit1), omega-amidase (nit2), nitrile hydratase (nthA), and genes related to purine degradation, including biuret hydrolase (biuH), oxamic transcarbamylase (allFGH), and catabolic carbamate kinase (allK). AOA often encoded an uncharacterized amidohydrolase collocated with biuH, rather than allophanate hydrolase (atzF). A small number of AOA encoded atzF, functioning in an unknown pathway. AOB and comammox were of relatively low abundance and taxonomic diversity and were present only at certain depths in WRB; however, they encoded triuret/biuret degradation genes (trtA, biuH, and atzH), and in comammox, these genes were also collocated with allFGHK. The genetic potential of ammonia oxidizers in the WRB floodplain suggests that organic N may support nitrification in this system. The proposed pathways for utilizing purine degradation products other than urea potentially expand the known metabolic capabilities of AOA, AOB, and comammox bacteria and reveal the possibility for cryptic N cycling between microbial community members.<br><br>IMPORTANCE: Floodplains are critical ecosystems where terrestrial and riverine systems meet. Floodplain sediments experience many, sometimes dramatic, changes in moisture and oxygen concentrations because of changes in water table height, flooding, and drought, leading to active microbial cycling of contaminants and nutrients. Nitrogen is one such nutrient that is not only essential for the building blocks of life but can also be used as an energy source by some microorganisms. Microorganisms that oxidize ammonia and nitrite are a crucial part of the nitrogen cycle and can lead to eventual nitrogen loss from a system. Investigating the genes present in microorganisms responsible for nitrification in a dynamic floodplain suggests that organic nitrogen-from decaying plants or potentially other sources, such as fertilizers, grazing livestock feces, or contaminants (e.g., pesticides, pharmaceuticals)-is an important nitrogen source to these microorganisms. This study identifies genes not previously described in nitrifying microorganisms, expanding their potential metabolic substrates.}, }
@article {pmid41080808, year = {2025}, author = {Zhang, Z and Huang, W}, title = {Exoskeleton Robot Gait Training and Its Impact on the Gut Microbiota-Brain Axis in Incomplete Spinal Cord Injury Patients: A Narrative Review of Rehabilitation Mechanisms.}, journal = {Journal of multidisciplinary healthcare}, volume = {18}, number = {}, pages = {6411-6430}, pmid = {41080808}, issn = {1178-2390}, abstract = {Exoskeleton robot-assisted gait training represents a significant advancement in neurorehabilitation for patients with incomplete spinal cord injury (iSCI). While its efficacy in improving motor function is increasingly documented, emerging evidence suggests these interventions may exert therapeutic effects through previously unrecognized physiological pathways involving the gut microbiota-brain axis. This review synthesizes current evidence regarding the bidirectional relationship between exoskeleton-based locomotor training and alterations in gut microbiome composition and function in the context of iSCI. Following spinal cord injury, significant dysbiosis occurs, characterized by reduced microbial diversity and altered taxonomic representation, which correlates with neuroinflammation, autonomic dysfunction, and impaired recovery. Exoskeleton-mediated gait rehabilitation appears to partially restore microbial homeostasis through multiple mechanisms, including autonomic nervous system regulation, altered intestinal transit time, modified intestinal barrier integrity, and immunomodulation. These microbiome modifications potentially facilitate neuroplasticity and functional recovery through microbiota-derived metabolites that traverse the blood-brain barrier or communicate via vagal afferents. The integration of metagenomic analysis with functional neuroimaging and detailed autonomic assessment in prospective studies represents a critical research direction. This emerging perspective extends beyond biomechanical rehabilitation, suggesting a comprehensive neurobiological effect that includes modulation of the microbiota-gut-brain axis, with significant implications for optimizing therapeutic strategies for individuals with incomplete spinal cord injury.}, }
@article {pmid41080802, year = {2025}, author = {Zhang, H and Zhang, H and Du, H and Zhang, Y and Zhang, M and Yu, X and Xu, Y}, title = {Metagenomic insights into viral dynamics and funcation in Baijiu.}, journal = {Current research in food science}, volume = {11}, number = {}, pages = {101189}, pmid = {41080802}, issn = {2665-9271}, abstract = {Baijiu fermentation represents a sophisticated microbial-driven biochemical process mediated by complex microbial consortium. Despite extensive characterization of bacterial and fungal roles in fermentation systems, the virus remains a critical knowledge gap. In this study,we employed metagenomics to profile the dynamics of viral community in fermented grains across five stages (day 0, 5, 10, 20 and 30) of a Baijiu fermentation. The metagenomics revealed 101 viral families, dominated by Metaviridae, Parvoviridae, Aliceevansviridae, Herelleviridae, Geminiviridae, Iridoviridae, and Genomoviridae, and lactic acid bacteria was identified as primary phage hosts. The results revealed that ssRNA viruses and ssDNA viruses were more abundant during 0-5 days, dsDNA viruses became dominant during 10-30 days. Multivariate analysis indicated that the viral community dynamics during the fermentation were primarily governed by microbes in succession, environmental factors (temperature,pH, moisture and glucose) and metabolites (lactic acid, acetate and ethanol) in the biosystem. Notably, predicting phages exhibited strong positive correlations with their respective hosts (P < 0.01, r > 0.6). We have identified viral auxiliary metabolic genes (AMGs) related to amino acid metabolism and vitamin biosynthesis. At 30 days of fermentation, the number and abundance of AMGs significantly increased. Our findings provide novel insights into the viral ecology in complex Baijiu fermentation ecosystem, shedding light on the intricate interactions within fermentation microbial communities.}, }
@article {pmid41080577, year = {2025}, author = {Wang, Z and Yu, J and Liu, Y and Gong, J and Hu, Z and Liu, Z}, title = {Role of the microbiota-gut-lung axis in the pathogenesis of pulmonary disease in children and novel therapeutic strategies.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1636876}, pmid = {41080577}, issn = {1664-3224}, mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; Child ; *Lung/immunology/microbiology/metabolism ; *Lung Diseases/therapy/microbiology/immunology/etiology/metabolism ; Dysbiosis ; Animals ; Fatty Acids, Volatile/metabolism ; }, abstract = {Emerging evidence highlights the microbiota-gut-lung axis (MGLA) as a pivotal regulator of pediatric respiratory health, yet mechanistic insights are lacking and therapeutic applications remain unclear. This review synthesizes cutting-edge findings to delineate how gut microbiota-derived metabolites, particularly short-chain fatty acids (SCFAs), orchestrate pulmonary immunity and disease pathogenesis in children. Leveraging multi-omics integration (metagenomics, metabolomics, transcriptomics), emerging studies have uncovered novel microbe-host interactions driving immune dysregulation in asthma, pneumonia, and cystic fibrosis. A comprehensive map of gut-lung crosstalk has been established across these conditions. Current studies suggest that early-life gut dysbiosis, shaped by delivery mode, antibiotics, and diet, disrupts SCFA-mediated immune homeostasis, amplifying T-helper 2 cell inflammation and impairing alveolar macrophage function. Crucially, we identified disease-specific microbial signatures (e.g., depletion of Lachnospira and Faecalibacterium in asthma) and demonstrated that fecal microbiota transplantation and probiotic interventions restore microbial balance, attenuating airway inflammation in preclinical models. This work pioneers the translation of MGLA insights into precision medicine strategies, highlighting dietary modulation and microbial therapeutics as viable alternatives to conventional treatments. By bridging microbial ecology and immune dynamics, our findings provide actionable biomarkers for early diagnosis and personalized interventions, addressing critical gaps in pediatric respiratory disease management. The integration of multi-omics frameworks not only advances mechanistic understanding but also positions the MGLA as a transformative target in reducing global childhood morbidity. Future research must prioritize longitudinal studies and clinical trials to validate these innovations, ultimately redefining therapeutic paradigms for GLA-driven pathologies.}, }
@article {pmid41080528, year = {2025}, author = {Wu, XT and Qiu, M and He, YQ and Wu, K and Zhao, JY and Wang, J and Ren, HY and Su, JY and Bao, P}, title = {Disproportionation of elemental sulfur by Exiguobacterium from marine sediment.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf168}, pmid = {41080528}, issn = {2730-6151}, abstract = {Elemental sulfur disproportionation is an ancient microbial metabolic process, and the phylogenetic distribution of elemental sulfur disproportionators may be broader than previously thought. We enriched a bacterial community capable of this process, with Exiguobacterium making up 99.45% of the total population. The results indicate that Exiguobacterium facilitates the formation of thiosulfate and sulfide through elemental sulfur disproportionation. This study represents the first report documenting elemental sulfur disproportionation by Bacilli. Metagenomic analysis shows that rhodanese-like sulfur transferase genes are significantly more abundant in the experimental group than in the control group, suggesting that they are implicated in elemental sulfur disproportionation in Exiguobacterium. These findings support the idea that Bacilli and/or Firmicutes are the oldest extant bacterial phyla. Our research fills a critical gap in understanding sulfur biogeochemical cycles. Given the widespread occurrence of Exiguobacterium across various environments, direct microbial transformations between elemental sulfur and thiosulfate are likely prevalent throughout ecological systems.}, }
@article {pmid41080188, year = {2025}, author = {Geniselli da Silva, V and Smith, NW and Mullaney, JA and Roy, NC and Wall, C and McNabb, WC}, title = {Mathematical models of the colonic microbiota: an evaluation of accuracy using in vitro fecal fermentation data.}, journal = {Frontiers in nutrition}, volume = {12}, number = {}, pages = {1623418}, pmid = {41080188}, issn = {2296-861X}, abstract = {Traditional approaches for studying diet-colonic microbiota interactions are time-consuming, resource-intensive, and often hindered by technical and ethical concerns. Metagenome-scale community metabolic models show promise as complementary tools to overcome these limitations. However, their experimental validation is challenging, and their accuracy in predicting colonic microbial function under realistic dietary conditions remains unclear. This study assessed the accuracy of the Microbial Community model (MICOM) in predicting major short-chain fatty acid (SCFA) production by the colonic microbiota of weaning infants, using fecal samples as a proxy. Model predictions were compared with experimental SCFA production using in vitro fecal fermentation data at the genus level. The model exhibited overall poor accuracy, with only a weak, significant correlation between measured and predicted acetate production (r = 0.17, p = 0.03). However, agreement between predicted and measured SCFA production improved for samples primarily composed of plant-based foods: acetate exhibited a moderate positive correlation (r = 0.31, p = 0.005), and butyrate a trend toward a weak positive correlation (r = 0.21, p = 0.06). These findings suggest that the model is better suited for predicting the influence of complex carbohydrates on the colonic microbiota than for other dietary compounds. Our study demonstrates that, given current limitations, modeling approaches for diet-colonic microbiota interactions should complement rather than replace traditional experimental methods. Further refinement of computational models for microbial communities is essential to advance research on dietary compound-colonic microbiota interactions in weaning infants.}, }
@article {pmid41080146, year = {2025}, author = {He, X and Yang, F and Qu, G and Zhang, H and Yi, M and Wang, X and Sun, S}, title = {Integrated microbial and proteomic analysis elucidates quality degradation mechanisms of fresh milk through the industrial processing stage.}, journal = {Food chemistry: X}, volume = {31}, number = {}, pages = {103062}, pmid = {41080146}, issn = {2590-1575}, abstract = {Fresh milk quality deterioration during processing is a major dairy challenge, with microbial-driven protein degradation mechanisms unclear. This study pioneers an integrated microbiome-proteome approach to systematically elucidate the dynamic interplay between microbial succession and protein quality changes during industrial processing. Microbial community analysis revealed oscillatory richness, with 2.3-fold and 1.8-fold increases during pre-treatment (PL) and refrigerated transport (RC), respectively. Pseudomonas (12.4 % → 31.7 %) and Acinetobacter (8.1 % → 19.3 %) dominated key phases, with proteomics showing significant nutrient loss (IgM: -69.8 %; IgG: -54.15 %). Integrating microbial metagenomics with proteolytic pathway analysis identified proteases from Pseudomonas and Acinetobacter as key drivers of protein degradation (68 % activity). Pasteurization cut microbial load by 82 % but paradoxically intensified nutrient loss via protein denaturation. Crucially, our data establish a time-dependent degradation model, revealing that combined microbial enzymatic action and thermal effects account for 76 % of total protein hydrolysis, providing a theoretical framework for developing targeted intervention strategies in dairy processing optimization.}, }
@article {pmid41079703, year = {2025}, author = {Akinnola, OO and Samuel, AE and Omonhinmin, CA}, title = {Dataset on characterisation of microbiome of prostate tissue and expressed prostatic secretions.}, journal = {Data in brief}, volume = {63}, number = {}, pages = {112098}, pmid = {41079703}, issn = {2352-3409}, abstract = {Prostate cancer (PCa) is the second most prevalent cancer in men, particularly affecting those of Black African descent. Nigeria currently has the fourth highest risk for PCa mortality in the world. The microbiome of the prostate has emerged as a critical factor in understanding the aetiology and progression of prostate diseases, such as prostate cancer (PCa), benign prostatic hyperplasia (BPH) , benign stromal hyperplasia (BSH) and prostatitis (PRO). This study to comparatively characterise the microbiome present in prostate tissue and expressed prostatic secretion (EPS) from 30 study subjects diagnosed with PCa, BPH, BSH and PRO and sampled from the urology clinic of Lagos State University Teaching Hospital Ikeja. Bacterial species community composition and diversity were analysed based on 16S rRNA metagenome nucleotide data to ensure the accuracy, reproducibility, and broader applicability of microbiological and genomic research. Data information allows for precise identification of organisms at the species or strain level, essential for verifying experimental results and comparisons of the isolated organism's genome with related strains, providing insights into genetic diversity, virulence factors, and metabolic pathways of the sample population microbiome.}, }
@article {pmid41079637, year = {2025}, author = {Tóth, AG and Nagy, S&#xc1; and Lakatos, I and Solymosi, N and Stágel, A and Paholcsek, M and Posta, K and Gömbös, P and Ferenczi, S and Szőke, Z}, title = {Impact of mycotoxins and glyphosate residue on the gut microbiome and resistome of European fallow deer.}, journal = {iScience}, volume = {28}, number = {10}, pages = {113539}, pmid = {41079637}, issn = {2589-0042}, abstract = {Some mycotoxins and herbicide residues pose threats to animal health. These toxins might affect the gut microbiome of fallow deer. The analyzation of the intestinal content samples of this valuable game species exposed to varying levels of zearalenone (ZEA) and other toxic compounds such as aflatoxin B1, deoxynivalenol, fumonisin B1, and glyphosate residues was performed. Metagenomic analysis revealed significant alterations in the bacterial community composition. Higher ZEA levels were associated with decreased alpha diversity, whereas higher aflatoxin levels had the opposite effect. Changes in the abundance of antibiotic resistance genes (ARGs) were also observed, suggesting a potential link between mycotoxin exposure and antimicrobial resistance. Furthermore, five complete bacterial genomes were assembled from the metagenomic data. These findings highlight the complex interplay between environmental toxins, gut microbiota, and animal health. Understanding these interactions is crucial for developing strategies to mitigate the negative effects of toxin exposure on wildlife populations.}, }
@article {pmid41079385, year = {2025}, author = {van Ede, JM and van der Steen, S and van der Kraan, GM and van Loosdrecht, MCM and Pabst, M}, title = {Discovery of microbial glycoside hydrolases via enrichment and metaproteomics.}, journal = {RSC chemical biology}, volume = {}, number = {}, pages = {}, pmid = {41079385}, issn = {2633-0679}, abstract = {The immense microbial diversity on Earth represents a vast genomic resource, yet discovering novel enzymes from complex environments remains challenging. Here, we combine a microbial enrichment with metagenomics and metaproteomics to facilitate the identification of microbial glycoside hydrolases that operate under defined conditions. We enriched microbial communities on the carbohydrate polymer pullulan at elevated temperatures under acidic conditions. Pullulan is a natural polysaccharide composed of maltotriose units linked by α-1,6-glycosidic bonds. Pullulan, along with its hydrolyzing enzymes, has broad applications across various industries. The enrichment inocula were sampled from thermophilic compost and from soil from the bank of a pond. In both cases, Alicyclobacillus was identified as the dominant microorganism. Metaproteomic analysis of the enriched biomass and secretome enabled the identification of several pullulan-degrading enzyme candidates from this organism. These enzymes were absent in the metagenomic analysis of the initial inoculum, which is highly complex with a wide diversity of species. This underscores the effectiveness of combining microbial enrichment with multi-omics for uncovering novel enzymes and sequence variants that operate under defined conditions from complex microbial environments.}, }
@article {pmid41078880, year = {2025}, author = {Goudarzi, R and Jahanshahi, DA and Kavousi, A and Ariaeenejad, S}, title = {Discovery and engineering of bifunctional enzymes for lignocellulose degradation: Metagenomic and computational approaches.}, journal = {Biotechnology reports (Amsterdam, Netherlands)}, volume = {48}, number = {}, pages = {e00926}, pmid = {41078880}, issn = {2215-017X}, abstract = {Efficient degradation of lignocellulosic biomass is vital for converting plant-based waste into renewable fuels and chemicals. Owing to its complex composition of cellulose, hemicellulose, and lignin, its enzymatic breakdown often requires multiple enzymes to act synergistically. Bifunctional enzymes that combine two catalytic activities in a single protein offer a promising solution. This review highlights recent advances in the identification and engineering of bifunctional enzymes for lignocellulose degradation, particularly through metagenomics, protein fusion and computational design. Functional pairings, such as cellulase/xylanase, were examined with a focus on their synergistic effects, substrate specificity, and stability. Promiscuous and naturally evolved bifunctional enzymes from extreme or uncultured environments are also discussed. Advances in silico modeling and directed evolution have enhanced enzyme properties such as thermostability and substrate range. The review concludes with an outlook on the challenges and opportunities of implementing bifunctional enzymes to improve the economic and technical viability of biomass conversion.}, }
@article {pmid41078518, year = {2025}, author = {Liu, J and Wang, L and Su, L and Chen, J and Su, R}, title = {Exploring the gut microbiota-Parkinson's disease link: preliminary insights from metagenomics and Mendelian randomization.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1654418}, pmid = {41078518}, issn = {1664-302X}, abstract = {INTRODUCTION: The relationship between the gut microbiome and Parkinson's disease (PD) has recently attracted significant attention, with most studies focused on analyzing microbial composition. However, our understanding of the potential causal relationship between the gut microbiota and PD remains limited.<br><br>METHODS: We extracted microbiome data from the metagenome for broad taxonomic coverage and accurate functional analysis. Subsequently, Mendelian randomization was employed to elucidate the causal relationship between the gut microbiome and PD.<br><br>RESULTS: The gut microbiota in PD patients was found to be systemically imbalanced, characterized by an abnormal enrichment of potential pathogenic bacteria, a significant reduction in key beneficial bacteria, and a reorganization of intestinal metabolic functions. This state of imbalance involves significant abnormalities in multiple metabolic and regulatory pathways, including the glucose metabolism, oxidative stress response, protein homeostasis regulation, and immune signaling pathways. These findings suggest that dysbiosis may influence host neural function through multilevel metabolic interventions. Additionally, specific microbial communities are clearly associated with disease risk, with some bacterial populations promoting disease onset and others demonstrating a potentially protective effect. Although metagenomic findings require validation in larger cohorts, the results of this study indicate that changes in gut microbiota composition and function are closely related to PD onset and progression.<br><br>CONCLUSION: This study revealed that certain microorganisms traditionally considered beneficial may contribute to PD risk. This finding challenges previous assumptions and highlights the complexity of host-microbiome interactions. The identification of altered metabolic and immune pathways, particularly those involving bacteria that produce short-chain fatty acids, underscores the critical role of the gut microbiota in PD pathophysiology. However, the relatively small sample size of the current metagenomic analysis limits the generalizability of these findings. Larger, more diverse cohorts are needed to validate these results. Despite this limitation, the study provides important insights into microbiome-targeted therapeutic strategies, emphasizing the need to reconsider the roles of both beneficial and harmful microorganisms in PD.}, }
@article {pmid41078512, year = {2025}, author = {Li, Y and You, J and Liao, Y and Wang, D and Wang, H and Su, Y}, title = {Daily fluctuation of genus Prevotella in porcine colon under ad libitum feeding and its association with nutrient substrates.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1688301}, pmid = {41078512}, issn = {1664-302X}, abstract = {The circadian rhythms of the gut microbiota are biologically significant for the host. However, the association between fluctuations in the relative abundance of the microbiota and nutrient substrates in the gut remains incompletely understood. Using swine as a model, this study employed continuous sampling at 9 time points over 24 h via a colonic T-shaped fistula. It investigated the temporal dynamics of nutrient substrates and Prevotella abundance in the colon of pigs over a 24-h period and further explored dynamic interactions among KEGG level-3 pathways, genes, and Prevotella using metagenomic approaches. Results revealed a significant 24-h periodicity in Prevotella abundance, peaking at T06-T09 and declining to minimal levels at T18-T21, with the nadir at T18. Dynamic correlation network analysis uncovered significant temporal associations between Prevotella rhythms and nutrient substrates: negative correlations with true protein (TP) and ammonia nitrogen (NH3-N), in contrast to positive correlations with starch and cellulose, exhibiting time lags ranging from -2 to 4 h. Prevotella copri exhibited high relative abundance and pronounced daily fluctuations, while Prevotella sp. MGM2 showed relatively high abundance but lacked daily fluctuations. Furthermore, differences existed in the dynamic correlations of genes and KEGG level-3 metabolic pathways of these two Prevotella species with nutrient substrates. The results revealed that the two Prevotella species in the colon exhibited different response strategies to nutrient substrates: Prevotella copri likely adopted a "rhythmic substrate-responsive strategy," while Prevotella sp. MGM2 followed a "sustained response strategy," which may explain their distinct daily fluctuations.}, }
@article {pmid41078511, year = {2025}, author = {Ren, G and Shi, W and Li, W and Wang, J and Wang, C and Zhao, G}, title = {Pyrolysis temperature shapes biochar-mediated soil microbial communities and carbon-nitrogen metabolism.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1657149}, pmid = {41078511}, issn = {1664-302X}, abstract = {INTRODUCTION: Biochar derived from agricultural residues has potential to improve soil quality and regulate microbial communities, but its effect depends strongly on pyrolysis temperature.<br><br>METHODS: In this study, biochar prepared from Flammulina velutipes residue at 200&#x202f;&#xb0;C, 300&#x202f;&#xb0;C, and 400&#x202f;&#xb0;C was applied to cucumber seedling cultivation to evaluate its influence on soil physicochemical properties, microbial community structure, and functional metabolism.<br><br>RESULTS: Results showed that soil pH increased significantly with biochar addition, from 5.00 in the control to 6.17 at 400&#x202f;&#xb0;C, while soil organic matter reached the highest level in the 400&#x202f;&#xb0;C treatment (90.03 g&#xb7;kg[-1]). Available phosphorus and potassium were also enhanced, with maximum values of 731.81 mg&#xb7;kg[-1] and 481.68 mg&#xb7;kg[-1], respectively. Seedling growth responded differently to pyrolysis temperatures: the 300&#x202f;&#xb0;C biochar treatment increased above-ground biomass to 0.18 g and total biomass to 0.214 g per plant, significantly higher than the control (0.124 g). Metagenomic sequencing revealed shifts in dominant microbial phyla, with Acidobacteriota enriched at higher temperatures, and alpha diversity indices (Chao1, ACE, Sobs) increased under 400&#x202f;&#xb0;C biochar. Functional analysis indicated that carbon metabolic genes (e.g., acetyl-CoA synthesis, TCA cycle) were optimized at moderate to high temperatures, whereas nitrogen metabolism showed divergent responses, with nitrate reduction favored at 300&#x202f;&#xb0;C and nitrite reduction at 400&#x202f;&#xb0;C. Regression analysis demonstrated a positive correlation between microbial diversity and carbon metabolism genes (R [2]&#x202f;=&#x202f;0.75), but a negative correlation with nitrogen metabolism genes (R [2]&#x202f;=&#x202f;0.56). Redundancy analysis further identified ammonium nitrogen, acid phosphatase, and catalase as key drivers of microbial community and functional gene structure.<br><br>DISCUSSION: Overall, these findings highlight that biochar from mushroom residue, particularly produced at 300-400&#x202f;&#xb0;C, improves soil fertility, regulates microbial community composition, and modulates carbon and nitrogen metabolic processes, thereby enhancing cucumber seedling growth.}, }
@article {pmid41078118, year = {2025}, author = {Wang, Y and Yang, J and Hou, H and Song, L and Cheng, X and Liu, YX}, title = {Advancing Plant Microbiome Research Through Host DNA Depletion Techniques.}, journal = {Plant biotechnology journal}, volume = {}, number = {}, pages = {}, doi = {10.1111/pbi.70379}, pmid = {41078118}, issn = {1467-7652}, support = {32470055//National Natural Science Foundation of China/ ; U23A20148//National Natural Science Foundation of China/ ; CAAS-BRC-CB-2025-01//Basic Research Center for Crop Biosafety Sciences/ ; CAAS-ZDRW202308//Agricultural Science and Technology Innovation Program/ ; }, abstract = {Plants provide ecological habitats for diverse microorganisms, making accurate metagenomic sequencing essential for understanding the complex interactions that support plant growth, development and disease resistance. However, host DNA contamination poses a major challenge in plant microbiome studies, obscuring microbial genetic signatures and complicating the accurate analysis of microbial genomes. This review provides a comprehensive overview of current host DNA depletion strategies, including physical separation (e.g., filtration, gradient centrifugation), selective lysis and enzymatic treatments targeting plant cell walls. Advanced techniques such as targeted sequence capture with magnetic beads, methylation-based enrichment and nanopore selective sequencing offer additional options for host DNA removal. Despite these advances, current methods still face challenges in efficiency, specificity and applicability, emphasising the need for tailored strategies and the exploration of novel approaches for microbial enrichment. Innovations like CRISPR-Cas9 and chromatin immunoprecipitation-based host DNA depletion methods are proposed to provide novel directions for addressing current limitations. The development and refinement of host depletion techniques tailored to plant systems are crucial for enabling high-resolution, cost-effective metagenomic studies. These efforts promise to deepen our understanding of microbial diversity and functionality, ultimately accelerating microbiome-based innovations in crop improvement, sustainable agriculture and ecosystem resilience.}, }
@article {pmid41078079, year = {2025}, author = {Shibata, R and Li, Y and Yaskolka Meir, A and Cregeen, SJ and Ross, MC and Espinola, JA and Sullivan, AF and Liang, L and Hasegawa, K and Camargo, CA and Zhu, Z}, title = {Nasopharyngeal Microbiome-Epigenome-Wide Association Analysis in Infants With Severe Bronchiolitis.}, journal = {Allergy}, volume = {}, number = {}, pages = {}, doi = {10.1111/all.70102}, pmid = {41078079}, issn = {1398-9995}, support = {/NH/NIH HHS/United States ; //Environmental influences on Child Health Outcomes (ECHO) Program Opportunities and Innovation Fund (OIF)/ ; //Massachusetts General Hospital/ ; //the Harvard University William F. Milton Fund/ ; //American Lung Association Innovation Award/ ; }, abstract = {BACKGROUND: Bronchiolitis exposes infants to both acute burdens (e.g., hospitalization in cases of severe bronchiolitis) and increased risks for chronic respiratory sequelae (e.g., asthma). In severe bronchiolitis, recent evidence suggests distinct pathobiological roles of microbiota (e.g., viruses, bacteria) and host responses influenced by genetic and epigenetic factors. However, the relationship of airway microbiota with host DNA methylation (DNAm) in infants with severe bronchiolitis remains unknown.<br><br>METHODS: In a multi-center prospective cohort of 504 multi-ethnic infants with severe bronchiolitis (age <&#x2009;1&#x2009;year), using nasopharyngeal microbiome (exposure) and blood DNAm (outcome, Infinium MethylationEPIC BeadChip, Illumina) data within 24&#x2009;h of the hospitalization, we conducted microbiome-epigenome-wide association studies (mbEWAS). We examined microbiota-associated differentially methylated CpGs (mbDMCs, false discovery rate [FDR]&#x2009;<&#x2009;0.05), regions (mbDMRs, FDR <&#x2009;0.05), and DNAm age acceleration. We also determined the associations of DNAm age acceleration with asthma development by age 6&#x2009;years. Furthermore, we focused on asthma-related pathogenic bacteria-Haemophilus influenzae, Moraxella catarrhalis, and Streptococcus pneumoniae-for functional analyses by examining serum mbDMR-related proteins (Proseek Multiplex, Olink) and their enriched pathways (FDR <&#x2009;0.10).<br><br>RESULTS: Across 23 common taxa-observed at least in 25% of the infants, we identified 1 mbDMC (S. pneumoniae, cg16594639, chr20: 39528675) and 96 mbDMRs (e.g., S. pneumoniae, chr5:27038497-27038802, CDH9; chr6:48068669-48068940, PTCHD4). A higher H. influenzae abundance was associated with DNAm age deceleration, and the deceleration was associated with a higher risk of developing asthma. In 29 mbDMRs of the asthma-related pathogenic bacteria, we identified 156 mbDMR-related proteins (e.g., MMP9, XCL1). These proteins were enriched in immune response-related pathways (e.g., regulation of ERBB signaling and eosinophil chemotaxis and migration pathways).<br><br>CONCLUSIONS: In this multi-center prospective cohort study of severe bronchiolitis, our mbEWAS suggested the microbiota-host associations that regulate immune responses.}, }
@article {pmid41077897, year = {2025}, author = {Rachtman, E and Jiang, Y and Mirarab, S}, title = {Machine Learning Enables Alignment-Free Distance Calculation and Phylogenetic Placement Using k-Mer Frequencies.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e70055}, doi = {10.1111/1755-0998.70055}, pmid = {41077897}, issn = {1755-0998}, support = {2137603//National Science Foundation (ACCESS Program)/ ; 2138259//National Science Foundation (ACCESS Program)/ ; 2138286//National Science Foundation (ACCESS Program)/ ; 2138296//National Science Foundation (ACCESS Program)/ ; 2138307//National Science Foundation (ACCESS Program)/ ; ACI-1540112//National Science Foundation (NRP/Natulius Program)/ ; CNS-2100237//National Science Foundation (NRP/Natulius Program)/ ; ACI-1541349//National Science Foundation (NRP/Natulius Program)/ ; CNS-1730158//National Science Foundation (NRP/Natulius Program)/ ; CNS-2120019//National Science Foundation (NRP/Natulius Program)/ ; OAC-1826967//National Science Foundation (NRP/Natulius Program)/ ; OAC-2112167//National Science Foundation (NRP/Natulius Program)/ ; 1R35GM142725/NH/NIH HHS/United States ; //Minderoo Foundation/ ; //Schmidt Foundation/ ; }, abstract = {A key application of phylogenetics in ecological studies is identifying unknown sequences with respect to known ones. This goal can be formalised as assigning taxonomic labels or inserting sequences into a reference phylogenetic tree (phylogenetic placement). Much attention has been paid to the phylogenetic placement of short fragments used in amplicon sequencing or metagenomics. However, placing longer pieces of DNA, such as assembled genomes, contigs, or long reads, is less studied. Placing long sequences should be easier than short reads due to their increased signal. However, handling larger inputs poses its own challenges including finding homologues and the computational burden. Here, we explore a phylogenetic placement method that uses k-mer frequencies to measure distances between long query sequences and reference genomes. Our proposed method, kf2vec, requires no alignment and can work on any region of the genome (needs no marker genes), thus simplifying analysis pipelines. A rich literature exists on using short k-mers frequencies to measure distances that correlate with phylogeny. Existing methods, however, have had moderate practical success despite enjoying strong theory. Instead of using predefined metrics, we train a deep neural network to estimate a distance from k-mer frequency vectors such that those distances match the path lengths on the reference phylogeny. The trained model is then used to characterise new samples. We demonstrate that kf2vec outperforms existing k-mer-based approaches in distance calculation and allows accurate phylogenetic placement and taxonomic identification of new samples from various types of long sequences.}, }
@article {pmid41077635, year = {2025}, author = {Noel, S and Patel, SK and White, J and Verma, D and Menez, S and Raj, D and Parikh, C and Rabb, H and , }, title = {Metagenomic Profiling of Gut Microbiota in Kidney Precision Medicine Project Participants With CKD and AKI.}, journal = {Comprehensive Physiology}, volume = {15}, number = {5}, pages = {e70058}, doi = {10.1002/cph4.70058}, pmid = {41077635}, issn = {2040-4603}, support = {U01DK133081//KPMP/ ; U01DK133091//KPMP/ ; U01DK133092//KPMP/ ; U01DK133093//KPMP/ ; U01DK133095//KPMP/ ; U01DK133097//KPMP/ ; U01DK114866//KPMP/ ; U01DK114908//KPMP/ ; U01DK133090//KPMP/ ; U01DK133113//KPMP/ ; U01DK133766//KPMP/ ; U01DK133768//KPMP/ ; U01DK114907//KPMP/ ; U01DK114920//KPMP/ ; U01DK114923//KPMP/ ; U01DK114933//KPMP/ ; U24DK114886//KPMP/ ; UH3DK114926//KPMP/ ; UH3DK114861//KPMP/ ; UH3DK114915//KPMP/ ; UH3DK114937//KPMP/ ; R01DK104662/DK/NIDDK NIH HHS/United States ; R01DK123342/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Renal Insufficiency, Chronic/microbiology ; *Acute Kidney Injury/microbiology ; Metagenomics/methods ; Precision Medicine/methods ; Female ; Male ; Middle Aged ; Adult ; Feces/microbiology ; }, abstract = {BACKGROUND: The gut microbiome plays an important role in human health and disease. Kidney Precision Medicine Project (KPMP) is a well-phenotyped, kidney biopsy-proven cohort of AKI and CKD patients. Comprehensive profiling of gut microbiota can uncover novel mechanistic, diagnostic, and therapeutic strategies for CKD and AKI patients.<br><br>METHODS: We performed metagenomic whole genome sequencing (mWGS; >&#x2009;25 million reads) on KPMP stool samples. mWGS data of healthy controls from 4 published studies was used. Kraken2 and MetaPhlAn3 were used for taxonomic assignment, and HUMAnN3 for functional annotation.<br><br>RESULTS: Kraken2 analysis showed significantly higher abundance of Ruminococcus bicirculans in CKD (6.47) compared to AKI (1.82) and healthy individuals (2.42; p&#x2009;=&#x2009;0.01). Furthermore, the abundance of Gordonibacter pamelaeae increased in CKD (0.30) compared to AKI (0.07; p&#x2009;=&#x2009;0.05) and healthy individuals (0.03). The percent mean abundance of genus Chryseobacterium was slightly higher in CKD (0.07) compared to AKI (0.05; p&#x2009;=&#x2009;0.05) but reduced compared to healthy individuals (0.20; p&#x2009;<&#x2009;0.001). MetaPhlAn3 identified alterations in Gordonibacter, Bacteroides, and Faecalibacterium with a significant increase in Clostridium asparagiforme in AKI (11.68) compared to CKD (0.03; p&#x2009;=&#x2009;0.06) and healthy (0.01; p&#x2009;=&#x2009;0.001) individuals. Roseburia hominis, Roseburia intestinalis, Dorea longicatena, and Gemmiger formicilis were significantly reduced in AKI compared to CKD and healthy individuals. LDA/HUMAnN3 analysis showed a significant correlation between several metabolites and bacterial species in this KPMP population.<br><br>CONCLUSION: Kidney biopsy-proven CKD and AKI patients show a distinct gut microbiota profile compared to healthy individuals. This high-quality dataset is a valuable resource for developing microbiome-based diagnostics and therapies for CKD and AKI.}, }
@article {pmid41077176, year = {2025}, author = {Agrawal, K and Hong, ASY and Cifuentes-González, C and Kumar, VS and Rojas-Carabali, W and Zhang, S and Wang, Q and de-la-Torre, A and Gijs, M and Gill, T and Rosenbaum, JT and Rajagopala, SV and Gangaputra, S and Conforti, A and Ross, RP and Yang, P and Wong, S and Agrawal, R}, title = {Microbiome Signatures and Their Role in Uveitis: Pathogenesis, Diagnostics, and Therapeutic Perspectives.}, journal = {Progress in retinal and eye research}, volume = {}, number = {}, pages = {101409}, doi = {10.1016/j.preteyeres.2025.101409}, pmid = {41077176}, issn = {1873-1635}, abstract = {Non-infectious uveitis is a group of complex inflammatory eye diseases shaped by genetic susceptibility, immune dysregulation, and environmental cues. Among these, the mucosal microbiome-including gut, oral, and ocular surface microbial communities-has emerged as a key player in modulating systemic and ocular immune responses. Recent evidence supports a gut-eye axis wherein microbial dysbiosis alters intestinal barrier function, perturbs T cell homeostasis, and drives systemic immune activation that can breach ocular immune privilege. Specific taxa, such as Prevotella and Faecalibacterium, as well as microbial metabolites including short-chain fatty acids, have been implicated in promoting or mitigating ocular inflammation. Human leukocyte antigen (HLA) alleles, notably HLA-B27 and HLA-A29, influence both microbiome composition and disease phenotype, suggesting a gene-microbiome-immunity triad of interaction in uveitis pathogenesis. Drawing on insights from metagenomics, metabolomics, in vitro and in vivo experimental and murine models, this review delineates four key mechanisms-immune imbalance, antigenic mimicry, epithelial barrier disruption, and bacterial translocation-that underpin the key roles of microbiome in uveitis. We combine current literature and integrate findings from our research programs to highlight diagnostic and therapeutic opportunities. Microbiome-informed strategies, such as rational probiotic design, dietary modulation, and targeted microbial therapies, hold promise for complementing existing immunosuppressive regimens. Translating these insights into clinical practice requires robust multi-omic studies, longitudinal cohorts, mechanistic studies, and precision-guided intervention trials. By framing uveitis within a mucosal immunological context, this review proposes a future precision medicine roadmap for integrating microbiome science into ocular inflammatory disease management.}, }
@article {pmid41076761, year = {2025}, author = {Jin, Y and Ping, J and Huang, X and Dai, J and Wang, X and Wang, S}, title = {Nanoscale zero-valent iron coupled with microorganisms enhances the removal of organochlorine pesticides in groundwater: Insights from the role of cascading effects and horizontal gene transfer.}, journal = {Water research}, volume = {288}, number = {Pt B}, pages = {124745}, doi = {10.1016/j.watres.2025.124745}, pmid = {41076761}, issn = {1879-2448}, abstract = {Nanoscale zero-valent iron (nZVIs) represent a promising approach for the remediation of organic chlorine-contaminated groundwater. However, the interaction between nZVIs and indigenous dechlorinating microorganisms is complex, which may have unpredictable effects on the dechlorination of organic chlorine, necessitating further investigation. In this study, we investigated an abandoned pesticide factory in southwest China, combined with microcosm experiment to reconstruct the metabolic pathway of biological dechlorination, and quantified the functional contribution of dechlorination genes and microorganisms. The results showed that the combined treatment of nZVIs and microorganisms significantly enhanced the degradation efficiency of HCHs, DDTs, and their six isomers, achieving removal rates of up to 99 % for HCHs and 87.73 % for DDTs. The concentrations of Cl[-] and Fe[2+] had a direct positive effect on the enrichment of microbial communities harboring HCHs degradation genes. Haloalkane dehalogenase encoded by the dhaA gene was identified as a key enzyme in the degradation of β-HCH precursors, which not only promoted the growth of facultative dehalogenators (particularly Acidovorax and Methyloversatilis) but also enhanced overall dechlorination activity. Importantly, we successfully reconstructed 7 near-complete bacterial metagenome-assembled genomes (MAGs) carrying the dhaA gene, representing taxonomically diverse novel dechlorinating microorganisms. Additionally, nZVIs significantly increased the abundance of mobile genetic elements (MGEs), with 17 MGEs detected within scaffolds harboring dhaA in the 7 MAGs. Integrases and transposases were identified as key drivers facilitating the spread of dhaA. This finding was supported by the shift of dhaA-harboring hosts, and by the incongruent evolutionary patterns observed between the genome-based tree and the dhaA protein phylogenetic tree. To be specific, cascading effects and horizontal gene transfer synergistically promoted the proliferation of dechlorinating microbes, providing novel strategies for managing and remediating organic chlorine-contaminated ecosystems.}, }
@article {pmid41076729, year = {2025}, author = {Burdon, IA and Psaltis, AJ}, title = {Changes in the sinus microbiome in health and chronic rhinosinusitis.}, journal = {Current opinion in otolaryngology &amp; head and neck surgery}, volume = {}, number = {}, pages = {}, pmid = {41076729}, issn = {1531-6998}, abstract = {PURPOSE OF REVIEW: This article synthesises the recent sinus microbiome literature, identifying common themes in research findings as well as surveying the varied methodological approaches used across these studies.<br><br>RECENT FINDINGS: While there remains no clear consensus as to which microbes define dysbiosis in chronic rhinosinusitis (CRS), certain trends are emerging. Increasingly, the evidence points towards a pathogenic role in the overabundance of Moraxella, Haemophilus and Pseudomonas species, whilst the genera Cutibacterium, Anaerococcus and Dolosigranulum tend towards commensalism. However, the roles of the most common genera in the sinus microbiome, Staphylococcus and Corynebacterium, remain uncertain. Given the diversity and abundance of species within these genera, species and function-level analyses are needed to clarify their contributions to the aetiopathogenesis of CRS. Comprehensive study of the sinus microbiome in healthy individuals further shows that community composition shifts with age, suggesting that dysbiosis may manifest differently across the lifespan. Beyond bacteria, growing evidence highlights the importance of fungi and viruses, underscoring the need to incorporate these microbionts into future analyses.<br><br>SUMMARY: Progress towards a clinically meaningful consensus will require standardised approaches to sequencing, species-level resolution in these analyses, and consideration of the heterogeneous clinical and immunological subgroups of CRS.}, }
@article {pmid41075638, year = {2025}, author = {Yin, D and Wang, K and Sun, S}, title = {Efficient sulfide bio-chemical removal by different crystalline FeOOH (α, β, γ, δ and amorphous) in sewers.}, journal = {Journal of hazardous materials}, volume = {499}, number = {}, pages = {140072}, doi = {10.1016/j.jhazmat.2025.140072}, pmid = {41075638}, issn = {1873-3336}, abstract = {H2S corrosion in sewers causes huge economic losses. However, effective control solutions have remained lacking for decades. This study proposes FeOOH as a long-lasting and cost-effective alternative to iron salts for H2S control in sewers. The effect of FeOOH crystalline structures, electrochemical activity, acid and thermal stability, and surface morphology on S and Fe microbial redox were investigated. δ-FeOOH exhibited nearly 100 % H2S removal efficiency and the highest S[2-] removal capacity of 369.6 mg S/g FeOOH (1.10 mol S/Fe) followed by α-, AMO-, β- and γ-FeOOH. α-FeOOH treatment showed the highest FeS-S precipitation (304.2 mg S/g) and longest duration for sulfide control. This was contributed to α-FeOOH's low surface area and high structure stability. SO4[2-]-S bio-reduction inhibition was highest in δ-FeOOH (92.4 mg S/g), attributed to its highest Fe(Ⅲ)/Fe(Ⅱ), abundant sulfide oxidation genes (fccB, soxY and SUOx), and minimal electron transfer resistance. Moreover, sewer microbes enhanced the sulfide removal capacity of FeOOH by up to 6.0 times. FeOOH redirected microbial electron transfer away from SO4[2-] reduction and formed hydrogen bond with proteins that influenced SO4[2-] transport and uptake. This study provides comprehensive insights into the impact of FeOOH crystalline structure on microbial sulfur metabolism and electron transfer in sewers.}, }
@article {pmid41075532, year = {2025}, author = {Ghafoor, D and Hayakijkosol, O and Prasetsincharoen, N and Chen, CCM and Noman, M and Chomchat, P and Kinobe, R}, title = {Characterisation of the gut microbiome and surveillance of antibiotic resistance genes in green sea turtles (Chelonia mydas).}, journal = {Marine environmental research}, volume = {212}, number = {}, pages = {107605}, doi = {10.1016/j.marenvres.2025.107605}, pmid = {41075532}, issn = {1879-0291}, abstract = {Green sea turtles (Chelonia mydas) are globally endangered marine herbivores that maintain the health of seagrass and coastal ecosystems. Their populations are declining due to human activities, including environmental pollution, which can disrupt gut microbial communities and compromise nutrition, immunity, and overall health. In this study, cloacal swabs from 139 green sea turtles categorised as captive juveniles, captive adults and wild stranded animals in the Gulf of Thailand, were analysed via shotgun metagenomic sequencing to elucidate bacterial taxonomic diversity and ARG profiles. In captive juveniles, Pseudomonadota was the most abundant phylum, followed by Ascomycota and Basidiomycota. In captive adults, Pseudomonadota exhibited an even greater predominance, with only minor contributions from unclassified bacteria and other taxa. In wild stranded green sea turtles, Pseudomonadota was dominant in their gut microbiome, but this was accompanied by notable levels of Actinomycetota, Bacteroidota, and Bacillota. Stranded turtles exhibited highest microbial diversity and variability, while captive adult turtles showed the lowest. Resistome profiling also revealed significant differences in the relative abundance of antibiotic resistance genes across all three groups. MacB (macrolide resistance) was the most abundant gene overall, with the highest abundance observed in juveniles (4.8 %). Stranded turtles exhibited elevated levels of TetA(58) (tetracycline resistance, 2.6 %) and msbA (nitroimidazole resistance, 2.2 %), while adults showed the greatest enrichment of Ecol_fabG_TRC (triclosan resistance, 3.8 %) and TxR (tetracycline resistance, 3.6 %). These data demonstrate that marked variability existed in the gut microbiome and resistome of green sea turtles across different life stages in captive or wild environments. This offers critical insights for the development of targeted conservation strategies and health management practices for both wild and captive green sea turtles. Strategies to mitigate the spread of antibiotic resistance should be developed.}, }
@article {pmid41073934, year = {2025}, author = {Zhu, X and Yan, J and Lai, X and Chen, M and Wang, Q}, title = {Hematogenous pulmonary abscess and septicemia due to infection with hypervirulent Pseudomonas aeruginosa in a nonimmunodeficient adolescent: a case report.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {1280}, pmid = {41073934}, issn = {1471-2334}, support = {No.LGF22H190004//Basic Public Welfare Research Project of Zhejiang Province, China/ ; No.LGF22H190004//Basic Public Welfare Research Project of Zhejiang Province, China/ ; No.LGF22H190004//Basic Public Welfare Research Project of Zhejiang Province, China/ ; No.LGF22H190004//Basic Public Welfare Research Project of Zhejiang Province, China/ ; No.LGF22H190004//Basic Public Welfare Research Project of Zhejiang Province, China/ ; No.2022KY927//, Health Science and Technology Planning Project of Zhejiang Province, China/ ; }, abstract = {BACKGROUND: Pseudomonas aeruginosa is a non-glucose-fermenting gram-negative bacillus and an opportunistic pathogen that typically causes localized or systemic infections in immunocompromised middle-aged and elderly individuals or children with congenital immune deficiencies. However, cases of pulmonary abscess with severe sepsis in normal individuals are rare and should be taken seriously.<br><br>CASE PRESENTATION: A 15-year-old nonimmunodeficient adolescent was hospitalized due to high fever and other clinical symptoms. The patient was diagnosed with a pulmonary abscess with severe sepsis. Etiological Examination showed that sensitive Pseudomonas aeruginosa. Subsequent inspection revealed this clinical isolate produces virulence factors ExoA and Pyocyanin, which was highly virulent. The patient&#x2019;s symptoms were improved after imipenem (IPM) treatment and discharged. At follow-up 3 months later, he had recovered well.<br><br>CONCLUSIONS: We report a case of a pulmonary abscess with severe sepsis caused by Pseudomonas aeruginosa in an immunocompetent patient. Compared with the vast majority of infections caused by P. aeruginosa, this patient was younger and had no immunodeficiency or basic diseases, and the characteristics of the lesions were also unique. For this P. aeruginosa isolate, the testings of antimicrobial drugs were generally sensitive, and the virulence factors ExoA and Pyocyanin by quantitative metagenomics next-generation sequencing may be the main factors for the severity.}, }
@article {pmid41075379, year = {2025}, author = {Pichler, I and Krischer, E and Obenhuber, T and Hirsch, B and Reinhold, I and Wiedmer, C and Ziltener, G and Weller, D and Roth, P and Weiss, T and Kufner, V and Bloemberg, GV and Trkola, A and Müller, NJ and Huber, M}, title = {Viral metagenomic sequencing reveals rare pathogens and improves diagnostic accuracy in neuroinflammatory disorders.}, journal = {Diagnostic microbiology and infectious disease}, volume = {114}, number = {2}, pages = {117140}, doi = {10.1016/j.diagmicrobio.2025.117140}, pmid = {41075379}, issn = {1879-0070}, abstract = {BACKGROUND: Neuroinflammatory disorders are frequently of unknown aetiology. Unbiased metagenomic next-generation sequencing of cerebrospinal fluid could help bridge the current diagnostic gap by identifying more infectious pathogens inducing central nervous system disorders. This study examined the advantages of adding viral metagenomics to standard testing procedures.<br><br>METHODS: Patients presenting with symptoms indicative of a neuroinflammatory disorder were enrolled at a Swiss tertiary care hospital through prospective and retrospective recruitment. Participants were diagnosed with infectious or autoimmune neuroinflammatory disorders based on the results of routine diagnostics and viral metagenomic sequencing.<br><br>RESULTS: Of the 70 study participants, 50 were classified as having an infectious disorder. Among these, a total of 37 pathogens were identified in 29 individuals (56 %), including 32 viral, three bacterial, one fungal, and one prion infection. Conventional virus testing and viral metagenomic sequencing produced the same positive and negative results for 13 and 21 cases, respectively. This resulted in an overall percent agreement of 59 %. Disparate viral results were observed in 19 cases. Ten cases were detected only by conventional testing, and nine were detected only by viral metagenomics. Notably, we report the detection of Toscana virus by viral metagenomic sequencing, a relatively rare pathogen in Switzerland that is not routinely screened for, underscoring the advantages of integrating viral metagenomics with conventional testing.<br><br>CONCLUSIONS: Viral metagenomic sequencing as a first-line diagnostic tool in combination with conventional methods yields the most comprehensive results to diagnose patients with infectious neuroinflammatory disorders. Its unbiased approach enables the detection of rare or unconsidered viruses.}, }
@article {pmid41075335, year = {2025}, author = {Ghaffar, A and Liljebjelke, K and Checkley, SL and Farooq, M and Abdul-Careem, MF}, title = {Exploring the indoor airborne microbiome and resistome in layer barns across Alberta, Canada.}, journal = {Research in veterinary science}, volume = {196}, number = {}, pages = {105930}, doi = {10.1016/j.rvsc.2025.105930}, pmid = {41075335}, issn = {1532-2661}, abstract = {The air in poultry barns carries a diverse range of microbial communities including potential opportunistic pathogens, which are important for both animal and human health. Bacteria carrying antimicrobial resistance genes (ARGs) can become airborne within poultry barns and be transmitted to animals and poultry workers, presenting a serious One Health concern. This study was aimed at characterizing the microbiome and resistome of bioaerosols sampled from layer chicken barns across Alberta. In total, 15 barns (9 cage housed and 6 floor housed) were sampled in this study using a microbial air sampler to characterize the microbiome and resistome using a shotgun metagenomic sequencing approach. The most abundant bacterial phyla found in the air of both housing systems for pullets were Bacilliota, Actinomycetota, and Bacteroidota. The respiratory pathogens such as Gallibacterium anatis, Ornithobacterium rhinotracheale, and Pasteurella multocida were relatively more abundant in the air of cage-housed barns, whereas Escherichia coli and Avibacterium paragallinarum were more prevalent in floor-housed barns. In total, 113 unique ARGs subtypes from 19 classes of antimicrobials were identified in this study. ARGs were significantly more abundant in the air of cage-housed barns compared to floor-housed barns. In particular, genes associated with resistance to tetracyclines, lincosamides, and macrolides were more frequently detected in cage-housed environments. Overall, both microbial and resistance gene levels were higher in the bioaerosols of cage-housed barns than in those from floor-housed pullet barns. The study results demonstrate the potential for air as a reservoir of ARGs and highlights microbial differences within cage and floor housing.}, }
@article {pmid41074949, year = {2025}, author = {Malik, MZ and Nizam, R and Jacob, S and Al Alqaderi, H and Al-Mulla, F and Alqaderi, H}, title = {Microbial dysbiosis in oral cavity determines obesity status in adolescents.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {82}, number = {1}, pages = {354}, pmid = {41074949}, issn = {1420-9071}, support = {Institutional Funding//Kuwait Foundation for the Advancement of Sciences/ ; }, mesh = {Humans ; Adolescent ; *Dysbiosis/microbiology ; Female ; Male ; *Mouth/microbiology ; *Obesity/microbiology ; Microbiota/genetics ; Saliva/microbiology ; Body Mass Index ; Kuwait ; }, abstract = {The prevalence of obesity is rapidly increasing among adolescents in Kuwait. The ecological and dynamic changes within the oral microbiota during this developmental stage remain elusive. This study aimed to investigate the impact of body mass index (BMI) on salivary microbiome diversity and composition in Kuwaiti adolescents by utilizing next-generation sequencing technologies. DNA was extracted from saliva samples of 62 Kuwaiti adolescents enrolled in the nationwide Kuwait Healthy Lifestyle Study, categorized as underweight, normal weight, overweight, and obese based on their BMI percentiles. The 16 S metagenomic profiling was performed to identify the key oral lineages and genera associated with obesity through comprehensive analysis involving taxonomic composition, co-occurrence networks, and key metabolic profiles. Our study reveals an inverse relationship between oral bacterial diversity and obesity status in Kuwaiti adolescents. The obese and overweight groups showed comparatively low microbial taxa compared to those of normal weight. We identified three potential microbial biomarkers linked to obesity and overweight: Prevotella melaninogenica, Veillonella dispar, and Veillonella parvula. The abundance of Neisseria subflava and Rothia mucilaginosa in normal weight adolescents indicates their role in weight homeostasis. In- silico analysis of differentially expressed microbiota revealed increased activity of major metabolic enzymes such as glucose- 6- phosphate dehydrogenase, pyruvate oxidase, and glycogen phosphorylase, along with oxidative stress- related enzymes including superoxide reductase and glutathione peroxidase in obese and over-weight adolescents. Conversely, normal weight adolescents exhibited heightened activity of pyruvate synthase and tRNA- methyltransferase, which are linked to antioxidative pathways and balanced energy metabolism. Our study highlights taxonomic and functional shifts in the oral microbiota of Kuwaiti adolescents across varying BMI categories, signifying key microbial markers that could pave the way for future research focused on microbiome- targeted interventions in obesity management.}, }
@article {pmid41074769, year = {2025}, author = {Tucker, SJ and Freel, KC and Eren, AM and Rappé, MS}, title = {Habitat-specificity in SAR11 is associated with a few genes under high selection.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf216}, pmid = {41074769}, issn = {1751-7370}, abstract = {The order Pelagibacterales (SAR11) is the most abundant group of heterotrophic bacteria in the global surface ocean, where individual sublineages likely play distinct roles in oceanic biogeochemical cycles. Yet, understanding the determinants of niche partitioning within SAR11 has been a formidable challenge due to the high genetic diversity within individual SAR11 sublineages and the limited availability of high-quality genomes from both cultivation and metagenomic reconstruction. Through an integrated metapangenomic analysis of 71 new SAR11 isolate genomes and a time-series of metagenomes from the prominent source of isolation, we reveal an ecological and phylogenetic partitioning of metabolic traits across SAR11 genera. We resolve distinct habitat preferences among genera for coastal or offshore environments of the tropical Pacific and identify a handful of genes involved in carbon and nitrogen metabolisms that appear to contribute to these contrasting lifestyles. Furthermore, we find that some habitat-specific genes experience high selective pressures, indicating that they are critical determinants of SAR11 fitness and niche differentiation. Together, these insights reveal the underlying evolutionary processes shaping niche-partitioning within sympatric and parapatric populations of SAR11 and demonstrate that the immense genomic diversity of SAR11 bacteria naturally segregates into ecologically and genetically cohesive units, or ecotypes, that vary in spatial distributions in the tropical Pacific.}, }
@article {pmid41074341, year = {2025}, author = {Zhang, Z and Wang, Y and Yao, Y and Li, Y and Xu, X and Hou, Q and Hu, X and Mei, X and Guo, Z}, title = {Microbial and flavor dynamics of medium-high temperature Daqu: regional influences and implications for Daqu quality optimization.}, journal = {Food research international (Ottawa, Ont.)}, volume = {220}, number = {}, pages = {117155}, doi = {10.1016/j.foodres.2025.117155}, pmid = {41074341}, issn = {1873-7145}, mesh = {*Taste ; China ; *Hot Temperature ; *Wine/microbiology/analysis ; Odorants/analysis ; *Food Microbiology ; Bacteria/classification/genetics/metabolism ; Metagenomics ; Microbiota ; Fermentation ; Humans ; }, abstract = {Medium-high temperature Daqu (MHTD) plays a crucial role in Chinese strong-flavor Baijiu production, yet its microbial dynamics and the drivers of regional variation remain underexplored. In this study, we investigated the microbial community structure, enzyme activity, and flavor profiles of MHTD from three geographically adjacent regions in China, using metagenomic sequencing, E-sensory analysis, and multivariate statistics. Despite significant regional differences in microbial diversity, community composition, and taste, aroma profiles were relatively consistent. Redundancy analysis revealed that water content and acidity were the primary environmental drivers of microbial and flavor variation. Notably, increased water content was positively correlated with microbial richness, enzyme activity, and flavor complexity. Functional annotation of metagenomic data uncovered key microbial pathways for starch, cellulose, and lignin degradation, as well as for the biosynthesis of pyrazines and guaiacol derivatives. Limosilactobacillus fermentum, the dominant species across all samples, was found to possess the genetic potential to produce both compound classes-representing a novel finding. Fungal species such as Thermoascus sp. and Rasamsonia emersonii appeared to cooperate in guaiacol synthesis, while Acetobacter pasteurianus and A. oryzoeni in MHTD from Chuzhou City contributed to pyrazine production. These findings highlight the microbial and environmental basis of flavor formation in MHTD and offer practical implications for MHTD production. Specifically, moisture regulation during fermentation and selective enrichment of functional strains like L. fermentum and Acetobacter spp. may help optimize flavor development and product consistency.}, }
@article {pmid41073968, year = {2025}, author = {Onohuean, H and Choonara, YE}, title = {Epidemiological distribution of bacterial meningitis infections in South Africa: a systematic review and meta-analysis.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {1284}, pmid = {41073968}, issn = {1471-2334}, mesh = {Humans ; South Africa/epidemiology ; *Meningitis, Bacterial/epidemiology/microbiology ; Prevalence ; Child ; Adolescent ; Child, Preschool ; Female ; Male ; Adult ; Infant ; Middle Aged ; Young Adult ; }, abstract = {Scientific evidence from public health findings can enhance the management, treatment, and prevention policies for bacterial meningitis (BM) infections. However, comprehensive epidemiological data on BM prevalence in South Africa is limited. We aimed to assess the prevalence and characteristics of laboratory-confirmed BM cases at the national population level. Using PRISMA standards, we retrieved data from electronic databases and selected reference articles. Out of 115,626 participants, 57,964 (50.13%) were infected with BM, with the highest prevalence (7.67%) in the age group 6-17 years. Our meta-analysis of 19 studies revealed an overall pooled prevalence of 38.01%, 95% confidence interval (CI: 0.26-0.50), with significant heterogeneity (I[2] = 99.86%, Q = 13117.45, p < 0.0001). The Egger test indicated publication bias (z = 3.4977, p = 0.0005). Subgroup analyses showed a higher prevalence in studies with sample sizes over 1000 (60.22%, 95% CI: 0.3899-0.7819, I[2] = 99.92%), over long study years (37.50%, 95% CI: 0.2642-0.5005, I[2] = 99.84%), cross-sectional study design (58.69%, 95%CI: 0.4906-0.6770, I2 = 99.72%), and particularly in Gauteng province (60.42%, 95% CI: 0.4539-0.7371, I[2] = 98.45%). The infectious types included Listeria (83.33%, 95% CI: 0.1936-0.9905, I[2] = 0.00%) and Neisseria (62.64%, 95% CI: 0.6126-0.6400, I[2] = 0.00%). Significant heterogeneity was noted in study design (R[2] = 52.93%, p < 0.0001), sample size (R[2] = 0.00%, p = 0.0117), and province (R[2] = 0.0%, p < 0.0001). These findings underscore a high prevalence of BM infections in South Africa's epidemiological landscape, highlighting the urgent need for targeted surveillance for effective prevention and treatment strategies.}, }
@article {pmid41073886, year = {2025}, author = {Mao, K and Lu, G and Qiu, Q and Zang, Y and Ouyang, K and Zhao, X and Song, X and Xu, L and Liang, H and Qu, M and Li, Y}, title = {Influence of creatine pyruvate on newly received cattle: insights from metagenomics and metabolomics.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {658}, pmid = {41073886}, issn = {1471-2180}, support = {CARS-37//the China Agriculture Research System of MOF and MARA/ ; CARS-37//the China Agriculture Research System of MOF and MARA/ ; 20232BCJ23016//the Young Talents Training Program for Academic and Technical Leaders of Major Disciplines in Jiangxi Province/ ; }, mesh = {Animals ; Cattle/growth &amp; development/microbiology ; Rumen/microbiology/metabolism ; *Creatine/pharmacology/administration &amp; dosage ; Metabolomics ; Metagenomics ; Gastrointestinal Microbiome/drug effects ; Metabolome/drug effects ; Animal Feed/analysis ; *Pyruvic Acid/pharmacology ; Bacteria/genetics/classification/metabolism ; }, abstract = {Transport stress is a critical factor affecting the health and growth performance of beef cattle, potentially leading to oxidative stress, inflammation, and metabolic disorders. Creatine pyruvate (CrPyr), as a potential stress alleviator, has unclear mechanisms of action. We monitored the growth of 17 Simmental calves (control, n = 8; CrPyr, n = 9) over 30 days post-transportation, collecting rumen and blood samples on days 1/4, and 30. This study aims to investigate the effects of CrPyr on the growth performance, rumen microbiome, and metabolome of calves subjected to transport stress. Results showed that CrPyr increased average daily gain and antioxidant capacity, while reducing the level of stress hormones and inflammation. In the 4 days post-transport, CrPyr mainly increases Ruminococcus abundance to boost ruminal nitrogen metabolism, providing substrates for microbial protein synthesis. CrPyr also provides energy for the proliferation of Ruminococcus by regulating ATP synthesis genes (ATPVC) and enriching purine metabolism products. Meanwhile, it strengthens the host's amino acid metabolism, especially aspartate, to enhance antioxidative capacity. By day 30, CrPyr primarily boosts Prevotella abundance to regulate VFA synthesis, supplying host energy. It regulates the ATP synthesis gene ATPF0A and enriches purine metabolism products, supporting Prevotella growth. Increased citric acid and ATP levels further aid host growth. The findings distinctly demonstrate that the mechanisms by which CrPyr alleviates transport stress through the regulation of the rumen microbiome and metabolome, and confirms that its effects are time-dependent. These findings provide a theoretical basis for the development of stress-alleviation strategies based on CrPyr and hold significant implications for enhancing the health and production performance of beef cattle.}, }
@article {pmid41073868, year = {2026}, author = {Leoni, C and Marzano, M and Filomena, E and D'Erchia, AM}, title = {Digital Droplet PCR (ddPCR) for Absolute Quantification of 16S rRNA Copy Number in Metagenomic Data.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2969}, number = {}, pages = {235-247}, pmid = {41073868}, issn = {1940-6029}, mesh = {*RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; *Polymerase Chain Reaction/methods ; *Gene Dosage ; DNA Copy Number Variations ; Fluorescent Dyes/chemistry ; }, abstract = {Digital Droplet PCR (ddPCR) is a quantitative PCR method that offers high sensitivity and accuracy in measuring the amount of nucleic acid in a sample, without the need of a standard curve. In ddPCR, a single sample is partitioned into up to 20,000 droplets, using the water-oil emulsion technology, and the amplification reaction occurs within each droplet using a fluorescent hydrolysis probe (Taqman) or a DNA-binding fluorescent dye. Following PCR, the emitted signals are individually measured in each droplet. Here, we describe a ddPCR optimized protocol for accurately quantifying the total copy number of the 16S rRNA gene in a metagenomic DNA sample. The protocol utilizes a primer pair, targeting the 16S V5-V6 hypervariable regions, in combination with a double-strand DNA-binding fluorescent dye.}, }
@article {pmid41073663, year = {2025}, author = {Yoo, JS and Jung, DJ and Goh, B and Heo, K and Zheng, W and Lee, CC and Seo, JI and Geva-Zatorsky, N and Wu, M and Park, SB and Kasper, DL and Oh, SF}, title = {Human gut bacteria produce structurally related monoglycolipids with contrasting immune functions.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {41073663}, issn = {2058-5276}, support = {K01-DK102771//U.S. Department of Health &amp; Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes &amp; Digestive &amp; Kidney Diseases)/ ; R01-AT010268//U.S. Department of Health &amp; Human Services | NIH | National Center for Complementary and Integrative Health (NCCIH)/ ; R01-AI165987//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 2021R1A6A3A14044113//National Research Foundation of Korea (NRF)/ ; RS-2024-00411992//National Research Foundation of Korea (NRF)/ ; RS-2024-00348702//National Research Foundation of Korea (NRF)/ ; 2021R1A6A3A14039202//National Research Foundation of Korea (NRF)/ ; RS-2023-00217123//National Research Foundation of Korea (NRF)/ ; 2014R1A3A2030423//National Research Foundation of Korea (NRF)/ ; 2012M3A9C4048780//National Research Foundation of Korea (NRF)/ ; }, abstract = {Gut symbiont Bacteroides fragilis can produce α-galactosylceramides (BfaGCs), sphingolipids with immunomodulatory functions that regulate colonic natural killer T (NKT) cells. However, their synthesis pathway and whether other human gut bacteria can produce them are unclear. Here, using genetic and metabolomic approaches, we mapped the sphingolipid biosynthesis pathway of B. fragilis and determined that α-galactosyltransferase (agcT) is essential and sufficient for colonic NKT cell regulation in mice. The distribution of agcT is restricted to only a few species among Bacteroidales. However, structural homologues of AgcT, such as BgsB, are widely distributed in gut microbiota and produce α-glycosyldiacylglycerols (aGDGs), particularly in Enterococcus. Analysis of infant gut metagenomes revealed that B. fragilis predominantly accounts for agcT abundance regardless of the cohort, but bgsB-encoding bacteria were taxonomically diverse and showed dynamic changes with host age. In addition, aGDGs from bgsB-encoding species act as antagonistic ligands for BfaGC-mediated NKT cell activation in vitro and in vivo. Our findings highlight the distinct natures of immunoactive glycolipid-producing symbionts and their relevance in the human gut microbiome, particularly in early life.}, }
@article {pmid41073345, year = {2025}, author = {Guo, WB and Wang, TT and Song, ZK and Liu, QY and Sun, JJ}, title = {[One case of occupational pulmonary anthrax].}, journal = {Zhonghua lao dong wei sheng zhi ye bing za zhi = Zhonghua laodong weisheng zhiyebing zazhi = Chinese journal of industrial hygiene and occupational diseases}, volume = {43}, number = {9}, pages = {705-707}, doi = {10.3760/cma.j.cn121094-20240719-00326}, pmid = {41073345}, issn = {1001-9391}, mesh = {Humans ; *Anthrax ; Male ; Bacillus anthracis ; *Occupational Diseases ; *Anthracosis ; Adult ; }, abstract = {Pulmonary anthrax is an acute zoonotic infectious disease caused by Bacillus anthracis infecting the human body. Humans can be infected by coming into contact with diseased animals and their products or by consuming diseased animals. According to the different infection routes, it can be classified into cutaneous anthrax, pulmonary anthrax and intestinal anthrax, etc. Among them, cutaneous anthrax is the most common, while case reports of pulmonary anthrax are rare. This article analyzes the clinical data of a case of occupational pulmonary anthrax diagnosed by metagenomic next-generation sequencing (mNGS) and successfully treated, so as to provide a reference for the clinical treatment of pulmonary anthrax.}, }
@article {pmid41072965, year = {2025}, author = {Odukwe, C and Abdelrahman, A and Zaidi, AN and Love, B and El-Hamamsy, I and Ghesani, M and Hopkins, KA}, title = {Culture-Negative Transcatheter Pulmonary Valve Endocarditis.}, journal = {JACC. Case reports}, volume = {30}, number = {31}, pages = {105324}, doi = {10.1016/j.jaccas.2025.105324}, pmid = {41072965}, issn = {2666-0849}, abstract = {CLINICAL CONDITION: We present a case of transcatheter pulmonary valve endocarditis in a 38-year-old woman with a history of atrial septal defect, pulmonary stenosis, and bicuspid aortic valve, all previously repaired with mechanical and bioprosthetic valve replacements. Despite negative initial studies, [18]F-fluorodeoxyglucose positron emission tomography-computed tomography revealed septic pulmonary emboli and abnormal uptake at the pulmonary valve. Metagenomic sequencing identified Haemophilus parainfluenzae as the pathogen.<br><br>KEY QUESTIONS: What is the differential diagnosis of a cardiac mass in this context? How should imaging and laboratory testing be approached in prosthetic valve endocarditis with negative studies? What surgical factors matter in patients with prior cardiac repairs?<br><br>OUTCOME: The patient underwent successful replacement of the pulmonary and aortic valves and completed a course of antibiotics, with full recovery.<br><br>TAKE-HOME MESSAGE: Consider bioprosthetic valve endocarditis in patients with persistent fevers and negative cultures. Use advanced diagnostics early when the clinical suspicion is high.}, }
@article {pmid41072853, year = {2025}, author = {Li, Y and Sun, C and Zhao, T and Ni, Y and Liu, Q and Song, M and Xu, X and Sun, W and Li, Y and Zhou, J and Li, D and Zhang, Q and Feng, C and Shi, J and Cao, M and Huang, B and Su, N and Lu, X and Wang, L and Lei, J and Sang, L and Zhou, W and Cai, X and Wang, J and Wang, Y and Cai, Y and Lu, Y and Zhong, J and Su, X}, title = {Etiology of Initial Treatment Failure in Non-immunosuppressed Adult Patients with Community-acquired Pneumonia.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {}, number = {}, pages = {108110}, doi = {10.1016/j.ijid.2025.108110}, pmid = {41072853}, issn = {1878-3511}, abstract = {OBJECTIVES: Initial treatment failure (ITF) of community-acquired pneumonia (CAP) is a significant clinical problem. The study aimed to explore the etiology of ITF using metagenomic next-generation sequencing (mNGS) and targeted next-generation sequencing (tNGS), and to provide optimized management strategies for patients with CAP.<br><br>METHODS: From June 2022 to August 2024, we conducted a prospective, multicenter study in 15 hospitals of non-immunosuppressed adult CAP patients with ITF in Jiangsu Province, China. Conventional microbiological tests (CMTs), mNGS, and tNGS were applied to detect microorganisms in bronchoalveolar lavage fluid.<br><br>RESULTS: ITF was mainly caused by responsible pathogens not covered by initial treatment (59.0%) despite the high compliance with guideline-recommended regimens. The top 5 responsible pathogens were Chlamydia psittaci (21.5%), Mycoplasma pneumoniae (16.7%), influenza virus (14.6%), SARS-CoV-2 (8.3%), and Pseudomonas aeruginosa (6.3%). The positive pathogen identification rate for mNGS and tNGS was 74.4% and 72.7%, respectively, while for CMTs it was 12.2%. Based on NGS results, treatment was optimized in 53.5% of patients, and 95.8% were improved or cured.<br><br>CONCLUSIONS: Atypical pathogens and viruses not covered by empirical treatment regimens were the main causes of ITF. mNGS and tNGS outperformed CMTs in identifying responsible pathogens and could optimize the treatment of patients with ITF.}, }
@article {pmid41072822, year = {2025}, author = {Chen, Z and Zhang, J and Lin, L and Sun, Y and Li, XY and Li, B}, title = {Enhanced fermentation for lactic acid production from food waste via hydrothermal pretreatment: performance evaluation and metagenomic analysis.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {133456}, doi = {10.1016/j.biortech.2025.133456}, pmid = {41072822}, issn = {1873-2976}, abstract = {Mixed-culture lactic acid fermentation of food waste (FW) commonly requests low pH conditions. However, this can pose the challenge of insufficient substrate hydrolysis. To address this, we investigated hydrothermal pretreatment coupled with centrifugal supernatant recovery as a technical strategy to enhance the FW hydrolysis and lactic acid production. The study characterized the supernatant substrate after the pretreatment at different temperatures (80-140 °C), focusing on organic solubilization, supernatant-solid separation for organic recovery, grease removal, and subsequently evaluated lactic acid production in 8-day batch fermentation. The results showed that hydrothermal pretreatment significantly boosted FW hydrolysis, improved organic recovery in the supernatant, and enhanced lactic acid yields. Optimal lactic acid production (12.4 g/L) representing a 68 % increase over the control without hydrothermal pretreatment, was achieved at 120 °C, despite the maximum hydrolysis occurring at 140 °C. Metagenomic sequencing further revealed that the pretreated substrate fostered the development of a lactic acid bacteria-dominated microbial community at low pH, notably enriched with Lactobacillus amylolyticus and Lactobacillus delbrueckii, along with functional genes associated with lactic acid production. Crucially, the absence of genes related to propionate and butyrate pathways in the dominant bacteria would explain the reduced byproduct spectrum and enhanced fermentation stability. These findings indicate that hydrothermal pretreatment improves both the quantity and quality of FW supernatant substrate, promoting a lactic acid bacteria-dominated community that drives favorable metabolic pathways under low pH conditions for more efficient and stable lactic acid production.}, }
@article {pmid41072348, year = {2025}, author = {Tang, Y and Khan, E and Gu, AZ and Tsang, DCW}, title = {Graphitic biochar-anammox achieved by multi-heme-based extracellular electron transfer.}, journal = {Water research}, volume = {288}, number = {Pt B}, pages = {124704}, doi = {10.1016/j.watres.2025.124704}, pmid = {41072348}, issn = {1879-2448}, abstract = {The anammox process decarbonizes nitrogen removal by avoiding greenhouse gas emissions and organic carbon demand, yet its reliance on nitrification and denitrification undermines these advantages. To address this, we developed a biochar-assisted anammox system that leverages graphitic defects as redox-active sites to enable interspecies, multi-heme extracellular electron transfer (EET). Biochar produced at 800 °C for 4 h (BC800-4 h) exhibited the greatest graphitic defect density and the highest electron accepting capacity, uniquely exceeding the daily stoichiometric electron demand for complete ammonium oxidation in the present study. Metagenomic and in vitro assays revealed that BC800-4 h promoted hydroxylamine-dependent ammonium oxidation by anaerobic ammonia-oxidizing bacteria (AnAOB) via EET. A cooperative microbial network was identified: AnAOB in suspension supplied heme precursors, while ammonia-oxidizing and denitrifying bacteria colonizing the biochar facilitated heme assembly and transport. This partitioning enabled direct electron transfer to biochar, achieving 62 % nitrogen removal without exogenous nitrite and reducing N2O emissions by 28 %. The pore-size-dependent reduction in graphitic defects suggests that large molecular-weight biological channels (>10 kDa) are essential for electron transfer between anammox consortia and biochar. Our findings indicate an opportunity to develop a biochar-anammox reactor-with suspended AnAOB and a fixed-bed biochar biofilm-to exploit this synergy for efficient and low-emission nitrogen removal.}, }
@article {pmid41072344, year = {2025}, author = {Yu, K and Xia, J and Zhu, D and He, B and Yu, Z and Zhu, DZ and Yao, Z}, title = {Public risk of sewage sediments in different functional areas - deciphered by metagenome assembly.}, journal = {Water research}, volume = {288}, number = {Pt B}, pages = {124691}, doi = {10.1016/j.watres.2025.124691}, pmid = {41072344}, issn = {1879-2448}, abstract = {Understanding public risk of sewage sediments, particularly those risks related to methane, sulfide emission and bio-risk, is critical for ensuring citizen safety. However, the underlying microbial mechanisms causing these risks remain unclear. This study employed metagenomic assembly to analyze methane/sulfur cycling pathways and bio-risks in sewage sediments from three typical functional areas: commercial, multifunctional, and residential. Results demonstrated that the sewage sediments in the multifunctional area exhibited the highest potential public risk levels, characterized by intensified methane/sulfur metabolic activity and increased abundance of mobile gene elements (MGEs) and high-risk antibiotic resistance genes (ARGs). In addition, the co-occurrence network complexity of ARGs, MGEs and pathogens were higher in the multifunctional sewage sediments. Intriguingly, we found genus Thiobacillus which participated in sulfur cycling, as the host of high risk ARGs, significantly enriched in the multifunctional area, also distributed in sewer systems around the world. Additionally, total organic carbon (TOC) emerged as key driver of sediment public risks. These findings highlight variations in sewage sediment public risks across different functional areas, providing a foundation for targeted risk mitigation strategies.}, }
@article {pmid41072198, year = {2025}, author = {Jamtsho, K and Lund, MA and Blake, D and Van Etten, E}, title = {Contrasting effects of impervious cover on riparian plant and soil bacterial communities in a rapidly urbanising Himalayan city.}, journal = {The Science of the total environment}, volume = {1003}, number = {}, pages = {180681}, doi = {10.1016/j.scitotenv.2025.180681}, pmid = {41072198}, issn = {1879-1026}, abstract = {Rapid urbanisation-particularly the expansion of impervious surfaces-is reshaping riparian landscapes worldwide. These areas are frequently targeted for development due to their favourable topography, abundant water resources, and aesthetic appeal. However, the impact of increasing impervious cover on soil bacterial communities in biodiverse urban riparian zones remains poorly understood, especially in developing countries, raising concerns about potential declines in essential ecosystem functions. In this study, we investigated the effects of impervious cover, quantified as the Percentage of Total Impervious Area (PTIA), on the taxonomic and functional diversity of riparian soil bacteria in Thimphu City, Bhutan. Using plot-based taxonomic profiling and metagenomic analysis across a PTIA gradient, we tested the hypothesis that bacterial diversity and functional pathways would decline beyond 40 % PTIA, mirroring patterns observed in riparian plant communities. Contrary to our hypothesis, plots with PTIA exceeding 40 % exhibited greater bacterial richness and functional diversity. These findings suggest opposing responses to impervious cover, with belowground microbial communities increasing in diversity while aboveground plant diversity declines. A significantly lower carbon-to‑nitrogen ratio in urban plots-likely driven by nutrient enrichment-emerged as the primary factor promoting bacterial diversity in high PTIA areas. This enrichment appeared to favour copiotrophic bacteria, enhancing both diversity and functional capacity. Our results suggest that bacterial communities may be effective bioindicators of riparian ecosystem health than plant communities. Incorporating microbial metrics into urban riparian management and monitoring could therefore provide valuable insights for sustaining ecosystem functions in rapidly urbanising regions.}, }
@article {pmid41072177, year = {2025}, author = {Uribarri, A and Henriquez, L and Beguiristain, I and Rodriguez, I and Alfaro, M and Sancho, I and Portillo, ME}, title = {Toward a clinical algorithm for the detection of periprosthetic joint infections using targeted NGS.}, journal = {Diagnostic microbiology and infectious disease}, volume = {114}, number = {2}, pages = {117133}, doi = {10.1016/j.diagmicrobio.2025.117133}, pmid = {41072177}, issn = {1879-0070}, abstract = {OBJECTIVES: Periprosthetic joint infection (PJI) represents a severe surgical complication, and despite advances have been made in PJI diagnosis, many cases remain microbiologically negative. In this context, metagenomic Next-Generation Sequencing (mNGS) emerged as a promising diagnostic tool for PJI. This study aimed to establish objective, widely-usable methodology and criteria for diagnosing PJI based on sequence analysis.<br><br>METHODS: We retrospectively analyzed sonication fluid samples from 34 patients who underwent surgical treatment for PJI in 2022. A 16S rRNA-based targeted NGS (tNGS) approach was carried out amplifying 16S rRNA gene for 25 and 35 cycles. Sequencing was performed on the Illumina MiSeq platform and data was processed using nf-core/ampliseq.<br><br>RESULTS: A significantly higher number of classifiable reads was observed in PJI cases (p < 0.0001). A negative control database was created using negative tNGS controls and samples from patients classified as aseptic failure. The database was then employed to establish three tNGS diagnostic criteria. The diagnostic efficacy of tNGS employing these criteria was assessed through receiver operating characteristic (ROC) curve analysis, which revealed optimal results after 25 cycles of 16S rRNA amplification (AUC = 0.924, p < 0.0001). An optimal cut-off of >12 % was calculated, obtaining a sensitivity of 100 % (95 % CI 75.3 %-100 %) and a specificity of 90.5 % (95 % CI 69.9 %-98.8 %). In both of our culture-negative PJI cases potential pathogens were detected: Listeria and Cutibacterium.<br><br>CONCLUSIONS: To the best of our knowledge, this is one of the few studies that attempts to establish standardized criteria and diagnostic cut-offs for the analysis of PJI tNGS data. We believe that these results could serve as a valuable reference for future PJI metagenomics diagnostic studies.}, }
@article {pmid41071829, year = {2025}, author = {Akanbi, DO and Abaye, BB and Averhoff, F and Berg, MG and Orf, GS and Lawan, KM and Beckett, GA and Omotoso, AB and Mata, M and Cloherty, GA and Chabuka, L and de Oliveira, T and Mac-Fisi, KW and Walter, A and Mark, II and Edeki, G and Sinayoko, A and Nasrullah, M and Justina, BI and Balogun, MS}, title = {Detection of dengue, malaria, and additional causes of acute febrile illness: The need for expanded testing, Bayelsa State, Nigeria.}, journal = {PLoS neglected tropical diseases}, volume = {19}, number = {10}, pages = {e0013060}, doi = {10.1371/journal.pntd.0013060}, pmid = {41071829}, issn = {1935-2735}, abstract = {Dengue virus (DENV) infection has not been previously reported from Bayelsa State, Nigeria. We aimed to determine the prevalence of dengue virus (DENV) infection, malaria, and coinfection, and other pathogens among febrile patients in the capital city, Yenagoa.We conducted a cross-sectional study among persons aged ≥1 year who presented with acute febrile illnesses (AFI) at four hospitals in Bayelsa State during 20 May - 15 June 2022. Blood samples from 443 participants were tested for DENV seromarkers (NS1, IgM, IgG), using serology and RT-PCR, and malaria was diagnosed by thick smear microscopy. Sociodemographic and risk factor data were collected using electronic questionnaires administered via smart phones/tablets and analyzed using univariate and multivariate methods. Metagenomic libraries were prepared and enriched by viral target capture and sequenced by NGS. The seroprevalence of acute DENV infection was 14.5% (n = 64) while the prevalence of malaria was 42.4% (n = 188); 6.5% (n = 29) of participants were coinfected with acute DENV infection and malaria. An additional 17.6% (n = 78) of participants had markers for past DENV infection. Rural/suburban residence and age ≥ 31 years were significantly correlated with having any dengue seromarker. Residence in a larger household (≥5 persons), and borehole water-use were predictors for malaria fever. RT-PCR results revealed multiple DENV serotypes, with serotype 3 dominant. Sequencing of unknown AFI cases revealed numerous viral causes such as adenovirus, EBV, and hepatitis A, as well as additional dengue and malarial infections missed by conventional testing. Of interest were Coxsackievirus A5 (hand, foot and mouth disease; HFMD) which has been diversifying locally for years in Nigeria and an mPox clade IIb (lineage A.2.3) strain that emerged in Nigeria during the 2022 global outbreak. The results of this study provide the first documentation of human DENV infection in Bayelsa State, Nigeria and suggests that dengue is an emerging and important cause of febrile illness in this area. Our findings support the need for routine testing to identify DENV among patients who present with acute febrile disease. Metagenomic NGS results highlight the benefits of unbiased surveillance to identify circulating and emerging pathogens.}, }
@article {pmid41070991, year = {2025}, author = {Brennan, C and Shaffer, JP and Belda-Ferre, P and Mohanty, I and Weng, Y and Cantrell, K and Ackermann, G and Allaband, C and Bryant, M and Farmer, S and González, A and McDonald, D and Martino, C and Meehan, MJ and Rahman, G and Salido, RA and Schwartz, T and Song, SJ and Tribelhorn, C and Tubb, HM and Dorrestein, PC and Knight, R}, title = {Streamlined extraction of nucleic acids and metabolites from low- and high-biomass samples using isopropanol and matrix tubes.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0191225}, doi = {10.1128/spectrum.01912-25}, pmid = {41070991}, issn = {2165-0497}, abstract = {UNLABELLED: An essential aspect of population-based research is collecting samples outside of a clinical setting. This is crucial because microbial populations are highly dynamic, varying significantly across hosts, environments, and time points, a variability that clinical sample collection alone cannot fully capture. At-home sample collection enables the inclusion of a larger and more diverse group of participants, accounting for differences in ethnicity, age, and other factors. However, managing large studies is challenging due to the complexities involved in sample acquisition, processing, and analysis. Building on our previous work demonstrating the effectiveness of single 1 mL barcoded, racked Matrix Tubes in reducing sample processing time and well-to-well contamination for paired DNA and metabolite extraction, we further validate this method against a previously benchmarked plate-based approach using the same extraction reagents. This validation focuses on samples from the built environment, human skin, human saliva, and feces from mice and humans. Importantly, we explore the impact of using a mix of bead sizes during bead-beating for cell lysis, demonstrating that it enhances taxonomic recovery compared to a single bead size. Finally, we assess the potential of 95% isopropanol for room-temperature sample preservation. Our results show that isopropanol performs comparably to 95% ethanol in many cases, suggesting it is viable as an alternative when ethanol is unavailable. Beyond minimizing contamination, halving processing time, eliminating human error during sample plating, and streamlining metadata curation, the Matrix tube approach produces metabolomic, 16S, and shotgun metagenomic data consistent with the Plate-based Method for both high- and low-biomass samples.<br><br>IMPORTANCE: Numerous studies have linked the microbiome to human and environmental health, yet many fundamental questions remain unanswered. Large-scale studies with robust statistical power are required to identify important covariates against a background of confounding factors. Cross-contamination, limited throughput, and human error have been identified as major setbacks when processing large numbers of samples. We present a streamlined method for sample accession and extraction of metabolites and DNA for both high- and low-biomass samples. This approach, previously shown to significantly reduce cross-contamination, employs an automation-friendly, single barcoded tube per sample. Additionally, we demonstrate that 95% isopropanol serves as an effective ambient-temperature storage solution for many sample types, providing an alternative in regions where ethanol is unavailable or restricted. This method has significant implications for the field, enabling large-scale studies to generate accurate insights with greater efficiency and expanded accessibility in situations in which ethanol is more costly or otherwise not available.}, }
@article {pmid41070134, year = {2025}, author = {Li, Q and Liu, F and Zhong, J and Fang, X and Zhang, X and Xiong, H and Li, G and Chen, H}, title = {Multi-cohort metagenomics reveals strain functional heterogeneity and demonstrates fecal microbial load correction improves colorectal cancer diagnostic models.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1656016}, pmid = {41070134}, issn = {1664-302X}, abstract = {INTRODUCTION: Colorectal cancer (CRC) is strongly associated with alterations in the gut microbiome. While numerous studies have examined this association, most focus on genus- or species-level taxonomic classifications, overlooking functional heterogeneity at the strain level.<br><br>METHODS: We integrated 1,123 metagenomic samples from seven global CRC cohorts to conduct multi-level metagenome-wide association studies (MWAS). Fecal microbial load (FML) correction was applied to mitigate technical confounding. We evaluated the performance of taxonomic models at various resolutions strain, species, and genus levels in classifying CRC status both within and across cohorts.<br><br>RESULTS: Strain-level analysis revealed conspecific strains with divergent associations to CRC. For instance, distinct strains of Bacteroides thetaiotaomicron exhibited both protective and risk-increasing effects across different cohorts. Genomic functional annotation suggested potential mechanistic bases for these opposing roles. Correction for FML reduced confounding and significantly improved the performance of within-cohort and cross-cohort CRC classification models. Interestingly, genus- and species-level models demonstrated superior predictive robustness compared to strain-level models, likely due to higher microbial abundance and greater cross-population conservation at these taxonomic ranks.<br><br>CONCLUSION: Our study underscores the biological relevance of strain level analysis in elucidating functional diversity within the microbiome. However, higher taxonomic levels provide more robust and clinically translatable diagnostic markers for CRC. Integrating FML correction with multi-level taxonomic profiling enhances both mechanistic insight into microbiom CRC interactions and the generalizability of diagnostic models across diverse populations.}, }
@article {pmid41070121, year = {2025}, author = {Long, C and Fu, X and Wu, Q and Wang, S and Zhou, X and Mao, J and Guo, L and Shi, W and Yang, H and Yang, T and Du, Y and Yue, J and Wu, D and Liu, H}, title = {Poncirus trifoliata vs. Citrus junos rootstocks: reshaping lemon rhizosphere microecology through microbial and metabolic reprogramming.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1650631}, pmid = {41070121}, issn = {1664-302X}, abstract = {INTRODUCTION: Trifoliate orange (Poncirus trifoliataL. Raf) and "Ziyang Xiangcheng" (Citrus junos Sieb. ex Tanaka) are the predominant rootstocks for lemon production in China, exhibiting distinct adaptations to soil pH and differential impacts on plant resilience. As pivotal mediators of scion-soil interactions, rootstocks have emerged as key research targets for their regulatory potential in rhizosphere microbial communities and metabolites.<br><br>METHODS: Pot-cultured systems were established with lemon (Citrus&#x202f;&#xd7;&#x202f;limon "Eureka") saplings grafted onto trifoliate orange (PTL) and "Ziyang Xiangcheng" (CJL) rootstocks. Integrated metagenomic and GC-MS metabolomic approaches were employed to analyze rhizosphere microbial communities and metabolites.<br><br>RESULTS: The results demonstrated no significant difference in rhizospheric microbial &#x3b1;-diversity (richness) between PTL and CJL, although PTL exhibited higher evenness. &#x3b2;-Diversity and LEfSe analysis revealed significant structural divergence in communities. A total of 15 differentially enriched genera across three phyla were identified, among which Pseudomonas, Cupriavidus, and Burkholderia in CJL, along with Sphingobium in PTL, exhibited strong effects. Random forest modeling identified 15 key differential metabolites, with 4 significantly upregulated in CJL and 11 in PTL. Microbial-metabolite correlation and GSEA analysis uncovered 10 core pathways involving genetic information processing, energy metabolism, environmental adaptation, and disease resistance mechanisms. Soil analysis showed CJL significantly surpassed PTL in organic matter content, catalase activity and plant height, whereas PTL exhibited superior cellulase, sucrase and urease activities. Mechanistically, PTL appears to recruit Pseudomonas mediterranea via 1-Monostearin secretion to activate glycerolipid metabolism, enhancing drought tolerance. Its caffeate and salicyl alcohol-&#x3b2;-glucoside secretions potentially mobilize Sphingobium and Ensifer adhaerens to regulate amino sugar metabolism, promoting carbon sequestration and root defense. Conversely, CJL likely employs L-alanine exudation to recruit Pseudomonas putida, triggering exopolysaccharide biosynthesis through arginine-proline metabolism as a key tolerance mechanism (such as drought tolerance and alkali tolerance).<br><br>DISCUSSION: The findings elucidate rootstock-specific modulation of rhizosphere microecosystems, highlighting distinct microbial-metabolite interactions and tolerance mechanisms. These results provide theoretical support for precision rootstock selection and microbiome engineering to advance sustainable citrus production.}, }
@article {pmid41070117, year = {2025}, author = {He, C and Yang, S and Dong, S and Wang, S and Zhang, P and Yang, Y and Xu, D and Yang, R and Zeng, B and Hu, Y and Zhang, Q}, title = {Fermentation-driven microbial and metabolic shifts in filler tobacco leaves of different grades.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1651289}, pmid = {41070117}, issn = {1664-302X}, abstract = {INTRODUCTION: Filler tobacco leaves (FTLs) serve as the primary raw material for cigar production, and notable differences in physicochemical properties and fermentation responsiveness exist across different grades. However, the underlying mechanisms governing microbial and metabolic evolution during FTL fermentation remain poorly understood. This study systematically investigated the microbial community structures and metabolomic profiles of FTLs of varying grades before and after fermentation using metagenomic sequencing and untargeted metabolomics.<br><br>RESULTS: Metagenomic analysis revealed marked differences in microbial composition among FTL grades at the onset of fermentation. The fermentation process further facilitated the enrichment of functional genera such as Bacillus, Escherichia, and Alternaria, while low-grade FTLs exhibited excessive accumulation of Corynebacterium, potentially contributing to off-flavors and undesirable odors. Untargeted metabolomics identified numerous significantly differential metabolites after fermentation, primarily enriched in pathways related to amino acid biosynthesis, sugar metabolism, and carotenoid biosynthesis. Principal component analysis and hierarchical clustering indicated partial continuity in metabolomic profiles within the same grade before and after fermentation. Correlation analysis further revealed strong positive associations between several dominant genera and flavor-related metabolites.<br><br>CONCLUSION: This study demonstrates that FTLs of different grades exhibit distinct patterns of microbial succession and metabolic remodeling during fermentation. The initial leaf grade plays a pivotal role in shaping microbial communities and metabolite accumulation. These findings offer mechanistic insights into the fermentation process of FTLs and provide theoretical and practical guidance for optimizing raw material grading and fermentation management in the cigar industry.}, }
@article {pmid41070051, year = {2025}, author = {Zhang, Y and Chen, A and Yang, C and Guan, L and Wang, C}, title = {Metagenomic next-generation sequencing assists in diagnosing Pneumocystis Jirovecii pneumonia in non-HIV patients: a case report.}, journal = {Respiratory medicine case reports}, volume = {58}, number = {}, pages = {102289}, pmid = {41070051}, issn = {2213-0071}, abstract = {BACKGROUND: Pneumocystis jirovecii Pneumonia (PJP) is a pulmonary opportunistic fungal infection with an incompletely elucidated pathogenesis. In recent years, non-human immunodeficiency virus (HIV) -infected PJP patients have exhibited rapid progression, poor prognosis, and a greater mortality rate compared to their HIV equivalents, necessitating timely detection and management, which are both critical and problematic.<br><br>CASE REPORT: We report a young patient admitted with diabetic ketoacidosis characterized by rapidly progressing acute respiratory failure with negative pathogen blood cultures, serum antibodies and polymerase chain reaction results, and a normal CD4[+] lymphocyte count. Anti-HIV antibody were negative. A computed tomography scan of the chest revealed patchy opacities in both lower lungs, a nonspecific manifestation. However, metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid detected high Pneumocystis jiroveci sequence counts and a markedly elevated 1,3-&#x3b2;-D-glucan test titer. Following the diagnosis of non-HIV-infected PJP, the patient was discharged after 13 days with a positive outcome, attained through systematic management involving Trimethoprim-sulfamethoxazole anti-infective medication and stringent glycemic control.<br><br>CONCLUSION: Insufficient glucose management may be an important susceptibility factor for immunocompetent persons with non-HIV-infected PJP patients. MNGS serves as an effective method for rapid diagnosis and medication adjustment when signs, symptoms, and imaging findings of PJP are nonspecific.}, }
@article {pmid41069861, year = {2025}, author = {George, C and Dharan, HM and Drescher, L and Lee, J and Qi, Y and Wang, Y and Chang, Y and Teo, SLM and Wainwright, BJ and Yung, C and Lauro, FM and Hazen, TC and Pointing, SB}, title = {Tropical intertidal microbiome response to the 2024 Marine Honour oil spill.}, journal = {Environmental science and ecotechnology}, volume = {28}, number = {}, pages = {100623}, pmid = {41069861}, issn = {2666-4984}, abstract = {Marine fuel oil (MFO) spills in tropical coastal environments are under-characterized despite increasing risk from maritime activities. Microbial and geochemical responses to the June 2024 Marine Honour MFO spill on Singapore's intertidal sediments were analyzed in real time over 185 days. Using metagenomics and hydrocarbon profiling, microbial community shifts and hydrocarbon degradation were quantified across visibly oiled (high-impact) and clean (low-impact) sites. Microbiomes at all sites adapted rapidly to the spill through increased diversity and abundance of genes encoding alkane and aromatic compound degradation, detoxification, and biosurfactant production. The dominant hydrocarbon-degrading bacteria differed markedly from those reported in other crude oil spills and in regions with different climates. Oil deposition intensity strongly influenced microbial succession and hydrocarbon-degrading gene profiles, and this reflected early toxicity constraints in heavily oiled areas. The persistence of hydrocarbon degradation genes beyond hydrocarbon detection in sediments suggested long-term functional priming may occur. The study provides novel genome-resolved insight into the microbial response to MFO pollution, advances understanding of marine environmental biodegradation, and provides urgently needed baseline data for oil spill response strategies in Southeast Asia and beyond.}, }
@article {pmid41069710, year = {2025}, author = {Burakova, I and Smirnova, Y and Gryaznova, M and Morozova, P and Kotarev, V and Lyadova, L and Ivanova, N and Denisenko, L and Syromyatnikov, M}, title = {Effect of interferon on broilers' fecal microbiome composition.}, journal = {Journal of advanced veterinary and animal research}, volume = {12}, number = {2}, pages = {487-496}, pmid = {41069710}, issn = {2311-7710}, abstract = {OBJECTIVE: The purpose of our study was to investigate the effect of chicken interferon on the intestinal microbiota of broiler chickens.<br><br>MATERIALS AND METHODS: The study used next-generation sequencing on the Ion Torrent pragmatic general multicast platform to target the V3 16S ribosomal ribonucleic acid hypervariable region gene, allowing us to analyze in detail changes in the composition of the broiler chicken microbiome.<br><br>RESULTS: Forty-one bacterial genera were identified in the studied groups of broilers. The highest abundance in both groups was observed for Lactobacillus, which was 31.08% &#xb1; 6.52 in the control group and 36.08% &#xb1; 7.25 in the interferon group. There was no clustering between the microbiome communities of the groups studied. We found a decrease or complete absence of Escherichia-Shigella, Eubacterium fissicatena group, Lachnospiraceae CHKCI001, and Pediococcus in the interferon-treated broiler group compared to the control group and an increase in the number of genera Ruminococcaceae CAG-352 and Turicibacter in the interferon group.<br><br>CONCLUSION: A decrease in E.-Shigella may indicate normalization of the intestinal microbiota of broilers, and it can also be concluded that the introduction of interferon helps to suppress opportunistic bacteria. In the interferon group, a sharp increase in the number of Turicibacter was observed. Representatives of this genus are among the most common members in the intestines of broilers.}, }
@article {pmid41069707, year = {2025}, author = {Rubio-Portillo, E and Arias-Real, R and Rodríguez-Pérez, E and Bañeras, L and Antón, J and de Los Ríos, A}, title = {Short-term virus-host interactions and functional dynamics in recently deglaciated Antarctic tundra soils.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf157}, pmid = {41069707}, issn = {2730-6151}, abstract = {Long-term chronosequence studies have shown that, as glaciers retreat, newly exposed soils become colonized through primary succession. To determine the key drivers of this process and their vulnerability to climate change, the short-term responses of these pioneering microbial communities also need to be elucidated. Here, we investigated how the taxonomic and functional structure of microbial communities, including viruses, changed over a 7-year period in an Antarctic glacier forefield. Using metagenomics and metatranscriptomics we assessed the influence of both abiotic and biotic factors on these communities. Our results revealed a highly heterogeneous bacteria-dominated microbial community, with Pseudomonas as the most abundant genus, followed by Lysobacter, Devosia, Cellulomonas, and Brevundimonas. This community exhibited the capacity for aerobic anoxygenic phototrophy, carbon and nitrogen fixation, and sulfur cycling, processes vital for survival in nutrient-poor environments. 52 high-quality metagenome-assembled genomes (MAGs) were recovered, representing both transient and cosmopolitan taxa, some of which were able to rapidly respond to environmental changes. A diverse and highly dynamic collection of lytic and temperate viruses was identified across all samples, with high clonal viral genomes typically detected in only one of the eight samples analyzed. Metatranscriptomic analyses confirmed the activity of lytic viruses, while prophage genomes featured much lower expression levels. Prophages appeared to influence host fitness through the expression of genes encoding membrane transporters. Additionally, the abundance of genes linked to antimicrobial compound synthesis and resistance, along with antiphage defense systems, highlights the importance of biotic interactions in driving microbial community succession and shaping short-term responses to environmental fluctuations.}, }
@article {pmid41069598, year = {2025}, author = {Wang, Z and Lin, X and Wu, J and Su, C and Luo, Y and Yu, G}, title = {Radix Pseudostellaria polysaccharides alleviate sepsis-induced liver injury by modulating the gut microbiota via the TLR4/NF-κB pathway.}, journal = {Frontiers in pharmacology}, volume = {16}, number = {}, pages = {1658147}, pmid = {41069598}, issn = {1663-9812}, abstract = {BACKGROUND: Sepsis-induced liver injury (SLI) is a life-threatening complication with limited therapeutic options. Radix Pseudostellariae polysaccharides (RPPS), a component of traditional Chinese medicine, exert immunomodulatory, anti-inflammatory, and antioxidant properties. Herein, we investigated the therapeutic effects and mechanisms of RPPS on SLI.<br><br>METHODS: A murine sepsis model was established using cecal ligation and puncture. Mice were pretreated with RPPS or saline for 14 days. Subsequently, multi-omics integration-including metagenomics, proteomics, and network pharmacology-was employed to elucidate the mechanisms of RPPS. Liver injury was assessed via serum biomarkers, histopathology, and transmission electron microscopy, while intestinal barrier integrity was evaluated through histopathological analysis. Gut microbiota composition and functional pathways were examined using metagenomic sequencing. Furthermore, Kyoto Encyclopedia of Genes and Genomes enrichment analyses of gut microbiota, liver proteomics, and network pharmacology data were integrated to predict key target pathways, which were experimentally validated in mice.<br><br>RESULTS: RPPS pretreatment significantly improved survival, reduced liver injury markers, attenuated hepatic necrosis and inflammation, and restored intestinal barrier integrity. RPPS also modulated the gut microbiota by enriching beneficial taxa and suppressing pathogens. Multi-omics integration identified the toll-like receptor 4 (TLR4)/nuclear factor kappa-light-chain-enhancer of activated B cells (NF-&#x3ba;B) pathway as the core mechanism, and experimental validation confirmed that RPPS inhibited TLR4 membrane expression, MyD88/IKK&#x3b1;/&#x3b2; activation, NF-&#x3ba;B p65 phosphorylation, and nuclear translocation. In conclusion, RPPS alleviates SLI by protecting the intestinal barrier, modulating gut microbiota, and suppressing the TLR4/NF-&#x3ba;B signaling pathway.<br><br>CONCLUSION: This study provides a scientific foundation for RPPS as a potential therapeutic candidate in sepsis treatment.}, }
@article {pmid41069450, year = {2025}, author = {Chen, W and Yang, P and Hu, J and Liu, X and Jiang, C and Wu, H and Wang, Y and Yan, Q and Lu, S and Xiong, J and Huang, X and Pan, Y and He, F and Chen, Q and Hu, S and Chen, M and Xiong, C}, title = {Echoes in the Deep: Revealing Influenza A Viruses' Persistence and Microbial Associations in Aquatic Ecosystems.}, journal = {Transboundary and emerging diseases}, volume = {2025}, number = {}, pages = {5586400}, pmid = {41069450}, issn = {1865-1682}, mesh = {*Influenza A virus/isolation &amp; purification/genetics/classification ; China/epidemiology ; Animals ; *Seawater/virology/microbiology ; Phylogeny ; Lakes/virology ; Ecosystem ; Humans ; *Water Microbiology ; Fresh Water/virology ; }, abstract = {BACKGROUND: Influenza A viruses (IAVs) are significant pathogens with complex transmission dynamics in aquatic ecosystems, yet their persistence, evolutionary relationships, and associations with environmental microorganisms remain poorly understood. This study aimed to elucidate the phylogenetic characteristics and ecological associations of IAV in freshwater and seawater ecosystems in Eastern China to inform public health strategies.<br><br>METHODS: Water samples were collected from three freshwater lakes and a coastal seawater site. Viral particles were concentrated, and nucleic acids were extracted for metatranscriptomic and metagenomic sequencing. Phylogenetic analyses, population dynamics assessments, and microbial association networks were constructed using bioinformatic tools. Statistical tests, including Tajima's D and Fu and Li's tests, were applied to evaluate evolutionary trends.<br><br>RESULTS: IAV fragments in seawater showed high homology with recent human H3N2 strains from North America (2021-2024), while freshwater-derived fragments aligned with historical avian strains from Asia. Microbial association networks revealed significant associations between IAV and environmental bacteria (e.g., Brevundimonas aurantiaca) and fungi (e.g., Thamnidium), implying potential ecological associations that may underpin viral persistence. Freshwater environments with higher abundances of Uroviricota exhibited more frequent IAV detection. PERMANOVA confirmed distinct overall microbial community compositions in IAV-positive versus IAV-negative samples across both freshwater and seawater ecosystems (p < 0.05).<br><br>CONCLUSION: Aquatic ecosystems, particularly freshwater habitats, may serve as reservoirs for IAV persistence and evolution, driven by complex microbial associations. Regional disparities in viral strain origins highlight the role of migratory waterfowl and environmental transmission routes. Integrated surveillance of aquatic IAV dynamics is critical to anticipate zoonotic risks and mitigate future outbreaks.}, }
@article {pmid41069107, year = {2025}, author = {Ozel, B and Agirman, B and Simsek, O and Erten, H}, title = {Effects of Backslopping on Yeast Diversity and the Volatile Profile of Tarhana.}, journal = {Yeast (Chichester, England)}, volume = {}, number = {}, pages = {}, doi = {10.1002/yea.70003}, pmid = {41069107}, issn = {1097-0061}, support = {//Cukurova University Academic Research Projects Unit (Project no: FDK-2017-7769)./ ; }, abstract = {The primary challenge in tarhana production is the occurrence of spontaneous fermentation, which leads to non-standardized products. Thus, we investigated the effects of backslopping, a traditional method for inoculating fermented foods, on the yeast and volatile aroma compound diversity of tarhana dough. Backslopping fermentations were conducted at different temperatures (25°C and 30°C), pHs (3.70 and 4.00), and inoculation rates (5%, 10%, and 15%). The results revealed that the fermentation temperature and pH significantly influenced the diversity of yeast species and the volatile compound profile of the tarhana dough. However, despite some variations in the PCR-DGGE profiles, the metagenomic analysis revealed that the inoculation rate had minimal effect on yeast diversity, with species diversity remaining relatively constant over the cycles. Kazachstania humilis, Kazachstania bulderi, and Pichia kluyveri were the most prevalent yeast species across all experimental conditions. Pichia membranifaciens was exclusively detected in doughs fermented at 25°C and pH 4.00, whereas Saccharomyces cerevisiae was observed only in doughs fermented at 30°C. Tarhana doughs had a wide range of volatile compounds, the most abundant of which were terpenes and terpenoids, followed by esters, alcohols, aldehydes, and phenols. Doughs fermented at 25°C and pH 3.70 were differentiated from other groups, particularly for their content of esters (e.g., ethyl acetate, ethyl lactate, ethyl decanoate, and ethyl octanoate) and alcohols (e.g., ethyl alcohol, isobutyl alcohol, benzyl alcohol). This study highlights the direct influence of backslopping on yeast diversity and its indirect impact on the aroma profile of tarhana dough, providing insights into the optimization of fermentation conditions for improved product standardization.}, }
@article {pmid41069041, year = {2025}, author = {Koketsu, A and Fukase, S and Tamahara, T and Saito, T and Ito, A and Higashi, Y and Kajita, T and Kurobane, T and Miyakoshi, M and Iikubo, M and Kumada, K and Li, B and Shimada, M and Shimizu, R and Takahashi, T and Yamauchi, K and Sugiura, T}, title = {Bacterial Involvement in Oral Squamous Cell Carcinoma and Potentially Malignant Oral Disorders.}, journal = {Oral diseases}, volume = {}, number = {}, pages = {}, doi = {10.1111/odi.70115}, pmid = {41069041}, issn = {1601-0825}, abstract = {OBJECTIVE: To clarify the relationship between oral squamous cell carcinoma (OSCC), potentially malignant oral disease (OPMD), and bacterial flora using metagenomic analysis.<br><br>METHODS: This cross-sectional observational study included 50 patients in the control group and 77 patients with OPMDs, 41 with early OSCCs, and 20 with advanced OSCCs. Patient saliva samples were subjected to high-throughput sequencing of 16S rRNA gene amplicons to evaluate the composition and diversity of the oral microbiome.<br><br>RESULTS: No significant differences were observed in patient backgrounds, other than sex. Patients with advanced OSCCs had greater oral bacterial diversity than those with early OSCC or OPMD. The advanced OSCC group formed a distinct cluster separate from the other groups. Sixteen and 275 species were identified at the phylum and genus levels, respectively. Compared with the control group, Actinomycetia and Streptococcus were significantly elevated in the early OSCC and OPMD groups. Peptostreptococcus and Fusobacterium were significantly higher in the advanced OSCC group than in the control, OPMD, and early OSCC groups.<br><br>CONCLUSIONS: The composition and diversity of oral microbiota may be associated with OPMD development and progression to OSCC. Consequently, the salivary microbiome may serve as a biomarker for oral cancer and help predict cancer progression.}, }
@article {pmid41068938, year = {2025}, author = {Xu, J and Chen, X and Ren, J and Xu, J and Zhang, L and Yan, F and Liu, T and Zhang, G and Huws, SA and Yao, J and Wu, S}, title = {Multi-omics insights into microbiome-rumen epithelium interaction mechanisms underlying subacute rumen acidosis tolerance in dairy goats.}, journal = {Genome biology}, volume = {26}, number = {1}, pages = {345}, pmid = {41068938}, issn = {1474-760X}, support = {32272829//National Natural Science Foundation of China/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024-KFKT-031//National Center of Technology Innovation for Dairy/ ; }, mesh = {Animals ; *Goats/microbiology ; *Rumen/microbiology/metabolism ; *Acidosis/veterinary/microbiology/metabolism ; *Gastrointestinal Microbiome ; Epithelium/metabolism/microbiology ; Fatty Acids, Volatile/metabolism ; Female ; *Goat Diseases/microbiology ; Hydrogen-Ion Concentration ; *Microbiota ; Transcriptome ; Multiomics ; }, abstract = {BACKGROUND: To address rising demand for dairy products, dairy goats are often fed high-concentrate diets, which lead to subacute rumen acidosis (SARA). The mechanisms behind individual variation in SARA tolerance are not well understood. This study aims to elucidate roles of rumen microbiome-host interactions in SARA-susceptibility and tolerance.<br><br>RESULTS: Goats susceptible or tolerant to SARA were selected by feeding diets with different levels of rumen degradable starch. SARA-susceptible goats present prolonged periods of rumen pH below 5.8 and volatile fatty acids (VFAs) accumulation. Metagenomic analysis reveals a decrease in cellulose- and hemicellulose-utilizing bacteria and enzymes, along with increased lysozymes, suggesting disrupted rumen homeostasis. Transcriptomic and single-nucleus transcriptome analyses reveal upregulated Th17 cells, IL-17 signalling, and inflammatory pathways in SARA-susceptible goats. In contrast, SARA-tolerant goats maintain stable pH levels and enhance VFAs absorption. Bifidobacterium adolescentis and other beneficial bacteria are enriched in the rumen of SARA-tolerant goats. These microbes are positively correlated with 3-methyl pyruvic acid, a key metabolite involved in branched-chain amino acid synthesis and epithelial cell proliferation. Both microbiome transplantation and B. adolescentis direct feeding experiments confirm the protective effects of SARA-tolerant microbiota including B. adolescentis, promoting rumen epithelial VFAs absorption and reducing ruminal inflammation.<br><br>CONCLUSIONS: This study highlights the importance of Th17-mediated immune responses in ruminal inflammation and the role of B. adolescentis in regulating rumen epithelial VFAs absorption. Modulating VFAs absorption in the rumen epithelium represents a promising strategy for improving animal health and enhancing rumen fermentation efficiency.}, }
@article {pmid41068590, year = {2025}, author = {Chen, Y and Miao, Q and Bao, R and Qu, H and Shen, J and Li, N and Luan, S and Yin, X and Pan, J and Hu, B}, title = {Distinct lung microbiota community states are associated with pulmonary nontuberculous mycobacterial disease prognosis.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {653}, pmid = {41068590}, issn = {1471-2180}, support = {2023ZSLC24//Zhongshan Hospital/ ; }, mesh = {Humans ; Male ; *Microbiota ; Female ; *Mycobacterium Infections, Nontuberculous/microbiology/diagnosis ; *Lung/microbiology ; Prognosis ; Middle Aged ; Bronchoalveolar Lavage Fluid/microbiology ; Aged ; *Nontuberculous Mycobacteria/genetics/isolation &amp; purification/classification ; Bacteria/classification/genetics/isolation &amp; purification ; Metagenomics ; Adult ; }, abstract = {BACKGROUND: The incidence of nontuberculous mycobacterial pulmonary disease (PNTM) is rising, but the available treatments have limitations. Currently, the understanding of the ecology of the airway microbiota in PNTM is limited, especially regarding community structure, dynamics, and their relationship with clinical outcomes.<br><br>METHODS: We used metagenomic sequencing to characterize the lung microbiota in bronchoalveolar lavage fluid (BALF). We evaluated the prognosis of patients with PNTM through respiratory specimen cultures and chest CT scans.<br><br>RESULTS: PNTM exhibit distinct airway microbiota characteristics compared to controls, however, no significant differences were observed in NTM species. A Dirichlet multinomial mixture model was used to identify two distinct community types (pneumotypes) and investigate their association with host immunity and prognosis. At the 13-month median follow-up, pneumotype 1 (including Mycobacterium, opportunistic pathogens, and anaerobes) presented a lower probability of sustained culture conversion (hazard ratio&#x2009;=&#x2009;0.29; 95% confidence interval&#x2009;=&#x2009;0.12-0.73; P&#x2009;=&#x2009;0.009) than pneumotype 2, indicating a worse prognosis. Based on microbial community abundance and interactions, Ralstonia (NetMoss score&#x2009;=&#x2009;1.0; log2FoldChange&#x2009;=&#x2009;3.6) and Dolosigranulum (NetMoss score&#x2009;=&#x2009;0.6; log2FoldChange&#x2009;=&#x2009;1.4) emerged as prominent taxa associated with the shift from pneumotype 1 to pneumotype 2, which correlated with differences in clinical outcomes.<br><br>CONCLUSION: Our research indicates that distinct baseline microbial characteristics in PNTM patients are associated with prognosis. Furthermore, we identified candidate microbes driving changes in the PNTM microbial community state, serving as potential therapeutic targets.}, }
@article {pmid41068306, year = {2025}, author = {Shin, AS and Xing, Y and Waseem, MR and Siwiec, R and James-Stevenson, T and Rogers, N and Bohm, M and Wo, J and Lockett, C and Gupta, A and Kadariya, J and Toh, E and Anderson, R and Dong, A and Xu, H and Gao, X}, title = {Microbiota and short chain fatty acid relationships underlie clinical heterogeneity and identify key microbial targets in irritable bowel syndrome (IBS).}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {35375}, pmid = {41068306}, issn = {2045-2322}, support = {K23DK122015/DK/NIDDK NIH HHS/United States ; R03DK132446/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Irritable Bowel Syndrome/microbiology/metabolism ; Female ; *Gastrointestinal Microbiome ; Male ; *Fatty Acids, Volatile/metabolism ; Feces/microbiology/chemistry ; Adult ; Middle Aged ; Bile Acids and Salts/metabolism ; Constipation/microbiology ; Metagenome ; Diarrhea/microbiology ; Bacteria/classification/genetics/metabolism ; }, abstract = {Short chain fatty acids (SCFA) are key microbial metabolites that modulate intestinal homeostasis and may influence irritable bowel syndrome (IBS) pathophysiology. We aimed to assess microbial features associated with SCFA and determine if features varied across IBS subtypes and endophenotypes. We analyzed stool microbial metagenomes, stool SCFA, and measurable IBS traits (stool bile acids, colonic transit, stool form) in 41 patients with IBS (IBS with constipation [IBS-C] IBS with diarrhea [IBS-D]) and 17 healthy controls. We used partial canonical correspondence analyses (pCCA), conditioned on transit, to quantify microbe-SCFA associations across groups. We further compared gut microbiome-encoded potential for substrate utilization across groups and within a subset of participants selected by their stool characteristics as well as stool microbiomes of patients with and without clinical bile acid malabsorption (BAM). Microbe-SCFA associations differed across groups and revealed key taxa including Dorea sp. CAG:317 and Bifidobacterium pseudocatenulatum in IBS-D and Akkermansia muciniphila and Prevotella copri in IBS-C that that could underlie subtype-specific microbially-mediated mechanisms. The greatest number of microbe-SCFA associations were observed in IBS-D. Several SCFA-producing species demonstrated inverse correlations with SCFA. Fewer bacterial taxa were associated with acetate to butyrate ratios in IBS compared to health. In participants selected by stool form, we demonstrated differential abundances of microbial genes/pathways for SCFA metabolism and degradation of carbohydrates and mucin across groups. SCFA-producing taxa were reduced in IBS-D patients with BAM. Keystone taxa responsible for SCFA production differ by IBS subtype and traits. IBS microbiomes appear exhibit reduced functional redundancy. Differences in substrate preferences are also linked to bowel functions. Focusing on taxa that drive SCFA profiles and stool form may be a rational strategy for identifying relevant microbial targets in IBS.}, }
@article {pmid40704526, year = {2025}, author = {Capps, B and Chadwick, R and Joly, Y and Lajaunie, C and Hauptmannova, I and Mackenzie, S and Mulvihill, JJ and Mumford, E and Rasmussen, SA and Sanghavi, K and Thaldar, DW and Yeates, J and Quinzin, MC and Lederman, Z}, title = {The Ecological Genome Project and the Promises of Ecogenomics for Society: Realising a Shared Vision as One Health.}, journal = {Bioethics}, volume = {39}, number = {9}, pages = {788-795}, doi = {10.1111/bioe.70020}, pmid = {40704526}, issn = {1467-8519}, mesh = {Humans ; *One Health/ethics ; *Genomics/ethics ; *Ecology/ethics ; *Metagenomics/ethics ; *Ecosystem ; }, abstract = {This paper develops a vision for The Ecological Genome Project: an aspirational, global endeavour to connect human genomic sciences with the ethos of ecological sciences. The Project's goal is to strengthen interdisciplinary networks that relate to diverse initiatives using genomic technologies, with respect to shared ethical frameworks and governance structures. To this end, this paper proposes a practical definition of ecogenomics to align various methodologies and values in a single environmental field using principles used to safeguard all forms of life in their habitats. We achieve this by using a One Health approach as a pretext for disparate disciplines to collaborate and also a lens to view the Ethical, Legal and Social Implications (ELSI) inherent in ecological systems.}, }
@article {pmid41068233, year = {2025}, author = {Giovannini, N and Limena, A and Ercolino, C and Renteria, SCU and Strati, F and Giuffrè, MR and Maragno, P and Carbone, IF and Facciotti, F and Ceriotti, F and Ferrazzi, E and Lattuada, D}, title = {Nasopharyngeal and oral microbiota profiling in SARS-CoV-2 infected pregnant women.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {35306}, pmid = {41068233}, issn = {2045-2322}, mesh = {Humans ; Female ; Pregnancy ; *COVID-19/microbiology/virology ; *Nasopharynx/microbiology ; Adult ; *Microbiota ; *Mouth/microbiology ; SARS-CoV-2/isolation &amp; purification ; *Pregnancy Complications, Infectious/microbiology/virology ; }, abstract = {Variations have been found in the upper respiratory tract microbiota in SARS-CoV-2 positive patients compared to healthy subjects, with different dominant species and diversity indexes detected, including a decrease in biodiversity and an increased abundance of bacterial pathogens. Moreover, these discrepancies were observed in patients with both mild and severe symptoms. Notably, the inflammatory state appears to be significantly influenced by the characteristics of the indigenous microbiota. This is particularly interesting in pregnant patients, as pregnancy involves an adaptive adjustment of the microbiota due to hormonal changes aimed at providing immune protection. The relationship between the microbiota of pregnant women and SARS-CoV-2 has not been deeply explored so far. The purpose of the present study is to investigate the relationship between SARS-CoV-2, nasopharyngeal and oral microbiota, and pregnancy. To our knowledge this is the first simultaneous investigation on both nasopharyngeal and oral microbiota in SARS-Cov-2 infected pregnant women. In this study, the nasopharyngeal and oral microbiota were analysed in 43 women in their third trimester of pregnancy enrolled from April 2020 to February 2021. The differential abundance of taxa was tested and alpha and beta diversity were evaluated. SARS-CoV-2 infected pregnant women showed an alteration of the nasopharyngeal and oral microbiota compared to healthy pregnant women. In both the nasopharyngeal and oral microbiota of the SARS-CoV-2 infected pregnant women, we found a variation in taxa, represented by an enrichment of pathobionts, which increased particularly with the severity of symptoms. Specifically, a significant reduction in microbial biodiversity has been identified within the nasopharyngeal microbiota of SARS-CoV-2 positive women. Furthermore, enrichment in pathobionts was noted in both asymptomatic and symptomatic women, with these changes being more pronounced in the nasopharyngeal microbiota compared to the oral one. The nasopharyngeal microbiota of asymptomatic and symptomatic SARS-CoV-2 infected women showed an enrichment of pathogens and pathobionts such as Corynebacterium, Fusobacterium, Neisseria, Streptococcus, Haemophilus, Mycobacterium and Porphyromonas compared with the control group. The oral microbiota showed an enrichment of pathobionts such as Neisseria, Fusobacterium and Streptococcus. A random forest classifier applied to metagenomic data from nasopharyngeal and oral swabs showed that the nasopharyngeal microbiota is the best sampling site to predict the patients' SARS-CoV-2 infection status. Gulbenkiania, Burkholderia and Actinomyces, all taxa significantly enriched in the control group compared to SARS-CoV-2 infected women, were the most important features selected by the classifier. Finally, correlations between the nasopharyngeal and oral microbiota and clinical parameters of pregnant women, particularly BMI and procalcitonin, were observed. SARS-CoV-2 infected pregnant women showed an alteration of the nasopharyngeal and oral microbiota compared to healthy pregnant women. We found a variation in taxa, represented by the enrichment of pathobionts in both the nasopharyngeal and oral microbiota of SARS-CoV-2 infected pregnant women, particularly increased in symptomatic individuals. The nasopharyngeal microbiota appears to be a better predictor of SARS-CoV-2 infection and its severity than the oral microbiota.}, }
@article {pmid41068119, year = {2025}, author = {Liu, S and Feng, B and Zhang, Z and Miao, J and Lai, X and Zhao, W and Xie, Q and Ye, X and Cao, C and Yu, P and Sun, J and Guo, J and Wang, Z and Wang, Q and Zhang, Z and Pan, Y}, title = {UPGG: expanding the taxonomic and functional diversity of the pig gut microbiome with an enhanced genome catalog.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {196}, pmid = {41068119}, issn = {2055-5008}, support = {LZ23C170003//Zhejiang Provincial Natural Science Foundation of China/ ; LZ23C170003//Zhejiang Provincial Natural Science Foundation of China/ ; 2021YFD1200802,2023YFF1001100//National Key Research and Development Program of China/ ; 2021YFD1200802,2023YFF1001100//National Key Research and Development Program of China/ ; 32272832//National Natural Science Foundation of China/ ; 32272832//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Swine/microbiology ; *Bacteria/genetics/classification/isolation &amp; purification ; *Archaea/genetics/classification/isolation &amp; purification ; Metagenome ; *Genome, Bacterial ; Interspersed Repetitive Sequences ; Phylogeny ; Metagenomics ; }, abstract = {The porcine gut microbiome is crucial for pig health and key to its production performance. However, genome-level analysis across multiple kingdoms remains limited. Here, we reconstructed the unified pig gastrointestinal genome (UPGG), including bacterial, archaeal, and annotated over 78 million non-redundant protein-coding genes using 5784 metagenome samples. We identified antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), and the distribution of 72,056 metabolic gene clusters within existing populations. We have constructed pan-genomes of 436 high-quality microbial species and, using these as references, discovered intraspecies genomic variations that revealed 23,350,975 single-nucleotide variants (SNVs). Finally, through comparative analysis of gut microbiome genomes conducted in this study, we observed that pigs may serve as a more suitable model than other animals for investigating human gut microbiota composition and functional patterns. In summary, we constructed a comprehensive reference catalog of the porcine gut microbiome and enhanced the understanding of the host-microbe coevolution.}, }
@article {pmid41068096, year = {2025}, author = {Wu, Y and Ji, G and Han, D and Zhang, Y and Zhu, X and Li, H and Li, M and Gao, Y and Xie, R and Xu, M and Lu, L and Deng, Z and Wei, Q and Qin, H and Bi, D}, title = {Fusobacterium lineage profiling facilitates the clarification of the associations between non-nucleatum Fusobacterium and colorectal cancer.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {197}, pmid = {41068096}, issn = {2055-5008}, support = {82072634//National Natural Science Foundation of China/ ; 82072236//National Natural Science Foundation of China/ ; SHDC2020CR2069B//Shanghai Municipal Hospital Development Center/ ; ZJ2022-ZD-005//Major Projects of Special Development Funds in Zhangjiang National Independent Innovation Demonstration Zone, Shanghai/ ; }, mesh = {*Colorectal Neoplasms/microbiology ; Humans ; *Fusobacterium/genetics/classification/isolation &amp; purification/pathogenicity ; Feces/microbiology ; *Fusobacterium Infections/microbiology ; Male ; Female ; Fusobacterium nucleatum/genetics ; Real-Time Polymerase Chain Reaction ; Middle Aged ; Aged ; Metagenomics ; }, abstract = {Non-nucleatum Fusobacterium may play a nonnegligible role in colorectal cancer (CRC) and certain Fusobacterium lineages (namely, L1 and L5) have shown specific associations with CRC. We aim to clarify the complex connections between Fusobacterium and CRC. We found that the widely adopted quantitative PCR (qPCR) method could overestimate F. nucleatum abundance and, in fact, reflect L1 levels in clinical samples. A lineage-specific qPCR assay targeting L1/L5 was developed and validated using mock and clinical samples. Its application in independent cohorts confirmed that L1 was overabundant in CRC, whereas L5 correlated with lymphovascular invasion. Importantly, faecal L1 abundance was more predictive of CRC than F. nucleatum, supported also by cross-population metagenomic data. CRC-associated virulence and colonisation genes were found in various L1 species other than F. nucleatum. Our results highlight the clinical importance of L1/L5 in CRC with high-diversity Fusobacterium contexts and suggest that non-nucleatum Fusobacterium may also contribute to CRC.}, }
@article {pmid41067450, year = {2025}, author = {Liu, N and Zhang, Y and Zhang, Y and Yang, Y and Long, H and Huang, A and Zeng, Y and Xie, Z}, title = {Quorum sensing mediates spatiotemporal microbial community dynamics and nitrogen metabolism in biofloc-based Litopenaeus vannamei aquaculture systems.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {133459}, doi = {10.1016/j.biortech.2025.133459}, pmid = {41067450}, issn = {1873-2976}, abstract = {Biofloc technology (BFT) enables sustainable aquaculture by leveraging microbial communities to enhance water quality and nutrient cycling. However, the role of quorum sensing (QS) in regulating microbial dynamics and metabolic functions within BFT systems remains poorly understood. This study examined how QS spatiotemporally regulates microbial succession and nutrient metabolism in a biofloc-based Litopenaeus vannamei aquaculture system over 82 days culture. Ammonia and nitrite concentrations shifted through four phases: initial (IP), rising (RP), declining (DP), and stabilization (SP). Notably, nitrite levels decreased rapidly from 1.21 mg/L to 0.03 mg/L during DP. Metagenomic analysis revealed Pseudomonadota, Actinomycetota, and Bacteroidota as the consistently dominant phyla, while dominant genera shifted over time. QS pathways displayed temporal heterogeneity: acyl-homoserine lactones (AHLs) and autoinducer-2 (AI-2) predominated during IP, whereas aromatic hydrocarbon kinases (AHKs) and cyclic dimeric guanosine monophosphate (c-di-GMP) were more enriched during SP. KEGG analysis indicated that nitrogen metabolism genes were more abundant in bioflocs than in the water. Genes associated with dissimilatory nitrate reduction and denitrification were significantly more abundant than those involved in other nitrogen metabolic processes (p < 0.05). Furthermore, QS signaling coordinated the complex interaction networks among 30 dominant bacterial genera (e.g., Amaricoccus and Ruegeria) involved in carbon, nitrogen, and sulfur metabolism, which is crucial for maintaining the stability and functionality of the biofloc system. This study elucidates the mechanisms through which microbial signaling orchestrates efficient nitrogen removal and sustains system stability, thereby providing a foundation for developing targeted bioaugmentation strategies to enhance sustainable aquaculture practices.}, }
@article {pmid41067299, year = {2025}, author = {Feng, Y and Yuan, Q and Kang, Y and Zheng, M and Li, Z}, title = {Deciphering the mobility, pathogenic hosts, and co-selection of antibiotic resistance genes in untreated wastewater from three different hospitals.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {}, number = {}, pages = {105840}, doi = {10.1016/j.meegid.2025.105840}, pmid = {41067299}, issn = {1567-7257}, abstract = {OBJECTIVE: Antibiotic resistance genes (ARGs) in hospital wastewater pose significant environmental and public health risks, yet the co-selection mechanisms involving metal/biocide resistance genes (MRGs/BRGs) and the role of mobile genetic elements (MGEs) remain poorly characterized. This study aimed to comprehensively assess the abundance, mobility, pathogenic hosts, and co-selection patterns of ARGs, MRGs, and BRGs in untreated wastewater from three types of hospitals.<br><br>METHODS: Untreated wastewater samples from nine sources across three hospital types (general, traditional Chinese medicine, and dental) were analyzed using metagenomic sequencing and assembly. ARGs, MRGs, and BRGs were identified via the SARG and BacMet databases. ARG hosts, mobility, and MGE co-occurrence were analyzed using PlasFlow and MOB-suite, with risk levels evaluated alongside pathogenic bacteria databases.<br><br>RESULTS: A total of 1911 ARGs (222 subtypes), 1662 MRGs (167 subtypes), and 916 BRGs (139 subtypes) were detected. Tetracycline, multidrug, and &#x3b2;-lactam resistance genes were predominant, with 46.43&#x202f;% of ARGs being plasmid-associated. Key pathogens including Klebsiella pneumoniae and Enterococcus spp. harbored high-risk ARGs such as KPC-2 and NDM-1. Notably, 76.2&#x202f;% of ARGs in traditional Chinese medicine hospital wastewater were classified as high-risk. Significant co-occurrence of ARGs with MGEs (e.g., DDE recombinases) and MRGs/BRGs was observed, underscoring the role of horizontal gene transfer and co-selection.<br><br>CONCLUSION: Untreated hospital wastewater represents a significant reservoir of ARGs, with risks exacerbated by pathogenic hosts, MGE-mediated HGT, and metal/biocide co-selection. These findings underscore the urgent need for optimized wastewater treatment strategies to curb the spread of antibiotic resistance and inform future intervention efforts.}, }
@article {pmid41067045, year = {2025}, author = {Li, LH and Pabst, M and van Loosdrecht, MCM and Pronk, M}, title = {Distinct roles of granules and flocs in aerobic granular sludge processes.}, journal = {Water research}, volume = {288}, number = {Pt B}, pages = {124671}, doi = {10.1016/j.watres.2025.124671}, pmid = {41067045}, issn = {1879-2448}, abstract = {Aerobic Granular Sludge (AGS) is an innovative and efficient biotechnology for wastewater treatment that has been successfully applied on full-scale worldwide. Full-scale municipal AGS systems typically contain both granular sludge (granules) and flocculent sludge (flocs). Studies on the different roles of granules and flocs remain limited. In this study, a laboratory-scale AGS reactor fed with complex synthetic wastewater was operated to simulate full-scale AGS systems and to study the different functional roles of granules and flocs. The laboratory reactor achieved a coexistence of granules and flocs with a floc mass fraction of 17 %. The activities of different size fractions were evaluated using batch experiments and compared for carbon, nitrogen, and phosphorus removal: flocs (FL; <0.2 mm), small granules (SG; 0.2∼1.0 mm), medium granules (MG; 1.0∼2.0 mm), and large granules (LG; >2.0 mm). During feeding, large granules and medium granules exhibited more substrate uptake than small granules and flocs due to preferential substrate access. For aerobic conversion, flocs and small granules showed higher biomass-specific nitrification rates, while medium granules and large granules showed higher phosphorus uptake and denitrification capacity. Furthermore, large granules and medium granules showed stronger mass transfer limitation of oxygen, which limits their nitrification capability. Microbial community analysis using metagenomics and metaproteomics was performed across size fractions, and distinct communities in granules and flocs were shown. Granules showed a high abundance of Candidatus Accumulibacter (polyphosphate-accumulating organisms, PAOs) and Candidatus Competibacter (glycogen-accumulating organisms, GAOs). Flocs showed a high abundance of Nitrosomonas (ammonium-oxidizing bacteria, AOB) and Tetrasphaera (fermentative PAOs) and a low abundance of Ca. Accumulibacter. The distribution of microbial activities and microbial community over sludge size fractions in the laboratory reactor is similar to full-scale AGS systems, indicating that this laboratory setup can simulate full-scale systems and can be used for future research. Overall, this study highlights the importance of maintaining a good balance between different granule sizes and flocs to optimize nutrient removal.}, }
@article {pmid41067043, year = {2025}, author = {Xu, D and Liu, T and Fan, J and Chen, W and Li, Y and Zhang, M and Zheng, P and Guo, J}, title = {Mechanical resistance of higher EPS contents in larger granules restricts anammox bacterial growth.}, journal = {Water research}, volume = {288}, number = {Pt B}, pages = {124705}, doi = {10.1016/j.watres.2025.124705}, pmid = {41067043}, issn = {1879-2448}, abstract = {Extracellular polymeric substances (EPS) are core granular components, playing critical roles in its structural stability. However, little is known about the effect of EPS on bacterial growth due to physical and mechanical resistances posed by EPS matrix. Herein, anaerobic ammonium oxidation (anammox) granules with different sizes and EPS contents were collected from a full-scale plant. Using [13]C isotope labelling and qPCR assays, we confirmed that larger granules with higher EPS content exhibited the higher maximum nitrogen removal activity but much lower bacterial growth yield, resulting in a significantly lower maximum specific growth rate (-26.8%), compared to smaller granules. Metagenomic sequencing revealed that anammox species were identical in different granules, and actual EPS production yields were similar in 15-day incubation, ruling out the possibility that more energy was diverted to produce additional EPS in larger granules. Interestingly, the EPS mechanical strength was significantly greater in large granules, which reduced cell membrane fluidity and severely deformed bacterial cells. These mechanical constraints imposed by the dense EPS matrix limited anammox bacterial proliferation and reduced their growth yield. Using low-intensity ultrasound to loosen EPS structure improved the growth yield of anammox bacteria in large granules, while also enhancing nitrogen removal activity. These together contributed to a substantial increase in bacterial growth rate (+153.3%). The findings highlight that physical and mechanical resistance imposed by EPS plays a previously overlooked role in bacterial growth, and provide the basis for promoting anammox bacterial proliferation within granules.}, }
@article {pmid41066987, year = {2025}, author = {Zhang, C and Zhang, Y and Diao, G and Hou, N and Zhao, X and Li, D}, title = {Decoding pyrene-induced reactive oxygen species production in the rhizosphere and their role in biodegradation: The repair mechanism of symbiotic driving by Fe(II) and microorganisms.}, journal = {Journal of hazardous materials}, volume = {499}, number = {}, pages = {140073}, doi = {10.1016/j.jhazmat.2025.140073}, pmid = {41066987}, issn = {1873-3336}, abstract = {Reactive oxygen species (ROS) are considered key drivers of biogeochemical processes. However, there is limited research on the factors influencing ROS generation in the rhizosphere due to polycyclic aromatic hydrocarbon (PAHs) pollution during plant-microbe joint remediation, as well as their role in biodegradation. This study demonstrated that exposure to pyrene at a concentration of 100 mg/kg significantly enhanced the release of hydrogen peroxide (H2O2), hydroxyl radicals (•OH), and superoxide anions (O2•[-]) in the rhizosphere of ryegrass during root development. The concentrations of these reactive oxygen species were 1.5-7.8 times higher than those in the control group. Additionally, the Fe(II) concentration increased by 37.5 ± 3.2 %, and the pyrene degradation rate reached 26.8 ± 1.4 %. These results indicate that pyrene serves as a major factor stimulating ROS generation in ryegrass. Among these processes, Fe(II) catalyzes the production of •OH, which directly attacks the benzene ring structure of pyrene. High-throughput analysis further revealed that ROS enhanced the diversity, cohesion, and robustness of the rhizosphere microbial community structure. Furthermore, Pseudomonas, Marmoricola, Nocardioides and Dietzia were identified as core microbial genera involved in pyrene degradation and ecological restoration. Metagenomics analysis suggests that rhizosphere microorganisms respond to ROS-induced oxidative stress by enhancing ATP synthesis, which provides energy for antioxidant-related protein production and damage repair, thereby accelerating pyrene degradation. These results elucidate the ROS-mediated driving mechanism behind microbial pyrene degradation in plant-microbe combined remediation systems, thereby providing a theoretical basis for optimizing bioremediation strategies for organically contaminated soils.}, }
@article {pmid41066873, year = {2025}, author = {Hou, J and Liu, M and Li, Y and Li, L and Yao, Y and Xu, H and An, Y}, title = {Seed-borne and environmental transmission mechanisms drive diverse heavy metal-resistant plant growth-promoting bacteria (PGPB) in rice.}, journal = {Environment international}, volume = {204}, number = {}, pages = {109840}, doi = {10.1016/j.envint.2025.109840}, pmid = {41066873}, issn = {1873-6750}, abstract = {Heavy metal-resistant plant growth-promoting bacteria (PGPB) play a crucial role in mitigating heavy metal stress and reducing heavy metal accumulation in plants. However, the origins and transmission mechanisms of PGPB and their associated heavy metal resistance genes (MRGs) in plants remain unclear. To fill this knowledge gap, we collected rice and related environmental samples from heavy metal-contaminated paddy fields. The microbial DNA was recovered from these rice and environmental samples and then analyzed using shotgun metagenomics at the metagenome-assembled genomes (MAGs) level. As a result, 805 MRG-PGPB combinations were detected in rice tissues and related environments under heavy metal contamination conditions. Core MRG-PGPB combinations shared across seed-rice (42.46%) and environment-rice (13.34%) interfaces collectively constituted 55.80% of the detected combinations, demonstrating that environmental translocation and seed-borne vertical transmission jointly drive over half of MRG-PGPB colonization in rice systems. Subsequent source-tracking analysis indicated that PGPBs present in rice primarily originated from seeds, with a substantial proportion also attributed to translocation within rice tissues. Phylogenetic analysis of dominant MRGs further demonstrated the seed-borne vertical transmission of MRGs-PGPB, while simultaneously elucidating that MRGs harbored by PGPB in rice could also be acquired via horizontal gene transfer (HGT) from environmental or seed-borne MRG-PGPB, particularly from atmospheric microbes such as Methylophilus and Serratia. These findings provide valuable insights into harnessing PGPB to enhance rice resilience against heavy metal contamination, thereby contributing to improved food security and sustainable agricultural practices.}, }
@article {pmid41066697, year = {2025}, author = {Li, Y and Gao, Y and Liu, X and Mao, Y and Wang, M and Qin, Y and Zhang, C and Chen, Q and Ning, K and Wang, Z and Han, M}, title = {Quantifying antibiotic resistome risks across environmental niches: the L-ARRAP for long-read metagenomic profiling.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {5}, pages = {}, doi = {10.1093/bib/bbaf535}, pmid = {41066697}, issn = {1477-4054}, support = {82300645//National Natural Science Foundation of China/ ; 41877409//National Natural Science Foundation of China/ ; U23A2059//National Natural Science Foundation of China/ ; 2408085Y039//Outstanding Youth Program of Anhui Provincial Natural Science Foundation/ ; YQZD202406//Key Project for cultivating outstanding young teachers of Higher Education in Anhui Province/ ; tsqn202312094//Taishan Scholars Program of Shandong Province/ ; 2023KJ034//Shandong Provincial Higher Education Institution Youth Innovation Teams/ ; XJ201916//Grants for Scientific Research of BSKY/ ; 2022zhyx-B15//Anhui Medical University, Research Fund of Anhui Institute of translational medicine/ ; }, mesh = {Humans ; *Metagenomics/methods ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; *Metagenome ; Risk Assessment ; Wastewater/microbiology ; *Drug Resistance, Bacterial/genetics ; *Bacteria/genetics/drug effects ; Feces/microbiology ; }, abstract = {The global dissemination of antibiotic resistance genes (ARGs) represents a critical challenge to One Health. Existing ARG risk assessment tools (e.g. MetaCompare, ARRI) are constrained by short-read sequencing data, limiting their utility for long-read platforms. To address this gap, we developed the Long-read based Antibiotic Resistome Risk Assessment Pipeline (L-ARRAP), which calculates the Long-read based Antibiotic Resistome Risk Index (L-ARRI) to quantify antibiotic resistome risks. Building upon our previous ARRI framework, L-ARRAP leverages long-read sequencing advantages to concurrently identify ARGs, mobile genetic elements, and human bacterial pathogens, integrating their interactions for risk scoring. Our results showed that L-ARRAP was not only able to accurately identify ARGs and evaluate the antibiotic resistance risk scores in samples of hospital wastewater (HWW), Chaohu lake, and human fecal samples, but also significantly distinguish the ARG risk in HWW samples between before and after disinfection groups, demonstrating the performance of L-ARRAP. Furthermore, L-ARRAP scores exhibited strong concordance with those generated by our laboratory-adapted MetaCompare variant (L-MetaCompare), corroborating its methodological reliability. Overall, to our knowledge, L-ARRAP is the first assessment pipeline of antibiotic resistome for long sequencing reads and has a great potential for monitoring the risk of ARGs in various environmental niches.}, }
@article {pmid41066275, year = {2025}, author = {Mutafcilar Velioglu, E and Arslan, U and Kayis, SA and Maçin, S and Kamada, N and Hakki, S}, title = {Correlation in the change of gut microbiota with clinical periodontal parameters in grade C periodontitis patients after non-surgical periodontal therapy.}, journal = {Journal of medical microbiology}, volume = {74}, number = {10}, pages = {}, doi = {10.1099/jmm.0.002065}, pmid = {41066275}, issn = {1473-5644}, mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; *Periodontitis/therapy/microbiology ; Middle Aged ; Adult ; Saliva/microbiology ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; Dysbiosis/microbiology ; }, abstract = {Introduction. Intestinal dysbiosis is associated with systemic health, and approaches targeting the microbiome can influence the host. Oral and intestinal microbiota are interrelated; therefore, we aimed to determine whether non-surgical periodontal treatment (NSPT) affects systemic health through its impact on the intestinal microbiota.Hypothesis/Gap Statement. Although the association between oral and gut microbiota has been suggested, there is limited evidence regarding how periodontal therapy may influence intestinal microbial composition. We hypothesized that NSPT in patients with periodontitis would lead to favourable changes in the gut microbiome, which may parallel improvements in clinical periodontal parameters.Aim. This study aimed to investigate the effect of NSPT on both oral and intestinal microbiota and to evaluate whether changes in gut microbial composition correlate with periodontal clinical outcomes.Methodology. Five systemically healthy individuals with grade C periodontitis and five systemically and periodontally healthy individuals were included. Saliva and stool samples were collected at baseline and 1 month after NSPT. DNA extractions were performed and subjected to 16S ribosomal RNA gene sequencing on the Illumina Novaseq at the V3-V4 hypervariable regions.Results. Grade C periodontitis patients displayed distinct oral and gut microbiomes compared to healthy individuals. NSPT resulted in a reduction in the diversity of both saliva and stool samples in healthy individuals (P>0.05). Salivary Fusobacteriota levels (P<0.05) and the gut Firmicutes/Bacteroides ratio decreased after NSPT. Moreover, changes in gut microbiota significantly correlated with improvements in periodontal probing depth and clinical attachment level in periodontitis patients.Conclusion. The improvement in clinical periodontal parameters after NSPT correlates with a positive shift in the gut microbiome towards health. Although the number of participants was limited, these findings support a strong relationship between periodontal and gut status. Further studies with larger cohorts and long-term follow-up are required to confirm these results.}, }
@article {pmid41066239, year = {2025}, author = {Cook, RA and Ponsero, AJ and Telatin, A and Yang, Y and Liang, Z and Wang, F and Chen, R and Wang, Z and Adriaenssens, EM and Clokie, MRJ and Millard, AD and Brightling, CE}, title = {Bacteriophage diversity declines with COPD severity in the respiratory microbiome.}, journal = {Cell reports}, volume = {44}, number = {10}, pages = {116413}, doi = {10.1016/j.celrep.2025.116413}, pmid = {41066239}, issn = {2211-1247}, abstract = {Chronic obstructive pulmonary disease (COPD) severity correlates with airway microbial dysbiosis, yet bacteriophage roles remain unexplored. We characterized the lung DNA virome by re-analyzing 135 sputum metagenomes from 99 COPD patients and 36 healthy controls. We identified 1,308 viral operational taxonomic units, revealing progressively lower viral diversity correlating with disease severity. While viral and bacterial diversity typically showed strong positive correlations, patients with frequent exacerbations uniquely exhibited decoupled viral-bacterial relationships, indicating disrupted ecological dynamics. Comparing all COPD patients to controls, phages infecting anaerobic oral bacteria showed disproportionately lower abundance-Porphyromonas phages were 40-fold less abundant, despite only 4-fold lower bacterial abundance-while pathogen-associated phages showed no significant differences. We detected virulence factor-encoding phages, including two neuA-carrying Haemophilus phages in 7.4% of Haemophilus-colonized patients, associated with 82-fold higher bacterial abundance. These findings establish altered bacteriophage ecology as an unrecognized feature of COPD pathobiology, with differential phage-bacteria relationships that reshape lung microbial ecosystems, offering new perspectives for microbiome-targeted interventions.}, }
@article {pmid41066109, year = {2025}, author = {Zhou, T and Delgado-Baquerizo, M and Ren, C and He, N and Zhou, Z and He, Y}, title = {Soil microbial life history strategies covary with ecosystem multifunctionality across aridity gradients.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {41}, pages = {e2511071122}, doi = {10.1073/pnas.2511071122}, pmid = {41066109}, issn = {1091-6490}, support = {202206600027//China Scholarship Council (CSC)/ ; 32522067//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {*Soil Microbiology ; *Microbiota/physiology ; *Ecosystem ; *Desert Climate ; Soil/chemistry ; }, abstract = {Aridity thresholds shape ecosystem functions worldwide. Despite the importance of soil microbiomes in engineering ecosystem processes, the specific strategies employed by soil microbiomes to support ecosystem multifunctionality (EMF) across aridity gradients remain virtually unknown. Here, we investigated 474 soil samples across a continental-scale aridity gradient and identified an aridity threshold beyond which plot-level EMF declines sharply. Microbial habitat and decomposition functions were among the last to respond to aridity, with thresholds occurring under more arid conditions compared to plant productivity and soil fertility. Combining metagenomic sequencing with physiological assays to characterize microbial life history strategies of high yield (Y), resource acquisition (A), and stress tolerance (S), we introduce a microbial trait-based framework to mechanistically link community-level microbial life history strategies to EMF. Our results reveal that microbial Y-strategy is positively correlated with EMF across aridity gradients, A-strategy exhibits a negative association with EMF across aridity gradients, and S-strategy is negatively correlated with EMF in arid ecosystems. Collectively, this study offers empirical evidence and insights into how aridification interacts with soil microbiomes in shaping EMF, highlighting the pivotal role of microbial life history strategies in understanding the mechanisms behind EMF variation in an increasingly arid world.}, }
@article {pmid41065113, year = {2025}, author = {Palacios, N and Gordon, S and Wang, T and Burk, R and Qi, Q and Huttenhower, C and Gonzalez, HM and Knight, R and De Carli, C and Daviglus, M and Lamar, M and Telavera, G and Tarraf, W and Kosciolek, T and Cai, J and Kaplan, RC}, title = {Gut microbiome and cognitive function in the Hispanic Community Health Study/Study of Latinos.}, journal = {Journal of Alzheimer's disease : JAD}, volume = {}, number = {}, pages = {13872877251376911}, doi = {10.1177/13872877251376911}, pmid = {41065113}, issn = {1875-8908}, abstract = {BackgroundThere is limited work on the association between the gut microbiome and Alzheimer's disease and related dementia (AD/ADRD) in Latinos.ObjectiveWe examined, within the Hispanic Community Health Study/Study of Latinos (HCHS/SOL) cohort, the association between gut microbiome and cognitive function.MethodsWe analyzed the fecal metagenomes of 2471 HCHS/SOL participants to identify microbial taxonomic and functional features associated with global cognitive function. Omnibus (PERMANOVA) and feature-wise analyses (MaAsLin2) were conducted to identify microbiome-cognition associations, and specific microbial species and pathways (Kyoto Encyclopedia of Genes and Genomes (KEGG modules) associated with cognition.ResultsEubacterium species (E. siraeum and E. eligens), and C phoceensis, among other species were associated with better cognition. Several KEGG modules, most strongly Ornithine, Serine biosynthesis and Urea Cycle, were associated with worse cognition.ConclusionsIn a large Hispanic/Latino cohort, we identified several microbial taxa and KEGG pathways associated with cognition.}, }
@article {pmid41064842, year = {2025}, author = {Kuswandi, W and Budiman, C and Khaerunnisa, I and Sumantri, C}, title = {Rearing system and immune status influence the small intestinal microbiota of IPB-D3 chickens: A full-length 16S rRNA metagenomic approach.}, journal = {Veterinary world}, volume = {18}, number = {8}, pages = {2206-2221}, pmid = {41064842}, issn = {0972-8988}, abstract = {BACKGROUND AND AIM: The small intestinal microbiota plays a pivotal role in poultry digestion and immune function. Rearing systems can influence their composition, thereby affecting the overall health and performance of the birds. This study aimed to investigate how rearing systems (intensive [IN] vs. free-range [FR]) and immune status, reflected by leukocyte profiles, influence the small intestinal microbiome of IPB-D3 chickens, a genetically improved Indonesian local breed.<br><br>MATERIALS AND METHODS: Ninety IPB-D3 chickens were reared for 12 weeks under either IN or FR systems. Hematological profiling was conducted to assess health status, with leukocyte counts used to stratify birds. Microbiota samples from the small intestine were analyzed using full-length 16S ribosomal RNA (V1-V9) sequencing on the Oxford Nanopore platform. Taxonomic identification was performed using the SILVA database. Statistical comparisons were made using t-tests, and microbial diversity was assessed through alpha and beta diversity metrics.<br><br>RESULTS: While most hematological parameters did not differ significantly between rearing systems, total leukocyte counts were higher in intensively reared chickens (p = 0.002). FR chickens exhibited significantly greater microbial diversity (p < 0.05) across multiple alpha diversity indices. A total of 1,294 unique species were identified in FR birds versus 720 in the IN group, with 1,761 shared species. Leukocyte level further influenced microbial profiles; chickens with high leukocyte (HL) counts were dominated by Ligilactobacillus aviarius, whereas low-leukocyte chickens had a higher abundance of Bacteroides caecigallinarum. Gallibacterium anatis, a potential pathogen, dominated in IN systems with elevated leukocytes.<br><br>CONCLUSION: This study demonstrates that both the rearing environment and immune status substantially influence small intestinal microbial composition in IPB-D3 chickens. FR systems promoted richer, more beneficial microbial communities, while IN systems, especially with HL levels, were associated with opportunistic pathogens. Leukocyte profiling may serve as a non-invasive biomarker for gut health, supporting future development of precision poultry management strategies and immune-responsive probiotics.}, }
@article {pmid41064771, year = {2025}, author = {Giraldo-Badillo, I and Pineda-Vélez, E and Carbonell-Medina, BA and Ardila, CM}, title = {Microbiological and Pharmacological Aspects Involved in Dentin-Pulp Complex Regeneration: A Scoping Review.}, journal = {Journal of clinical and experimental dentistry}, volume = {17}, number = {9}, pages = {e1149-e1158}, pmid = {41064771}, issn = {1989-5488}, abstract = {BACKGROUND: The regeneration of the dentin-pulp complex represents a pivotal challenge in endodontics, requiring a delicate balance between microbial eradication and tissue repair. This scoping review, conducted in accordance with PRISMA-ScR guidelines, synthesizes current evidence on microbiological and pharmacological factors influencing regenerative outcomes.<br><br>MATERIAL AND METHODS: A systematic search of PubMed, Scopus, Web of Science, and Cochrane Library identified 242 studies, with 15 meeting inclusion criteria after screening.<br><br>RESULTS: The review highlights the dominance of anaerobic biofilm-forming pathogens (Enterococcus faecalis, Porphyromonas gingivalis) in periapical lesions, their virulence mechanisms (e.g., proteolytic enzymes, immune evasion), and the rising threat of antibiotic resistance driven by &#x3b2;-lactamases and efflux pumps. Pharmacologically, while triple/double antibiotic pastes promote dentin thickening, their cytotoxicity at high concentrations and disruption of commensal microbiota underscore the need for optimized dosing. Emerging alternatives-such as antimicrobial peptides, calcium hypochlorite, and immunomodulatory biomolecules-demonstrate superior biocompatibility and dual action against pathogens while supporting stem cell viability.<br><br>CONCLUSIONS: Future directions emphasize microbiome-targeted therapies, advanced biomaterials, and personalized approaches leveraging metagenomics. This review underscores the imperative to integrate selective antimicrobial strategies with regenerative biology to advance endodontic outcomes. Key words:Dentin-pulp regeneration, endodontic infections, biofilm, antimicrobial resistance, regenerative endodontics.}, }
@article {pmid41064045, year = {2025}, author = {Zhao, S and Wang, F and Song, L and Zhu, S and Liu, S and Zhao, K and Liu, R and Li, YY}, title = {Interspecies electron transfer as one of key drivers of methanogenic consortia succession within quorum sensing regulation.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf165}, pmid = {41064045}, issn = {2730-6151}, abstract = {Robust interspecies interactions are essential for efficient methanogenesis in anaerobic digestion. This study investigated the impact of quorum sensing (QS) enhancement on the succession of methanogenic communities during anaerobic digestion. The QS stimulation via exogenous N-acyl-homoserine lactones enhanced methane production by 18.8%-22.1%. Moreover, QS shaped microbial community succession toward a more deterministic assembly, selectively enriching key syntrophs (Pelotomaculum, Smithella), and methanogens (Methanobacterium, Methanothrix). Metagenomic analysis revealed that QS induced genes related to transcription, transport, and cofactor biosynthesis instead of directly regulating carbon metabolism. In this context, interspecies electron transfer emerges as a critical factor regulating interspecies interactions under QS regulation. Specifically, QS enhancement boosted redox mediator secretion, and the concentration of 2-amino-3-carboxy-1,4-naphthoquinone and phenazine increased by 7.8- and 4.8-fold, respectively. QS enhancement also induced higher abundance of c-type cytochromes. Moreover, the higher electron transfer coefficients were detected with 40.2%-89.9% increase. Further, QS also enhanced relative abundance of genes involved in Complex I/III and ferredoxin-dependent hydrogenases, promoting electron flow from syntrophs to methanogens. These effects induced higher relative abundance of genes associated with syntrophic propionate/butyrate oxidation and hydrogenotrophic/acetotrophic methanogenesis. Collectively, given that the similar regulation pathway is widely distributed in anaerobes, these findings identify QS as a critical ecological signal that drives functional microbial succession.}, }
@article {pmid41063294, year = {2025}, author = {Sun, S and Wang, H and Han, B and Wu, H and Wang, Y and Xu, T}, title = {Combined effects of low temperature, hyperosmolarity and seawater-conditioned pathogens on open fracture healing in a rat model simulating circumpolar environments.}, journal = {Journal of orthopaedic surgery and research}, volume = {20}, number = {1}, pages = {875}, pmid = {41063294}, issn = {1749-799X}, mesh = {Animals ; Rats, Sprague-Dawley ; Male ; *Seawater/microbiology/adverse effects ; Rats ; *Fracture Healing/physiology ; *Cold Temperature/adverse effects ; *Fractures, Open/microbiology/diagnostic imaging ; Disease Models, Animal ; *Femoral Fractures/microbiology/diagnostic imaging ; }, abstract = {OBJECTIVE: To investigate the factors influencing the healing of open fractures in circumpolar latitude region seawater immersion conditions.<br><br>MATERIALS AND METHODS: A femoral fracture model was established in ninety 6-to-8-week-old male Sprague-Dawley rats, randomly assigned to five groups (n&#x2009;=&#x2009;18 per group): (1) fracture only, (2) fracture with circumpolar seawater immersion, (3) fracture with low-temperature isotonic solution immersion, (4) fracture with aseptic circumpolar seawater immersion, and (5) fracture with low-temperature aseptic circumpolar seawater immersion. Fractures were confirmed postoperatively by radiographs on days 7, 21, and 42. Micro-CT and H&amp;E staining were performed on day 42 to assess bone healing. Bacterial cultures from internal fixation devices were analyzed on day 3. Blood samples were collected on days 3, 7, and 14 to assess leukocyte and neutrophil counts, and serum ALP and VEGF levels were measured on days 7, 14, and 21. Pathogenic microorganisms in the seawater were identified by metagenomic analysis. Fracture healing and callus formation rates were compared using the Log-rank test.<br><br>RESULTS: X-ray, micro-CT, and histological analyses revealed significantly impaired fracture healing in the group exposed to circumpolar seawater immersion compared to the fracture-only group (P&#x2009;<&#x2009;0.05). Bacterial colony counts on internal fixation devices were highest in the circumpolar seawater group (P&#x2009;<&#x2009;0.05). Leukocyte and neutrophil levels were significantly elevated in this group on days 3 and 7 (P&#x2009;<&#x2009;0.05), with no significant differences observed on day 14 (P&#x2009;>&#x2009;0.05). Serum ALP and VEGF levels were significantly reduced on days 7, 14, and 21 (P&#x2009;<&#x2009;0.05), although ALP levels on day 21 showed no significant difference (P&#x2009;>&#x2009;0.05). Log-rank analysis indicated that the bone union and callus maturation rates were significantly lower in the circumpolar seawater group compared to the other four groups. Metagenomic analysis identified Flavobacterium, Rhodobacter, and Bacteroides as the dominant pathogens in circumpolar seawater.<br><br>CONCLUSIONS: This study demonstrates that hyperosmolarity, low temperature, and exposure to opportunistic pathogens under circumpolar seawater conditions collectively delay open fracture healing. Among these factors, opportunistic pathogens exert the most significant impact, highlighting microbial contamination as the primary barrier to bone regeneration in such environments and providing direction for future therapeutic strategies.<br><br>CLINICAL TRIAL NUMBER: not applicable.}, }
@article {pmid41062579, year = {2025}, author = {Wang, Y and Wang, Y and Hou, L and Zhong, L and Yang, H and Kang, X and Zhou, Y and Pan, J}, title = {Assessment of airborne and surface microbes on leather cultural relics in museums of arid regions represented by xinjiang, China.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {35107}, pmid = {41062579}, issn = {2045-2322}, support = {2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; }, mesh = {China ; *Museums ; *Air Microbiology ; *Bacteria/genetics/classification/isolation &amp; purification/drug effects ; Microbiota ; }, abstract = {This study investigates the airborne microbial contamination in three museums located in the dry region of Xinjiang region, China-Bayingolin, Hami, and Turpan. Airborne microbial concentrations in these museums were found to be relatively low, ranging from 7.5 to 38.3 CFU/m[3], which is advantageous for the preservation of cultural relics, especially in comparison to humid regions where higher microbial concentrations have been reported. The microbial communities were dominated by bacteria, with Firmicutes being the most abundant phylum, followed by Proteobacteria and Bacteroidetes. Notably, Pseudomonas sp., Bacillus sp., and Staphylococcus hominis were identified as potential threats to the degradation of leather cultural relics. Additionally, Mycobacterium sp., Pantoea sp., and Priestia aryabhattai were first identified in the context of cultural heritage conservation. Metagenomic sequencing revealed a significant presence of salt-tolerant, spore-forming bacteria, which are characteristic of dry environments. Antibacterial tests showed that 0.5% K100 exhibited the best antimicrobial effect. This study provides valuable insights into the microbial ecology of museums in rid climates and suggests the need for targeted preservation strategies to mitigate microbial-induced biodeterioration, particularly through the use of antimicrobial agents and environmental management.}, }
@article {pmid41062543, year = {2025}, author = {Prast-Nielsen, S and Granström, AL and Kiasat, A and Ahlström, G and Edfeldt, G and Rautiainen, S and Boulund, F and Andersson, FO and Lindberg, J and Schuppe-Koistinen, I and Gustafsson, UO and Engstrand, L}, title = {Associations of the intestinal microbiota with plasma bile acids and inflammation markers in Crohn's disease and ulcerative colitis.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {35039}, pmid = {41062543}, issn = {2045-2322}, mesh = {Humans ; *Bile Acids and Salts/blood ; *Gastrointestinal Microbiome ; *Crohn Disease/blood/microbiology ; *Colitis, Ulcerative/blood/microbiology ; Female ; Male ; Adult ; Biomarkers/blood ; Middle Aged ; *Inflammation/blood ; Case-Control Studies ; Feces/microbiology ; }, abstract = {Our study explores signatures for Crohn's disease (CD) and Ulcerative Colitis (UC) reflecting an interplay between the intestinal microbiota, systemic inflammation, and plasma bile acid homeostasis. For this, 1,257 individuals scheduled for colonoscopy were included and completed a comprehensive questionnaire. Individuals with IBD ('CD' n = 64 and 'UC' n = 55), were age- and gender-matched to controls without findings during colonoscopy. Shotgun metagenomic profiles of the fecal microbiota and plasma profiles of inflammatory proteins and bile acids were used to build disease classifiers. Omics integration identified associations across datasets. B. hydrogenotrophica was associated with CD and C. eutactus, C. sp. CAG167, B. cellulosilyticus, C. mitsuokai with controls. Ten inflammation markers were increased in CD, and eleven bile acids and derivatives were decreased in CD, while 7a-Hydroxy-3-oxo-4-cholestenoate (7-HOCA) and chenodeoxycholic acid (CDCA) were increased compared to controls.In UC, commensals such as F. prausnitzii and A. muciniphila were depleted. CCL11, IL-17A, and TNF were increased in UC and associated to gut microbial changes. Correlations between taxa and bile acids were all positive. For both CD and UC, taxonomic differences were primarily characterized by a reduction in commensal gut microbes which exhibited positive correlations with secondary bile acids and negative correlations with inflammation markers.}, }
@article {pmid41062510, year = {2025}, author = {Feng, S and Zhang, B and Wang, H and Xiong, Y and Tian, A and Yuan, X and Pan, C and Guo, X}, title = {Enhancing peptide identification in metaproteomics through curriculum learning in deep learning.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {8934}, pmid = {41062510}, issn = {2041-1723}, support = {R15LM013460//U.S. Department of Health &amp; Human Services | NIH | U.S. National Library of Medicine (NLM)/ ; R01AT011618//U.S. Department of Health &amp; Human Services | NIH | National Center for Complementary and Integrative Health (NCCIH)/ ; R01AT011618//U.S. Department of Health &amp; Human Services | NIH | National Center for Complementary and Integrative Health (NCCIH)/ ; }, mesh = {*Deep Learning ; *Proteomics/methods ; *Peptides/analysis ; Humans ; Gastrointestinal Microbiome ; Neural Networks, Computer ; Databases, Protein ; Metagenome ; }, abstract = {Metaproteomics offers a powerful window into the active functions of microbial communities, but accurately identifying peptides remains challenging due to the size and incompleteness of protein databases derived from metagenomes. These databases often contain vastly more sequences than those from single organisms, creating a computational bottleneck in peptide-spectrum match (PSM) filtering. Here we present WinnowNet, a deep learning-based method for PSM filtering, available in two versions: one using transformers and the other convolutional neural networks. Both variants are designed to handle the unordered nature of PSM data and are trained using a curriculum learning strategy that moves from simple to complex examples. WinnowNet consistently achieves more true identifications at equivalent false discovery rates compared to leading tools, including Percolator, MS[2]Rescore, and DeepFilter, and outperforms filters integrated into popular analysis pipelines. It also uncovers more gut microbiome biomarkers related to diet and health, highlighting its potential to support advances in personalized medicine.}, }
@article {pmid41062486, year = {2025}, author = {Tu, Z and Sun, H and Wang, T and Liu, Y and Xu, Y and Peng, P and Qin, S and Tu, C and He, B}, title = {Node role of wild boars in virus circulation among wildlife and domestic animals.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {8938}, pmid = {41062486}, issn = {2041-1723}, mesh = {Animals ; *Sus scrofa/virology ; *Animals, Wild/virology ; Swine/virology ; *Animals, Domestic/virology ; China/epidemiology ; Disease Reservoirs/virology ; Virome/genetics ; Humans ; *Viruses/genetics/classification/isolation &amp; purification ; *Swine Diseases/virology ; Zoonoses/virology ; Phylogeny ; }, abstract = {Wild boars are considered pest animals in most of their distribution ranges, but their role as virus reservoirs has long been overlooked, with the circulation dynamics of their viruses rarely investigated. Here we prepared a data set, that is, BrCN-Virome, of 9281 viral metagenomes by pan-viromic analyses of 2535 organ and 274 blood samples from 466 healthy and 50 dead wild boars across 127 locations in 26 provincial regions of China. Compared to domestic pigs, BrCN-Virome shows different viromic composition, with a great expansion in the DNA virus diversity. Some wild boar viruses are traced to humans, domestic animals, wildlife, and arthropods, with several evidently or potentially related to epizootics or zoonoses. Pig pathogens spread widely in wild boars and are responsible for a substantial portion of wild boar mortality, with occurrences of co-infection with multiple African swine fever viruses. These results indicate that wild boars are a node animal connecting different animal taxa in the virus circulation network, and that their viruses not only pose a major threat to the pig industry but also challenge wildlife conservation and public health, highlighting the need for routine surveillance of wild boar viruses and active control of the wild boar population.}, }
@article {pmid41062001, year = {2025}, author = {Ghaffar, T and Valeriani, F and Romano Spica, V}, title = {The Sex Related Differences in Health and Disease: A Systematic Review of Sex-Specific Gut Microbiota and Possible Implications for Microbial Pathogenesis.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {108094}, doi = {10.1016/j.micpath.2025.108094}, pmid = {41062001}, issn = {1096-1208}, abstract = {BACKGROUND: The gut microbiota, a complex ecosystem influenced by various physiological and environmental factors, has been increasingly recognized for its role in health and disease. Emerging evidence suggests that sex differences, particularly mediated by sex hormones and physiological variations, significantly influence the composition and diversity of the gut microbiome. This systematic review aimed to evaluate and synthesize the current knowledge on sex-related variations in gut microbiota across human and animal studies.<br><br>METHODS: We conducted a systematic review of 24 eligible studies, selected from an initial 13,205 articles, focusing on healthy populations and next-generation sequencing-based microbiota profiling in both humans and animal models.<br><br>RESULTS: The results reveal sex-specific differences in microbial diversity and taxa abundance; however, the consistency and significance of these findings vary across studies, with females generally exhibiting higher levels of Akkermansia and Bifidobacterium, while males showed increased levels of Prevotella and Escherichia. These findings suggest that sex may be a contributing, but not necessarily dominant, biological variable shaping microbiome architecture across various species, including mice, pigs, deer, and humans, and highlight the influence of hormonal fluctuations, body composition, and lifestyle factors on gut microbial ecosystems.<br><br>CONCLUSION: Our findings underscore the importance of considering sex as a key biological variable in microbiome research and its potential implications for disease susceptibility, therapeutic interventions, and microbiome-targeted strategies in microbial pathogenesis. Moreover, evidence from human studies remains limited, especially those using 16S rRNA gene sequencing, which may lack the resolution to detect strain-level or functional differences. Incorporating multi-omics approaches such as metagenomics, metatranscriptomics, and metabolomics may offer deeper insights into sex-dependent microbial dynamics.However, these implications remain largely associative and require mechanistic validation in future studies.}, }
@article {pmid41061960, year = {2025}, author = {Wang, H and Sheng, J and Zhang, Y and Lan, H and Lu, X and Li, X and Zhao, X}, title = {Detection of zoonotic Coxiella burnetii causing chronic Q fever endocarditis in a Chinese geriatric patient by mNGS.}, journal = {Journal of global antimicrobial resistance}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jgar.2025.09.015}, pmid = {41061960}, issn = {2213-7173}, abstract = {OBJECTIVES: Q (query) fever, caused by Coxiella burnetii, is often linked to negative bacterial cultures. Infective endocarditis with negative cultures is difficult to diagnose and treat. Our case demonstrates that metagenomic next-generation sequencing (mNGS) can provide a rapid and accurate method for pathogenetic diagnosis in infectious diseases.<br><br>CASE PRESENTATION: We reported a case of infective endocarditis with negative blood cultures in a male patient with a history of sheep farming and previous aortic valve replacement (AVT) and atrial septal defect atrial septal defect (ASD) repair. Blood tests showed positive serum immunofluorescent antibodies to rickettsia, while mNGS of perivalvular abscess tissue suggested C. burnetii. Doxycycline 0.1 g q12h and hydroxychloroquine 0.2 g q12h were used for postoperative antibiotic treatment. The genome of the C. burnetii C2245173Z was assembled on the Illumina platform, and no known antibiotic resistance genes were detected. Phylogenetic analysis of C. burnetii genomes shows a genetic relationship between animal-derived strains and human-derived strains.<br><br>CONCLUSIONS: The application of mNGS could provide a rapid and accurate assay in clinical diagnosis and play a decisive role in the pathogenetic diagnosis of some infectious diseases. Doxycycline plus hydroxychloroquine remains an effective treatment for chronic Q fever endocarditis. In addition, phylogenetic tree analysis indicates that C. burnetii infection may pose a potential risk to humans working with livestock.}, }
@article {pmid41061540, year = {2025}, author = {Zhang, L and Gao, X and Li, G and Xu, Z and Luo, W}, title = {Metagenomic insights to effective elimination of resistomes in food waste composting by lime addition.}, journal = {Journal of hazardous materials}, volume = {499}, number = {}, pages = {140065}, doi = {10.1016/j.jhazmat.2025.140065}, pmid = {41061540}, issn = {1873-3336}, abstract = {Food waste contains abundant resistomes, including antibiotic and heavy metal resistance genes (ARGs and MRGs), which pose risks to the environment and human health. Composting can be used for food waste treatment, but it fails to effectively eliminate these resistomes. Thus, this study investigated the performance of lime to regulate the dynamics and mobility of ARGs and MRGs in food waste composting by metagenomics. Genome-resolved analysis was further conducted to identify the ARGs and MRGs hosts and their horizontal gene transfer (HGT) events. Results showed that lime addition at 1 % (wet weight) could significantly promote temperature and pH increase to sterilize hosts, particularly pathogen bacteria (e.g. Acinetobacter johnsonii and Enterobacter cloacae), thus reducing the abundance of resistomes by more than 57.1 %. This sterilization notably reduced the number of mobile ARGs and MRGs driven by mobile genetic elements (MGEs). The contribution of MGEs located on chromosomal sequences to horizontally transfer ARGs and MRGs was significantly higher than that on mobilizable plasmids. Further analysis indicated that the reduced resistomes by lime was mainly attributed to effective sterilization of hosts rather than decreased HGT diversity. Thus, this study provides valuable insights into use lime as a low-cost control of resistomes in waste recycling.}, }
@article {pmid41061488, year = {2025}, author = {Yang, M and Huang, Y and Liu, J and Wang, G and Mei, Y and Ge, L and Du, Q and Li, H and Zhao, N}, title = {Characterisation of microbial succession and exploration of the stability maintenance strategy of phage community on microbes in radish paocai.}, journal = {International journal of food microbiology}, volume = {444}, number = {}, pages = {111479}, doi = {10.1016/j.ijfoodmicro.2025.111479}, pmid = {41061488}, issn = {1879-3460}, abstract = {Previous research focused on the safety control of phages in food. In recent years, numerous phages have been extensively characterised in fermented foods, where they change along with fermentation process but do not compromise product quality. However, the potential roles of phages in fermented foods remain unclear. Microbial steady state is critical for maintaining normal radish paocai fermentation. To explore stability maintenance strategies for phages, their structure and interactions with microbes were investigated across two microbial structural systems during fermentation. Microbial counts showed the absence of fungi in the non-steady-state environment (NE), whereas high fungal levels (6.78 ± 0.09 log colony-forming units/mL) were detected in the steady-state environment (SE). Metagenomic analysis revealed that microbial structure remained stable in SE but changed markedly in NE. Pediococcus ethanolidurans and Lactococcus lactis were the species that differed significantly between SE and NE. Microbial succession exhibited a significant association with physicochemical environments in NE (P < 0.05), whereas microbial abundance fluctuations were unaffected by physicochemical stress in SE. Caudoviricetes was identified as the dominant viral class. Cluster analysis showed that NE systems displayed high variability with dramatic shifts across multiple viral genera (Clusters 3-6). In NE, 25 lytic and 226 lysogenic phages were identified, while 3 lytic and 29 lysogenic phages were found in SE. Phage host prediction indicated preferential targeting of harmful bacteria (e.g., Escherichia) in NE, contrasted with phage predation on fermentation-associated lactic acid bacteria in SE. Genomic analysis indicated that Lactiplantibacillus abundance and its corresponding phages remained stable in SE but increased sharply in NE on day 3. Lactiplantibacillus phages isolated from NE and SE displayed strict host specificity at the strain level and exhibited potent lytic activity across different fermented food matrices. This study advances our understanding of steady-state maintenance mechanisms in vegetable fermentation systems and offers new insight for cross-system phage applications.}, }
@article {pmid41060906, year = {2025}, author = {Sawyer, FM and Stossi, F and Nachman, E and Britton, RA and Bolt, MJ and Mancini, MA and Estes, MK and Blutt, SE}, title = {A pipeline for rapid, high-throughput imaging and quantitative analysis of human intestinal organoids.}, journal = {PloS one}, volume = {20}, number = {10}, pages = {e0332418}, doi = {10.1371/journal.pone.0332418}, pmid = {41060906}, issn = {1932-6203}, mesh = {Humans ; *Organoids/cytology/metabolism ; *Intestinal Mucosa/cytology ; *High-Throughput Screening Assays/methods ; Microscopy, Confocal/methods ; Image Processing, Computer-Assisted/methods ; *Intestines/cytology ; Cell Proliferation ; }, abstract = {Human intestinal organoids (HIOs) are a model system for studying human intestinal epithelium. Utilizing HIOs for high-throughput studies remains inefficient, as analyzing their cellular composition and responses to varying experimental conditions requires extensive time and labor. We describe a 96-well plate-based automated pipeline for rapidly imaging and quantifying fluorescent labeling in HIOs using a high-throughput confocal microscope and image analysis software. The pipeline was leveraged to quantify varying levels of cell proliferation among donor HIO lines in response to microbial products. Cytoplasmic fluorescence via antibody labeling was also quantified with the pipeline, enabling measurement of the prevalence of specific cell types in HIOs. This platform offers a novel approach to efficiently and rapidly image and quantify fluorescent staining and immunolabeling in HIOs and has many potential applications, including drug screening, toxicity testing, intestinal barrier integrity and transport studies, microbiome and host-pathogen interaction studies, and lineage tracking.}, }
@article {pmid41060725, year = {2025}, author = {Liu, Y and Tang, J and Wang, Y and Cui, F and Yang, Y}, title = {Intracranial infection caused by Mycoplasma hominis after neurosurgical operation: an easily overlooked but serious condition.}, journal = {Journal of infection in developing countries}, volume = {19}, number = {9}, pages = {1425-1431}, doi = {10.3855/jidc.20729}, pmid = {41060725}, issn = {1972-2680}, mesh = {Humans ; Male ; *Mycoplasma hominis/isolation &amp; purification/genetics ; *Mycoplasma Infections/diagnosis/drug therapy/microbiology ; Aged ; Anti-Bacterial Agents/therapeutic use ; *Neurosurgical Procedures/adverse effects ; *Postoperative Complications/microbiology/diagnosis/drug therapy ; }, abstract = {INTRODUCTION: Mycoplasma hominis (M. hominis) is a commensal that mainly colonizes in the microflora of the genitourinary tracts and is associated with urogenital tract infections. There are reports of central nervous system (CNS) infections in neonates caused by M. hominis. Nevertheless, M. hominis CNS infections in non-neonatal patients are extremely rare. Herein, we have reported a case of a man who suffered from intracranial infection secondary to M. hominis after neurosurgical operation. Additionally, we reviewed the relevant published literature to raise awareness on such infections and highlight the importance of proper treatments.<br><br>CASE PRESENTATION: A 68-year-old man underwent emergence craniotomy for intracerebellar hemorrhage. He presented with a moderate fever unresponsive to piperacillin-tazobactam on the seventh day after the surgery. His body temperature continued to increase, and he presented with signs of CNS infection. The antimicrobial therapy was switched to meropenem and vancomycin. No obvious reduction in the body temperature was observed. The cerebrospinal fluid (CSF) obtained previously revealed tiny point colonies which were morphologically consistent with M. hominis and subsequently confirmed by metagenomic next-generation sequencing (mNGS). Thus, M. hominis induced intracranial infection was diagnosed, and a combination therapy with moxifloxacin and minocycline was implemented. Fortunately, the patient's body temperature decreased to normal range after effective antibiotic therapy.<br><br>CONCLUSIONS: Based on the lesson of our case and a thorough review of published literature, the possibility of M. hominis induced CNS infections after neurosurgical intervention should not be ignored, especially when there is no response to standard antimicrobial therapy.}, }
@article {pmid41060484, year = {2025}, author = {Khan, MF}, title = {Enhancing stability of enzymes for industrial applications: molecular insights and emerging approaches.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {41}, number = {10}, pages = {362}, pmid = {41060484}, issn = {1573-0972}, support = {82930-NP//University College Dublin/ ; }, mesh = {Enzyme Stability ; *Enzymes/chemistry/metabolism/genetics ; Protein Engineering/methods ; Hydrogen-Ion Concentration ; Biocatalysis ; Biotechnology ; }, abstract = {The growing demand for robust biocatalysts in industrial bioprocesses has intensified the pursuit of enzymes capable of functioning under extreme physicochemical conditions. This work critically examines the molecular determinants of enzyme stability, including thermostability, pH tolerance, halotolerance, resistance to solvents and oxidative stress, mechanical resilience to shear and pressure, and storage stability. These traits are essential for sustained catalytic performance in sectors such as bioenergy, pharmaceuticals, food, textiles, and environmental remediation. Recent advances in structure-guided engineering, molecular dynamics, and mutational profiling have enabled rational strategies to enhance enzyme resilience. By adopting a multi-parametric lens, this study bridges specific molecular adaptations with industrial challenges, offering a systems-level framework often lacking in single-condition analyses. It also explores emerging frontiers, including AI-assisted enzyme design, metagenomic discovery from extremophiles, and synthetic reconstruction of adaptive pathways, paving the way for next-generation biocatalysts optimised for scalability, performance, and sustainability. The novelty of this work lies in its integrative approach combining molecular insight, environmental origin, and computational tools to guide the development of industrially robust enzymes.}, }
@article {pmid41060313, year = {2025}, author = {Hays, MD and Fuchsman, CA}, title = {SAR11 ecotypes across ocean basins change with depth due to changes in light and oxygen.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf221}, pmid = {41060313}, issn = {1751-7370}, abstract = {SAR11 bacteria are ubiquitous and abundant heterotrophs that are important mediators of marine biogeochemical cycles. Within the SAR11 clade smaller ecotypes inhabit different ecological niches. Using metagenomic read placement onto a phylogenetic tree of RNA polymerase (rpoB), we were able to determine the distribution of different ecotypes both geographically and by depth. Our method avoids biases from the absence of quality sequenced genomes for deep SAR11 ecotypes. Depth profiles that range from the surface to the bathypelagic were analyzed at 30 stations in 6 ocean basins. In the euphotic zone, changes in the dominant primary producer from eukaryotic algae to cyanobacteria, did not cause the abundance of SAR11 to shift between stations. However, specific SAR11 ecotypes did correlate with eukaryotic phytoplankton (1a.3 and 1a.4) or picocyanobacteria (1b.2, 1b.4, and IIaB). In the lower euphotic and mesopelagic zones, group IIb.x was overwhelmingly the dominant species but group 1c was also present, and we found several new deep sub-ecotypes of 1b. The shift between the surface SAR11 community, dominated by 1a and surface 1b sub-ecotypes, and the mesopelagic ecotype groups, corresponded to the maximum decrease in the light-dependent proteorhodopsin/rpoB ratio, indicating that many deep ecotypes did not possess proteorhodopsin. This ecotype switch repeatedly corresponded to the maximum in Low Light I Prochlorococcus, leading to the hypothesis that changes in light motivates the ecotype switch. Environmentally abiotic factors like light and temperature appear to be determining factors in the SAR11 ecotype distribution throughout the global oceans.}, }
@article {pmid41060304, year = {2025}, author = {Bueno de Mesquita, CP and Olm, MR and Bissett, A and Fierer, N}, title = {High strain-level diversity of Bradyrhizobium across Australian soils.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf222}, pmid = {41060304}, issn = {1751-7370}, abstract = {Global surveys of soil bacteria have identified several taxa that are nearly ubiquitous and often the most abundant members of soil bacterial communities. However, it remains unclear why these taxa are so abundant and prevalent across a wide range of soil types and environmental conditions. Here we use genome-resolved metagenomics to test the hypothesis that strain-level differences exist in these taxa that are not adequately captured with standard marker gene sequencing, and that distinct strains harbor unique traits that reflect adaptations to different soil environments. We analyzed data from 331 natural soils spanning Australia to assess strain differentiation in Bradyrhizobium, a dominant soil bacterial genus of ecological importance. We developed a workflow for strain-level bacterial analyses of complex soil metagenomes, combining genomes from pre-existing databases with new genomes generated via targeted assembly from metagenomes to detect 181 Bradyrhizobium strains across the soil collection. In addition to a high degree of phylogenetic variation, we observed substantial variation in pangenome content and inferred traits, highlighting the breadth of diversity within this widespread genus. Although members of the genus Bradyrhizobium were detected in >80% of samples, most individual strains were restricted in their distributions. The overall strain-level community composition of Bradyrhizobium varied significantly across geographic space and environmental gradients, and was particularly associated with differences in temperature, soil pH, and soil nitrate and metal concentrations. Our work provides a general framework for studying the strain-level ecology of soil bacteria and highlights the ecological and pangenomic diversity within this dominant soil bacterial genus.}, }
@article {pmid41059692, year = {2025}, author = {Bedi de Silva, A and Polson, SW and Schvarcz, CR and Steward, GF and Edwards, KF}, title = {Genomic diversity and global distribution of four new prasinoviruses from the tropical north Pacific.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0258324}, doi = {10.1128/spectrum.02583-24}, pmid = {41059692}, issn = {2165-0497}, abstract = {Viruses that infect phytoplankton are an integral part of marine ecosystems, but the vast majority of viral diversity remains uncultivated. Here, we introduce four near-complete genomic assemblies of viruses that infect the widespread marine picoeukaryote Micromonas commoda, doubling the number of reported genomes of Micromonas dsDNA viruses. All host and virus isolates were obtained from tropical waters of the North Pacific, a first for viruses infecting green algae in the order Mamiellales. Genome length of the new isolates ranges from 205 to 212 kb, and phylogenetic analysis shows that all four are members of the genus Prasinovirus. Three of the viruses form a clade that is adjacent to previously sequenced Micromonas viruses, while the fourth virus is relatively divergent from previously sequenced prasinoviruses. We identified 61 putative genes not previously found in prasinovirus isolates, including a phosphate transporter and a potential apoptosis inhibitor novel to marine viruses. Forty-eight genes in the new viruses are also found in host genome(s) and may have been acquired through horizontal gene transfer. By analyzing the coding sequences of all published prasinoviruses, we found that ~25% of prasinovirus gene content is significantly correlated with host genus identity (i.e., Micromonas, Ostreococcus, or Bathycoccus), and the functions of these genes suggest that much of the viral life cycle is differentially adapted to the three host genera. Mapping of metagenomic reads from global survey data indicates that one of the new isolates, McV-SA1, is relatively common in multiple ocean basins.IMPORTANCEThe genomes analyzed here represent the first viruses from the tropical North Pacific that infect the abundant phytoplankton order Mamiellales. Comparing isolates from the same location demonstrates high genomic diversity among viruses that co-occur and presumably compete for hosts. Comparing all published prasinovirus genomes highlights gene functions that are likely associated with adaptation to different host genera. Metagenomic data indicate these viruses are globally distributed, and one of the novel isolates may be among the most abundant marine viruses.}, }
@article {pmid41059690, year = {2025}, author = {Venkatachalam, S and Granskog, MA and Gonçalves-Araujo, R and Divine, DV and Vipindas, PV and Jabir, T and Shereef, A and Jain, A}, title = {Distinct bacterial community structures with abundant carbon degradation and sulfur metabolisms found in different sea-ice types from the Central Arctic Ocean.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0129125}, doi = {10.1128/spectrum.01291-25}, pmid = {41059690}, issn = {2165-0497}, abstract = {The rapid decline of sea ice in the relatively understudied Central Arctic Ocean has a significant impact on bacterial biodiversity and the ecological functions they support. We investigated the bacterial community composition and the associated metabolic functions from three geographically distinct sea-ice floes: first-year ice (FYI) at the North Pole and western Nansen Basin and second-year or multi-year ice (SYI/MYI) in the western Amundsen Basin. We resolved the sea-ice bacterial community diversity at species-level precision using a long-read amplicon (n = 18) and metagenomic (n = 3) sequencing approach. The amplicon sequencing highlighted marked differences in bacterial community structure driven by ice age, floe origin, and environmental factors, demonstrating pronounced vertical structuring among ice horizons. Bacterial taxa like Paraglaciecola psychrophila, Hydrogenophaga crassostreae, Octadecabacter arcticus, and Polaribacter irgensii mainly dominated the bottom layers of SYI/MYI, whereas species Actimicrobium antarcticum, Polaromonas cryoconiti, O. antarcticus, and Rhodoferax sp. dominated the FYI. Similarly, notable taxonomic differences were observed in bacterial taxa inhabiting the surface and interior layers of FYI and SYI/MYI (e.g., F. frigoris and Hydrogenophaga sp.). The metagenomic analysis showed the prevalence of sulfur cycling-associated (assimilatory and dissimilatory sulfur metabolism) and complex carbon degradation processes in sea ice. We also elucidated the potential ecological role of novel metagenome-assembled genomes belonging to the genus Aquiluna through phylogenomic and pangenomic analyses. Overall, our findings revealed novel insights on the distinct bacterial communities that inhabit ice horizons and their associated ecological functions correlating with sea-ice type, origin, and habitat characteristics in the Central Arctic Ocean.IMPORTANCEThe Arctic region is warming nearly four times faster than the global average, leading to the continuous replacement of its thick multi-year sea ice with thinner first-year ice. The reduction in Arctic sea-ice cover was previously shown to have cascading effects on sea-ice-associated microbial communities and their role in the functioning of the ecosystem. This study provides the first high-resolution, species-level insight into the bacterial community composition and metabolic potential across different sea-ice types in the Central Arctic Ocean-an understudied yet rapidly changing environment. By combining long-read amplicon and metagenomic sequencing, we uncover distinct bacterial assemblages and functional metabolic roles that were shaped by the ice age and other physicochemical properties. Our findings highlight the ecological importance of sea-ice associated bacterial communities and the prevalence of sulfur metabolism and carbon degradation processes in different sea-ice types found in the central Arctic Ocean through genome-resolved metagenomics.}, }
@article {pmid41059063, year = {2025}, author = {Hu, J and Cyle, KT and Yuan, W and Shi, W}, title = {Metagenomic evidence clarifies the texture-dependent cascading effects of organic degradation on soil hypoxia and N2O emission.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1670657}, pmid = {41059063}, issn = {1664-302X}, abstract = {INTRODUCTION: Soil pore-scale aeration is a crucial yet often overlooked factor influencing the effectiveness of nitrous oxide (N2O) emission mitigation strategies. Our previous work revealed a hundred-fold variation in N2O emissions among soils under apparently aerobic conditions and texture-dependent mitigation effects of biochar-manure co-compost (BM) compared to manure compost (M).<br><br>METHODS: We analyzed soils of three textures-clay loam (CL), silt loam (SL), and sand (SA)-amended with BM or M. Metagenomic sequencing was used to profile microbial community composition and functional genes, with a focus on aeration-sensitive taxa and pathways.<br><br>RESULTS: We demonstrate that these changes of N2O emissions are aligned with variations in aeration-sensitive microbes and genes. SA, with the highest N2O emissions, was most abundant in obligate and facultative anaerobes and denitrification-related genes, while CL, with the lowest emissions, had more genes related to fermentation and dissimilatory nitrate reduction. Compared to M, BM in CL favored genes for microbial processes requiring a more reducing environment, likely because biochar-induced finer pores, exacerbating oxygen diffusion limitations. This severe oxygen restriction in CL after BM addition was substantiated by greater reductions in CO2 efflux and C-cycling genes than in the other soils.<br><br>DISCUSSION: Our findings suggest that hypoxic pore abundance and the severity of pore anaerobiosis imparted by degradation of organic amendments varied with soil texture and are the overriding factors of soil greenhouse gas (GHG) emissions. Metagenomic traits provide a sensitive tool for detecting pore-scale environmental shifts, improving our mechanistic understanding of soil-dependent GHG emissions following organic amendments.}, }
@article {pmid41059058, year = {2025}, author = {Wang, Y and Bai, Z and Liu, Y and Wang, Y and Xu, J and Lai, Z}, title = {Influence of the gut microbiota on the pharmacokinetics of tacrolimus in liver transplant recipients: insights from microbiome analysis.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1616985}, pmid = {41059058}, issn = {1664-302X}, abstract = {INTRODUCTION: Tacrolimus is crucial for immunosuppression after liver transplantation, but its pharmacokinetics vary markedly among individuals. Emerging evidence suggests that the gut microbiota may influence its metabolism, although the underlying mechanisms remain unclear.<br><br>METHODS: This study analyzed the fecal microbiota from 38 postliver transplant patients and 31 healthy controls via 16S rDNA amplicon and shotgun metagenomic sequencing. Patients were stratified into three groups on the basis of oral tacrolimus dosage and blood concentration: LDLBC (low dose, low blood concentration), LDHBC (low dose, high blood concentration), and SDLBC (standard dose, low blood concentration).<br><br>RESULTS: Posttransplant patients presented significantly reduced gut microbial diversity. Specific bacterial taxa, including Enterococcus raffinosus, Intestinibacter bartlettii, and Bacteroides fragilis, were enriched in patients with lower tacrolimus blood concentrations. In contrast, Phascolarctobacterium faecium and Streptococcus salivarius were associated with increased drug levels. Functional analysis revealed differences between patient subgroups in ATP-binding cassette (ABC) transporters and drug efflux pumps, suggesting a potential microbial influence on tacrolimus absorption and metabolism. Additionally, antibiotic resistance genes were more abundant in patients with lower tacrolimus blood concentrations, particularly in the Escherichia coli-enriched groups.<br><br>DISCUSSION: These findings underscore the influence of the gut microbiota on tacrolimus pharmacokinetics and support the potential of microbial composition as a biomarker for optimizing immunosuppressive therapy.}, }
@article {pmid41059040, year = {2025}, author = {Zhu, N and Gao, J and Wu, R and Jia, S and Guo, X and Sun, D and Guan, Q}, title = {Metagenomic insights into respiratory viral signatures in lower respiratory tract infections with and without respiratory failure.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1637352}, pmid = {41059040}, issn = {2235-2988}, mesh = {Humans ; *Respiratory Tract Infections/virology/microbiology/complications ; *Metagenomics ; Male ; Middle Aged ; Female ; Bacteria/classification/genetics/isolation &amp; purification ; *Viruses/classification/genetics/isolation &amp; purification ; *Virome ; Bronchoalveolar Lavage Fluid/virology/microbiology ; Microbiota ; Aged ; *Respiratory Insufficiency/virology/microbiology ; Adult ; }, abstract = {OBJECTIVE: Lower respiratory tract infections (LRTIs) are a significant cause of morbidity and mortality worldwide, with the respiratory microbiome playing a pivotal role in disease pathogenesis. Comprehensive profiling of the lower respiratory tract virome allows investigation of potential differences between LRTIs and non-LRTIs, helps identify virus-associated taxa linked to pulmonary disease, and provides insights into virome-host interactions involved in respiratory health.<br><br>METHODS: In this study, we compared viral and bacterial microbiome characteristics of LRTI patients with non-LRTI controls by &#x3b1;-diversity, &#x3b2;-diversity (PCoA, NMDS, ANOSIM), and differential abundance (LEfSe) analyses using metagenomic sequencing of bronchoalveolar lavage fluids, and further performed these comparisons similarly in respiratory failure (RF) patients and non-RF patients in the LRTI group. In addition, virus-bacteria co-occurrence patterns, the correlations between viral and bacterial abundance profiles, and the associations between microbial features and host clinical indicators were assessed using Spearman correlation analysis.<br><br>RESULTS: Overall, no significant differences in viral and bacterial &#x3b1;- or &#x3b2;-diversity were detected between LRTI (n=39) and non-LRTI (n=9) groups. However, among LRTI patients with RF (n=5), distinct viral taxonomic signatures were observed, including enrichment of Phixviricota, Malgrandaviricetes, Petitvirales, and Microviridae lineages. Despite taxonomic shifts, overall viral diversity remained similar between RF and non-RF subgroups. Bacterial communities showed no notable stratification across clinical categories. Correlation analyses revealed that uncultured human fecal viruses were negatively associated with lymphocyte counts, while Streptococcus-related bacteriophages correlated positively with C-reactive protein (CRP) levels.<br><br>CONCLUSION: The overall composition and diversity of the respiratory microbiome were insufficient to distinguish LRTI from non-LRTI conditions. However, within the LRTI cohort, patients with RF exhibited distinct viral taxonomic profiles compared to non-RF individuals. Additionally, several viral taxa were correlated with host clinical indicators irrespective of clinical subgroup. These findings highlight virome compositional differences associated with RF within LRTI patients, but do not imply causal effects, and warrant further investigation.}, }
@article {pmid41059035, year = {2025}, author = {Huang, Y and Zhang, M and Tian, Y and Lan, X and Jin, W and Bai, Y and Zang, Q and Chen, M and Su, Z and Zhang, W and Aishan, G and Geng, M and Xie, J and Tong, P}, title = {A novel broad-spectrum lytic phage vB_EcoM_P3322: isolation, characterization, and therapeutic potential against avian pathogenic Escherichia coli.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1645263}, pmid = {41059035}, issn = {2235-2988}, mesh = {Animals ; *Escherichia coli/virology/pathogenicity ; *Escherichia coli Infections/therapy/veterinary/microbiology ; *Myoviridae/isolation &amp; purification/classification/ultrastructure/genetics/physiology ; Host Specificity ; *Phage Therapy/methods ; Wastewater/virology ; *Coliphages/isolation &amp; purification/classification/ultrastructure/physiology/genetics ; Columbidae/microbiology ; Genome, Viral ; Phylogeny ; Poultry Diseases/therapy/microbiology ; Hydrogen-Ion Concentration ; }, abstract = {INTRODUCTION: The widespread misuse of antibiotics has accelerated the emergence of multidrug-resistant bacterial strains, presenting a major threat to global public health. Bacteriophages (phages), owing to their host-specific lytic activity and self-replicating nature, have emerged as promising alternatives or adjuncts to conventional antibiotic therapies.<br><br>METHODS: In this study, a lytic phage targeting avian pathogenic Escherichia coli (APEC) was isolated from farm wastewater. The phage's morphological characteristics, host range, optimal multiplicity of infection (MOI), one-step growth curve, pH stability, thermal stability, chloroform sensitivity, and in vitro antibacterial activity were determined. Subsequently, the therapeutic efficacy of the phage was evaluated in a pigeon model.<br><br>RESULTS: In this study, we isolated and characterized a lytic phage, designated vB_EcoM_P3322, from farm wastewater targeting APEC. Transmission electron microscopy classified vB_EcoM_P3322 within the Myoviridae family. The phage exhibited broad lytic activity against five Escherichia coliserotypes (O8:H10, O15:H18, O51:H20, O149:H20, and O166:H6). Optimal biological parameters included a multiplicity of infection (MOI) of 1, a latent period of 10 minutes, an 80-minute burst period, and a burst size of 252 PFUs/cell. vB_EcoM_P3322 maintained stable lytic activity across a pH range of 5-9 and temperatures from 4&#xb0;C to 50&#xb0;C, although it was sensitive to chloroform. In vitro, the phage effectively suppressed bacterial growth within 6 hours at MOIs of 0.1, 1, and 10. Whole-genome sequencing revealed a 151,674 bp double-stranded DNA genome encoding 279 predicted open reading frames. No virulence factors, toxin genes, antibiotic resistance genes, or lysogeny-related elements were identified, affirming its safety for therapeutic application. Phylogenetic analysis indicated 98.44% nucleotide identity (97% coverage) with phage vB_EcoM_Ro121c4YLVW (GenBank: NC_052654), suggesting a close evolutionary relationship. In a pigeon infection model, vB_EcoM_P3322 treatment significantly improved survival and reduced histopathological damage in the liver and spleen. Metagenomic analysis of duodenal contents revealed a marked reduction (P < 0.01) in E. coli abundance in the treatment group, indicating selective pathogen clearance and modulation of gut microbiota.<br><br>DISCUSSION: In summary, vB_EcoM_P3322 displays broad-spectrum lytic activity, robust environmental stability, potent antibacterial efficacy both in vitro and in vivo, and a safe genomic profile. These attributes support its potential as a novel biocontrol agent for managing APEC infections in poultry farming.}, }
@article {pmid41058886, year = {2025}, author = {Liu, Y and Li, L and Yang, L and Yang, Y and An, H and Li, D and Wang, X}, title = {Clinical Features and Treatment Strategies of Q Fever Spinal Infection: A Pooled Analysis of 39 Cases and Narrative Review of the Literature.}, journal = {Open forum infectious diseases}, volume = {12}, number = {10}, pages = {ofaf584}, pmid = {41058886}, issn = {2328-8957}, abstract = {BACKGROUND: The incidence of spinal infections is increasing; However, pathogen identification remains challenging. Although Q fever spinal infection is reported infrequently, its accrual incidence is likely underestimated. The causative agent, Coxiella burnetii, cannot be routinely cultured. Consequently, physicians often misdiagnose Q fever spinal infection as spinal tuberculosis, leading to severe patient harm. Thus, improving clinicians' awareness of the clinical characteristics of Q fever spinal infection is urgently needed.<br><br>METHODS: We present a case of Q fever spinal infection and conducted literature searches in PubMed and the Chinese core journals of the Wanfang Database using keywords including "Q fever," "Coxiella burnetii," "spinal infection," "osteomyelitis," "spondylodiscitis," and "psoas abscess." Additional reports were identified through cross-referencing, with a cutoff date of 6 November 2024. Cases were included if patient age, sex, and baseline medical history were documented. Clinical data were retrospectively analyzed, and clinical features were compared between the aneurysm-associated group and the isolated spinal infection group. Fisher's exact probability test was used to evaluate the incidence difference.<br><br>RESULTS: A total of 39 adult patients were enrolled (mean age: 67.82 &#xb1; 10.51 years, male: 34,87.2%), Eleven cases reported potential pathogen exposure. Thirty-three cases presented with early-onset of lower back pain, and 13 developed fever during the disease course. Thirty-four cases involved the lumbar spine, exhibiting continuous lesions of 1-3 vertebral bodies, with imaging features of vertebral osteomyelitis, discitis, paravertebral soft-tissue swelling, and/or adjacent aneurysmal changes. Among 21 cases with routine blood tests, 2 showed elevated leukocyte counts, 5 had mild anemia, and the remainder were normal. Serological testing was performed in 34 cases, with 29 testing positive on the first time; PCR testing was conducted in 25 cases, with 23 cases detecting positive specimens; and rapid diagnosis confirmed in all 3 cases via metagenomic next-generation sequencing (mNGS). Inflammatory reactions were identified in all 21 biopsied cases, with inflammatory granulomas reported in 7 and explicitly excluded in 4. There were 24 cases complicated with aneurysm and 15 cases with isolated spinal infection. A significant difference in CRP elevation rate was observed between the two groups (14/15, 93.33% vs 4/8, 50.00%, P = .033). Early local lesion debridement combined with doxycycline-based multidrug therapy showed favorable outcomes. Serological monitoring demonstrated low sensitivity for assessing therapeutic efficacy.<br><br>CONCLUSIONS: This study systematically summarizes the clinical characteristics of Q fever spinal infection and, for the first time, reports features associated with its distinct clinical subtypes. Q fever should be considered in case of chronic spinal infections-especially those complicated with vascular lesions. Based on clinical history evaluation, rapid diagnosis may be achieved through mNGS of specimens from local lesions. Combined with early initiation of doxycycline-based regimens, timely debridement of necrotic tissues and purulent material may improve treatment outcomes. Further investigations are needed to identify reliable biomarkers for monitoring therapeutic efficacy and to establish optimal treatment strategies for subtypes of Q fever spinal infection.}, }
@article {pmid41058622, year = {2025}, author = {Cai, ZZ and Zeng, DM and Lei, LW and Xiao, S}, title = {Rotavirus gastroenteritis complicating meningitis caused by Bacteroides uniformis detected using mNGS: a case report and literature review.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1601953}, pmid = {41058622}, issn = {2296-858X}, abstract = {This case report describes a rare instance of pediatric meningitis caused by Bacteroides uniformis (B. uniformis) following rotavirus gastroenteritis in a 1-year-4-month-old boy, diagnosed using metagenomics next-generation sequencing (mNGS). Bacterial meningitis (BM) is a life-threatening disease in children, particularly those under 5 years old, and early identification of the pathogen is crucial for reducing mortality and improving prognosis. B. uniformis, a Gram-negative, non-spore-forming, obligate anaerobic bacillus and common gut commensal, is rarely implicated in human infections, particularly pediatric meningitis. The child presented with vomiting, diarrhea, convulsions, and syncope, and was initially treated for meningitis and rotavirus gastroenteritis. Despite negative bacterial cultures, mNGS identified B. uniformis in the cerebrospinal fluid (CSF). Treatment was switched from ceftriaxone to meropenem (0.45 g, IV every 8 h) based on its good blood-brain barrier penetration and likely susceptibility of B. uniformis. The child's condition improved significantly, with follow-up lumbar puncture showing normal CSF parameters and no detectable pathogens. The case suggests that rare anaerobic meningitis may occur against the backdrop of rotavirus gastroenteritis and underscores the importance of using mNGS for accurate pathogen detection in bacterial meningitis, as well as the need for early initiation of appropriate antimicrobial therapy.}, }
@article {pmid41058503, year = {2025}, author = {Castro, M and Vida, R and Galeano, J and Cuesta, JA}, title = {Scarce data, noisy inferences and overfitting: the hidden flaws in ecological dynamics modelling.}, journal = {Journal of the Royal Society, Interface}, volume = {22}, number = {231}, pages = {20250183}, doi = {10.1098/rsif.2025.0183}, pmid = {41058503}, issn = {1742-5662}, support = {//Agencia Estatal de Investigaci&#xf3;n/ ; }, mesh = {*Models, Biological ; *Ecosystem ; Bayes Theorem ; *Microbiota ; Humans ; }, abstract = {Metagenomic data has significantly advanced microbiome research by employing ecological models, particularly in personalized medicine. The generalized Lotka-Volterra (gLV) model is commonly used to understand microbial interactions and predict ecosystem dynamics. However, gLV models often fail to capture complex interactions, especially when data are limited or noisy. This study critically assesses the effectiveness of gLV and similar models using Bayesian inference and a model reduction method based on information theory. We found that ecological data often leads to non-interpretability and overfitting due to limited information, noisy data and parameter sloppiness. Our results highlight the need for simpler models that align with the available data and propose a distribution-based approach to better capture ecosystem diversity, stability and competition. These findings challenge current bottom-up ecological modelling practices and aim to shift the focus towards a statistical mechanics view of ecology based on distributions of parameters.}, }
@article {pmid41058431, year = {2025}, author = {Jiménez-Arroyo, C and Molinero, N and Del Campo, R and Delgado, S and Moreno-Arribas, MV}, title = {Human gut microbiome study through metagenomics: Recent advances and challenges for clinical implementation.}, journal = {Enfermedades infecciosas y microbiologia clinica (English ed.)}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.eimce.2025.09.011}, pmid = {41058431}, issn = {2529-993X}, abstract = {Metagenomics has decisively advanced the study of the gut microbiome, enabling a better understanding of its importance for human health. Metataxonomics, based on the sequencing of the 16S rRNA gene, provides taxonomic profiles of prokaryotes, while shotgun metagenomics allows a comprehensive characterization of all DNA present in a sample. With adequate sequencing depth, the latter increases taxonomic resolution to the strain level and provides detailed information on the functional potential of the microbiota. However, the lack of standardization in sample collection and processing, sequencing technologies, and data management limits the comparability of results and their implementation in clinical laboratories. This review offers a practical and updated framework on metagenomic methodologies, data analysis, and the application of artificial intelligence tools, highlighting advances and best practices to facilitate the integration of functional microbiome analysis into clinical practice and to overcome current challenges.}, }
@article {pmid41057946, year = {2025}, author = {Ren, Y and Wu, YH and Chen, J and Luo, ZH and Xu, XW}, title = {New insights into the evolution and metabolism of the bacterial phylum Candidatus Acidulodesulfobacteriota through metagenomics.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {127}, pmid = {41057946}, issn = {2524-6372}, support = {42376133//National Natural Science Foundation of China/ ; 2021YFF0501303//National Key R&amp;D Program of China/ ; }, abstract = {Candidatus Acidulodesulfobacterales, a formerly proposed bacterial order within the Deltaproteobacteria lineage, represents an ecologically significant group in sulfur-rich environments. Their diversity and functional potential in artificial acid mine drainage (AMD) ecosystems have been well studied; however, their distribution and ecological role in marine hydrothermal sulfides remain poorly understood. Here we integrated publicly available metagenome-assembled genomes (MAGs) with a newly reconstructed MAG from hydrothermal sulfides to perform comprehensive phylogenetic, metabolic, and host-virus interaction analyses. Phylogenomic and 16S rRNA gene analyses indicated that this lineage represents a distinct phylum-level clade, leading us to propose the designation Ca. Acidulodesulfobacteriota. Metabolic reconstructions indicated a versatile lifestyle, encompassing pathways for carbon fixation, nitrogen fixation, sulfur metabolism, iron oxidation, and hydrogen oxidation. Notably, the concatenated DsrAB protein phylogeny and the mixed enzyme types involved in Dsr-dependent dissimilatory sulfur metabolism suggest that Ca. Acidulodesulfobacteriota may represent a transitional lineage in the evolutionary shift from reductive to oxidative Dsr metabolism. Viral auxiliary metabolic genes (AMGs) associated with this phylum were predicted to modulate host metabolic pathways, including folate biosynthesis and sulfur metabolism, highlighting intricate host-virus interactions. These findings advance our understanding of the evolution, metabolic potential, and ecological roles of Ca. Acidulodesulfobacteriota in biogeochemical cycling.}, }
@article {pmid41057624, year = {2025}, author = {Han, D and Liu, C and Yang, B and Yu, F and Liu, H and Lou, B and Shen, Y and Tang, H and Zhou, H and Zheng, S and Chen, Y}, title = {Metagenomic fingerprints in bronchoalveolar lavage differentiate pulmonary diseases.}, journal = {NPJ digital medicine}, volume = {8}, number = {1}, pages = {599}, pmid = {41057624}, issn = {2398-6352}, support = {2023YFC2308300//Key Technologies Research and Development Program/ ; 82472371//National Natural Science Foundation of China/ ; }, abstract = {Recent advances in unbiased metagenomic next-generation sequencing (mNGS) enable simultaneous examination of microbial and host genetic material. We developed a multimodal machine learning-based diagnostic approach to differentiate lung cancer and pulmonary infections by analyzing 402 bronchoalveolar lavage fluid (BALF) mNGS datasets, including lung cancer (n = 123), bacterial infections (n = 114), fungal infections (n = 79), and pulmonary tuberculosis (n = 86). The training cohort revealed differences in microbial profiles, bacteriophage abundance, host gene and transposable element expression, immune cell composition, and tumor fraction derived from copy number variation (CNV). The integrated model (Model VI) achieved an AUC of 0.937 (95% CI, 0.910-0.964) in the training cohort and 0.847 (95% CI, 0.776-0.918) in the test cohort. A rule-in/rule-out strategy further improved accuracy in differentiating lung cancer from tuberculosis (accuracy = 0.896), fungal (accuracy = 0.915), and bacterial (accuracy = 0.907) infections. These findings highlight the potential of mNGS-based multimodal analysis as a cost-effective tool for early and accurate differential diagnosis.}, }
@article {pmid40631202, year = {2025}, author = {Palmer, SN and Mishra, A and Gan, S and Liu, D and Koh, AY and Zhan, X}, title = {Identifying Optimal Machine Learning Approaches for Human Gut Microbiome (Shotgun Metagenomics) and Metabolomics Integration with Stable Feature Selection.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.06.21.660858}, pmid = {40631202}, issn = {2692-8205}, support = {U01 AI169298/AI/NIAID NIH HHS/United States ; T32 AI005284/AI/NIAID NIH HHS/United States ; R01 GM126479/GM/NIGMS NIH HHS/United States ; R56 HG011035/HG/NHGRI NIH HHS/United States ; P01 AI179406/AI/NIAID NIH HHS/United States ; R01 HG011035/HG/NHGRI NIH HHS/United States ; }, abstract = {UNLABELLED: Microbiome research has been limited by methodological inconsistencies. Taxonomy-based profiling presents challenges such as data sparsity, variable taxonomic resolution, and the reliance on DNA-based profiling, which provides limited functional insight. Multi-omics integration has emerged as a promising approach to link microbiome composition with function. However, the lack of standardized methodologies and inconsistencies in machine learning strategies has hindered reproducibility. Additionally, while machine learning can be used to identify key microbial and metabolic features, the stability of feature selection across models and data types remains underexplored, despite its importance for downstream experimental validation and biomarker discovery. Here, we systematically compare Elastic Net, Random Forest, and XGBoost across five multi-omics integration strategies: Concatenation, Averaged Stacking, Weighted Non-negative Least Squares (NNLS), Lasso Stacking, and Partial Least Squares (PLS), as well as individual omics models. We evaluate performance across 588 binary and 735 continuous models using human gut microbiome-derived metabolomics and taxonomic data derived from metagenomics shotgun sequencing data. Additionally, we assess the impact of feature reduction on model performance and feature selection stability. Among the approaches tested, Random Forest combined with NNLS yielded the highest overall performance across diverse datasets. Tree-based methods also demonstrated consistent feature selection across data types and dimensionalities. These results demonstrate how integration strategies, algorithm selection, data dimensionality, and response type impact both predictive performance and the stability of selected features in multi-omics microbiome modeling.<br><br>KEY POINTS: A total of 1,323 models were developed to comprehensively evaluate prediction performance and the robustness of feature selection for human gut microbiome (metabolomics and taxonomy from metagenomics shotgun sequencing) datasets. These models included three widely used machine learning algorithms - Elastic Net, Random Forest and XGBoost - applied across five integration strategies and single-omics approaches on datasets with binary and continuous outcomes.For continuous outcomes, Random Forest combined with NNLS integration achieved the highest performance and maintained strong predictive performance across full-dimensional and feature-reduced datasets.For binary outcomes, Random Forest consistently performed well regardless of the integration strategy. Notably, single-omics models, especially those using metabolomics data, outperformed integrative approaches.Tree-based models demonstrated greater consistency in feature selection across different dimensionalities and integration strategies.}, }
@article {pmid39764050, year = {2025}, author = {Nasr, E and Pechlivanis, N and Strepis, N and Amato, P and Bernt, M and Bhardwaj, A and Blankenberg, D and Brites, D and Cumbo, F and Do, K and Ferrari, E and Griffin, TJ and Gruening, B and Hiltemann, S and Hyde, CJ and Jagtap, P and Mehta, S and Métris, KL and Momin, S and Nelson, TM and Oba, A and Pavloudi, C and Péguilhan, R and Price, GR and Psomopoulos, F and Rosic, N and Schatz, MC and Schiml, VC and Siguret, C and Soranzo, N and Stubbs, A and Van Heusden, P and Vohra, M and ,  and Zierep, P and Batut, B}, title = {Microbiology Galaxy Lab: The first community-driven gateway for reproducible and FAIR analysis of microbial data.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.12.23.629682}, pmid = {39764050}, issn = {2692-8205}, support = {U24 AI183870/AI/NIAID NIH HHS/United States ; U41 HG006620/HG/NHGRI NIH HHS/United States ; }, abstract = {The explosion of microbial omics data has outpaced the ability of many researchers to analyze it, with complex tools and limited computational resources creating barriers to discovery. To address this gap, we present the Microbiology Galaxy Lab: a free, globally accessible, community-supported platform that combines state-of-the-art analytical power with user-friendly accessibility. Supported by the Galaxy and global microbiology communities, this platform integrates over 315 tool suites and 115 curated workflows, enabling comprehensive metabarcoding, (meta)genomic, (meta)transcriptomic, and (meta)proteomic data analysis within a FAIR-aligned environment. It also supports research in the health and infectious disease sectors, as well as in environmental microbiology. The platform's utility is exemplified through various use cases, including antimicrobial resistance tracking, biomarker prediction, microbiome classification, and functional annotation of key microbes. Built on reproducibility and community engagement, it supports creation, sharing, and updating of best-practice workflows. Over 35 tutorials and learning paths empower scientists, fostering an ecosystem that keeps resources at the forefront of microbial science. The Microbiology Galaxy Lab enables collective analysis, democratising research, thereby accelerating discovery across the global microbiology community (microbiology.usegalaxy.org, .eu, .org.au, .fr).}, }
@article {pmid41059288, year = {2023}, author = {Cameron, ES and Blaxter, ML and Finn, RD}, title = {plastiC: A pipeline for recovery and characterization of plastid genomes from metagenomic datasets.}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {475}, pmid = {41059288}, issn = {2398-502X}, abstract = {The use of culture independent molecular methods, often referred to as metagenomics, have revolutionized the ability to explore and characterize microbial communities from diverse environmental sources. Most metagenomic workflows have been developed for identification of prokaryotic and eukaryotic community constituents, but tools for identification of plastid genomes are lacking. The endosymbiotic origin of plastids also poses challenges where plastid metagenomic assembled genomes (MAGs) may be misidentified as low-quality bacterial MAGs. Current tools are limited to classification of contigs as plastid and do not provide further assessment or characterization of plastid MAGs. plastiC is a workflow that allows users to identify plastid genomes in metagenome assemblies, assess completeness, and predict taxonomic association from diverse environmental sources. plastiC is a Snakemake workflow available at https://github.com/Finn-Lab/plastiC. We demonstrate the utility of this workflow with the successful recover of algal plastid MAGs from publicly available lichen metagenomes.}, }
@article {pmid41056780, year = {2025}, author = {Chang, X and Ma, Y and Zhang, J and Wang, T and Li, H and Wang, L}, title = {Size-specific effects of polyethylene microplastics (100-10,000 nm) on the soil resistome and pathogens revealed via metagenomics and machine learning.}, journal = {Journal of environmental management}, volume = {394}, number = {}, pages = {127517}, doi = {10.1016/j.jenvman.2025.127517}, pmid = {41056780}, issn = {1095-8630}, abstract = {Microplastics (MPs) and antibiotic resistance genes (ARGs) are widespread, persistent environmental contaminants. However, the influence of MP particle size on ARGs dissemination and soil ecosystem health remains unclear. Herein, polyethylene MPs of three sizes (100, 1,000, and 10,000 nm) were incubated in ARG-contaminated soils for 45 days to evaluate their effects on soil physicochemical properties, microbial communities, ARGs, mobile genetic elements (MGEs), and pathogen abundance. MP exposure significantly increased soil water (up to 4.07-fold), total nitrogen (up to 50.34 %), and ammonium nitrogen (up to 38.54 %) contents. Conversely, soil organic carbon content decreased with increasing MP size. MPs markedly reduced the activities of key enzymes, including alkaline phosphatase (by 87.65 %), sucrase (by 10.96 %), and urease (by 54.17 %). Microbial α-diversity increased; however, the abundance of potentially pathogenic Pseudomonadota increased by up to 41.88 %, whereas that of beneficial Actinobacteria and Chloroflexi declined. MPs promoted the expression of 44 ARGs and 15 MGEs, with smaller MPs exhibiting stronger enrichment. They also increased the expression of virulence factors and the abundance of human- and plant-associated pathogens. Random forest modeling revealed that smaller MPs primarily drove these changes by altering soil physicochemical properties and microbial dynamics. Collectively, these findings demonstrate that MPs, especially smaller particles, simultaneously alter soil chemistry, suppress enzyme activities, reshape microbial communities, and enhance ARGs expression and pathogen proliferation, underscoring their significant ecological and human health risks in agricultural soils.}, }
@article {pmid41056245, year = {2025}, author = {Roongpiboonsopit, D and Wairit, S and Nithisathienchai, C and Pakdee, A and Cheibchalard, T and Sayasathid, J and Wilantho, A and Tongsima, S and Somboonna, N}, title = {Oral microbiome dysbiosis in acute ischemic stroke and transient ischemic attack patients.}, journal = {PloS one}, volume = {20}, number = {10}, pages = {e0333676}, doi = {10.1371/journal.pone.0333676}, pmid = {41056245}, issn = {1932-6203}, mesh = {Humans ; Male ; Female ; *Dysbiosis/microbiology ; *Ischemic Attack, Transient/microbiology ; *Microbiota/genetics ; Middle Aged ; Case-Control Studies ; Aged ; *Ischemic Stroke/microbiology ; RNA, Ribosomal, 16S/genetics ; Prospective Studies ; Saliva/microbiology ; Bacteria/genetics/classification ; *Mouth/microbiology ; }, abstract = {Oral microbiome (bacterial community) may influence systemic inflammation and vascular health, which both are critical factors in a pathogenesis of ischemic stroke. This study aimed to evaluate differences in the saliva microbiome of acute ischemic stroke (AIS) and transient ischemic attack (TIA) patients compared with matched healthy controls, hypothesizing that AIS and TIA patients are associated with oral microbiome shift. A prospective case-control study was conducted in Naresuan University Hospital, Thailand, to compare the saliva microbiome of AIS and TIA stroke patients of Thai ethnic with matched healthy controls. Microbial profiles were analyzed by metagenomics combined 16S rRNA gene sequencing to assess microbial alpha diversity, taxonomic composition, beta diversity, and microbial functional pathways.Forty-one patients (31 AIS and 10 TIA) and 20 age- and sex-matched stroke-free healthy controls were included in this study. Baseline characteristics were comparable between groups, apart from higher rates of hypertension, diabetes, and smoking in the patient group. Patients exhibited significantly higher alpha-diversity genus richness by OTUs and Chao1 index than controls (p < 0.001), highlighting an altered microbial community structure. Phylum-level analysis revealed an increased abundance of Bacillota (p = 0.0285) in the patient group, with a statistically decreasing trend for Bacteroidota, Actinomycetota and Pseudomonadota (p < 0.05). At the genus level, Streptococcus was more significantly abundant in the patients (p = 0.0171), while Prevotella was reduced. The patient and control groups were statistically separated in beta-diversity analysis (PERMANOVA, p < 0.001), with species biomarker analysis by LEfSe (Linear discriminant analysis effect size) could suggest species markers for each group. Functional pathway analysis showed the patient group the significantly higher in functional categories of, for examples, xenobiotics biodegradation and metabolism, cardiovascular diseases, signal transduction, and membrane transport (Welch's t-test, p < 0.05). In conclusion, this study demonstrated the statistical alterations in the saliva microbiome of AIS and TIA patients, characterized by increased genus richness diversity and relatively distinct microbial shifts that may be associated with stroke-related inflammation. The findings suggest the saliva microbiome analysis as potential as a non-invasive biomarker for stroke risk and its role in stroke pathophysiology.}, }
@article {pmid41056240, year = {2025}, author = {Brenner, LN and Huang, CY and Kim, M and Bringhurst, L and Richards, CJ and Sicilian, L and Neuringer, I and Putman, MS and Lai, PS}, title = {Dysglycemia and the airway microbiome in cystic fibrosis.}, journal = {PloS one}, volume = {20}, number = {10}, pages = {e0331847}, doi = {10.1371/journal.pone.0331847}, pmid = {41056240}, issn = {1932-6203}, mesh = {Humans ; *Cystic Fibrosis/microbiology/complications ; *Microbiota ; Male ; Female ; Adult ; Sputum/microbiology ; *Diabetes Mellitus/microbiology/etiology ; Glucose Tolerance Test ; Young Adult ; Lung/microbiology ; Respiratory Function Tests ; Pseudomonas aeruginosa ; }, abstract = {BACKGROUND: Cystic fibrosis-related diabetes (CFRD) is one of the most common non-pulmonary complications in people living with cystic fibrosis (pwCF), seen in up to 50% of adults. Even when correcting for severity of CFTR mutations, those with CFRD have more pulmonary exacerbations, lower lung function, and increased mortality than those with normal glucose tolerance (NGT).<br><br>METHODS: Expectorated sputum samples were collected from 63 pwCF during routine outpatient visits (29 with CFRD, 12 with IGT and 22 with NGT). Oral glucose tolerance test results, A1c levels, and pulmonary function tests closest to the time of sputum collection were obtained from the medical record. Samples underwent metagenomics sequencing and raw reads were processed through the bioBakery workflow for taxonomic profiling at the species level as well as predicted functional profiling and antibiotic resistance profiling. Viral profiling was performed with Marker-MAGu. Differences in alpha diversity, beta diversity, and differential abundance were assessed. Microbiome and phage signatures of CFRD were generated using sparse partial least squares models which were subsequently used as a primary predictor of lung function using multivariate linear regression.<br><br>RESULTS: In linear models, CFRD status compared to NGT was associated with a lower alpha diversity (reciprocal Simpson -1.98 [-3.80,-0.16], p&#x2009;=&#x2009;0.033) and differences in microbial community composition (Bray Curtis dissimilarity PERMANOVA R2 0.17, p&#x2009;=&#x2009;0.011). Pseudomonas aeruginosa and Streptococcus gordonii had higher relative abundance in CRFD vs NGT participants (2.43 [0.027, 4.82], unadjusted p&#x2009;=&#x2009;0.056 and 1.11 [0.58, 1.64] unadjusted p=&#x2009;<&#x2009;.001 respectively). There were global differences between CFRD vs NGT in both functional pathways and antibiotic resistance genes. In multivariate models adjusting for age, sex, antibiotic use, and modulator therapies, virome but not microbiome signatures of CFRD were associated with lower FEV1 percent predicted (-6.4 [95% CI -10.2, -2.6]%, p&#x2009;=&#x2009;0.001 for each 10% increase in virome score).<br><br>CONCLUSION: Differences in the airway microbiome in those with dysglycemia in CF are associated with poorer lung function.}, }
@article {pmid41055380, year = {2025}, author = {Du, J-Y and Zhang, Z-J and Tan, L and Yang, J-Y and Yang, R-N and Chen, Y-L and Tan, G-F and Li, J and Li, W-J and Yang, L and Cai, J and Shen, D-L and Zhu, H-R and Fan, Z-X and Yuan, M-L and Zhang, W}, title = {Gut microbiota dysbiosis and metabolic perturbations of bile/glyceric acids in major depressive disorder with IBS comorbidity.}, journal = {mBio}, volume = {}, number = {}, pages = {e0244725}, doi = {10.1128/mbio.02447-25}, pmid = {41055380}, issn = {2150-7511}, abstract = {Major depressive disorder (MDD) and irritable bowel syndrome (IBS) exhibit high comorbidity, yet their shared pathophysiology remains unclear. Previous studies have primarily focused on the psychological health in the IBS population, without considering psychiatric diagnoses or stratifying different psychological states, potentially leading to biased findings. This study employed multi-omics approaches to characterize gut microbiota and serum metabolites in 120 MDD patients (47 with IBS and 73 without IBS) and 70 healthy controls (HCs). MDD with IBS patients showed significantly higher depression (Hamilton depression scale [HAMD-17]) and anxiety (Hamilton anxiety scale [HAMA-14]) scores than MDD-only patients (P < 0.05). Metagenomic sequencing of fecal samples revealed increased alpha diversity (Chao1/Shannon indices) and Firmicutes dominance in both MDD groups vs HC, while Actinobacteria enrichment specifically marked MDD with IBS. Functionally, MDD with IBS uniquely activated D-amino acid/glycerolipid metabolism pathways (Kyoto Encyclopedia of Genes and Genomes). Serum metabolomics identified comorbid-specific perturbations: downregulation of bile acids (CDCA, GCDCA, GCDCA-3S) and upregulation of glyceric acid/glutaconic acid. Our study also found that Eggerthella lenta and Clostridium scindens are differentially abundant bacteria that are involved in bile acid metabolism, and that microbial genes (e.g., K03738) are associated with glyceric acid production. These findings implicate gut microbiota-driven bile acid/glyceric acid dysregulation in MDD with IBS comorbidity, supporting the gut-brain axis as a therapeutic target for probiotics or microbiota transplantation.IMPORTANCEMajor depressive disorder (MDD) exhibits a high comorbidity rate with irritable bowel syndrome (IBS). Our study, conducted on 120 MDD patients (47 of whom were comorbid with IBS) and a control group of 70 individuals, revealed that MDD-IBS comorbid patients demonstrated significantly higher depression/anxiety scores. Multi-omics analysis indicated substantial alterations in the gut microbiota (e.g., Firmicutes, Actinobacteria) and serum metabolites (e.g., bile acids, glyceric acid) among MDD-IBS patients, which were associated with specific metabolic pathways. Therefore, the new aspect of this study was the inclusion of patients with MDD but without IBS symptoms, which provided a deeper understanding of the intestinal microbiota dysregulation associated with comorbid IBS and MDD. These findings suggest that there may be involvement of the gut-brain axis, providing new research directions for potential therapeutic targets.CLINICAL TRIALSThis study is registered with the Chinese Clinial Trial Registry as ChiCTR2100041598.}, }
@article {pmid41055333, year = {2025}, author = {Sharma, S and Narahari, HP and Raman, K}, title = {Harnessing machine learning for metagenomic data analysis: trends and applications.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0164224}, doi = {10.1128/msystems.01642-24}, pmid = {41055333}, issn = {2379-5077}, abstract = {Metagenomic sequencing has revolutionized our understanding of microbial ecosystems by enabling high-resolution profiling of microbes across diverse environments. However, the resulting data are high-dimensional, sparse, and noisy, posing challenges for downstream data analysis. Machine learning (ML) has provided an arsenal of tools to extract meaningful insights from such large and complex data sets. This review surveys the existing state of ML applications in metagenomic data analysis, from traditional supervised and unsupervised learning to time-series modeling, transfer learning, and newer directions such as causal ML and generative models. We highlight certain key challenges and delve into important issues like model interpretability, emphasizing the importance of explainable AI (XAI). We also compare ML with mechanistic models, commenting on their relative advantages, disadvantages, and prospects for synergy. Finally, we preview future directions, such as the incorporation of multi-omics data, synthetic data generation, and Agentic AI systems, highlighting the increasingly prominent role that AI and ML will play in the future of microbiome science.}, }
@article {pmid41054501, year = {2025}, author = {Wang, W and Mo, Q and Ding, X and Pan, J}, title = {Metagenomic Next-Generation Sequencing Reveals Tannerella forsythia in Lung Abscesses: A Retrospective Case Series Linking Smoking, Oral Health, and Diagnostic Challenges.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {5193-5205}, pmid = {41054501}, issn = {1178-6973}, abstract = {PURPOSE: Tannerella forsythia (T. forsythia) is a Gram-negative anaerobic bacterium commonly found in the oral cavity of patients with periodontitis, but lung abscesses caused by this pathogen are extremely rare in the literature. This study aimed to characterize the clinical features, diagnostic challenges, and treatment outcomes of T. forsythia-associated lung abscesses through four case analyses.<br><br>PATIENTS AND METHODS: We retrospectively reviewed four patients treated between April 2023 and May 2024 with lung abscesses confirmed by chest computed tomography (CT) and T. forsythia detection via metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF). Conventional cultures were performed but yielded negative results. Clinical data, including demographics, symptoms, imaging findings, and treatment regimens, were analyzed.<br><br>RESULTS: All patients had oral diseases, and 75% were long-term smokers. The primary clinical manifestations were nonspecific respiratory symptoms, including cough, fever, chest pain, and hemoptysis. Chest CT revealed consolidation and cavitation in the upper lobes of the lungs. T. forsythia was successfully detected by mNGS of BALF, while conventional cultures failed to identify pathogens in all cases. All patients received combination antibiotic therapy based on metronidazole and piperacillin-tazobactam, with some cases requiring additional antibiotics. Following treatment, significant clinical improvement was observed, and follow-up imaging demonstrated gradual resolution of the lesions.<br><br>CONCLUSION: This study is limited by its small sample size and the lack of confirmatory tests, which warrant validation in larger prospective cohorts. Our findings highlight the advantages of mNGS in detecting fastidious pathogens (such as the anaerobic bacterium T. forsythia), providing new insights for the diagnosis of similar infections in the future. Additionally, the results identify smoking and poor oral health as common features that may be associated with the development of T. forsythia-associated lung abscesses.}, }
@article {pmid41053880, year = {2025}, author = {Shittu, OE and Enagbonma, BJ and Babalola, OO}, title = {Deciphering the influence of fertilization systems on the Allium ampeloprasum rhizosphere microbial diversity and community structure through a shotgun metagenomics profiling approach.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {126}, pmid = {41053880}, issn = {2524-6372}, support = {CRP/ZAF22-03)//ICGEB, Italy/ ; NRF//South African National Research Foundation/ ; }, abstract = {BACKGROUND: Chemical fertilizer application in agriculture over the years has been a vital instrument to boost agricultural yields and soil fertility, but has threatened the diversity of the rhizosphere microbiomes in the soil. However, knowledge about the impacts of biofertilizers (BF) as well as chemical fertilizers (CF) on Allium ampeloprasum rhizosphere's microbiomes is still limited. Hence, this study investigated the metagenomic profiling of A. ampeloprasum rhizosphere under different fertilization systems and in bulk soils, to obtain a depiction of their associated microbial diversity and community structure, which will inform best agricultural practices.<br><br>METHOD: The entire DNA sample&#xa0;was mined from soil samples taken from an independent uncultivated bulk soil and the rhizosphere of A. ampeloprasum treated with chemical and biofertilizer and subjected to shotgun metagenomics sequencing.<br><br>RESULTS: The taxonomic analysis of our metagenome unveiled that while all soil samples exhibited similar core microbial phyla, Bacteroidota and Verrucomicrobiota were exclusive to the biofertilizer (G2) plot. Actinobacteria and Pseudomonadota (Proteobacteria) were predominant in the biofertilizer plot (G2), chemical fertilizer (G1), and bulk soil (G3) plots, respectively. Genera such as Dyadobacter, Verrucomicrobium, Streptomyces, and Haliangium were exclusively detected in the biofertilizer plot (G2). Alpha diversity analysis showed that G2 harboured the most diverse microbial community, followed by G3, with the lowest diversity found in the G1 plot, highlighting the importance of biofertilizer in increasing microbial diversity. The observed differences in the microbial diversity and community structure are highly linked to the nature of fertilizer applied and the distinct physicochemical parameters of the three plots. However, redundancy analysis subsequently highlighted total nitrogen and carbon as the key environmental influencers impacting the microbial community structure and composition.<br><br>CONCLUSION: This study underscores the potential of biofertilizers in boosting the rhizosphere microbial diversity, improving soil health, and offer a sustainable alternative to chemical fertilizers, thereby supporting long-term agricultural sustainability and resilience in food production systems.}, }
@article {pmid41053318, year = {2025}, author = {Vitry, G and Angdisen, J and Sawant, MA and Arriaga, P and Irgen-Gioro, S and Peshette, P and Vuong, DC and Ilhardt, P and Fehr, J and Cwikla, B and Ponnaiya, B and Inman, JL and Snijders, AM and Hamid, S and Caballero-Lima, D and Garty, G and Apfeldorf, K and Laiakis, EC}, title = {Using a full thickness bioengineered human skin equivalent as a model for radiation biology research.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {34702}, pmid = {41053318}, issn = {2045-2322}, support = {W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; }, mesh = {Humans ; *Skin/radiation effects/microbiology/metabolism ; Animals ; Mice ; Microbiota/radiation effects ; Bioengineering ; Cell Proliferation/radiation effects ; Dose-Response Relationship, Radiation ; }, abstract = {Radiation exposure from radiological or nuclear events, medical treatments, or spaceflight poses significant health risks, yet human-specific models to investigate radiation effects on skin remain limited. This study establishes a novel in vitro platform using a full-thickness bioengineered human skin equivalent colonized with natural mixed human microbiota (coHSEs) to assess radiation-induced biological responses. We exposed coHSEs to acute doses of up to 4 Gy with x-rays and evaluated their viability, structural integrity, and molecular responses over 25 days. The coHSE model demonstrated sustained viability without dose-dependent opportunistic microbial overgrowth when procedural optimizations were applied. Radiation-induced epidermal remodeling did not compromise tissue architecture or swabbing-based sample collection. Cell proliferation analyses revealed dose- and time-dependent dynamics, with consistent dermal cell density maintained across radiation doses. Comparative multi-omic analyses, including untargeted metabolomics, targeted lipidomics, and 16 S metagenomics, revealed conserved metabolic and microbial responses to radiation in both coHSEs and skin from irradiated mice. Enriched pathways such as arachidonic acid and fatty acid metabolism, along with shifts in microbial taxa including Lachnospiraceae, support the translational relevance of the coHSE model. This system offers a scalable, ethical, and physiologically relevant platform for radiation biology, biodosimetry, and therapeutic development, advancing terrestrial health research with promising application for space research.}, }
@article {pmid41052982, year = {2025}, author = {Cao, Y and Fan, X and Zang, T and Qiu, T and Fang, Q and Bai, J and Liu, Y}, title = {Prenatal depression-associated gut microbiota induces depressive-like behaviors and hippocampal neuroinflammation in germ-free mice.}, journal = {Translational psychiatry}, volume = {15}, number = {1}, pages = {383}, pmid = {41052982}, issn = {2158-3188}, support = {2023AFB710//Natural Science Foundation of Hebei Province (Hebei Provincial Natural Science Foundation)/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Female ; *Hippocampus/metabolism/pathology/immunology ; Mice ; Pregnancy ; Fecal Microbiota Transplantation ; *Depression/microbiology/metabolism ; *Dysbiosis/microbiology/complications ; Humans ; Lipopolysaccharides/blood ; Germ-Free Life ; *Neuroinflammatory Diseases/metabolism/microbiology ; Microglia ; *Pregnancy Complications/microbiology ; Disease Models, Animal ; Behavior, Animal ; Interleukin-6/metabolism ; Tumor Necrosis Factor-alpha/metabolism ; }, abstract = {Numerous studies have described the role of the microbiome-gut-brain axis in depression. However, the molecular mechanisms underlying the involvement of gut microbiota in the development of prenatal depression are limited. In this study, fecal microbiota from women with prenatal depression was transplanted into germ-free mice to investigate the potential causal relationships between the gut microbiota and depressive phenotypes. Shotgun metagenomic sequencing and untargeted metabolomics approaches were used to investigate the characteristics of gut microbiota and microbial metabolites. The levels of neuroinflammation in the brain were detected using immunofluorescence and real-time quantitative PCR. We found significant changes in gut microbiota composition and metabolites in mice with fecal microbiota transplantation (FMT) from women with prenatal depression, including decreased Ligilactobacillus, increased Akkermansia, and abnormal glycerophospholipid metabolism. Besides, significant increase in plasma lipopolysaccharide (LPS) levels and significant proliferation of microglia in the hippocampus were observed in mice receiving FMT from women with prenatal depression, accompanied by a significant increase in the expression of nuclear factor-κB (NF-κB) p65, tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6) mRNA. The gut microbiota and its metabolites were strongly associated with depressive-like behaviors, plasma LPS and neuroinflammation. Our study collectively demonstrates that dysbiosis of the gut microbiota may play a causal relationship in the development of prenatal depression. This process potentially involves the activation of neuroinflammation through the LPS-NF-κB signaling pathway.}, }
@article {pmid41052966, year = {2025}, author = {Tang, W and Hexter, C and Dai, R and Fortin, SG and Tracey, JC and Intrator, N and Kunes, MA and Wan, XS and Jayakumar, A and Shi, D and Ward, BB}, title = {Substrate Effect on the Contribution of Ammonium and Urea to Marine Nitrification and Nitrous Oxide Production.}, journal = {Environmental microbiology}, volume = {27}, number = {10}, pages = {e70187}, doi = {10.1111/1462-2920.70187}, pmid = {41052966}, issn = {1462-2920}, support = {OCE-1946516//National Science Foundation/ ; 675459//Simons Foundation/ ; //University of South Florida/ ; }, mesh = {*Nitrification ; *Nitrous Oxide/metabolism ; *Urea/metabolism ; *Archaea/metabolism/genetics ; *Ammonium Compounds/metabolism ; Oxidation-Reduction ; *Seawater/microbiology/chemistry ; Ammonia/metabolism ; Nitrites/metabolism ; }, abstract = {Nitrification (microbial oxidation of ammonia to nitrite and nitrate) controls nitrogen speciation and is the main source of nitrous oxide (N2O) in the ocean. It was recently shown that the most abundant marine ammonia oxidizers, the ammonia-oxidising archaea (AOA), are also capable of oxidising urea, providing a previously ignored source of nitrite. Here, we show that the relative magnitude of urea and ammonia oxidation rates, and the relative rates of N2O production from the two substrates, is correlated with the ratio of the substrate concentrations. By examining all reported measurements of urea and ammonium concentrations and the paired urea and ammonia oxidation rates, we show that this relationship likely holds across the global ocean. Examination of newly acquired and previously published metagenomic data shows that the fraction of AOA with the genetic capability for urea oxidation increases with the urea:ammonium ratio, rather than depending on the urea or ammonium concentration alone. These results corroborate the correlation between substrate ratios and oxidation rate ratios, and extend it to N2O production. This may help explain the distribution of nitrification rates and N2O production in the ocean.}, }
@article {pmid41052412, year = {2025}, author = {Dias, ME and Breyer, GM and Torres, MC and Wuaden, CR and Rebelatto, R and Kich, JD and Dorn, M and Siqueira, FM}, title = {Overview of the microbiome and resistome of swine manure in commercial piglet farms and its application in grazing soils.}, journal = {Environmental technology}, volume = {}, number = {}, pages = {1-11}, doi = {10.1080/09593330.2025.2566429}, pmid = {41052412}, issn = {1479-487X}, abstract = {The environmental spread of antimicrobial resistance genes (ARGs) through the use of animal manure in agriculture has become a significant concern. This study investigated the impact of applying swine manure treated through biodigestion on the spread of ARGs in agricultural soils in the Midwest region of Brazil. Samples of untreated and treated manure, fertilized soil, and unfertilized soil were collected from three piglet production units. Bacterial communities and ARGs were characterized through metagenomic sequencing and bioinformatics. Bacterial profiles in fertilized and unfertilized soils were highly similar across all farms. In contrast, biodigestion reduced the total number of ARGs in treated manure. Of the 399 ARGs detected in fertilized soils, 67% were also found in unfertilized soils, and 12% were shared exclusively with treated manure. The presence of numerous ARGs in unfertilized soils highlights the role of environmental dissemination routes, such as runoff, dust, or wildlife, in shaping soil resistomes even in areas without manure application. These findings suggest a stable bacterial and resistome profile in soils, regardless of manure application. Although antimicrobial residues were not evaluated, the results reinforce the need for responsible antibiotic use and effective manure management to minimize environmental ARG dissemination.}, }
@article {pmid41052332, year = {2025}, author = {Ni, G and Wang, M and Walker, N and Muetzel, S and Schmidt, O and Fischer, A and Stemmler, RT and Leung, PM and Zhang, X and Li, Q and Jain, S and Jespersen, M and Grinter, R and Archer, SDJ and Pacheco, D and Lowe, K and Pope, PB and Müller, V and Pitta, DW and Janssen, PH and Watson, M and Attwood, GT and Ver Loren van Themaat, E and Kindermann, M and Greening, C}, title = {Methanogenesis inhibition remodels microbial fermentation and stimulates acetogenesis in ruminants.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {41}, pages = {e2514823122}, doi = {10.1073/pnas.2514823122}, pmid = {41052332}, issn = {1091-6490}, support = {APP1178715//Federal Government | DHAC | National Health and Medical Research Council (NHMRC)/ ; FT240100502//Department of Education and Training | Australian Research Council (ARC)/ ; }, mesh = {Animals ; *Methane/metabolism/biosynthesis ; *Fermentation/drug effects ; *Rumen/microbiology/metabolism ; Cattle ; *Gastrointestinal Microbiome/drug effects ; *Propanols/pharmacology ; Animal Feed ; *Ruminants/microbiology/metabolism ; Microbiota/drug effects ; Fatty Acids, Volatile/metabolism ; }, abstract = {Rumen microbiota enable ruminants to grow on fibrous plant materials, but also produce methane, driving 5% of global greenhouse gas emissions and leading to a loss of gross energy content. Methanogenesis inhibitors such as 3-nitrooxypropanol (3-NOP) decrease methane emissions in ruminants when supplemented in feed. Yet we lack a system-wide, species-resolved understanding of how the rumen microbiota remodels following inhibition and how this influences animal production. Here, we conducted a large-scale trial with 51 dairy calves to analyze microbiota responses to 3-NOP, pairing host performance, emissions, and nutritional profiles with genome-resolved metagenomic and metatranscriptomic data. 3-NOP supplementation decreased methane emissions by 62%, modulated short-chain fatty acid and H2 levels, and did not affect dietary intake or animal performance. We created a rumen microbial genome catalogue (27,884 genomes) that mapped to the meta-omic data at high rates. There was a strong reduction of methanogens and stimulation of reductive acetogens, primarily uncultivated lineages such as "Candidatus Faecousia." However, there was a shift in major fermentative communities away from acetate production in response to hydrogen gas accumulation. In vitro incubations recapitulated these results and showed an enrichment of acetate from reductive acetogenesis. Altogether, the divergent responses of the fermentative and hydrogenotrophic communities lead to net hydrogen build-up and limit potential productivity gains from methane reduction. By linking ruminant greenhouse gas emissions and productivity to specific microbial species, this study emphasizes the importance of microbiota-wide analysis for optimizing methane mitigation strategies and identifies promising strategies to simultaneously reduce emissions while increasing animal production.}, }
@article {pmid41052251, year = {2025}, author = {Qin, Z and Yang, Z and Zhang, Y and Qi, L and Peng, Y and Deng, S and Wang, Y}, title = {Biotin Limitation Attenuates Streptococcus mutans Cariogenicity by Disrupting Metabolic Flux and Virulence Pathways.}, journal = {Caries research}, volume = {}, number = {}, pages = {1-24}, doi = {10.1159/000548822}, pmid = {41052251}, issn = {1421-976X}, abstract = {INTRODUCTION: Our previous metagenomic analysis revealed higher frequencies of biotin-related genes (i.e., bioY, bioM, bccP) in caries-active children, indicating a potential role of biotin in caries pathogenesis. This study investigated a biotin limitation strategy against the primary cariogenic bacterium Streptococcus mutans (S. mutans), including its effects on cariogenic phenotypes, gene expression, and metabolomics.<br><br>METHODS: S. mutans UA159 was cultured in biotin-free medium supplemented with different biotin concentrations. The cariogenic phenotypes of the strain, including growth kinetics, biofilm formation, exopolysaccharide (EPS) production, lactate synthesis, acid/oxidative tolerance, and membrane fluidity, were measured and compared across biotin concentrations. Biofilm architecture was visualized via confocal laser-scanning microscopy (CLSM) and scanning electron microscopy (SEM). Quantitative real-time polymerase chain reaction (RT-qPCR) was employed to analyze the expression of genes associated with virulence and biotin metabolism. Metabolomic analysis was performed to characterize metabolic perturbations induced by biotin limitation in S. mutans.<br><br>RESULTS: Under biotin limitation, S. mutans exhibited significantly reduced cariogenic phenotypes, accompanied by cell elongation and reduced membrane fluidity. At the molecular level, biotin limitation suppressed the expression of key virulence-associated genes and induced a compensatory upregulation of genes involved in biotin uptake and biotin-dependent carboxylases. Metabolomic analysis under biotin-limited conditions in S. mutans revealed perturbed pathways in central carbon metabolism and nucleotide metabolism.<br><br>CONCLUSION: Biotin limitation significantly reduced the cariogenic potential of S. mutans by disrupting metabolic flux and virulence gene expression, highlighting biotin uptake and metabolism as potential targets for anti-caries therapies.}, }
@article {pmid41051042, year = {2025}, author = {Nancy,  and Lakhawat, SS and Kumar, R and Sharma, PK}, title = {Cloning, Expression, Purification, and Characterization of Superoxide Dismutase from the Soil Metagenome.}, journal = {Protein and peptide letters}, volume = {}, number = {}, pages = {}, doi = {10.2174/0109298665415743250926072254}, pmid = {41051042}, issn = {1875-5305}, abstract = {INTRODUCTION: Superoxide Dismutases (SODs) are enzymes that catalyze the conversion of toxic free radicals generated during stress conditions into nontoxic forms. Thus, the enzyme superoxide dismutase contributes to the adaptation and survival of microorganisms across a variety of environmental conditions, making it an indispensable enzyme during the response to stress. In this study, we embarked upon investigating and characterizing a Superoxide Dismutase (SOD) from DNA extracted directly from garden soil, where the average temperature ranges from 4°C- 45°C.<br><br>MATERIALS AND METHODS: Metagenomic DNA was extracted by employing a kit. The gene was amplified using PCR. The amplified PCR product was gel eluted and ligated into the pGEMT-easy vector and subcloned into an expression vector. The protein was purified using Ni-NTA chromatography and characterized using biophysical, biochemical, and computational approaches.<br><br>RESULTS: The recombinant SOD was expressed and purified; the purified protein exhibited activity and stability over a broad pH and temperature range, with optimal activity observed at 40&#xb0;C and pH 8, respectively. The enzyme remains completely stable at 40&#xb0;C for 3 h. However, in contrast, it loses 50% of its activity when incubated at 50&#xb0;C and 60&#xb0;C for 3 h. The biophysical investigation revealed stable confirmation of the secondary structure of the protein, as evident from circular dichroism and intrinsic Tryptophan (Trp) fluorescence studies. In silico sequence and structural analysis revealed a close similarity of the SOD reported in this study to the Mn SOD of multi- Bacillus species. Molecular simulation dynamics experiments revealed the all-over conformational stability of protein structures at varying pH, indicating broad pH functioning of the enzyme.<br><br>DISCUSSION: The study provides a comprehensive analysis of the structure and function of a superoxide dismutase enzyme derived from a soil metagenome. A Mn2+ binding site identified in the study offers an opportunity to further facilitate engineering and design of mutant SOD.<br><br>CONCLUSION: The enzyme exhibits distinct attributes that hold significant industrial relevance. Owing to the wide functionality of SOD at different pH and temperature, it can be tailored for its potential industrial applications, which include its therapeutic potential, thus opening new avenues for enhanced antioxidant therapies and novel biocatalyst designing.}, }
@article {pmid41050906, year = {2025}, author = {Wiese, M and Klaassens, ES and Hatt, V and Kreikamp, A and Baak, ML and Heerikhuisen, M and Van Der Vossen, JMBM}, title = {Demonstration of phage inhibitory action against Clostridium perfringens LMG 11264 within a complex chicken cecal microbiota in vitro.}, journal = {Frontiers in antibiotics}, volume = {4}, number = {}, pages = {1599939}, pmid = {41050906}, issn = {2813-2467}, abstract = {INTRODUCTION: Clostridium perfringens strains may cause foodborne illness, and 95% of human infections are linked to the consumption of contaminated meat, including chicken products. In poultry, C. perfringens infection may cause necrotic enteritis, and infections are associated with high mortality rates partially due to antibiotic resistance, which hampers efficient treatment. In-vitro screening approaches of alternative treatment options, for instance, specific phages, represent a promising strategy for the selection of novel interventions to combat infections.<br><br>MATERIAL AND METHODS: In this study, we explored the application of a C. perfringens strain LMG 11264-specific phage #7 introduced at 10[4] pfu/mL to inhibit the growth of C. perfringens at 10[6] cfu/mL compared to two antibiotics (amoxicillin at 10 &#xb5;g/mL and clindamycin at 10 &#xb5;g/mL) within complex chicken cecal microbiota in vitro. Samples for gDNA isolation, qPCR, and metagenome sequencing were taken at the beginning and after 24 and 48 h of incubation.<br><br>RESULTS: The C. perfringens strain LMG 11264 proliferated within the untreated complex microbiota and reached levels of approximately 10[8] and 10[9] genome equivalents per mL after 24 and 48 h of incubation, respectively. The phage intervention with phage #7 inhibited the growth of C. perfringens LMG 11264 significantly; the inhibitory effects were similar to those exerted by the antibiotic intervention with amoxicillin and stronger than the inhibitory effects with clindamycin. In the absence of the C. perfringens challenge, we found a significant effect of amoxicillin (p = 0.040) or clindamycin (p = 0.000017) compared to the untreated control after 24 h of incubation, and the phage addition did not affect the alpha diversity expressed as Chao index significantly (p = 1). In addition, the endogenous C. perfringens in the chicken microbiota appeared insensitive to phage #7. The phage titer of phage #7 only increased in the presence of the inoculated C. perfringens strain LMG 11264. In conclusion, the i-screen model can be implemented to test the efficacy and specificity of phage therapy in vitro.}, }
@article {pmid41050878, year = {2025}, author = {Chetty, C and Mafunda, N and Happel, AU and Khan, A and Cooley Demidkina, B and Yende-Zuma, N and Saidi, Y and Mahabeer Polliah, A and Lewis, L and Osman, F and Radebe, P and Passmore, JS and Kwon, D and Ravel, J and Ngcapu, S and Liebenberg, L and Symul, L and Holmes, S and Mitchell, CM and Potloane, D}, title = {Randomized trial of multi-strain Lactobacillus crispatus vaginal live biotherapeutic products after antibiotic therapy for bacterial vaginosis: study protocol for VIBRANT (vaginal lIve biotherapeutic RANdomized trial).}, journal = {Contemporary clinical trials communications}, volume = {48}, number = {}, pages = {101554}, pmid = {41050878}, issn = {2451-8654}, abstract = {BACKGROUND: Globally, approximately 30 % of women have bacterial vaginosis (BV). Antibiotic treatment is frequently followed by recurrence, likely due to lack of colonization with beneficial lactobacilli.<br><br>METHODS: This is a Phase 1, randomized, placebo-controlled trial of vaginal live biotherapeutic products (LBP) after antibiotic treatment for BV to establish Lactobacillus colonization. The LBP are vaginal tablets containing 6&#xa0;L. crispatus strains (LC106) or 15&#xa0;L. crispatus strains (LC115), at 2 x 10[9] colony forming units (CFU) per dose. Participants with BV in the United States and South Africa will receive seven days of oral metronidazole twice daily and will be randomized 1:1:1:1:1 to: seven days placebo; seven days LC106; three days LC106/four days placebo; seven days LC106 starting day 3 of the metronidazole course; or seven days LC115. Safety will be assessed by the number and percentage of &#x2265; Grade 2 related adverse events during or after product use. The primary outcome is LBP colonization defined as relative abundance &#x2265;5&#xa0;% of any LBP strain or &#x2265;10&#xa0;% of a combination of LBP strains by metagenomic sequencing any time in the 5 weeks after randomization. A generalized linear model will measure the association between treatment group and colonization, adjusting for site.<br><br>CONCLUSIONS: This study seeks to establish proof of concept for a multi-strain LBP to promote vaginal L. crispatus colonization in two geographically distinct populations.<br><br>TRIAL REGISTRATION: South African National Clinical Trials Registry (SANCTR DOH-27-102023-8342; October 27, 2023) and ClinicalTrials.gov (NCT06135974; November 11, 2023).<br><br>PROTOCOL VERSION: 2.0 dated October 03, 2023.}, }
@article {pmid41050761, year = {2025}, author = {Zhou, X and Yang, C and Liu, X and Wang, J and Li, Y and Pan, L and Peng, S and Yu, H and Deng, X}, title = {Clinical performance of metagenomic next-generation sequencing for distinction and diagnosis of Mucorales infection and colonization.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1631960}, pmid = {41050761}, issn = {2235-2988}, mesh = {Humans ; *Mucormycosis/diagnosis/microbiology/drug therapy ; *Mucorales/genetics/isolation &amp; purification/classification ; Male ; Female ; Middle Aged ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Aged ; Adult ; ROC Curve ; Antifungal Agents/therapeutic use ; Microbiota ; }, abstract = {Mucormycosis is a lethal fungal infection disease with high mortality rate. However, investigations assessing the value of metagenomic next-generation sequencing (mNGS) for distinguishing Mucorales infection from colonization are currently insufficient. A retrospective analysis of clinical date from 71 patients at Sichuan Provincial People's Hospital from September 2021 to September 2024 was conducted. The performance of mNGS in distinguishing Mucorales infection from colonization, along with the differences in patients' characteristics, imaging characteristics, antimicrobial adjustment, and microbiota, were examined. Among the 71 patients, 51 were identified as Mucorales infection group (3 proven and 48 probable cases), and 20 were colonization group (possible cases). Receiver operating characteristic (ROC) curve for mNGS indicated an area under the curve of 0.7662 (95%CI: 0.6564-0.8759), with an optimal threshold value of 51 for discriminating Mucorales infection from colonization. The infection group exhibited a higher proportion of antimicrobial adjustments compared to the colonization group (64.71% vs. 35.00%, P < 0.05), with antifungal agent changed being more dominant (43.14% vs. 10.00%, P < 0.01). Mucorales RPTM value, length of hospital stays, hsCRP, immunocompromised, malignant blood tumor, and antifungal changed were significantly positively correlated with Mucorales infection. Rhizomucor pusillus showed significant differences between the two groups. The abundance of Torque teno virus significantly increased in the infection group, whereas the colonization group exhibited higher abundance of Rhizomucor delemar. mNGS is a valuable tool for differentiating colonization from infection of Mucorales. Malignant blood tumor, immunocompromised, length of hospital stays and hsCRP were significant different indicators between patients with Mucorales infection from colonization.}, }
@article {pmid41050671, year = {2025}, author = {Duan, H and Xu, B and Luo, P and Chen, T and Zou, J}, title = {Microbial metabolites and their influence on the tumor microenvironment.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1675677}, pmid = {41050671}, issn = {1664-3224}, mesh = {Humans ; *Tumor Microenvironment/immunology ; *Neoplasms/immunology/metabolism/therapy/microbiology ; Animals ; Immunotherapy ; *Microbiota/immunology ; Fatty Acids, Volatile/metabolism ; }, abstract = {While tumor immunotherapy has achieved remarkable progress in many hematological malignancies, its efficacy remains limited by key challenges, including the immunosuppressive microenvironment of solid tumors, metabolic abnormalities, and drug resistance. As a central mechanism underlying impaired immune function, metabolic reprogramming of immune cells has emerged as a pivotal focus for unraveling tumor immune evasion and therapeutic resistance. Advances in metagenomics have highlighted the significance of the human commensal microbiome as a 'second genome.' Microbial metabolites, whether circulating systemically or accumulating locally, serve as key messengers linking the microbiota to tumor immunometabolism. This review comprehensively examines the regulatory roles and metabolic mechanisms through which microbial metabolites-including short-chain fatty acids (SCFAs), bile acids, tryptophan metabolites, and lipopolysaccharides (LPS)-modulate tumor immunity and immunotherapeutic responses via immune cell metabolism. These metabolites shape the tumor immune microenvironment and influence immunotherapeutic efficacy by reprogramming immune cell metabolic and biosynthetic pathways. This review underscores the central regulatory role of microbial metabolites as the 'second genome' in tumor immunometabolism, offering a theoretical foundation and potential targets to elucidate mechanisms of immunotherapeutic resistance and advance microbiota metabolism-based precision interventions.}, }
@article {pmid41050203, year = {2026}, author = {Wang, Q and Shan, S and Sun, Q and Zhao, X and Yuan, C and Mou, Y and Wang, J and Yan, C and Wang, Q and Rui, Q and Li, C}, title = {The coupling effect of Penicillium baileys W2 in the Aspergillus flavus inhibition and peanut growth promotion.}, journal = {Synthetic and systems biotechnology}, volume = {11}, number = {}, pages = {127-140}, pmid = {41050203}, issn = {2405-805X}, abstract = {Aspergillus flavus is a significant plant pathogen, and peanut crops are particularly vulnerable to aflatoxin contamination. This vulnerability underscores the need for more effective control methods. In this study, the strain Penicillium baileys W2 was isolated from the rhizosphere soils of healthy peanut seedlings. The fermentation extract exhibited concentration-dependent inhibition of pathogenic A. flavus growth, with a minimum inhibitory concentration (MIC) of 55 % and a minimum fungicidal concentration (MFC) of 60 %. Physiological data and transcriptome analysis demonstrated that the W2 fermentation supernatant inhibited A. flavus growth by disrupting membrane permeability. Metabolomics analysis identified active compounds, including propylparaben, taxifolin, and phloretin, which exhibited significant antagonistic effects against A. flavus. Additionally, we evaluated the impact of the W2 fermentation broth on peanut growth promotion and on rhizosphere microbial community structure using metagenomic sequencing. The reduction of harmful soil microorganisms contributed to the maintenance of soil health, whereas the increased abundance of beneficial microorganisms enhanced peanut seedling growth by facilitating soil nutrient cycling. These findings indicate that the development and application of P. baileys strain W2 or its fermentation extract aligns with sustainable agricultural principles and offers a promising biological control approach.}, }
@article {pmid41049781, year = {2025}, author = {Wang, B and He, T and Cheng, Y and Chen, H and Hu, Y and Liu, Y and Wang, F and Chen, L}, title = {Targeted enhancement strategies for Sojae Semen Praeparatum: Impact of Aspergillus oryzae and Bacillus subtilis on microbial communities, flavor substances, and functional components.}, journal = {Food chemistry: X}, volume = {30}, number = {}, pages = {102931}, pmid = {41049781}, issn = {2590-1575}, abstract = {Sojae Semen Praeparatum (SSP), a traditional Chinese fermented soybean product, was optimized through novel single/double enhancement fermentation using Aspergillus oryzae and Bacillus subtilis. Enhanced fermentation significantly increases the production of flavor amino acids. Using headspace solid-phase extraction microextraction gas chromatography-mass spectrometry (HS-SPEM-GC-MS) technology, 51 critical flavor substances were identified, confirming that enhanced fermentation improves the flavor profile of SSP. Isoflavone quantification revealed that enhancement strategies promoted isoflavone conversion. Enzyme inhibition and antioxidant activities were superior in the double enhancement fermentation group. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis demonstrated a significant increase in SSP's enrichment in the flavone and flavonol biosynthesis pathway. Screening identified 19 key flavonoid components strongly correlated with bioactivity, and enhancement fermentation notably enhancing their accumulation. Metagenomic sequencing revealed 14 key differential microorganisms, essential to flavor development and activity enhancement in SSP. This study offers valuable insights for optimizing fermentation processes to enhance product quality.}, }
@article {pmid41049190, year = {2025}, author = {Liu, C and Li, B and Wu, Q and Chen, D and Zhou, W and Ao, J}, title = {The effects and mechanism of urease inhibitor and its combination with nitrification inhibitor on nitrous oxide emission across four soil types.}, journal = {Frontiers in plant science}, volume = {16}, number = {}, pages = {1663261}, pmid = {41049190}, issn = {1664-462X}, abstract = {Nitrogen (N) fertilization is essential for ensuring crop productivity, while excessive N application significantly increases greenhouse gases (GHGs) emissions, particularly nitrous oxide (N2O). Urease inhibitors (UI) and combined urease and nitrification inhibitors (UN) have demonstrated potential in mitigating GHGs emission, though their efficiency with great variation across different soils types. In this study, controlled incubation experiments were conducted using four types of agricultural soils to evaluate the mitigation potential of UI and UN application and to investigate their underlying mechanisms. N fertilization significantly increased N2O emissions by 5.1~99.9-fold and elevated CO2 emissions by 13.6~65.4% across all soil types. The UI treatment decreased the peak of NO2 [-] concentrations in two alkaline soils, while the UN treatment decreased both NO2 [-] and NO3 [-] concentrations in all four soils. In terms of GHG mitigation, UI treatment reduced N2O emissions by 16.5~57.4% in alkaline soils and reduced CO2 emissions by 6.5~49.3% across four soil types. The UN treatment demonstrated superior efficacy, reducing N2O emissions by 52.5~92.4% and CO2 emissions by 4.2~87.2% across all soils. Metagenomic sequencing revealed that both UI and UN significantly inhibited the relative abundances of key functional genes associated with nitrification (hao and nxrAB), dissimilatory nitrate reduction (narGHI/napAB), nitrite reduction (nirS/nirK), and nitric oxide reduction (norBC). Random forest identified key factors influencing the N2O mitigation efficiency of UI and UN. These included soil properties such as soil pH, total nitrogen, organic matter, available potassium, water-filled pore space, texture. Additionally, partial functional genes related to nitrification, denitrification, carbon and methane metabolism, sulfur and phosphorus cycling were also identified as key contributors. Overall, these findings provide valuable insights for the region-specific application of UI and UN to effectively mitigate GHGs emissions. The identification of key soil abiotic and biotic factors offers a theoretical foundation for optimizing inhibitors application and enhancing their mitigation efficiency.}, }
@article {pmid41049022, year = {2025}, author = {Cohodes, M and Fernandez, A and Ashkin, D and Reed, C and Park, S and Banaei, N and Fung, M and Jacobson, K and Goswami, ND}, title = {Curated cases from the TB expert network: Unplugged! Series: Use of plasma microbial cell-free DNA metagenomic sequencing to diagnose Mycobacterium tuberculosis.}, journal = {Journal of clinical tuberculosis and other mycobacterial diseases}, volume = {41}, number = {}, pages = {100563}, pmid = {41049022}, issn = {2405-5794}, abstract = {A 52-year-old U.S.-born man with diabetes and a kidney transplant 3 months prior presented with fever of unknown origin and left-sided weakness. On admission, he was found to have right internal carotid artery thrombus and cerebral infarct. He developed respiratory failure and underwent treatment for Pseudomonas bacteremia. Fevers continued through hospital day 30 and computed tomography (CT) scans demonstrated an esophageal mass, hepatic lesions, and pulmonary nodules, which were new compared to pre-transplant imaging 2 years prior. While awaiting results from acid-fast bacilli (AFB) cultures from sputum and tissue, plasma microbial cell-free DNA (mcfDNA) metagenomic sequencing was ordered on day 29 and was positive for Mycobacterium Tuberculosis (Mtb). Based on the results of mcfDNA sequencing, clinical presentation, and radiographic findings, a diagnosis of tuberculosis disease was made, and anti-tuberculosis treatment was initiated. While awaiting results from acid-fast bacilli (AFB) cultures and molecular studies from sputum and tissue, plasma microbial cell-free DNA (mcfDNA) metagenomic sequencing was ordered on day 29 and was positive for Mycobacterium Tuberculosis (Mtb). The patient was discharged on hospital day 60; 27 days after discharge, 58 days after the Mtb PCR resulted positive from tissue biopsy, and 60 days after the positive mcfDNA, sputum cultures returned positive for Mycobacterium tuberculosis.}, }
@article {pmid41048510, year = {2025}, author = {Mieremet, A and van der Wurff, M and Pagan, L and Ferrer-González, E and Seo, J and Schuren, FHJ}, title = {Taxonomic and functional profiling of the vulvar microbiome indicates variations related to ecological signatures, aging, and health status.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1633147}, pmid = {41048510}, issn = {1664-302X}, abstract = {INTRODUCTION: The vulvar microbiome is adjacent to that of the skin and the vagina and connects microbiomes present on a stratified epithelial barrier to that of a mucosal barrier. Yet, the characterization of the microbiome in the vulvar region of the body is understudied, although dysbiosis in the microbiome of the skin or vagina have been linked to impairments in women's health.<br><br>METHODS: To better understand the role of the vulvar microbiome during healthy aging or during presentation of vulvar diseases, we analyzed the vulvar microbiome by shotgun metagenomic sequencing on composition at species level and for functional capacity. This was performed in a large population enrolled in the Vulvar Microbiome Leiden Cohort (VMLC), including a total of 58 healthy women in a broad age range (22-82 years). Moreover, we analyzed vulvar microbiome derived from 9 participants presenting a vulvar disease, including vulvar lichen sclerosus (LS; N = 6), or high-grade squamous intraepithelial lesion (HSIL; N = 3).<br><br>RESULTS: Compositional analyses showed a skin-, vagina-, or multispecies mixture- dominant bacterial signature, which revealed differences in the alpha diversity and functional capacity of the microbiome. Upon aging the presence of Lactobacillus iners, L. crispatus, and L. gasseri in the vulvar microbiome shifted toward reduction. In the microbiome of individuals with a vulvar disease, higher abundance of Staphylococcus hominis, Micrococcus luteus, Corynebacterium amycolatum, and Corynebacterium simulans was detected, and an altered functional capacity for the L-histidine pathway.<br><br>DISCUSSION: In conclusion, we identified variations in microbial taxa and functional capacities in the vulvar microbiome that are associated with age and disease (LS and HSIL), which can be targeted to develop microbiome-based vulvar therapies promoting women's health.}, }
@article {pmid41048504, year = {2025}, author = {Ai, X and Huang, C and Liu, Q and Duan, R and Ma, X and Li, L and Shu, Z and Miao, Y and Shen, H and Lv, Y and Jiang, Z and Luo, H and Long, Z}, title = {Gut microbiome dynamics and functional shifts in healthy aging: insights from a metagenomic study.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1629811}, pmid = {41048504}, issn = {1664-302X}, abstract = {INTRODUCTION: Population aging represents a significant challenge in contemporary society. The gut microbiome plays a critical role in maintaining host health and physiological functions, and its alterations with advancing age are closely associated with the process of healthy aging.<br><br>METHODS: This study conducted a comprehensive analysis of the gut microbiome in hundred healthy elderly individuals (aged &#x2265;60) residing in Changshou Town, Zhongxiang City, Hubei Province, utilizing metagenomic sequencing technology. The primary objective was to investigate the changes in the gut microbiome and its potential functions during the latter stages of life. Participants were categorized into three distinct age groups: the Young-Old group (YO, ages 60-74), the Middle-Old group (MO, ages 75-89), and the Long-Lived Old group (LO, ages 90-99).<br><br>RESULTS: The findings indicate that the diversity of the gut microbiome tends to diminish with age. However, a significant reversal was observed among healthy longevity elderly individuals. Our analysis specifically focused on the trends in the alterations of gut microbiome species and their potential functions as age increases, revealing that the changes in major differential functions closely align with the trends in major differential species, demonstrating a strong positive correlation. The YO group exhibited a more diverse array of differential microbial characteristics and functional traits. Notably, there was a significant enrichment of Bacteroides stercoris in the YO group, which displayed a continuous decline with age, alongside a marked enrichment of pathways associated with xenobiotic biodegradation and metabolism. Furthermore, species significantly linked to aging-related pathways, such as oxidative phosphorylation, were identified through species functional correlation analysis. Specifically, Collinsella bouchesdurhonensis and Prevotella stercorea were enriched in the LO and YO groups, respectively. In total, we successfully obtained two hundred and thirty eight high-quality bins through metagenomic assembly, which included the identification of four species with 100% completeness, as well as the genomic information of the Methanobrevibacter smithii A across all groups.<br><br>DISCUSSION: This study characterizes the age-associated trends in gut microbiome composition and function during later-life healthy aging, providing exploratory insights that may inform future microecological intervention strategies, pending validation in longitudinal studies.}, }
@article {pmid41048502, year = {2025}, author = {Peng, X and Wei, Y and Zhou, X}, title = {Enhancing pathogen identification through AI-assisted metagenomic sequencing.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1634194}, pmid = {41048502}, issn = {1664-302X}, abstract = {INTRODUCTION: To address the limitations of current metagenomic identification approaches, we proposed a principled AI-assisted architecture that enhances accuracy, scalability, and biological interpretability through three core innovations.<br><br>METHODS: Firstly, we developed a structured probabilistic model that formulates pathogen detection as a hierarchical and compositional inference task under taxonomic and ecological constraints. This framework enables the integration of phylogenetic priors and sparsity-aware mechanisms, reducing noise and ambiguity. By modeling taxonomic structure and ecological dependencies, the approach ensures more accurate identification, especially in complex or low-abundance microbial communities. Secondly, we introduced the Taxon-aware Compositional Inference Network (TCINet), a deep learning model that processes sequencing reads to produce taxonomic embeddings. TCINet estimates abundance distributions via masked neural activations that enforce sparsity and interpretability, while also propagating uncertainty through log-normal variance modeling. Designed to respect microbial phylogeny and co-occurrence patterns, TCINet enables scalable, biologically plausible inference across diverse clinical and environmental datasets. Thirdly, we presented the Hierarchical Taxonomic Reasoning Strategy (HTRS), a post-inference module that refines predictions by enforcing compositional constraints, propagating evidence across taxonomic hierarchies, and calibrating confidence using entropy and variance-based metrics. HTRS includes context-aware thresholding and co-occurrence priors to adaptively optimize performance based on dataset characteristics.<br><br>RESULTS: Together, these innovations create a unified framework for metagenomic identification that combines probabilistic modeling, deep learning, and structured reasoning.<br><br>DISCUSSION: The architecture delivers robust and interpretable results, making it suitable for applications in clinical diagnostics, environmental monitoring, and ecological research.}, }
@article {pmid41048492, year = {2025}, author = {Chen, X and Yu, D and Yan, Y and Yuan, C and He, J}, title = {Soil viruses drive carbon turnover during subtropical secondary forest succession.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1633379}, pmid = {41048492}, issn = {1664-302X}, abstract = {INTRODUCTION: Soil viruses are increasingly recognized as key regulators of microbial ecology and ecosystem function, yet their roles in forest ecosystems, particularly during natural secondary succession, remain largely unexplored.<br><br>METHODS: We examined soil viral communities across five successional stages of secondary forests to investigate their taxonomic dynamics and functional potential. Using high-throughput viral metagenomics, we characterized viral community structure, abundance, and auxiliary metabolic gene content.<br><br>RESULTS: Our results demonstrate that soil viral abundance and community composition shift significantly with forest stand age. Viral richness increased during succession, with compositional transitions observed across stages; however, tailed bacteriophages consistently dominated. Structural equation modeling and linear mixed-effects analysis identified soil pH and bacterial diversity as primary environmental determinants of viral diversity. Functionally, soil viruses harbored auxiliary metabolic genes related to carbohydrate metabolism, indicating their potential involvement in modulating host metabolic processes. Successional trends in viral functional profiles revealed a transition from carbon assimilation to carbon release pathways, suggesting viral mediation of carbon turnover. Notably, the enrichment of glycoside hydrolase and glycosyl transferase genes across forest ages implies a role for viruses in shaping microbial carbon processing capacities through carbohydrate-active enzyme contributions.<br><br>DISCUSSION: These findings provide novel evidence that soil viruses actively participate in ecosystem succession by influencing microbial functional potential and biogeochemical cycling. This study underscores the ecological importance of soil viral communities in regulating carbon dynamics during secondary forest development.}, }
@article {pmid41048389, year = {2025}, author = {Kong, S and Abrams, E and Binik, Y and Cappelli, C and Chu, M and Cornett, T and Culbertson, I and Garcia, E and Henry, J and Lam, K and Lampman, DB and Morenko, G and Rivera, I and Swift, T and Torres, I and Velez, R and Waxman, E and Wessely, S and Yuen, A and Lardner, CK and Weissman, JL}, title = {Metagenomes and metagenome-assembled genomes from tidal lagoons at a New York City waterfront park.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e20081}, pmid = {41048389}, issn = {2167-8359}, mesh = {New York City ; *Metagenome ; *Parks, Recreational ; Metagenomics ; Humans ; *Seawater/microbiology ; Microbiota/genetics ; *Water Microbiology ; }, abstract = {New York City parks serve as potential sites of both social and physical climate resilience, but relatively little is known about how microbial organisms and processes contribute to the functioning of these deeply human-impacted ecosystems. We report the sequencing and analysis of 15 shotgun metagenomes, including the reconstruction of 129 high-quality metagenome-assembled genomes, from tidal lagoons and bay water at Bush Terminal Piers Park in Brooklyn, NY sampled from July to September 2024. Our metagenomic database for this site provides an important baseline for ongoing studies of the microbial communities of public parks and waterfront areas in NYC. In particular, we provide rich functional and taxonomic annotations that enable the use of these metagenomes and metagenome-assembled genomes for a wide variety of downstream applications.}, }
@article {pmid41048206, year = {2025}, author = {Tao, H and Zheng, W}, title = {Non-Tuberculous Mycobacterial Infections of the Skin and Soft Tissue in a Chinese Population: A Retrospective Analysis of 15 Cases.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {5139-5147}, pmid = {41048206}, issn = {1178-6973}, abstract = {BACKGROUND: Non-tuberculous mycobacteria (NTM) skin and soft tissue infections (SSTIs) are increasingly recognized but underdiagnosed in China.<br><br>METHODS: This retrospective study analyzed 15 confirmed cases of NTM SSTIs treated at a southern Chinese hospital from 2012 to 2022. Clinical data, including demographics, clinical presentations, comorbidities, diagnostic methods, treatment regimens, and outcomes, were collected and analyzed. Diagnostic efficacy of conventional culture and metagenomic next-generation sequencing (mNGS) was compared.<br><br>RESULTS: The median age of patients was 57 years, and 66.7% were farmers. Pathogens identified included Mycobacterium abscessus (20.0%), M. marinum (13.3%), and rapidly growing mycobacteria (13.3%). Immunocompromised states, such as anti-interferon-gamma autoantibody positivity, were present in 40.0%. mNGS demonstrated superior diagnostic performance, achieving a detection rate of 86.7% (13/15 cases), compared to 26.7% for culture. Treatment regimens, including clarithromycin, rifampin, ethambutol, and moxifloxacin, lasted 1-24 months. Outcomes showed cure in 8 patients (53.3%), improvement in 6 (40.0%), and 1 lost to follow-up.<br><br>CONCLUSION: NTM SSTIs present significant diagnostic and therapeutic challenges, with clinical variability and frequent association with immunocompromised states. M. abscessus, M. marinum, and M. avium were the predominant pathogens. mNGS improves detection but still should complement culture. Precise pathogen identification and tailored therapy are essential for achieving optimal outcomes, and further studies are needed to refine diagnostics and treatment strategies.}, }
@article {pmid41048034, year = {2025}, author = {Wright, SL and Abdul-Aziz, M and Blaha, GN and Ta, CK and Gancz, A and Ademola-Popoola, IJ and Szécsényi-Nagy, A and Sereno, PC and Weyrich, LS}, title = {Wet Lab Protocols Matter: Choice of DNA Extraction and Library Preparation Protocols Bias Ancient Oral Microbiome Recovery.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e70054}, doi = {10.1111/1755-0998.70054}, pmid = {41048034}, issn = {1755-0998}, abstract = {Ancient DNA (aDNA) analysis of archaeological dental calculus has provided a wealth of insights into ancient health, demography and lifestyles. However, the workflow for ancient metagenomics is still evolving, raising concerns about reproducibility. Few systematic investigations have examined how DNA extraction methods and library preparation protocols influence ancient oral microbiome recovery, despite evidence from modern populations suggesting that they do. This leaves a gap in our understanding of how wet-lab protocols impact aDNA recovery from dental calculus. In this study, we apply two DNA extraction and two library preparation methods in the aDNA field on dental calculus samples from Hungary and Niger. Samples from each context have similar chronological ages, but differences in their levels of aDNA preservation are notable, providing additional insights into how the efficacy of wet-lab protocols is impacted by sample preservation. Several metrics were employed to assess intra- and inter-sample variability, such as DNA fragment length recovery, GC content, clonality, endogenous content, DNA deamination and microbial composition. Our findings indicate that both DNA extraction and library preparation protocols can considerably impact ancient DNA recovery from archaeological dental calculus. Furthermore, no single protocol consistently outperformed the others across all assessments, and the effectiveness of specific protocol combinations depended on the preservation of the sample. These findings highlight the challenges of meta-analyses and underscore the need to account for technical variability. Lastly, our study raises the question of whether the field should strive to standardise methods for comparability or optimise protocols based on sample preservation and specific research objectives.}, }
@article {pmid41046791, year = {2025}, author = {Wang, H and Chen, H and Ruan, C and Liao, J and Schwarz, C and Shi, B and Alvarez, PJJ and Yu, P}, title = {Nanoplastics induce prophage activation and quorum sensing to enhance biofilm mechanical and chemical resilience.}, journal = {Water research}, volume = {288}, number = {Pt B}, pages = {124712}, doi = {10.1016/j.watres.2025.124712}, pmid = {41046791}, issn = {1879-2448}, abstract = {Despite the prevalence of nanoplastics (NPs) in natural and engineered water systems and their association with microbial risks, bacterium-phage interactions have been largely overlooked in the context of biofilm formation. Here, we investigated the effects of positively (PS-NH2) and negatively (PS-COOH) charged polystyrene nanoplastics (PS-NPs) on dual-species biofilms composed of Escherichia coli (λ+) and Pseudomonas aeruginosa. PS-NPs promoted biofilm formation and stability at environmentally relevant concentrations (e.g., 100-1000 ng/L), with PS-NH2 exhibiting higher influence. The cellular internalization of PS-NPs increased the reactive oxygen species (ROS) levels by 2.18-2.25 folds, triggered prophage λ activation followed by lysis of E. coli (λ+) after exposure to PS-NPs. Transcriptomic analyses revealed that PS-NPs, especially PS-NH2, activated the SOS response (2.35-2.63-fold), λ phage replication (2.68-3.97-fold), and interspecies quorum sensing (2.24-5.13-fold), which was verified by the proteomic analyses. Therefore, PS-NPs stimulated protective extracellular polymeric substances (EPS) secretion with eDNA content increased to 325.8-433.8 μg/cm[2]. Enhanced EPS production contributed to improved biofilm mechanical properties (1.46-1.57-fold as measured by atomic force microscopy) and increased resistance to chlorine disinfection. Metagenomic analysis of pipeline biofilm demonstrated that PS-NPs promoted bacterium-phage interactions and enhanced bacterial antiviral defense systems, which stimulated multi-species biofilm formation and enhanced environmental resilience. Overall, our findings provide novel insights into the interplay between nanoplastics and bacterium-phage dynamics, highlighting increased microbial risks associated with waterborne nanoplastics.}, }
@article {pmid41046720, year = {2025}, author = {Yang, J and Wang, S and Heal, KV and Chen, L and Zhou, C}, title = {Microbial functional groups activate insoluble rhizosphere phosphorus to mitigate P limitation of Chinese fir plantations.}, journal = {Journal of environmental management}, volume = {394}, number = {}, pages = {127503}, doi = {10.1016/j.jenvman.2025.127503}, pmid = {41046720}, issn = {1095-8630}, abstract = {The decline in soil phosphorus (P) reserves and its low solubility pose significant challenges in long-term plantation cultivation. In P-limited subtropical environments, the rhizosphere microbial community and associated genes play a crucial role in driving P cycling and availability during the long-term development of forest plantations. Using the space-for-time substitution method, we investigated rhizosphere P cycling in Chinese fir (Cunninghamia lanceolata) plantations at different growth stages in Fujian Province, southern China. We utilized the modified Hedley fractionation method and metagenomic sequencing for rhizosphere soil samples from stand ages of 6, 26, 45, and 102 years. The results revealed that, with stand development, rhizospheric concentrations of total, stable and moderately labile P decreased significantly, whereas labile P became progressively enriched (P < 0.05). Genes involved in organic P mineralization and P transport were positively correlated with labile P concentrations in the rhizosphere (P < 0.05), whereas P metabolism regulatory genes were negatively correlated with moderately labile P (P < 0.05). Additionally, the dominant P-solubilizing bacteria-Bacteroidetes and Rudaea-exerted significant positive effects on labile P and negative effects on stable P, respectively (P < 0.05). Overall, rhizospheric P reserves were significantly depleted in the Chinese fir plantations during their developmental progression. However, this unsustainable trend in P reserves was mitigated through synergistic interactions between P-solubilizing bacteria and P metabolism genes, which catalyzed the conversion of insoluble P into labile P, while enhancing plant P uptake efficiency. Consequently, we propose science-informed management practices-such as optimizing P fertilization management, inoculating P-solubilizing microbial agents, utilizing organic fertilizers, and introducing native broadleaf species-to sustain functional stability and long-term productivity of subtropical plantation ecosystems.}, }
@article {pmid41000811, year = {2025}, author = {Konnaris, MA and Saxena, M and Lazar, N and Silverman, JD}, title = {Uncertainty Modeling Outperforms Machine Learning for Microbiome Data Analysis.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41000811}, issn = {2692-8205}, abstract = {Microbiome sequencing measures relative rather than absolute abundances, providing no direct information about total microbial load. Normalization methods attempt to compensate, but rely on strong, often untestable assumptions that can bias inference. Experimental measurements of load (e.g., qPCR, flow cytometry) offer a solution, but remain costly and uncommon. A recent high-profile study proposed that machine learning could bypass this limitation by predicting microbial load from sequencing data alone. To evaluate this claim, we assembled mutt, the largest public database of paired sequencing and load measurements, spanning 35 studies and over 15,000 samples. Using mutt, we show that published machine learning models fail to generalize: on average they perform worse than a naive baseline that always predicted the training set mean. These failures stem from covariate shift-limited shared taxa between studies, differences in community composition, and differences in preprocessing pipelines-that silently derail model inputs. In contrast, Bayesian partially identified models do not attempt to impute microbial load, but instead propagate scale uncertainty through downstream analyses. Across 30 benchmark datasets, Bayesian partially identified models consistently outperformed normalization and machine learning approaches, providing a principled and reproducible foundation for microbiome inference.}, }
@article {pmid41046693, year = {2025}, author = {Theysgeur, S and Dugardin, C and Louvel, B and Lemière, S and Muchembled, J and Taminiau, B and Daube, G and Siah, A and Ravallec, R and Hilbert, JL and Lucau-Danila, A}, title = {Assessment of health effects of potato crop phytopharmaceuticals and storage products in a murine model.}, journal = {The Science of the total environment}, volume = {1002}, number = {}, pages = {180630}, doi = {10.1016/j.scitotenv.2025.180630}, pmid = {41046693}, issn = {1879-1026}, abstract = {Potatoes are among the most widely consumed staple foods worldwide, but their cultivation and storage frequently involve multiple phytopharmaceutical products (PPPs), raising concerns about the health risks of dietary pesticide residues. The health effects of multi-residue PPPs used in potato cultivation were assessed in an in vivo murine model, involving 36 mice, and evaluated through omics analyses. Two field cultivation methods (conventional and organic) and two post-harvest storage conditions (using 1,4-dimethylnaphthalene and mint essential oil as sprout inhibitor treatments) were considered. Potato tubers were processed into flour and administered to the animals at a moderate daily dose for 20 consecutive days. Nutrigenomic analyses revealed significant gene deregulations, with 70 genes affected in the liver, 56 in the jejunum, and 52 in the brain, suggesting disturbances in cellular proliferation, nervous system functions, lipid and carbohydrate metabolism, reproductive health, and immune responses. Metagenomic analyses indicated microbiota imbalances, including a shift in the Firmicutes/Bacteroidota ratio and changes in 2 bacterial genera with potentially adverse effects. The main residues suspected of producing these effects include propamocarb, carfentrazone, 1,4-dimethylnaphthalene, copper derivatives, and peppermint essential oil. These findings highlight the importance of large-scale omics approaches in uncovering potential biological disruptions, underscore the health risks associated with chronic dietary exposure to pesticide residues, particularly in mixtures, and emphasize the need to reassess regulatory standards to promote agricultural practices that minimize pesticide residues to better protect the environment and human health.}, }
@article {pmid41046691, year = {2025}, author = {Zhang, N and Li, W and Wang, H and Lv, G}, title = {Metabolomic insights into rhizosphere microbial dynamics in desert plants under drought stress.}, journal = {The Science of the total environment}, volume = {1002}, number = {}, pages = {180653}, doi = {10.1016/j.scitotenv.2025.180653}, pmid = {41046691}, issn = {1879-1026}, abstract = {Drought hinders plant growth and development. However, studies on rhizospheric metabolism and microbial composition of desert plants under drought stress are limited. This study used untargeted metabolomics to detect that the differential metabolites included mainly alkaloids and their derivatives, benzenoids, lipids, and lipid molecules under drought stress. A Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that the differences between drought stress in the rhizosphere environment were usually reflected in microbial metabolism, plant hormone biosynthesis, and secondary metabolite biosynthesis in different environments. Metagenomic analysis showed that the relative abundances of Chloroflexi, Firmicutes, and Gemmatimonadetes in the mild drought rhizosphere group (MiR) were significantly higher than those in the severe drought rhizospheric soil group (SR) in the phylum of the microorganisms; the relative abundance of Proteobacteria in the SR group was also significantly higher. Through the analysis of the correlation network, it is found that there is a significant correlation between microorganisms and differential metabolites. During drought stress, plants can indirectly influence the support of soil microbes by modifying the structure and concentration of metabolites, which helps to enhance drought tolerance. This study provides a theoretical basis for exploring new stress adaptation strategies and protecting soil microecology.}, }
@article {pmid41046678, year = {2025}, author = {Alhaboub, A and Deschenes, NM and Li, XX and Williams, VR and Katz, KC and Park, SY and Aftanas, P and Wong, H and Sjaarda, C and Tozer, K and Maguire, F and Leis, J and Sheth, P and Kozak, R}, title = {Some assembly required: Comparison of bioinformatic pipelines for analysis of viral metagenomic sequencing from nosocomial respiratory virus outbreaks.}, journal = {Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology}, volume = {181}, number = {}, pages = {105877}, doi = {10.1016/j.jcv.2025.105877}, pmid = {41046678}, issn = {1873-5967}, abstract = {INTRODUCTION: Metagenomic sequencing (mGS) is a useful tool for identifying pathogens in patient samples. During nosocomial outbreaks of respiratory viruses, mGS allows for the identification of viral strains and provides insight into their genetic relatedness. Multiple bioinformatics analysis assembler are available for processing data, but a comprehensive comparison of their performance in for respiratory virus outbreaks has not been conducted.<br><br>METHODS: This study sequenced samples from five separate nosocomial outbreaks of RNA respiratory viruses. RNA was extracted from the samples, and cDNA was synthesized using random hexamers, and then sequenced on an Illumina Miniseq following Nextera DNA Flex library preparation. The data from each outbreak were analyzed using four different assemblers: MEGAHIT, rnaSPAdes, rnaviralSPAdes, and coronaSPAdes, to evaluate their analytical performance.<br><br>RESULTS: The mGS confirmed the viral identification and provided accurate strain identification for both coronavirus and parainfluenza virus samples. However, differences were observed between the assemblers in terms of the largest contigs produced and the proportion of the viral genome aligned with reference genomes. Notably, coronaSpades outperformed the other pipelines for analyzing seasonal coronaviruses, generating more complete data and covering a higher percentage of the viral genome.<br><br>CONCLUSION: Achieving a higher percentage of the viral genome sequence is crucial for a more detailed characterization, which is especially valuable for outbreak analysis where viral strains may only differ by a few genetic changes. Comparison of assemblers will allow for clinical laboratories to determine the bioinformatic pipeline that is optimal for helping clinicians better manage outbreaks.}, }
@article {pmid41046586, year = {2025}, author = {Kwiatkowska, AM and Guzmán, JA and Lafaurie, GI and Castillo, DM and Cardona, AF}, title = {Exploring the role of the oral microbiome in saliva, sputum, bronchoalveolar fluid, and lung cancer tumor tissue: A systematic review.}, journal = {Translational oncology}, volume = {62}, number = {}, pages = {102557}, doi = {10.1016/j.tranon.2025.102557}, pmid = {41046586}, issn = {1936-5233}, abstract = {OBJECTIVE: To explore the association between the oral microbiome and the presence or progression of lung cancer (LC) using metagenomic sequencing techniques.<br><br>METHODS: Databases, including PubMed and EMBASE, were reviewed. Eligible studies included the study of oral microorganisms via genomic sequencing and molecular mechanisms associated with LC in saliva, sputum, bronchoalveolar lavage fluid (BALF), or tumor tissue from LC patients. A quality analysis of the studies was carried out, and a qualitative synthesis was performed according to the localization and sample type. Meta-analysis was performed on alpha diversity indexes.<br><br>RESULTS: Of the 1880 scrutinized articles, 50 studies were selected, comprising 29 cross-sectional, 7 case-control, and 14 cohort studies. The quality analysis sheds light on potential biases. The findings revealed a conspicuous overgrowth of specific microbial taxa in LC patients' saliva BALF samples of Veillonella and Streptococcus. Conversely, the Bacteroides genus, related to periodontal disease, exhibited no significant correlation with LC. Microorganisms in tumoral tissue were associated with poor prognosis. Veillonella was associated with a better response to ICIs therapy. Oral microorganisms were related to metabolic reprogramming with xenobiotic biodegradation, amino acid, sugar, sucrose, and lipidic metabolism, immune modulation, and proinflammatory responses.<br><br>CONCLUSION: Overgrowth of specific oral microorganisms in the saliva and BALF is associated with diagnosis, poor prognosis, and low response to immunotherapy. Veillonella could be a marker for response to ICIs therapy. Further well-designed studies should evaluate the impact of the oral microbiome on the response to ICIs.}, }
@article {pmid41045990, year = {2025}, author = {Liu, Y and Zheng, Y and Wang, L and Guo, Y and Huang, G and Yuan, Z and Wang, F and Gai, W and Xing, J}, title = {Bacteriophage combined with mNGS enhances the specificity of bacterial infection diagnosis.}, journal = {The Journal of infection}, volume = {}, number = {}, pages = {106618}, doi = {10.1016/j.jinf.2025.106618}, pmid = {41045990}, issn = {1532-2742}, abstract = {INTRODUCTION: Metagenomic next-generation sequencing (mNGS) is an important tool for enhancing pathogen detection in infected patients. However, distinguishing between specimens that are infected or colonized is still a major challenge.<br><br>OBJECTIVES: To explore the composition of bacteriophages in the blood and respiratory tract of the human body, the association between bacteriophage detection and bacterial infections, and whether bacteriophages can assist in differentiating infectious pathogens according to mNGS results.<br><br>METHODS: Clinical samples from hospitalized patients were collected between January 2023 and February 2024. DNA and cell-free DNA were extracted from BALF and plasma retrospectively to identify the pathogens present, and bacteriophage annotations were conducted.<br><br>RESULTS: A total of 299 samples, comprising 136 blood samples and 163 BALF samples, were obtained from 218 patients. Compared with the samples negative for bacteria, both blood and bronchoalveolar lavage fluid (BALF) samples infected with Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa, and S. aureus showed a corresponding increase in the proportions of phages related to these pathogens. In BALF samples with Acinetobacter baumannii infection, the proportions of Autographiviridae, Siphoviridae, and Myoviridae were significantly greater than those in the Acinetobacter baumannii colonization group. The sensitivity of Myoviridae for differentiating between infection and colonization was 86.36%, and the specificity was 52.94%.<br><br>CONCLUSION: In sepsis, compared with conventional mNGS methods alone, the use of bacteriophages combined with mNGS was more effective in identifying causative pathogens and had higher specificity. These findings may provide new ideas and tools for improving clinical infection diagnosis.}, }
@article {pmid41045972, year = {2025}, author = {Song, X and Meng, H and Yang, T and Li, Y and Zheng, F and Yan, X}, title = {Female accessory reproductive glands of Paederus fuscipes serve as a reservoir of symbiotic pederin-producing bacteria.}, journal = {Insect biochemistry and molecular biology}, volume = {}, number = {}, pages = {104408}, doi = {10.1016/j.ibmb.2025.104408}, pmid = {41045972}, issn = {1879-0240}, abstract = {Paederus fuscipes, an ecologically and medically important species, is known for its blistering toxin pederin in hemolymph. Evidence demonstrates that the toxin is synthesized by the uncultured symbiotic pederin-producing bacteria (PPB) in P. fuscipes, but the biological characteristics of PPB within the beetle host remain poorly characterized. Here, we investigated PPB abundance variations in P. fuscipes across different factors (sexes, life stages, habitats, and organs), along with their colonization sites and metabolic potentials. The findings revealed that the PPB abundance in female P. fuscipes at the level of individuals and tissues exhibited stable colonization patterns, independent of habitat and time changes. Notably, PPB dominated the bacterial community in females (relative abundance ≥ 66.08%) and nearly occupied reproductive organs (relative abundance ≥ 96.31%). Moreover, our results indicated that PPB were predominantly enriched in the accessory glands of female reproductive organs, which could serve as a reservoir for PPB proliferation. Although PPB were not cultured in this study, metagenomic binning yielded the draft genome of PPB (CheckM completeness = 85.14%, contamination = 0), in which genes related to pederin biosynthesis were identified. Phylogenetic analyses revealed that PPB formed a sister clade to Pseudomonas aeruginosa rather than nesting within the P. aeruginosa lineage. Metabolic module prediction analysis revealed specific deficiencies in PPB's energy metabolism and amino acid biosynthesis pathways, suggesting limited free-living potential for PPB. Collectively, this study provides insights into PPB biological characteristics within their beetle host and paves the way for biotechnological exploitation related to pederin production.}, }
@article {pmid41045941, year = {2025}, author = {Alcolea-Medina, A and Snell, LB and Humayun, G and Al-Yaakoubi, N and Ward, D and Alder, C and Patel, V and Vivian, F and Meadows, CIS and Wyncoll, D and Paul, R and Barratt, N and Batra, R and Edgeworth, J and Nebbia, G and Whitehorn, J}, title = {Rapid pan-microbial metagenomics for pathogen detection and personalised therapy in the intensive care unit: a single-centre prospective observational study.}, journal = {The Lancet. Microbe}, volume = {}, number = {}, pages = {101174}, doi = {10.1016/j.lanmic.2025.101174}, pmid = {41045941}, issn = {2666-5247}, abstract = {BACKGROUND: Most clinical metagenomic studies do not provide rapid results, detect pathogens from all microbial kingdoms, or measure clinical impacts. We aimed to evaluate the feasibility, performance, and clinical impacts of a rapid pan-microbial respiratory metagenomic service for patients admitted to intensive care units (ICUs).<br><br>METHODS: This was a single-centre observational study of a rapid metagenomics service that tests respiratory samples from ICU patients at Guy's and St Thomas' hospitals, London, UK, between Dec 5, 2023, and April 12, 2024. Testing used a previously published pan-microbial metagenomics workflow, which simultaneously detects bacteria, fungi, and DNA and RNA viruses; provides same-day preliminary results after 2 h; and provides final results after 24 h. Patients were included if they were aged 18 years or older, admitted to the ICU, had confirmed respiratory failure requiring supplemental oxygen or advanced airway support, and had at least one of the following: (1) clinical suspicion of lower respiratory tract infection based on clinical, biochemical, or radiological findings, (2) sepsis of unknown origin, and (3) concern from an intensive care physician regarding inflammatory pathology. Patients with a suspected or confirmed containment level three organism were excluded. The outcome was performance characteristics of the metagenomic test compared with routine diagnostic testing, detection of additional pathogens by metagenomics, change in antimicrobial prescribing within 24 h of testing, and initiation of immunomodulation.<br><br>FINDINGS: We processed 114 samples (1-5 per day) from 74 patients (39 [53%] female and 35 [47%] male). 107 (94%) of 114 samples passed quality control, of which 101 (94%) provided same-day preliminary results. Bacteria were detected in 45 (43%) of 104 tested specimens, fungal organisms in 17 (16%) of 104 tested specimens, and viruses in 28 (34%) of 83 tested specimens. Sensitivity in lower respiratory tract samples after 24 h was 97% (95% CI 87-100) for bacteria, 89% (65-99) for fungi, and 89% (71-98) for viruses, with only one false positive for bacteria. Metagenomics identified 42 pathogens not detected by other tests in 32 (30%) of 107 samples. Antimicrobial therapy was changed after metagenomic results from 30 (28%) of 107 samples: 22 (21%) were de-escalated and eight (7%) were escalated. Metagenomics contributed to the initiation of immunomodulation in 15 (20%) of 74 patients for a range of inflammatory conditions. Pathogens with clinical significance to local infection control or national public health were found in ten (14%) of 74 patients, including three invasive Group A streptococci, two parvovirus B19, and one each of HIV-1, measles virus, Mycobacterium tuberculosis, Neisseria meningitidis, and Mycoplasma pneumoniae.<br><br>INTERPRETATION: Respiratory metagenomics for ICU patients showed good performance and turnaround time, and diverse clinical and public health benefits. This ability to inform both personalised patient therapy and infectious disease surveillance needs evaluation in multicentre studies.<br><br>FUNDING: None.}, }
@article {pmid41045876, year = {2025}, author = {Gebert, J and Böhnke-Brandt, S and Zander, F and Indenbirken, D and Bergmann, L and Krohn, I and Perner, M}, title = {Linking microbial community composition, microbial biomass and extracellular polymeric substances to organic matter lability gradients in sediments of the tidal Elbe River.}, journal = {The Science of the total environment}, volume = {1002}, number = {}, pages = {180614}, doi = {10.1016/j.scitotenv.2025.180614}, pmid = {41045876}, issn = {1879-1026}, abstract = {The port of Hamburg represents a transition zone between upstream, shallow regions of high net primary production and downstream deep and more turbulent waters in the tidal Elbe River in northwestern Germany. Correspondingly, strong gradients of degradable organic matter (OM) on a distance of a few river kilometers had been identified. This study links microbial community composition using 16S metagenomic amplicons and extracellular polymeric substances (EPS) composition to the observed gradients of sediment OM lability. It was hypothesized that lability gradients caused by higher concentrations of biogenic, autochthonous OM upstream and greater share of already stabilized OM downstream reflect in gradients of microbial community composition, diversity and EPS characteristics. Indeed, available OM was found to act as key driver regulating syntrophic microbial community composition and associated metabolic features, with location-specific overriding the effect of seasonal variations. Upstream sites with high available OM featuring lower bacterial but increased archaeal diversity and elevated methane and carbon dioxide fluxes, whereas lower OM lability downstream fostered a more diverse bacterial but decreased archaeal diversity. The ratio between microbial taxon richness and biomass correlated inversely with OM transformation rates. These patterns also reflected in increased EPS concentration produced in response to metabolic needs (i.e. polysaccharides and proteins), whereas structural components such as lipids, which can be more resistant under the prevailing anoxic conditions, remained more evenly distributed along the transect. Although bacterial relative abundances exceeded archaeal abundances (<1 %) by far, archaeal functional significance remained pivotal for the final release of carbon as methane and carbon dioxide under the mostly reducing conditions in the deposited sediment.}, }
@article {pmid41045656, year = {2025}, author = {Tuffou, R and Windal, L and Delmotte, S and Skorski, G and Metton, I and Voisin, SN and Surribas, A and Beytur, S and Leborgne, M and Blanquart, H and Salducci, X and Feugier, A}, title = {Combining fermentation and vermicomposting for sustainable pet food waste management: Effects of waste profile and inoculum source.}, journal = {Waste management (New York, N.Y.)}, volume = {208}, number = {}, pages = {115176}, doi = {10.1016/j.wasman.2025.115176}, pmid = {41045656}, issn = {1879-2456}, abstract = {Ingredient production is the main driver of pet-food GHGs and land use. Indeed, the pet food industry uses nearly 495,000 km[2] of land annually. Yet, waste streams from production and declassified products remain underexplored as resources to produce high quality soil amendment. This study proposes an integrated approach to valorise such organic wastes through microbial fermentation prior to vermicomposting. Two experiments were conducted. (1) the effects of kibble incorporation ratio (15 % vs. 30 %), fibre source (spruce flakes, SF vs. beech sawdust, BS), and container size (50 L vs. 500 L) on fermentation dynamics, worm preference, and vermicompost properties were assessed. (2) the functional equivalence of commercial inoculum (EM®) and locally sourced indigenous microorganisms (IMO) was evaluated. Results showed that fibre type significantly influenced fermentation outcomes at low kibble incorporation, with BS lowering pH (from 9 in SF30% to 5.2 in BS15%, P < 0.001) and increasing redox potential (+213 %, P < 0.001). Electroconductivity was strongly affected by both kibble ratio (+110 %, P < 0.001) and fibre source (+130 %, P < 0.001). Worms displayed strong preference for BS-based substrates (+493 % density in 7 days, P < 0.001). Vermicompost derived from SF exhibited slower nitrogen and carbon mineralisation than BS. Container size had no effect on fermentation. EM® and IMO performed equivalently in fermentation efficiency, worm attraction, and functional microbial activity (metagenomic/metaproteomic analyses). This work demonstrates that combining microbial pre-digestion with vermicomposting can upcycle pet food waste into valuable soil amendments, while supporting local circular bioeconomy and sustainable waste management.}, }
@article {pmid41044998, year = {2025}, author = {Modin, O and Zheng, D and Schnürer, A and Lundwall, T and Bolanos, SE and Olsson, J}, title = {From Low-Loaded Mesophilic to High-Loaded Thermophilic Anaerobic Digestion: Changes in Reactor Performance and Microbiome.}, journal = {Microbial biotechnology}, volume = {18}, number = {10}, pages = {e70238}, doi = {10.1111/1751-7915.70238}, pmid = {41044998}, issn = {1751-7915}, support = {//K&#xe4;ppalaf&#xf6;rbundet/ ; //The Swedish Research Council (VR)/ ; }, mesh = {*Bioreactors/microbiology ; Anaerobiosis ; *Sewage/microbiology ; Methane/metabolism ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Temperature ; *Microbiota ; *Archaea/classification/genetics/metabolism ; Metagenomics ; }, abstract = {This study investigated temporal dynamics in reactor performance and microbial community structure during anaerobic digestion of sewage sludge when the temperature was changed from 37°C to 55°C, followed by an increase in organic loading rate (OLR). Performance instability was observed immediately following the temperature increase and in the end of the study when the OLR was 11.1 ± 0.3 kgVS m[-3]d[-1]. The specific methane production peaked at 0.31 ± 0.06 Nm[3] kg[-1] volatile solids (VS) during thermophilic operation and when the OLR was 3.5 ± 0.9 kgVS m[-3]d[-1]. Using metagenomic sequencing, 304 species-representative genome bins (SGB) were assembled. Network analysis revealed that 186 SGB were associated with thermophilic conditions and several new species putatively involved in key reactor functions were identified. When reactor function initially stabilised, two hydrogenotrophic and one aceticlastic methanogen (Methanothermobacter spp. and Methanosarcina thermophila), the hydrolytic Coprothermobacter proteolyticus, and putative syntrophic propionate oxidisers (e.g., Pelotomaculaceae) had high relative abundance. During the peak in specific gas production, the community was dominated by one hydrogenotrophic Methanothermobacter species coexisting with syntrophic acetate oxidising bacteria (Thermacetogenium phaeum and other species). Finally, when the reaction function deteriorated due to high OLR, new hydrolytic taxa emerged and the same aceticlastic methanogen as seen during the initial acclimatisation phase returned.}, }
@article {pmid41044758, year = {2025}, author = {Pérez-Pérez, L and Galisteo, C and Sanjuán, JMO and Cobo-Díaz, JF and Puente, H and Rubio, P and Carvajal, A and Arguello, H}, title = {Severity of Brachyspira hyodysenteriae colitis correlates to the changes observed in the microbiota composition and its associated functionality in the large intestine.}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {105}, pmid = {41044758}, issn = {2524-4671}, support = {PRE2020-093762//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; JDC2023-051122-I//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; LE088P23//Junta de Castilla y Le&#xf3;n/ ; }, abstract = {BACKGROUND: The gut microbiota is essential for maintaining nutritional, physiological and immunological processes, but colonic infections such as swine dysentery, caused by Brachyspira hyodysenteriae (B. hyo) disrupt this homeostasis. This study uses shotgun and full-length 16S rRNA sequencing in faeces, colonic contents and mucosa from pigs challenged with B. hyo to provide a high-resolution characterisation of the taxa, functions and metagenome-assembled genomes (MAGs) of interest, disclose their association with the primary pathogen and how they are affected by the pathological changes of the infection.<br><br>RESULTS: Changes in the microbiota were associated with disease severity. In early infection, no major findings were observed in diversity or abundance analyses, whereas in acute infection, B. hyo load, mucosal neutrophil infiltration, epithelial ulceration and mucosal thickness were clearly associated with changes in microbiota ordination, which were also associated with a decrease in species richness. Changes included a significant increase in Acetivibrio ethanolgignens, Campylobacter hyointestinalis and Roseburia inulinivorans, which, with the exception of C. hyointestinalis, established themselves as part of the core microbiota and shifted the colonic enterotype in acutely infected animals. MAGs analyses revealed that no major virulence genes were detected in the genomes of the species co-interacting with B. hyo in acute infection. Similarly, functional changes were observed only after the onset of clinical signs, with an increase in functions related to inflammation and toxic effects on the colonic epithelium.<br><br>CONCLUSIONS: Our study shows that in colitis caused by B. hyo, changes in the microbiota are mainly a consequence of the lesions that occur in the intestine, with no differences observed in early infection. Similarly, the bacterial species that are increased at the onset of clinical signs may promote intestinal inflammation caused by B. hyo infection, but the analysis of their genomes rule out their participation in the primary infection.}, }
@article {pmid41044750, year = {2025}, author = {Kang, L and Li, Y and Wang, J and Fu, J and Li, Q and Jiang, Q and Zhou, H and Xiao, H and Zhang, Z and Hong, M}, title = {Seasonal dynamics, dietary patterns, and bamboo leaf nutrition shape the phyllosphere-associated gut microbiota of red pandas.}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {104}, pmid = {41044750}, issn = {2524-4671}, support = {grant no. 32470516//National Natural Science Foundation of China/ ; grant no. KCXTD2022-7//Innovation Team Funds of China West Normal University/ ; grant no. 2024NSFSC2082//Sichuan Natural Science Foundation/ ; }, abstract = {BACKGROUND: The gut microbiota of bamboo-eating red pandas (Ailurus fulgens) comprises a intricate and multifaceted ecosystem influenced by numerous factors. Despite considerable research dedicated to captive red pandas, the microbial dynamics observed in wild populations are still not well understood. To address this research gap, our study employed advanced techniques such as high-throughput sequencing and metagenomic analysis to characterize the microbial communities and their functional profiles in fresh fecal samples from wild red pandas and in samples of their primary food source. Our objective was to conduct a thorough examination of how seasonality, diet, bamboo leaf nutrition, and phyllosphere-associated microorganisms affect the gut microbiota of red pandas.<br><br>RESULTS: Our findings reveal that seasonal variations have a notable impact on the composition, structure, and functionalities of red pandas' gut microbiota. Specifically, autumn and winter exhibit heightened microbial diversity and richness. Moreover, during different feeding phases (leaf-feeding, shoot-feeding, and mixed-feeding), the gut microbiota displays varied cellulose-digesting abilities, marked by increased expression of key enzymes during high-fiber dietary phases. Our analysis reveals robust correlations between bamboo nutrients and microbial communities in both bamboo and red panda guts. Notably, bamboo's crude protein and phosphorus content are pivotal in shaping the phyllosphere and gut microbial communities, while crude fat, crude protein, and phosphorus emerge as key drivers of microbial structure. Seasonal fluctuations in microbial populations of both bamboo and red panda guts with shared genera, underscore their tight linkage and interconnected seasonal adaptations.<br><br>CONCLUSIONS: In conclusion, our study provides a comprehensive understanding of how seasonality, diet, and bamboo leaf nutrition shape the gut microbiota of red panda connected to bamboo microbiome. It underscores the gut microbes' indispensable role in facilitating red pandas' adaptation to their bamboo-based diet, crucial for their survival in natural habitats.}, }
@article {pmid41044404, year = {2025}, author = {Rodríguez-Gijón, A and Pacheco-Valenciana, A and Milke, F and Dharamshi, JE and Hampel, JJ and Damashek, J and Wienhausen, G and Rodriguez-R, LM and Garcia, SL}, title = {Widely-distributed freshwater microorganisms with streamlined genomes co-occur in cohorts with high abundance.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {34482}, pmid = {41044404}, issn = {2045-2322}, mesh = {*Fresh Water/microbiology ; Metagenome ; *Genome, Bacterial ; Genome Size ; Ecosystem ; *Bacteria/genetics/classification ; }, abstract = {Genome size is known to reflect the eco-evolutionary history of prokaryotic species, including their lifestyle, environmental preferences, and habitat breadth. However, it remains uncertain how strongly genome size is linked to prokaryotic prevalence, relative abundance and co-occurrence. To address this gap, we present a systematic and global-scale evaluation of the relationship between genome size, relative abundance and prevalence in freshwater ecosystems. Our study includes 80,561 medium-to-high quality genomes, from which we identified 9,028 species (ANI > 95%) present in a manually curated dataset of 636 freshwater metagenomes. Our results show that prokaryotes with reduced genomes exhibited higher prevalence and relative abundance, suggesting that genome streamlining may promote cosmopolitanism. Furthermore, network analyses revealed that the most prevalent prokaryotes have streamlined genomes that are found in co-occurrent cohorts potentially sustained by metabolic dependencies. Overall, species in these groups possess a diminished capacity for synthesizing different essential metabolites such as vitamins, amino acids and nucleotides, potentially fostering metabolic complementarities within the community. Moreover, we found the presence of the essential biosynthetic functions to be usage-dependent: nucleotide and amino acids biosynthesis are the most complete, whereas vitamin biosynthesis is most incomplete. Our results underscore genome streamlining as a central eco-evolutionary strategy that both shapes and is shaped by community dynamics, ultimately fostering interdependences among prokaryotes.}, }
@article {pmid41044010, year = {2025}, author = {Bleidorn, C and Sandberg, F and Martin, S and Vogler, AP and Podsiadlowski, L}, title = {The untapped potential of short-read sequencing in biodiversity research.}, journal = {Trends in genetics : TIG}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tig.2025.09.001}, pmid = {41044010}, issn = {0168-9525}, abstract = {The power of short-read DNA sequencing in biodiversity research and evolutionary genomics is rapidly growing due to advances in technology and bioinformatics. Short-read sequencing offers powerful solutions for taxonomic identification, biomass estimation, and phylogenetic reconstruction. Moreover, short-read data enable robust estimation of genome size and repeat content, offering valuable insights into genome evolution. Though growing in popularity, long-read genome assemblies are often not feasible with material from museum collections or raw biodiversity samples. With the growing demand for DNA-based approaches in biodiversity research, short-read genomics provides an easily generated universal data source spanning all levels from individual genomes to ecosystems, and including all species on Earth, to achieve the objectives of the Global Biodiversity Framework (GBF) for the preservation of biodiversity.}, }
@article {pmid41043962, year = {2025}, author = {Sessions, AL and Magnabosco, C and Barton, HA and Burkhardt, C and Dworkin, JP and Freissinet, C and French, KL and Glavin, DP and Leys, N and Maixner, F and Olsson-Francis, K and Probst, AJ and Quitté, G and Rampe, E and Steele, A and Carrier, BL and Hays, LE and Thiessen, F and Paardekooper, D and Hutzler, A and Harrington, AD and Teece, BL}, title = {Planning Considerations Related to Contamination Control for the Return and Analysis of Martian Samples.}, journal = {Astrobiology}, volume = {}, number = {}, pages = {}, doi = {10.1177/15311074251382157}, pmid = {41043962}, issn = {1557-8070}, abstract = {The joint National Aeronautics and Space Administration and European Space Agency Mars Sample Return (MSR) Campaign is a proposed multi-mission effort to bring selected geological samples from Mars to Earth for the purpose of scientific investigation. Significant parts of these investigations could be affected by Earth-sourced contamination that is either misinterpreted as having a martian origin or that masks a martian signal. The Mars 2020 Perseverance rover implemented strict contamination control requirements to limit contamination of the samples during sample collection. Contamination control and contamination knowledge requirements have not yet been established for the samples after they arrive on Earth. The MSR Sample Receiving Facility (SRF) Contamination Panel (SCP) was tasked with defining the terrestrial biological, organic, and inorganic contamination limits for martian samples during their residence inside the SRF. To reach our recommendations, the SCP studied (i) the previously proposed limits and rationale of the Organic Contamination Panel, (ii) cleanliness levels achieved for sampling hardware by the M2020 mission, (iii) recent improvements in analytical technology and detection limits, (iv) updated information regarding the organic content of martian samples (e.g., from the Sample Analysis at Mars instrument on the Curiosity rover and laboratory analyses of martian meteorites), and (v) information about the composition and geologic context of samples being collected by the Perseverance rover for return to Earth.}, }
@article {pmid41039216, year = {2025}, author = {Ma, Y and Wang, D and Yu, X and Fan, Y and Yang, Z and Gao, X and Huang, X and Meng, J and Cheng, P and Liu, X and Liu, Z and Li, X}, title = {Moderate altitude exposure induced gut microbiota enterotype shifts impacting host serum metabolome and phenome.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {591}, pmid = {41039216}, issn = {1471-2180}, support = {2023YFE0114300//National key research and development program intergovernmental key projects/ ; No.2024A1515012697//Guangdong Provincial Basic and Applied Basic Research Fund Project/ ; No. 202206010044//Science and Technology Program of Guangzhou, China/ ; No. U24A20652//The Joint Funds of the Natural Science Foundation of China/ ; No. 82272246//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Consistent patterns of gut microbiota variations, particularly in relative abundance, have been identified in the adult human gut. Enterotype, another general measure of the gut microbiota, is a valuable approach for categorizing the human gut microbiota into distinct clusters. The impact of different enterotypes on human health varies, and the changes induced by moderate altitude exposure remain unclear. This study aimed to conduct a comprehensive investigation of the cascade effects triggered by enterotype shifts following moderate altitude exposure.<br><br>RESULTS: Using shotgun metagenome sequencing, participants before and after moderate-altitude exposure were classified into cluster BL (dominated by Blautia) and cluster BA (dominated by Bacteroides). Relative to cluster BL, cluster BA consisted predominantly of individuals exposed to moderate altitude. Compared to cluster BL, Cluster BA exhibited rewired metabolism of serum metabolites (i.e., amino acids, fatty acids and bile acids) and gut microbiota, lower inflammatory factor levels (i.e., tumor necrosis factor-&#x3b1; (TNF-&#x3b1;)), and sparser correlations among these parameters. Individuals with baseline BL enterotype who transitioned to the BA enterotype following moderate-altitude exposure showed prominent improvement in fasting blood glucose (FBG) levels, with higher abundance of Bacteroidetes species (e.g., Bacteroides thetaiotaomicron, and Bacteroides uniformis), but lower Proteobacteria species abundance (e.g., Escherichia coli) and decreased L-Glutamic acid levels. Furthermore, fecal microbiota transplantation (FMT) from moderate-altitude exposed individuals to high-fat diet (HFD) fed mice confirmed increased Bacteroides abundance shifts associated with improvements in glucose homeostasis regulation and rewired amino acid metabolism. In addition, significant increases in alanine aminotransferase (ALT) levels but decreased serum creatinine (Scr), arterial oxygen saturation (SaO2), 4-Hydroxyproline, L-Glutamic acid, L-Asparagine, L-Threonine, L-Citrulline, L-Lysine and Isovaleric acid levels were identified as potentially important signals for individuals upon moderate altitude exposure, regardless of the gut microbiota enterotype.<br><br>CONCLUSIONS: Moderate altitude exposure could induce enterotype switching, and a Bacteroides-dominant enterotype may be a beneficial pattern of the gut microbiome related to host metabolism. Moderate-altitude exposure has potential implications for glycemic control, suggesting new avenues for managing FBG levels in future.<br><br>GRAPHICAL ABSTRACT: [Image: see text]<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-025-04245-4.}, }
@article {pmid41043636, year = {2025}, author = {Ba, XQ and Wang, MF and Huang, WL and Ye, XF and Xu, YY and Li, MM and Jiang, RF and Chen, CN}, title = {Talaromyces Marneffei Infection Involving the Central Nervous System in a Patient with Acquired Immunodeficiency Syndrome: A Case Report and Literature Review.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {}, number = {}, pages = {108096}, doi = {10.1016/j.ijid.2025.108096}, pmid = {41043636}, issn = {1878-3511}, abstract = {BACKGROUND: Talaromycosis, an opportunistic deep invasive mycosis, is caused by the fungus Talaromyces marneffei and is predominantly observed in individuals with acquired immunodeficiency syndrome (AIDS). Involvement of the central nervous system (CNS) is exceedingly rare and presents significant diagnostic challenges, often associated with high mortality rates.<br><br>CASE PRESENTATION: This report details a case of CNS Talaromyces marneffei infection in an AIDS patient who initially presented with epileptic seizures. Neuroimaging identified a ring-enhancing lesion within the right frontal lobe, concurrent with a marked elevation in serum &#x3b2;-D-glucan levels. The diagnosis was confirmed through a multimodal approach, including histopathological examination and metagenomic next-generation sequencing (mNGS). Postoperative management involved a sequential regimen of amphotericin B followed by voriconazole, leading to a favorable recovery. The patient is currently on a maintenance elvitegravir-based antiretroviral therapy regimen.<br><br>CONCLUSIONS: CNS Talaromyces marneffei infection in AIDS patients often lacks specific clinical manifestations, which complicates diagnosis and treatment. This case report contributes to the existing body of knowledge by presenting a successfully managed case, thereby enhancing the understanding of diagnostic and therapeutic strategies for similar future presentations.}, }
@article {pmid41043345, year = {2025}, author = {Yu, C and Zhu, H and He, Y and Weng, R}, title = {Comparison of sulfur cyclings coupled with anaerobic ammonium oxidation in response to different river remediations.}, journal = {Journal of environmental management}, volume = {394}, number = {}, pages = {127523}, doi = {10.1016/j.jenvman.2025.127523}, pmid = {41043345}, issn = {1095-8630}, abstract = {The evolution from 'malodor' to 'algae bloom' in remediated urban rivers has received an ever-increasing attention due to relatively high nitrogen (N) loadings. As pivotal autotrophic processes, anaerobic ammonium oxidation (anammox) and sulfur-driven denitrification (SDD) represent promising candidates for N removal in remediated rivers with low C/N ratios. However, how and to what extent SDD is coupled with anammox remained largely unknown. Our investigations of four remediated urban rivers revealed that SDD was more prevalent than anammox, with Thiobacillus (0.13 %-2.51 %) dominating over Candidatus_Brocadia (0-0.02 %). The injection of Ca(NO3)2 greatly enhanced the coupling of SDD and anammox (SDDA) in anaerobic environments, achieving a maximum total nitrogen (TN) removal of 93.89 %. Metagenomic and metatranscriptomic analyses identified Thiobacillus, Thermomonas, and Candidatus_Brocadia as key microbial players, with their activities increased by 0.060 %, 0.015 %, and 0.498 %, respectively. Differently, Sulfurisoma, Dechloromonas, and Candidatus_Scalindua emerged as key players in Na2S2O3-group, while Sulfurisoma, Sulfurimonas, and Candidatus_Scalindua played pivotal roles in FeS2-group. Additionally, river simulations revealed that Na2S2O3-group showed the strongest SDDA coupling, supported by the highest abundances of soxB (0.14 %), narG (0.05 %), nirS (5.92 %), and hzsB (6.14 %). The FeS2-group demonstrated moderate coupling, whereas the Ca(NO3)2-group displayed the weakest performance. Moreover, Na2S2O3-group also exhibited excellent TN removal (87.58 %) in real river scenarios, indicating its potential as one promising N removal strategy for practical application. This study contributes to the understanding of S-N cyclings in river ecosystems and provides insights into manipulating N-reduction for possible application in remediated urban rivers.}, }
@article {pmid41043307, year = {2025}, author = {Ji, Z and Liu, S and Tian, Z and Guo, N and Wei, W and Jiang, Q}, title = {Tooth Loss-Induced Gut Dysbiosis Promotes Neuroinflammation via L-Asparagine-Mediated Neuronal Toxicity.}, journal = {International dental journal}, volume = {75}, number = {6}, pages = {103929}, doi = {10.1016/j.identj.2025.103929}, pmid = {41043307}, issn = {1875-595X}, abstract = {INTRODUCTION AND AIMS: Tooth loss is not only a dental issue but also affects gut microbial composition and downstream physiological responses. This study investigates how tooth loss-induced alterations in the gut microbiota influence metabolic and neural function. This study aimed to elucidate the mechanistic links between microbiota dysbiosis, metabolic imbalance, and neuroinflammation following tooth loss.<br><br>METHODS: Using a murine model, the first molars of C57BL/6 mice were extracted, followed by the collection of fecal samples, serum, and brain tissue for subsequent metagenomic sequencing, metabolomics, and transcriptomics. Pro-inflammatory markers (IL-6, TNF-&#x3b1;) and PSD95 expression were assessed. The neurotoxic effects of key metabolite L-Asparagine were validated using HT22 neuronal cell models.<br><br>RESULTS: Tooth loss induced gut microbiota dysbiosis, which subsequently mediated pathological alterations in brain tissue, characterised by a reduction in beneficial Butyribacter and an increase in pathogenic taxa. Corresponding shifts in systemic metabolism were observed, along with changes in brain gene expression, particularly in genes related to neuroinflammation. In vitro experiments further demonstrated that L-Asparagine directly induced neurotoxicity in HT22 hippocampal neurons through ROS overproduction, apoptosis, and inflammatory activation.<br><br>CONCLUSION: Tooth loss induced gut microbiota dysbiosis, systemic metabolic disruptions, and neuroinflammatory responses. Our findings demonstrated that tooth loss exacerbated neuroinflammation via gut-derived L-Asparagine, providing a mechanistic link in the oral-gut-brain axis.<br><br>CLINICAL RELEVANCE: This study demonstrated that molar extraction in mice disrupted gut microbiota and promoted neuroinflammation via L-Asparagine, suggesting that maintaining oral integrity might help preserve neurological health. This could open new avenues for microbiota-targeted interventions in neurodegenerative disease prevention.}, }
@article {pmid41043233, year = {2025}, author = {Sun, C and Liu, X and Wang, M and Zhang, Q and Geng, H and Ji, X and Wang, H and Li, S and Jin, E and Zhang, F}, title = {Metagenome-metabolome responses to linarin alleviate hepatic inflammatory response, oxidative damage, and apoptosis in an ETEC-challenged weaned piglet model.}, journal = {Ecotoxicology and environmental safety}, volume = {304}, number = {}, pages = {119145}, doi = {10.1016/j.ecoenv.2025.119145}, pmid = {41043233}, issn = {1090-2414}, abstract = {Enterotoxigenic Escherichia coli (ETEC), present in contaminated food, water, and environments, can induce hepatic injury via the gut-liver axis, posing a serious threat to ecological systems and public health. Linarin, a flavonoid extracted from Chrysanthemum indicum, exhibits anti-inflammatory and antioxidant properties, but its protective effects against ETEC-induced hepatic injury remain unclear. In this study, 24 weaned piglets were randomly assigned to four groups: BD+NB (basal diet + nutrient broth), LN+NB (basal diet + 150 mg/kg linarin + nutrient broth), BD+ETEC (basal diet + ETEC challenge), and LN+ETEC (basal diet + 150 mg/kg linarin + ETEC challenge). Dietary linarin significantly increased ADFI and the genes related to oxidative damage and bile acid metabolism, while decreasing F:G ratio, liver index, serum liver function-related parameters, and the genes related to inflammatory response and apoptosis. It also significantly altered the relative abundances of gut microbiota, which were closely associated with key hepatic metabolic pathways, including nicotinate and nicotinamide metabolism and fatty acid biosynthesis. Our study suggests that linarin alleviated ETEC-induced hepatic inflammation and apoptosis, enhanced antioxidant capacity, and regulated bile acid metabolism. The potential mechanism involves linarin modulating gut microbiota-mediated key hepatic metabolic pathways to exert protective effects. In contrast to previous flavonoid-ETEC studies that primarily focused on the gut, this study, based on the gut-liver axis, investigates the potential mechanisms by which linarin is associated with the alleviation of ETEC-induced hepatic injury through integrated analysis of gut microbiome metagenomics and liver metabolomics.}, }
@article {pmid41042849, year = {2025}, author = {Shen, LQ and Lin, D and Ye, YQ and Liu, Y and Ni, B and Wu, D and Wang, L and Zhu, D}, title = {Combined pesticide pollution enhances the dissemination of the phage-encoded antibiotic resistome in the soil under nitrogen deposition.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {40}, pages = {e2516722122}, doi = {10.1073/pnas.2516722122}, pmid = {41042849}, issn = {1091-6490}, support = {2024YFE0106300//MOST | National Key Research and Development Program of China (NKPs)/ ; 22193062//MOST | National Natural Science Foundation of China (NSFC)/ ; 42207013//MOST | National Natural Science Foundation of China (NSFC)/ ; 42222701//MOST | National Natural Science Foundation of China (NSFC)/ ; 2023321//Youth Innovation Promotion Association of the Chinese Academy of Sciences (CAS YIPA)/ ; 2022A-163-G//Ningbo Yongjiang Talent Project/ ; }, mesh = {*Bacteriophages/genetics ; *Nitrogen ; *Soil Microbiology ; *Pesticides/toxicity ; Soil/chemistry ; Bacteria/genetics/virology/drug effects ; *Drug Resistance, Microbial/genetics ; *Soil Pollutants ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; }, abstract = {Phage-mediated dissemination of antibiotic resistance genes (ARGs) intensifies health threat in the environment. Increasing amounts of pesticides are entering the soil ecosystem, yet their potential influence on phage-mediated ARG spread, particularly under conditions of global change, remains poorly understood. In this study, we performed a long-term field experiment simulating pesticide contamination under nitrogen deposition and examined the role of soil phages in ARG spread and host adaptation using metagenomic and viromic sequencing. Combined pesticide markedly elevated the abundance of phage-encoded ARGs under nitrogen deposition. By enhancing phage-host interactions and increasing the co-occurrence of auxiliary metabolic genes with ARGs, phages may further facilitate the transfer of ARGs to bacterial hosts, conferring hosts a competitive edge in intensified microbial competition driven by combined pesticide exposure under nitrogen deposition. The phage-driven mechanism was supported by in vitro cultivation experiments, demonstrating that phages harboring ARGs, shaped by long-term combined pesticide exposure under nitrogen deposition, can infect bacterial hosts and confer resistance. Collectively, our findings underscore the pivotal role of phages in ARG mobilization under environmental stressors, reinforcing the importance of accounting for phage activity in ARG risk assessments under global change.}, }
@article {pmid41042593, year = {2025}, author = {Varliero, G and Bauder, A and Stierli, B and Qi, W and Frey, B}, title = {Host-virome associations in the weathering crust of a rapidly retreating temperate Alpine glacier.}, journal = {Microbial genomics}, volume = {11}, number = {10}, pages = {}, doi = {10.1099/mgen.0.001524}, pmid = {41042593}, issn = {2057-5858}, mesh = {*Ice Cover/microbiology/virology ; *Bacteria/genetics/virology/classification ; *Microbiota/genetics ; *Viruses/genetics/classification/isolation &amp; purification ; Switzerland ; Metagenomics/methods ; Ecosystem ; Host Specificity ; }, abstract = {Glaciers are retreating rapidly, altering ecosystem dynamics and increasing meltwater outflow into populated areas. Understanding microbial-virome interactions is crucial for predicting the consequences of this release. We sampled ice from four shallow pits in the weathering crust of the Rhonegletscher, Swiss Alps, and found a microbiome dominated by bacteria and microeukaryotes, alongside a metavirome infecting both groups. Viruses exhibited variable host specificity, with some targeting particular taxa and others showing a broader infectivity range. Variable genomic regions, including metagenomic and metaviromic islands, were enriched in genes related to replication, recombination, repair and transposable elements. Detected auxiliary metabolic genes were primarily involved in host coenzyme biosynthesis, uptake or utilization and in altering bacterial methylation patterns to evade detection. These findings underscore the major role of viruses in regulating microbial dynamics in glaciers and their potential downstream environmental impacts.}, }
@article {pmid41042396, year = {2025}, author = {Wu, J and Zhou, J and Zhao, Q and Yang, C and Bai, Y}, title = {Metagenomic analysis of microbial community dynamics in konjac rhizosphere during soft rot disease progression.}, journal = {Applied microbiology and biotechnology}, volume = {109}, number = {1}, pages = {212}, pmid = {41042396}, issn = {1432-0614}, support = {32072558//the Nature Science Foundation of China/ ; 2024-620-000-001-007//Hubei Agricultural Science and Technology Innovation Center Innovation Team Project/ ; }, mesh = {*Rhizosphere ; *Plant Diseases/microbiology ; *Soil Microbiology ; Metagenomics ; *Amorphophallus/microbiology ; *Microbiota/genetics ; Bacteria/classification/genetics/isolation &amp; purification ; Fungi/genetics/classification ; }, abstract = {Amorphophallus konjac, the sole glucomannan-rich species in the Araceae family, faces significant yield and quality losses due to soft rot disease. Understanding the relationship between soil microbial communities and soft rot incidence is critical for sustainable konjac production. Metagenomic profiling was employed to systematically characterize the spatiotemporal dynamics of rhizosphere microbiomes during disease progression. Microbial alpha diversity (Chao1 index) exhibited a significant peak in the rhizosphere of diseased plants at the mature stage, contrasting with stable diversity patterns in healthy and latently infected groups, indicating dysbiosis-associated richness inflation during disease progression. Principal coordinate analysis (PCoA) revealed significant divergence in rhizosphere microbial structures between diseased and healthy/latently infected groups, with higher compositional variability observed in diseased samples. At the phylum level, Chloroflexi and Acidobacteria abundances in healthy mature plants exceeded those in diseased plants by 11.54% and 4.6%, respectively, while pathogenic Rhizopus arrhizus and Rhizopus microsporus were significantly enriched in diseased mature plants. Correlation analyses demonstrated predominantly negative associations between bacterial species and soil factors, contrasting with positive fungal correlations. KEGG pathway annotation identified carbohydrate metabolism and amino acid synthesis as core microbial functions in the konjac rhizosphere. Collectively, Chloroflexi and Acidobacteria were validated as putative biocontrol agents, while Rhizopus spp. emerged as key drivers of soft rot development. These findings provide mechanistic insights for designing microbiome-based biocontrol strategies to mitigate konjac soft rot, offering a sustainable alternative to conventional agrochemical reliance. KEY POINTS: • Diseased konjac microbial richness peaks; healthy plants enrich Chloroflexi/Acidobacteria. • Rhizopus pathogens drive soft rot; bacteria and fungi show opposing soil factor links. • Lays groundwork for microbiome approaches to cut agrochemicals in konjac rot control.}, }
@article {pmid41041976, year = {2025}, author = {Breusing, C and Hauer, MA and Hughes, IV and Becker, JS and Casagrande, D and Phillips, BT and Girguis, PR and Beinart, RA}, title = {Contrasting Genomic Responses of Hydrothermal Vent Animals and Their Symbionts to Population Decline After the Hunga Volcanic Eruption.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {e70126}, doi = {10.1111/mec.70126}, pmid = {41041976}, issn = {1365-294X}, support = {//Schmidt Ocean Institute/ ; EPSCoR Cooperative Agreement OIA-#1655221//National Science Foundation/ ; OCE-0732369//Division of Ocean Sciences/ ; OCE-1536331//Division of Ocean Sciences/ ; OCE-1736932//Division of Ocean Sciences/ ; 1747454//National Science Foundation Graduate Research Fellowship Program/ ; //Argonne National Laboratory/ ; }, abstract = {Genetic bottlenecks are evolutionary events that reduce the effective size and diversity of natural populations, often limiting a population's ability to adapt to environmental change. Given the accelerating human impact on ecosystems worldwide, understanding how populations evolve after a genetic bottleneck is becoming increasingly important for species conservation. Ash deposits from the 2022 Hunga volcanic eruption in the Southwest Pacific led to a drastic decline of animal symbioses associated with hydrothermal vents in this region, allowing insights into the effects of population bottlenecks in the deep sea. Here, we applied metagenomic sequencing to pre- and post-eruption samples of mollusc-microbial symbioses from the Lau Basin to investigate patterns of genetic variation and effective population size. Our data indicate that animal host populations currently show only small changes in genome-wide diversity but in most cases experienced a long-term decline in effective size that was likely intensified by the volcanic impact. By contrast, host-associated symbiont populations exhibited a notable decrease in genomic variation, including potential loss of certain habitat-specific strains. However, detection of environmental sequences resembling mollusc symbionts suggests that lost host-associated symbiont diversity might be recovered from the free-living symbiont pool. The differences between host and symbiont populations might be related to their contrasting genetic structures and pre-existing levels of connectivity, although the full extent of population bottlenecks in the host animals might only be recognisable after a few generations. These results add to our understanding of the evolutionary dynamics of animal-microbe populations following a natural disturbance and help assess their resilience to both natural and anthropogenic impacts.}, }
@article {pmid41041810, year = {2025}, author = {Oskolkov, N and Jin, C and Clinton, SL and Guinet, B and Wijnands, F and Johnson, E and Kutschera, VE and Kinsella, CM and Heintzman, PD and van der Valk, T}, title = {Improving taxonomic inference from ancient environmental metagenomes by masking microbial-like regions in reference genomes.}, journal = {GigaScience}, volume = {14}, number = {}, pages = {}, doi = {10.1093/gigascience/giaf108}, pmid = {41041810}, issn = {2047-217X}, support = {KAW 2021.0048 [P.D.H., F.W.]//Knut and Alice Wallenberg Foundation/ ; KAW 2022.0033 [P.D.H.]//Knut and Alice Wallenberg Foundation/ ; //National Bioinformatics Infrastructure Sweden at SciLifeLab/ ; VR 2020-04808//Swedish Research Council/ ; KAW 2020.0239//SciLifeLab and Wallenberg Data Driven Life Science Program/ ; }, mesh = {*Metagenome ; *Metagenomics/methods ; *DNA, Ancient/analysis ; Animals ; Phylogeny ; Archaea/genetics/classification ; }, abstract = {Ancient environmental DNA is increasingly vital for reconstructing past ecosystems, particularly when paleontological and archaeological tissue remains are absent. Detecting ancient plant and animal DNA in environmental samples relies on using extensive eukaryotic reference genome databases for profiling metagenomics data. However, many eukaryotic genomes contain regions with high sequence similarity to microbial DNA, which can lead to the misclassification of bacterial and archaeal reads as eukaryotic. This issue is especially problematic in ancient eDNA datasets, where plant and animal DNA is typically present at very low abundance. In this study, we present a method for identifying bacterial- and archaeal-like sequences in eukaryotic genomes and apply it to nearly 3,000 reference genomes from NCBI RefSeq and GenBank (vertebrates, invertebrates, plants) as well as the 1,323 PhyloNorway plant genome assemblies from herbarium material from northern high-latitude regions. We find that microbial-like regions are widespread across eukaryotic genomes and provide a comprehensive resource of their genomic coordinates and taxonomic annotations. This resource enables the masking of microbial-like regions during profiling analyses, thereby improving the reliability of ancient environmental metagenomic datasets for downstream analyses.}, }
@article {pmid41041613, year = {2025}, author = {Ma, R and Xu, B and Chen, X and Sun, Q and Li, Y and Zheng, Q and Jiao, N and Zhang, R}, title = {Prophages in marine Citromicrobium: diversity, activity, and interaction with the host.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf148}, pmid = {41041613}, issn = {2730-6151}, abstract = {Lysogeny was frequently detected in marine ecosystems, while how temperate phage genomes (prophages) impact marine microbial population or individual dynamics remained poorly understood. Using marine Citromicrobium strain collection as a model system, we revealed that 58% (22/38) were lysogens harboring 31 prophages that can be grouped into five novel genera (φA-φE). Prophage-encoded genes constituted 9% of host accessory genome, significantly expanding the microdiversity among citromicrobial clonal strains. Metagenomic abundance correlations indirectly supported the "Piggyback-the-Winner" dynamics for φA/φE, evidenced by their sublinear growth pattern with increasing host abundance. Most prophages were capable of spontaneous induction and exhibited high lytic activity when triggered by mitomycin C. Importantly, host-range profiling revealed these prophages deployed a dual "Kill-the-Relatives" and "Colonize-the-Relatives" strategy, and meanwhile, they protected parental host strains through superinfection immunity and enhanced phage resistance with greater prophage carriage. Sequencing data showed the dominance of Mu-like phages over non-Mu-like partners upon induced from the double lysogens. Our analysis further hinted at a unique Mu-type within-host competitive strategy: selectively targeting genes of co-resident prophages and host hypothetical genes, while avoiding self-damage and host metabolic genes potentially essential for phage lytic growth or progeny release. Collectively, this work establishes prophages as key architects of bacterial adaptation and provides new perspectives for prophage-driven evolution in marine bacterial hosts.}, }
@article {pmid41041524, year = {2025}, author = {Happi, A and Sijuwola, A and Omah, IF and Ogunsanya, O and Saibu, F and Ayinla, A and Adedokun, O and Fadele, J and Nwofoke, C and Adelabu, A and Ogundana, E and Lawal, O and Elias, O and Okokoh, E and Colquhoun, R and Achonduh-Atijegbe, O and Nta, H and Onimajesin, A and Momoh, F and Mari-Saez, A and Redding, D and Murray, K and Hanefeld, J and Sesay, AK and Rambaut, A and Happi, C}, title = {Metagenomics reveals cryptic circulation of zoonotic viruses in Nigeria.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-7630852/v1}, pmid = {41041524}, issn = {2693-5015}, abstract = {Zoonotic spillover events pose an ongoing threat to global health, with historic and recent viral diseases of international concern emerging from animal reservoirs 1-6. In Nigeria, limited surveillance of animal hosts at the human and animal interface continues to hinder our understanding of viruses that are cryptically circulating in animals near human dwellings with potential for consequential spillover events. We performed unbiased metagenomic next‑generation sequencing (mNGS) on tissue and swab samples collected from 240 individual animals across 11 taxa (rodents, shrews, bats, goats, sheep, pigs, dogs, cats, chickens, cattle egrets, and lizards) in two Lassa‑affected Nigerian states (Ondo and Ebonyi). Host‑depleted sequencing reads were assembled into contigs, taxonomically classified, and subjected to phylogenetic analyses to characterize viral diversity, host associations, and evidence of cross‑species transmission. Across all samples, we identified 214 distinct viral taxa spanning 33 families, of which 41% (n = 83) represent novel species by ICTV criteria. Positive‑sense RNA viruses dominated (Coronaviridae, Picornaviridae, Astroviridae), followed by negative‑sense RNA, single‑ and double‑stranded DNA, and double‑stranded RNA viruses. Notably, human‑associated enteroviruses-including Hepatitis A virus (genotype 1b), echoviruses, coxsackieviruses, and noroviruses-were detected in goats, pigs, dogs, and chickens, indicating cryptic circulation of human pathogens in peridomestic and domesticated animals. Phylogenetic reconstructions revealed multiple cross‑species viral sharing events, particularly among rodents, goats, sheep, and pigs, and extensive recombination within Nigerian Betacoronavirus 1 lineages. Interestingly we found a putative novel avian like coronavirus in rodents, goats and sheep. Ecological modelling demonstrated that host species identity, sample type, and sampling effort were primary drivers of viral richness and abundance, and that higher overall viral diversity strongly predicted cross‑species transmission potential. Our integrated mNGS approach uncovered a rich and dynamic virome within animals inhabiting human‑dominated environments in Nigeria, including undetected circulation of human enteric viruses. These findings underscore the importance of broad‑taxonomic, real‑time surveillance at human-animal interfaces to inform early‑warning systems and pandemic preparedness, particularly in low‑resource settings.}, }
@article {pmid41041139, year = {2025}, author = {Berlanga, M and Martín-García, A and Guerrero, R and Riu-Aumatell, M and López-Tamames, E}, title = {Changes in healthy Wistar rat gut microbiome by short-term dietary cava lees intervention.}, journal = {Frontiers in nutrition}, volume = {12}, number = {}, pages = {1641612}, pmid = {41041139}, issn = {2296-861X}, abstract = {INTRODUCTION: The gut microbiome plays a crucial role in host health through complex host-microbe interactions. Beta-glucans, structural polysaccharides found in yeast cell walls, have emerged as promising modulators of immune function and microbial ecology. Cava lees, a by-product of sparkling wine production composed of Saccharomyces cerevisiae cell walls, represent a rich source of beta-glucans that could be upcycled for nutritional and therapeutic applications.<br><br>METHODS: Twenty-four Wistar rats (12 males, 12 females) were randomly divided into control and treatment groups. The treatment group received daily doses of 2,000&#x202f;mg lees/kg body weight for 14&#x202f;days. Shotgun metagenomic analysis was performed to assess microbial composition and functional changes.<br><br>RESULTS: A 14-day cava lees supplementation study revealed significant shifts in gut microbiota composition and function. Baseline microbiota was dominated by Bacillota (64-72%) and Bacteroidota (23-32%) with sex-specific differences at the family level. Post-supplementation analysis showed increased Shannon diversity across both sexes, with beneficial enrichment of Bifidobacteriaceae and Rikenellaceae families and reduction of Eubacteriaceae. While global metabolic profiles remained stable, targeted functional pathways were significantly changed, including butyrate production genes. Females exhibited particularly elevated secondary bile acid modification genes (Mann-Whitney-Wilcoxon test p&#x202f;=&#x202f;0.032), and male oxidative stress response pathways (Mann-Whitney-Wilcoxon test p&#x202f;=&#x202f;0.016) showing both a potentially sex-dependent responses to dietary intervention.<br><br>CONCLUSION: Working with healthy individuals provides a clear understanding of the normal, baseline microbiota composition and function before any intervention. These findings suggest a degree of plasticity of the gut microbiome and its responsiveness to dietary modifications. Beta-glucans from cava lees appear to create a favorable environment for beneficial bacteria, with sex-specific changes of certain bacterial families and functions. These findings provide a foundation for future translational research in humans. Nonetheless, to establish their true impact on human health, these observations in rodent models must be validated through appropriately designed human clinical studies.}, }
@article {pmid41040987, year = {2025}, author = {Li, Y and Zhang, L and Ma, G and Li, C and Hu, W and Ren, R and Zang, Y and Ying, D and Qiu, S and Jin, S and Qiu, C and Cao, X}, title = {Optimization of decision thresholds for Mycobacterium tuberculosis can effectively improve the performance of mNGS in tuberculosis diagnosis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1646194}, pmid = {41040987}, issn = {2235-2988}, mesh = {Humans ; *Mycobacterium tuberculosis/genetics/isolation &amp; purification ; Female ; *Tuberculosis, Pulmonary/diagnosis/microbiology ; Male ; Middle Aged ; Adult ; *High-Throughput Nucleotide Sequencing/methods ; ROC Curve ; Bronchoalveolar Lavage Fluid/microbiology ; Sensitivity and Specificity ; *Metagenomics/methods ; Aged ; Young Adult ; }, abstract = {BACKGROUND: Pulmonary tuberculosis (TB) diagnosis remains challenging due to limitations in traditional methods. This study aimed to optimize the metagenomic next-generation sequencing (mNGS) threshold for Mycobacterium tuberculosis complex (MTBC) detection and evaluate its efficacy compared to standard diagnostic approaches.<br><br>METHODS: A total of 264 bronchoalveolar lavage fluid (BALF) samples were collected from patients with suspected pulmonary TB at Yongkang First People's Hospital between January 2022 and June 2023. After excluding patients with incomplete data, 59 clinically confirmed TB patients and 111 with non-tuberculous conditions were enrolled. mNGS data were analyzed to calculate reads per million (RPM) for MTBC, and thresholds of 0.02, 0.05, and 0.10 RPM were evaluated for diagnostic efficacy using clinical diagnosis as the gold standard.<br><br>RESULTS: The area under the receiver operating characteristic (ROC) curve (AUC) for mNGS in diagnosing TB at RPM thresholds of &#x2265;0.02, &#x2265;0.05, and &#x2265;0.10 were 0.881, 0.873, and 0.814, respectively. The optimal detection threshold was found at RPM &#x2265; 0.05. Comparative analysis showed mNGS (AUC = 0.873) outperformed routine culture (0.718), PCR (0.741), and Xpert (0.763). Combining mNGS with these methods improved AUC values to 0.837, 0.868, and 0.873, respectively.<br><br>CONCLUSION: Optimizing the mNGS threshold to &#x2265;0.05 significantly enhances MTBC detection in pulmonary TB. Combining mNGS with traditional methods further improves diagnostic efficacy, suggesting a potential role for mNGS in clinical TB management.}, }
@article {pmid41040929, year = {2025}, author = {Cho, HY and Park, HJ and Choi, JS and Kim, SH and Ryu, MO and Seo, KW}, title = {Delineating the fecal microbiome of healthy domestic short-hair cats in South Korea.}, journal = {Frontiers in veterinary science}, volume = {12}, number = {}, pages = {1571107}, pmid = {41040929}, issn = {2297-1769}, abstract = {BACKGROUND: The gut microbiome is a vital component of an organism's health, influencing metabolism, immune function, and overall homeostasis. In this study, we aimed to characterize the gut microbiota of healthy domestic short-hair cats in South Korea and evaluate the effects of age, body condition score (BCS), sex, and diet on microbial composition.<br><br>METHODS: From August to December 2023, 40 healthy cats aged 1-14&#x202f;years with a body condition score (BCS) of 5-9 were selected. Cats were excluded if they had taken probiotics or antibiotics, exhibited gastrointestinal symptoms within the last 6&#x202f;months, or had blood work abnormalities. DNA quantification was performed, and libraries targeting the V3 and V4 regions were prepared according to the Illumina 16S metagenomic sequencing protocol with a read length of 2&#x202f;&#xd7;&#x202f;300 bp. The relative abundance of bacteria at the phylum, genus, and species levels was assessed according to the age, sex, diet, and BCS of the cats, with major bacterial groups selected for chart analysis.<br><br>RESULTS: Examination of the fecal samples from 40 healthy cats (aged 0.5-14&#x202f;years) using 16S rRNA gene sequencing revealed 2,721 bacterial amplicon sequence variants. The predominant phyla were Bacillota, Bacteroidota, and Actinomycetota. Although age did not significantly affect alpha diversity, a trend toward increased diversity was observed in cats aged 7-14&#x202f;years. Phocaeicola was more abundant in older cats, suggesting a possible association with age-related conditions. Furthermore, Verrucomicrobiota was enriched in cats with a BCS of 8-9, and Ruminococcus torque was positively correlated with higher BCS. Sex-based differences indicated increased levels of Pseudomonadota, Finegoldia magna, and Sutterella massiliensis in neutered males, potentially linked to inflammatory pathways. Dietary analysis revealed an increased abundance of Blautia and Lachnoclostridium following a combination of dry and wet food.<br><br>CONCLUSION: Our findings provide critical insights into the core microbiota of domestic short-hair cats in South Korea, emphasizing the influence of geographic, physiological, and environmental factors on gut microbial diversity. The results offer a valuable foundation for advancing feline gut health research and enhancing health management strategies for felines, particularly in South Korea.}, }
@article {pmid41040912, year = {2025}, author = {Matsumura, M and Mitsui, H and Woo, T and Suzuki, T and Arai, H and Koike, C and Kataoka, T and Motooka, D and Fukushima, K and Okudela, K}, title = {Identification of key molecules in micropapillary progression of lung adenocarcinoma: A comprehensive gene expression analysis study using the spatial gene expression solution methodology.}, journal = {Oncology letters}, volume = {30}, number = {5}, pages = {533}, pmid = {41040912}, issn = {1792-1082}, abstract = {The micropapillary histological subtype is a high-grade element and a poor prognostic marker in lung adenocarcinoma (LUAD). This subtype develops through the lepidic-filigree micropapillary (filigree)-conventional/overt micropapillary (mPAP) pathway. The present study aimed to identify key molecules that promote this progression. To this end, gene expression profiles specific to lepidic, filigree and mPAP elements were investigated in histological sections obtained from 4 different LUAD cases. The 10× Genomics Visium Spatial Gene Expression Solution was used due to its superior resolution compared with conventional microdissection techniques. Cellular retinoic acid binding protein 2 (CRABP2), carcinoembryonic antigen-related cell adhesion molecule 5 (CEACAM5) and mucin 21 (MUC21) were identified as common molecules with significantly elevated levels along the lepidic-filigree-mPAP pathway. Furthermore, the present findings indicated that CRABP2 may serve an important role in the early stage of this process, as its level significantly increases during the transition from the lepidic to the filigree substage. Immunohistochemical analysis of the expression of CRABP2, CEACAM5 and MUC21 proteins in 207 surgically resected LUAD samples (expanded sample size) was performed. The present study revealed an increase in the expression levels of CRABP2 between the lepidic and filigree elements, and between filigree and mPAP for CEACAM5 and MUC21. Thus, these three proteins were demonstrated to serve roles in the lepidic-filigree-mPAP pathway at different stages. Notably, these molecules were associated with poor prognosis, characterized by an elevated recurrence rate and poor survival rate. In conclusion, crucial molecules that promote the lepidic-filigree-mPAP pathway, and exhibit potential clinical utility as prognostic markers and molecular therapeutic targets, were identified.}, }
@article {pmid41040880, year = {2025}, author = {Wang, J and Gu, H and Gao, H and Zhang, T and Li, B and Zhang, M and Jiang, F and Song, P and Liang, C and Fan, Q and Xu, Y and Zhang, R}, title = {Developmental dynamics and functional adaptation of gut microbiota in Mongolian wild asses (Equus hemionus hemionus) across ontogenetic stages in arid desert ecosystems.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1659661}, pmid = {41040880}, issn = {1664-302X}, abstract = {Understanding the composition and function of gut microbiota is essential for elucidating how wild animals adapt to arid environments. The Mongolian wild ass (Equus hemionus hemionus), which inhabits harsh desert ecosystems, offers an ideal model for such investigations. This study employed metagenomic sequencing of fecal samples to characterize the composition and structure of the gut microbiota in adult, subadult, and juvenile Mongolian wild asses, with functional annotation based on the KEGG, CARD, and CAZy databases. Our study revealed that Bacillota and Bacteroidota were the dominant phyla, together accounting for over 85% of relative abundance, with their ratio (B/B value) showing clear age-dependent shifts. Juveniles were dominated by Bacillota (high B/B value), consistent with adaptation to a milk-based, protein- and lactose-rich diet, whereas adults shifted toward Bacteroidota dominance (low B/B value), with relative abundance increasing from 39.53% to 64.92%, reflecting enhanced polysaccharide and fiber degradation, thereby providing microecological support for adaptation to low-energy, high-fiber desert vegetation resources. Alongside this transition, α-diversity significantly increased with age, while β-diversity patterns shifted from dispersed to clustered, indicating a more complex, stable, and mature gut community. Over 58% of predicted genes were assigned to metabolic pathways, highlighting the essential contribution of gut microbes to herbivore digestion. Polysaccharide lyases, enriched in adults and subadults, were positively correlated with Bacteroidota abundance, highlighting their central role in fiber degradation and stable energy supply, thereby supporting adaptation to arid desert habitats. In contrast, juveniles were characterized by enrichment of the galactose metabolism pathway, high abundance of Pseudomonadota (LEfSe LDA > 4), and the largest number of antibiotic resistance genes (AROs), including 17 potential key AROs, reflecting greater microbial plasticity and higher environmental exposure risks during early development. This study provides the first systematic characterization of age-related gut microbiome dynamics and functional adaptations in the endangered Mongolian wild ass, offering novel insights into microbial contributions to host energy optimization and resilience in arid ecosystems, with implications for conservation strategies.}, }
@article {pmid41040879, year = {2025}, author = {Hoepfner, C and Guzmán, D and Vidal-Veuthey, B and Foronda, V and Beggs, A and Cárdenas, JP and Vargas, VA and Alfaro, FD}, title = {Functional stratification and enzymatic arrangement in microbial communities across a hypersaline depth gradient.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1624058}, pmid = {41040879}, issn = {1664-302X}, abstract = {Extreme environments comprise a significant portion of Earth's terrestrial surface, posing challenges, such as extreme temperatures, pressure, pH extremes, oxygen and nutrient scarcity, and high salinity. Hypersaline ecosystems, such as those in the Andean Cold Deserts, exemplify extreme environments where microbial life has evolved specialized survival mechanisms. The Central Andean Mountains host extensive salt flats exposed to extreme temperature fluctuations, intense ultraviolet radiation, and high soil salinity. While most studies focus on surface layers, the impact of soil depth on functional diversity remains poorly understood. This study utilized shotgun metagenomics and functional annotation to explore enzymatic diversity across a 8-meter depth gradient in the Uyuni Salt Flat aiming to understand microbial adaptations to depth and abiotic stress. Our findings revealed a complex, stratified microbial ecosystem. Surface layers showed high abundance of amylases, enzymes that degrade accessible carbohydrates, likely derived from photosynthetic communities or surface-imported organic matter. These patterns suggest a dominance of strategies for rapid carbon decomposition. Intermediate depths exhibited elevated lipase and peroxidase activity, reflecting the presence of complex lipids and oxidative stress management, essential for survival in oxygen-limited, high-salinity zones. Lipase support lipid utilization as a carbon source, while peroxidase activity points to redox adaptations for microbial resilience under fluctuating oxidative conditions. Deeper sediment layers showed a shift toward protease and peptidase activity, indicating organic nitrogen recycling in nutrient-deprived environments and suggesting an efficient protein degradation system among halophilic archaea. Peroxidases remained abundant even at these depths, supporting sustained redox regulation and biogeochemical cycling thus enabling microbes to manage redox imbalances in high-salinity, low-oxygen settings. The enzymatic diversity across the depth gradient demonstrates functional stratification and remarkable microbial adaptability to hypersaline conditions. This functional resilience underpins nutrient cycling and organic matter decomposition deep in the salt flats. Notably, the identified halophilic enzymes, stable and active under high-salinity conditions, hold significant potential for biotechnological applications. This study contributes to our understanding of microbial life's complexity in hypersaline environments, enhancing our ability to harness extremophilic enzymes for biotechnological applications while underscoring the ecological value of these unique habitats.}, }
@article {pmid41040656, year = {2025}, author = {Wilkins, L and Yuen, B and Petersen, J and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and ,  and ,  and ,  and ,  and , }, title = {The chromosomal genome sequence of the mollusc, Ctena decussata (O.G.Costa, 1829) and its bacterial endosymbiont Candidatus Thiodiazotropha sp. CDECU1 (Chromatiales).}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {435}, pmid = {41040656}, issn = {2398-502X}, abstract = {We present a genome assembly from a specimen of Ctena decussata (Mollusca; Bivalvia; Lucinida; Lucinidae). The genome sequence has a total length of 1,658.05 megabases. Most of the assembly (97.83%) is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 53.28 kilobases in length. The genome of Candidatus Thiodiazotropha sp. CDECU1, a bacterium associated with C. decussata was also assembled.}, }
@article {pmid41040369, year = {2025}, author = {Rehman, Y and Kim, Y and Tong, M and Blaby, IK and Blaby-Haas, CE and Beatty, JT}, title = {Mining thermophile photosynthesis genes: a synthetic operon expressing Chloroflexota species reaction center genes in Rhodobacter sphaeroides.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.09.22.677880}, pmid = {41040369}, issn = {2692-8205}, abstract = {Photosynthesis is the foundation of the vast majority of life systems, and therefore the most important bioenergetic process on earth, and the greatest diversity in photosynthetic systems are found in microorganisms. However, understanding of the biophysical and biochemical processes that transduce light to chemical energy has derived from the relatively small subset of proteins from microbes that are amenable to cultivation, in contrast to the huge number of microbial DNA sequences encoding proteins that catalyze the initial photochemical reactions that has been deposited in databases, such as from metagenomics. We describe the use of a Rhodobacter sphaeroides laboratory strain for expression of heterologous photosynthesis genes to demonstrate the feasibility of mining this resource, focusing on hot spring Chloroflexota gene sequences. Using a synthetic operon of genes, we produced a photochemically active complex of reaction center proteins in our biological system. We also present bioinformatic analyses of anoxygenic type II reaction center sequences from metagenomic samples collected from hot (42-90° C) springs available through the JGI IMG database, to generate a resource of diverse sequences that potentially are adapted to photosynthesis at such temperatures. These data provide a view into the natural diversity of anoxygenic photosynthesis, through a lens focused on high-temperature environments. The approach we took to express such genes can be applied for potential biotechnology purposes as well as for studies of fundamental catalytic properties of these heretofore inaccessible protein complexes.}, }
@article {pmid41040146, year = {2025}, author = {He, W and Bobanga, T and Piantadosi, A and Popkin-Hall, ZR and Vulu, F and Collins, MH and Kashamuka, MM and Tshefu, AK and Juliano, JJ and Parr, JB}, title = {Evidence of dengue virus transmission and a diverse Aedes mosquito virome on the Democratic Republic of Congo-Angola border.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.01.16.633031}, pmid = {41040146}, issn = {2692-8205}, abstract = {Aedes mosquitoes are widely distributed across the Democratic Republic of Congo (DRC), and are major vectors of dengue (DENV), Zika, chikungunya (CHIKV), and yellow fever (YFV) viruses. While the high burden of malaria in the DRC receives considerable attention, arboviruses remain understudied. In the setting of recent CHIKV and YFV outbreaks in southwestern DRC, we collected Aedes mosquitoes in three areas of Kimpese, DRC, near the Angola border, to investigate their virome. Metagenomic and targeted sequencing of eight randomly selected field mosquito pools, comprising 155 mosquitoes from three collection sites, confirmed high-confidence DENV reads and human blood meals in six (75%) and eight (100%) pools, respectively. We find diverse mosquito viromes including other known and putative human and animal viruses. Our findings provide strong evidence of endemic DENV transmission along the DRC-Angola border and illustrate the potential of wild-caught mosquitoes for xenosurveillance of emerging pathogens.}, }
@article {pmid41039672, year = {2025}, author = {Silvester, R and Webster, G and Perry, WB and Farkas, K and Rushton, L and Craine, N and Cross, G and Kille, P and Weightman, AJ and Jones, DL}, title = {Genome-resolved metagenomics uncovers antimicrobial resistance gene carriers in hospital and municipal wastewater environments.}, journal = {The Science of the total environment}, volume = {1002}, number = {}, pages = {180607}, doi = {10.1016/j.scitotenv.2025.180607}, pmid = {41039672}, issn = {1879-1026}, abstract = {Wastewater-based epidemiology (WBE) is a powerful approach to study antimicrobial resistance (AMR) dynamics at the population level. Using genome-resolved metagenomics, we recovered 3978 metagenome-assembled genomes (MAGs) from archived metagenome sequences generated under the national wastewater surveillance programme across Wales, UK. Taxonomic profiling of MAGs revealed a diverse bacterial community, with significant compositional shifts observed across seasons and sample sources. Approximately 13.6 % of the MAGs carried one or more antimicrobial resistance genes (ARGs), with genes conferring resistance to tetracycline and oxacillin being the most prevalent within the wastewater microbiomes. We also recovered yet-uncultivated microbial genomes- often referred to as "microbial dark matter" harbouring clinically relevant ARGs, offering insights into previously uncharacterised resistance reservoirs in wastewater. ARG-host associations shifted between untreated influent and treated effluent, with effluent profiles also varying significantly between secondary and tertiary treatments, revealing the impact of treatment type on ARG host composition. This study represents the first comprehensive genome-resolved metagenomic characterisation of ARG carriers across both hospital and municipal wastewater in Wales, effectively bridging clinical and environmental compartments. Our findings highlight the need to integrate high-resolution genome-resolved metagenomic surveillance into national AMR monitoring frameworks to track emerging threats, characterise ARG reservoirs and inform targeted public health interventions.}, }
@article {pmid41039256, year = {2025}, author = {Jin, W and Zhang, Y and Su, X and Xie, Z and Wang, R and Wang, Y and Qiu, Y and He, Y}, title = {Effects of different land use on functional genes of soil microbial carbon and phosphorus cycles in the desert steppe zone of the Loess Plateau.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {607}, pmid = {41039256}, issn = {1471-2180}, support = {32072394//National Natural Science Foundation of China/ ; 23ZSCQ030//Gansu Province Intellectual Property Project/ ; 2022-01//Chinese Academy of Sciences regional development projects for young scholars/ ; }, mesh = {*Soil Microbiology ; *Phosphorus/metabolism ; China ; Soil/chemistry ; Grassland ; *Carbon/metabolism ; Desert Climate ; *Carbon Cycle/genetics ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; Microbiota ; Metagenomics ; }, abstract = {Desert grassland ecosystems on China's Loess Plateau are characterized by diverse land use types and varying human disturbances. We aimed to evaluate how land use influences soil microbial communities and functional genes related to carbon (C) and phosphorus (P) cycling. To do this, we selected five representative land use types: natural grassland, 20-year abandoned farmland, 12-year alfalfa grassland, 5-year Lanzhou lily farmland, and 17-year Platycladus orientalis forest. High-throughput metagenomic sequencing and soil physicochemical analyses were conducted. Proteobacteria dominated the nutrient-rich lily soil, while Actinobacteria were more abundant in the other soils. Available phosphorus (AP) had the strongest influence on microbial community structure and gene composition (p < 0.01). The relative abundance of ppdK, rpiB, glpX, and epi (C fixation genes), and purS (purine metabolism) was significantly higher in forest soil than in abandoned farmland (p < 0.05). Similarly, forest soil showed elevated levels of mttB and acs (methanogenesis), sdhA (TCA cycle), pstS (P transport), and pps (pyruvate metabolism) compared to alfalfa soil. Lily soil exhibited significantly higher abundance of acr genes (involved in the hydroxypropionate-hydroxybutylate cycle) and phnE (an ATP-binding cassette transporter) than natural grassland and alfalfa soils (p < 0.05). Microbial networks involved in C and P cycling were simpler but more functionally specialized in forest soil. Positive microbial interactions related to C and P cycling were strongest in lily soil. These findings provide important insights into soil microbial functional adaptation and offer a foundation for sustainable land use management on the Loess Plateau.}, }
@article {pmid41039213, year = {2025}, author = {IJdema, F and Arias-Giraldo, LM and Vervoort, E and Struyf, T and Van den Ende, W and Raaijmakers, JM and Lievens, B and De Smet, J}, title = {Metagenome-based identification of functional traits of the black soldier fly gut microbiome associated with larval performance.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {612}, pmid = {41039213}, issn = {1471-2180}, support = {S008519N//ENTOBIOTA/ ; IMP20028//KU Leuven Impuls grant/ ; C3/22/041//KU Leuven CHITINERY grant/ ; G0C4622N//Fonds Wetenschappelijk Onderzoek/ ; }, mesh = {Animals ; Larva/microbiology/growth &amp; development ; *Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism ; *Metagenome ; *Diptera/microbiology/growth &amp; development ; Animal Feed/analysis ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Diet ; Phylogeny ; Chickens ; }, abstract = {BACKGROUND: The relationship between microbiomes and their hosts has been the subject of intensive study in recent years. For black soldier fly larvae (BSFL) (Hermetia illucens L., Diptera: Stratiomyidae), correlations between shifts in its microbial gut community composition and its health and performance suggest that the BSFL gut microbiome encodes important functions that complement the insect's own immune system and metabolism. To date, most BSFL microbiome studies have been based on 16S rRNA sequencing data. Because this approach derives a lot of information from very short sequencing reads, it was hypothesized that more insight into bacterial functionality could be generated using more extensive sequencing technologies. Here, whole genome shotgun (WGS) metagenomic sequencing was employed to investigate which microbiome-associated taxa and functions were associated with increased performance of larvae reared on a chicken feed (CF) or artificial supermarket food waste (SFW) based diet.<br><br>RESULTS: Taxonomic and functional profiling of the BSFL gut microbiome revealed a significant shift in response to diet, where bacterial genes encoding specific metabolic functions, such as the metabolism of sorbitol, were significantly enriched in the microbiome of larvae reared on SFW-diet. This indicates that the nutritional composition of the substrate alters the gut bacterial composition by providing competitive benefits or new niches for specific bacteria that can utilise these compounds. Moreover, specific microbial functions, such as cobalamin synthesis, appear to be correlated with larval performance. Aside from metabolic functions, biosynthetic gene cluster analysis revealed potential antimicrobial competition and protective functions among bacterial species. Improved taxonomic resolution provided by WGS led to the identification of several metagenome assembled genomes (MAGs), including a potentially novel BSFL-associated Scrofimicrobium species. Furthermore, there were differences in larval performance between rearing diets, and larval growth was correlated with high abundance of several MAGs.<br><br>CONCLUSIONS: Variation in the nutritional and bacterial load of a diet can result in functional shifts in the gut microbiome of the larvae. Analysis of the BSFL metagenome identified several bacteria that are positively correlated with larval performance, which could potentially provide beneficial metabolic functions for the host that should be further explored.}, }
@article {pmid41039197, year = {2025}, author = {Mpai, T and Diale, MO and Shargie, N and Gerrano, AS and Mtsweni, PN and Bopape, FL and Bairu, M and Hassen, AI}, title = {Functional and taxonomic profiles of soil microbial communities of tropical legume soils from smallholder farmers' fields in Tzaneen, Limpopo province, South Africa.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {601}, pmid = {41039197}, issn = {1471-2180}, support = {PHP012403000067//Department of Agriculture (DoA), South Africa/ ; PHP012403000067//Department of Agriculture (DoA), South Africa/ ; PHP012403000067//Department of Agriculture (DoA), South Africa/ ; PHP012403000067//Department of Agriculture (DoA), South Africa/ ; PHP012403000067//Department of Agriculture (DoA), South Africa/ ; PHP012403000067//Department of Agriculture (DoA), South Africa/ ; PHP012403000067//Department of Agriculture (DoA), South Africa/ ; PHP012403000067//Department of Agriculture (DoA), South Africa/ ; }, abstract = {BACKGROUND: Soil microorganisms play a vital role as the major indicators of soil health in sustainable agricultural farming systems. However, intensive cultivation and unrecommended farmers' soil management practices negatively affect the soil microbial communities, and hence that of the soil health. Here, we investigated the functional and taxonomic diversity of soil microorganisms on six selected smallholder farmers that grow Bambara groundnut (Vigna subterranea) and dry bean (Phaseolus vulgaris) in Limpopo Province, South Africa using metagenomics and phenotypic profiles studies. Five soil samples, randomly collected per farm and pooled into a single representative sample were used. Metagenomics raw read quality control, genome assembly and annotation were performed on the KBase platform while the community level physiological profile analysis was done using Biolog Ecoplates™.<br><br>RESULTS: The results indicated that the soil microbial communities in Chosen Generation farm had higher rates of carbon source utilization. Likewise, it showed greater microbial abundance of varying taxonomy in which Actinobacteria, Firmicutes and Proteobacteria were the predominant phyla while Bacillus, Streptomyces, Microvirga and Bradyrhizobium were the most represented genera.<br><br>CONCLUSIONS: This study reports that soils from the six farms studied are enriched with genetically and physiologically diverse microorganisms that are responsible for crop growth. While soil physico-chemical properties can be associated with microbial diversity in this study, further studies on farming practices such as fertilizer and irrigation are recommended to further explore their possible effects on soil microbes.}, }
@article {pmid41039183, year = {2025}, author = {Al-Shaibani, MM and Zin, NM and Remali, J and Sidik, NM and Al-Mekhlafi, NA and Mariappan, V and Sukri, A}, title = {Anticancer compounds from Streptomyces: insights from metagenomics and mechanistic perspective.}, journal = {Folia microbiologica}, volume = {}, number = {}, pages = {}, pmid = {41039183}, issn = {1874-9356}, support = {FRGS/1/2016/STG05/UKM/02/5//Ministry of Higher Education/ ; }, abstract = {Cancer continues to be a leading cause of death globally, driving the ongoing search for novel bioactive compounds with therapeutic potential. Metagenomic sequencing has revolutionized this pursuit by enabling the direct detection and genomic assembly of previously uncultured Streptomyces species from environmental DNA, circumventing traditional cultivation limitations. This review explores recent advances in metagenomics-driven discovery of anticancer compounds derived from Streptomyces, with a focus on identifying biosynthetic gene clusters (BGCs) responsible for producing bioactive secondary metabolites. Over the past decade, metagenomic approaches have been adopted to uncover new species of Streptomyces and anticancer compounds. Although metagenomics has been adopted in research and discovery of new Streptomyces, its application in the discovery of Streptomyces-related pathways pertaining to anticancer compounds remains limited. Furthermore, clinical translation remains limited, highlighting the need for further research. By examining metagenomic methodologies and the mechanisms of action of these compounds, this review provides an updated and focused perspective on Streptomyces-derived anticancer agents and their potential for future drug development.}, }
@article {pmid41038565, year = {2025}, author = {Habiba, U and Noor, M and Kayani, MUR and Huang, L}, title = {Horizontal gene transfers differentially shape the functional potential of the infant gut metagenome.}, journal = {Life sciences}, volume = {}, number = {}, pages = {124006}, doi = {10.1016/j.lfs.2025.124006}, pmid = {41038565}, issn = {1879-0631}, abstract = {Horizontal gene transfer (HGT) is a major driver of microbial evolution, influencing the metabolic potential of microbial communities. Despite its significance, the consequences of HGT in shaping the microbial metabolic potential remain poorly understood, particularly in complex environments such as the human gut. This study aimed to assess the impact of HGT in infant gut microbiome from Caesarean section (CSD) and vaginal delivery (VD) groups during the first year of life. At Month 0, CSD infants exhibited a higher number of HGT events than VD infants. However, the numbers converged around Month 2 and remained comparable until Month 9, with no significant differences between groups (p > 0.05). HGT in VD was primarily driven by Coprococcus catus and Ruminococcus sp_5_1_39BFAA, while in CSD, Salmonella enterica and Klebsiella pneumoniae were dominant donors and acceptors. Functional analysis revealed that HGT in VD enriched genes related to carbohydrate metabolism and immune responses, whereas CSD was enriched for metabolic processes and biofilm formation. Additionally, HGT events were associated with Neonatal Intensive Care Unit Admission and diet transitions. These results suggest that HGT events in the VD and CSD groups differently shape the functional potential of the infant gut microbiome, with possible health implications that require further investigation. However, experimental validation is needed to establish a causal link.}, }
@article {pmid41038529, year = {2025}, author = {Liu, J and Dong, Y and Huang, Y and Xie, M and Wang, H and Wang, Q and Wang, S and Wang, N and Jiang, Y and Zhang, W and Wang, M and Chen, J and Huang, L and Cai, H}, title = {Clinical metagenomic next-generation sequencing test for diagnosis of central nervous system infections in ICU: A multicenter retrospective study.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {}, number = {}, pages = {108094}, doi = {10.1016/j.ijid.2025.108094}, pmid = {41038529}, issn = {1878-3511}, abstract = {BACKGROUND: Central nervous system (CNS) infections impose a substantial global burden of morbidity and mortality, necessitating accurate and timely diagnosis for optimal clinical management. Metagenomic next-generation sequencing (mNGS) has been demonstrated as a valuable tool for pathogen detection in patients with suspected CNS infections.<br><br>METHODS: From December 2019 to June 2023, we conducted a comprehensive analysis of 520 cerebrospinal fluid samples collected from patients with suspected intracranial infections across six intensive care units. All pathogen-positive results identified through metagenomic next-generation sequencing were subsequently validated by an independent laboratory.<br><br>RESULTS: Metagenomic NGS detected 105 microbial species in 520 clinical samples, comprising 64 bacterial species (61.0%), 16 DNA viruses (15.2%), 13 fungal species (12.4%), and 7 RNA viruses (6.7%). The 30-day mortality rate among all study participants was 18.5%. Metagenomic NGS identified 172 infection cases, whereas conventional culture methods detected only 31 cases. For CNS infections, mNGS demonstrated diagnostic sensitivity, specificity, and accuracy rates of 59%, 90.5%, and 72.5%, respectively.<br><br>CONCLUSIONS: Metagenomic NGS testing facilitates accelerated diagnosis of CNS infections and informs evidence-based clinical management decisions.}, }
@article {pmid41038519, year = {2025}, author = {Surgers, L and Lafont, C and Lamoureux, C and Demontant, V and N'Debi, M and Cheval, J and Boizeau, L and Trawinski, E and Pawlotsky, JM and Woerther, PL and Rodriguez, C and , }, title = {Shotgun metagenomics for the diagnosis of infections: A prospective study.}, journal = {The Journal of infection}, volume = {}, number = {}, pages = {106619}, doi = {10.1016/j.jinf.2025.106619}, pmid = {41038519}, issn = {1532-2742}, abstract = {BACKGROUND: Shotgun metagenomics (SMg) promises to significantly improve the microbiological diagnosis of infectious diseases. However, the prospective evaluation of its clinical utility in different infectious syndromes remains poorly documented.<br><br>METHODS: We conducted a prospective study including all patients who underwent SMg as part of their care at the French Henri Mondor Hospital National Reference Laboratory for accredited SMg between February 2018 and January 2020. Patients were categorized as having either a "high likelihood" or "low likelihood" of infection based on their clinical presentation. The contribution of the SMg to the final diagnosis was assessed by a multidisciplinary team of infectious disease specialists.<br><br>FINDINGS: 202 patients were enrolled in the study. Of the 123 patients considered to have a high likelihood of infection, SMg confirmed the cause of infection in 38 cases (30.9%), including 12 cases (9.8%) diagnosed exclusively by this method. In the 79 patients classified as having a "low likelihood" of infection, SMg did not detect any microorganisms compatible with an infectious cause. In particular, patients undergoing immunosuppressive treatment within the latter group showed no deterioration after 6 months.<br><br>INTERPRETATION: SMg facilitated microbiological diagnosis in over 30% of complex cases, regardless of sample type or site of infection. Compared with conventional techniques, SMg provided diagnoses in 10% more cases, highlighting its broad utility across different infectious diseases. Our results suggest that SMg is a promising tool for documenting complex infectious diseases alongside traditional microbiology tools. Furthermore, negative SMg results are useful for the management of patients with a low likelihood of infection.<br><br>FUNDING: This study was conducted as part of patient care.}, }
@article {pmid41038405, year = {2025}, author = {Jin, H and Feng, B and Gong, W and Chen, X and Wang, D and Li, Y and Huang, W and Peng, W}, title = {Evaluation of gut microbial diversity and correlation in asymptomatic and symptomatic patients with hand, foot and mouth disease.}, journal = {Genomics}, volume = {}, number = {}, pages = {111126}, doi = {10.1016/j.ygeno.2025.111126}, pmid = {41038405}, issn = {1089-8646}, }
@article {pmid41038354, year = {2025}, author = {Qing, Z and Haibei, H and Hanxue, Y and Juan, S}, title = {Mitigation of tetracycline resistance genes in silage through targeted lactic acid bacteria inoculation.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {133416}, doi = {10.1016/j.biortech.2025.133416}, pmid = {41038354}, issn = {1873-2976}, abstract = {The dissemination of antibiotic resistance genes (ARGs) in silage ecosystems poses a critical challenge to ecological stability and public health security. This investigation focuses on tetracycline resistance genes (TRGs), the most prevalent subtype of ARGs in silage, employing a targeted selection strategy for lactic acid bacteria (LAB) inoculants. From 226 isolated LAB strains, four candidates (LP1-3: Lactiplantibacillus plantarum; LC1: Lacticaseibacillus paracasei) demonstrating superior growth kinetics (OD600 > 1.6 within 24 h) and rapid acidification capacity (pH < 3.9 within 24 h) were selected. Strains LP3 and LC1 exhibited minimal intrinsic TRGs content. These four strains reduced (p < 0.001) pH, ammonia-N concentration, and coliform bacterial counts of stylo silage. Metagenomic analysis revealed that strains LP1-3 promoted Lactiplantibacillus dominance (0.709-0.975 vs. 0.379-0.509 in the control), while LC1 enhanced Lacticaseibacillus abundance (0.449-0.612 vs. 0.002-0.013 in the control). Ensiling process downregulated 367 and upregulated 227 ARGs. Inoculation with the four LAB strains further enhanced the suppression of ARGs. Among the top 30 TRGs, 22 were reduced by strains LP1-3 and 20 by LC1. Quantitative PCR results showed that strains LP1-3 decreased (p < 0.05) the contents of tetA and tetG during 30 days fermentation. Among the TRGs increased, tetA(60), tetB(58), tet(T) were positively correlated with Lactiplantibacillus spp., tetA(58), tetB(60), tetA(46), tetB(46), tet(43) were significantly correlated with Lacticaseibacillus spp. (R > 0.4, p < 0.001). In conclusion, the fermentation process induced substantial ARGs profile modifications, LAB-mediated microbiome engineering enables TRGs suppression, providing a scientific foundation for precision silage management strategies targeting antimicrobial resistance mitigation.}, }
@article {pmid41038122, year = {2025}, author = {Zhao, F and Yang, Z and Xiao, Y and Han, G and Hardie, KR and Bartlam, M and Wang, Y}, title = {Enantioselective interactions of silver nanoparticles and chiral antibiotics in driving resistance evolution in activated sludge.}, journal = {Water research}, volume = {288}, number = {Pt B}, pages = {124656}, doi = {10.1016/j.watres.2025.124656}, pmid = {41038122}, issn = {1879-2448}, abstract = {The stereochemistry of antibiotics significantly affects resistance development. With rising antibiotic resistance, nanotechnology is emerging as a promising solution, potentially increasing the likelihood of nanoparticle coexistence with antibiotics in wastewater treatment plants (WWTPs). However, the influence of nanoparticles on chiral antibiotics induced resistance remains unclear. This study employed chemical characterization, metagenomics, and molecular docking to comprehensively elucidate the resistance mechanisms induced by the combination of silver nanoparticles (AgNPs) and chiral antibiotics (ofloxacin: OFL and levofloxacin: LEV). AgNPs significantly altered the abundance and composition of antibiotic and metal resistance genes, as well as the conjugative transfer of the RP4 plasmid among activated sludge communities, with the OFL_AgNPs combination exhibiting a higher resistance potential than LEV_AgNPs. Mechanistic studies revealed that chiral antibiotics selectively interact with AgNPs, promoting Ag[+] release, enhancing antibiotic uptake, and forming stable complexes. These interactions reshaped microbial functions, including cell membrane permeability, oxidative stress response, quorum sensing, and extracellular secretion, thereby shaping resistance profiles. This study reveals previously overlooked enantiomer-specific risks associated with nanoparticle-antibiotic interactions and provides a foundation for strategies to mitigate ARG dissemination in wastewater treatment and broader environmental systems.}, }
@article {pmid41037216, year = {2025}, author = {Pan, F and Yu, F and Zhang, H and Chen, P and Weng, W}, title = {Clinical application of metagenomic next-generation sequencing (mNGS) in children with suspected bloodstream infection.}, journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {}, number = {}, pages = {}, pmid = {41037216}, issn = {1435-4373}, abstract = {BACKGROUND: Accurate and comprehensive pathogen diagnosis methods are urgently required for the diagnosis of bloodstream infection (BSI).This study retrospectively evaluated the clinical application of metagenomic next-generation sequencing (mNGS) in children with suspected BSI.<br><br>METHODS: Between July 8, 2021 to December 31, 2022, mNGS tests and conventional methods tests (CMTs) were performed simulataneously on samples from children with suspected BSI. The diagnostic performance of mNGS was assessed in comparison CMTs .<br><br>RESULTS: A total of 191 patients with suspected BSI were included in the final analysis after excluding 9 patients due to lost to follow-up or duplicated entries. The mNGS yielded positive results in 111 cases, with a positive rate of 58.1% (111/191), significantly higher than that of CMTs (13.1%, 25/191) (P&#x2009;<&#x2009;0.05). Using CMTs as standard, the sensitivity, specificity, positive predictive value and negative predictive value for mNGS and CMTs were 73.8% vs. 25.0%, 54.2% vs. 96.3%, 55.9% vs. 84.0%, and 72.5% vs. 62.0%, respectively. Among 111 mNGS-positive cases, 46 cases (41.4%) showed ploymicrobial infections, with Torque teno virus, human betaherpesvirus 5, and human gammaherpesvirus 4 being most frequently identified pathogens. Of them, 62 cases (55.9%) were clinically diagnosed as BSI regarded as true positive results, while 49 cases (44.1%) positive for pathogens were diagnosed as non-BSI. The diagnostic time of mNGS was significantly shorter than that of CMTs (30.6&#x2009;&#xb1;&#x2009;7.7&#xa0;h vs. 70.5&#x2009;&#xb1;&#x2009;11.6&#xa0;h, P&#x2009;<&#x2009;0.05). It is worth noting that mNGS results guided adjustments to antimicrobial therapy in 50.8% (97/191) patients, including escalation in 74 cases and de-escalation in 23 cases.<br><br>CONCLUSIONS: The mNGS significantly improves the detection rate for the pathogens in children with suspected BSI, especially for viruses, which serve as a complement to CMTs.}, }
@article {pmid41037127, year = {2025}, author = {Arunrat, N and Mhuantong, W and Sereenonchai, S}, title = {Land-use legacies shape soil microbial communities and nutrient cycling functions in rotational shifting cultivation fields of Northern Thailand.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {102}, pmid = {41037127}, issn = {1432-184X}, support = {MU-SRF-RS-21 B/67//Mahidol University (Strategic Research Fund: 2024)/ ; }, mesh = {*Soil Microbiology ; Thailand ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Soil/chemistry ; *Microbiota ; Nitrogen/metabolism ; Nitrification ; *Agriculture/methods ; Nitrogen Fixation ; Nitrogen Cycle ; }, abstract = {How land-use history-particularly in contrasting systems such as rotational shifting cultivation (RSC) and continuously fallow (CF) fields-influences soil microbial communities and their biogeochemical functions remains insufficiently understood. In this study, shotgun metagenomic sequencing was used to compare the taxonomic composition and functional gene profiles of soils under RSC and CF systems in Northern Thailand. The results revealed distinct microbial assemblages and metabolic potentials shaped by land-use legacy. RSC soils were characterized by a higher abundance of nitrifiers and nitrogen-fixing taxa, including Nitrosocosmicus and Streptomyces, along with enriched genes involved in nitrification (e.g., amoC_B, nxrB) and nitrogen fixation (nifD, nifK), reflecting an enhanced potential for nitrogen acquisition and retention. In contrast, CF soils showed enrichment in Bradyrhizobium, Halobaculum, and Russula, and exhibited higher expression of denitrification-related genes (norB, narJ), suggesting increased nitrogen loss via gaseous emissions. Functional genes related to phosphate metabolism (phoX, glpQ) and nutrient signal transduction were more abundant in RSC soils, indicating active nutrient cycling in response to recent disturbance. Conversely, CF soils demonstrated broader metabolic capabilities, including genes for sulfur oxidation and redox regulation, suggesting microbial adaptation to more stable but nutrient-limited conditions. These findings demonstrate that land-use legacies strongly influence microbial composition and function, with important implications for nutrient cycling and soil fertility restoration in shifting cultivation landscapes.}, }
@article {pmid41036867, year = {2025}, author = {Venturini, AM and Gontijo, JB and Berrios, L and Mazza Rodrigues, JL and Peay, KG and Tsai, SM}, title = {A catalog of metagenome-assembled genomes from Amazonian forest and pasture soils.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0064225}, doi = {10.1128/mra.00642-25}, pmid = {41036867}, issn = {2576-098X}, abstract = {The Amazon rainforest is facing multifaceted anthropogenic pressures, and we previously showed that forest-to-pasture conversion has led to soil microbial communities with distinct genomic traits. Here, we present 69 archaeal and bacterial metagenome-assembled genomes and detail their virulence- and antimicrobial resistance-associated genes.}, }
@article {pmid41036845, year = {2025}, author = {Du Plessis, I and Snyder, H and Calder, R and Rolando, JL and Kostka, JE and Weitz, JS and Dominguez-Mirazo, M}, title = {Viral community diversity in the rhizosphere of the foundation salt marsh plant Spartina alterniflora.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0023425}, doi = {10.1128/msphere.00234-25}, pmid = {41036845}, issn = {2379-5042}, abstract = {Viruses of microorganisms impact microbial population dynamics, community structure, nutrient cycling, gene transfer, and genomic innovation. In wetlands, root-associated microbial communities mediate key biogeochemical processes important for plants involved in ecosystem maintenance. Nonetheless, the presence and role of microbial viruses in salt marshes remain poorly understood. In this study, we analyzed 24 metagenomes retrieved from the root zone of Spartina alterniflora, a foundation plant in salt marshes of the eastern and Gulf coasts of the U.S. The samples span three plant compartments-bulk sediment, rhizosphere, and root-and two cordgrass plant phenotypes: short and tall. We observed differentiation between phenotypes and increased similarity in viral communities between the root and rhizosphere, indicating that plant compartment and phenotype shape viral community composition. The majority of viral populations characterized are novel at the genus level, with a subset predicted to target microorganisms known to carry out key biogeochemical functions. The findings contribute to ongoing efforts to understand plant-associated viral diversity and community composition and to identify potential targets for exploring viral modulation of microbially mediated ecosystem functioning in intertidal wetlands.IMPORTANCESalt marshes are vital coastal ecosystems. Microbes in these environments drive nutrient cycling and support plant health, with Spartina alterniflora serving as a foundation species. This study explores viral communities associated with S. alterniflora, revealing how plant compartments and phenotypes shape viral composition. The discovery of numerous novel viruses, some potentially influencing microbes involved in key biogeochemical processes, highlights their ecological significance. Given the increasing pressures on coastal ecosystems, understanding virus-microbe-plant interactions is essential for predicting and managing ecosystem responses to environmental change.}, }
@article {pmid41036842, year = {2025}, author = {Zeng, J and Hu, W and Chang, L and Hua, Z and Wu, G and Fang, Y and Wang, G and Xiao, C and Liu, J}, title = {Genome-resolved insights into the bacterial phylum WOR-3: hydrogenotrophic metabolism and unique carbon fixation via archaeal form III RuBisCO.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0117825}, doi = {10.1128/msystems.01178-25}, pmid = {41036842}, issn = {2379-5077}, abstract = {The WOR-3 phylum is widely distributed in various environments, including hot springs, marine ecosystems, and hydrothermal vents, yet its ecological roles and metabolic capabilities remain poorly understood. In this study, we analyzed 181 medium- to high-quality metagenome-assembled genomes, including 59 newly reconstructed from environmental samples and 122 retrieved from public databases. Phylogenetic analyses resolved the WOR-3 lineage into four subgroups (subgroup 1-4). Metabolic reconstruction revealed significant divergence of the carbon, sulfur, nitrogen, and hydrogen metabolism pathways among the different subgroups. Subgroup 1 was characterized by fermentative metabolism involving formate and ethanol and uniquely exhibited potential for carbon fixation via the Calvin cycle, as indicated by the presence of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) gene. Notably, WOR-3 RuBisCO is phylogenetically affiliated with archaeal form III, although the carbon fixation pathway follows the canonical bacterial Calvin cycle-a feature of potential evolutionary significance. Subgroup 3 exhibits metabolic versatility, including genes for dissimilatory sulfate reduction, sulfur oxidation, partial denitrification, and fatty acid degradation. In addition, all subgroups harbored key components of hydrogen metabolism, including widespread NiFe hydrogenases, supporting H2-dependent electron transfer and energy conservation. Within the WOR-3 lineage, the coexistence of two respiratory enzyme systems-the Rnf complex and the oxidative phosphorylation respiratory chain-indicates distinct anaerobic and aerobic metabolic lifestyles, respectively. Collectively, this study expands the genomic framework for the WOR-3 phylum and provides novel insights into the metabolic versatility and ecological functions of this previously uncharacterized lineage in biogeochemical cycles of carbon, nitrogen, and sulfur.IMPORTANCEThe WOR-3 phylum represents a widespread but poorly understood bacterial lineage inhabiting diverse various environments. By integrating 181 metagenome-assembled genomes, including 59 newly reconstructed, this study provides the most comprehensive genomic framework to date for WOR-3. Phylogenomic and metabolic reconstruction revealed four distinct subgroups with divergent capacities for carbon, sulfur, and nitrogen metabolism. Notably, subgroup 1 encodes a complete Calvin-Benson-Bassham cycle featuring an archaeal-type form III ribulose-1,5-bisphosphate carboxylase/oxygenase, suggesting an unusual evolutionary trajectory for carbon fixation in this lineage. Subgroup 3 exhibits versatile metabolic potential, including dissimilatory sulfur metabolism, partial denitrification, and fatty acid degradation, highlighting its possible roles in multiple biogeochemical processes. These findings not only expand the taxonomic and functional landscape of the WOR-3 phylum but also offer key insights into its ecological roles in global element cycling.}, }
@article {pmid41036698, year = {2025}, author = {Bulteau, S and Braud, M and Petrier, M and Castain, L and Anani, H and Peltier, C and Mobuchon, L and Bouras, M and Flattres, D and Poschmann, J and Josset, L and Roquilly, A and Bressollette-Bodin, C}, title = {Interferon Gamma Injection and Its Effect on the Respiratory Anelloviridae Population in ICU Ventilated Patients.}, journal = {Journal of medical virology}, volume = {97}, number = {10}, pages = {e70612}, doi = {10.1002/jmv.70612}, pmid = {41036698}, issn = {1096-9071}, support = {//This work was supported by the Horizon 2020 Research and Innovation Framework Programme (grant agreement no. 847782, HAP2 project, https://hap2-project.com). S.B. was also supported by a grant from Region Pays de la Loire./ ; }, mesh = {Humans ; Male ; Female ; Intensive Care Units ; Middle Aged ; *Interferon-gamma/administration &amp; dosage/therapeutic use ; Aged ; *Respiration, Artificial/adverse effects ; Viral Load ; DNA, Viral ; Adult ; Metagenomics ; *Healthcare-Associated Pneumonia/prevention &amp; control/virology ; *Immunologic Factors/administration &amp; dosage ; Critical Illness ; }, abstract = {Immune dysfunctions induced by critical illness are associated with an increased risk of hospital-acquired pneumonia (HAP) in intensive care unit (ICU) patients. The use of immunomodulatory molecules in this setting is under evaluation. The presence of persistent viruses, such as anelloviruses (AVs) or herpesviruses, which are frequently detected in respiratory samples, may indicate immune dysfunction. Herpesvirus infections are associated with increased morbidity in ICU patients, and variations in AV DNA loads are associated with rejection events in immunocompromised patients. We investigated the respiratory viral landscape of 94 patients during the first week under invasive mechanical ventilation using quantitative PCR and targeted metagenomics after capture probe enrichment. The patients were included in a placebo-controlled randomized clinical trial testing IFNγ for the prevention of HAP. We measured AV and herpes simplex virus-1 (HSV-1) DNA loads over time in respiratory samples collected at admission (n = 54), and on Days 3 (n = 73) and 7 (n = 57) after admission. There were no significant differences in mortality, HAP, the development of acute respiratory distress syndrome (ARDS), HSV, or AV DNA detection between patients treated with IFNg and those who received a placebo. Patients who developed HAP had a significantly higher AV DNA load in tracheal aspirates over time (p = 0.011) than those who did not. Target enrichment analysis revealed AV presence in all respiratory samples, with no differences observed in AV composition between IFNg-treated and placebo patients, or between HAP and noHAP patients. Trial Registration: CPP Ouest II 17/02/2021 (avis N°2021/03); ClinicalTrial.gov number: NCT04793568.}, }
@article {pmid41036626, year = {2025}, author = {Xia, Y and Liang, L and Wang, X and Chen, Z and Liu, J and Yang, Y and Xie, H and Ding, Z and Huang, X and Long, S and Wang, Z and Xu, X and Ding, C and Chen, Q and Feng, Q}, title = {MetaflowX: a scalable and resource-efficient workflow for multi-strategy metagenomic analysis.}, journal = {Nucleic acids research}, volume = {53}, number = {18}, pages = {}, doi = {10.1093/nar/gkaf954}, pmid = {41036626}, issn = {1362-4962}, support = {2022YFA1304100//National Key R&amp;D Program of China/ ; 82&#xa0;270&#xa0;980//National Natural Science Foundation of China/ ; 82071122//National Natural Science Foundation of China/ ; 82&#xa0;202&#xa0;539//National Natural Science Foundation of China/ ; 2023ZD0501406//National Science and Technology Major Program/ ; 2019//National Young Scientist Support Foundation/ ; ZR2021JQ29//Excellent Young Scientist Foundation of Shandong Province/ ; 2019//Taishan Young Scientist Project of Shandong Province/ ; 2021GXRC021//Periodontitis innovation team of Jinan City/ ; 2021SFGC0502//Major Innovation Projects in Shandong Province/ ; 2020KJK001//Oral Microbiome Innovation Team of Shandong Province/ ; 2021ZDSYS18//Shandong Province Key Research and Development Program/ ; #202412A001//horizontal cooperation project with Shenzhen 01 Life Institute/ ; #202112E401//horizontal cooperation project with Shenzhen 01 Life Institute/ ; }, mesh = {*Metagenomics/methods ; Workflow ; *Software ; *Metagenome/genetics ; *Microbiota/genetics ; Humans ; }, abstract = {Microbiomes play crucial roles in diverse ecosystems, spanning environmental, agricultural, and human health domains. However, in-depth metagenomic data analysis presents significant technical and resource challenges, particularly at scale. Existing computational pipelines are typically limited to either reference-based or reference-free approaches and exhibit inefficiencies in process large datasets. Here, we introduce MetaflowX (https://github.com/01life/MetaflowX), an open-resource workflow integrating both analytical paradigms for enhanced metagenomic investigations. This modular framework encompasses short-read quality control, rapid microbial profiling, hybrid contig assembly and binning, high-quality metagenome-assembled genome (MAG) identification, as well as bin refinement and reassembly. Benchmarking tests showed that MetaflowX completed full metagenomic analyses up to 14-fold faster and with 38% less disk usage than existing workflows. It also recovered the highest number of high-quality and taxonomically diverse MAGs. A dedicated reassembly module further improved MAG quality, increasing completeness by 5.6% and reducing contamination by 53% on average. Functional annotation modules enable detection of key features, including virulence and antibiotic resistance genes. Designed for extensibility, MetaflowX provides an efficient solution addressing current and emerging demands in large-scale metagenomic research.}, }
@article {pmid41036540, year = {2025}, author = {Pei, Y and Cai, S and Xue, Y and Fu, Y and Zhang, J and Shen, Q and Ji, L and Wu, P and Wang, H and Wang, Y and Zhang, W and Yang, S}, title = {First detection of two cycloviruses in cormorant fecal samples in China by high-throughput sequencing technology.}, journal = {Frontiers in veterinary science}, volume = {12}, number = {}, pages = {1677378}, pmid = {41036540}, issn = {2297-1769}, abstract = {INTRODUCTION: The Great Cormorant (Phalacrocorax carbo) is widely distributed across China. As an apex predator in aquatic ecosystems, it plays a tripartite ecological role: acting as a natural host, transmission vector, and indicator species for viruses. Current research confirms that cormorants carry diverse viral pathogens from the families including Flaviviridae, Orthomyxoviridae, Paramyxoviridae, and Polyomaviridae. Significant knowledge gaps persist regarding their virome diversity.<br><br>METHODS: In this study,46 cormorant fecal swab samples were collected at Xiamen Garden Expo Park, and viralmetagenomics method was conducted to identify two Cycloviruses.<br><br>RESULTS: This study identified two novel cycloviruses, Corcyclo-1 (1,856 bp) and Corcyclo-2 (1,831 bp), from cormorant fecal samples using viral metagenomics. Genomic analyses revealed hallmark features of the genus Cyclovirus, including inversely oriented open reading frames (ORFs) encoding the capsid protein (Cap) and replication-associated protein (Rep), as well as a conserved stem-loop sequence TAATACTAT. The Rep gene of Corcyclo-1 contained a 166-bp intron and shared >96.9% amino acid identity with human-, wild boar-, and chicken-derived cyclovirus strains (HaCV-8) from Vietnam and Madagascar, classifying it as a novel strain of HaCV-8. In contrast, Corcyclo-2 harbored a 98-bp intron in its Rep gene and clustered with unclassified cyclovirus strains from bats and mongooses in China and Saint Kitts and Nevis (>97.4% identity), constituting a putative new species. Phylogenetic and pairwise sequence analyses further supported their taxonomic positions. Epidemiological screening demonstrated a high prevalence of Corcyclo-1 (82.6%, 38/46) and Corcyclo-2 (32.6%, 15/46) in cormorant feces. Cross-species surveillance detected Corcyclo-2 in chickens (25.8%, 16/62) and ducks (11.7%, 9/77), whereas Corcyclo-1 was absent in these hosts.<br><br>CONCLUSION: This study represents the first report of cormorant-associated cycloviruses, highlighting their potential for cross-species transmission and providing new insights into the ecological diversity and evolutionary mechanisms of cyclovirus.}, }
@article {pmid41036230, year = {2025}, author = {Xin, L and Jiao, X and Gong, X and Yu, J and Zhao, J and Lv, J and Feng, Q and Yuan, Y and Pan, W}, title = {Diagnostic value of metagenomic next generation sequencing of bronchoalveolar lavage fluid in immunocompromised patients with pneumonia.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1602636}, pmid = {41036230}, issn = {2235-2988}, mesh = {Humans ; *Immunocompromised Host ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Male ; *Bronchoalveolar Lavage Fluid/microbiology/virology ; Female ; Middle Aged ; Sensitivity and Specificity ; Aged ; *Pneumonia/diagnosis/microbiology ; Bacteria/genetics/isolation &amp; purification/classification ; Adult ; Fungi/genetics/isolation &amp; purification/classification ; Viruses/genetics/isolation &amp; purification/classification ; }, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) enables simultaneous sequencing of DNA fragments for comprehensive pathogen identification. Pneumonia in immunocompromised patients-characterized by atypical clinical manifestations and rapid progression-poses diagnostic challenges. Conventional microbiological testing (CMT), which relies on pathogen culture and serological assays, is limited by prolonged turnaround times and suboptimal detection rates. This study was performed to evaluate the clinical utility of mNGS through comparative analysis with CMT in detecting pathogens among immunocompromised patients with pneumonia.<br><br>METHODS: We conducted a retrospective cohort study of 146 immunocompromised patients with suspected pneumonia. The mNGS and CMT results were systematically analyzed. Pathogen detection rates and microbial spectrum concordance were visualized using pie and bar charts. Diagnostic performance was compared using McNemar's test and Kappa (&#x3ba;) statistics for inter-method agreement. The sensitivity, specificity, accuracy, and area under the curve were calculated for pathogen-specific evaluations.<br><br>RESULTS: mNGS demonstrated superior detection efficacy, identifying pathogens in 98 cases versus 50 by CMT, with 48 overlapping positives. The microbial spectrum showed substantial differences: mNGS detected 73 bacterial, 46 fungal, and 45 viral pathogens, whereas CMT identified 38 bacterial, 27 fungal, and 21 viral agents. mNGS outperformed CMT across all infection types, including single-pathogen infections (bacterial, fungal, or viral only) and mixed infections (bacterial + fungal, bacterial + viral, fungal + viral, or bacterial + fungal + viral). Bacterial and fungal detections showed low inter-method concordance, while viral detection exhibited moderate agreement (&#x3ba; = 0.510, p < 0.001). Notably, mNGS achieved significantly higher detection rates for Enterococcus faecalis and Pneumocystis jirovecii in intensive care unit (ICU)-admitted patients with severe pneumonia (p < 0.05). Clinical outcomes improved in 45 patients following mNGS-guided therapeutic adjustments.<br><br>CONCLUSIONS: mNGS and CMT demonstrate complementary strengths in bacterial and fungal detection in immunocompromised patients with pneumonia. mNGS provides enhanced diagnostic accuracy for key pathogens such as E. faecalis and P. jirovecii, particularly in severe and ICU-admitted cases. As a high-throughput diagnostic tool, mNGS may improve pathogen detection and clinical management in immunocompromised populations.}, }
@article {pmid41035885, year = {2025}, author = {Velasco Cardona, DC and Cardona-Acevedo, S and Valencia-Arias, A and Pérez-Delgado, O and Pinella Vega, M}, title = {Bibliometric analysis of the application of artificial intelligence techniques in bacteriology: a PRISMA-guided research agenda.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1641967}, pmid = {41035885}, issn = {1664-302X}, abstract = {INTRODUCTION: The integration of artificial intelligence (AI) into bacteriology has marked a pivotal advancement by enabling the analysis of large-scale microbiological datasets. Despite growing adoption, significant research gaps persist, hindering the full exploitation of AI's potential in bacterial research and diagnostics.<br><br>OBJECTIVE: To analyze global scientific production on the application of AI techniques in bacteriology and propose a future research agenda based on bibliometric trends.<br><br>METHODS: This study conducts a bibliometric analysis of artificial intelligence (AI) applications in bacteriology, explicitly guided by the PRISMA 2020 framework. Unlike traditional reviews, this approach combines PRISMA's methodological rigor with bibliometric techniques to map scientific production. Metadata were retrieved from Scopus and Web of Science using predefined search strategies. Quantitative indicators, co-occurrence networks, and thematic mapping were applied to examine the field's temporal evolution and conceptual structure. The findings provide an evidence-based overview of research trends and gaps, supporting the design of a future research agenda on AI integration in bacteriology.<br><br>RESULTS: The findings reveal exponential growth in scientific output, especially between 2022 and 2024. Leading authors include Singh and Waegeman, with high-impact journals such as Frontiers in Microbiology and MSystems. The United States and China are the most productive countries. Thematic evolution shows a shift from early topics like microbial spoilage toward advanced applications including bacterial classification and diagnostic modeling. Key conceptual clusters were identified around microbiomes, classification, and bioinformatics. Emerging terms such as "diagnosis," "metagenomics," and "transfer learning" indicate future research directions.<br><br>CONCLUSION: AI applications in bacteriology are expanding rapidly yet still rely heavily on traditional machine learning methods. There is a need to incorporate advanced approaches such as deep learning and transformer-based models. The findings support a strategic agenda for promoting interdisciplinary collaboration and technological innovation in bacteriological research.}, }
@article {pmid41035876, year = {2025}, author = {Jiang, W and Zhai, J and Li, B and Ma, J and Zhang, S}, title = {Pulmonary Rhizopus arrhizus infection treated with high-dose liposomal amphotericin B in a heart transplant recipient under ECMO: a case report.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1631873}, pmid = {41035876}, issn = {2296-858X}, abstract = {Pulmonary mucormycosis caused by Rhizopus arrhizus is an emergent, fulminant threat in immunocompromised hosts, yet therapeutic success remains elusive when extracorporeal membrane oxygenation (ECMO) is required. While liposomal amphotericin B (L-AMB) is endorsed as first-line therapy, its pharmacokinetics are profoundly altered by ECMO-dilution, circuit sequestration, and impaired lung penetration all conspire to sub-therapeutic exposure. We report the first documented case in which these challenges were systematically overcome. A 52-year-old cardiac-transplant recipient, supported on veno-venous ECMO for refractory hypoxaemia, developed rapidly progressive pneumonia. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid returned a definitive Rhizopus arrhizus signature within 24 h, prompting immediate escalation to high-dose L-AMB (10 mg/kg/day). Therapeutic drug monitoring confirmed sustained trough levels above 7 μg/mL despite a 3.5-fold increase in volume of distribution. Serial mNGS quantification demonstrated a logarithmic decline in fungal reads to undetectable levels by day 10, accompanied by radiological resolution and preserved renal function. After 28 days of intravenous therapy, the patient was discharged on oral isavuconazole with no relapse at 6 months. This case establishes that early pathogen identification by mNGS, coupled with aggressive L-AMB dose optimisation under rigorous pharmacokinetic guidance, can achieve cure of pulmonary mucormycosis even in the most pharmacologically hostile environment of ECMO support.}, }
@article {pmid41035666, year = {2025}, author = {Liu, H and Ding, Z and Xu, L and Guo, T}, title = {Severe Legionella pneumonia mimicking immune-related pneumonitis after chemoimmunotherapy for lung cancer: a case report.}, journal = {Frontiers in oncology}, volume = {15}, number = {}, pages = {1663978}, pmid = {41035666}, issn = {2234-943X}, abstract = {BACKGROUND: Immune checkpoint inhibitors (ICIs) have significantly improved survival outcomes and quality of life in patients with various malignancies. Nevertheless, their associated toxicities must not be overlooked. Although not the most common immune-related adverse event (irAE), CIP is recognized as one of the most serious. In particular, grade 3-4 CIP that is not promptly treated may compromise subsequent immunotherapy and can result in respiratory failure or even death. Legionnaires' disease, caused by Legionella pneumophila, is an uncommon but potentially life-threatening form of atypical pneumonia. With the expanding use of ICIs, especially in combination with chemotherapy, early stage CIP and Legionella pneumonia may share similar radiological features, such as ground-glass opacities, which makes early differential diagnosis difficult. However, timely differentiation is critical because the management strategies differ substantially: CIP requires systemic corticosteroids, whereas Legionella pneumonia necessitates quinolone antibiotics. Traditional diagnostic methods for Legionella infection, including culture on specialized media and urine antigen testing, are limited by low sensitivity and the risk of false-negative results. In recent years, targeted next-generation sequencing (tNGS) has emerged as a valuable diagnostic tool. Compared with metagenomic next-generation sequencing (mNGS), tNGS offers a shorter turnaround time, higher sensitivity and specificity, and greater cost-effectiveness. As such, it is becoming increasingly important in the accurate identification of atypical pathogens in pulmonary infections.<br><br>CASE SUMMARY: We report the case of a patient with squamous cell lung cancer who developed severe pneumonia following combined chemotherapy and immunotherapy. The initial working diagnosis was immune checkpoint inhibitor-related pneumonia (ICI-P) complicated by bacterial infection. However, sputum-targeted next-generation sequencing (tNGS) subsequently identified Legionella pneumophila infection. Following the administration of quinolone-sensitive antibiotics, the patient's clinical condition improved markedly, and he was discharged in a stable state. A 70-year-old male farmer with a history of lung cancer, type 2 diabetes, and chronic obstructive pulmonary disease (COPD) was admitted on February 4, 2025,with fever, cough, and dyspnea following chemoimmunotherapy. He had received paclitaxel, cisplatin, and tislelizumab on January 24.Initial tests revealed leukopenia, neutropenia, and chemotherapy-induced myelosuppression. On admission, the patient exhibited hypoxemia, hyponatremia, and elevated inflammatory markers, raising suspicion for ICI-P complicated by bacterial infection. Despite empirical broad-spectrum antibiotics and corticosteroids, his condition deteriorated, requiring transfer to the Respiratory Intensive Care Unit (RICU). On February 13, tNGS of sputum identified Legionella pneumophila, Enterococcus faecium, Epstein-Barr virus (EBV),and Herpesvirus-1 (HSV-1). The high relative abundance of Legionella pneumophila indicated it was the primary pathogen; EBV and HSV-1 were presumed latent. Antimicrobial therapy was adjusted to moxifloxacin, cefepime, and ganciclovir, leading to clinical improvement and resolution of hypoxemia. Follow-up chest CT showed partial resolution of pulmonary infiltrates. The patient was discharged with home oxygen and outpatient follow-up.The patient is currently undergoing regular anti-tumor treatment.<br><br>CONCLUSIONS: In the era of chemoimmunotherapy, the presence of pulmonary ground-glass interstitial lesions should prompt consideration not only of immune checkpoint inhibitor-related pneumonia (ICI-P) but also of infections caused by uncommon pathogens such as Legionella, particularly when there is no significant improvement after corticosteroid therapy. It is necessary to consider applying advanced molecular diagnostic techniques such as targeted next-generation sequencing (tNGS) as early as possible to make a clear diagnosis of the pathogen and guide individualized treatment.}, }
@article {pmid41035224, year = {2025}, author = {Farini, A and Strati, F and Molinaro, M and Mostosi, D and Saccone, S and Tripodi, L and Troisi, J and Landolfi, A and Amoroso, C and Cassani, B and Blanco-Míguez, A and Leonetti, E and Bazzani, D and Bolzan, M and Fortunato, F and Caprioli, F and Facciotti, F and Torrente, Y}, title = {Immunoproteasome Inhibition Positively Impacts the Gut-Muscle Axis in Duchenne Muscular Dystrophy.}, journal = {Journal of cachexia, sarcopenia and muscle}, volume = {16}, number = {5}, pages = {e70054}, doi = {10.1002/jcsm.70054}, pmid = {41035224}, issn = {2190-6009}, support = {M6/C2_CALL 2022//PNRR/ ; FRRB-2022//Unmet Medical Needs, Fondazione Regionale per la Ricerca Biomedica/ ; GJC21084//Cariplo Telethon Alliance GJC2021-2022/ ; //NextGenerationEU/ ; //MUR/ ; PR-0394//Gruppo familiari beta-sarcoglicanopatie/ ; PNC-E3-2022-23683266-CUP: C43C22001630001//Hub Life Science-Diagnostica Avanzata/ ; //Associazione Centro Dino Ferrari/ ; }, mesh = {Animals ; *Muscular Dystrophy, Duchenne/drug therapy/metabolism/pathology ; Mice ; Gastrointestinal Microbiome/drug effects ; *Proteasome Inhibitors/pharmacology/therapeutic use ; *Muscle, Skeletal/drug effects/metabolism ; Disease Models, Animal ; Mice, Inbred mdx ; Male ; *Proteasome Endopeptidase Complex/metabolism ; Mice, Inbred C57BL ; }, abstract = {BACKGROUND: Duchenne Muscular Dystrophy (DMD) features immune-muscle crosstalk, where muscle fibre degeneration enhances pro-inflammatory macrophage infiltration, worsening inflammation and impairing regeneration.<br><br>METHODS: We investigated the impact of immunoproteasome (IP) inhibition on the gut-muscle axis in mdx mice, a well-established model of DMD. We employed microbiota perturbation models, including broad-spectrum antibiotic treatment (ABX) and faecal microbiota transplantation (FMT) from IP-inhibited mdx mice. IP inhibition effects were assessed by analysing gut microbiota composition, intestinal inflammation, muscle integrity and associated metabolic and inflammatory pathways.<br><br>RESULTS: IP inhibitor ONX-0914 significantly impacted the intestinal inflammatory microenvironment and gut microbiota of mdx mice. ONX-0914 treatment increased gastrointestinal transit (increased wet/dry faecal weights, p&#x2009;=&#x2009;0.0486 and p&#x2009;=&#x2009;0.0112, respectively) and partially restored intestinal barrier integrity (reduced FITC-dextran leakage, p&#x2009;=&#x2009;0.0449). JAM-A was significantly upregulated (p&#x2009;<&#x2009;0.0001). Colonic CD206+ M2 macrophages increased, while CD68&#x2009;+&#x2009;M1 cells partially decreased. ONX-0914 downregulated IP isoforms in macrophages (PSMB8: p&#x2009;=&#x2009;0.0022; PSMB9: p&#x2009;=&#x2009;0.0186) as well as FOXO-1 (p&#x2009;=&#x2009;0.0380) and TNF-&#x3b1; (p&#x2009;=&#x2009;0.0487). Antibiotic-induced microbiota depletion abrogated these effects. Metagenomic analysis revealed significant differences in microbiota composition between C57Bl controls and mdx mice (PERMANOVA p&#x2009;<&#x2009;0.001), with ONX-0914 inducing enrichment of stachyose degradation pathways. Metabolomic analysis showed enrichment of bacterial metabolites, fatty acid and sugar metabolism pathways, with increased glutathione, galactose, glycerol, glyceraldehyde and TCA cycle intermediates. ONX-0914 improved mitochondrial activity in skeletal muscle, as increased expression of ETC complexes (mdx vs. mdx+ONX: Complex II, p&#x2009;=&#x2009;0.0338; Complex IV, p&#x2009;=&#x2009;0.0023) and TCA enzymes (mdx vs. FTMmdx+ONX: IDH p&#x2009;=&#x2009;0.0258; FH p&#x2009;=&#x2009;0.0366). This led to a shift towards oxidative muscle fibres and improved muscle morphology (increased fibre size, p&#x2009;<&#x2009;0.0001 mdx vs. mdx+ONX and mdx vs. FTMmdx+ONX). Muscle performance was enhanced with reduced CPK levels (p&#x2009;=&#x2009;0.0015 mdx vs. mdx+ONX) and fibrosis (decreased TGF&#x3b2;: mdx vs. mdx+ONX, p&#x2009;=&#x2009;0.0248; mdx vs. FTMmdx+ONX, p&#x2009;=&#x2009;0.0279). ONX-0914 reduced CD68+ (mdx vs. mdx+ONX, p&#x2009;=&#x2009;0.0024; mdx vs. FTMmdx+ONX, p&#x2009;<&#x2009;0.0001) and increased CD206+ (mdx vs. FTMmdx+ONX: p&#x2009;=&#x2009;0.0083) macrophages in muscle, downregulated inflammatory genes (mdx vs. mdx+ONX: ccl2 p&#x2009;=&#x2009;0.0327, vcam-1p&#x2009;=&#x2009;0.0378) and reduced pro-inflammatory proteins (MCP1, mdx vs. mdx+ONX, p&#x2009;=&#x2009;0.0442). Inflammatory cytokines and endothelial vessel density in ONX-0914 treated mdx were restored to wild type mice. These data demonstrate that ONX-0914 enhances muscle function through microbiota-dependent mechanisms.<br><br>CONCLUSIONS: Our study advances the understanding of the role of dysbiosis in DMD disease and identifies IP inhibition as a potential therapeutic strategy to modulate the dystrophic gut-muscle axis, offering new perspectives for microbiota-targeted therapies.}, }
@article {pmid41035142, year = {2025}, author = {Wang, B and Fu, Y and Xu, D and Liu, J and Tian, T and Xie, W}, title = {Successful Management of a Rare Keratitis Caused by Mycobacterium Immunogenum After a Series of Misdiagnoses.}, journal = {Eye &amp; contact lens}, volume = {}, number = {}, pages = {}, doi = {10.1097/ICL.0000000000001228}, pmid = {41035142}, issn = {1542-233X}, abstract = {This case report presents the successful diagnosis and management of a rare case of Mycobacterium immunogenum keratitis. A 34-year-old immunocompetent female presented with a 6-month history of recurrent right eye redness and blurred vision. Previous treatment at other hospitals with oral antivirals, topical corticosteroids, and ganciclovir ointment for presumed herpetic keratitis had failed, with progressive vision decline from 20/20 to 20/50. The causative pathogen identification revealed Mycobacterium immunogenum through comprehensive diagnostic workup including microbiological culture, acid-fast staining, and metagenomic next-generation sequencing (mNGS). Initial therapy with topical amikacin proved ineffective and caused significant ocular toxicity, whereas adjunctive oral azithromycin showed no clinical benefit. Subsequent treatment with 0.3% gatifloxacin eye gel resulted in dramatic improvement. During the healing phase, 0.02% fluorometholone was added to control scarring. Complete resolution was achieved within 4 months, with only mild residual scarring and final uncorrected visual acuity of 20/30. The patient remained recurrence-free throughout 4 years of follow-up. This case demonstrates that Mycobacterium immunogenum keratitis does not necessarily occur in immunocompromised individuals or those with a history of trauma or surgery. It is easily misdiagnosed in the early stages, whereas mNGS can aid in pathogen identification. Treatment with 0.3% gatifloxacin eye gel suggests potentially superior efficacy and safety in such condition.}, }
@article {pmid41034963, year = {2025}, author = {Lewis, ZJ and Scott, A and Madden, C and Vik, D and Zayed, AA and Smith, GJ and Justice, SS and Rudinsky, A and Hokamp, J and Hale, VL}, title = {Evaluating urine volume and host depletion methods to enable genome-resolved metagenomics of the urobiome.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {199}, pmid = {41034963}, issn = {2049-2618}, support = {Canine Intramural Grant//College of Veterinary Medicine, Ohio State University/ ; DBI 20222070//National Science Foundation/ ; 1K08ES034821-01A1/NH/NIH HHS/United States ; }, mesh = {*Metagenomics/methods ; Animals ; Dogs ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation &amp; purification ; Humans ; Metagenome ; *Microbiota/genetics ; DNA, Bacterial/genetics ; *Urinary Tract/microbiology ; *Urine/microbiology ; Gastrointestinal Microbiome/genetics ; }, abstract = {BACKGROUND: The gut microbiome has emerged as a clear player in health and disease, in part by mediating host response to environment and lifestyle. The urobiome (microbiota of the urinary tract) likely functions similarly. However, efforts to characterize the urobiome and assess its functional potential have been limited due to technical challenges including low microbial biomass and high host cell shedding in urine. Here, to begin addressing these challenges, we evaluate urine sample volume (100 ml-5 mL) and host DNA depletion methods and their effects on urobiome profiles in healthy dogs, which are a robust large animal model for the human urobiome. We collected urine from seven dogs and fractionated samples into aliquots. One set of samples was spiked with host (canine) cells to model a biologically relevant host cell burden in urine. Samples then underwent DNA extraction followed by 16S rRNA gene and shotgun metagenomic sequencing. We then assembled metagenome-assembled genomes (MAGs) and compared microbial composition and diversity across groups. We tested six methods of DNA extraction: QIAamp BiOstic Bacteremia (no host depletion), QIAamp DNA Microbiome, Molzym MolYsis, NEBNext Microbiome DNA Enrichment, Zymo HostZERO, and propidium monoazide.<br><br>RESULTS: In relation to urine sample volume,&#x2009;&#x2265;&#x2009;3.0&#xa0;mL resulted in the most consistent urobiome profiling. In relation to host depletion, individual (dog) but not extraction method drove overall differences in microbial composition. DNA Microbiome yielded the greatest microbial diversity in 16S rRNA sequencing data and shotgun metagenomic sequencing data and maximized MAG recovery while effectively depleting host DNA in host-spiked urine samples. As proof-of-principle, we then mined MAGs for select metabolic functions including central metabolism pathways and environmental chemical degradation.<br><br>CONCLUSIONS: Our findings provide guidelines for studying the urobiome in relation to sample volume and host depletion and lay the foundation for future evaluation of urobiome function in relation to health and disease. Video Abstract.}, }
@article {pmid41034825, year = {2025}, author = {Chen, Y and Bai, Y and Li, M and Gan, X and Wang, Y and Zhou, Y and Niu, T}, title = {Machine learning model for differentiating Pneumocystis jirovecii pneumonia from colonization and analyzing mortality risk in non-HIV patients using BALF metagenomic sequencing.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {1222}, pmid = {41034825}, issn = {1471-2334}, support = {No. ZYJC21007//1.3.5 Project for Disciplines of Excellence/ ; No. GYYX24003//1.3.5 Project of High Altitude Medicine/ ; No. ZYAI24039//1.3.5 Project for Artificial Intelligence/ ; No. 2023YFS0031//West China Hospital, Sichuan University , Key Research and Development Program of Sichuan Province/ ; No. 82370192, U24A20680//National Natural Science Foundation of China/ ; No. 2022YFC2502600, 2022YFC2502603//West China Hospital, Sichuan University, National Key Research and Development Program of China/ ; }, }
@article {pmid41034705, year = {2025}, author = {Bruscadin, JJ and Cardoso, TF and Conteville, LC and da Silva, JV and Ibelli, AMG and Pena, GAC and Porto, T and de Oliveira, PSN and Andrade, BGN and Zerlotini, A and Regitano, LCA}, title = {HolomiRA: a reproducible pipeline for miRNA binding site prediction in microbial genomes.}, journal = {BMC bioinformatics}, volume = {26}, number = {1}, pages = {236}, pmid = {41034705}, issn = {1471-2105}, support = {2022/06281-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2019/04089-2//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2019/04089-2//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 456191/2014-3//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, mesh = {*MicroRNAs/metabolism/genetics ; Binding Sites ; *Software ; Humans ; Animals ; *Computational Biology/methods ; Cattle ; *Genome, Microbial ; *Genome, Bacterial ; }, abstract = {BACKGROUND: Small RNAs, such as microRNAs (miRNAs), are candidates for mediating communication between the host and its microbiota, regulating bacterial gene expression and influencing microbiome functions and dynamics. Here, we introduce HolomiRA (Holobiome miRNA Affinity Predictor), a computational pipeline developed to predict target sites for host miRNAs in microbiome genomes. HolomiRA operates within a Snakemake workflow, processes microbial genomic sequences in FASTA format using freely available bioinformatics software and incorporates built-in data processing methods. The pipeline begins by annotating protein-coding sequences from microbial genomes using Prokka. It then identifies candidate regions, evaluates them for potential host miRNA binding sites and the accessibility of these target sites using RNAHybrid and RNAup software. The predicted results that meet the quality filter parameters are further summarized and used to perform a functional analysis of the affected genes using SUPER-FOCUS software.<br><br>RESULTS: In this paper, we demonstrate the use of the HolomiRA pipeline by applying it to publicly available metagenome-assembled genomes obtained from human feces, as well as from bovine feces and ruminal content. This approach enables the prediction of bacterial genes and biological pathways within microbiomes that could be influenced by host miRNAs. It also allows for the identification of shared or unique miRNAs, target genes, and taxonomies across phenotypes, environments, or host species.<br><br>CONCLUSIONS: HolomiRA is a practical and user-friendly pipeline designed as a hypothesis-generating tool to support the prediction of host miRNA binding sites in prokaryotic genomes, providing insights into host-microbiota communication mediated by miRNA regulation. HolomiRA is publicly available on GitHub: https://github.com/JBruscadin/HolomiRA .}, }
@article {pmid41029837, year = {2025}, author = {Cabrera, C and Carrión, N and Mateo, D and Vicens, P and Pinzón, A and Heredia, L and Forcadell-Ferreres, E and Pino, M and Yerga, B and Zaragoza, J and Vicente-Pascual, M and Moral, A and Arco, T and Arjó, M and Martínez, E and Galvez, S and Lozano, MJ and Torrente, M}, title = {Gut microbiota characterization in ageing, mild cognitive impairment, and Alzheimer's disease in the context of mediterranean lifestyle in a Spanish population.}, journal = {Alzheimer's research &amp; therapy}, volume = {17}, number = {1}, pages = {211}, pmid = {41029837}, issn = {1758-9193}, support = {PID2019-103888RB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2019-103888RB-I00//Agencia Estatal de Investigaci&#xf3;n/ ; }, abstract = {BACKGROUND: Alzheimer’s disease (AD) is a neurodegenerative disorder often preceded by a prodromal stage of Mild Cognitive Impairment (MCI). Previous research suggests that gut microbiota (GMB) dysbiosis may contribute to cognitive decline via the microbiota-gut-brain axis (MGBA). Notably, GMB composition patterns can vary across populations and stages of dementia. This study aimed to characterize the GMB in a cohort of older adults from Tarragona (Spain) diagnosed with AD or MCI, or presenting a healthy cognitive status (HC), all of whom follow a Mediterranean lifestyle (ML).<br><br>METHODS: The present cross-sectional, multicenter case&#x2013;control study analyzed fecal samples from 99 individuals,including 31 with AD, 30 with MCI, and 38 HC,aged 60&#x2013;85 years, recruited from seven hospitals and specialized cognitive centers in the province of Tarragona, Spain. Shotgun metagenomic sequencing was conducted with taxonomic profiling using Kraken2. APOE genotyping was performed from fecal DNA using TaqMan assays. Richness, alpha and beta diversity, differential abundance, multivariate linear modeling, and Jonckheere&#x2013;Terpstra trend tests were conducted to identify GMB species signatures associated with MCI and AD.<br><br>RESULTS: Richness, alpha and beta diversity did not differ across groups. Differential abundance analysis identified 109 taxa, of which ten microbial species were shared across comparisons. Notably, several species, including Coprococcus comes and Odoribacter splanchnicus, emerged as replicable candidates, showing both discriminatory value and severity-related declines, alongside taxa with context-dependent or adverse associations.<br><br>CONCLUSIONS: Overall GMB diversity did not differ across cognitive groups, but specific taxa, particularly short-chain fatty acid producers, showed consistent associations with cognitive decline in this ML cohort. These findings support a role for the GMB in AD pathology and suggest that targeting key microbial species may provide novel avenues for prevention and intervention.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13195-025-01862-z.}, }
@article {pmid41001489, year = {2025}, author = {Prakash, H and Perez, RK and Ross, M and Tisza, M and Cregeen, SJJ and Deegan, J and Petrosino, JF and Boerwinkle, E and Clark, JR and Maresso, AW}, title = {Wastewater Sequencing Reveals Persistent Circulation and Rising Prevalence of Several Oncogenic Viruses Across Texas.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {41001489}, abstract = {BACKGROUND: Oncogenic viruses cause high-risk cancers in humans and are responsible for nearly 20% of all cancer cases worldwide. Currently, very limited data exists in the realm of wastewater-based viral epidemiology (WBE) of cancer-causing viruses, with existing studies using targeted approaches (i.e PCR-based approaches) which lack scalability. Our study aims to carry out WBE with hybrid-capture probes to detect and track multiple oncogenic viruses simultaneously in wastewater across Texas, USA, overcoming the drawbacks associated with targeted approaches.<br><br>METHODS: Here, we used a hybrid-capture approach to detect, filter and sequence oncogenic virus signals from wastewater samples collected over a duration of three years, from May 2022 to May 2025. Once viral reads were sequenced, we utilized established computational tools to characterize reads into their respective virus of origin. Next, viral abundances of each characterized oncogenic virus were tracked over time and read coverage across their genomes was measured using read mapping techniques.<br><br>FINDINGS: We detected six known oncogenic viruses, along with three suspected oncogenic viruses across all sampling locations within Texas. Over three years, viral abundance gradually increased, with distinct peaks and dips over the summer and winter months. The prevalence of high-risk viruses such as HPV and EBV rose sharply, with increases in abundance observed post-2024. We also obtained nearly 100% genome coverage with viral reads captured using a hybrid-capture technique for almost all oncogenic viruses and their types.<br><br>INTERPRETATIONS: Our study shows that a hybrid-capture method can efficiently overcome the challenges faced with using targeted approaches for WBE. Using this method, we get broader read coverage, coupled with concurrent and consistent real-time tracking dynamics of multiple oncogenic viruses. Our findings also emphasize the persistent circulation and rising prevalence of high-risk cancer-causing viruses, underscoring the need for sustained public health interventions to protect communities and assess viral prevalence in high-risk populations.<br><br>FUNDING: This work was supported by S.B. 1780, 87th Legislature, 2021 Reg. Sess. (Texas 2021), the Baylor College of Medicine and the Alkek Foundation Seed Funds.}, }
@article {pmid41000896, year = {2025}, author = {Dillard, BA and Sanders, JG and Husain, AP and Yule, KM and Moeller, AH}, title = {Isolation by distance promotes strain diversification in the wild mouse gut microbiota.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41000896}, issn = {2692-8205}, abstract = {Bacterial species within the mammalian gut microbiota exhibit considerable strain diversity associated with both geography and host genetic ancestry. However, because geography and host ancestry are typically confounded, disentangling their contributions to the diversification of gut bacterial strains has remained challenging. Here, we show through joint profiling of gut bacterial and mitochondrial genomes from wild-living populations of deer mice (Peromyscus maniculatus) sampled across the United States that isolation by distance (IBD) drives gut bacterial strain diversification independently of the effects of host ancestry. Analyses revealed significant IBD in 27 predominant gut bacterial species, including members of the Muribaculaceae and Lachnospiraceae, but limited evidence for co-inheritance of gut bacterial genomes with mitochondria during the diversification of extant mouse populations. Gut bacterial species capable of forming spores exhibited reduced IBD independently of phylogenetic history, indicating that adaptations facilitating bacterial dispersal can mitigate the geographic structuring of strain diversity. These results show that the diversification of gut bacterial strains within rodent species has been mediated by geographic separation of host populations rather than host genealogical divergence.}, }
@article {pmid41033729, year = {2025}, author = {Chan, CSY and Georgakopoulos-Soares, I}, title = {From nonexistence to novel applications: Nullomers and related k-mer based concepts in bioinformatics.}, journal = {Advances in clinical chemistry}, volume = {129}, number = {}, pages = {191-206}, doi = {10.1016/bs.acc.2025.06.009}, pmid = {41033729}, issn = {2162-9471}, mesh = {*Computational Biology/methods ; Humans ; Genomics ; Proteomics ; Neoplasms/diagnosis/genetics ; }, abstract = {Underrepresented k-mer sequences, provide insights into evolutionary constraints, molecular mechanisms, and organismal fitness. Analysis of these sequences have broad applications across genomics and proteomics, such as in biomarker development, cancer diagnostics, phylogenetic analysis, synthetic biology and novel drug discovery. Absent sequences (nullomers and neomers) show promise for cancer detection and tissue-of-origin identification using nucleic acids derived from liquid biopsies, while quasi-primes serve as genomic fingerprints that offer potential for evolutionary studies for understanding trait evolution, and in metagenomics, as biomarkers of organismal presence. The chapter also discusses computational challenges associated with analyzing absent sequences and highlights available k-mer based resources and databases. With the continuous expansion of genomic and proteomic data, absent sequences present an innovative framework for addressing fundamental biological questions and advancing applications in basic and translational research.}, }
@article {pmid41033716, year = {2025}, author = {Garima,  and Dhanawat, M and Wilson, K and Chaubey, P}, title = {High-throughput sequencing technologies for cancer genomics.}, journal = {Methods in cell biology}, volume = {198}, number = {}, pages = {103-133}, doi = {10.1016/bs.mcb.2025.02.018}, pmid = {41033716}, issn = {0091-679X}, mesh = {Humans ; *Neoplasms/genetics ; *High-Throughput Nucleotide Sequencing/methods ; *Genomics/methods ; Genome, Human ; Transcriptome ; }, abstract = {In investigations about transcriptomics, epigenomics, and genomics, high-throughput sequencing technologies have become indispensable. Several hundred million of DNA molecules may be sequenced at once thanks to high throughput sequencing (HTS) technologies, which can simultaneously analyze many DNA molecules. Traditionally, sequencing information has been clarified utilizing a low throughput technique known as Sanger sequencing. This added value makes it feasible to employ HTS to generate tremendous amounts of data, which enhances the comprehension of the transcriptome and genetic fingerprints of cells during various stages of evolution and pathology. By identifying somatic changes, morphological deviations, and repetitive changes across the human genome, techniques such as whole exome sequencing (WES) and whole genome sequencing (WGS) provide information about cancer formation as well as prospective therapies. Identifying tumor biology and discovering biomarkers rely on the examination of aberrant networks and variations in gene expression that RNA DNA sequencing, or RNA-Seq, offers. By identifying rare cell kinds and their function in carcinogenesis, the sequencing of one cell offers illumination on the wide range of cells observed across tumors. Metagenomics and chromatin immunoprecipitation sequencing (ChIP-Seq) delivers essential knowledge by discovering alterations that affect the epigenetic configuration and the microenvironment that accompanies tumors. Integrating these recent developments will allow the development of personalized treatments that use unique genetic traits to determine every cancer patient, offering more individualized treatments. The revolutionary implications of high-throughput genome sequencing for cancer research and treatment are addressed in this book chapter, particularly concerning cancer precision as well as effective treatment outcomes.}, }
@article {pmid41033677, year = {2025}, author = {Ilbağı, H and Kanakala, S and Masonbrink, R and Lozier, Z and Miller, WA}, title = {Metagenomic Sequencing of Maize Reveals Abundant Genomic RNA of a Comovirus, a Genus Previously Known to Infect Only Dicots.}, journal = {The plant pathology journal}, volume = {41}, number = {5}, pages = {656-670}, doi = {10.5423/PPJ.OA.06.2025.0077}, pmid = {41033677}, issn = {1598-2254}, support = {//The Scientific and Technological Research Council of Turkey/ ; NKUBAP.03.GA.21.289//Tekirda&#x11f; Nam&#x131;k Kemal University/ ; 4308//The Iowa Agriculture and Home Economics Experiment Station, Ames, IA/ ; //The Iowa State University Plant Sciences Institute/ ; //DARPA Insect Allies Program/ ; }, abstract = {To better understand the diversity of viral pathogens in Türkiye, a major exporter of cereals in Europe, we performed high-throughput sequencing of total RNA from maize plants collected in the Trakya region. Certain maize plants exhibiting mosaic and mottle symptoms, gathered from Tekirdağ province in Trakya, yielded large numbers of reads corresponding to the genome of a divergent strain of a comovirus, which corresponds to turnip ringspot virus (TuRSV), a recognized species of the genus Comovirus. This finding is unexpected because all known comoviruses infect only dicotyledonous species, and the known host range of TuRSV has been limited to plants in the Brassicaceae family. The nearly complete and partial nucleotide sequences of the bipartite genome of the maize isolate, as named TuRSVTR59, consist of 6,027 nt TuRSV-TR59 RNA1 and 3,920 nt TuRSV-TR59 RNA2, excluding poly (A) tails. RNA1 and RNA2 each encode a single ORF of 1,860 and 1,096 codons, respectively. Phylogenetic analysis demonstrated that TuRSV-TR59 from Türkiye clustered with other TuRSV isolates from diverse hosts and regions, showing highest identity to isolates from Germany, Czech Republic, and Croatia (80.56-77.77% and 92.09-90.50% nucleotide and amino acid sequence identities, respectively). The ability of TuRSV-TR59 isolate to infect maize was confirmed by reverse transcription polymerase chain reaction. Surveys in the Tekirdağ province of Türkiye, done in 2022-2025, revealed that 2 out of 145 maize samples (1.38%) and 8 out of 116 canola samples (6.89%) were found infected with TuRSV. This is the first report of a comovirus in maize from a monocotyledonous plant species.}, }
@article {pmid41033626, year = {2025}, author = {Kong, F and Guan, DX and Lu, L and Lu, S and Xu, J and Wang, H}, title = {Multi-element amendment reshaped rhizosphere microbiome: A microbially driven Fe/Mn/S synergistic action for Cd immobilization.}, journal = {Environmental research}, volume = {}, number = {}, pages = {122985}, doi = {10.1016/j.envres.2025.122985}, pmid = {41033626}, issn = {1096-0953}, abstract = {Cadmium (Cd) contamination in soils threatens rice safety, necessitating effective remediation strategies. While the silicon-calcium-magnesium amendment (FSY) is known to reduce Cd bioavailability, its precise microbial mechanisms remain underexplored. This study integrated metagenomics and machine learning to investigate FSY's impact on the rice rhizosphere microbiome and to elucidate the biological drivers of Cd immobilization. FSY application and rice growth stage were the core factors that significantly reshaped bacterial and archaeal community structures, shifting archaeal community assembly toward deterministic processes, while the fungal community remained relatively stable. Co-occurrence network analysis revealed that FSY enhanced the complexity and stability of microbial interactions, strengthening the roles of key functional taxa. Crucially, functional profiling showed that FSY significantly upregulated genes related to multi-barrier systems: (1) iron/manganese oxidation (e.g., feoB) associated with iron-manganese plaque (IP) formation; (2) sulfate reduction (e.g., dsrA) linked to cadmium sulfide (CdS) precipitation; and (3) microbial Cd resistance (e.g., the czcA gene). Machine learning identified 14 core species, including key taxa in Campylobacterota and Thermoproteota, as the pivotal drivers of synergistic Fe/Mn/S-Cd interaction. These findings substantiated the microbially driven Fe/Mn/S synergistic model for Cd immobilization through three interconnected mechanisms: enhanced microbially mediated mineral fixation (IP thickening and CdS precipitation), and strengthened community-level Cd resistance. This research provided a deep mechanistic understanding of how chemical amendments induced microbial functions to mitigate heavy metal risks, thereby offering a scientifically-grounded strategy for remediation and safe use of Cd-contaminated field.}, }
@article {pmid41033498, year = {2025}, author = {Saejung, C and Akkahat, S}, title = {Light color-based proliferation of purple phototrophic bacteria in a microbial consortium for sustainable wastewater treatment and bioproduct generation.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {133411}, doi = {10.1016/j.biortech.2025.133411}, pmid = {41033498}, issn = {1873-2976}, abstract = {Purple phototrophic bacteria (PPB) offer distinct advantages for wastewater treatment. However, the application of pure cultures of PPB in large-scale wastewater treatment is constrained by isolation challenges and microbial competition. Therefore, we investigated light color treatment as a tool to enrich PPB within a natural microbial consortium for integrated wastewater treatment and bioproduct generation. We used metagenomics to assess PPB population dynamics and measured bioproduct yields of pigments, protein, biomass, and polyhydroxybutyrate as well as chemical oxygen demand removal (COD). While an initial enrichment yielded low PPB abundance (12 %), subsequent exposure to specific light color greatly altered the community composition. White light (465 nm) enriched the consortium with 76 % PPB abundance, dominated by Rhodopseudomonas sp., which maximized bacterial biomass, polyhydroxybutyrate accumulation, and COD removal. Conversely, red light (616 nm) suppressed PPB proliferation but enhanced specific yields of photosynthetic pigments and protein, indicating a metabolic trade-off between growth and bioproduction. Thus, light color treatment may be a simple and powerful strategy to boost PPB abundance and performance within a microbial consortium, creating a cost-effective platform for wastewater biorefineries.}, }
@article {pmid41033373, year = {2025}, author = {Yarim, D and Abay, S}, title = {First Comprehensive Genome Analysis and Antimicrobial Resistance Profile of Clostridium innocuum from a Domestic Cat.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {108076}, doi = {10.1016/j.micpath.2025.108076}, pmid = {41033373}, issn = {1096-1208}, abstract = {This study aimed to investigate the molecular and phenotypic properties of a C. innocuum isolate from a healthy cat, which was previously misidentified as C. difficile by molecular testing (tpi-PCR). To resolve the misidentification and obtain more information on the isolate at the genetic level, whole genome sequencing (WGS) on the long-read sequencing platform Oxford Nanopore PromethION was performed. WGS data were analysed to identify virulence factors, antibiotic resistance, and hypothetical prophage genes. The isolate was identified as C. innocuum as a result of WGS. While several virulence genes, including pilM, yabQ, HrcA, and CptIN family toxins, were detected, toxin-coding genes in other Clostridium species were not detected. Four prophage regions were detected; three appeared as intact phage sites, while one was incomplete. The isolate was susceptible to ampicillin, clindamycin, vancomycin, and metronidazole but was resistant to meropenem using the E-test method. The genome also contained resistance genes such as tet(M), aph(2'')-Ia, and VanT, VanW, VanY, VanG, and VanZ. Genetic similarities between our isolate and those obtained from global human-derived metagenome-associated genomes (MAGs) and non-MAG genomes from healthy humans and animals were illustrated through WGS-SNP-based phylogenetic analyses. This study provides insights into the phenotypic and genotypic characteristics of C. innocuum, an emerging pathogen. Taken together, the isolation of this agent-possessing intrinsic resistance mechanisms and emerging after the treatment of C. difficile infections from a domestic cat highlights its potential threat to public health. Nevertheless, many clinical questions remain unanswered, underscoring the need for further research to deepen our understanding of this pathogen and to develop effective control and treatment strategies.}, }
@article {pmid41033148, year = {2025}, author = {Luo, L and Wong, JWC and Yan, B and Xu, S and Rabaey, K}, title = {Mechanistic insights into fermentative pathway control during solid-state food waste acidogenesis under autogenic pressure.}, journal = {Water research}, volume = {288}, number = {Pt B}, pages = {124679}, doi = {10.1016/j.watres.2025.124679}, pmid = {41033148}, issn = {1879-2448}, abstract = {The efficiency of two-phase anaerobic digestion hinges on the acidogenic phase, where acidogenic off-gas generates autogenic pressure that alters the physicochemical environment and may affect microbial activity, pathways, and intermediates. However, its mechanistic role under solid-state conditions remains unclear. To address this knowledge gaps, we investigated the effects of autogenic pressure on solid-state food waste acidogenesis, focusing on soluble microbial product (SMP) formation and the associated metabolic responses at the molecular level. Autogenic pressure enhanced acidogenic decomposition, increasing SMP yields from 365.3 ± 10.5 g COD/kg VSadded to 407.1 ± 7.3 g COD/kg VSadded. It initially promoted lactate production, followed by enhanced conversion of lactate to butyrate and acetate functioning by Megasphaera. Metagenomic and metabolite analyses revealed that autogenic pressure increased the abundance of functional genes associated with homoacetogenesis and butyrate synthesis. Incubation experiments further confirmed that acetate, stimulated by autogenic pressure, played a key role in driving the reverse β-oxidation pathway while suppressing the acrylate pathway during lactate conversion. As a result, butyrate production increased by 25 %, while propionate decreased by 43 %. These findings provide new insights into how SMP-producing microbial communities respond to autogenic pressure and demonstrate the potential of self-regulation to enhance product yield and process controllability. This strategy advances sustainable solid waste management and promotes the development of circular bioeconomy.}, }
@article {pmid41032862, year = {2025}, author = {Ghosh Chowdhury, M and Singh, AA and Bhattacharyya, M and Muthukumar, V and Kapoor, S and Srivastava, A and Kumar, H and Shard, A}, title = {Thiazole-Based Tumor Pyruvate Kinase M2 Inhibitors: A Paradigm-Shifting Therapeutic Strategy Targeting Metabolic and Microbial Synergy in Colorectal Cancer.}, journal = {Journal of medicinal chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jmedchem.5c02169}, pmid = {41032862}, issn = {1520-4804}, abstract = {Colorectal cancer (CRC) remains a major global health burden, with current treatments primarily focused on eradicating cancer cells. However, chemotherapy-induced gut dysbiosis exacerbates inflammation and disease progression, necessitating innovative therapeutic strategies. While various metabolic inhibitors and microbiome-modulating approaches have been explored separately, no reported agent to date simultaneously targets both cancer cell survival and gut microbiome restoration. We designed thiazole-based pyruvate kinase M2 (PKM2) inhibitors, hypothesizing that selective modulation may suppress tumor growth while restoring gut microbial balance. 10j selectively inhibited PKM2 in a cell-free assay (0.01 ± 0.0009 μM) and in CRC cells (4.21 ± 0.04 μM), disrupting key pathways driving CRC progression. Remarkably, metagenomic analysis revealed that 10j restored gut microbiota balance. These findings suggest that dual-function anticancer agents, which kill cancer cells while simultaneously restoring gut microbiota, represent an unexplored therapeutic avenue. Thiazole-based PKM2 inhibitors are pioneering this novel strategy in CRC treatment.}, }
@article {pmid41032855, year = {2025}, author = {Qi, YL and Zou, DY and Hou, JJ and Zhang, ZF and Du, H and Pan, YP and Hua, ZS and Zhang, CJ and Li, M}, title = {Temporal and Spatial Dynamics of Microbial Community Composition and Functional Potential in Mangrove Wetlands over a Seven-Year Period.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c01564}, pmid = {41032855}, issn = {1520-5851}, abstract = {Microbial communities are essential to sustaining ecosystem functions in mangrove wetlands, yet their long-term responses to environmental changes remain poorly characterized. Here, we conducted a seven-year multiomics investigation (2017-2023) of microbial diversity, functionality, and evolutionary dynamics in the Futian Mangrove National Nature Reserve, Shenzhen, China. This region has experienced ecological degradation followed by phased restoration efforts since 2007. By analyzing 81 metagenomes, 8474 microbial metagenome-assembled genomes (MAGs) were successfully reconstructed, representing 13 archaeal phyla, 70 bacterial phyla, and up to 95% newly identified species. Community composition was primarily influenced by sediment depth and seasonal variations. Integrating 72 metatranscriptomes revealed marked temporal shifts in gene expression linked to carbon, nitrogen, and sulfur cycling, including enhanced transcription of genes involved in organic carbon oxidation, sulfate reduction, denitrification, and nitrogen fixation during later stages restoration. Evolutionary analyses demonstrated pervasive purifying selection across microbial lineages, with environmental fluctuations and genome size acting as key determinants of selective pressures. Additionally, a new class Candidatus Shennongiarchaeia within Thermoplasmatota was proposed, exhibited anaerobic, facultatively heterotrophic characteristics and bioactive compound synthesis potential. These findings demonstrate that microbial communities in restored mangrove wetlands undergo structural and functional reorganization, characterized by the enrichment of anaerobic lineages, upregulation of key metabolic pathways, and environmentally driven selective pressures. This long-term study deepens our understanding of microbial resilience and adaptation in mangrove ecosystems, with implications for future conservation and restoration strategies in coastal wetlands.}, }
@article {pmid41032194, year = {2025}, author = {Naderian, R and Alibabaei, F and Paraandavaji, E and Dehghan, P and Eslami, M}, title = {Phage-Microbiota Interactions in the Gut: Implications for Health and Therapeutic Strategies.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {41032194}, issn = {1867-1314}, abstract = {The diversified ecology of microorganisms, including bacteria, archaea, fungi, protozoa, and viruses known collectively as the gut microbiota, which includes bacteriophages, is crucial to human health because it affects functions like immune system regulation, vitamin production, and pathogen protection. Bacteriophages are viruses that infect bacteria and are increasingly recognized as a viable treatment option for antibiotic-resistant strains, owing to their high host specificity, which enables precise targeting of drug-resistant bacteria while sparing commensal microbiota. The complex relationships between bacteriophages and gut microbiota are examined, with emphasis on their roles in maintaining health and contributing to disease. Gut microbiota homeostasis is influenced by a number of factors, including age, nutrition, and drugs. Bacteriophages, via lytic cycles and lysogenic conversion, influence the gut microbiota composition and microbial community structure. Gaining an understanding of these processes is crucial to appreciating their contribution to the stability and variety of microbes. Recent research highlights the gut phageome's potential for therapeutic interventions by demonstrating its substantial influence on immunological responses and metabolic problems. The study of phage-microbiota interactions has been transformed by cutting-edge technologies, including high-throughput sequencing, CRISPR-Cas systems, and viral metagenomics, which allow for thorough research and the creation of new therapeutics. Even though tailored medicine and pathogen management hold great potential, obstacles such as regulatory difficulties and bacterial resistance call for additional investigation. Phage-based therapeutic strategies are rapidly advancing, ranging from genetically engineered phages and phages with modified capsid proteins designed to enhance efficacy to phage cocktails that target multiple bacterial strains.}, }
@article {pmid41031628, year = {2025}, author = {Yu, D and Kang, Y and Lu, W and Chen, B}, title = {Progress in diagnosis and treatment of primary spondylodiscitis: a systematic literature review.}, journal = {EFORT open reviews}, volume = {10}, number = {10}, pages = {815-828}, doi = {10.1530/EOR-2025-0041}, pmid = {41031628}, issn = {2058-5241}, abstract = {OBJECTIVE: Primary spondylodiscitis poses significant diagnostic and therapeutic challenges, with delayed diagnosis or improper treatment potentially resulting in severe complications. This systematic review aimed to summarize the latest diagnostic and therapeutic approaches for primary spondylodiscitis.<br><br>METHODS: Adhering to PRISMA 2020 guidelines, we conducted a systematic literature review. PubMed was comprehensively searched for English-language original studies from January 1, 1990, to October 31, 2024. Structured queries combined keywords and MeSH terms relevant to spondylodiscitis, vertebral osteomyelitis, spinal infection, and associated treatments. Two reviewers independently screened titles, abstracts, and full texts, with manual bibliography searches as a supplement. A total of 147 articles were finally included.<br><br>RESULTS: The literature indicates that diagnosis can be based on clinical suspicion, using serological, radiological, and microbiological tests. Newer methods such as metagenomics next-generation sequencing (mNGS) and positron emission tomography-computed tomography (PET-CT) can enhance diagnostic sensitivity and specificity. For confirmed cases, appropriate antibiotic therapy is crucial. Surgical treatment can benefit patients with neurological deficits, sepsis, spinal instability/deformity, epidural abscesses, or failed conservative treatment, accelerating recovery and reducing complications. Minimally invasive surgical approaches may also serve as an alternative to open surgery for select patients.<br><br>CONCLUSION: Although new technologies have improved diagnostic accuracy and treatment success rates for primary spondylodiscitis, establishing a robust staging system is vital to ensure patients receive effective, evidence-based treatment options.}, }
@article {pmid41031110, year = {2025}, author = {Slunečko, J and Kogoj, R and Zakotnik, S and Suljič, A and Knap, N and Bosilj, M and Strle, F and Avšič-Županc, T and Bogovič, P and Korva, M}, title = {Development and performance evaluation of a clinical metagenomics approach for identifying pathogens in the whole blood from patients with undifferentiated fever.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1667422}, pmid = {41031110}, issn = {2235-2988}, mesh = {Humans ; *Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; *Fever ; *Bacteria/genetics/isolation &amp; purification/classification ; *Blood/microbiology/virology ; Computational Biology ; Sensitivity and Specificity ; Molecular Diagnostic Techniques/methods ; Female ; Male ; }, abstract = {INTRODUCTION: Blood culture is the cornerstone of microbiological diagnostics for patients with acute undifferentiated fever and no obvious localization of infection; however, up to 50% of cases remain undiagnosed. Infections caused by arboviruses, fastidious or even uncultivable bacteria, or parasites often go undiagnosed without the use of target-specific molecular methods. These are typically performed in a stepwise manner, increasing cost and delaying results. Metagenomic next-generation sequencing (mNGS) has recently gained recognition as a potential universal pathogen detection tool for such cases. Our study aimed to develop a streamlined mNGS workflow for simultaneous detection of intracellular and cell-free pathogens within a single sequencing library.<br><br>METHODS: Total nucleic acid was isolated separately from 200 EDTA blood samples. The plasma isolate was processed with DNase, followed by the depletion of host ribosomal and messenger RNA, reverse transcription, and sequence-independent single primer amplification (SISPA). The whole blood isolate was only reverse transcribed, with no other pre-processing manipulation. Finally, the two fractions were combined prior to library preparation and sequencing using either Oxford Nanopore Technologies or Illumina. Following established bioinformatics analysis, we developed a mathematical ranking approach (ClinSeq score) that enabled quick identification of relevant pathogens in approximately one hour.<br><br>RESULTS: The mNGS workflow reached 79.5% (159/200) overall sensitivity. For bacteria the sensitivity was 88.6% (70/79), DNA viruses, 66.7% (10/15) and for RNA viruses 73.8% (76/103). Pathogen detections by individual sequencing methods showed overall sensitivity of Illumina and ONT to be 80.0% (76/95) and 79.1% (83/105) respectively. The ClinSeq score correctly highlighted the pathogen in 126/200 (63.0%) samples effectively with a Cohen's kappa (&#x3ba;) agreement of 0.61 with manual analysis.<br><br>CONCLUSION: Developed comprehensive mNGS workflow detects a wide range of pathogens in patients with acute undifferentiated fever. The unified workflow improves sensitivity for intracellular bacteria and RNA viruses, reduces time, cost and complexity by eliminating the need for separate library preparations, enabling faster turnaround suitable for clinical settings. The ClinSeq score effectively differentiates true pathogen signals from background noise, reducing false positives and manual interpretation time. Overall, the workflow demonstrates flexible, and efficient pathogen detection, supporting its potential for clinical diagnostics and improved patient management.}, }
@article {pmid41031025, year = {2024}, author = {Waterworth, SC and Solomons, GM and Kalinski, JJ and Madonsela, LS and Parker-Nance, S and Dorrington, RA}, title = {The unique and enigmatic spirochete symbiont of latrunculid sponges.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.05.23.595633}, pmid = {41031025}, issn = {2692-8205}, abstract = {Bacterial symbionts are critical members of many marine sponge holobionts. Some sponge-associated bacterial lineages, such as Poribacteria, SAUL, and Tethybacterales appear to have broad host ranges and associate with a diversity of sponge species, while others are more species-specific, having adapted to the niche environment of their host. Host-associated spirochete symbionts that are numerically dominant have been documented in several invertebrates including termites, starfish, and corals. However, dominant spirochete populations are rare in marine sponges, thus far only observed in Clathrina clathrus and various species within the Latrunculiidae family, where they are co-dominant alongside Tethybacterales symbionts. This study aimed to characterize these spirochetes and their potential role in the host sponge. Analysis of metagenome-assembled genomes from eight latrunculid sponges revealed that these unusual spirochetes are relatively recent symbionts and are phylogenetically distinct from other sponge-associated spirochetes. Functional comparative analysis suggests that the host sponge may have selected for these spirochetes due to their ability to produce terpenoids and/or possible structural contributions.}, }
@article {pmid41030903, year = {2025}, author = {Li, Y and Jiang, X and Ji, J and Yao, B and Zhao, F and Zhang, J and Yu, Y and Fu, Y}, title = {Case report: Laboratory diagnosis methods on brain abscess pathogens caused by anaerobic species and Streptococci constellatus.}, journal = {IDCases}, volume = {42}, number = {}, pages = {e02373}, pmid = {41030903}, issn = {2214-2509}, abstract = {Brain abscess (BA) represents a severe, intracranial infection associated with high morbidity and mortality. Multiple pathogens may contribute to BA development, some of which are difficult to detect using conventional diagnostic methods alone. With the wide utilization of metagenomic next-generation sequencing (mNGS), more experiences are concluded in authenticity practice except for being regarded as a comprehensive method for detecting all pathogens. Here, we report a severe case of BA in a patient diagnosed by CT imaging, who subsequently underwent surgical removal of the abscess. To identify the causative pathogen and support anti-infection treatment, Gram staining, culture, and mNGS were performed on the abscess specimen. Interesting, we found the results were discordant: the Streptococcus constellatus was identified by culture, whereas mNGS predominantly detected anaerobic bacteria. Following additional human DNA removal, sequencing detected S. constellatus in the specimen as well. In conclusion, we highlight that a combined diagnostic strategy, leveraging both conventional culture and mNGS, is critical for comprehensive pathogen identification and informed clinical decision-making in BA.}, }
@article {pmid41030838, year = {2025}, author = {Maqsood, S and Arshad, MT and Ikram, A and Al-Aoh, HA and Gnedeka, KT}, title = {Foodomics in Diabetes Management: A New Approach.}, journal = {Food science &amp; nutrition}, volume = {13}, number = {10}, pages = {e71021}, pmid = {41030838}, issn = {2048-7177}, abstract = {Critical information regarding the interactions among food components, human metabolism, and disease is contained in foodomics, an interdisciplinary field that bridges food science with contemporary omics technologies (genomics, proteomics, metabolomics, and lipidomics). In order to gain a better understanding of the metabolic dysregulation in type 2 diabetes mellitus (T2DM), foodomics examines bioactive compounds derived from food (e.g., polyphenols, fibers, and lipids) alongside host molecular responses. For the enhancement of glycemic control and the prevention of diabetes-related complications, the current study is concerned with how foodomics enables personalized dietary interventions that are aligned with one's metabolic and genetic characteristics. We investigate deeper into the role of the gut microbiota in T2DM progress and how foodomics-informed methodologies, such as metabolomics and metagenomics, can be functional to discover treatments intended at the microbiota. In addition, we discover the prospective that functional foods enriched with bioactive elements, comprising β-glucans and flavonoids, may influence metabolic processes in diabetes. In addition, foodomics improves food safety by recognizing conceivable diabetes-causing contaminants (endocrine disruptors). Foodomics has incredible potential for improving precision nutrition in the prevention and treatment of T2DM, though experiments in data integration and standardization are present. Through the integration of dietary concepts, molecular biology, and clinical consequences, this method offers revolutionary strategies towards metabolic wellness.}, }
@article {pmid41030555, year = {2025}, author = {Worku, AT and Sciarretta, A and Guarnieri, A and Falcone, M and Brancazio, N and Minwuyelet, A and Cutuli, MA and Atenafu, G and Nicolosi, D and Colacci, M and Yewhalaw, D and Di Marco, R and Petronio Petronio, G}, title = {Microbial gatekeepers: midgut bacteria in Aedes mosquitoes as modulators of arboviral transmission and targets for sustainable vector control.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1656709}, pmid = {41030555}, issn = {1664-302X}, abstract = {Arboviral diseases such as Dengue virus, Zika virus, Chikungunya virus, and West Nile virus pose significant global public health and economic challenges, particularly in tropical and subtropical regions. The absence of effective vaccines and sustainable vector control strategies continues to drive high morbidity and mortality rates. Symbiotic bacteria residing in the mosquito midgut can produce antimicrobial compound, stimulate the host immune response, disrupt nutrient pathways critical for pathogen development, and interfere with the pathogen's lifecycle and dissemination. Additionally, these microbes may reduce vector reproduction and shorten the lifespan of both immature and adult stages. Genetically modified symbiotic bacteria can release effector molecules that target pathogens without harming mosquitoes. Advances in genomic and metagenomic tools have deepened our understanding of the mosquito gut microbiome. This review highlights current knowledge of gut bacteria and arbovirus interactions and explores strategies to reduce arboviral transmission. Comprehensive literature searches were conducted using global databases, including PubMed, Web of Science, and Scopus, with a focus on English-language publications.}, }
@article {pmid41030552, year = {2025}, author = {Zhang, B and Yang, T and Cheng, C and Li, T and Zhang, N and Wang, F and Chen, W and Zhong, Z and Liu, Z and Gu, G and Lin, X and Xie, X}, title = {Multi-omics analysis reveals the alleviating effect of oxidation remediation on tobacco quinclorac stress.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1625585}, pmid = {41030552}, issn = {1664-302X}, abstract = {The extensive use of the herbicide quinclorac has led to significant residues in agricultural soil, posing adverse effects on crop safety and high-quality production. In this study, using the tobacco variety CB-1 as material, we found that oxidizing agent K2S2O8 can significantly reduce quinclorac-induced phytotoxicity symptoms in tobacco. Furthermore, we integrated biochemical methods, metagenomics, metabolomics, and transcriptomics to investigate the effects of K2S2O8 on both quinclorac-contaminated soil and tobacco plants. Soil physicochemical properties analysis showed that the incorporation of K2S2O8-based remediation significantly mitigated the negative effects of quinclorac and largely restored the soil properties affected by quinclorac stress. Metagenomic analysis found that quinclorac significantly reduced soil species diversity, while K2S2O8-based remediation soil exhibited higher richness of microbial communities, with increased abundance of Sphingomonas and Bradyrhizobium, and decreased abundance of Alphaproteobacteria. Differential gene expression analysis showed significant up-regulation and down-regulation of genes under C10H5Cl2NO2 stress, which was partially mitigated by K2S2O8 treatment. Gene Ontology (GO) enrichment analysis indicated that these genes were mainly involved in cellular processes, metabolic pathways, and biological regulation. Metabolomic analysis further confirmed significant changes in metabolite profiles, with K2S2O8 treatment restoring many metabolites to near control levels. Integrated metabolomic-transcriptomic analysis revealed enrichment of differentially expressed genes (DEGs) and metabolites in six key pathways: (1) lysine degradation, (2) stilbenoid diarylheptanoid and gingerol biosynthesis, (3) arginine and proline metabolism, (4) phenylalanine biosynthesis, (5) tyrosine metabolism, and (6) flavonoid biosynthesis. Additionally, the levels of 4-hydroxyphenylacetylglutamic and 5-aminovaleric acid were down-regulated, along with the expression of genes associated with these metabolites, when quinclorac residual soil was treated by K2SO8. The results of this study provide a theoretical basis for the remediation of pesticide residue soil in rice tobacco rotation areas, offering valuable insights for sustainable agricultural practices.}, }
@article {pmid41030387, year = {2025}, author = {Zheng-Qiang, L and Jun, L and Rui, A and Rui, L and Wei, D and Ping, M and Xu, Y and Rong, S and Xiao-Yan, Y and Wen, X}, title = {A probiotic for preventing microplastic toxicity: Clostridium dalinum mitigates microplastic-induced damage via microbiota-metabolism-barrier interactions.}, journal = {Current research in food science}, volume = {11}, number = {}, pages = {101200}, pmid = {41030387}, issn = {2665-9271}, abstract = {Microplastics (MPs) are widely distributed and accumulated in the environment, making it nearly impossible for humans to avoid ingestion. Their toxicity can cause serious health damage and pose a threat to human health. In this context, developing strategies to prevent and restore toxic damage from their ingestion is extremely urgent. This study comprehensively employs various techniques, including metagenomics and metabolomics, to explore the pre-protective and restorative effects of Clostridium dalinum, a potential probiotic with excellent antioxidant and anti-inflammatory capabilities, on damage induced by exposure to polystyrene microplastics (PS-MPs) in mice. The results show that exposure to PS-MPs leads to significant intestinal damage in mice; preemptive intake of C. dalinum for pre-protection, or post-exposure intake of C. dalinum for restorative treatment, both significantly reduced the damage caused by MPs exposure, as evidenced by changes in intestinal length (PS-MPs exposure vs C. dalinum pre-protection vs C. dalinum restoration vs control = 36.55 vs 39.94 vs 40.12 vs 41.05 cm), barrier protein content (27.12 % vs 97.28 % vs 97.73 % vs 100.00 %), and inflammation levels (284.56 % vs 101.05 % vs 98.17 % vs 100.00 %). Mechanistically, the pre-protective and restorative effects of C. dalinum both rely on upregulating the expression of barrier proteins such as ZO-1 and Occludin and inhibiting the TLR4/NF-κB inflammatory signaling pathway. Meanwhile, the two intervention modes also exhibit specific mechanisms: in the pre-protection mode, C. dalinum enhances lipid metabolic balance and antioxidant reserves by pre-activating the PPARγ/GPR43 pathway, and enriches the ABC transporters pathway to promote toxin efflux capacity, thereby preventing PS-MPs-induced damage; in the restoration mode, C. dalinum repairs intestinal damage by enriching the beneficial bacterium Lachnospiraceae NK4A136 and inhibiting the pro-inflammatory bacterium Desulfovibrio, and regulating intestinal metabolites. In summary, this study is the first to confirm that C. dalinum can effectively prevent and restore intestinal damage caused by PS-MPs exposure through the synergistic pathway of "microbiota-metabolism-barrier". Importantly, this study is the first to reveal the potential and unique mechanisms of probiotics in preventing and restoring MPs exposure toxicity, providing a theoretical basis for the future development of probiotic-based defense strategies.}, }
@article {pmid41030376, year = {2025}, author = {Aldeguer-Riquelme, B and Rodriguez-R, LM and Konstantinidis, KT}, title = {Differences in metagenome coverage may confound abundance-based and diversity conclusions and how to deal with them.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf140}, pmid = {41030376}, issn = {2730-6151}, abstract = {The importance of rarefying ecological or amplicon sequencing data to a standardized level of diversity coverage for reliable diversity comparisons across samples is well recognized. However, the importance of diversity coverage, i.e. the fraction of the genomic diversity of a sample sequenced, in comparative shotgun metagenomic studies remains frequently overlooked. Using both in silico and natural metagenomes from a wide range of environments, we demonstrate that uneven metagenome coverage can result in misleading biological conclusions, particularly for identifying differentially abundant features, i.e. groups of genes or genomes assigned to the same protein family or taxonomic rank, respectively, and for comparing diversity between samples. The main underlying cause is that not all members of a feature may be detectable, and thus counted, across such unevenly covered metagenomes depending on the sequencing effort applied and the underlying member-abundance curves. Unfortunately, 99.5% of previous comparative metagenomic studies have overlooked this metric, suggesting that their reported results might be misleading. We show that achieving high Nonpareil coverage (≥0.9), a metric that estimates metagenome diversity coverage, is the most reliable strategy to mitigate this issue. When high Nonpareil coverage is not achievable, such as for highly diverse and complex samples like soils, we show that standardizing (or subsampling) metagenomic datasets to the same Nonpareil coverage, rather than sequencing effort, prior to comparative analysis provides for more accurate results. We provide a set of practical recommendations and the corresponding Python scripts to help researchers to assess and standardize metagenome diversity coverage for their comparative analyses.}, }
@article {pmid41030375, year = {2025}, author = {Sheridan, PO and Meng, Y and Bodington, D and Coutts, D and Williams, TA and Gubry-Rangin, C}, title = {Genomic recovery from rare terrestrial microbes enabled by DNA-based GC-fractionation.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf152}, pmid = {41030375}, issn = {2730-6151}, abstract = {Genome reconstruction from metagenomic samples has dramatically increased our understanding of uncultivated lineages of life. However, untargeted metagenomic sequencing is biased towards the more abundant microbes, neglecting less abundant lineages playing important ecological roles, such as the ammonia-oxidising archaea. Here, we demonstrate that separating soil molecular DNA using a bisbenzimide-CsCl guanine-cytosine (GC)-content-based DNA fractionation approach separates microbial DNA along a GC-content gradient. The fractions from both extremes of the GC-content gradient possess different 16S rRNA gene composition than the original unfractionated DNA. The high diversity in the lower GC-content fractions (< 45%) contrasts with the higher DNA abundance in the higher GC-content fractions (50%-70%), highlighting the low GC fractions as an enriched source of rare microbe DNA. Metagenomic sequencing of specific low- and high-GC fractions enabled the reconstruction of 204 taxonomically diverse metagenome-assembled genomes from 31 microbial phyla, with at least 63 of these originating from rare (< 0.1% relative abundance) or very rare (< 0.01% relative abundance) microbial families. Therefore, this approach facilitates genomic assembly of rare taxa in resulting pseudo-communities. Ultimately, this technique enables a semi-targeted metagenomic approach to recover genomes from low-abundance microbes with GC-contents that differ significantly from the environmental microbial community of interest. As mounting evidence suggests that rare microbes drive critical ecosystem functions, this approach will facilitate a deeper understanding of their metabolic potential in the environment.}, }
@article {pmid41029845, year = {2025}, author = {Rey-Velasco, X and Auladell, A and Deulofeu-Capo, O and Lundin, D and Pinhassi, J and Ferrera, I and Sánchez, O and Gasol, JM}, title = {Decoding the genetic drivers of marine bacterial blooms through comparative genomics.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {198}, pmid = {41029845}, issn = {2049-2618}, support = {PID2021-125469NB-C31//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2021-125469NB-C31//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2021-125469NB-C31//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2021-125469NB-C31//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2021-125469NB-C31//Ministerio de Ciencia e Innovaci&#xf3;n/ ; SPIP2020-02595//Ministerio para la Transici&#xf3;n Ecol&#xf3;gica y el Reto Demogr&#xe1;fico/ ; SPIP2020-02595//Ministerio para la Transici&#xf3;n Ecol&#xf3;gica y el Reto Demogr&#xe1;fico/ ; SPIP2020-02595//Ministerio para la Transici&#xf3;n Ecol&#xf3;gica y el Reto Demogr&#xe1;fico/ ; SPIP2020-02595//Ministerio para la Transici&#xf3;n Ecol&#xf3;gica y el Reto Demogr&#xe1;fico/ ; FPU20/01625//Ministerio de Universidades/ ; }, mesh = {*Bacteria/genetics/classification/growth &amp; development/isolation &amp; purification ; *Genome, Bacterial ; *Seawater/microbiology ; *Genomics/methods ; *Microbiota/genetics ; Phytoplankton ; Metagenome ; Eutrophication ; Metagenomics/methods ; }, abstract = {BACKGROUND: While oligotrophic bacteria are known to dominate most marine microbial habitats, under certain conditions, such as during phytoplankton blooms, copiotrophs can dramatically increase in abundance and reach towering proportions of the bacterial communities. We are uncertain whether the bacteria exhibiting this capacity, which we denote as "bloomers," have specific functional characteristics or if, instead, they are randomly selected from the broader pool of copiotrophs. To explore the genomic determinants of this ecological trait, we conducted a comparative genomic analysis of bacterial genomes from microcosm experiments where grazer and viral presence was reduced and nutrient availability was increased, conditions that triggered bacterial blooms.<br><br>RESULTS: We tested which functional genes were overrepresented in the bacteria that responded to the treatments, examining a total of 305 genomes from isolates and metagenome-assembled genomes (MAGs) that were categorized as copiotrophs or oligotrophs according to their codon usage bias (CUB). The responsive bacteria were enriched in genes related to transcriptional regulation in response to stimuli (mostly via two-component systems), transport, secretion, cell protection, catabolism of sugars and amino acids, and membrane/cell wall biosynthesis. These genes confer on them capabilities for adhesion, biofilm formation, resistance to stress, quorum sensing, chemotaxis, nutrient uptake, and fast replication. They were overrepresented mainly in copiotrophic genomes from the families Alteromonadaceae, Vibrionaceae, Rhodobacteraceae, Sphingomonadaceae, and Flavobacteriaceae. Additionally, we found that these responsive bacteria, when abundant, could affect biogeochemical cycling, particularly the phosphorus cycle.<br><br>CONCLUSIONS: In this study, we provide insights into the functional characteristics that enable certain bacteria to rapidly respond to changes in the environment and bloom. We also hint at the ecological meaning and implications of these phenomena that could affect biogeochemical cycles in the oceans. Video Abstract.}, }
@article {pmid41029787, year = {2025}, author = {Lemieux, &#xc9; and Monger, XC and Saucier, L and Charette, SJ and Guay, F and Pouliot, &#xc9; and Fournaise, S and Vincent, AT}, title = {Effect of an antibiotic and a probiotic on phage communities in the swine gut microbiota.}, journal = {BMC research notes}, volume = {18}, number = {1}, pages = {402}, pmid = {41029787}, issn = {1756-0500}, support = {RGPIN-2022-03321//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Animals ; *Probiotics/pharmacology/administration &amp; dosage ; *Gastrointestinal Microbiome/drug effects ; Swine/microbiology ; *Bacteriophages/drug effects/genetics ; *Anti-Bacterial Agents/pharmacology ; Feces/microbiology/virology ; Cross-Over Studies ; }, abstract = {OBJECTIVE: The impact of dietary treatments on the phage community of porcine intestinal microbiota is not well understood. An antibiotic (tylvalosin), a probiotic (Pediococcus acidilactici), and a combination of these were given to six cannulated pigs in a double crossover design study. Samples of ileal digesta and feces were collected and whole genome shotgun sequencing was performed. The variations in phage and bacterial communities were compared for each treatment and sample type.<br><br>RESULTS: The bacteriophages present in the gut microbiome exhibited greater variations in both &#x3b1;- and &#x3b2;-diversity between sample types (digesta, feces) than between treatments. &#x3b2;-diversity and differential abundance showed that the effect of the combined antibiotic and probiotic treatment was the same as with the antibiotic alone. However, the effects of the probiotic and antibiotic treatments were statistically significantly different in the fecal samples. &#x3b2;-diversity was different in those two treatments, and differential abundance analysis identified multiple phages as markers for each treatment. No significant variations in relative abundance were found in phage lifestyle (i.e., virulent, temperate) between treatments.}, }
@article {pmid41029310, year = {2025}, author = {Huang, J and Dong, T and Yang, C}, title = {Diagnosis of pleural aspergillosis caused by Aspergillus infection via metagenomic next-generation sequencing from a patient with unexplained pleural effusion: a case report.}, journal = {BMC pulmonary medicine}, volume = {25}, number = {1}, pages = {434}, pmid = {41029310}, issn = {1471-2466}, mesh = {Humans ; Male ; Middle Aged ; High-Throughput Nucleotide Sequencing ; *Pleural Effusion/microbiology ; *Aspergillus fumigatus/genetics/isolation &amp; purification ; Metagenomics ; *Aspergillosis/diagnosis/drug therapy/microbiology/complications ; Antifungal Agents/therapeutic use ; Voriconazole/therapeutic use ; }, abstract = {Pleural aspergillosis is a severe pathological condition triggered by Aspergillus species and commonly affects immunocompromised individuals. This case report describes a 63-year-old man with normal immune function who was admitted to the hospital due to a 20-day history of right-sided chest pain and cough. He was diagnosed with an infection-related pleural effusion of unknown origin. Metagenomic next-generation sequencing (mNGS) identified Aspergillus fumigatus in the pleural effusion intrapleurally, and pathological examination revealed granulomatous inflammation. The patient received three months of antifungal treatment with voriconazole tablets. A six-month follow-up examination showed complete resolution of both pleural and pulmonary abnormalities. This case highlights the utility of mNGS as a diagnostic tool for detecting clinical fungal pathogens with atypical features, thereby improving diagnostic accuracy and therapeutic strategies for such conditions.}, }
@article {pmid41029068, year = {2025}, author = {Gao, J and Lao, C and Chen, J}, title = {Chlamydia psittacosis infection complicating cerebral infarction: A case report and literature review.}, journal = {Medicine}, volume = {104}, number = {39}, pages = {e44854}, doi = {10.1097/MD.0000000000044854}, pmid = {41029068}, issn = {1536-5964}, support = {No.2024ZL175//Chinese Medical Science and Technology Project of Zhejiang Province/ ; }, mesh = {Humans ; Female ; Middle Aged ; *Cerebral Infarction/etiology/complications/therapy/microbiology ; *Psittacosis/complications/diagnosis/drug therapy ; Anti-Bacterial Agents/therapeutic use ; *Chlamydophila psittaci/isolation &amp; purification ; }, abstract = {RATIONALE: Chlamydia psittaci (CP) pneumonia is a rare zoonosis. Severe infection predisposes patients to thrombotic complications; however, only 2 documented cases of delayed cerebral infarction occurring during anticoagulant therapy exist in the literature.<br><br>PATIENT CONCERNS: A 60-year-old female with a history of hypertension and a concealed history of avian exposure presented with fever, chest tightness, and dyspnea. Examination revealed severe hypoxemia (PaO2 46.8&#x2005;mm&#x2005;Hg), systemic inflammation (C-reactive protein 343.65&#x2005;mg/L), and multi-organ dysfunction.<br><br>DIAGNOSES: CP pneumonia; cerebral infarction.<br><br>INTERVENTIONS: Following definitive diagnosis via metagenomic next-generation sequencing of bronchoalveolar lavage fluid, targeted antimicrobial therapy with omadacycline (100&#x2005;mg daily) and moxifloxacin (400&#x2005;mg daily) was initiated immediately. Concurrent interventions included mechanical ventilation and prophylactic anticoagulation with enoxaparin (5000&#x2005;IU daily). Upon development of an acute cerebral infarction, the antithrombotic strategy was modified: anticoagulation was discontinued and dual antiplatelet therapy (aspirin 100&#x2005;mg/d&#x2005;+&#x2005;clopidogrel 75&#x2005;mg/d) was commenced, alongside early rehabilitation in a dedicated stroke unit.<br><br>OUTCOMES: By day 5 of antimicrobial therapy, inflammatory markers decreased significantly and oxygenation improved. Neurological function showed partial recovery by day 14 postinfarction (National Institutes of Health Stroke Scale score reduced from 8 to 3), enabling successful weaning from ventilation and hospital discharge.<br><br>LESSONS: Active screening for avian contact history and early application of metagenomic next-generation sequencing should be considered in patients with severe pneumonia. CP infection can trigger immunothrombosis, warranting vigilance for delayed stroke even during anticoagulation. Multidisciplinary management is crucial for optimizing outcomes in infection-associated cerebral infarction.}, }
@article {pmid41029053, year = {2025}, author = {Wang, CC and Chen, Y and Li, MJ and Xie, B and Shan, Q and Guo, H and Huang, QC and Guo, BM}, title = {Acute fibrinous and organizing pneumonia presents as right lung upper lobe cavitary lesion: Case report and literature review.}, journal = {Medicine}, volume = {104}, number = {39}, pages = {e44915}, doi = {10.1097/MD.0000000000044915}, pmid = {41029053}, issn = {1536-5964}, mesh = {Humans ; Male ; Middle Aged ; Tomography, X-Ray Computed/methods ; Diagnosis, Differential ; *Cryptogenic Organizing Pneumonia/diagnosis/drug therapy/diagnostic imaging ; *Lung/pathology/diagnostic imaging ; *Pneumonia/diagnosis/drug therapy ; Methylprednisolone/therapeutic use/administration &amp; dosage ; Organizing Pneumonia ; }, abstract = {RATIONALE: The upper lobe of the right lung, due to its unique anatomical structure that is prone to tumor occurrence, poses a challenge for the differential diagnosis of focal cavitary lesions. Cases of acute fibrinous and organizing pneumonia presenting as cavitary lesions in the upper lobe of the right lung are extremely rare in the previous literature.<br><br>PATIENT CONCERNS: This case presents a 59-year-old man who was hospitalized with a cough, phlegm, and low-grade fever after a bout of strenuous exercise and exposure to rain. A chest computed tomography (CT) revealed a cavitary lesion (lesions maximum diameter 9&#x2009;cm, hollow maximum diameter of 3.5&#x2009;cm) in the upper lobe of the right lung.<br><br>DIAGNOSES: Initially, he was incorrectly diagnosed with community-acquired pneumonia, and the empirical anti-infective and antiviral therapies proved ineffective. The flexible bronchoscopy lavage fluid showed negative results in metagenomic Next-Generation Sequencing (mNGS), but the pathological micrograph indicated a suspected diagnosis of acute fibrinous and organizing pneumonia.<br><br>INTERVENTIONS: He was taken off antibiotics, changed to 40&#x2009;mg of methylprednisolone intravenously each day.<br><br>OUTCOMES: Six days after receiving methylprednisolone, the cough disappeared. A reexamination chest CT showed a significant reduction of the lesion. Additionally, the patient did not report any discomfort during the 6 months of follow-up.<br><br>LESSONS: This case highlights the particular characteristics of the focal cavitary lesions in the upper lobe of the right lung and emphasizes the role of liquid-based cytology in the diagnosis of acute fibrinous and organizing pneumonia, rather than mNGS.}, }
@article {pmid41028724, year = {2025}, author = {Li, Z and Wei, T and He, L and Qian, H and Zhu, YG and Wang, Y}, title = {Genomic potential for mercury biotransformation in marine sediments across marginal slope to hadal zone.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {8655}, pmid = {41028724}, issn = {2041-1723}, support = {42376149//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Geologic Sediments/microbiology/chemistry ; *Mercury/metabolism ; Metagenome/genetics ; Biotransformation/genetics ; China ; Seawater/microbiology/chemistry ; *Water Pollutants, Chemical/metabolism ; Oceans and Seas ; Phylogeny ; Genomics ; Methyltransferases/genetics/metabolism ; Methylation ; Ecosystem ; }, abstract = {Mercury accumulates in the deep sea, but its ecological impact on deep-sea ecosystems remains poorly understood. We conduct an analysis of 32 sediment cores, comprising 101 layers for the study of metagenomes, and additional 41 global reference sediment metagenomes. These sediment cores are collected from two deep-sea regions: the South China Sea and Mariana Trench, followed by revealing high mercury accumulation in the South China Sea. In these metagenomes, we find that the mercury methylation genes hgcAB are abundant in marginal seas but negligible in open oceans. Genomics result indicates that some Hg-methylating microorganisms affiliated with Desulfobacterota, Spirochaetota, and Zixibacteria in the deep-sea sediments encode MttB, the sole corrinoid-dependent methyltransferase identified in these taxa, which may interact with HgcA to transfer methyl groups from possibly osmolyte-derived trimethylamine for methylation. The demethylation gene merB is widely distributed and exhibits higher abundance in the open ocean. Moreover, we identify a large number of novel Hg demethylating taxa that are associated with horizontal transfer of the merB gene potentially involving methane generation. Our results expand the diversity of Hg-transforming taxa and reveal their unique ecophysiological adaptations in deep-sea sediments.}, }
@article {pmid41028597, year = {2025}, author = {Maile-Moskowitz, A and Brown, CL and Rumi, MA and Moumi, NA and Majeed, H and Finkielstein, CV and Ceci, A and Gonzalez, R and Xia, K and McDaniel, L and Baffoe-Bonnie, A and Rao, J and Zhang, L and Pruden, A and Vikesland, PJ}, title = {Relating antimicrobial use to wastewater resistance gene patterns via metagenomic analysis of two neighboring treatment plants circa the COVID-19 pandemic.}, journal = {npj antimicrobials and resistance}, volume = {3}, number = {1}, pages = {82}, pmid = {41028597}, issn = {2731-8745}, support = {1545756//National Science Foundation/ ; 1545756//National Science Foundation/ ; 2004751//National Science Foundation/ ; 2004751//National Science Foundation/ ; 2004751//National Science Foundation/ ; 1545756//National Science Foundation/ ; 1545756//National Science Foundation/ ; 1545756//National Science Foundation/ ; }, abstract = {Minimizing antimicrobial use is a recommended strategy to reduce the evolution and spread of antibiotic resistance; however, efficacy is elusive to measure. Wastewater-based surveillance provides a promising means to relate trends in microbial community antibiotic resistance profiles as a function of interventions and other factors. We examined influent sewage metagenomes for two neighboring wastewater treatment plants (WWTPs) serving a university and a nearby community. We compared antibiotic resistance gene (ARG) profiles as a function of diagnoses of COVID-19 and other illnesses, antibiotic use, antibiotic/antimicrobial and disinfectant/quaternary ammonium compound concentrations, and COVID-19-related behavioral shifts. Diversity and abundances of ARGs unique to the corresponding sewage were consistently higher for the community WWTP, but converged in 2022 when antibiotic prescriptions surged in the university zip code. Decreases in ARG diversity/abundance were not apparent during periods of decreased antibiotic usage, indicating that extended times may be required for wastewater ARG signals to attenuate following interventions.}, }
@article {pmid41028522, year = {2025}, author = {Moon, SJ and Kim, HJ and Lim, JE and Hong, S and Won, HH and Jeong, BC and Kim, JH}, title = {HSF1-DBC1 axis drives prostate cancer progression by activating a metastatic transcriptional program.}, journal = {Experimental &amp; molecular medicine}, volume = {}, number = {}, pages = {}, pmid = {41028522}, issn = {2092-6413}, support = {2023R1A2C1005018//National Research Foundation of Korea (NRF)/ ; 2022R1I1A1A01064189//National Research Foundation of Korea (NRF)/ ; 2022R1I1A1A01053377//National Research Foundation of Korea (NRF)/ ; 2021R1A2C1004656//National Research Foundation of Korea (NRF)/ ; }, abstract = {Heat shock factor 1 (HSF1) is a key stress-protective transcription factor that acts as a guardian of proteostasis. HSF1 also plays multifaceted roles in tumor-associated processes including proliferation and metastasis. HSF1 is frequently overexpressed and activated in a wide range of cancers, including prostate cancer, and hijacked by cancer cells to promote their survival in harsh tumor microenvironments and during metastasis. However, mechanisms underlying the persistent activation of HSF1 and its coregulators in malignancies are largely unknown. Here we show that HSF1 is highly activated and required for metastatic spread and growth of metastatic castration-resistant prostate cancer (mCRPC) cells. The HSF1-driven transcriptional program and its genome occupancy in mCRPC cells were distinct from those of castration-resistant prostate cancer cells and massively reprogrammed during the metastatic progression of castration-resistant prostate cancer cells. In addition, we report DBC1 as a key coregulator of HSF1. DBC1 positively regulated HSF1-mediated transcription and genome-wide chromatin binding of HSF1. Moreover, DBC1 was required for super-enhancer formation and activation of super-enhancer-associated HSF1 target genes, including MMP11, involved in metastasis. Mechanistically, DBC1 activated and stabilized HSF1 by enhancing trimerization and DYRK2-mediated phosphorylation of HSF1 and inhibiting CHIP-mediated HSF1 ubiquitination, thereby increasing the transcriptional activity and genome-wide binding of HSF1. Importantly, DBC1 loss suppresses the metastatic growth of mCRPC cells, and HSF1-DBC1 double-high expression correlated with worse outcomes in patients with mCRPC. Our results highlight the critical role of HSF1 as a metastasis-promoting transcription factor and a novel regulatory mechanism of HSF1 activity and stability by DBC1. Thus, targeting the HSF1-DBC1 axis could be a promising therapeutic strategy for metastatic cancers.}, }
@article {pmid41028378, year = {2026}, author = {Sahil, R and Jain, M}, title = {A Multi-omics Approach for Microbiome Data Analysis in Legumes.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2977}, number = {}, pages = {181-196}, pmid = {41028378}, issn = {1940-6029}, mesh = {*Microbiota/genetics ; *Metagenomics/methods ; *Fabaceae/microbiology/genetics ; *Computational Biology/methods ; Data Analysis ; Metagenome ; Multiomics ; }, abstract = {Microbiome plays a crucial role in influencing the health and function of living beings as well as in regulating the biogeochemical cycles. The plant microbiome, in particular, has garnered significant research interest aimed at exploring the microbes that play a crucial role in regulating plant growth and nutrient acquisition. Recent advancements in omics sciences have played a crucial role in uncovering the complexities of these relationships. While techniques such as amplicon and shotgun metagenomics provide taxonomic profiling up to the species level and even the strain level, metatranscriptomics further elucidates the functional roles of these microbes. These techniques are being rapidly and widely adopted to understand the influence of microbes on the host. However, the challenge lies in their integration. Most studies to date rely on only one of these techniques, which limits the scope of holistic understanding of host-microbe interactions. Additionally, there is currently no well-established workflow that effectively combines these techniques to provide comprehensive biological insights. In this work, we describe an integrated approach for microbiome data analysis to provide biologically meaningful insights.}, }
@article {pmid41028236, year = {2025}, author = {Ning, Z and Liu, J and Zhang, J and Zhong, W and Yang, T and Huang, Y and Qin, X and Zhang, X and Xu, X}, title = {Enhancement of short-chain fatty acids production by biochar-supported zero-valent iron in anaerobic fermentation: focusing on metabolic reactions and electron transport.}, journal = {Bioprocess and biosystems engineering}, volume = {}, number = {}, pages = {}, pmid = {41028236}, issn = {1615-7605}, abstract = {Carbon-based and iron-based materials have been widely reported as effective promoters in biogas fermentation due to the promotion of electron transport. However, the effect of these materials, especially in combination, on short-chain fatty acids (SCFAs) production has been scarcely reported. In this study, the production of short-chain fatty acids (SCFAs) from green cabbage waste was promoted by adding biochar (BC) and biochar-supported zero-valent iron (BC@ZVI). The underlying mechanisms, focusing on metabolic pathways and electron transport, were subsequently investigated through metagenomic analysis. The optimal SCFAs yields were achieved with BC (5 g·L[-]1) and BC@ZVI (15 g·L[-]1). While BC notably enhanced n-butyrate production (89.4-fold), BC@ZVI balancedly promoted acetate and n-butyrate. Metagenomics revealed that BC@ZVI's superiority stemmed from its enhanced ability to enrich functional microbes and facilitate electron transfer. Metagenomic analysis revealed that BC@ZVI enriched Sphaerochaeta and Herbinix, which could participate in the direct interspecies electron transfer process. The abundance of almost all functional enzymes involved in carbohydrate hydrolysis and the synthesis of acetate and n-butyrate were remarkably increased by BC@ZVI. BC and BC@ZVI lead to a notable enrichment of conductive pili genes, including pilB, pilC, and pilM. BC@ZVI enriched both conductive pili and c-type cytochromes, which could be considered a more effective selection than BC. Notably, BC@ZVI was more effective than BC in stimulating n-butyrate-type fermentation, significantly shortening the lag phase and the overall fermentation cycle, thereby exhibiting better comprehensive performance, enhancing pH buffering capacity, and strengthening electron transfer and substrate hydrolysis. The results proved the potential of BC@ZVI in SCFAs fermentation and deciphered the underlying mechanisms, which provided a new perspective to promote resource recovery of organic waste by anaerobic system.}, }
@article {pmid41028186, year = {2025}, author = {Chen, J and Lou, H and Yao, Y and Chen, Q and Liu, C and Zhou, H}, title = {Metagenomic next-generation sequencing for concurrent diagnosis of infections and malignancies in patients with lung lesions: a single-center prospective study.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {33721}, pmid = {41028186}, issn = {2045-2322}, support = {2022YFC2504502//the Key R&amp;D Plan of the Ministry of Science and Technology of China/ ; 2023C03068//the Research and Development Program of Zhejiang Province/ ; 82272338//the National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Lung Neoplasms/diagnosis/genetics ; Male ; *High-Throughput Nucleotide Sequencing/methods ; Prospective Studies ; Female ; Middle Aged ; *Metagenomics/methods ; Aged ; Bronchoalveolar Lavage Fluid/microbiology ; DNA Copy Number Variations ; Adult ; Sensitivity and Specificity ; Diagnosis, Differential ; }, abstract = {Metagenomic next-generation sequencing (mNGS) offers sensitive and rapid pathogen detection and has the added advantage of analyzing chromosomal copy number variations (CNVs) of the host in the same test. This study aimed to evaluate the dual diagnostic performance of mNGS in clinical cases where pulmonary infections and malignancies are difficult to be distinguished. A single-center prospective study was conducted at the First Affiliated Hospital, Zhejiang University School of Medicine. The study recruited patients with lung lesions from October 2021 to October 2022 that required differential diagnosis of infection, malignancy, or other pulmonary diseases. The mNGS was used to detect both pathogens and potential CNVs of the host chromosomes to inform presence of neoplasm, and the results were compared to conventional microbiological tests (CMTs), bronchoalveolar lavage fluid (BALF) cytology, histology, and clinical composite diagnoses. The mNGS demonstrated a significantly higher sensitivity of infection diagnosis (56.5% vs.39.1% for CMTs, P < 0.05). The CNVs analysis showed moderate sensitivity (38.9%) and high specificity (100%) for diagnosing malignancy, which helped determine lung cancer in 4 cases who were initially considered as pneumonia. Combining CNVs analysis with BALF cytology has increased the sensitivity for detecting malignancy from 38.9% to 55.6%. Furthermore, the sensitivity of CNVs analysis was higher (50%) when bronchoscopy directly found positive signs, such as neoplasm or bronchial mucosal infiltration. This study highlights the dual capacity of mNGS to simultaneously detect infections and malignancies. The integration of both pathogen and tumor detection could significantly enhance clinical decision-making, particularly for patients with overlapping symptoms of infection and cancer.}, }
@article {pmid41028005, year = {2025}, author = {Xu, H and Ba, W and Yu, R and He, Z and Wang, P and Gou, X and Zhang, X and Wang, F}, title = {Fructophilic Apilactobacillus kunkeei alleviates high-fructose diet-induced lipid accumulation by modulating gut microbiota and intestinal barrier function in mice.}, journal = {NPJ science of food}, volume = {9}, number = {1}, pages = {201}, pmid = {41028005}, issn = {2396-8370}, support = {32402039//National Natural Science Foundation of China/ ; }, abstract = {Excessive fructose consumption is strongly linked to metabolic syndrome, with gut microbiota playing a pivotal role in mediating fructose metabolism and associated metabolic disturbances. In this study, we aimed to characterize Apilactobacillus (A.) kunkeei, a fructophilic lactic acid bacterium from honey, and evaluate its probiotic function in male C57BL/6 J mice fed a high-fructose diet (HFD). Transcriptome analysis was carried out to analyze the activation of pathways under various culture conditions. Pathway inhibitors were used in cell culture and a hepatectomy mouse model to study the function of different pathways in hepatocyte growth and liver regeneration. Our results showed that A. kunkeei FM01 exhibited strong tolerance to simulated gastrointestinal stress in vitro, indicating good probiotic potential. Administration of A. kunkeei FM01 significantly reduced body weight gain, improved glucose tolerance, and attenuated hepatic and visceral (perirenal and epididymal) lipid accumulation in HFD-fed mice. Serum lipid profiling and targeted lipidomic analysis revealed that A. kunkeei FM01 lowered triglycerides, phosphatidylcholine, and lysophosphatidylcholine levels while increasing beneficial phospholipids such as phosphatidylethanolamine. Metagenomic analysis demonstrated that A. kunkeei FM01 modulated gut microbiota composition by reducing pro-inflammatory and fructose-metabolizing taxa, including Alistipes, Oscillibacter, Desulfovibrio, Lawsonibacter, and Enterococcus, while enriching beneficial species, including Kineothrix alysoides and Faecalibaculum rodentium. These microbial shifts were associated with increased abundances in genes encoding carbohydrate-active enzymes and amino acid biosynthesis pathways. Furthermore, A. kunkeei FM01 restored intestinal barrier integrity by upregulating tight junction proteins (Zonula Occludens-1 and occludin) and reduced serum lipopolysaccharide and diamine oxidase levels. Collectively, these findings suggest that A. kunkeei FM01 exerts protective effects against HFD-induced metabolic dysfunction through multi-targeted mechanisms involving lipid metabolism, gut microbiota modulation, and intestinal barrier restoration. This study identifies A. kunkeei FM01 as a promising probiotic candidate for preventing and managing fructose-associated metabolic disorders.}, }
@article {pmid41027803, year = {2025}, author = {Blank, RB and Bu, K and Zhang, X and Chen, W and Cunningham, I and Sokolove, J and Lahey, L and Heguy, A and Medina, R and Ubeda, C and Nayak, RR and Hu, J and Cantor, A and Lee, J and Williams, FMK and Clemente, JC and Scher, JU}, title = {Short-chain fatty acids and their gut microbial pathways distinguish rheumatoid arthritis in discordant monozygotic twins.}, journal = {Annals of the rheumatic diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ard.2025.08.029}, pmid = {41027803}, issn = {1468-2060}, abstract = {OBJECTIVES: Although genetic risk factors, such as HLA-DRB1 alleles, contribute to the pathogenesis of rheumatoid arthritis (RA), the concordance rate in monozygotic (MZ) twins is low, suggesting that other factors are involved in disease development. Further, the relative contribution of nongenetic elements in identical twins has not been characterised. Here, we aimed to characterise host and microbial biomarkers of RA by studying MZ twins discordant for disease using a multiomics approach.<br><br>METHODS: Eight pairs of MZ twins discordant for RA (N = 16) were enrolled in the United States (US). The gut microbiome was assessed using shotgun metagenomic sequencing. Autoantibodies, cytokines, and plasma proteins were measured in both plasma and faeces. Levels of short-chain fatty acids (SCFAs) from serum and faeces were quantified using gas chromatography mass spectrometry (GC-MS). Metagenomic data from a UK twin registry (TwinsUK) (N = 14) were used to validate findings in the US population.<br><br>RESULTS: Although microbiome diversity and composition did not differ between twins, we observed a significant decrease in the SCFA-producing bacteria Blautia faecis and significantly lower concentrations of faecal butyrate and propionate in affected RA twins in the US. TwinsUK showed a similar reduction in the SCFA-producers Gemmiger formicilis and Faecalicatena fissicatena, as well as bacterial SCFA metabolism pathways.<br><br>CONCLUSIONS: Multiomics biomarkers differentiate MZ twins discordant for RA. Faecal butyrate and propionate, as well as SCFA-producing bacteria, were decreased in affected twins. We found a similar decrease in SCFA-producing taxa in affected twins in a geographically distinct cohort in the UK. Our results suggest that, if further validated in larger cohorts, multiomics approaches may improve our understanding of RA pathogenesis and, potentially, contribute to more accurate diagnostics and coadjuvant therapies.}, }
@article {pmid41027356, year = {2025}, author = {Kahwage, S and Lanzarini, NM and de Paula, BB and Saggioro, EM and Motta, ATF and Mannarino, CF and Miagostovich, MP}, title = {Viral genetic diversity in surface and groundwater at a non-operational dumpsite and its surrounding neighborhood.}, journal = {The Science of the total environment}, volume = {1002}, number = {}, pages = {180604}, doi = {10.1016/j.scitotenv.2025.180604}, pmid = {41027356}, issn = {1879-1026}, abstract = {Inappropriate municipal solid waste disposal areas lack waterproof base liners, drainage systems, treatment of waste degradation by-products, mass coverages, and vector control. Leachate is a by-product derived from water percolation through solid waste disposal sites, comprising an environmental and health contamination source when not adequately collected and treated. This study aimed to describe surface and groundwater viral diversity in a dumpsite area non-operational for over a decade and its surrounding neighborhood in the metropolitan Rio de Janeiro region employing shotgun metagenomic analysis. Between May 2021 and March 2023, 100 leachate samples (2 L each) were collected from 21 sampling points and subsequently organized into five pooled samples. Nucleic acids were extracted employing the Biopur Nucleo-mag Virus kit, followed by purification with AMpure XP beads and quantification via Qubit 4.0, Next-Generation Sequencing was performed on a NextSeq 2000 sequencer (Illumina, USA). Sequencing analysis identified 578 operational taxonomic units, of which 312 (54 %) were classified into 46 viral families, while 266 (46 %) remained unclassified, the Microviridae family was the most abundant. Viral sequences linked to pathogenic hosts were detected, including canine circovirus. Comparable viral family profiles were observed between the dumpsite and the residential area suggesting that some of the shared viral families may be influenced by groundwater flow originating from the closed dumpsite. Although irregular land use hinders precise attribution of contamination sources, the detection of potentially pathogenic viruses in waters intended for human use raises significant public health concerns. These findings support long-term virome-based surveillance of groundwater near closed dumpsite.}, }
@article {pmid41027219, year = {2025}, author = {Li, X and Zhu, S and Wang, H and Zhen, Q and She, D}, title = {Silicon-modified lignin biochar outperforms hydrochar in heavy metal remediation: stochastic microbial assembly and functional gene reprogramming drive soil multifunctionality.}, journal = {Journal of hazardous materials}, volume = {498}, number = {}, pages = {139966}, doi = {10.1016/j.jhazmat.2025.139966}, pmid = {41027219}, issn = {1873-3336}, abstract = {Heavy metal contamination severely threatened soil health, microbial stability, and food safety worldwide. While lignin-based biochar had shown potential in mitigating metal toxicity, its regulatory effects on soil microbiomes and ecosystem functions remained inadequately understood, especially across different carbonization strategies. A cross-scale remediation framework using silicon-modified lignin-based hydrochar (Si-LHB) and pyrochar (Si-LPB) was developed to restore cadmium (Cd)/zinc (Zn)-contaminated soil ecosystems. In a pot experiment combined with metagenomics and biochemical assays, metal speciation, microbial dynamics, nitrogen cycling, and soil multifunctionality were evaluated. Results showed that both Si-LHB and Si-LPB effectively enhanced metal stabilization and plant growth, yet Si-LPB outperformed Si-LHB by significantly reducing acid-soluble Cd and Zn (by 16.22 % and 48.43 %) and increasing residual fractions up to 72.70 %, primarily via silicate precipitation and microenvironment modulation. Compared to Si-LHB, Si-LPB more effectively restructured bacterial communities, enriching Pseudomonadota and increasing community stochasticity (NST＞50 %). It also selectively upregulated nitrogen transport genes (e.g., narK, nrtP) and suppressed denitrification genes (e.g., nirK, nosZ), enhancing nitrogen retention and carbon fixation. Consequently, Si-LPB improved soil multifunctionality by 72.13 % and reduced Cd/Zn accumulation in plants by up to 99.66 %. This study demonstrates that silicon-enhanced lignin biochars, particularly Si-LPB, restore soil ecological functions through functional redundancy and enrichment of keystone taxa rather than by increasing diversity, offering a promising carbon-silicon-microbe strategy for sustainable remediation.}, }
@article {pmid41027192, year = {2025}, author = {Xu, H and Chen, C and Pang, Z and Zhang, G and Zhang, W and Kan, H}, title = {Effects of microplastics and excessive nitrogen pollution on oat growth and soil nitrogen cycling.}, journal = {Ecotoxicology and environmental safety}, volume = {304}, number = {}, pages = {119119}, doi = {10.1016/j.ecoenv.2025.119119}, pmid = {41027192}, issn = {1090-2414}, abstract = {Both excessive nitrogen (N) and microplastic (MPs) pollution pose global change challenges to ecosystems and human health. The effects of MPs coexisting with excessive N on plant growth and N cycling are still largely unknown. This study employed a pot experiment to assess how polypropylene (PP) MPs influence oat (Avena sativa L.) growth and soil N cycling under conditions of excessive N fertilization. In the treatments of excessive N treatment, 2 % PP MPs significantly increased underground biomass (54.5 %). [15]N stable isotope results showed that 2 % PP MPs treatment significantly reduced the percentage of N from fertilizer in oat by 10.4 %. Compared to without N treatment, excessive N treatment reduces the Shannon index of the rhizosphere soil bacterial community. Only at the 0.5 % PP MPs level, excessive N treatment significantly reduced the diversity of bacterial communities in the bulk soil compared to the without N treatment. The Shannon index of fungal community was not affected by N treatment and MPs. Microbial biomass nitrogen (MBN) and pH were significant related to sensitive species in microbial communities. The coexistence of excess N and 2 % PP MPs significantly reduced the abundance of genes (norB, nosZ and nirB) related to denitrification process. Structural equation modeling showed that MPs could promote underground biomass, reduce soil pH, inorganic N content, and reduce N uptake efficiency, thus resisting growth damage caused by high N. In the future, the effects of different concentrations and types of MPs and different nitrogen forms on soil and crops should be further investigated.}, }
@article {pmid41027153, year = {2025}, author = {Zhang, S and Gao, W and Gao, X and Xu, W and Liu, Y and Guo, Z and Liu, G and Zhang, P and Shi, H and Chang, X}, title = {Astragaloside VI attenuates mechanical stress-induced cardiac remodeling through piezo1-VDAC1 dependent endoplasmic reticulum unfolded protein response.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {148}, number = {}, pages = {157288}, doi = {10.1016/j.phymed.2025.157288}, pmid = {41027153}, issn = {1618-095X}, abstract = {BACKGROUND: The dysregulation of protein homeostasis is a condition associated with mechanical stress-induced cardiac remodeling (CR) due to endoplasmic reticulum (ER) dysfunction and stress.<br><br>PURPOSE: This research explores the effect of Piezo1 on the ER unfolded protein response (UPR) in cardiomyocytes following hypoxic stress, specifically through its interaction with VDAC1. In addition, the study evaluates the therapeutic potential that this mechanism holds for treating CR and cardiomyocyte hypertrophy.<br><br>STUDY DESIGN: Considering the relative limitation of potential therapeutic drugs for CR, our goal is to utilize a multi-omics approach to confirm the process by which Astragaloside IV (AS) alleviates CR through the Piezo1-VDAC1 dependent UPR.<br><br>METHODS: We utilized multiple omics studies, such as single-cell sequencing, network pharmacology, and metagenomics, for the validation of AS's targets and phenotypic mechanisms. Following this, we created Piezo1/VDAC1 transgenic mice (Piezo1[TG]/VDAC1[TG]) and wild-type mice, which were then subjected to transverse aortic constriction (TAC) to induce myocardial damage. We performed assessments of cardiac function, myocardial injury staining, and cardiomyocyte hypertrophy on these animal models both before and after the drug intervention. The analysis into the interaction between Piezo1-VDAC1 and the structural integrity of cytoskeletal proteins and the ER was conducted utilizing laser confocal microscopy, immunofluorescence, and molecular biology experiments.<br><br>RESULTS: The regulation of mechanical stress-induced cardiac remodeling crucially involves Piezo1-VDAC1. Data from single-cell sequencing and network pharmacology suggest that ER damage, mitochondrial energy metabolism dysfunction, and the dysregulation of subcellular organelles are important phenotypes that mediate this process. Our animal experiments demonstrated that AS is capable of improving cardiac function after TAC, inhibiting myocardial injury and the associated inflammatory reaction, and suppressing excessive UPR stress. The therapeutic effect of the drug was eliminated by the transgenic treatment of Piezo1. In vitro experiments also offered confirmation that AS can ameliorate cardiomyocyte damage through the ER pathway. This is achieved by regulating the Piezo1-VDAC1 interaction mechanism, which restores ER structural collapse after hypoxic injury, enhances energy metabolism levels, and inhibits excessive UPR stress.<br><br>CONCLUSION: The abnormal activation of the UPR, which is mediated by Piezo1-VDAC1, constitutes the pathological mechanism behind mechanical stress-induced cardiac remodeling. By regulating the Piezo1-VDAC1 interaction, AS inhibits excessive UPR stress and improves the breakdown of ER structure and functional abnormalities. These actions further normalize ER function and ameliorate cardiac function and myocarditis-related injury. This work offers a promising strategy for utilizing natural medicine to treat mechanical stress-induced cardiac remodeling.}, }
@article {pmid41026933, year = {2025}, author = {Greco, M and Coculo, D and Conti, A and Agresti, S and Pontiggia, D and Mélida, H and Favaro, L and Lionetti, V}, title = {Biorefining of Anaerobic Digestates for the Recovery of Biostimulants and Bioelicitors for Immune Priming and Plant Protection.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c03321}, pmid = {41026933}, issn = {1520-5851}, abstract = {Olive oil production is a major global agricultural industry that generates significant waste, particularly olive pomace, which poses environmental and economic challenges. Anaerobic digestion emerges as a promising solution for its valorization into biogas. However, the resulting digestate remains underutilized and its long-term environmental impact is uncertain. Traditional disposal methods are costly and inefficient, underscoring the need for more sustainable approaches. In this study, olive pomace digestate was biorefined, and its components were upcycled into soil amendments and plant immunostimulants. Metagenomic analysis revealed a diverse microbial community in the liquid fraction. A microbial-enriched protein extract (MIPE) was obtained, containing precursors of microbe- and damage-associated molecular patterns, including Flagellin, Elongation Factor Tu, and the plant phytocytokine Golven. Plant treatment with MIPE triggered a rapid immune response, characterized by oxidative burst, mitogen-activated protein kinase activation, and the upregulation of defense-related genes such as CYP81F2, FRK1, and WRKY53. MIPE-induced priming enhanced Arabidopsis and tomato resistance to Botrytis cinerea and Pseudomonas syringae. Our findings highlight olive pomace digestate as a valuable growth biostimulant, with its liquid fraction also representing a promising resource of immunity bioelicitors. This refinement valorizes olive mill waste, providing a sustainable alternative to chemical fertilizers and pesticides and supporting sustainable agriculture.}, }
@article {pmid41026643, year = {2025}, author = {Wu, D and Van Goethem, MW and Graham, DW and Zhang, X and Li, Z and Shi, G}, title = {Antarctic Environmental Resistomes Closely Associated with Human and Animal Waste Releases.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c06023}, pmid = {41026643}, issn = {1520-5851}, abstract = {Antarctica harbors a diverse spectrum of antibiotic resistance genes (ARGs) across lake, soil, and seawater environments. However, linkages between resistomes in waste-impacted and pristine settings are not well understood in polar settings, especially how phage, plasmids, and microbial community assembly influence the spatial distribution of ARGs. Metagenomic sequencing of 85 Antarctic samples showed 10-fold greater ARG abundances near animal and human waste-impacted sites compared with more remote settings, including glacial, lake, soil, and offshore seawater sites (-1.9 to -0.1 log10(ARGs/cell), P < 0.01), although (except for glaciers) resistome compositions were broadly similar. Based on metagenomic data, plasmids appear to be more associated with ARGs than phages in the Antarctic samples, with Pseudomonas, Staphylococcus, Bacillus, and Mycobacterium being primarily associated with ARG prevalence because they dominate local microbial assemblages. These primary taxa exhibit wide cross-setting prevalence and are not significantly impacted by local environmental selection (P > 0.05, SNPs-RDA). As such, human- and animal-waste-impacted locations, which have higher microbial migration rates (m = 10.8, NCM), are primary sources of ARG-containing and assembly predominant bacteria in Antarctic settings. Thus, better management of waste releases from human settlements must be central to retaining "pristine" Antarctic environments against the globally expanding resistomes.}, }
@article {pmid41026231, year = {2025}, author = {Qian, M and Zhou, J and Chen, P and Jiang, N and Wang, T and Chen, X and Xu, H and Zhou, F and Yang, Y and Lin, X and Yang, Q and Shao, L and Ruan, Q and Zhang, W}, title = {A Novel Compound Heterozygous Mutation in the IL12RB1 Gene Causes Susceptibility To Mycobacterium Tilburgii Infection.}, journal = {Journal of clinical immunology}, volume = {45}, number = {1}, pages = {133}, pmid = {41026231}, issn = {1573-2592}, support = {82271794//National Natural Science Foundation of China/ ; KY2024-664//Clinical Research Project of Huashan Hospital, Fudan University./ ; }, mesh = {Humans ; Female ; *Receptors, Interleukin-12/genetics ; *Genetic Predisposition to Disease ; Adult ; Heterozygote ; *Mycobacterium Infections/genetics/diagnosis/drug therapy/immunology ; *Mutation ; *Mycobacterium ; Interferon-gamma ; }, abstract = {Mendelian susceptibility to mycobacterial disease (MSMD) is a rare clinical syndrome that is characterized by selective vulnerability to intracellular pathogens. Deficiency in IL12RB1 is the most common type of MSMD but the heterogeneity of its clinical Manifestation Makes precise diagnosis difficult. Here, we report a previously healthy 29 year-old woman who had suffered from disseminated infection with Mycobacterium tilburgii, which is a rare, unculturable environmental mycobacteria, for over 2 years. We used whole exome sequencing to detect a novel compound heterozygous variant in the IL12RB1 gene. Immunological analysis of the patient's peripheral lymphocytes showed a barely detectable level of IL-12Rβ1, a reduced population of follicular helper T (Tfh) cells and impaired production of IFN-γ in response to IL-12/IL-23 stimulation. Metagenomic next-generation sequencing was used to identify the causative pathogen and to analyze drug susceptibility. The infection was contained by a combination of anti-mycobacterial drugs and IFN-γ supplementary treatment. An RNA-seq analysis, using follow-up blood samples, revealed the limited success of these treatments over 6 months. Our findings support the screening for inherited immunological problems in patients with difficult-to-treat mycobacterial infections. The suboptimal response to prolonged anti-mycobacterial drugs and IFN-γ supplementation warrants the development of novel therapeutic strategies for MSMD patients.}, }
@article {pmid41026172, year = {2025}, author = {Gao, H and Ma, X and Lu, M and Wang, Y and Liu, H and Hu, X and Nie, Y}, title = {Population and Spatial Features Impact the Gut Phageome-Bacteriome Structure and Interactions in a Mammal Species Living in Fragmented Habitats.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {98}, pmid = {41026172}, issn = {1432-184X}, support = {32225033//National Natural Science Foundation of China/ ; 2022YFF1301500//Ministry of Science and Technology of China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Bacteriophages/genetics/classification/physiology/isolation &amp; purification ; *Bacteria/classification/genetics/isolation &amp; purification/virology ; *Ecosystem ; RNA, Ribosomal, 16S/genetics ; *Antelopes/microbiology/virology ; Metagenome ; Feces/microbiology ; }, abstract = {The mammalian gut microbiome composition has been shown to promote host adaptation to ecological environments. However, the variation in the gut phageome and bacteriome composition at both the population level and spatial scale in wild animals has not been well investigated. Here, we used viral metagenomes and 16S rRNA gene sequencing to explore how these characteristics affect the gut microbiome of Przewalski's gazelle, an endangered group-living ungulate that lives in several fragmented habitats due to anthropogenic activities. The results revealed that population and habitat geographic characteristics collectively explained much more of the variation in phageome and bacteriome compositions than did host-associated factors. Both gut phage and bacterial diversity were positively associated with population size, and differentiation in gut microbiome diversity increased with geographic distance among populations. Additionally, the gut phage and the bacterial hosts displayed similar patterns in composition across habitats, indicating that the microbiome may exhibit complex interactions in response to the environment. For the first time, our study reveals the important roles of population and habitat geographic characteristics in driving spatial patterns of gut microbiome structures in wild animals and highlights the interactions between gut phages and the bacteriome in adaptation to living environments under the influence of human disturbances.}, }
@article {pmid41026152, year = {2025}, author = {Nassirnia, S and Scherz, V and Greub, G and Caruana, G and Taffé, P and Jaton, K and Papis, S and Posfay-Barbe, KM and Mornand, A and Rochat-Guignard, I and Bertelli, C and Asner, SA}, title = {Concordance between upper and lower airway microbiota in children with cystic fibrosis.}, journal = {Journal of medical microbiology}, volume = {74}, number = {9}, pages = {}, doi = {10.1099/jmm.0.002079}, pmid = {41026152}, issn = {1473-5644}, mesh = {Humans ; *Cystic Fibrosis/microbiology ; *Sputum/microbiology ; *Microbiota ; Child ; *Pharynx/microbiology ; Male ; Female ; *Bacteria/classification/genetics/isolation &amp; purification ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Child, Preschool ; Adolescent ; Longitudinal Studies ; *Respiratory System/microbiology ; Metagenomics ; Infant ; }, abstract = {Introduction. Sputum is the most used sample type to monitor the lower respiratory tract microbiota in cystic fibrosis (CF), but young patients often cannot expectorate.Hypothesis. We hypothesized that throat swabs could reflect lower airway colonization and assessed the concordance of bacterial community composition between paired sputum and throat swab samples from children with CF.Aim. We aimed to compare bacterial community diversity and composition between sputum and throat swabs in the full cohort and in patients with paired samples from the same visit.Methodology. The prospective longitudinal multicentre MUCOVIB cohort included 379 samples from 61 CF children. Using V3-V4 16S rRNA amplicon metagenomics, we compared bacterial community diversity and composition between sputum and throat swabs in the full cohort and in 11 patients with paired samples from the same visit.Results. Sputum and throat swabs exhibited similar bacterial diversity, regardless of the exacerbation status, and presented a substantial agreement for detecting pathogens (Cohen's kappa: 0.6). Differences in bacterial abundance were observed (P=0.001), but not presence/absence (P=0.098). Community typing revealed three distinct community types, with 86% of paired samples falling into the same cluster, highlighting the homogeneity between sputum and throat swab microbiota. Network analysis demonstrated slight, non-random similarities in microbial interactions between sample types (adjusted Rand index=0.08 and 0.10). The average beta-diversity distances between samples collected from the same visit were shorter (0.505±0.056 95% confidence interval), compared with sputum (0.695±0.017) or throat swab (0.704±0.045) from the same patient collected during different visits.Conclusion. Throat swabs can provide representative information on lower respiratory microbiota. Clinicians should collect throat swabs rather than relying on sputum samples from previous visits to guide antibiotic prescriptions in CF children unable to expectorate.}, }
@article {pmid41026097, year = {2025}, author = {Patyka, M and Wang, R and Honchar, A and Patyka, T and Khablak, S}, title = {Modulation of the rhizosphere microbiome structure and optimization of beneficial functions in winter wheat induced by Bacillus subtilis: a metagenomic and phenotypic study.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaf097}, pmid = {41026097}, issn = {1574-6941}, abstract = {The rhizosphere microbiome critically determines plant health and productivity. This study investigated the impact of Bacillus subtilis H38 on the taxonomic and functional profiles of the winter wheat (Triticum aestivum L.) rhizosphere microbiome under typical chernozem conditions using 16S rRNA gene sequencing and shotgun metagenomics, complemented by plant phenotypic evaluation and targeted metabolite analysis. Inoculation with B. subtilis H38 significantly restructured the rhizosphere bacterial community, increasing alpha-diversity (Shannon index from 5.8 to 6.7) and showing distinct clustering in beta-diversity analysis. The relative abundance of putative plant-beneficial genera, including Bacillus, Pseudomonas, Azotobacter, and Streptomyces, was significantly elevated. Shotgun metagenomic analysis revealed enrichment of functional genes associated with nitrogen fixation, phosphorus mobilization, phytohormone biosynthesis, siderophore production, and synthesis of antimicrobial compounds. Targeted metabolomic analysis confirmed elevated levels of indole-3-acetic acid (IAA) and key siderophores. Concurrently, treated wheat plants exhibited an 18.0% increase in above-ground biomass and a 25.0% increase in root length under field conditions. These findings underscore the potential of B. subtilis to beneficially reshape the rhizosphere microbiome and its metagenome, leading to enhanced plant growth, and highlight its utility as a potent biofertilizer for improving wheat productivity. This research reinforces the potential of harnessing beneficial plant-microbe interactions to enhance agricultural productivity while minimizing dependence on synthetic agrochemicals.}, }
@article {pmid41025937, year = {2025}, author = {Garvey, SM and Blonquist, TM and Brutscher, LM and Walsh, DM and Kaden, VN and Beckman, DB and Zeng, M and Bruno, RS and Cook, CM and Spears, JL}, title = {Dietary Supplementation with the Probiotic Bacillus velezensis BV379 Decreases Abdominal Bloating Without Perturbing the Commensal Gut Microbiota: A Randomized, Double-Blind, Placebo-Controlled Trial in Healthy Adults.}, journal = {Journal of the American Nutrition Association}, volume = {}, number = {}, pages = {1-16}, doi = {10.1080/27697061.2025.2563894}, pmid = {41025937}, issn = {2769-707X}, abstract = {OBJECTIVE: Various bacterial Bacillaceae and Bacillus strains have demonstrated health benefits, but less is known about probiotic characteristics of strains of Bacillus velezensis. In this randomized, double-blind, placebo-controlled clinical trial, we investigated the safety and efficacy of B. velezensis BV379 supplementation for 8 weeks (2 × 10[9] colony-forming units (CFU)/day).<br><br>METHODS: During the baseline and final weeks, GI symptoms were recorded daily using the 8-item Gastrointestinal Tolerance Questionnaire (GITQ). The primary outcome was the proportion of participants showing an improvement from baseline to week 8 in the 7-day, 3-item composite score for abdominal distention/bloating, burping, and gas/flatulence. Plasma chemistry, hematology, intestinal permeability, and fecal metagenomes were also investigated.<br><br>RESULTS: Eighty participants (54% female; age: 50.3&#x2009;&#xb1;&#x2009;10.1&#x2009;years) were randomized to BV379 (n&#x2009;=&#x2009;39) or placebo (n&#x2009;=&#x2009;41). At end of study, no significant difference was observed in the percentage of participants with improvement in the 3-item composite GITQ score (BV379: 36.1%; placebo: 28.2%; p&#x2009;=&#x2009;0.46). Analysis of individual GI symptoms showed that more participants experienced improvement in abdominal distention/bloating with BV379 compared to placebo (38.9% vs 17.9%; p&#x2009;=&#x2009;0.044). There were no clinically meaningful changes in plasma chemistry, hematology, or intestinal permeability between groups. Fecal metagenomic analyses showed no overall shifts in microbial composition between groups. In addition to B. velezensis, a few commensal species such as Lacticasei bacillus casei were significantly enriched in the BV379 group.<br><br>CONCLUSION: Despite not significantly improving the composite GITQ score of distention/bloating, burping, and gas/flatulence, BV379 supplementation was a well-tolerated approach to specifically lower abdominal bloating.}, }
@article {pmid41025824, year = {2025}, author = {Li, Z and Li, S and Han, C and Chen, Y and Zhen, H and Sun, Y and Zhou, X and Chen, Y and Zheng, Y and Han, L and Krutmann, J and Nie, C and Wang, J and Xia, J}, title = {A comprehensive reference catalog of human skin DNA virome reveals novel viral diversity and microenvironmental influences.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0117825}, doi = {10.1128/spectrum.01178-25}, pmid = {41025824}, issn = {2165-0497}, abstract = {UNLABELLED: Human skin serves as a dynamic habitat for a diverse microbiome, including a complex array of viruses whose diversity and roles are not fully understood. A total of 2,760 skin metagenomes from 6 published skin studies were collected. A skin virome catalog was constructed using standard methods in the viromics field. Viral characteristics were identified through cross-cohort meta-analysis and used to characterize viral features across different skin environments. We identified 20,927 viral sequences, which clustered into 2,873 viral operational taxonomic units (vOTUs), uncovering a substantial breadth of viral diversity on human skin. The results also highlight significant differences in viral communities that are associated with varying skin microenvironments. The oily skin is enriched in Papillomaviridae, the dry skin area is enriched in Autographiviridae and Inoviridae, and the moist skin is enriched in Herelleviridae. We also investigated the relationship between bacteriophages and bacteria on the skin surface. We found that skin bacteria such as Pseudomonas, Klebsiella, and Staphylococcus are predicted to be infected by phages from the class Caudoviricetes. This comprehensive skin DNA viral catalog significantly advances our understanding of the virome's role within the skin ecosystem.<br><br>IMPORTANCE: This study presents a comprehensive reference catalog of the human skin DNA virome, constructed from 2,760 metagenomic datasets collected globally. It identified 20,927 viral sequences, with 90.85% representing previously unknown viruses, greatly expanding our understanding of skin viral diversity. The findings reveal significant differences in viral communities between distinct skin microenvironments (oily, dry, and moist) and highlight close interactions between bacteriophages and their bacterial hosts, suggesting a potential role for the virome in maintaining microbial balance and skin health. This extensive skin viral catalog constitutes a crucial resource for future epidemiological and therapeutic research, potentially facilitating the development of novel phage therapies and diagnostic markers for skin disorders.}, }
@article {pmid41025799, year = {2025}, author = {Buckner, AM and Glendinning, L and Palma Hidalgo, JM and van Munster, JM and Stevens, M and Watson, M and Newbold, CJ}, title = {The selective culture and enrichment of major rumen bacteria on three distinct anaerobic culture media.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0056325}, doi = {10.1128/spectrum.00563-25}, pmid = {41025799}, issn = {2165-0497}, abstract = {Ruminants play an important part in global food security, but also emit methane, which contributes to global warming. Rumen microbes strongly influence the energy retention efficiency from the host's plant-based diet and produce methane as a by-product. While thousands of novel microbial genomes have been assembled from metagenomic sequence data, their culturability is ill-defined. Here, different media (Med10, Med2, and MedTC) were used to isolate co-cultures of microbes from rumen fluid. Thirty-four OTUs were identified belonging to the phyla Bacillota (75.28 ± 6.34%), Bacteroidota (19.99 ± 4.85%), Pseudomonadota (2.46 ± 2.01%), and Actinomycetota (2.09 ± 1.07%). The most abundant genera were Selenomonas (28.08 ± 11.71%), Streptococcus (22.67 ± 6.06%), Prevotella (18.71 ± 4.02%), and unclassified Lachnospiraceae (11.50 ± 2.54%), and 31 significantly enriched on at least one medium, with each medium successfully culturing a distinct range of microbes. The composition of the source rumen fluid was vastly different from those cultured. Bacteroidota (52.53 ± 5.10%) predominated, with Bacillota (41.00 ± 3.96%), Methanobacteriota (5.12 ± 1.94%), Pseudomonadota (1.22 ± 0.78%), and Actinomycetota (0.12 ± 0.08%) comprising the rest. The most abundant genera were Prevotella (29.13 ± 4.16%), Butyrivibrio (18.21 ± 2.08%), Succiniclasticum (15.57 ± 5.03%), unclassified Bacteroidetes (13.91 ± 1.67%), and unclassified Prevotellaceae (9.50 ± 2.01%). These data further emphasize the importance of using defined media to select for different microbial taxa. This is essential to understand the complex workings of the rumen microbes to enhance digestion efficiency and reduce the loss of energy that could potentially be utilized by the host.IMPORTANCEThis research demonstrates that using a range of culture media, containing a wide variety of substrates, can lead to the culture of key rumen microbes. The knowledge of which of these microbes is selectively enriched on each medium is essential to understand how to grow these microbes in co-culture and isolate them in pure culture for further investigation. In addition, this research shows the stark disparity between the population of rumen microbes grown in co-culture and those found in the rumen itself. This further demonstrates the need for a targeted approach to growing and isolating these microbes. Learning how these microbes respond to culture media with different nutritional compositions will lead to a better understanding of the rumen microbiota, and this research provides a valuable insight into how selective media can target the enrichment of different microbes. This knowledge will contribute to increasing ruminant digestion efficiency and reducing methane production.}, }
@article {pmid41025782, year = {2025}, author = {Boyd, AI and Kafer, LA and F Escapa, I and Kambal, A and Tariq, H and Hilsenbeck, SG and Nguyen-Phuc, H and Rajan, A and Lensmire, JM and Patras, KA and Piedra, PA and Blutt, SE and Lemon, KP}, title = {Nasal microbionts differentially colonize and elicit cytokines in human nasal epithelial organoids.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0049325}, doi = {10.1128/msphere.00493-25}, pmid = {41025782}, issn = {2379-5042}, abstract = {UNLABELLED: Nasal colonization by Staphylococcus aureus or Streptococcus pneumoniae is associated with an increased risk of infection by these pathobionts, whereas nasal colonization by Dolosigranulum species is associated with health. Human nasal epithelial organoids (HNOs) differentiated at air-liquid interface (ALI) physiologically recapitulate human nasal respiratory epithelium with a robust mucociliary blanket. Due to their natural stem-like properties, HNO lines are a long-term experimental resource that offers genetic diversity based on the different donors. To develop HNOs as a new model system for bacterial nasal colonization, we reproducibly monocolonized HNOs differentiated at ALI with S. aureus, S. pneumoniae, or Dolosigranulum pigrum for up to 48 h with varying kinetics across species. HNOs tolerated bacterial monocolonization with localization of bacteria to the mucus layer and with minimal cytotoxicity compared to uncolonized HNOs. Human nasal epithelium exhibited both species-specific and general cytokine responses, without induction of type I interferons, which is consistent with colonization rather than infection. Only live S. aureus colonization robustly induced epithelial cell production of interleukin-1 family cytokines, suggestive of inflammasome signaling. D. pigrum and live S. aureus decreased CXCL10, whereas S. pneumoniae increased CXCL11, chemokines involved in antimicrobial responses to both viruses and bacteria. Overall, HNOs are a new model system for uncovering microbe-epithelial cell dynamics at the human nasal mucosa.<br><br>IMPORTANCE: Human nasal microbiota often includes highly pathogenic members, many of which are antimicrobial resistance threats, e.g., methicillin-resistant Staphylococcus aureus and drug-resistant Streptococcus pneumoniae. Preventing colonization by nasal pathobionts decreases infections and transmission. In contrast, nasal microbiome studies identify candidate beneficial bacteria that might resist pathobiont colonization, e.g., Dolosigranulum pigrum. Learning how these microbionts interact with the nasal epithelium and identifying new means to reduce pathobiont colonization are key goals in the field. As a tool to advance this research, we developed human nasal epithelial organoids (HNOs) differentiated at an air-liquid interface as a new model system of bacterial nasal colonization. HNOs accurately represent the mucosal surface of the human nasal passages, enabling exploration of bacterial-epithelial interactions, which is important since the epithelium is an instigator of the initial innate immune response to bacteria. Here, we identified differential epithelial cytokine responses to these three bacteria, setting the stage for future research.}, }
@article {pmid41025644, year = {2025}, author = {Saito, D and Saito, CPB and Cannavan, FDS and Tsai, SM}, title = {Draft genome sequences of six Rothia mucilaginosa strains assembled from the human oral microbiome.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0050825}, doi = {10.1128/mra.00508-25}, pmid = {41025644}, issn = {2576-098X}, abstract = {We report draft metagenome-assembled genomes (MAGs) of six Rothia mucilaginosa strains recovered from the oral microbiome of distinct human subjects. MAGs were retrieved according to a species-specific genome mapping approach, displaying high average nucleotide identities (≥95.85%) to R. mucilaginosa ATCC 25296's genome and minimal contamination levels (≤3.75%).}, }
@article {pmid41025564, year = {2025}, author = {Zeng, S and Wang, H and Zhang, L and Li, S and Yuan, Y and Tian, M and Qu, Y and Ying, J and Zhou, M and Hu, Y and Huang, J and Zou, R and Zhao, F and Su, X and Liu, Q and He, Y and Feng, J and Huang, W and Luo, Y and Zhou, Z and Shen, W and Mu, D and Wang, S}, title = {The Gut Resistome Atlas in Preterm Infants Enables Prediction of Necrotizing Enterocolitis Onset.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e05154}, doi = {10.1002/advs.202505154}, pmid = {41025564}, issn = {2198-3844}, support = {2021YFC2701704//National Key Research and Development Program/ ; 2021YFC2701700//National Key Research and Development Program/ ; 82402025//National Natural Science Foundation of China/ ; 82241036//National Natural Science Foundation of China/ ; 82271749//National Natural Science Foundation of China/ ; 82371717//National Natural Science Foundation of China/ ; 82201905//National Natural Science Foundation of China/ ; 82571980//National Natural Science Foundation of China/ ; 82530056//National Natural Science Foundation of China/ ; 2025ZNSFSC1677//Department of Science and Technology of Sichuan Province/ ; SCU2023D006//Fundamental Research Funds for the Central University/ ; SZSM202311027//Sanming Project of Medicine in Shenzhen/ ; }, abstract = {The accelerating threat from antimicrobial resistance (AMR) has become a global health issue. The properties of AMR in the gut microbiome of preterm infants and its clinical relevance with necrotizing enterocolitis (NEC) remain unknown. In-depth integrative analyses of 5,684 gut metagenomes are performed to build an AMR genes (ARGs) landscape. A subset of 107 preterm infants who developed NEC is sampled to examine the trajectory and predictive potential of ARGs preceding NEC onset. The variation and core set of ARGs, their higher burden and diversity, and potential ARGs-enriched gut bacteria in preterm infants compared to full-term infants are comprehensively discovered, reflecting a strain shift in genomic functions. Moreover, the gut resistome converged over 9 days before NEC onset is observed, which is driven by 24 ARGs. Machine learning analysis reveals potential usage of the gut resistome as an indicator for predicting NEC onset in an external validation preterm birth cohort (the area under the receiver operating characteristic curve, AU-ROC = 0.823), which is significantly higher than that based on the bacterial species (AU-ROC = 0.727). Overall, the findings can be referenced to mitigate the burden and spread of ARGs, and specific ARGs have potential for disease risk stratification to improve clinical management.}, }
@article {pmid41025248, year = {2025}, author = {Park, YJ and Lim, JK and Lee, YJ and Kwon, KK}, title = {Protocol for efficient recovery of high-quality DNA from microbiome of marine invertebrates.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {63}, number = {9}, pages = {e2507003}, doi = {10.71150/jm.2507003}, pmid = {41025248}, issn = {1976-3794}, support = {EA0311//Ministry of Oceans and Fisheries/ ; KIMST 20210469//Ministry of Oceans and Fisheries/ ; }, mesh = {Animals ; *Microbiota/genetics ; *DNA, Bacterial/isolation &amp; purification/genetics ; *Aquatic Organisms/microbiology ; *Bacteria/genetics/isolation &amp; purification/classification ; *Porifera/microbiology ; Symbiosis ; Republic of Korea ; *Invertebrates/microbiology ; Anthozoa/microbiology ; RNA, Ribosomal, 16S/genetics ; High-Throughput Nucleotide Sequencing ; Polymerase Chain Reaction ; }, abstract = {Marine organisms often form symbiotic relationships with various microorganisms to adapt and thrive in harsh environments. These symbiotic microbes contribute to host survival by providing nutrition, modulating the hosts' immune system, and supporting overall physiological stability. Advances in high-throughput sequencing technologies have enabled a deeper understanding of the structure and function of symbiotic microbial communities, as well as host-microbe interactions. Notably, symbiotic bacteria associated with marine invertebrates such as corals and sponges are recognized as a potential source of useful bioactive compounds, including antibiotics and enzymes. However, obtaining high-quality microbial DNA from host tissues still remains a technical challenge due to the presence of unknown substances. This study focuses on optimizing sample preparation and DNA extraction procedures and additional purification to improve the recovery of microbial DNA while minimizing host DNA contamination. Comparison between several methods was conducted using sponge samples to evaluate DNA quality and microbial recovery. A sample designated as 2110BU-001 was collected from the east coast of the Republic of Korea and used for culture-independent microbial cell isolation. Total bacterial DNA was extracted by using a manual Phenol-Chloroform protocol and three commercial kits. DNA extracted using the standard manual method showed both the highest yield and the largest fragment size. However, PCR (Polymerase chain reaction) test showed that quality of manually extracted DNA was not enough for sequencing. Therefore, the quality of DNA was improved through additional purification steps. Briefly, host eukaryotic cells were removed by mechanical process and almost only bacterial DNA was successfully obtained by combination of manual extraction method and further purification processes. The established protocol was successfully introduced to extraction of metagenomic DNA from mussel and jellyfish microbiomes, indicating that it can be widely applied to various marine organisms.}, }
@article {pmid41024883, year = {2025}, author = {Abdelwahab, MM and Ghattas, AS and Tawheed, A}, title = {Implications of gut microbiota in hepatic and pancreatic diseases: Gut-liver-pancreas axis.}, journal = {World journal of hepatology}, volume = {17}, number = {9}, pages = {109965}, pmid = {41024883}, issn = {1948-5182}, abstract = {The gut-liver-pancreas axis (GLPA) is a critical network shaped by gut microbiota (GM) and their metabolites, essential for maintaining metabolic and immune balance. Disruption of this microbial equilibrium, known as dysbiosis, contributes to the development and progression of various hepatic and pancreatic diseases. Through mechanisms such as increased intestinal permeability and exposure to microbial products-including lipopolysaccharide, trimethylamine-N-oxide, and secondary bile acids-dysbiosis promotes inflammation, oxidative stress, insulin resistance, and carcinogenesis. These changes are linked to conditions including metabolic dysfunction-associated steatotic liver disease, alcohol-associated liver disease, cirrhosis, hepatocellular carcinoma, pancreatitis, pancreatic ductal adenocarcinoma, and diabetes. Emerging tools like stool metagenomics and serum metabolomics help identify microbial biomarkers for diagnosis and risk stratification. While interventions such as probiotics, dietary changes, and fecal microbiota transplantation aim to restore microbial balance, their success remains inconsistent. This work aims to highlight the pathogenic role of GM across the GLPA, with special emphasis on the underexplored gut-pancreas connection. Advancing our understanding of the GLPA can unlock novel microbiota-targeted approaches for early diagnosis and treatment of hepatopancreatic diseases.}, }
@article {pmid41024767, year = {2025}, author = {Ezzat, WM}, title = {Machine learning as an artificial intelligence application in management of chronic hepatitis B virus infection.}, journal = {World journal of gastroenterology}, volume = {31}, number = {35}, pages = {109776}, pmid = {41024767}, issn = {2219-2840}, mesh = {Humans ; *Hepatitis B, Chronic/therapy/microbiology/diagnosis/virology ; *Machine Learning ; *Gastrointestinal Microbiome ; *Hepatitis B virus/pathogenicity ; Algorithms ; Artificial Intelligence ; Antiviral Agents/therapeutic use ; Supervised Machine Learning ; }, abstract = {Let's review the role of gut microbiota in pathogenesis of chronic hepatitis B infection as addressed in by Zhu et al. Zhu et al used high-throughput technology to characterize the microbial ecosystems, which led to an explosion of various types of molecular profiling data, such as metagenomics, metatranscriptomics, and metabolomics. To analyze such data, machine learning (ML) algorithms have shown to be useful for identifying key molecular signatures, discovering potential patient stratifications, and, particularly, for generating models that can accurately predict phenotypes. Strong evidence suggests that such gut microbiome-based stratification could guide customized interventions to benefit human health. Supervised learning includes designing an algorithm to fix a pre-identified problem. To get an answer, ML software must access data that have been nominated. On the other hand, unsupervised learning does not address any pre-defined problems. Bias should be eliminated as much as possible. In unsupervised learning, an ML algorithm works to identify data patterns without any prior operator input. This can subsequently lead to elements being identified that could not be conceived by the operator. At the intersection between supervised and unsupervised learning is semi-supervised ML. Semi-supervised learning includes using a partially labeled data set. The ML algorithm utilizes unsupervised learning to label data (that has not yet been labelled) by drawing findings from the labeled data. Then, supervised techniques can be used to solve defined problems involving the labeled data. Reinforcement learning, which is similar to supervised learning in the meaning, is goal-oriented. Reinforcement learning does not need labeled data, instead, it is provided with a set of regulations on a problem. An algorithm will carry out operations to try to answer questions involving the problem. Based on obtained data of gut microbiota, various therapeutic modalities can be applied: Prebiotics, probiotics, postbiotics, engineered bacteria, bacteriophage, and novel microbe-materials therapeutic system and fecal transplantation. In conclusion, ML is an artificial intelligence application that helps in providing new perspectives on tailored therapy. Furthermore, assessing the impact of gut microbiota modification is a critical step in advanced liver disease management. These new artificial intelligence techniques although promising, still require further analysis and validation in future studies.}, }
@article {pmid41024212, year = {2025}, author = {Wang, Y and Gong, L and Dong, D and Li, X}, title = {Metagenomic binning reveals community and functional characteristics of sulfur- and methane-oxidizing bacteria in cold seep sponge ground.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {122}, pmid = {41024212}, issn = {2524-6372}, support = {KEXUE2020GZ01//The Senior User Project of R/V Kexue/ ; 42176114//The National Natural Science Foundation of China/ ; ZR2023MD100//Natural Science Foundation of Shandong Province/ ; }, abstract = {BACKGROUND: Cold seep sponges typically reside in the carbonate rock areas surrounding the vents, often comprising only a few individuals of a limited number of species. Previous limited studies have indicated that sponges living in seeps or vents host chemolithotrophic microorganisms, including sulfur-oxidizing bacteria (SOB) and methane-oxidizing bacteria (MOB), regardless of their feeding habits. This suggests that they may utilize compounds from their environment. However, when multiple sponge species are found co-occurring in a single sponge ground sharing identical environmental and material conditions, it remains unclear how their symbiotic community structure will behave. Specifically, it is uncertain whether the community will exhibit greater similarity or, as seen in most studies, demonstrate host specificity.<br><br>RESULTS: We utilize metagenomics and binning analysis to characterize six new sponge species belonging to two classes and two distinct dietary habits, all discovered in the same cold seep. Our findings reveal that their associated microbial communities, primarily composed of SOB and MOB from the phylum Proteobacteria, exhibit a high abundance of groups with the same chemosynthetic functions. Binning recovered diverse, novel MAGs (metagenome-assembled genomes) primarily dominated by order PS1 (SOB) and order Methylococcales (MOB). This similarity extends beyond the dietary habits and higher taxonomic levels of the sponge hosts. Phylogenetic and abundance difference analyses of MAGs indicate significant host specificity in the selection of symbiotic microbial species among different sponge species. Notably, these MOB and SOB exhibit potential novelty within their clade compared to known taxa. Furthermore, the genomes of these SOB and MOB contain abundant functions related to their adaptation to the chemoautotrophic environment and symbiotic lifestyle within the cold seep.<br><br>CONCLUSIONS: The chemosynthetic environment shapes the high relative abundance of key functional groups that dominate the symbiotic community, while the species differences among host sponges determine the strain selection within these groups. The metabolic functions expressed by this "convergence with divergence" community structure collectively endow the holobionts with the ability to adapt to the cold seep environment.}, }
@article {pmid41024198, year = {2025}, author = {Altalhi, S and Schultz, J and Jamil, T and Diercks, I and Sharma, S and Follmann, J and Alam, I and Raman, K and Augustin, N and van der Zwan, FM and Rosado, AS}, title = {Decoding microbial diversity, biogeochemical functions, and interaction potentials in red sea hydrothermal vents.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {118}, pmid = {41024198}, issn = {2524-6372}, support = {BAS/1/1096-01-0//King Abdullah University of Science and Technology/ ; BAS/1/1096-01-0//King Abdullah University of Science and Technology/ ; BAS/1/1096-01-0//King Abdullah University of Science and Technology/ ; FCC/1/1973-43-01//King Abdullah University of Science and Technology/ ; FCC/1/1973-43-01//King Abdullah University of Science and Technology/ ; BAS/1/1096-01-0//King Abdullah University of Science and Technology/ ; }, abstract = {BACKGROUND: Hydrothermal vents along mid-ocean ridges host diverse microbial communities and are crucial to global elemental cycling. The Red Sea, known for its unique environmental conditions-including low nutrient levels, high year-round temperatures, bottom-water temperatures of 21 °C, and elevated salinity-hosts recently discovered active low-temperature hydrothermal vent fields at the axial Hatiba Mons volcano. These vents, characterized by large iron oxide mounds and abundant microbial mats, offer an extreme environment for studying the diversity and functions of prokaryotes involved in elemental cycling in this system. In this study, we used 16S rRNA sequencing and shotgun metagenomics to examine the microbial diversity and metabolic capabilities of precipitates and microbial mats from five vent sites.<br><br>RESULTS: We recovered 314 non-redundant metagenome-assembled genomes (MAGs), including 250 bacterial and 64 archaeal MAGs, representing 34 bacterial and 11 archaeal phyla. Functional annotations revealed diverse nutrient and metal cycling potentials, with notable enrichment in iron redox genes. Key players include Bathyarchaeia and Chloroflexi in the precipitates (contributing to carbon, nitrogen, sulfur, and metal cycling potentials) and Pseudomonadota members in the microbial mats and upper precipitates (involved in iron and sulfur metabolism and carbon fixation through the CBB cycle). Carbon fixation in precipitate potentials primarily occurs through the Wood-Ljungdahl pathway. Sulfur and nitrogen cycling genes are distributed across various genomes, indicating collaborative cycling.<br><br>CONCLUSION: Our genome-resolved analysis positions the Hatiba Mons vents as an iron-rich system that provides new insights into oligotrophic hydrothermal environments, with potential relevance for understanding novel metabolic pathways, extremophilic adaptations, and their roles in element cycling and biotechnological applications.}, }
@article {pmid41024077, year = {2025}, author = {Zhang, Y and Guo, S and Lu, L and Li, Y and Wu, Y}, title = {Metagenomic next-generation sequencing for pathogen detection of pulmonary infections in persons living with HIV.}, journal = {AIDS research and therapy}, volume = {22}, number = {1}, pages = {95}, pmid = {41024077}, issn = {1742-6405}, support = {kq2403197//Natural Science Foundation of Changsha/ ; 2025JJ80470//Natural Science Foundation of Hunan Province/ ; }, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; Male ; Female ; *HIV Infections/complications/virology ; Retrospective Studies ; *Metagenomics/methods ; Middle Aged ; Adult ; Bronchoalveolar Lavage Fluid/microbiology/virology ; CD4 Lymphocyte Count ; *Lung Diseases/diagnosis/microbiology/virology ; Sensitivity and Specificity ; *Respiratory Tract Infections/diagnosis/microbiology/virology ; }, abstract = {BACKGROUND: This study aimed to evaluate the diagnostic utility of metagenomic next-generation sequencing (mNGS) in detecting pulmonary infections in persons living with HIV(PLWH).<br><br>METHODS: We conducted a retrospective study involving 246 PLWH with pulmonary infections. Bronchoalveolar lavage fluid (BALF) specimens were collected from all patients. mNGS and traditional microbial cultures were performed in parallel to compare the differences in pathogen identification. Patients were stratified by immune status based on CD4[+] T cell counts, and the association between pathogen profiles and immunodeficiency severity was analyzed.<br><br>RESULTS: mNGS demonstrated a significantly higher pathogen detection sensitivity (98.0%) compared to traditional cultures (32.1%). The spectrum of pathogens detected by mNGS and culture methods differed significantly. mNGS identified 123 pathogenic microorganisms, whereas cultures detected only 17. mNGS detected additional pathogens, including viruses (e.g., Epstein-Barr virus and cytomegalovirus) and fastidious microorganisms (e.g., Pneumocystis jirovecii). Furthermore, mNGS revealed a significant correlation between PLWH-associated immunodeficiency and pathogen profiles. The diversity of pathogens, particularly fungi and viruses, increased with declining CD4[+] T cell counts (p&#x2009;<&#x2009;0.05).<br><br>CONCLUSION: mNGS comprehensively characterizes the complex pathogen spectrum in PLWH-associated pulmonary infections, significantly enhancing detection sensitivity for mixed and fastidious infections, thereby guiding targeted anti-infective therapy. Immunosuppression severity strongly correlates with opportunistic pathogen profiles and the risk of specific pathogen detection, highlighting the importance of immune status-guided clinical strategies. mNGS serves as a valuable adjunct to conventional diagnostic methods, enhancing the detection and prognostic assessment of infectious complications in PLWH.}, }
@article {pmid41023882, year = {2025}, author = {Luo, Y and Zhao, C and Chen, H and Lin, Z and Xia, J and Liu, X and Li, X}, title = {Clinical value of metagenomic next-generation sequencing in diagnosis of Coxiella burnetii infection.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {1219}, pmid = {41023882}, issn = {1471-2334}, support = {No. 2023A1515220226//Basic and Applied Basic Research Foundation of Guangdong Province/ ; No. 2420004000311//Science and technology plan project in the field of social development of ZhuhaiScience and technology plan project in the field of social development of Zhuhai/ ; }, mesh = {Humans ; *Q Fever/diagnosis/microbiology/drug therapy ; *Coxiella burnetii/genetics/isolation &amp; purification ; Adult ; Male ; Female ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing/methods ; Middle Aged ; *Metagenomics/methods ; Aged ; Young Adult ; }, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) is a new pathogen detection technique, but the current experience of clinical application in Coxiella burnetii infection is relatively limited. This study aimed to investigate the clinical application value of mNGS in diagnosis of Coxiella burnetii infection.<br><br>METHODS: We conducted a retrospective study that included patients with Coxiella burnetii infection detected by mNGS from December 2018 to August 2024. Their clinical information and mNGS test results were retrieved for analysis.<br><br>RESULTS: A total of 70 patients with Coxiella burnetii infection were included in this study. The mean age of these patients was 43.5 years and the common clinical manifestations were fever (67/70, 95.7%), followed by headache (43/70, 61.4%), weakness (36/70, 51.4%), and muscle and joint pain (27/70, 38.6%). The mean length of hospitalization was five days. 92.9% (65/70) patients were discharged with improvement, and one patient died. The median duration of fever for these patients was seven days. Most patients temperatures returned to normal within 2-3 days after receiving targeted antibiotic therapy. No correlation was observed between the duration of fever and the reads of mNGS in febrile patients. The specimens tested by mNGS were mainly blood specimens. The reads of mNGS detected fluctuated from one to 826, with the range of one to 50 being the most frequent. 43 (61.4%) samples of mNGS detected only Coxiella burnetii. Pathogens detected along with Coxiella burnetii include viruses, bacteria, and fungi. None of the 63 patients followed up for six months had clinical manifestations of chronic Q fever.<br><br>CONCLUSIONS: Q fever is a disseminated infectious disease that deserves attention for its nonspecific clinical symptoms. mNGS emerges as a powerful novel tool for pathogen detection, demonstrating significant value in diagnosing Q fever, particularly in where conventional serological and PCR testing is unavailable or inconclusive.}, }
@article {pmid41023790, year = {2025}, author = {Cao, L and Sun, H and Wang, Y and Wei, Z and Zhang, J and Wang, Y and Yan, J and Zhu, Y and Cheng, N and He, S and Liu, X and Li, T and Wang, M and Li, E}, title = {Comparative analysis of metagenomics between high- and medium-temperature daqu, and microbial succession in Jiang-Nong Jianxiang Baijiu fermentation.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {852}, pmid = {41023790}, issn = {1471-2164}, mesh = {*Fermentation ; *Metagenomics/methods ; *Alcoholic Beverages/microbiology ; *Microbiota ; *Bacteria/genetics/classification ; Temperature ; Phylogeny ; }, abstract = {BACKGROUND: The mixture of high-temperature Daqu and medium-temperature Daqu can be used to produce Chinese Jiang-Nong Jianxiang Baijiu. This study used metagenomic sequencing and physicochemical analysis to investigate the microbial community and functionality of high-temperature Daqu and medium-temperature Daqu. In addition, exploring the changes of microbial communities during the Jiang-Nong Jianxiang Baijiu fermentation process.<br><br>RESULTS: The results showed that Lichtheimia ramose and Saccharopolyspora rectivirgula were the significantly different species in high-temperature Daqu. However, Paecilomyces variotii, Aspergillus chevalieri, and Rasamsonia emersonii were the significantly different species in medium-temperature Daqu. The medium-temperature Daqu had higher saccharifying power (101.20&#x2009;&#xb1;&#x2009;1.85 U/g) than high-temperature Daqu (60.00&#x2009;&#xb1;&#x2009;0.58 U/g). And the protease activity of high-temperature Daqu (62.47&#x2009;&#xb1;&#x2009;5.84 U/mg) was significantly higher than medium-temperature Daqu (36.10&#x2009;&#xb1;&#x2009;1.13 U/mg). The community structure analysis results of the stack fermentation stage showed that the mixture of high-temperature Daqu and medium-temperature Daqu inherited the community advantages of both high-temperature Daqu and medium-temperature Daqu. With Jiang-Nong Jianxiang Baijiu fermentation, the significantly different species changed from Pichia sp., Acetobacter sp., and Lactobacillus sp. to Pediococcus sp., Lactobacillus sp., Lentilactobacillus sp., Saccharomyces sp., Thermoactinomyces sp., and Saccharopolyspora sp., implying the importance of acid-resistant and ethanol-resistant microorganisms for the production of flavor substances in the late Baijiu fermentation.<br><br>CONCLUSIONS: Our research revealed the difference in microbial communities between high-temperature Daqu and medium-temperature Daqu, and demonstrated the shifts and functionality of microbiota during Jiang-Nong Jianxiang Baijiu fermentation. This study provides a theoretical reference for utilizing core synergistic microbiota and their functional traits in Baijiu fermentation starters to improve Baijiu quality.}, }
@article {pmid41023748, year = {2025}, author = {Soto-López, JD and García-Martín, JM and Lizana-Ciudad, D and Lizana, M and Hernández-Tabernero, L and Fernández-Soto, P and Velásquez-González, OE and Aragón, SL and Belhassen-García, M and Muro, A}, title = {Taxonomic and functional profiling of bat guano microbiota from hiking trail-associated tunnels: a potential risk for human health?.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {123}, pmid = {41023748}, issn = {2524-6372}, support = {Orden EDU/1868/2022//Predoctoral Fellowship Program of Junta de Castilla y Leon - Fondo Social Europeo Plus (FSE +)/ ; }, abstract = {Metagenomic studies have significantly expanded our understanding of the bacterial communities present in bat guano. Several studies have reported the presence of common human pathogenic bacteria, including enteric foodborne species, zoonotic pathogens, unusual Gram-negative bacteria, and multidrug-resistant strains. These findings have reinforced the perception of bat guano as a potential reservoir of pathogens. Despite this, research conducted in sites with frequent human contact remains limited. Caves and tunnels such as those along the Camino del Hierro in northeastern Spain represent environments with regular human exposure, making them areas of particular interest from a public health perspective. In this study, we conducted an extensive analysis of the guano microbiome during both the breeding season and hibernation period in bats inhabiting this touristic site, using shotgun metagenomics and a comprehensive bioinformatic pipeline. Our results revealed marked differences in the relative microbial composition across samples from fresh and desiccated bat guano. The most abundant viral order detected was Herpesvirales, while among bacterial genera, Bacillus, Burkholderia, Lactobacillus, Pseudomonas, Salmonella and Streptococcus were dominant. The presence of these taxa in the tunnels poses a potential risk not only to visitors but also to park staff who are regularly exposed to bat guano, particularly due to the presence of species associated with various human viral and bacterial diseases. No significant differences were observed in the overall abundance of detected organisms between seasons. However, distinct seasonal patterns emerged when analyzing metabolic pathways and virulence factors. During the breeding season, there was a notable predominance of metabolic pathways related to cell proliferation, along with virulence factors associated with strategies for surface attachment and biofilm formation. Overall, our findings highlight an underrecognized and unmonitored risk of pathogen transmission for both visitors and personnel at this tourist site, underscoring the need for increased awareness and further investigation into the health implications of human-bat interactions in such environments.}, }
@article {pmid41023693, year = {2025}, author = {Yang, M and Zhang, HX and Zhou, YL and Selvarajan, R and Xu, PK and Gao, ZM and Wang, Y}, title = {Viral ecogenomics across oxic and anoxic zones of the Yongle Blue Hole.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {119}, pmid = {41023693}, issn = {2524-6372}, support = {ZDKJ2021028//Major Science and Technology Plan Project of Hainan Province/ ; 2022YFC2805304//National Key Research and Development Program of China/ ; 42376149//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Deep ocean blue holes are characterized by distinct physicochemical gradients and complex biological processes, and Yongle Blue Hole (YBH) in the South China Sea (SCS) is the world's deepest (301 m) underwater cavern with unique environmental characteristics. So far, studies investigated the bacterial community structure with different lifestyles of the YBH; however, our understanding of viruses in the YBH remains limited. Here, we utilized a metagenomic approach to investigate viral communities in both the "viral fraction" and "cellular fraction" of seawater samples in oxic and anoxic zones within YBH.<br><br>RESULTS: A total of 1,730 viral operational taxonomic units (vOTUs) were identified, with over 70% affiliated with the classes Caudoviricetes and Megaviricetes, particularly within the families Kyanoviridae, Phycodnaviridae and Mimiviridae. Gene-sharing network analyses indicated that the deeper anoxic layers contain a high proportion of novel viral genera, while the oxic layer's viral genera overlap with those found in the open water samples from SCS. Virus-linked prokaryotic hosts predominantly belong to the phyla Patescibacteria, Desulfobacterota, and Planctomycetota. Notably, the detected putative auxiliary metabolic genes (AMGs) suggest that these viruses may influence photosynthetic and chemosynthetic pathways, as well as methane, nitrogen, and sulfur metabolisms, especially with several high-abundance AMGs potentially involved in prokaryotic assimilatory sulfur reduction.<br><br>CONCLUSIONS: Together, these findings highlight the potential ecological roles and diversity of viral communities within YBH and shedding light on niche-separated viral speciation.}, }
@article {pmid41023631, year = {2025}, author = {Lan, Q and Deng, Z and Li, C and Huang, H and Zhou, Z and Jiang, L and Li, F and Wu, D and Zheng, M and Zhou, M and Chen, Q and Xu, F}, title = {Evaluation of hybrid capture-based targeted and metagenomic next-generation sequencing for pathogenic microorganism detection in infectious keratitis.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {1211}, pmid = {41023631}, issn = {1471-2334}, support = {2025GXNSFDA069056//Natural Science Foundation of Guangxi Zhuang Autonomous Region/ ; Z2016623//Guangxi Medical Health Appropriate Technology Development and Application Project/ ; 2020036//Science and Technology Plan Project of Qingxiu District in Nanning City/ ; AD19245193//Guangxi clinical ophthalmic research center/ ; 20233071//Nanning City Science Research and Technology Development Program/ ; }, }
@article {pmid41023192, year = {2025}, author = {Vishal, V and Thakur, P and Tigga, SS and Lal, S}, title = {A metagenomic assessment of overburden dump of coal mine soil bacterial consortium from Jharkhand, India.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {10}, pages = {1161}, pmid = {41023192}, issn = {1573-2959}, mesh = {*Soil Microbiology ; India ; *Bacteria/classification/genetics ; *Coal Mining ; *Environmental Monitoring ; *Soil Pollutants/analysis ; Metagenomics ; Soil/chemistry ; *Microbial Consortia ; Biodegradation, Environmental ; RNA, Ribosomal, 16S ; Coal ; }, abstract = {Overburden dump (OBD) of coal mine waste soils is arguably a major source of heavy metals and metalloids, leading to both public health and ecological consequences. This study employed hypervariable V3-V4 region of 1.5 kbp 16S rDNA gene-based amplicon metagenomic sequencing to analyze unexplored bacterial diversity and its phenotypical and hypothetical functions, emphasizing the significance of these studies for assessing the potential of bioremediation. Triplicate coal OBD soil samples were collected from the coal dumping yard of Sarubera Colliery from Atna-Chainpur and agricultural soils from Ramgarh Cantonment, Jharkhand. There were 30 phyla And 320 operational taxonomic units (OTUs) recorded in coal OBD soil, while agricultural soil had 26 phyla And 240 OTUs. Proteobacteria were the predominant phylum in both environments. Firmicutes, Actinobacteria, and Bacteroidetes were the most prevalent phyla in the coal OBD soil, whereas Acidobacteria, Planctomycetes, and Nitrospirae were most frequently found in agricultural soil. Alphaproteobacteria and Gammaproteobacteria was the most abundant classes, and whereas the mesophilic Acinetobacter were the most abundant genus detected in coal OBD soil. The PICRUSt2 pipeline predicted hypothetical functional categories, identifying 2404 EC numbers, 7813 KO terms, And 442 MetaCyc pathways. The most enriched categories were RNA polymerase sigma-70 factor, ABC transporters, And 3-oxoacyl-[acyl-carrier-protein] reductase, aerobic respiration pathways, and pyruvate fermentation biosynthesis pathways. Taxonomy-to-phenotypic mapping was used to record phenotypic categories like oxygen requirement, temperature range, energy sources, biotic relationships, and Gram stain nature between the two habitats. The presence of nitrogen-fixing and phosphate-solubilizing bacteria in coal OBD soil offers their key roles of biodegrading polycyclic aromatic hydrocarbons (PAHs), speeding mineralization, and ameliorating environmental issues that threaten plant viability.}, }
@article {pmid41022942, year = {2025}, author = {Halifu, S and Deng, X and Yang, L and Qian, L and Yang, L}, title = {Metagenomic analysis of pathogenicity of puccinia xanthii on invasive plant xanthium italicum.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {33530}, pmid = {41022942}, issn = {2045-2322}, support = {KX031042//PhD research startup foundation of Shihezi University/ ; KX6107//a program of Shihezi University/ ; }, mesh = {*Plant Diseases/microbiology ; Plant Leaves/microbiology ; *Xanthium/microbiology ; *Metagenomics/methods ; *Puccinia/genetics/pathogenicity ; Introduced Species ; Photosynthesis ; China ; }, abstract = {Biological invasion refers to the establishment and proliferation of non-indigenous species in previously unoccupied areas, where they form wild populations. Xanthium italicum, an invasive species in Xinjiang, China, negatively affects local ecosystems, agriculture, and animal husbandry. In this study, we investigated the pathogenicity of Puccinia xanthii on the leaves of X. italicum by exploring the morphological characteristics of the pathogenic fungi, leaf enzyme activity measurement, photosynthesis measurement, and metagenomic sequencing. This study showed that P. xanthii infects the leaves of X. italicum, significantly reducing the activities of lyase, oxidoreductase, and antioxidant enzymes, including phenylalanine ammonia-lyase (PAL), superoxide dismutase (SOD), polyphenol oxidase (PPO), and catalase (CAT), as well as impairing photosynthesis. Furthermore, metagenomic analysis indicated that P. xanthii infection reduced the homogeneity and richness of phyllosphere microorganisms and increased the abundance of P. xanthii in the phyllosphere. Functional analysis also revealed that P. xanthii infection altered the diversity of microbial functions and eventually led to the development of disease symptoms and the demise of leaves through activated oxidative phosphorylation.}, }
@article {pmid41022717, year = {2025}, author = {Song, K and Xiao, Y and Wang, Y and Deng, M and Zhou, S and Huang, Y and Yeerken, S and Li, L and Wu, F}, title = {Electron shuttling promotes denitrification and mitigates nitrous oxide emissions in lakes.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {8564}, pmid = {41022717}, issn = {2041-1723}, support = {42222709//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42307505//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42107277//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Nitrous Oxide/metabolism/analysis ; *Denitrification/physiology ; *Lakes/microbiology/chemistry ; Electron Transport ; Geologic Sediments/microbiology/chemistry ; Bacteria/metabolism/genetics ; Oxidation-Reduction ; Electrons ; Eutrophication ; }, abstract = {Eutrophication is an emerging global issue that is becoming increasingly severe due to the rising nutrient inputs and limited availability of electron donors for nitrogen removal. In sediments where redox conditions fluctuate dramatically, extracellular electron transfer (EET) critically supports microbial metabolism. However, the biogeochemical significance of EET-coupled denitrification and its EET mechanisms remain unclear. Here, through field investigations and laboratory [15]N isotope experiments, we reveal that humic substance (HS)-mediated electron shuttling significantly enhances denitrification primarily by stimulating bacterial outer membrane c-type cytochrome. Specifically, EET mitigates the emission of greenhouse gas nitrous oxide by enriching nosZII-type reducers. Notably, the efficacy of exogenous HS amendment attenuates in sediment with high native HS concentration. Metagenomic binning further reveals multiple cytochromes forming a complete EET-coupled denitrification electron transport chain. Our findings elucidate the microbial mechanisms underlying electron shuttling-driven denitrification in lakes, thereby expanding the understanding of biogeochemical cycles.}, }
@article {pmid41022706, year = {2025}, author = {Füssy, Z and Lampe, RH and Arrigo, KR and Barry, K and Brisbin, MM and Brussaard, CPD and Decelle, J and de Vargas, C and DiTullio, GR and Elbourne, LDH and Frischer, ME and Goodstein, DM and Grigoriev, IV and Hayes, RD and Healey, AL and James, CC and Jenkins, JW and Juery, C and Kumar, M and Kustka, AB and Maumus, F and Novák Vanclová, AMG and Oborník, M and Paulsen, IT and Probert, I and Saito, MA and Schmutz, J and Skalický, T and Tec-Campos, D and Tomelka, H and Věchtová, P and Venepally, P and Wilson-Mortier, B and Zengler, K and Zheng, H and Allen, AE}, title = {Genome-resolved biogeography of Phaeocystales, cosmopolitan bloom-forming algae.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {8559}, pmid = {41022706}, issn = {2041-1723}, support = {NA15OAR4320071//United States Department of Commerce | National Oceanic and Atmospheric Administration (NOAA)/ ; NA19NOS4780181//United States Department of Commerce | National Oceanic and Atmospheric Administration (NOAA)/ ; NSF OCE-1756884//National Science Foundation (NSF)/ ; 970820//Simons Foundation/ ; }, mesh = {Phylogeny ; *Haptophyta/genetics/classification/metabolism ; Phylogeography ; Gene Transfer, Horizontal ; Metagenome ; Oceans and Seas ; Genome ; Genomics ; }, abstract = {Phaeocystales, comprising the genus Phaeocystis and an uncharacterized sister lineage, are nanoplanktonic haptophytes widespread in the global ocean. Several species form mucilaginous colonies and influence key biogeochemical cycles, yet their underlying diversity and ecological strategies remain underexplored. Here, we present new genomic data from 13 strains, including three high-quality reference genomes (N50 > 30 kbp), and integrate previous metagenome-assembled genomes to resolve a robust phylogeny. Divergence timing of P. antarctica aligns with Miocene cooling and Southern Ocean isolation. Genomic traits reveal metabolic flexibility, including mixotrophic nitrogen acquisition in temperate waters and gene expansions linked to polar nutrient adaptation. Concordantly, transcriptomic comparisons between temperate and polar Phaeocystis suggest Southern Ocean populations experience iron and B12 limitation. We also identify signatures of horizontal gene transfer and endogenous giant virus/virophage insertions. Together, these findings highlight Phaeocystales as an ecologically versatile and geographically widespread lineage shaped by evolutionary innovation and adaptation to contrasting environmental stressors.}, }
@article {pmid41021050, year = {2025}, author = {Kishk, M and Rahmeh, R and Asiri, F and Karam, H and Al-Muhanna, K and Hejji, AB and Shajan, A and Al-Salem, SM}, title = {Substrate-specific microbial community shifts during mesophilic biodegradation of polymers in compost amended soil.}, journal = {Biodegradation}, volume = {36}, number = {5}, pages = {93}, pmid = {41021050}, issn = {1572-9729}, support = {FB187K//Kuwait Institute for Scientific Research/ ; }, mesh = {Biodegradation, Environmental ; *Soil Microbiology ; *Soil/chemistry ; *Polymers/metabolism ; *Composting ; *Bacteria/metabolism/genetics/classification ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Fungi/metabolism/genetics/classification ; Starch/metabolism ; }, abstract = {Plastics are widely utilized across various industries, but their persistent accumulation in the environment has become a major ecological concern. Biodegradable alternatives offer a potential solution to plastic pollution; however, their degradation behavior under environmentally relevant conditions remains underexplored. This study evaluates the aerobic biodegradation of four polymer materials: starch, commercial thermoplastic starch of polyester origin (TPS1), linear low-density polyethylene (LLDPE), and a co-polyester thermoplastic starch (TPS2), over 180 days at 25 °C in a compost-soil matrix using the testing protocols of ASTM D5988-18 for carbon dioxide (CO2) evolution. Microbial community dynamics were profiled using 16S rRNA and ITS2 amplicon sequencing. TPS2 reached complete mineralization (~ 100%) in 28 days, followed by starch at 71.1% by day 180. TPS1 showed partial mineralization of 38.6%, while LLDPE showed minimal mineralization (21.9%) as expected. Alpha diversity revealed higher bacterial richness in starch treatments and a marked reduction in fungal diversity in TPS1 and LLDPE. Differential abundance testing revealed significant microbial shifts between treatments. Linear discriminant analysis Effect Size (LEfSe) identified polymer-specific microbial biomarkers, including Paenibacillus and Botryotrichum for starch, Acrophialophora and Mycothermus for TPS2, and the Mycobacterium for LLDPE. Subgroup 10 Acidobacteria was uniquely enriched in TPS2-treated samples. These taxa reflect substrate-driven microbial selection. Coupling CO2 mineralization with microbial profiling offers a practical framework to evaluate polymer biodegradability and guide the design of soil-degradable bioplastics. Overall, these findings demonstrate that polymer composition significantly influences microbial community structure and mineralization performance under mesophilic conditions.}, }
@article {pmid41020900, year = {2025}, author = {Aziez, M and Yanat, B and Rodriguez-Diaz, C and Suharoschi, R and Vulturar, R and Heghes, SC and Guenaoui, N and Ali, AM and Garcia-Fuentes, E and Bribi, N}, title = {Pharmacological Potential of Arthrospira platensis in Mitigating Sub-Chronic Colitis: Redox Homeostasis and Gut Microbiota Modulation.}, journal = {Current issues in molecular biology}, volume = {47}, number = {9}, pages = {}, doi = {10.3390/cimb47090778}, pmid = {41020900}, issn = {1467-3045}, abstract = {Inflammatory bowel diseases (IBDs) are complex disorders involving interconnected immune, oxidative, and microbial dysregulations. Arthrospira platensis (Spirulina) is a rich source of bioactive compounds with antioxidant, anti-inflammatory, and immunomodulatory properties. This study investigates the pharmacological efficacy of its aqueous extract (APA) in mitigating 2,4-Dinitrobenzene Sulfonic Acid (DNBS)-induced sub-chronic colitis with a focus on restoring redox balance and modulating gut microbiota composition. APA's antioxidant capacity was assessed in vitro by 2,2-diphenyl-1-picrylhydrazyl (DPPH), 2,2'-azino-bis (3-ethylbenzthiazoline-6-sulphonic) acid (ABTS) radical scavenging, and metal chelation assays. In vivo, BALB/c mice received two DNBS inductions to establish sub-chronic colitis and were treated with APA (50, 100, and 200 mg/kg). Therapeutic efficacy was assessed through clinical scoring, histopathological assessment, biochemical analysis, and gut microbiota profiling based on 16S rRNA gene sequencing. APA exhibited strong antioxidant activity and significantly attenuated colitis severity, as evidenced by reduced Disease Activity Index (DAI) scores, decreased colon inflammation, suppression of Myeloperoxidase (MPO)-mediated neutrophil infiltration, and modulation of redox biomarkers. Moreover, metagenomic profiling revealed APA-induced modulation of the gut microbiota, mainly through a decreased abundance of pathogenic genera such as Staphylococcus and Enterobacteriaceae. APA demonstrates potent antioxidant, anti-inflammatory, and microbiota-modulating activities, supporting its potential as a complementary therapy for IBDs and encouraging further clinical studies.}, }
@article {pmid41020604, year = {2025}, author = {Mohr, J and Albers, A and Schaumburg, F and Paulus, W and Brokinkel, B and Stummer, W and Spille, DC and Thomas, C}, title = {Deep 16S rDNA Sequencing of Chronic Subdural Hematomas Suggests Involvement of Bacterial Infection in Recurrences.}, journal = {Neurosurgery}, volume = {}, number = {}, pages = {}, doi = {10.1227/neu.0000000000003754}, pmid = {41020604}, issn = {1524-4040}, support = {TH222202//Medizinische Fakult&#xe4;t,&#xa0;Westf&#xe4;lische Wilhelms-Universit&#xe4;t M&#xfc;nster/ ; }, abstract = {BACKGROUND AND OBJECTIVES: Chronic subdural hematoma (CSDH) is an encapsulated blood collection between the dura mater and arachnoid that often follows mild head trauma. It involves pronounced inflammation and angiogenesis, and recurrence remains common despite advances in surgical management. Subclinical bacterial involvement has been hypothesized as a potential factor in these recurrent cases. We aimed to determine whether bacteria are present in CSDH outer membranes and to define accompanying histological and transcriptomic changes.<br><br>METHODS: A total of 39 Formalin-fixed paraffin-embedded outer-capsule specimens from 19 patients (17 primary, 22 recurrent) underwent: (1) ultra-deep Nanopore 16S rDNA profiling; (2) histomorphology with Gram staining, lipopolysaccharide immunohistochemistry and quantitative immune-cell counts; and (3) RNA-seq of 3 matched primary-recurrent pairs, followed by differential-expression and pathway analysis.<br><br>RESULTS: Gram staining revealed bacteria in 2 recurrent samples (5%) from a single patient, whereas lipopolysaccharide immunohistochemistry was negative in all cases. Notably, 16S rDNA sequencing detected bacterial DNA exclusively in recurrent lesions (6 samples from 4 patients), with none in primary cases (P = .02, &#x3c7;2 test). The identified bacterial genera included Staphylococcus, Neisseria, Prevotellamassilia, and Paracoccus. Histopathological evaluation showed no significant differences in eosinophils, myeloperoxidase-positive cells, CD3-positive T-cells, or CD20- positive B-cells when comparing primary with recurrent lesions, or infected to uninfected membranes. Unsupervised clustering of matched primary and recurrent CSDH samples revealed distinct transcriptomic profiles, identifying 184 differentially expressed genes (including consistent Toll-like receptor 4 upregulation) and highlighting pathways related to development, protein biosynthesis, and wound healing.<br><br>CONCLUSION: These findings suggest that bacterial DNA is present in a subset of recurrent CSDH, suggesting that bacteria could be involved in recurrences. Further research with larger cohorts is needed to determine whether antimicrobial or anti-inflammatory strategies might help reduce recurrence.}, }
@article {pmid41020558, year = {2025}, author = {Diallo, D and Sene, O and Ngom, D and Khoulé, A and Faye, ET and Dieng, I and Ndione, MHD and Faye, O and Simon-Lorière, E and Diagne, MM and Diallo, M and Sakuntabhai, A and Fall, G}, title = {Detection and genetic characterization of arboviruses and other viruses from mosquitoes collected in southeastern and central Senegal, October 2022.}, journal = {Medical and veterinary entomology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mve.70017}, pmid = {41020558}, issn = {1365-2915}, support = {U01AI151758//National Institute of Allergy and Infectious Diseases, National Institues of Health/ ; }, abstract = {The knowledge of the distribution of viruses and their associated mosquito species is still incomplete in Senegal. Additionally, data on the genetic characterization of these viruses are limited. The aim was to update knowledge on the diversity, distribution and genetic relationships of mosquito-associated viruses in Senegal through entomological and molecular surveillance. Mosquitoes were collected in October 2022 across 10 districts in Senegal. Samples were identified morphologically and processed for virome characterization using qRT-PCR and next-generation sequencing. The most common species were Culex cinereus Theobald, 1901, Culex quinquefasciatus Say, 1823, Culex neavei Theobald, 1904, and Culex poicilipes Theobald, 1904 (Diptera: Culicidae). The number of mosquitoes collected varied by habitat and district. We detected 42 isolates of 7 viruses, including Bagaza (BAGV), Barkedji, Sindbis (SINV), Usutu (USUV), Dezidougou, Densovirus and Pestivirus A (PESVA), in 6 mosquito species (Mansonia uniformis, Cx. neavei Theobald, 1901, Anopheles coustani, Cx. cinereus Laveran, 1900, Aedes aegypti Linnaeus, 1762 and Aedes vexans Meigen, 1830) (Diptera: Culicidae). The viruses were mainly detected in mosquitoes collected near ponds (92.9%). BAGV and SINV were detected for the first time in southeastern Senegal. This is also the first association of PESVA with mosquitoes in the field. Phylogenetic analyses revealed that PESVA clustered with strains from Asia and Egypt, BAGV with strains from Senegal and Spain, USUV with strains from Senegal and SINV with strains from Spain and Kenya. This study expands the understanding of mosquito-virus associations in Senegal, revealing new geographic distributions and vectors for several viruses, with implications for arbovirus emergence and surveillance strategies.}, }
@article {pmid41020500, year = {2025}, author = {Yang, Y and Kang, D and Mihalache, B and Vexler, S and Jain, S and Peng, H and Annabi, N and Yang, S and Chen, IA}, title = {Metagenome-inspired libraries to engineer phage M13 for targeted killing of Gram-negative bacterial species.}, journal = {Nucleic acids research}, volume = {53}, number = {18}, pages = {}, doi = {10.1093/nar/gkaf984}, pmid = {41020500}, issn = {1362-4962}, support = {R35GM148249/GF/NIH HHS/United States ; T32GM145388/GM/NIGMS NIH HHS/United States ; UL1TR001881/TR/NCATS NIH HHS/United States ; 32201100//National Natural Science Foundation of China/ ; //UCLA/ ; }, mesh = {*Metagenome ; *Bacteriophage M13/genetics ; Pseudomonas aeruginosa/virology/drug effects ; Anti-Bacterial Agents/pharmacology ; *Gram-Negative Bacteria/virology/drug effects ; Humans ; *Peptide Library ; Phage Therapy ; }, abstract = {Given concerning trends in antibiotic resistance, phages have been increasingly explored as promising antimicrobial agents. However, a major problem with phage therapy is the overly high specificity of phages for their hosts, which is currently addressed by a personalized approach involving screening a bank of wild-type phages against each clinical isolate. To shorten this process, we propose that a focused library of synthetic phages could be rapidly selected for a member binding to a given clinical isolate. We created libraries of recombinant M13 phages expressing receptor-binding proteins based on the collective metagenome of inovirus phages, a diverse group whose members appear to infect nearly all bacterial phyla. Using two rounds of a pull-down selection, phage variants were identified against several Gram-negative pathogens, including a variant (M13PAB) that bound to several Pseudomonas aeruginosa strains, including clinical isolates. To confer bactericidal activity to the nonlytic phage, a last-line but nephrotoxic lipopeptide, colistin, was cross-linked to the M13PAB virions. The colistin-M13PAB phage conjugate lowered the minimal inhibitory concentration of colistin by 1-2 orders of magnitude for multiple strains of P. aeruginosa and showed a lack of hemolytic or cytotoxic activity in vitro, suggesting high potency combined with low toxicity. Thus, a metagenome-inspired library displayed on the M13 phage scaffold, when subjected to a short selection for binding to a bacterial clinical isolate, could yield a phage variant that targets the specified strain. This approach may improve the speed, consistency, and cost-effectiveness of personalized phage therapy.}, }
@article {pmid41020266, year = {2025}, author = {Back, F and Sandoval, A and Vu, LM and Hong, VM and Bhaskara, A and Rodriguez, SR and O'Brien, JT and Kolber, BJ and Kroener, S and Ploski, JE}, title = {Adeno-associated viral vector resource for the RNA-targeting Cas13d: A comparison of high-fidelity variants, DjCas13d and hfCas13d.}, journal = {Molecular therapy. Methods &amp; clinical development}, volume = {33}, number = {4}, pages = {101565}, pmid = {41020266}, issn = {2329-0501}, abstract = {RNA-targeting CRISPR-Cas systems have emerged as alternatives to RNA-interference technology to knock down specific RNA transcripts. In particular, Cas13d derived from Ruminococcus flavefaciens (CasRx, RfxCas13d) has generated interest due to its superior knockdown efficiencies; however, accumulating evidence indicates that CasRx is prone to inducing transcriptome alterations due to its tendency to cleave bystander RNAs. High-fidelity Cas13d (hfCas13d) derived from CasRx and DjCas13d, an ortholog of Cas13d derived from Ruminococcus sp. UBA7013 (gut metagenome), are two recently identified variants that are superior to CasRx, as they both show a reduced tendency to cleave bystander RNAs. In this study, we created a resource of adeno-associated viral (AAV) vectors designed to deliver Cas13d, including hfCas13d and DjCas13d. We directly compared hfCas13d and DjCas13d for their on- and off-target potential in 293FT and neuro 2A cells. Specifically, we examined their ability to knockdown several endogenous and ectopically expressed transcripts using several different guide RNAs (gRNAs), and we examined knockdown specificity using a combination of reporter assays, RNA integrity analysis, and RNA sequencing (RNA-seq). We report that while both of these enzymes exhibit generally similar levels of knockdown potential, with DjCas13d sometimes outperforming hfCas13d, hfCas13d consistently caused significantly fewer transcriptome alterations when targeting highly expressed genes compared to DjCas13d.}, }
@article {pmid41020244, year = {2025}, author = {Yang, YM and Guo, J and Dang, NN}, title = {Case Report: Diagnosis of Nocardia asteroides infection using metagenomic next-generation sequencing of lymph node puncture tissue.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1626685}, pmid = {41020244}, issn = {2296-858X}, abstract = {The Nocardia genus is an aerobic, Gram positive, opportunistic pathogen that primarily affects cell-mediated immunosuppressed patients. The clinical manifestation of nocardiosis varies widely, making it challenging to diagnose. In this report, we describe a 48 year old woman with a muscular abscess caused by Nocardia asteroides. Venous blood, skin biopsy specimen, muscle tissue, and inguinal lymph node puncture tissue cultures yielded negative results. Using metagenomic next-generation sequencing (mNGS), the pathogen was identified as Nocardia asteroides. Whole-exome sequencing of the peripheral blood showed that the patient had a monoallelic mutation in the lipopolysaccharide-responsive beige-like anchor protein (LRBA) gene. The mNGS detected Nocardia asteroides in the patient, and the administration of accurate treatment led to her complete recovery.}, }
@article {pmid41020144, year = {2025}, author = {Tan, Y and Li, X and Xie, Y and Zhang, Z and Liu, J and Zhou, G and Liu, M}, title = {A Rare Case of Yersinia Pseudotuberculosis Infection with Septic Shock and Splenic Infarction.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {5057-5065}, pmid = {41020144}, issn = {1178-6973}, abstract = {Yersinia pseudotuberculosis is a Gram-negative bacterium of the family Yersiniaceae, primarily transmitted via the gastrointestinal tract. Progression to sepsis is uncommon, and the combination of septic shock and splenic infarction is exceedingly rare. We report a 40-year-old male who initially presented with fever, abdominal pain, and distension, which rapidly progressed to sepsis and multi-organ dysfunction. Definitive diagnosis of Y. pseudotuberculosis infection was established by blood culture and metagenomic next-generation sequencing, supported by imaging evidence of splenic infarction. The patient was managed with stepwise antimicrobial regimens (including piperacillin-tazobactam, meropenem, levofloxacin, linezolid, and daptomycin), plasma exchange, continuous renal replacement therapy, and organ function support. Following comprehensive treatment, the patient recovered and was discharged in stable condition. This case highlights the importance of considering Y. pseudotuberculosis in atypical sepsis presentations and demonstrates that timely diagnosis and multidisciplinary management are crucial to improving outcomes in such rare and life-threatening infections.}, }
@article {pmid41019955, year = {2025}, author = {Hajjar, J and Voigt, AY and Conner, ME and Swennes, AG and Fowler, S and Calarge, C and Mendonca, DD and Armstrong, D and Chang, CY and Walter, JE and Butte, MJ and Savidge, T and Oh, J and Kheradmand, F and Petrosino, JF}, title = {Gut dysbiosis patterns in CVID patients with noninfectious complications observed in a germ-free mouse model through fecal microbiota transplantation.}, journal = {Journal of human immunity}, volume = {1}, number = {1}, pages = {}, pmid = {41019955}, issn = {3065-8993}, abstract = {Patients with common variable immunodeficiency (CVID) who develop noninfectious complications (NIC) have worse clinical outcomes than those with infections only (INF). While gut microbiome aberrations have been linked to NIC, reductionist animal models that accurately recapitulate CVID are lacking. Our aim in this study was to uncover potential microbiome roles in the development of NIC in CVID. We performed whole-genome shotgun sequencing on fecal samples from CVID patients with NIC, INF, and their household controls. We also performed fecal microbiota transplants from CVID patients to germ-free mice. We found potentially pathogenic microbes Streptococcus parasanguinis and Erysipelatoclostridium ramosum were enriched in gut microbiomes of CVID patients with NIC. In contrast, Fusicatenibacter saccharivorans and Anaerostipes hadrus, known to suppress inflammation and promote healthy metabolism, were enriched in gut microbiomes of INF CVID patients. Fecal microbiota transplant from NIC, INF, and their household controls into germ-free mice revealed gut dysbiosis patterns only in recipients from CVID patients with NIC, but not in those from INF CVID or household controls recipients. Our findings provide a proof of concept that fecal microbiota transplant from CVID patients with NIC to germ-free mice recapitulates microbiome alterations observed in the donors.}, }
@article {pmid41019762, year = {2025}, author = {Vazzana, R and Mularoni, A and Vaiana, C and Cona, A and Mulè, G and Amato, C and Ranucci, G and Conaldi, PG and Agnese, V and Cuscino, N and Gallo, A}, title = {Shotgun metagenomics detects the human pegivirus complete genome in a pediatric patient with acute hepatitis of unknown etiology: a case report.}, journal = {Frontiers in genetics}, volume = {16}, number = {}, pages = {1653082}, pmid = {41019762}, issn = {1664-8021}, abstract = {Human pegivirus (HPgV) is a positive-sense, single-strand RNA virus belonging to the Flaviviridae family. Although not conclusively linked to a specific disease, an increasing number of studies have recently reported an association between this virus and different human pathologies. In this study, we present a 6-month-old female infant admitted to the hospital for severe acute hepatitis. Her clinical history started with a one week of fever and diarrhea treated with paracetamol and amoxicillin-clavulanate for a total of 4 days. The persistence of the symptoms, high levels of transaminases, coagulopathy, increased lymphocytosis, and C-reactive protein (CRP) in the blood suggested an acute hepatitis episode. Serological and molecular biology tests for hepatotropic and non-hepatotropic viruses, including hepatitis B virus (HBV), hepatitis A virus (HAV), hepatitis C virus (HCV), hepatitis E virus (HEV), Epstein-Barr virus (EBV), cytomegalovirus (CMV), herpes simplex virus (HSV), enterovirus, and adenovirus, were negative. Metabolic and genetic alterations, deficiency of alpha-1 antitrypsin, and Wilson's disease were ruled out following negative results. The child was thus treated with supportive therapy. Metagenomic next-generation sequencing (mNGS) performed to identify other possible infective agents undetected with the classical tests, showed the presence of the complete genome of human HPgV-1. This case provides further evidence supporting the hypothesis of the pathogenic role of HPgV-1 and warrants particular attention, especially in the pediatric population. Moreover, here we confirmed the diagnostic power of metagenomic-NGS in the detection of unusual pathogens.}, }
@article {pmid41019524, year = {2025}, author = {Shang, KM and Liu, R and Ni, HB and Ma, H and Su, JW and Yu, HL and Guo, L and Chen, BN and Zhang, XX and Yang, X}, title = {Bile acid pathways in Caprinae gut microbiota: adaptive shifts in microbial metabolism and community structure.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1648896}, pmid = {41019524}, issn = {1664-302X}, abstract = {INTRODUCTION: The gut microbiota plays a central role in host metabolism and immunity, in part through bile acid (BA) biotransformation. In Caprinae animals such as goats and sheep, this process is critical for nutrient absorption, immune regulation, and intestinal homeostasis, yet the microbial taxa and functional pathways involved remain poorly characterized.<br><br>METHODS: By leveraging 7,530 high-quality non-redundant metagenome-assembled genomes (MAGs) from Caprinae gut microbiomes, this study systematically characterized microbial diversity, taxonomic composition, and bile acid (BA)-related metabolic pathways through genome annotation, phylogenetic inference, and statistical analyses.<br><br>RESULT: The results revealed a diverse gut microbiota across 28 phyla, with Bacillota_A being the most dominant. A significant number of genes (8,290) from 5,217 genomes were identified to be involved in BA transformation pathways, including deconjugation, oxidation, and dehydroxylation. Bacteria from the Bacillota_A phylum were the primary carriers of BA-related genes. Among the MAGs, 1,845 encoded bile salt hydrolase (BSH), an enzyme crucial for the initial step of BA metabolism. Comparative analysis with human and pig gut microbiota highlighted a distinct BA metabolic profile in Caprinae animals, characterized by a higher proportion of BSH-related genes. Functional profiling of BSH-carrying MAGs within the genus Alistipes revealed significant differences in carbohydrate-active enzymes (CAZymes), indicating distinct metabolic repertoires that may reflect divergent ecological roles in the intestinal environment. Microbial taxonomic composition and bile acid (BA)-metabolizing potential varied markedly across the ten intestinal segments of Ovis aries, with the colon, cecum, and rectum showing the highest microbial diversity and functional gene abundance. Key BA-transforming enzymes (BSH, 7&#x3b1;-HSDH, and baiB) were widely distributed, with particularly high abundances in the jejunum and ileum, indicating region-specific specialization in BA metabolism.<br><br>DISCUSSION: This study provides new insights into the ecological and metabolic functions of gut microbiota in Caprinae animals, emphasizing the unique BA metabolic profiles and the functional potential of BSH-carrying MAGs, which have broader implications for understanding host-microbiota interactions in health and disease.}, }
@article {pmid41019405, year = {2025}, author = {Song, H and Li, X and Luo, J and Wang, J and Wu, F and Jiang, J and Chen, J and Cheng, Y and Yong, Y and Duan, M and Zhu, G}, title = {The Influence of Diet on the Composition and Function of Gut Microbiota in Four Snake Species.}, journal = {Ecology and evolution}, volume = {15}, number = {10}, pages = {e72204}, pmid = {41019405}, issn = {2045-7758}, abstract = {Diet plays an important role in shaping the intestinal flora, especially as demonstrated in non-mammalian studies. However, the precise associations underlying the interaction between the snake gut microbiota and diet remain poorly understood. Our findings indicate that the gut microbiomes of four snake species exhibit distinct characteristics influenced by their dietary preferences. Significant variations in gut microbial composition were observed among snakes with different diets. Similarities were noted between the gut microbiomes of Jerdon's pitviper (Protobothrops jerdonii: PJ) and Black-browed ratsnake (Elaphe taeniura: ET), which share similar food preferences. Chinese slug-eating snake (Pareas chinensis: PC), which primarily feeds on snails and slugs, displayed the highest gut microbiota diversity, suggesting a higher level of functional specificity associated with its specialized diet. Chiwen keelback (Rhabdophis chiwen: RC), which consumes fireflies and earthworms, exhibited a significantly higher abundance of antimicrobial resistance genes (ARGs) compared to other snake groups. Opportunistic pathogens such as Plesiomonas, Aeromonas, and Salmonella were relatively abundant in RC, ET, and PJ. The results of this study provide comprehensive data to differentiate the gut microbiota composition structures among four snake species with distinct dietary preferences, explore their potential functions, and identify possible correlations between gut microbial composition and diet. Furthermore, it provides a foundation for the analysis of the influence of genetic and environmental factors on the evolution of gut microbial communities.}, }
@article {pmid41019383, year = {2025}, author = {Qu, D and Wang, Y and Cao, L and Hou, Q and Liu, Z and Zhong, J and Guo, Z}, title = {Combined microbiome and metabolome analysis of Dacha and Ercha fermented grains of Fen-flavor Baijiu.}, journal = {Food chemistry. Molecular sciences}, volume = {11}, number = {}, pages = {100298}, pmid = {41019383}, issn = {2666-5662}, abstract = {Fen-flavor Baijiu is produced via two fermentation rounds (Dacha and Ercha), and quality is shaped by microbes in fermented grains. We hypothesized that the two rounds select distinct lactic acid bacteria (LAB) consortia with different metabolic potentials that associate with stage-specific metabolites and flavor compounds. We profiled 24 fermented-grain samples using shotgun metagenomics and untargeted metabolomics. Ercha showed lower alpha-diversity and a composition distinct from Dacha. Lactobacillus acetotolerans dominated Dacha, whereas Acetilactobacillus jinshanensis dominated Ercha. We detected 225 differential metabolites; 12 involved in flavonoid biosynthesis were higher in Dacha, while pyrimidine metabolism was more prominent in Ercha. Several LAB species-including L. acetotolerans, Lentilactobacillus hilgardii, Lactobacillus amylovorus, and Lactobacillus amylolyticus-showed positive correlations with these flavonoids. Genes encoding L-lactate dehydrogenase and acetate kinase were mainly carried by L. acetotolerans and associated with acetic acid and ethyl acetate in fermented grains. These outcomes supported our hypothesis and suggested actionable levers for production: stage-targeted monitoring of marker taxa/genes and rational starter design to steer flavor formation in Fen-flavor Baijiu.}, }
@article {pmid41019081, year = {2025}, author = {Liu, M and Cheng, Y and Wang, X and He, Z and Yang, K and Chen, K and Fan, Y and Wang, W}, title = {Diagnosing Rickettsia felis infection with Metagenomic Next-Generation Sequencing (mNGS) in a patient with ankylosing spondylitis: a case report and literature review.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1643599}, pmid = {41019081}, issn = {1664-3224}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; Middle Aged ; *Spondylitis, Ankylosing/complications/diagnosis ; *Rickettsia felis/genetics ; *Metagenomics/methods ; *Rickettsia Infections/diagnosis/microbiology/drug therapy ; Male ; }, abstract = {Rickettsia felis, an emerging flea-borne pathogen with global distribution potential, is a neglected cause of undifferentiated febrile illness, although reported human cases remain sparse. The development of molecular diagnostic methods, along with the application of metagenomic next-generation sequencing (mNGS), has improved the diagnostic accuracy of infectious fevers. A case of Rickettsia felis infection was diagnosed by mNGS in a 55-year-old patient with pre-existing ankylosing spondylitis. Five previously reported cases of Rickettsia felis infection were systematically reviewed, with a comprehensive analysis of their epidemiological characteristics, clinical manifestations, and therapeutic regimens. This study highlights the clinical features and diagnostic approaches of the disease through a case report and literature review.}, }
@article {pmid41018968, year = {2025}, author = {Dai, Q and He, Y and Wu, J and Zhou, L and Jiang, G and Chen, F}, title = {Effects of neutral detergent fiber levels on apparent nutrient digestibility and intestinal microbiota composition and function in forest musk deer.}, journal = {Frontiers in veterinary science}, volume = {12}, number = {}, pages = {1658189}, pmid = {41018968}, issn = {2297-1769}, abstract = {This experiment was conducted to explore the effects of different neutral detergent fiber (NDF) levels on nutrient apparent digestibility and intestinal microbiota composition and function in adult male forest musk deer (FMD) (Moschus berezovskii). A total of 18 adult male forest musk deer (FMD) (aged 4-10 years) with an initial average body weight of 7.09 ± 0.82 kg were selected and randomly divided into three groups with different NDF levels: L: 21.60%, M: 25.14%, and H: 28.47%. The FMD were used in a 50-day trial. The results showed that the apparent digestibility of NDF and acid detergent fiber (ADF) first increased and then decreased as NDF levels rose, with the M group showing the highest digestibility (p < 0.05). The H group exhibited significantly higher (p < 0.05) Chao1 and ACE indices compared to the L group. In addition, at the phylum level (the relative abundance > 0.5%), no significant differences were observed among the three groups, except for Mycoplasmatota, which showed higher (p < 0.05) relative abundance in the M group compared to the L group. At the genus level (the relative abundance > 1%), the three groups did not change (p > 0.05) significantly. In the KEGG function analysis, differentially expressed genes were primarily enriched in pathways related to organismal systems and human diseases. In the CAZy functional analysis, significant differences (p < 0.05) were observed in glycoside hydrolases (GHs) and carbohydrate-binding modules (CBMs), with the M group showing clear enrichment in fiber-degrading enzymes. Overall, the M group demonstrated superior NDF apparent digestibility and enhanced fiber degradation capacity. Therefore, a dietary NDF level of approximately 25% is recommended as optimal for adult male FMD.}, }
@article {pmid41018817, year = {2025}, author = {Zhou, X and Li, Q and Zhang, S and Wang, W and Wang, R and Zhang, X and Tan, Z and Wang, M}, title = {GCompip: a pipeline for estimating the gene abundance in microbial communities.}, journal = {Bioinformatics advances}, volume = {5}, number = {1}, pages = {vbaf207}, pmid = {41018817}, issn = {2635-0041}, abstract = {MOTIVATION: Gene abundance in metagenome datasets is commonly represented in terms of Counts or Copies Per Million. However, above term lack the consideration of the size of the microbial communities. To reflect the gene abundance in the microbial communities (GAM), GCompip, a comprehensive pipeline for estimating GAM, was developed based on specialized universal single copy genes (USCG) database, stringent alignment parameters, and rigorous filtering criteria.<br><br>RESULTS: GCompip showed high specificity without compromising computational efficiency, and improved the precision of downstream GAM estimations across diverse six ecological environments (i.e. human gut, rumen, freshwater, marine, hydrothermal sediment, and glacier). In contrast, the comparative annotation tools (i.e. KofamScan, eggNOG-mapper and HUMAnN3) showed larger error intervals, higher susceptibility to false positives, or overestimation of USCG abundance, primarily due to more relaxed thresholds, multifamily matches, or less stringent alignment settings. To facilitating the applicability of GCompip, we provided both Linux command line and R package versions. Overall, this GCompip presented an accurate, robust, user-friendly, and efficient computational pipeline designed to calculate GAM using metagenomic sequencing data. The developed pipeline makes it accessible to researchers seeking to evaluate the metabolic capabilities of microbial communities, and improve the capacity of interpreting metagenomic data related to microbial communities.<br><br>GCompip package source code and documentation are freely available for download at https://github.com/XiangZhouCAS/GCompip. A separate Linux command line version is available at https://github.com/XiangZhouCAS/GCompip_onlinux.}, }
@article {pmid41018532, year = {2025}, author = {Wang, J and Yu, C and Qiu, M and Xiong, X and Peng, H and Zhu, S and Chen, J and Song, X and Hu, C and Xia, B and Xiong, Z and Du, L and Yang, C and Zhang, Z}, title = {Whole-genome Metagenomic Sequencing Reveals Gut Microbiota Composition and Function Associated with Differential Growth Performance in Two Chicken Breeds.}, journal = {The journal of poultry science}, volume = {62}, number = {}, pages = {2025028}, pmid = {41018532}, issn = {1349-0486}, abstract = {Growth performance, an important trait in the broiler industry, is defined by both the host genome and gut microbiota. At present, it is not known how gut microbiota contribute to the growth of Dahen broilers, a commercially important breed in China. In this study, we used metagenome sequencing to compare the taxonomic composition and functional implications of cecal microbiota in fast-growing Dahen broilers and slow-growing Tibetan chickens. A total of 2,207,811 unique genes were assembled in the non-redundant set, and 99% of them were taxonomically annotated as having a bacterial origin. The fast-growing group displayed a higher alpha diversity than the slow-growing group in terms of ACE, Chao1, and Good's coverage statistics. The two groups presented also significantly different (P < 0.05) relative abundances of the genera Collinsella, Olsenella, Pyramidobacter, Basidiobolus, and Mieseafarmvirus, along with that of eight species (e.g., Olsenella timonensis and Victivallis sp. Marseille Q1083). Although not statistically significant, we found a higher expression of several energy metabolism-related eggNOG terms in the fast-growing group. In summary, the present study identifies gut microbiota associated with growth performance in Dahen broilers and offers new tools for gut microbiome-related intervention in this breed.}, }
@article {pmid41017911, year = {2025}, author = {Devarajalu, P and Attri, SV and Kumar, J and Dutta, S and Kabeerdoss, J}, title = {Characterization of gut microbiota signatures in Indian preterm infants with necrotizing enterocolitis: a shotgun metagenomic approach.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1649384}, pmid = {41017911}, issn = {2235-2988}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Infant, Premature ; India/epidemiology ; Infant, Newborn ; *Enterocolitis, Necrotizing/microbiology/epidemiology ; Feces/microbiology ; *Metagenomics/methods ; Male ; Female ; Enterobacteriaceae/genetics/isolation &amp; purification/classification ; }, abstract = {INTRODUCTION: Necrotizing enterocolitis (NEC) is an inflammatory bowel disease that primarily affects preterm infants. Predisposing risk factors for NEC include prematurity, formula feeding, anemia, and sepsis. To date, no studies have investigated the gut microbiota of preterm infants with NEC in India.<br><br>METHOD: In the current study, shotgun metagenomic sequencing was performed on fecal samples from premature infants with NEC and healthy preterm infants (n = 24). Sequencing was conducted using the NovaSeq X Plus platform, generating 2 &#xd7; 150 bp paired-end reads. The infants were matched based on gestational age and postnatal age.<br><br>RESULT: The median time to NEC diagnosis was 9 days (range: 1-30 days). Taxonomic analysis revealed a high prevalence of Enterobacteriaceae at the family level, with the genera Klebsiella and Escherichia particularly prominent in neonates with NEC. No statistically significant differences in alpha or beta diversity were observed between stool samples from infants with and without NEC. Linear regression analysis demonstrated that Enterobacteriaceae were significantly more abundant in stool samples from infants with NEC than without NEC (q < 0.05). Differential abundance analysis using Linear Discriminant Analysis Effect Size (LEfSe) identified Klebsiella pneumoniae and Escherichia coli as enriched in the gut microbiota of preterm infants with NEC. Functional analysis revealed an increase in genes associated with lipopolysaccharide (LPS) O-antigen, the type IV secretion system (T4SS), the L-rhamnose pathway, quorum sensing, and iron transporters, including ABC transporters, in stool samples from infants with NEC.<br><br>CONCLUSION: The high prevalence of Enterobacteriaceae and enrichment of LPS O-antigen and T4SS genes may be associated with NEC in Indian preterm infants.}, }
@article {pmid41017909, year = {2025}, author = {Maan, S and Batra, K and Rajendhran, J and Joseph, R and Singh, VK and Chaudhary, D and Sindhu, S and Kadian, V and Kumar, A and Maan, NS and Mor, S}, title = {Exploring viral diversity in diarrheic porcine feces: a metagenomic analysis from an Indian swine farm.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1653342}, pmid = {41017909}, issn = {2235-2988}, mesh = {Animals ; Swine ; *Feces/virology ; *Swine Diseases/virology/epidemiology ; *Metagenomics ; India/epidemiology ; *Viruses/genetics/classification/isolation &amp; purification ; Phylogeny ; *Diarrhea/veterinary/virology ; Farms ; Genome, Viral ; Virome ; *Virus Diseases/veterinary/virology ; High-Throughput Nucleotide Sequencing ; }, abstract = {BACKGROUND: Pig husbandry is a vital sector in India, providing nutritional security and employment for marginalized communities. Pigs are advantageous due to high reproduction rates and fecundity, shorter generation intervals, and efficient feed conversion, requiring minimal housing. However, the swine industry encounters significant disease challenges, particularly viral gastroenteritis, which poses serious public health risks, especially in developing countries. Pigs serve as natural reservoirs and amplifiers for numerous viruses with zoonotic potential, making disease surveillance essential.<br><br>MATERIALS: In this study, we conducted a metagenomic analysis of 15 fecal samples from diarrheic pigs on a farm in India, marking the first exploration of the fecal virome diversity in this region. Our next-generation sequencing approach has enabled the unbiased detection of multiple viral agents in the porcine fecal samples, detecting both known and novel viral agents without prior target knowledge.<br><br>RESULTS: The key and novel viruses obtained in our study were porcine circovirus, porcine parvovirus 7, porcine mamastrovirus 3, porcine sapelovirus A, and porcine enterovirus G. This work resulted in the generation of full genomes for multiple porcine viruses, including Circovirus, Enterovirus, Sapelovirus, and Mamastrovirus, along with partial genomes of Parvovirus, Picobirnavirus, Porcine stool-associated RNA virus (Porcine Posavirus), Kobuvirus, and Rotavirus, all subjected to phylogenetic analysis.<br><br>CONCLUSION: Our survey indicates frequent co-infections with diverse viruses, creating conducive environments for viral recombination and reassortment. Continuous surveillance of viral pathogens in animal populations is essential for understanding the dynamics of both known and novel viruses and for detecting emerging pathogens, along with their zoonotic and pathogenic potential.}, }
@article {pmid41017724, year = {2025}, author = {Zhang, Y and Mo, C and He, X and Xiao, Q and Yang, X}, title = {Gut microbial community of patients with Parkinson's disease analyzed using metagenome-assembled genomes.}, journal = {Neural regeneration research}, volume = {}, number = {}, pages = {}, doi = {10.4103/NRR.NRR-D-25-00420}, pmid = {41017724}, issn = {1673-5374}, abstract = {Previous investigations into gut microbiota dysbiosis in patients with Parkinson's disease have relied on 16S rRNA amplicon sequencing and assembly-free metagenomic approaches. However, there is an urgent need to study the function of the gut microbiome at the genome level using metagenome-assembled genomes. Here, we conducted single-sample metagenomic binning analysis using shotgun metagenomic sequencing data and retrieved 2837 metagenomeassembled genomes to explore the gut microbiota profile at the genome level. Reconstructing microbial genomes from metagenomic sequences greatly enriched the diversity and number of microbial genomes, especially those of uncultivable strains. By integrating the analysis of metagenome-assembled genomes with clinical parameters, we observed higher α-diversity indexes and a very different composition of microbial communities in patients with Parkinson's disease. We also identified microbial species and metagenome-assembled genomes that were significantly associated with clinical characteristics, including disease severity, medication, motor complications, and non-motor symptoms. The genes of Parkinson's disease severity-associated metagenomeassembled genomes were distributed across multiple pathways, such as carbon metabolism, phosphonate metabolism, carbohydrate metabolism, amino acid metabolism, fatty acid metabolism, bile acid metabolism, metabolism of cofactors and vitamins, neuroprotective molecules, immunogenic components, toxic metabolites, translation, and bacterial secretion. Our work provides a comprehensive resource for investigating the gut microbiota-Parkinson's disease relationship at the genome level, which may enhance our comprehension of the underlying mechanisms of this disease.}, }
@article {pmid41017070, year = {2025}, author = {Guo, C and Pan, Y and Yu, J and Yao, L and He, Y and Cui, J and Gao, M and Pang, Y}, title = {Disseminated Blastomycosis Mimicking Tuberculosis, China.}, journal = {Emerging infectious diseases}, volume = {31}, number = {10}, pages = {2046-2048}, doi = {10.3201/eid3110.250671}, pmid = {41017070}, issn = {1080-6059}, mesh = {Humans ; Male ; *Blastomyces/genetics/isolation &amp; purification ; *Blastomycosis/diagnosis/drug therapy/microbiology ; China ; Diagnosis, Differential ; Tomography, X-Ray Computed ; *Tuberculosis/diagnosis ; Adult ; }, abstract = {Blastomycosis is endemic in central and southern North America but rare in China. It can mimic community-acquired pneumonia, tuberculosis, or cancer. We describe a patient who initially had tuberculosis diagnosed and later had blastomycosis diagnosed through metagenomic detection, which aided diagnosis and treatment. Clinicians should consider blastomycosis in differential diagnoses for respiratory diseases.}, }
@article {pmid41016664, year = {2025}, author = {Dong, Y and Zheng, JS and Yang, Y and Wang, T and Li, F and Wu, P and Lai, Y and Wang, Y and He, X and Zhang, P and Zhang, S and Wu, N and Li, S and Yuan, J and Shan, D and Liu, X and Liu, G and Hu, Y and Pan, A and Pan, XF}, title = {Associations between Combined Healthy Lifestyle and Adverse Birth Outcomes in Two Prospective Cohorts: Roles of Gut Microbiota and Serum Metabolites.}, journal = {The American journal of clinical nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ajcnut.2025.09.036}, pmid = {41016664}, issn = {1938-3207}, abstract = {BACKGROUND: Maternal lifestyle factors are reported to be associated with adverse birth outcomes (ABOs). These factors may also dynamically influence gut microbiota composition and serum metabolic profiles.<br><br>OBJECTIVE: To investigate the associations between combined healthy lifestyle and ABOs, and the mediating roles of gut microbiota and serum metabolites.<br><br>METHODS: This study was conducted based on the Tongji-Huaxi-Shuangliu Birth Cohort (THSBC), comprising 1086 participants with repeated multi-omics data collected at three time points. An independent validation was performed using 161 participants from the Huaxi Birth Cohort (HBC), with available multi-omics data at five time points. Participants were classified into three lifestyle categories (unhealthy, low healthy, and highly healthy) according to diet, physical activity, smoking, drinking, sleep, and body mass index. Gut microbiota were characterized using 16S rRNA gene sequencing in the THSBC and metagenomics in the HBC, while serum metabolites were profiled using untargeted liquid chromatography-mass spectrometry. Clinical data on birth outcomes, such as gestational age, birth weight, and sex were collected in the THSBC.<br><br>RESULTS: A highly healthy lifestyle was associated with lower risks of macrosomia (MAC) (odds ratio: 0.43; 95% confidence interval: 0.33, 0.57), preterm birth (PTB) (0.60; 0.46, 0.79), and large for gestational age (LGA) (0.44; 0.35, 0.56). Among the identified mediators, gut microbiota and serum metabolites, including Eisenbergiella, Tyzzerella, Megamonas, pro-Ile, and 1-amino-1-cyclobutane-carboxylic acid were negatively associated with a healthy lifestyle, while Lachnospiraceae NK4A136 group, 4-methoxyestrone, and LPC (0:0/18:3) were positively associated. Mediation analyses showed that Eisenbergiella and 4-methoxyestrone explained 11.4% and 13.0% of the inverse association between a highly healthy lifestyle and PTB, respectively, while the other microbiota and metabolites mediated 5%-7% of the associations with MAC and LGA.<br><br>CONCLUSION: Maternal healthy lifestyle was associated with lower risks of ABOs, with gut microbiota and serum metabolites serving as important mediators in these relationships.}, }
@article {pmid39345108, year = {2025}, author = {Yu, L and Mu, C and Lan, X and Cheng, L and Li, H and Li, Z and Feng, Y and Cui, Z}, title = {A Patient With Cryptococcal Meningitis Accompanied With Acute Intracranial Hypertension Treated by Ventricular Abdominal-wall Drainage.}, journal = {The Journal of craniofacial surgery}, volume = {36}, number = {2}, pages = {e109-e111}, doi = {10.1097/SCS.0000000000010699}, pmid = {39345108}, issn = {1536-3732}, mesh = {Humans ; *Meningitis, Cryptococcal/complications ; *Intracranial Hypertension/etiology/therapy/surgery ; *Drainage/methods ; Male ; Antifungal Agents/therapeutic use ; *Abdominal Wall/surgery ; Tomography, X-Ray Computed ; Acute Disease ; Adult ; }, abstract = {Intracranial hypertension is considered a common and severe complication of cryptococcal meningitis (CM), contributing to early mortality and neurological sequelae. Timely and effective control of elevated intracranial pressure is crucial for the management of CM. Herein, the authors present a case of ventricular abdominal wall drainage for CM accompanied with acute intracranial hypertension. Notably, the patient has a history of taking immunosuppressants for thoracic and abdominal diffuse lymphangiomatosis. After continuous drainage of cerebrospinal fluid combined with standardized antifungal treatment, the patient recovered well.}, }
@article {pmid41019634, year = {2023}, author = {McCulloch, JA and Badger, JH and Cannon, N and Rodrigues, RR and Valencia, M and Barb, JJ and Fernandes, MR and Balaji, A and Crowson, L and O'hUigin, C and Dzutsev, A and Trinchieri, G}, title = {JAMS - A framework for the taxonomic and functional exploration of microbiological genomic data.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.03.03.531026}, pmid = {41019634}, issn = {2692-8205}, abstract = {Shotgun microbiome sequencing analysis presents several challenges to accurately and consistently depict sample composition and functional potential. Here we present a two-part framework - JAMS (Just a Microbiology System) - whereby with raw fastq files and metadata as input, meaningful analysis within a sample and between a sample can be performed with ease for either shotgun or 16S sequences. JAMS is the first package to provide seamless deconvolution of functions into their taxonomic contributors. We validated our JAMS framework on two human gut shotgun metagenome test datasets against the popular tool MetaPhlAn 4. We further demonstrate the application of the JAMS package, particularly the plotting functions, on a mouse shotgun dataset.}, }
@article {pmid41016593, year = {2025}, author = {Ma, S and Li, Y and Chen, C and Dong, Y and Huang, P and Tu, R and Liu, X and Zhou, R and Wu, C}, title = {Metabolic interactions drive microbial community succession and functional expression of Nongxiangxing (Strong-flavor) daqu.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2025.09.052}, pmid = {41016593}, issn = {2090-1224}, abstract = {INTRODUCTION: Nongxiangxing daqu is a wheat-based fermentation starter used in the production of Baijiu (a traditional Chinese distilled spirit), whose fermentation process during storage directly affects its quality. However, the dynamics of microbial succession and metabolism during daqu storage, particularly the functional contributions of specific microorganisms to enzyme formation and their metabolic interactions, remain unclear.<br><br>OBJECTIVES: This study aimed to investigate the temporal dynamics of microbial community structure, function, and enzymatic activity in daqu during storage, with a focus on metabolic interactions such as cross-feeding and metabolic division of labor (MDOL).<br><br>METHODS: Metagenomic and metaproteomic analyses were integrated to profile microbial taxa, functional genes, and protein expression across storage time points. Weighted gene co-expression network analysis (WGCNA) linked gene modules to storage time. Genome-scale metabolic models (GEMs) were constructed to infer metabolic interaction networks among microbes.<br><br>RESULTS: Paecilomyces variotii, Rasamsonia emersonii, Rhizopus microsporus, Rhizopus delemar, Kroppenstedtia eburnea, and Weissella confusa were dominant species. In total, 14,588 protein groups were identified, including 6,801 enzymes enriched in carbohydrate, amino acid, and energy metabolism. Glucosidase activity was primarily attributed to Rasamsonia, Thermoascus, Aspergillus, Thermomyces, and Paecilomyces. Functional genes and enzymes declined sharply after month 1, reached a nadir at month 3, and partially rebounded by month 4. WGCNA identified 16 gene modules associated with storage (maximum r&#x202f;=&#x202f;0.97, P < 0.01). Cross-feeding patterns were identified among Weissella confusa, Kroppenstedtia eburnea, Saccharopolyspora rectivirgula, and Enterobacteriaceae. The MDOL model revealed cooperative metabolic roles among Actinomycetota, Bacillota, Ascomycota, and Mucoromycota in converting raw materials into flavor compounds.<br><br>CONCLUSION: These findings improve the understanding of microecological dynamics during daqu storage and provide a theoretical basis for regulating and optimizing the fermentation process during the storage period.}, }
@article {pmid41016209, year = {2025}, author = {Zhao, Q and Yu, C and Liu, X and Hu, X and Yang, Q}, title = {Multi-omics reveals the systematical influence of composite heavy metal(loid)s on soil microbial function: Elemental cycling and microbial adaptation mechanisms.}, journal = {Journal of hazardous materials}, volume = {498}, number = {}, pages = {139973}, doi = {10.1016/j.jhazmat.2025.139973}, pmid = {41016209}, issn = {1873-3336}, abstract = {As the core of soil material cycling, soil microecosystems contaminated by combined heavy metal(loid)s have attracted widespread concern. Previous studies mostly focused on community-level ecological functions, neglecting genomic-level investigations and comprehensive microbial adaptation mechanisms. Here, we integrated multi-omics (metagenomics, genome assemblies, comparative genomics) with field and lab studies to explore responses from community to genomic scales. We found that metal(loid)s altered the assembly of microbial functional genes and weakened functional networks linking carbon, nitrogen, phosphorus, and sulfur cycling. They reduced the potential of carbohydrate metabolism, carbon fixation, and sulfur metabolism involved in protein synthesis and disrupted normal organic matter decomposition (via certain CAZymes). Conversely, they increased the potential of methanogenesis, denitrification, and organic phosphorus mineralization, as well as stimulating dissimilatory sulfate reduction and sulfur disproportionation. Microbes employed multi-level strategies to combat persistent heavy metal(loid)s stress, including reducing metal ion uptake, facilitating intracellular detoxification, and activating efflux pathways. They underwent adaptive evolution through mechanisms such as enhancing the synthesis and transportation of siderophores, strengthening DNA damage repair, and promoting genome streamlining. Notably, our analysis revealed that horizontal gene transfer, mediated by mobile genetic elements, drives the acquisition of resistance genes. This study provides systematic genomic evidence for such adaptive mechanisms in functional microbes, greatly advancing our understanding of their bioremediation potential.}, }
@article {pmid41016077, year = {2025}, author = {Wirth, R and Pap, B and Szuhaj, M and Bagi, Z and Farkas, Z and Kovács, KL and Maróti, G}, title = {Functional resistomes in municipal wastewater treatment plants pose challenges to public health.}, journal = {Water research}, volume = {288}, number = {Pt B}, pages = {124663}, doi = {10.1016/j.watres.2025.124663}, pmid = {41016077}, issn = {1879-2448}, abstract = {Wastewater treatment plants (WWTPs) are essential for controlling antimicrobial resistance, but also serve as hotspots for resistance gene persistence and dissemination. In this study, a novel combinatory approach using genome-resolved metagenomics and metatranscriptomics was employed to examine the resistome of a full-scale municipal WWTP across treatment stages and seasons. Results reveal that although human-associated, potentially pathogenic, antibiotic resistance gene (ARG)-harbouring metagenome-assembled genomes (ARBMAGs) declined in abundance during treatment, many ARGs remained transcriptionally active, particularly efflux, beta-lactam, and macrolide-lincosamide-streptogramin genes conferring resistance against fluoroquinolones, cephalosporins, and macrolides. Environment and treatment-adapted microbes become increasingly dominant, with plasmids identified as major vectors of mobile resistance. Dominant potential pathogenic human-associated ARBMAGs were abundant during spring and summer, whereas environmental ARBMAGs predominated in colder seasons. Fluoroquinolone resistance genes displayed varying expression levels across ARBMAG types, with the lowest levels observed during the anaerobic phase of treatment. Although clinically relevant ARGs were detected at low relative abundance and expression levels, one of the carriers was Citrobacter freundii ARBMAG, a human-associated potential pathogen. These findings underscore the value of integrating genomic and transcriptomic data to assess site-specific and ARBMAG-type-specific resistance and to strengthen antibiotic resistance monitoring in engineered systems.}, }
@article {pmid41015769, year = {2025}, author = {Sheppard, SK and Arning, N and Eyre, DW and Wilson, DJ}, title = {Machine learning and statistical inference in microbial population genomics.}, journal = {Genome biology}, volume = {26}, number = {1}, pages = {313}, pmid = {41015769}, issn = {1474-760X}, support = {088786/C/09/Z//Wellcome/ ; 101237/Z/13/B//Wellcome/ ; MR/L015080/1//UK Research and Innovation/ ; BB/M011224/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 101237/Z/13/B//Royal Society/ ; }, mesh = {*Machine Learning ; *Genomics/methods ; *Metagenomics/methods ; *Genome, Microbial ; }, abstract = {The availability of large genome datasets has changed the microbiology research landscape. Analyzing such data requires computationally demanding analyses, and new approaches have come from different data analysis philosophies. Machine learning and statistical inference have overlapping knowledge discovery aims and approaches. However, machine learning focuses on optimizing prediction, whereas statistical inference focuses on understanding the processes relating variables. In this review, we outline the different aspirations, precepts, and resulting methodologies, with examples from microbial genomics. Emphasizing complementarity, we argue that the combination and synthesis of machine learning and statistics has potential for pathogen research in the big data era.}, }
@article {pmid41015602, year = {2025}, author = {Nazrin, MRR and Pavan, JS and Gouda, MNR and Kumaranag, KM and Suroshe, SS and Kamil, D and Subramanian, S}, title = {Host-Driven Functional Divergence in Gut Microbiota of Honeybees Apis cerana and Apis mellifera: Implications for Pollination, Nutrition, and Sustainable Apiculture.}, journal = {Current microbiology}, volume = {82}, number = {11}, pages = {531}, pmid = {41015602}, issn = {1432-0991}, mesh = {Bees/microbiology/physiology ; Animals ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Pollination ; }, abstract = {Honeybees are indispensable in sustaining natural ecosystems and global crop production by pollinating key food crops. Understanding their gut microbiota is crucial for insights into their health, nutrition, and behavior, with broader ecological and agricultural relevance. This study compares the gut microbiota of Apis cerana and Apis mellifera, focusing on bacterial composition, diversity, and functional roles. Using culture-dependent and metagenomic methods, core bacteria such as Lactobacillus, Fructobacillus, Gilliamella apicola, Bartonella apis, and Snodgrassella alvi were identified, linked to carbohydrate and nitrogen metabolism, immune modulation, and polysaccharide degradation. A. mellifera exhibited greater microbial and functional diversity, reflected in higher Shannon (1.22 vs. 1.08) and Simpson (0.675 vs. 0.655) indices. Strong intraspecies correlations and weaker interspecies correlations (Pearson's r = 0.6486) indicated distinct microbial profiles, supported by PCA (75.3% variation) and Adonis test (P = 0.04, R[2] = 0.723). Functional analysis via MG-RAST and UniFrac-based PCoA showed species-specific differences in key metabolic pathways. Enzymatic profiling revealed Fructobacillus fructosus with high invertase activity (7.31 ± 0.30) and Apilactobacillus apinorum with strong pectinolytic activity (4.707 ± 0.36), enhancing honeybee nutrition. These findings have significant implications for pollination efficiency, probiotic development, and sustainable apiculture, ultimately supporting conservation strategies and the resilience of honeybee populations.}, }
@article {pmid41015591, year = {2025}, author = {Raziq, K and Saleem, R and Zafar, S and Sanaullah, T and Nazir, MM and Ummara, UE and Abbasi, A}, title = {Environmental resistomes and antimicrobial resistance: integrating the One Health framework.}, journal = {Naunyn-Schmiedeberg's archives of pharmacology}, volume = {}, number = {}, pages = {}, pmid = {41015591}, issn = {1432-1912}, abstract = {Antimicrobial resistance (AMR) has emerged as a critical global health challenge, exacerbated by the interconnected dynamics of human, animal, and environmental health systems. The "One Health" approach, which integrates these domains, offers a comprehensive framework for addressing AMR at its roots. This review explores the environmental dimension of AMR by examining the role of environmental microbiomes as reservoirs and transmission vectors of antimicrobial resistance genes (ARGs). It highlights emerging evidence, transmission pathways, detection methodologies, and policy gaps, with an emphasis on low- and middle-income countries (LMICs). An in-depth literature synthesis was conducted across environmental, clinical, and molecular microbiology studies to understand the eco-evolutionary dynamics of resistance, routes of ARG transmission, and effectiveness of current surveillance models. Emphasis was placed on novel detection technologies and integrated policy frameworks. Environmental resistomes present in soil, water, air, and waste play a pivotal yet underappreciated role in ARG dissemination via horizontal gene transfer, mobile genetic elements, and co-selectors like heavy metals and biocides. The complexity of microbial communities in diverse ecological matrices fosters the persistence and evolution of resistance. Current surveillance systems often neglect environmental inputs, particularly in LMICs, limiting the effectiveness of AMR mitigation efforts. A paradigm shift is required to recognize the environmental microbiome as a central component of AMR. Integrated "One Health" strategies, improved environmental surveillance, policy reforms, and novel technological interventions are critical for global AMR control. Bridging the research-policy gap and empowering local surveillance infrastructure can significantly enhance resistance management and public health outcomes.}, }
@article {pmid41015495, year = {2025}, author = {Castells-Nobau, A and Fumagalli, A and Del Castillo-Izquierdo, &#xc1; and Rosell-Díaz, M and de la Vega-Correa, L and Samulėnaitė, S and Motger-Albertí, A and Arnoriaga-Rodríguez, M and Garre-Olmo, J and Puig, J and Ramos, R and Burokas, A and Coll, C and Zapata-Tona, C and Perez-Brocal, V and Ramio, L and Moya, A and Swann, J and Martín-García, E and Maldonado, R and Fernández-Real, JM and Mayneris-Perxachs, J}, title = {Gut microbial modulation of 3-hydroxyanthranilic acid and dopaminergic signalling influences attention in obesity.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2025-336391}, pmid = {41015495}, issn = {1468-3288}, abstract = {BACKGROUND: Obesity-related alterations in the gut microbiota have been linked to cognitive decline, yet their relationship with attention remains poorly understood.<br><br>OBJECTIVE: To evaluate the possible relationships among gut metagenomics, plasma metabolomics and attention.<br><br>DESIGN: We conducted faecal shotgun metagenomics and targeted plasma tryptophan metabolomics across three independent cohorts (n=156, n=124, n=804) with functional validations in preclinical models, including three faecal microbiota transplantation (FMT) experiments in mice and Drosophila melanogaster.<br><br>RESULTS: Obesity was consistently associated with reduced attention. Metagenomics analyses identified Proteobacteria species and microbial functions related to tryptophan biosynthesis from anthranilic acid (AA) as negatively associated with attention in obesity. Plasma tryptophan metabolic profiling and machine learning revealed that 3-hydroxyanthranilic acid (3-HAA) was positively associated with attention, particularly in obesity, while AA showed a negative association. Bariatric surgery improved attention and enriched microbial species linked to attention. In mice, diet-induced obesity (DIO) and microbiota depletion reduced 3-HAA and 5-hydroxy-indole acetic acid (5-HIAA) concentrations in the prefrontal cortex (PFC), which were restored by FMT. Global metabolic profiling (>600 metabolites) of PFC from the FMT group identified 3-HAA and the tryptophan and tyrosine pathways among the most significant in mice receiving microbiota from high-attention donors. A second FMT experiment also revealed a consistent enrichment of the tryptophan and tyrosine metabolism at the transcriptional level in the PFC, with Haao (3-hydroxyantrhanilic acid dioxygenase) and Aox4 (aldehyde oxidase 4), key in 3-HAA and 5-HIAA degradation, among the significantly regulated genes. In a third FMT study, attentional traits were transmitted from humans to mice alongside modulation of serotonergic and dopaminergic pathways. In Drosophila, mono-colonisation with Enterobacter cloacae and DIO induced attention deficit-like behaviours, which were mitigated by 3-HAA supplementation.<br><br>CONCLUSIONS: We have identified the microbiota and 3-HAA as potential therapeutic targets to improve attention, especially in obesity.}, }
@article {pmid41015376, year = {2025}, author = {Zhao, JX and Wang, XY and Zhang, X and Tang, LY and Xie, SC and Lv, YH and Zheng, Z and Gao, YQ and Jiang, J and Zhang, XX and Ma, H}, title = {Toxoplasma gondii alters gut microbiota and systemic metabolism in cats: A multi-omics approach.}, journal = {Veterinary journal (London, England : 1997)}, volume = {}, number = {}, pages = {106455}, doi = {10.1016/j.tvjl.2025.106455}, pmid = {41015376}, issn = {1532-2971}, abstract = {Toxoplasma gondii (T. gondii) is an obligate intracellular parasite with a complex life cycle that culminates in cats-its only definitive host. While its immunological impact is well studied, how T. gondii shapes the feline gut microbiota and systemic metabolism remains largely unexplored. To investigate host-parasite-microbiome interactions, we performed a multi-omics study combining metagenomic sequencing and untargeted serum metabolomics in cats before and after T. gondii infection. Fecal samples were used to construct a comprehensive microbial gene catalog and assess functional shifts, while serum samples were analyzed via liquid chromatography-tandem mass spectrometry (LC-MS/MS) to capture systemic metabolic changes. Infection with T. gondii, particularly during its sexual replication phase, significantly disrupted gut microbial diversity, composition, and function. Functional annotation revealed downregulation of microbial genes involved in vitamin, cofactor, and energy metabolism, alongside upregulation of carbohydrate metabolism pathways. Concurrently, metabolomic profiling showed marked alterations in lipid profiles, amino acid pathways, and folate-mediated one-carbon metabolism. Integrated analysis uncovered strong correlations between specific microbial taxa-such as Bifidobacterium adolescentis and Ligilactobacillus animalis-and host metabolites, underscoring a tight link between microbial function and host metabolic responses to infection. To our knowledge, this is the first study to comprehensively map the microbiome and metabolic landscape of T. gondii infection in the feline host. Our findings reveal profound parasite-induced shifts in microbial function and systemic metabolism, offering new insights into the molecular interplay between host, parasite, and microbiota. These insights may inform future strategies for therapeutic modulation of host responses in toxoplasmosis.}, }
@article {pmid41015315, year = {2025}, author = {Miao, H and Zeng, W and Zhan, M and Hao, X and Wang, R and Peng, Y}, title = {Overcoming elemental sulfur bioavailability limitations with sponge iron coupling for enhanced nitrate removal: Novel perspective on electron transfer and iron-nitrogen-sulfur metabolism.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {133390}, doi = {10.1016/j.biortech.2025.133390}, pmid = {41015315}, issn = {1873-2976}, abstract = {This study developed a novel sponge iron (sFe[0]) and elemental sulfur (S[0]) coupled autotrophic denitrification biofilter (S[0]-sFe[0]AD). At the ratio Fe[0] to S[0] of 0.5 and a hydraulic retention time of 1.5 h, the system achieved high nitrate and phosphate removal rates of 969.7 mgN·L[-1]·d[-1] and 56.1 mgP·L[-1]·d[-1], with efficiencies over 98.5 %. Activated biochemical sulfidogenic pathways enabled in situ regeneration of highly bioavailable FeS. This process not only expanded electron donor pool but also reduced sulfate production by facilitating multi-pathway denitrification. Moreover, FeS-mediated direct extracellular electron transfer promoted iron-sulfur redox cycling. Metagenomic analysis further revealed enhanced iron and energy metabolism within the coupled system. The enriched iron-sulfur redox bacteria (Thiobacillus, Desulfurivibrio and Geothrix) and genes (narB, mtrC, sox, fccAB and sir) facilitated the establishment of a self-sustaining iron-sulfur cycle, thereby extending system longevity. This study provides novel insights for developing efficient iron-sulfur coupled autotrophic denitrification technology for sustainable wastewater treatment.}, }
@article {pmid41015306, year = {2025}, author = {Hou, DJ and Guo, WL and Yang, HW and Liu, QR and Fan, NS and Jin, RC}, title = {Behaviors and adaptive strategies of anammox microbiota in response to typical ionic liquid: Metabolic compensation and gene regulation.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {133395}, doi = {10.1016/j.biortech.2025.133395}, pmid = {41015306}, issn = {1873-2976}, abstract = {Ionic liquids (ILs) have been used to replace organic solvents, thereby causing challenges for wastewater treatment. Anaerobic ammonium oxidation (anammox) had been recognized to treat high-strength ammonium wastewater, but its response to ILs remains unclear. Metagenomic sequencing, granule characterization and molecular docking simulation were employed to investigate the comprehensive effects of 1-ethyl-3-methylimidazolium acetate ([EMIM][Ac]) on anammox consortia. [EMIM][Ac] of 2 mg L[-1] reduced the specific anammox activity (SAA) by 46.0 %. [EMIM][Ac] also induced oxidative stress. The higher abundance of denitrifying bacteria and functional genes (nirK and nirS) compensated for the reduced nitrogen removal efficiency. In P2, the total abundance of nirK and nirS in R1 was 16.2 % higher than its initial value, and also 9.6 % higher than that in R0. This study elucidated how anammox microbiota resisted ILs via metabolic regulation and EPS secretion, providing a theoretical support for improving the feasibility and efficiency of anammox-based wastewater treatment systems.}, }
@article {pmid41015263, year = {2025}, author = {Moore, CM and Secor, EA and Fairbanks-Mahnke, A and Everman, JL and Elhawary, JR and Witonsky, JI and Pruesse, E and Chang, CH and Contreras, MG and Eng, C and Canales, K and Rosado, T and Hu, D and Huntsman, S and Jackson, ND and Li, Y and Lopez, N and Valentin, AM and Medina, V and Montanez-Lopez, CA and Morin, A and Nieves, NA and Oh, SS and Otero, RA and Colon, R and Rodriguez, L and Sajuthi, SP and Salazar, S and Serrano, G and Morales, EV and Vazquez, G and Morales, NV and Williams, BJM and Zhang, P and Sheppard, D and Santana, JRR and Seibold, MA}, title = {Independent and interactive effects of viral species on early-life lower respiratory tract illness.}, journal = {The Journal of infection}, volume = {}, number = {}, pages = {106616}, doi = {10.1016/j.jinf.2025.106616}, pmid = {41015263}, issn = {1532-2742}, abstract = {OBJECTIVES: To determine the association between viral species and odds of severe lower respiratory tract illnesses (sLRI) versus upper respiratory illness (URI) among children under 2 years of age.<br><br>METHODS: Infants (n=2,061) enrolled in the Puerto Rican Infant Metagenomic and Epidemiologic Study of Respiratory Outcomes were surveilled for respiratory illnesses until age 2 years (March 2020 to April 2024). Nasal swabs from 1,363 illnesses (774 participants) were screened for 21 pathogens.<br><br>RESULTS: RSV infections occurred in 23% of sLRIs and increased odds of sLRI vs URI (OR=9.28; 95% CI, 5.43-15.85). Metapneumovirus, parainfluenza, and non-SARS-CoV-2 coronavirus also increased odds of sLRIs, while SARS-CoV-2 was associated with lower risk of sLRIs. Rhinovirus (43%) and bocavirus (16.1%) were commonly detected, but were not associated with sLRI risk. Co-infection with multiple viral species was associated with 2.92-fold greater odds of sLRI (95% CI, 2.05-4.16) compared to single viral species infections. Rhinovirus-bocavirus was the most common co-infection, and interaction between these viruses was associated with increased odds of sLRI.<br><br>CONCLUSIONS: Diverse viral pathogens drive early-life sLRIs. Some (e.g. RSV and metapneumovirus) have intrinsic propensity to cause sLRIs, while other viruses' lower airway pathogenicity depends on other factors, including co-infection.}, }
@article {pmid41015172, year = {2025}, author = {Luo, S and Yuan, J and Song, Y and Qi, J and Zhu, M and Feng, H and Zhao, Y and Mei, W and Fu, F and Li, X and Song, C}, title = {Bacterial network complexity drives carbon, nitrogen and phosphorus metabolism potential under short-term soil water content changes in wetlands.}, journal = {Environmental research}, volume = {}, number = {}, pages = {122952}, doi = {10.1016/j.envres.2025.122952}, pmid = {41015172}, issn = {1096-0953}, abstract = {Wetland soil microbial communities play pivotal roles in biogeochemical cycling; however, how their network complexity mediates carbon (C), nitrogen (N), and phosphorus (P) metabolism in response to soil water content (SWC) changes remains unclear. In this study, soil samples from the Zhalong, Momoge and Xianghai wetlands in Songnen Plain of China were incubated under natural (CK), drought (10% SWC), and high SWC (50% SWC) conditions, followed by metagenomic sequencing to evaluate the impact of SWC changes on bacterial community structure and function. The results showed that soil bacterial diversity and network complexity decreased under drought but recovered under high SWC, with Proteobacteria and Actinobacteria displaying divergent responses. C fixation pathways (rTCA and DC-HB cycles) were significantly enriched under 50% SWC, which correlated strongly with enhanced bacterial interactions. The abundance of denitrification genes (norBC, nosZ) decreased under drought but increased under high SWC. P metabolism (purine metabolism and two-component systems) showed strong SWC dependence, with key genes (PstS, phnDC) increased in abundance under 50% SWC. Notably, bacterial network complexity tightly coupled with metabolic pathways, indicating SWC driven community restructuring regulates wetland soil C, N and P cycling. These findings underscore the critical importance of hydrological management in maintaining bacterial-mediated nutrient cycling functions of wetland ecosystem under climate change.}, }
@article {pmid41015028, year = {2025}, author = {Luan, T and Cepeda-Espinoza, VP and Liu, B and Bowen, Z and Ayyangar, U and Almeida, M and Koren, S and Treangen, TJ and Porter, A and Pop, M}, title = {Reference-guided assembly of metagenomes with MetaCompass.}, journal = {Cell reports methods}, volume = {}, number = {}, pages = {101186}, doi = {10.1016/j.crmeth.2025.101186}, pmid = {41015028}, issn = {2667-2375}, abstract = {Metagenomic studies have primarily relied on de novo assembly for reconstructing genes and genomes from microbial mixtures. While reference-guided approaches have been employed in the assembly of single organisms, they have not been used in a metagenomic context. Here, we develop an effective approach for reference-guided metagenomic assembly that can complement and improve upon de novo metagenomic assembly methods for certain organisms. Such approaches will be increasingly useful as more genomes are sequenced and made publicly available.}, }
@article {pmid41015012, year = {2025}, author = {Zhou, Y and Gu, WH and Bai, JF and Wang, RX and Zhang, CL and Guo, YG and Lu, C and Chen, SP}, title = {Metagenomic insights into the synergistic properties and mechanisms of sludge microbial communities degrading polystyrene and polypropylene.}, journal = {Journal of hazardous materials}, volume = {498}, number = {}, pages = {139929}, doi = {10.1016/j.jhazmat.2025.139929}, pmid = {41015012}, issn = {1873-3336}, abstract = {Microplastic pollution is a prominent global environmental challenge, with polystyrene (PS) and polypropylene (PP) accumulating over time due to poor degradability, harboring ecological risks. This study used metagenomics to dissect the synergistic characteristics and biodegradation mechanisms of a sludge microbial consortium-enriched from plastic-contaminated industrial activated sludge-with dual-degradation capacity for PS/PP. Bacillota and Pseudomonadota are the dominant phyla, with Bacillus initiating the degradation process and Achromobacter regulating intermediate metabolism, forming an "initiation-metabolism" network. A 60-day experiment revealed direct degradation without pretreatment, with weight loss rates of 13.4 ± 2.3 % for PS microplastics and 23.2 ± 2.4 % for PP microplastics. Multi-dimensional characterization revealed surface disruption, reduced hydrophobicity, and decreased molecular weight in microplastics. PS undergoes benzene ring hydroxylation and carbonylation, producing phenolic and aldehydic metabolites that are then integrated into the tricarboxylic acid (TCA) cycle through aromatic compound degradation pathways, according to analyses using Fourier transform infrared spectroscopy (FTIR) and gas chromatography-mass spectrometry (GC-MS). In contrast, PP exhibit a sequential oxidative pathway of "hydroxylation→carbonylation→esterification" through fatty acid degradation mechanisms. Metagenomic annotation confirmed functional complementarity between Bacillus-encoded initial hydrolytic enzymes and Achromobacter-encoded metabolic enzymes, the molecular basis for efficient degradation. This study supports PS/PP microplastic in situ bioremediation and advances understanding of microbial synergistic degradation.}, }
@article {pmid41014789, year = {2025}, author = {Ge, SH and Yang, MZ and Qian, WY and Zhuang, LL and Wu, HM and Chen, Z and Wang, XX and Zhang, J}, title = {Attached microalgae-simulated plants enhanced multiple-pollutant removal in a tidal flow constructed wetland: quantified efficiencies, pathways, and biological mechanisms.}, journal = {Water research}, volume = {288}, number = {Pt A}, pages = {124654}, doi = {10.1016/j.watres.2025.124654}, pmid = {41014789}, issn = {1879-2448}, abstract = {Active microalgae have great potential for releasing organic carbon and oxygen, which can be utilized as electron donors/acceptors, to enhance pollutant removal in constructed wetlands (CWs). In this study, we proposed a tidal flow CW with attached microalgae-simulated plants (AMSP) and verified the superiorities and mechanisms of microalgae's contribution to pollutant removal. The CWs with AMSP achieved high removal efficiencies for NH4N (87.6 %), TN (62.7 %), TP (56.4 %), and COD (98.8 %), which were 45.7 %, 16.3 %, and 20.5 % higher for NH4N, TN, and TP compared with those without AMSP. AMSP were found to enhance the abundance of functional microorganisms and genes involved in nitrogen metabolism, and to reduce the pH values in the bed filler to improve phosphate adsorption. Furthermore, the enhancement of NH4N and TP removal by AMSP was far beyond that of plants. Under the stress of 5 mg/L sulfamethazine (SMZ), the AMSP improved their photosynthetic efficiency and biomass accumulation, mitigated the impact of SMZ on the microbial community structure and diversity in the bed filler of CWs, increased the SMZ removal efficiency by 10.4 %, and reduced the release of antibiotics resistance genes into the environment by 49.7-89.6 %. These results demonstrated an effective integration of microalgal cultivation and CWs for treating wastewater containing emerging contaminants.}, }
@article {pmid41014671, year = {2025}, author = {Zhao, Y and Song, T and Ren, P and Wu, X and Luo, Q and Xie, J and Lai, H and Li, X and Wen, Y and Liao, X and Zhou, J}, title = {Integrating metagenomics, lipidomics and proteomics to explore the effect and mechanism of ginsenoside Rb1 on atherosclerosis co-depression disease.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {148}, number = {}, pages = {157301}, doi = {10.1016/j.phymed.2025.157301}, pmid = {41014671}, issn = {1618-095X}, abstract = {BACKGROUND: The comorbidity of atherosclerosis (AS) and depression presents a significant clinical challenge. Its pathogenesis entails complex abnormalities in inflammatory responses, lipid metabolism, and gut microbiota homeostasis. Ginsenoside Rb1 (GRb1)-a bioactive compound derived from the dried roots of Panax ginseng (Araliaceae)-demonstrates anti-inflammatory, antioxidant, lipid-lowering, and neuroprotective properties. However, GRb1's therapeutic potential and underlying mechanisms in AS co-depression remain inadequately characterized.<br><br>PURPOSE: This study aims to elucidate the mechanism of GRb1 in AS co-depression disease, identify potential therapeutic targets, and thereby develop novel therapeutic strategies for this condition.<br><br>METHODS: An AS co-depression comorbidity model was established using ApoE[&#x207b;/&#x207b;] mice fed a high-fat diet and subjected to chronic restraint stress. To evaluate GRb1's therapeutic efficacy, we assessed serum lipid profiles, performed aortic Oil Red O staining, and conducted behavioral tests for depressive-like phenotypes. Furthermore, we employed an integrated multi-omics approach-combining metagenomics, targeted lipid metabolomics, and proteomics-to identify key alterations in gut microbiota, lipid metabolites, and proteins, with subsequent correlation analysis. Key differential proteins and associated pathways identified through multi-omics were validated using both in vivo (AS co-depression mouse model) and in vitro (HT22 cells) experiments. Finally, GRb1's effects on ferroptosis and specific signaling pathways (CD44/Gls2, ACSL4/LPCAT3/ALOX15, SLC7A11/GPX4) were examined via Western blotting, immunofluorescence, and transmission electron microscopy in both mouse tissues and HT22 cells.<br><br>RESULTS: Proteobacteria, Helicobacter, and Helicobacter_typhlonius represent significant intestinal microbiota components. Their primary differential lipids include phosphatidylethanolamine (PE), phosphatidylcholine (PC), and lysophosphatidylcholine (LPC), while key differential proteins encompass CD44, Gls2, and Snrpf. Notably, a strong correlation exists among Helicobacter_typhlonius, PE, and CD44. GRb1 modulates PE metabolic dysregulation by reducing the relative abundance of Helicobacter_typhlonius, thereby inhibiting lipid peroxidation and ameliorating oxidative stress. Furthermore, GRb1 suppresses the CD44/Gls2 axis, ACSL4/LPCAT3/ALOX15 pathway, and activates the SLC7A11/GPX4-mediated ferroptosis pathway, thereby exerting its anti-AS co-depression effects through these multi-target mechanisms.<br><br>CONCLUSION: GRb1 regulates the intestinal microbiota, abnormal lipid metabolism, modulates protein function, inhibits lipid peroxidation, improves oxidative stress, inhibits ferroptosis, regulates the CD44/Gls2, ACSL4/LPCAT3/ALOX15, SLC7A11/ GPX4 signaling pathways, and prevents the progression of AS co-depression disease.}, }
@article {pmid41014594, year = {2025}, author = {Huang, R and Yang, D and Ji, Q and Nie, L and Lyu, Y and Wang, S and Wang, L and Feng, Z}, title = {Angucystemycins, Highly Oxygenated Acetylcysteine-Angucycline Hybrid Conjugates Derived from a Soil Metagenomic Library.}, journal = {Journal of natural products}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jnatprod.5c00642}, pmid = {41014594}, issn = {1520-6025}, abstract = {A type II polyketide biosynthetic gene cluster (agc) was identified from a soil metagenomic library. The gene cluster harbors several distinct oxidoreductase genes, suggesting that the heterologous expression of the agc gene cluster could yield novel polycyclic aromatic polyketides featuring unique redox-driven modifications. Eight angucycline derivatives were isolated from Streptomyces albus J1074 harboring the agc gene cluster, including two new S-bridged acetylcysteine-angucycline compounds, angucystemycins (1-2), a new angucycline congener, emycin H (3), along with five known analogues, rubiginone B2 (4), emycin C (5), rubiginone B1 (6), ochromycinone (7), and emycin A (8). Their structures were elucidated based on detailed High-Resolution Electrospray Ionization Mass Spectrometry and 1D and 2D NMR spectroscopy. The proposed biosynthetic pathway of angucystemycins indicated that the angucycline core and the acetylcysteine moiety are derived from the agc biosynthetic gene cluster and S. albus J1074, respectively. In addition, emycin H (3) and emycin C (5) exhibited inhibitory activity against Bacillus subtilis 168 and B. pumilus CMCC 63202. Structural analysis suggested that the saturated bond between C-5 and C-6 contributes to the activity, whereas the introduction of a C-8 O-methyl group diminishes the antimicrobial activity of the compounds of this structural class, implying a potential structure-activity relationship.}, }
@article {pmid41013652, year = {2025}, author = {Pérez-Carrasco, V and Soriano-Lerma, A and Guzzi, C and García-Martín, ML and Tello, MJ and Linde-Rodríguez, &#xc1; and Sánchez-Martín, V and Ortiz-González, M and ,  and Gutiérrez-Fernández, J and Alarcón-Riquelme, ME and Soriano, M and Marañón, C and García-Salcedo, JA}, title = {Identification of urinary bacterial genes as biomarkers for non-invasive diagnosis of renal lupus.}, journal = {Biomarker research}, volume = {13}, number = {1}, pages = {117}, pmid = {41013652}, issn = {2050-7771}, support = {115565; 831434//Innovative Medicines Initiative Joint Undertaking and Innovative Medicines Initiative 2 Joint Undertaking/ ; }, abstract = {BACKGROUND: Systemic lupus erythematosus (SLE) is a complex autoimmune disease that often affects the kidneys, causing lupus nephritis. Diagnosis of this affection currently relies on kidney biopsy, an invasive and complex procedure. This study explores the diagnostic value of biomarkers based in the urobiome - the microbial community of the urinary tract - in patients with renal SLE.<br><br>METHODS: This study enrolled 585 female subjects including Healthy controls, non-renal and renal SLE patients. The taxonomic and functional differences of the urobiome in patients with SLE, as well as in the metabolites of interest, were identified by 16S rRNA profiling with PICRUSt functional inference and nuclear magnetic resonance (NMR). The accuracy of the identified biomarkers was tested by building random forest (RF) classification models. Furthermore, the results were validated in an independent cohort composed by 30 controls, 30 non-renal and 30 renal SLE patients.<br><br>RESULTS: Bacterial gene-based biomarkers with an AUC value of 0.7&#x2009;&#xb1;&#x2009;0.07 and 0.67&#x2009;&#xb1;&#x2009;0.07 to distinguish renal from non-renal SLE cases were identified. These biomarkers were validated in a validation cohort using quantitative PCR (qPCR), demonstrating their robust diagnostic performance. Furthermore, our analysis uncovered significant urobiome dysbiosis and distinct bacterial functional profile in both groups of SLE patients, with notable differences in amino acid metabolism pathways, particularly those involving valine and leucine, which were assessed by NMR-based urinary metabolite quantification.<br><br>CONCLUSIONS: Some bacterial genes have been identified in the urobiome of SLE patients that allow differentiation between those with renal and non-renal lupus. These findings offer valuable insight into the association between the urobiome and SLE presentation, and lay the foundation for developing novel diagnostic tools that overcome the limitations of current methods, thereby improving patient care.}, }
@article {pmid41013651, year = {2025}, author = {Buigues, J and Viñals, A and Martínez-Recio, R and Monrós, JS and Sanjuán, R and Cuevas, JM}, title = {Rodents as potential reservoirs for toroviruses.}, journal = {Virology journal}, volume = {22}, number = {1}, pages = {305}, pmid = {41013651}, issn = {1743-422X}, support = {PID2020-118602RB-I00//Spanish Ministerio de Ciencia e Innovaci&#xf3;n (MICINN)/ ; PID2020-118602RB-I00//Spanish Ministerio de Ciencia e Innovaci&#xf3;n (MICINN)/ ; CIAICO/2022/110//Conselleria de Educaci&#xf3;n, Universidades y Empleo (Generalitat Valenciana)/ ; 101019724-EVADER//ERC Advanced Grant/ ; }, mesh = {Animals ; Phylogeny ; Genome, Viral ; Feces/virology ; Spain ; *Disease Reservoirs/virology ; *Torovirus/genetics/isolation &amp; purification/classification ; High-Throughput Nucleotide Sequencing ; *Rodentia/virology ; Open Reading Frames ; *Torovirus Infections/virology/veterinary/transmission ; }, abstract = {BACKGROUND: Emerging zoonotic viruses pose a significant threat to global health. The order Nidovirales includes diverse viruses, such as coronaviruses, which are well known for their zoonotic potential. Toroviruses are a less-studied genus within Nidovirales primarily associated with gastrointestinal diseases in ungulates, although some evidence suggests their presence in humans.<br><br>METHODS: We set out to describe full-length genomes of potentially emerging viruses by collecting feces from dozens of small mammals, mainly rodents, captured in different regions of Spain. Viral reads were obtained by high-throughput Illumina sequencing and analyzed phylogenetically.<br><br>RESULTS: In this study, we report the discovery of a novel torovirus from a fecal sample of a dormouse (Eliomys quercinus) in Spain, which we named Dormouse torovirus (DToV). This represents the first complete genome of a rodent-associated torovirus. The 28,555-nucleotide genome encodes the six characteristic torovirus open reading frames, but these exhibit low amino acid sequence identity (44.3-86.3%) compared to other toroviruses, indicating that DToV likely represents a new viral species. Moreover, the basal phylogenetic position of DToV suggests that rodents may represent a reservoir for this viral genus.<br><br>CONCLUSIONS: Our findings expand the known torovirus host range, underscore their potential for cross-species transmission, and highlight the importance of continued surveillance of wildlife viruses.}, }
@article {pmid41013611, year = {2025}, author = {Kazarina, A and Sarkar, S and Adams, B and Vogt, B and Rodela, L and Pogranichny, S and Powell, S and Wiechman, H and Heeren, L and Reese, N and Thompson, D and Ran, Q and Hartung, E and Akhunova, A and Akhunov, E and Johnson, L and Jumpponen, A and Lee, STM}, title = {Interaction of plant-derived metabolites and rhizobiome functions enhances drought stress tolerance.}, journal = {Genome biology}, volume = {26}, number = {1}, pages = {310}, pmid = {41013611}, issn = {1474-760X}, support = {2020-67019-3180//National Institute of Food and Agriculture/ ; 2238633//National Science Foundation CAREER Award/ ; OIA-1656006//National Science Foundation Award/ ; INV-004430/GATES/Gates Foundation/United States ; }, mesh = {*Rhizosphere ; *Stress, Physiological ; *Plant Roots/microbiology/metabolism ; *Droughts ; Soil Microbiology ; *Microbiota ; }, abstract = {BACKGROUND: Plants have evolved alongside microbes, enabling plants to better cope with abiotic and biotic stress. Interactions between plant roots and local soil microbes are critical for environmental adaptation and plant health. Plants actively regulate the microbial community composition in their rhizospheres to recruit specific microorganisms that enhance their fitness in the ecosystem they inhabit. This study builds on prior research suggesting that plants exhibit a "home field advantage" by preferentially recruiting microbes unique to their native environments, likely through mutual recognition and selective recruitment mechanisms.<br><br>RESULTS: Using gene- and genome-centric approaches, we assess the functional potential of root-associated microbes and profile their host metabolites to uncover the metabolic outputs potentially regulating host&#x2012;microbe interactions in Andropogon gerardii. We find that plants adapted to drier environments experience less stress, producing fewer stress-related metabolites and impacting the recruitment of microbes with genes linked to stress relief pathways. In particular, plant-derived trimethyllysine is highly associated with microbial populations capable of improving nutrient uptake, producing plant growth-promoting compounds, and modulating stress responses.<br><br>CONCLUSIONS: This study highlights the critical interplay between host exudates and microbial substrate uptake as the primary mechanism of rhizosphere assembly. We demonstrate that plants actively produce metabolites to recruit microbial populations with the functional potential to enhance their ability to thrive in stressful environments. This research provides insights into the mechanisms of plant-microbe communication, rhizosphere recruitment, and the complex interplay of plant-microbe interactions. Furthermore, it highlights promising avenues for manipulating rhizosphere microbiomes to support conservation agriculture when coping with climate change.}, }
@article {pmid41013568, year = {2025}, author = {Lei, Y and Zheng, Y and Yan, Y and Zhang, K and Sun, X and Yang, B and Ge, L and Meng, Z and Cao, X and Zhang, X and Yan, X and Xu, Y and Zhang, T and Shi, J and Chen, S and Qiu, Q and Chen, Y and Deng, L and Li, Z and Wang, X and Zhang, K}, title = {Deciphering functional landscapes of rumen microbiota unveils the role of Prevotella bryantii in milk fat synthesis in goats.}, journal = {Genome biology}, volume = {26}, number = {1}, pages = {311}, pmid = {41013568}, issn = {1474-760X}, support = {2022YFD1300203//the National Key Research and Development Program of China/ ; 2022ZD04014//the Biological Breeding-Major Projects/ ; CARS-39-03//the China Agricultural Research System/ ; 32402785//the National Natural Science Foundation of China/ ; 2024PT-ZCK-71-3//the Key Research and Development Program of Shaanxi Province/ ; }, mesh = {Animals ; *Rumen/microbiology/metabolism ; *Goats/microbiology ; *Milk/metabolism ; *Prevotella/genetics/metabolism ; Female ; *Gastrointestinal Microbiome ; Lactation ; *Microbiota ; Lipid Metabolism ; Niacinamide/metabolism ; }, abstract = {BACKGROUND: The rumen microbiome is critical for regulating milk synthesis in dairy livestock, yet the molecular mechanisms linking microbial functions to host lipid metabolism remain poorly understood. While host genetics and microbial composition have been studied, integrative analyses of the rumen-blood-mammary gland axis remain lacking.<br><br>RESULTS: Here, we present the goat rumen microbial reference gene catalog and 5514 metagenome-assembled genomes (MAGs) from 160 multi-breed rumen samples. Integrating this resource with lactation data from 177 Saanen dairy goats, we identify Prevotella spp. as keystone taxa driving concurrent increases in milk yield and fat percentage. Functional and metabolomic profiling reveals that Prevotella bryantii B14 synthesizes nicotinate, which is converted to nicotinamide in circulation. Using in vitro and in vivo models, we demonstrate that nicotinamide activates the mTORC1 pathway in mammary epithelial cells via GPR109A, which upregulates transcription factors SREBP and PPAR-&#x3b3; and the downstream lipogenic genes FASN, ACC&#x3b1;, and SCD1 to promote milk fat synthesis. In contrast, the relative deficiency of P. bryantii B14 and the associated reduction in nicotinamide levels in the rumen of poor lactating dairy goats may represent a significant contributor to impaired lactation performance. Additionally, the enhanced hydrogenotrophic methanogenesis activity may also adversely affect their lactation phenotype.<br><br>CONCLUSIONS: Our study establishes a causal link between rumen microbial metabolism and mammary lipid synthesis mediated by nicotinamide-mTORC1 signaling and identifies Prevotella abundance as a biomarker for precision breeding. These findings advance the understanding of microbiome-host crosstalk in lactation and provide actionable strategies for enhancing dairy productivity through microbiota-targeted interventions.}, }
@article {pmid41013350, year = {2025}, author = {Zhu, N and Lin, S and Zhang, Y and Chen, M and Chen, L and Cao, C}, title = {Evaluating the diagnostic efficacy of metagenomic next-generation sequencing in bronchoalveolar lavage fluid for pulmonary cryptococcosis with different clinical and imaging characteristics.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {1143}, pmid = {41013350}, issn = {1471-2334}, mesh = {Humans ; Male ; Female ; *Bronchoalveolar Lavage Fluid/microbiology ; Middle Aged ; *Cryptococcosis/diagnosis/microbiology ; Sensitivity and Specificity ; Aged ; Adult ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; *Lung Diseases, Fungal/diagnosis/microbiology ; }, abstract = {OBJECTIVE: This study aimed to explore the diagnostic value of bronchoalveolar lavage fluid metagenomic next-generation sequencing (BALF-mNGS) in patients with pulmonary cryptococcosis (PC) exhibiting different clinical and imaging characteristics, thereby enhancing clinical physicians' understanding and application of BALF-mNGS in diagnosing PC.<br><br>METHODS: A total of 84 patients with PC and 84 non-cryptococcosis patients admitted to the First Affiliated Hospital of Ningbo University from February 2020 to April 2025 were enrolled in this study. Data on basic demographics, medication history, comorbidities, clinical presentations, laboratory test results, imaging findings, and serological test results were collected. The sensitivity and specificity of BALF-mNGS for diagnosing PC and its diagnostic sensitivity across different clinical features were analyzed.<br><br>RESULTS: Among the 84 patients with PC, 46 were males and 38 were females. BALF-mNGS results were positive in 72 cases and negative in 12 cases. All 84 non-cryptococcosis patients tested negative using BALF-mNGS. The sensitivity of BALF-mNGS for detecting PC was 85.71%, whereas the specificity and positive predictive value were both 100.00%. Among the 48 patients presenting with cough or sputum, BALF-mNGS was positive in 45 cases, yielding a sensitivity of 93.33%, significantly higher than that of patients without cough or sputum (P&#x2009;<&#x2009;0.05). Among the 38 patients with lesions located in the right lung, BALF-mNGS was positive in 36 cases, resulting in a sensitivity of 94.74%, higher than that for patients with lesions in the left lung or both lungs (P&#x2009;<&#x2009;0.05). Of the 57 patients with multiple lesions, 53 tested positive with BALF-mNGS, resulting in a sensitivity of 92.98%, significantly higher than that of patients with single lesions (P&#x2009;<&#x2009;0.05).<br><br>CONCLUSIONS: BALF-mNGS demonstrated high sensitivity for diagnosing PC, particularly in patients presenting with cough or sputum, right lung lesions, or multiple lesions. This serves as a valuable tool for the early diagnosis of PC.}, }
@article {pmid41013333, year = {2025}, author = {Wei, S and Meng, D and Qin, J and Mo, S and Jiang, Z and Zhang, P}, title = {Disseminated Mycobacterium kansasii disease complicating Talaromyces marneffei infection in patient with anti-IFN-γ autoantibodies: a case report.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {1157}, pmid = {41013333}, issn = {1471-2334}, mesh = {Humans ; Male ; Middle Aged ; *Mycobacterium Infections, Nontuberculous/drug therapy/complications/microbiology/immunology/diagnosis ; *Talaromyces/isolation &amp; purification ; *Mycobacterium kansasii/isolation &amp; purification ; *Interferon-gamma/immunology ; *Autoantibodies/immunology/blood ; *Mycoses/microbiology/complications/immunology/drug therapy ; *Coinfection/microbiology ; }, abstract = {BACKGROUND: Patients with immunodeficiency syndromes associated with anti-interferon-gamma (IFN-γ) autoantibodies are prone to a wide range of infections, particularly those caused by intracellular pathogens such as nontuberculous mycobacteria (NTM) or Talaromyces marneffei (T. marneffei). However, disseminated Mycobacterium kansasii (M. kansasii) infection co-occurring with T. marneffei infection is relatively rare. Here, we present a case of disseminated M. kansasii disease complicated by T. marneffei infection in a patient with anti-IFN-γ autoantibodies.<br><br>CASE PRESENTATION: A 52-year-old man presented with a persistent cough, back pain, fever, generalized rash, and multiple enlarged lymph nodes. Chest computed tomography (CT) revealed hilar Masses, and technetium 99m (Tc-99m) skeletal scintigraphy showed multifocal increased osteoblastic activity. Histopathological examination of the hilar mass biopsy specimens revealed chronic suppurative inflammation. Metagenomic next-generation sequencing (mNGS) of the right submandibular lymph node identified M. kansasii, while blood culture isolated T. marneffei. The patient was diagnosed with disseminated M. kansasii infection co-existing with T. marneffei infection. Additionally, he tested positive for anti-IFN-&#x3b3; autoantibodies. Combination therapy for NTM-comprising isoniazid, clarithromycin, moxifloxacin, and linezolid-in conjunction with antifungal therapy (amphotericin B followed by itraconazole) achieved a favorable clinical outcome.<br><br>CONCLUSIONS: Patients with anti-IFN-&#x3b3; autoantibodies are at risk of developing multiple opportunistic bacterial infections, which may occur concurrently or sequentially, complicating diagnosis. Early detection using mNGS is critical in these cases, as it enables timely therapeutic adjustments and improves clinical outcomes.}, }
@article {pmid41013192, year = {2025}, author = {Child, HT and Wierzbicki, L and Joslin, GR and Roper, K and Haxhiraj, Q and Tennant, RK}, title = {Automated environmental metagenomics using Oxford nanopore sequencing.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {835}, pmid = {41013192}, issn = {1471-2164}, support = {CW648947-PT34767//Shell Research Ltd/ ; CW648947-PT34767//Shell Research Ltd/ ; CW648947-PT34767//Shell Research Ltd/ ; CW648947-PT34767//Shell Research Ltd/ ; }, mesh = {*Metagenomics/methods ; *Nanopore Sequencing/methods ; Metagenome ; Automation ; High-Throughput Nucleotide Sequencing/methods ; Gene Library ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: Long-read sequencing has revolutionised metagenomics through improved metagenome assembly, taxonomic classification and functional characterisation. Automation can enhance the throughput, reproducibility, and accuracy of library preparation. However, the validation of automated library preparation protocols remains undetermined for metagenomic workflows, which are particularly sensitive to methodological perturbation. Here, we compare long-read metagenomic sequencing of environmental samples through parallel manual and automated protocols.<br><br>RESULTS: Although automated library preparation led to minor reduction in read and contig lengths, taxonomic classification rate and alpha diversity was slightly higher than manual libraries, including the detection of more rare taxa. Despite this, no significant difference in microbial community structure was identified between manual and automated libraries.<br><br>CONCLUSIONS: Despite minor differences in sequencing and classification metrics, automated and manual library preparation resulted in comparable characterization of environmental community metagenomes. These findings demonstrate the suitability of automation for high-throughput long-read metagenomics, with broad applicability to automated long-read sequencing for improved efficiency and reproducibility.}, }
@article {pmid41012834, year = {2025}, author = {Liu, S and Zhou, B and Liu, L and Zhong, J and Zhang, X and Jiang, W and Liu, H and Zhou, Z and Peng, G and Zhong, Y and Zhang, K and Zhong, Z}, title = {Effects and Microbiota Changes Following Oral Lyophilized Fecal Microbiota Transplantation Capsules in Canine with Chronic Enteropathy After Parvovirus Infection: Case Report.}, journal = {Veterinary sciences}, volume = {12}, number = {9}, pages = {}, doi = {10.3390/vetsci12090909}, pmid = {41012834}, issn = {2306-7381}, support = {CGF2024001//the Study on Key Technologies for Conservation of Wild Giant Panda Populations and Its Habitats within Giant Panda National Park System/ ; }, abstract = {(1) Background: Chronic enteropathy (CE) in canines is associated with persistent microbiome dysbiosis, and conventional therapies (e.g., special diets, antimicrobials, and immunosuppressive drugs) are sometimes ineffective. Currently, fecal microbiota transplantation (FMT) has proven successful in treating CE in canines via invasive methods (e.g., enemas or endoscopy) or via oral frozen liquid capsules, which must be stored at -80 °C. However, due to the invasiveness of the administration methods and the storage constraints of the liquid capsules, FMT is not widely used in veterinary clinical practice. (2) Methods: The case of a four-year-old Siberian Husky with a three-year history of CE following canine parvovirus infection received lyophilized FMT capsules for thirty days. Stool samples were collected for metagenomic sequencing and quantification of fecal short-chain fatty acids (SCFAs), both pre- and post-FMT. Blood samples were analyzed using complete blood count (CBC) and biochemical testing. Ultrasound was used to assess the wall thickness of the stomach, duodenum, jejunum, and colon. (3) Results: Post-FMT, improvements in clinical outcomes were observed: fecal scores improved from 6 (unformed stools with mucus) to 2 (formed stool), and body weight increased by 8.3% (from 24.2 kg to 26.2 kg). Abnormal CBC and biochemical parameters were restored to reference ranges, including hematocrit (from 60.6% to 55.7%), hemoglobin (from 208 g/L to 190 g/L), creatinine (from 167 μmol/L to 121 μmol/L), and urea (from 11.9 mmol/L to 7.1 mmol/L). Ultrasound results showed that colonic wall thickness decreased from 0.23 ± 0.03 cm (pathological) to 0.18 ± 0.01 cm (physiological). Metagenomic analysis revealed that microbial richness (operational taxonomic units (OTUs) from 151 to 183) and diversity (Shannon and Simpson indices from 3.16 to 4.8 and from 0.87 to 0.94, respectively) all increased. The microbiota composition of the recipient exhibited a decline in the relative abundance of Firmicutes, falling from 99.84% to 35.62%, concomitant with an increase in Actinobacteria (from 0.08% to 4.78%), indicating a convergence toward a donor-like profile. Fecal SCFAs analysis revealed a 251.4% increase in propionate (from 0.0833 to 0.2929 mg/g) and elevated acetate (from 0.4425 to 0.4676 mg/g). These changes are functionally linked to enriched propanoate metabolism (Z = 0.89) in KEGG pathways. (4) Conclusions: Oral lyophilized FMT capsules resolved clinical signs of CE, enhanced microbial diversity and richness, and restored donor-like abundances of gut microbiota, particularly SCFA-producing taxa. Microbial restructuring increased microbial metabolite output, notably SCFA concentrations, and enriched functional metabolic pathways. Importantly, lyophilized FMT overcomes storage limitations and administration barriers, demonstrating its high clinical viability for treating canine CE.}, }
@article {pmid41012745, year = {2025}, author = {Pacini, MI and Forzan, M and Sgorbini, M and Cingottini, D and Mazzei, M}, title = {Metagenomic Analysis of the Fecal Virome in Wild Mammals Hospitalized in Pisa, Italy.}, journal = {Veterinary sciences}, volume = {12}, number = {9}, pages = {}, doi = {10.3390/vetsci12090820}, pmid = {41012745}, issn = {2306-7381}, support = {Fondi Ateneo 2020//University of Pisa/ ; }, abstract = {Emerging infectious diseases, particularly those of zoonotic origin, often originating from wildlife reservoirs represent a growing threat to global health. Human-driven environmental changes such as habitat fragmentation, climate change, and urban expansion have intensified interactions at the wildlife-domestic animal-human interface, facilitating cross-species viral transmission. Despite their epidemiological importance, systematic virological surveillance of wildlife remains challenging. In this study, we employed shotgun metagenomic sequencing to characterize the virome of wild animals rescued in the Pisa area and hospitalized at the "Mario Modenato" Veterinary Teaching Hospital (VTH) at the University of Pisa. Fecal samples collected from injured wildlife admitted between September 2020 and September 2021 were analyzed to detect both known and novel viruses. This approach builds upon previous PCR-based investigations of the same biological material, enabling a more comprehensive assessment of viral diversity. We adopted a shotgun approach for analyzing six sample pools-four were positive for at least one viral target-identifying diverse viral families, including Astroviridae, Circoviridae, Picornaviridae, Adenoviridae, and Retroviridae, in asymptomatic wildlife admitted to a veterinary hospital, highlighting their potential role as reservoirs. Our findings provide insights into the influence of environmental and anthropogenic factors on wildlife virome composition and highlight the value of hospital-based sampling strategies for urban viral surveillance. The results contribute to the development of integrated monitoring and prevention strategies within a One Health framework.}, }
@article {pmid41012703, year = {2025}, author = {Johnson, ML and Boezen, D and Grum-Grzhimaylo, AA and van der Vlugt, RAA and de Visser, JAGM and Zwart, MP}, title = {Living Together Apart: Quantitative Perspectives on the Costs and Benefits of a Multipartite Genome Organization in Viruses.}, journal = {Viruses}, volume = {17}, number = {9}, pages = {}, doi = {10.3390/v17091275}, pmid = {41012703}, issn = {1999-4915}, support = {016.VIDI.171.061/NWO_/Dutch Research Council/Netherlands ; }, mesh = {*Genome, Viral ; *Plant Viruses/genetics/physiology ; Host Specificity ; Metagenomics ; Plant Diseases/virology ; Plants/virology ; }, abstract = {BACKGROUND: Multipartite viruses individually package their multiple genome segments into virus particles, necessitating the transmission of multiple virus particles for effective viral spread. This dependence poses a cost in the form of reduced transmission compared to monopartite viruses, which only have a single genome segment. The notable cost of a multipartite genome organization has spurred debate on why multipartite viruses are so common among plant viruses, including a search for benefits associated with this organizational form.<br><br>METHODS: We investigated the costs and benefits of multipartite viruses with three approaches. First, we reanalyzed dose-response data to measure the cost of multipartition to between-host transmission for multipartite viruses. Second, we developed a simulation model to explore when the sharing of viral gene products between cells is beneficial. Third, we tested whether multipartite viruses have a broad host range by estimating the host range for plant viruses using metagenomics data.<br><br>RESULTS: We find that the observed cost to transmission exceeds theoretical predictions. We predict that a virus gene-product-sharing strategy only confers benefits under limited conditions, suggesting that this strategy may not be common. Our results suggest that multipartite and segmented viruses have broader host ranges than monopartite viruses.<br><br>CONCLUSIONS: Our analyses also suggest there is limited evidence for the costs and benefits of a multipartite organization, and we argue that the diversity of multipartite virus-host systems demands pluralistic explanatory frameworks.}, }
@article {pmid41012687, year = {2025}, author = {Nunes Neto, JP and Dias, DD and Nascimento, BLSD and da Silva, SP and da Silva, SLS and Reis, LAM and Reis, HCF and da Silva, FS and da Silva E Silva, LH and Vieira, DBR and Brandão, RCF and Rosário, WO and Paiva, FADS and Júnior, JWR and Nunes, BTD and Martins, LC and Casseb, LMN and Cruz, ACR}, title = {Molecular Detection of Yellow Fever Virus in Haemagogus janthinomys Mosquitoes (Diptera: Culicidae) in a Rural Settlement in the State of Pará, Brazilian Amazon, 2024.}, journal = {Viruses}, volume = {17}, number = {9}, pages = {}, doi = {10.3390/v17091258}, pmid = {41012687}, issn = {1999-4915}, mesh = {Animals ; Brazil/epidemiology ; *Yellow fever virus/genetics/isolation &amp; purification/classification ; *Mosquito Vectors/virology ; *Yellow Fever/virology/epidemiology/transmission ; *Culicidae/virology/classification ; Phylogeny ; Rural Population ; }, abstract = {Yellow fever (YF) is an acute and potentially fatal hemorrhagic disease caused by the Yellow Fever virus (YFV), endemic to sub-Saharan Africa and several tropical countries, including Brazil. In Brazil, the Amazon region is considered the main endemic area. YFV is maintained in a sylvatic cycle involving Neotropical primates and mosquitoes of the genera Haemagogus and Sabethes, acting as primary and secondary vectors, respectively. In March 2024, entomovirological surveillance was conducted in Santa Bárbara do Pará, Pará, Brazil. A total of 286 mosquitoes were collected, classified into 13 species across nine genera, and grouped into 33 pools. Seventeen pools were tested by RT-qPCR for Orthoflavivirus (YFV, DENV, WNV, SLEV), Alphavirus (CHIKV, MAYV), and Orthobunyavirus (OROV). YFV was detected in four Haemagogus janthinomys pools, with Ct values ranging from 22.2 to 27.9. Metagenomic sequencing confirmed the presence of YFV with assigned reads and >99% protein identity. Notably, the detection occurred without human cases or primate deaths, enabling timely vaccination of the local population. These findings confirm YFV circulation in forested areas of the Belém metropolitan region and reaffirm Hg. janthinomys as a key vector. Our study reinforces the relevance of early entomovirological surveillance and preventive strategies, such as vaccination, to mitigate yellow fever reemergence.}, }
@article {pmid41012679, year = {2025}, author = {Hernández, LHA and da Silva, FS and da Paz, TYB and Dias, DD and de Barros, BCV and Nunes, BTD and Casseb, LMN and da Silva, SP and da Costa Vasconcelos, PF and Cruz, ACR}, title = {Virome Analysis of Small Mammals from the Brazilian Amazon.}, journal = {Viruses}, volume = {17}, number = {9}, pages = {}, doi = {10.3390/v17091251}, pmid = {41012679}, issn = {1999-4915}, support = {3286/2013//Coordena&#xe7;&#xe3;o de Aperfeicoamento de Pessoal de N&#xed;vel Superior/ ; 88887.636166/2021-00//Coordena&#xe7;&#xe3;o de Aperfeicoamento de Pessoal de N&#xed;vel Superior/ ; 310295/2021-1//National Council for Scientific and Technological Development/ ; 406490/2023-6//National Council for Scientific and Technological Development/ ; 314522/2021-2//National Council for Scientific and Technological Development/ ; 406360/2022-7//Instituto Nacional de Ci&#xea;ncia e Tecnologia em Viroses Emergentes e Reemergentes/ ; }, mesh = {Animals ; Brazil ; *Virome ; *Chiroptera/virology ; *Viruses/genetics/classification/isolation &amp; purification ; Genome, Viral ; Phylogeny ; High-Throughput Nucleotide Sequencing ; *Opossums/virology ; *Rodentia/virology ; Animals, Wild/virology ; *Mammals/virology ; }, abstract = {The municipalities of Peixe-Boi and Santa Bárbara do Pará, both in the Pará State (eastern Amazon), have more than half of their territory deforested. Understanding the viral diversity in wildlife that inhabits the surroundings of human communities contributes to strengthening surveillance. Samples from eleven bats, seven opossums, and eight rodents from the two locations were screened by high-throughput sequencing for virome analysis. Viral reads were assigned into twenty viral families, from which the most abundant was Retroviridae. Host order, tissue type, and season showed a significant effect on viral composition. Five viral genomes of bat ERVs with intact genes were recovered, showing the need to understand their endogenous nature. In addition, a new Buritiense virus (Hantaviridae) strain was also obtained, supporting its circulation in Santa Bárbara do Pará and expanding its genomic information. Together, these findings reinforce the need for continuous surveillance in wild animals, especially in the Amazon region, to anticipate potential threats to public health.}, }
@article {pmid41011853, year = {2025}, author = {Saylam, E and Özden, &#xd6; and Yerlikaya, FH and Sivrikaya, A and Yormaz, S and Arslan, U and Topkafa, M and Maçin, S}, title = {Investigation of Intestinal Microbiota and Short-Chain Fatty Acids in Colorectal Cancer and Detection of Biomarkers.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {9}, pages = {}, doi = {10.3390/pathogens14090953}, pmid = {41011853}, issn = {2076-0817}, support = {22401140//Sel&#xe7;uk University/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Colorectal Neoplasms/microbiology/diagnosis/pathology/metabolism ; Male ; Female ; *Fatty Acids, Volatile/metabolism/analysis ; Middle Aged ; Feces/microbiology/chemistry ; Haptoglobins ; Aged ; Protein Precursors ; Acute-Phase Proteins/analysis ; Cholera Toxin/blood ; *Biomarkers, Tumor ; Carrier Proteins/blood ; Membrane Glycoproteins/blood ; Biomarkers ; Bacteria/classification/genetics/isolation &amp; purification ; Adult ; }, abstract = {Colorectal cancer (CRC) is one of the most common cancers worldwide and a significant global health issue. The human gut microbiota, a complex ecosystem hosting numerous microorganisms such as bacteria, viruses, fungi, and protozoa, plays a crucial role. Increasing evidence indicates that gut microbiota is involved in CRC pathogenesis. In this study, the gut microbiota profiles, short-chain fatty acids, zonulin, and lipopolysaccharide-binding protein levels of newly diagnosed CRC patients were analyzed along with healthy controls to elucidate the relationship between CRC and the gut microbiota. The study included 16 newly diagnosed CRC patients and 16 healthy individuals. For microbiota analysis, DNA isolation from stool samples was performed using the Quick-DNA™ Fecal/Soil Microbe Miniprep Kit followed by sequencing using the MinION device. Data processing was conducted using Guppy software (version 6.5.7) and the Python (3.12) programming language. ELISA kits from Elabscience were utilized for analyzing LBP and zonulin serum levels. Fecal short-chain fatty acids were analyzed using GC-MS/MS equipped with a flame ionization detector and DB-FFAP column. Microbial alpha diversity, assessed using Shannon and Simpson indices, was found to be lower in CRC patients compared to healthy controls (p = 0.045, 0.017). Significant differences in microbial beta diversity were observed between the two groups (p = 0.004). At the phylum level, Bacteroidota was found to be decreased in CRC patients (p = 0.027). Potential biomarker candidates identified included Enterococcus faecium, Ruminococcus bicirculans, Enterococcus gilvus, Enterococcus casseliflavus, Segatella oris, and Akkermansia muciniphila. Serum zonulin levels were higher in CRC patients (CRC = 70.1 ± 26.14, Control = 53.93 ± 17.33, p = 0.048). There is a significant relationship between gut microbiota and CRC. A multifactorial evaluation of this relationship could shed light on potential biomarker identification and the development of new treatment options for CRC.}, }
@article {pmid41011835, year = {2025}, author = {Ezzat, A and Abd El Wahed, A and Ceruti, A and El Asely, AM and Khalifa, MS and Winters, AD and Truyen, U and Shaheen, AA and Faisal, M}, title = {Exploring the Virome of Nile Tilapia (Oreochromis niloticus) Using Metagenomic Analysis.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {9}, pages = {}, doi = {10.3390/pathogens14090935}, pmid = {41011835}, issn = {2076-0817}, mesh = {Animals ; *Cichlids/virology ; *Virome/genetics ; *Metagenomics/methods ; Phylogeny ; *Fish Diseases/virology ; *Viruses/genetics/classification/isolation &amp; purification ; Egypt ; DNA Viruses/genetics/classification/isolation &amp; purification ; Metagenome ; }, abstract = {Nile tilapia (Oreochromis niloticus) is an indispensable source of high-quality protein worldwide. Along with the exponential expansion of tilapia aquaculture, several novel pathogenic viruses have emerged, and some cause significant economic losses. Unfortunately, there is scarce information on the biology and epidemiology of these viruses. This exploratory metagenomic study used Oxford Nanopore Technology (ONT) sequencing to profile the virome compositions of both wild and farmed Nile tilapia across five regions in Egypt. The Nile tilapia virome was dominated by two double-stranded DNA bacteriophages, Muvirus mu and M. sfmu, which constituted 79.8% of the detected sequences. Eukaryotic viruses, including members of the families Amnoonviridae, Peribunyaviridae, and Baculoviridae, were also identified. Two giant DNA viruses known to infect Acanthamoeba spp., Mollivirus sp., and Pandoravirus sp. were identified in the spleen virome of tilapia from a single sampling site. The diversity analysis showed no significant differences among tissue types or sampling sites. Phylogenetic analyses were performed on a single virus detected of potential pathogenicity, an amnoonvirus. The analyses demonstrated that the detected virus is a member of the family Amnoonviridae and placed it alongside members of the Tilapinevirus genus. The virus, however, was distinct from the other two members in the genus: T. tilapae and T. poikilos. This study underscores the usefulness of ONT in providing a foundational understanding of the Nile tilapia virome.}, }
@article {pmid41011708, year = {2025}, author = {Rakhalaru, P and Mampholo, BM and Mamphogoro, TP and Thantsha, MS}, title = {Endophytic and Epiphytic Microorganisms as Biocontrol Agents: Mechanisms, Applications, and Metagenomic Approaches in Tomato Cultivation.}, journal = {Molecules (Basel, Switzerland)}, volume = {30}, number = {18}, pages = {}, doi = {10.3390/molecules30183816}, pmid = {41011708}, issn = {1420-3049}, support = {A148/API012403000048//Department of Agriculture, South Africa/ ; }, mesh = {*Solanum lycopersicum/microbiology/growth &amp; development ; *Metagenomics/methods ; *Endophytes/physiology/genetics ; *Biological Control Agents ; *Plant Diseases/microbiology/prevention &amp; control ; Bacteria/genetics ; Fungi ; }, abstract = {Tomato (Solanum lycopersicum) is an essential crop worldwide, yet it remains highly vulnerable to severe fungal and bacterial diseases. Traditional chemical-based disease management strategies, aimed at controlling these diseases face increasing scrutiny, due to concerns regarding pathogen resistance, environmental degradation, and potential health risks to humans. This has catalyzed the exploration of sustainable alternatives, with biological control emerging as a viable and promising strategy. Endophytic and epiphytic microorganisms are pivotal as biocontrol agents (BCAs), employing diverse strategies, such as generating antimicrobial substances, enzymes, and volatile organic compounds (VOCs), to suppress pathogen growth and enhance plant health. The efficacy of these antagonistic microorganisms is influenced by the cultivation systems employed, with significant variations observed between soil and hydroponic environments. Factors such as nutrient dynamics and microbial interactions play crucial roles in determining the success of BCAs in these different settings. The advent of metagenomic tools has transformed the landscape of microbial community research, facilitating the identification of functional genes associated with antagonistic activities and the adaptation of these microorganisms to diverse environmental conditions. This review aims to elucidate the potential of endophytic and epiphytic microorganisms in biological control, examining their mechanisms of action, the impact of cultivation systems on their effectiveness, and the application of metagenomics to optimize their use in sustainable disease management strategies for tomato crops.}, }
@article {pmid41011536, year = {2025}, author = {Cai, P and Gan, S and Ning, Z and Zhang, M}, title = {Synergistic Potential of Contamination Remediation and Carbon Fixation: Functional Resilience of Carbon Fixation in Petroleum Hydrocarbon-Degrading Microbial Communities Under Enhanced Natural Attenuation.}, journal = {Microorganisms}, volume = {13}, number = {9}, pages = {}, doi = {10.3390/microorganisms13092205}, pmid = {41011536}, issn = {2076-2607}, support = {42407064//the National Natural Science Foundation of China/ ; }, abstract = {Enhanced Natural Attenuation (ENA) can accelerate pollutant degradation by adding electron acceptors or nutrients. However, its impact on carbon-fixing microorganisms, which are widely found in the natural attenuation process, remains unclear. In this study, four types of ENA materials were added in batch experiments. Chemical analysis and metagenomic sequencing were employed to analyze the degradation kinetics of petroleum hydrocarbons, the consumption pattern of nitrate, as well as the functional genes and population evolution characteristics of carbon-fixing microorganisms. Results showed that nitrate-based enhancement materials significantly improved the petroleum hydrocarbon degradation rate but suppressed the expression of some carbon fixation genes, such as those involved in the Calvin-Benson-Bassham cycle. Nevertheless, the overall abundance of carbon fixation genes did not show a notable decline. Dominant bacterial genera such as Pseudomonas and Achromobacter possessed both hydrocarbon degradation and carbon fixation capabilities. Although the calcium peroxide treatment group only achieved a 40% petroleum hydrocarbon degradation rate, it significantly promoted the abundance of carbon fixation genes involved in the reductive tricarboxylic acid cycle pathway. Therefore, ENA alters carbon fixation pathways but does not diminish carbon fixation potential, indicating its potential for synergistically achieving pollution remediation and carbon fixation.}, }
@article {pmid41011523, year = {2025}, author = {Gomes, AG and Sousa, AC and Carreira, JS and Oliveira, A and Justino, MC and Santos, CA}, title = {Unveiling Bacterial Diversity in Portuguese Red Wine Effluents Through a Metagenomic Approach.}, journal = {Microorganisms}, volume = {13}, number = {9}, pages = {}, doi = {10.3390/microorganisms13092192}, pmid = {41011523}, issn = {2076-2607}, support = {101023567//REDWine project funded from Bio-based Industries Joint/ ; }, abstract = {The sustainable reuse of agro-industrial effluents requires a detailed understanding of their microbial composition, especially in the context of integrated vineyard-winery ecosystems. This study investigated the bacterial communities present in winery effluents generated during the early stages of red wine production, using samples collected at a winery in the Setúbal Peninsula, Portugal. Metagenomic analysis targeting the 16S rRNA gene was used to characterise microbial diversity and identify taxa with potential relevance for biotechnology and environmental applications. The effluents exhibited a diverse microbiome, including Prevotella paludivivens, species from the Lactobacillus genus, and members of the Clostridiaceae family, the latter representing about 5% of the total community. Functional profiling of lactic acid bacteria revealed the predominance of Oenococcus and Lactobacillus genera, highlighting adaptive traits that may be beneficial under stress conditions. These results suggest that winery effluents, often considered waste, harbour microbial communities with functional potential that extends beyond fermentation, contributing to a broader grape-wine microbial system. The findings emphasise the value of studying winemaking byproducts as reservoirs of microbial diversity and as resources for developing innovative and sustainable applications in biotechnology and environmental management within the wine industry.}, }
@article {pmid41011518, year = {2025}, author = {Lu, C and Qian, G and Luo, L and Peng, Y and Ren, H and Yan, B and Xu, Y}, title = {Elucidation of Mechanism of Soil Degradation Caused by Continuous Cropping of Dictyophora rubrovalvata Using Metagenomic and Metabolomic Technologies.}, journal = {Microorganisms}, volume = {13}, number = {9}, pages = {}, doi = {10.3390/microorganisms13092186}, pmid = {41011518}, issn = {2076-2607}, support = {2020-530622-01-01-034399//the Basic Research Program of Yunnan Province/ ; FWCY-ZNT2024021//the Science and Technology Program of Yunnan Universities Serving Key Industries/ ; }, abstract = {Dictyophora rubrovalvata is a soil-cultivated edible fungus with high economic and medicinal value, yet its continuous cultivation is frequently hindered by cropping obstacles. To elucidate the underlying ecological mechanisms, this study employed metagenomic sequencing and untargeted metabolomics (UHPLC-OE-MS) to analyze the changes in soil microbial communities and metabolite profiles under different continuous cropping treatments (CC0: Uncultivated; CC1: one cropping cycle; CC2: two cropping cycle; CC3: three cropping cycle.). Continuous cropping significantly decreased soil pH from 7.94 to 7.52 and available phosphorus (AP) from 213.69 mg/kg to 15.7 mg/kg, while increasing available nitrogen (AN) from 284.5 mg/kg to 886.33 mg/kg. The Shannon index of fungal communities rose from 3.15 to 4.55. Notably, the relative abundance of the beneficial bacterium Sphingomonas declined from 15.63% to 1.12%, whereas the pathogenic fungus Aspergillus increased from 0.06% to 3.06%. A total of 1408 secondary metabolites were detected, with 39 significantly upregulated and 416 downregulated in CC3 compared to CC0. Several autotoxic compounds, including ferulic acid, hydroxycinnamic acid derivatives, and jasmonic acid, were enriched and positively correlated with pathogenic fungi. These results suggest that continuous cropping may reshape the soil microecosystem by promoting autotoxic metabolite accumulation and pathogenic Microbial enrichment, thereby contributing to soil degradation and cropping obstacles.}, }
@article {pmid41011492, year = {2025}, author = {Wedemeyer, J and Lechleiter, N and Vernunft, A and Junker, J and Homeier-Bachmann, T}, title = {Impact of Organic and Conventional Husbandry Systems on the Gut Microbiome and Resistome in Pigs.}, journal = {Microorganisms}, volume = {13}, number = {9}, pages = {}, doi = {10.3390/microorganisms13092161}, pmid = {41011492}, issn = {2076-2607}, support = {28KIDA001//Federal Ministry of Agriculture, Food and Regional Identity (BMLEH)/ ; }, abstract = {The gut microbiome of pigs is important for energy supply and impacts the animals' health. Additionally, the microbiota can act as a reservoir for antimicrobial resistance genes (ARG). Different husbandry systems in pig farming can influence the microbiome and the overall composition of the resistome, i.e., the complete collection of ARG. In this study, pooled fecal samples were collected repeatedly in one pig farm over a period of two years. One group of animals was kept in organic husbandry conditions with access to an outdoor run, while the other group was kept according to conventional standards. Shotgun metagenomic sequencing was performed on the samples. Additionally, E. coli isolates were subjected to whole-genome sequencing and antimicrobial susceptibility testing. Significant differences were observed in alpha and beta diversity in the microbiome between the two husbandry systems. Families enriched in the organic group included Prevotellaceae, Lachnospiraceae, and Cellulosilyticaceae, while Methanobacteriaceae showed a higher abundance in the conventional group. In the resistome, the differences were smaller, and the dominant genes were the same in both groups. However, there was a significant difference in beta diversity. In addition, the overall frequency of ARG, normalized by 16S rRNA gene content, was on average higher in the organic group. Overall, the husbandry system shaped the microbiome and-albeit to a lesser extent-the resistome in pigs from the same farm.}, }
@article {pmid41011466, year = {2025}, author = {Wang, Z and Hu, L and Wang, L and Liu, R}, title = {Halogenation and Dehalogenation Potential of Microorganisms in Yangtze River Waters.}, journal = {Microorganisms}, volume = {13}, number = {9}, pages = {}, doi = {10.3390/microorganisms13092133}, pmid = {41011466}, issn = {2076-2607}, support = {42276149, 92251303//National Natural Science Foundation of China/ ; }, abstract = {The discharge of pollutants into rivers has been increasing with the rapid industrial development and extensive agricultural use of pesticides and herbicides. Halogenated organic compounds (HOCs) represent a significant class of environmental pollutants. It has been found that microorganisms have the ability not only to degrade HOCs but also to synthesize them. Little is known about the halogenation and dehalogenation potential of microorganisms in river waters. In this study, we investigated the halogenation and dehalogenation potentials of microorganisms in the Yangtze River, which originates from the Tibetan Plateau, flows through southwestern, central and eastern China, and finally joins the East China Sea. A systematic metagenomic and bioinformatics analysis identified and quantified genes encoding four dehalogenases and two halogenases, providing fundamental data for the halogen cycle in the Yangtze River water body. The study showed that the microbial community in the Yangtze water body was mainly associated with dehalogenation potential, and the relative abundance of dehalogenase genes was higher than that of halogenase genes. Among the microorganisms with halogenation and dehalogenation potentials, Pseudomonadota and Actinomycetota dominated. Some microorganisms possessed both halogenation and dehalogenation functions, suggesting a potential adaptive strategy to environmental fluctuations. The presence of diverse and complete dehalogenation metabolic pathways highlights the microbial potential for bioremediation. These microorganisms not only contribute to the degradation of halogenated organic matter but also play crucial roles in carbon, nitrogen, and sulfur cycling. This study provides essential data for understanding microbial halogenation and dehalogenation potential in the Yangtze River, offering insights into the microbial-driven biogeochemical cycling mechanisms in its waters.}, }
@article {pmid41011452, year = {2025}, author = {Ramírez-Hernández, MDC and Gaytán-Cervantes, J and González-Torres, C and Loyola-Cruz, M&#xc1; and García-Mendiola, RE and Cruz-Cruz, C and Cortés-Ortíz, IA and García-Moncada, E and López-Flores, T and Durán-Manuel, EM and Gómez-Mancilla, N and Oviedo-López, MF and Jiménez-Zamarripa, CA and Rojas-Bernabé, A and García-Hernández, OA and Puente-Rivera, J and López-Ornelas, A and Nieto-Velázquez, NG and Blanco-Hernández, DMR and Castañeda-Ortega, JC and Hernández-Castellanos, B and Anaya-Saavedra, G and Calzada-Mendoza, CC and Bello-López, JM}, title = {Oral Microbiota Dysbiosis in Male HIV Patients: Comparative Analysis of Candidiasis and HPV-Associated Lesions.}, journal = {Microorganisms}, volume = {13}, number = {9}, pages = {}, doi = {10.3390/microorganisms13092121}, pmid = {41011452}, issn = {2076-2607}, abstract = {Progressive immune damage associated with Human Immunodeficiency Virus (HIV) alters mucosal homeostasis, favouring oral microbial imbalance and the development of opportunistic infections. The aim of this study was to characterize the composition and structure of the oral microbiota in different clinical conditions of HIV infection. A cross-sectional study was conducted in 99 Mexican men divided into five groups: HIV-negative controls, newly diagnosed without antiretroviral treatment, virally suppressed, with oral candidiasis, and with HPV infection. Metagenomic DNA was obtained from salivary samples, and the V1-V3 region of the 16S rRNA gene was massively sequenced. Taxonomic profiles, alpha/beta diversity, differential abundance, microbial co-occurrence networks and degree of dysbiosis were analysed. The results showed distinctive profiles between the groups. Alpha and beta diversity was significantly higher in the groups with oral Candida and HPV lesions, reflecting a disturbance of microbial balance. Differential abundance analysis revealed an increase in Streptococcus, Veillonella, Lactobacillus and Actinomyces genera in HIV patients, while healthy subjects showed higher abundance of Neisseria, Treponema, and Rothia, associated with a eubiotico state. The group of patients with HPV lesions had the highest number of taxa with differential abundance, suggesting an ecological environment altered by the lesion. Analysis of co-occurrence networks revealed a progressive pattern of microbial complexity: controls presented simple networks with weak positive correlations, while HIV groups showed increased connection density and appearance of structured nuclei. The group of patients with HPV lesions presented the highest connectivity, with multiple strongly correlated cores and core nodes such as Prevotella melaninogenica and Shuttleworthia. The dysbiosis score increased progressively from healthy subjects to those with HPV lesions, indicating a gradient of oral microbial disruption. These findings suggest that HIV immunosuppression and the presence of oral lesions are associated with enhanced dysbiosis, although their individual contributions could not be independently assessed due to the absence of non-HIV lesion controls. The integration of microbial networks and dysbiosis scores could be useful for assessing mucosal and immune health in people with HIV and used as biomarkers of clinical progression.}, }
@article {pmid41011430, year = {2025}, author = {Hu, CY and Yao, SF and Li, YF and Wang, QZ and Li, YJ and Sun, C and Liu, J and Zhao, ZX}, title = {Differences in Non-Pathogenic Lung-Colonizing Bacteria Among Patients with Different Types of Pneumonia: A Retrospective Study.}, journal = {Microorganisms}, volume = {13}, number = {9}, pages = {}, doi = {10.3390/microorganisms13092099}, pmid = {41011430}, issn = {2076-2607}, support = {81970038//Natural Science Foundation of Guangdong Province/ ; SL2022A04J00473//Science and Technology Projects in Guangzhou, China/ ; SL2023A04J00962//Science and Technology Projects in Guangzhou, China/ ; 202201020299//Science and Technology Projects in Guangzhou, China/ ; }, abstract = {The clinical impact of non-pathogenic colonizing bacteria in pneumonia remains poorly understood. This retrospective study analyzed the mutual influence of pneumonia and non-pathogenic bacterial flora in the lungs. Bronchoalveolar lavage fluid samples from 483 patients were analyzed using metagenomic next-generation sequencing, and differences in colonizing bacteria in different pneumonia types and their impact on disease prognosis were determined. Patients with bacterial pneumonia exhibited higher and lower colonization rates of Granulicatella adiacens and Streptococcus parasanguinis, respectively, than those without. Fungal pneumonia showed lower and higher colonization rates of Abiotrophia defectiva and Veillonella parvula, respectively; viral pneumonia showed higher colonization rates of Abiotrophia defectiva and Streptococcus mitis. Rothia mucilaginosa was associated with shorter duration of fever, and lower risks of sepsis and multiple organ dysfunction syndrome (MODS). Prevotella melaninogenica was associated with lower risks of sepsis and MODS. These findings suggest that select non-pathogenic bacteria might influence disease severity and also highlight the need for further investigation into microbiome-based therapeutic strategies, potentially guiding personalized pneumonia treatments.}, }
@article {pmid41011405, year = {2025}, author = {Malcom, HB and Bowes, DA}, title = {Use of Wastewater to Monitor Antimicrobial Resistance Trends in Communities and Implications for Wastewater-Based Epidemiology: A Review of the Recent Literature.}, journal = {Microorganisms}, volume = {13}, number = {9}, pages = {}, doi = {10.3390/microorganisms13092073}, pmid = {41011405}, issn = {2076-2607}, abstract = {Antimicrobial resistance (AMR) presents a global health challenge, necessitating comprehensive surveillance and intervention strategies. Wastewater-based epidemiology (WBE) is a promising tool that can be utilized for AMR monitoring by offering population-level insights into microbial dynamics and resistance gene dissemination in communities. This review (n = 29 papers) examines the current landscape of utilizing WBE for AMR surveillance with a focus on methodologies, findings, and gaps in understanding. Reported methods from the reviewed literature included culture-based, PCR-based, whole genome sequencing, mass spectrometry, bioinformatics/metagenomics, and antimicrobial susceptibility testing to identify and measure antibiotic-resistant bacteria and antimicrobial resistance genes (ARGs) in wastewater, as well as liquid chromatography-tandem mass spectrometry to measure antibiotic residues. Results indicate Escherichia coli, Enterococcus spp., and Pseudomonas spp. are the most prevalent antibiotic-resistant bacterial species with hospital effluent demonstrating higher abundances of clinically relevant resistance genes including bla, bcr, qnrS, mcr, sul1, erm, and tet genes compared to measurements from local treatment plants. The most reported antibiotics in influent wastewater across studies analyzed include azithromycin, ciprofloxacin, clindamycin, and clarithromycin. The influence of seasonal variation on the ARG profiles of communities differed amongst studies indicating additional factors hold significance when examining the conference of AMR within communities. Despite these findings, knowledge gaps remain, including longitudinal studies in multiple and diverse geographical regions and understanding co-resistance mechanisms in relation to the complexities of population contributors to AMR. This review underscores the urgent need for collaborative and interdisciplinary efforts to safeguard public health and preserve antimicrobial efficacy. Further investigation on the use of WBE to understand these unique population-level drivers of AMR is advised in a proposed framework to inform best practice approaches moving forward.}, }
@article {pmid41011396, year = {2025}, author = {Sultankulova, KT and Kozhabergenov, NS and Shynybekova, GO and Chervyakova, OV and Usserbayev, BS and Alibekova, DA and Zhunushov, AT and Orynbayev, MB}, title = {Metagenomic Detection of RNA Viruses of Hyalomma asiaticum Ticks in the Southern Regions of Kazakhstan.}, journal = {Microorganisms}, volume = {13}, number = {9}, pages = {}, doi = {10.3390/microorganisms13092064}, pmid = {41011396}, issn = {2076-2607}, abstract = {Hyalomma ticks are known for their ability to transmit a wide range of pathogens, posing a significant threat to both human and animal health. The viral communities associated with Hyalomma asiaticum ticks in Kazakhstan remain largely unexplored. Using high-throughput sequencing on the Ion Torrent platform, nine RNA viruses belonging to seven families were identified. These viruses were associated with H. asiaticum ticks collected in 2024 in southern Kazakhstan. The detected viruses-including Bole tick virus 1 (Phenuiviridae), Bole tick virus 3 (Chuviridae), Bole tick virus 4 (Flaviviridae), Hubei toti-like virus 24 (Totiviridae), Kashgar totiv tick virus 1 (Totiviridae), Lonestar tick totivirus (Totiviridae), Qingyuan parti tick virus 1 (Partitiviridae), and Taishun tick virus (Rhabdoviridae)-had previously been reported only in China. This study provides the first documented evidence of the presence of RNA viruses previously unreported in Kazakhstan within H. asiaticum tick populations. A newly isolated Kazakhstan strain of Wad Medani virus (Sedoreoviridae), identified from H. asiaticum, shares genetic similarities with Russian strains, suggesting a common epidemiological landscape across Central Eurasia. The detection of novel RNA viruses in Kazakhstan highlights the need for ongoing surveillance, as their impact on human and animal health remains insufficiently understood.}, }
@article {pmid41011387, year = {2025}, author = {Wang, Y and Deng, C and Sui, M and Wei, P and Duan, B and Li, Z and Zou, F}, title = {Acute Toxoplasma gondii Infection Drives Gut Microbiome Dysbiosis and Functional Disruption in Mice as Revealed by Metagenomic Sequencing.}, journal = {Microorganisms}, volume = {13}, number = {9}, pages = {}, doi = {10.3390/microorganisms13092056}, pmid = {41011387}, issn = {2076-2607}, support = {202449CE340019//the Yunnan Key Laboratory of Veterinary Etiological Biology/ ; U2202201//the NSFC-Yunnan Joint Fund/ ; 202401AT070440//the Yunnan Fundamental Research Projects/ ; 2024Y339//the Scientific Research Fund of Education Department of Yunnan Province/ ; No.XXX//the Yunnan Provincial University Key Industry Service Science and Technology Program/ ; }, abstract = {Toxoplasma gondii is a widely distributed intracellular parasite that disrupts host immune and metabolic homeostasis. Although accumulating evidence highlights the role of gut microbiota in parasitic infections, the effects of acute T. gondii infection on host gut microbial ecology remain poorly understood. In this study, metagenomic sequencing technology was used to systematically analyze the composition and functional alterations of the ileal microbiota in BALB/c mice on day 10 post-infection. Compared to uninfected controls, T. gondii infected mice exhibited a significant reduction in microbial diversity and a pronounced shift in community structure. Notably, there was an expansion of Proteobacteria, particularly the Enterobacteriaceae family, alongside a marked decline in beneficial taxa such as Actinobacteria and Bacillota. Functional annotation using the KEGG and CAZy databases revealed enrichment of metabolic pathways related to glycolysis/gluconeogenesis, O-antigen nucleotide sugar biosynthesis, bacterial secretion systems, and biofilm formation-Escherichia coli in the infected microbiota. These findings provide novel insights into the dysbiosis of gut microbiota and host-microbe interactions during acute T. gondii infection.}, }
@article {pmid41011380, year = {2025}, author = {Gao, X and Chen, Q and Sha, Y and He, Y and Liu, X and Chen, X and Shao, P and Huang, W and He, Y and Li, M and Hao, Z and Shi, B and Xu, J}, title = {Study on the Plateau Adaptive Synergistic Mechanism of Rumen Microbiome-Metabolome-Resistome in Tibetan Sheep.}, journal = {Microorganisms}, volume = {13}, number = {9}, pages = {}, doi = {10.3390/microorganisms13092049}, pmid = {41011380}, issn = {2076-2607}, support = {2025CYZC-043//Industrial Support Program for Universities in Gansu Province/ ; 32260820//National Natural Science Foundation of China/ ; GAU-XKTD-2022-21//Discipline Team Project of Gansu Agricultural University/ ; 2025CXZX-824//Post-graduate Innovation Star Project of Gansu Province/ ; 24ZYQL003//Projects of the Central Government's Funds for Guiding Local Scientific and Technological Development/ ; }, abstract = {Tibetan sheep are an important livestock breed adapted to the extreme environment of the Qinghai-Tibet Plateau (QTP). Their energy metabolism and environmental adaptability are highly dependent on the rumen microbiome. However, systematic comparisons of the rumen microbiome, its functions, and the resistome between plateau-adapted breeds and lowland breeds remain insufficient. In this study, 6 Tibetan sheep (TS) and 6 Hu sheep (HS) were selected. All the selected sheep had a body weight of 34 kg (±0.5 kg) and an age of 1 year (±1 month) and were all managed under local traditional natural grazing (without supplementary feeding). Using metagenomics and metabolomics techniques, systematic comparative analysis was conducted on the differences in rumen microbial community structure, functions, resistome, and metabolites between the two breeds. Metagenomic analysis showed that at the phylum level, the abundance of Bacteroidetes in the rumen of TS was significantly higher than that in HS (p < 0.05); at the genus level, the abundance of Bacteroides in TS was also significantly higher (p < 0.05). Carbohydrate-active enzymes (CAZy) analysis indicated that the abundance of Glycosyltransferases (GTs) and Carbohydrate-Binding Modules (CBMs) in the rumen of TS were significantly upregulated (p < 0.05), while HS was rich in various Glycoside Hydrolases (GHs). Comprehensive Antibiotic Resistance Database (CARD) analysis revealed that more than 60% of the Antibiotic Resistance Genes (ARGs) in the rumen of HS were present at higher levels than those in TS. Metabolomics identified a large number of differential metabolites, among which metabolites such as 2E,6Z,8Z,12E-hexadecatetraenoic acid, Leukotriene F4, and Tenurin were significantly upregulated in the rumen of TS. Correlation analysis showed that rumen microbial flora and their metabolites jointly act to regulate rumen ARGs. Specifically, microorganisms including Firmicutes and Succiniclasticum had a significantly positive correlation with ARGs such as rpoB2 (p < 0.05), while differential metabolites like endomorphin-1 and Purothionin AII exhibited a significantly negative correlation with ARGs such as rpoB2 (p < 0.05). Therefore, compared with HS, the synergistic effect of the rumen microbial flora, their metabolites, and the resistome in TS is an important characteristic and strategy for their adaptation to the hypoxic environment of the QTP, and also contributes to the formation of their unique rumen resistome. Despite being reared in the same plateau environment, the rumen microbiome of HS still retains low-altitude characteristics, which are manifested as high GHs activity and high ARGs abundance.}, }
@article {pmid41011379, year = {2025}, author = {Trogu, T and Carrera, M and Tolini, C and Nucci, A and Canziani, S and Grilli, G and Rapi, MC and Manfredini, S and Rubini, S and Lelli, D and Carta, V and Bertasio, C and Sozzi, E and Lavazza, A and Moreno, A}, title = {Identification of Reassortant Mammalian Orthoreovirus Strains in European Hedgehogs (Erinaceus europaeus): Genomic Insights and Host Association.}, journal = {Microorganisms}, volume = {13}, number = {9}, pages = {}, doi = {10.3390/microorganisms13092047}, pmid = {41011379}, issn = {2076-2607}, support = {PE00000007, INF-ACT//NextGeneration EU-MUR PNRR Extended Partnership initiative on Emerging Infectious Diseas-es/ ; B93C22001210001//Italian Health Ministry, CCM_SURVEID, Pilot Study For Surveillance Of Potential Emerging Infectious Disease (Eids) Threats Of Viral Origin Using A Diagnostic Platform Based On Next-Generation Metagenomic Sequencing (Mngs)/ ; }, abstract = {Thanks to its ethological and physiological characteristics, the hedgehog is a synanthropic species of particular importance for the maintenance and possible spread of pathogens, some of which are zoonotic. Among these, we can include the mammalian orthoreovirus (MRV), which is characterized by respiratory, gastrointestinal, and neurological symptoms in both animals and humans. MRV is characterized by a high capacity for genetic reassortment and intragenic rearrangement, and the ability to infect a wide range of mammals. This work aims to investigate the presence of MRVs and its genomic characterization in hedgehogs. During the two-year period from 2022 to 2023, the intestine and lungs were collected from 293 hedgehogs and subjected to real-time PCR to detect the L1 gene. Positive samples were subjected to a typing RT-PCR targeting a portion of the S1 gene and then to sequencing. A total of 38 hedgehogs tested positive by real-time PCR (p = 13%). Typing RT-PCR demonstrated the positivity of 25 samples for serotype 3. Four samples, representative of the main groups recognized during the phylogenetic analysis, underwent whole genome sequencing, revealing the presence of reassortment phenomena between strains related to bats, chamois, and human MRVs.}, }
@article {pmid41011356, year = {2025}, author = {Masirika, LM and Hewins, B and Toloue Ostadgavahi, A and Dutt, M and Mambo, LM and Udahemuka, JC and Ndishimye, P and Mbiribindi, JB and Siangoli, FB and Kelvin, P and Langille, MGI and Kelvin, DJ and Flores, L and Sganzerla Martinez, G and Kumar, A}, title = {The Trans-Kingdom Spectrum of Mpox-like Lesion Pustules of Suspect Patients in the Mpox Clade Ib Outbreak in Eastern Democratic Republic of the Congo.}, journal = {Microorganisms}, volume = {13}, number = {9}, pages = {}, doi = {10.3390/microorganisms13092025}, pmid = {41011356}, issn = {2076-2607}, support = {CIHR MZ1 187236/CAPMC/CIHR/Canada ; 2023-2565//Research Nova Scotia/ ; N/A//Dalhousie Medical Research Foundation/ ; N/A//Li-Ka Shing Foundation/ ; }, abstract = {During infectious disease outbreaks, acquiring genetic data across various kingdoms offers essential information to tailor precise treatment methodologies and bolster clinical, epidemiological, and public health awareness. Metagenomics sequencing has paved the way for personalized treatment approaches and streamlined the monitoring process for both co-infections and opportunistic infections. In this study, we conducted long-read metagenomic DNA sequencing on mpox-like lesion pustules from six suspected patients who were positive and confirmed to be infected with MPXV during the MPXV subclade Ib outbreak in the Eastern Democratic Republic of the Congo. The sequenced data were taxonomically classified as bacterial, fungal, and viral in composition. Our results show a wide spectrum of microorganisms present in the lesions. Bacteria such as Corynebacterium amycolatum, Gardnerella vaginalis, Enterococcus faecium, Enterobacter clocae, Staphylococcus epidermidis, and Stenotrophomonas maltophilia were found in the lesions. The viral classification of the reads pointed out the absolute predominance of the monkeypox virus. Taken together, the outcomes of this investigation underscore the potential involvement of microorganisms in mpox lesions and the possible role that co-infections played in exacerbating disease severity and transmission during the MPXV subclade Ib outbreak.}, }
@article {pmid41011355, year = {2025}, author = {Black, CA and So, W and Benavides, R and Mercer, JA and Dallas, SS and Shurko, JF and Bandy, SM and Encino, BA and Lipscomb, JS and Vargus, A and Frei, CR and Lee, GC}, title = {Pathoadapative Genomic Determinants of Staphylococcus aureus Community Skin Infections and Nasal Colonization.}, journal = {Microorganisms}, volume = {13}, number = {9}, pages = {}, doi = {10.3390/microorganisms13092023}, pmid = {41011355}, issn = {2076-2607}, abstract = {Staphylococcus aureus is a leading cause of skin and soft tissue infections (SSTIs), yet the bacterial genomic adaptations underlying the transition from nasal colonization to invasive infection remain incompletely defined. We sequenced and analyzed 157 S. aureus isolates (126 from SSTIs and 31 from asymptomatic nasal colonization) from a primary care network in South Texas. Using genome-wide association studies, non-synonymous single-nucleotide variant (NSNV) profiling, and machine learning, we identified strain-specific adaptations in metabolic and regulatory pathways. SSTI isolates exhibited significant enrichment of nitrogen assimilation, purine biosynthesis, menaquinone production, and anaerobic respiration genes. Elevated copy number and colocalization of phage-linked metabolic genes-including nirB, narH, and nifR3-suggest a pathoadaptive genomic island supporting infection-specific energy generation. The enrichment of α/β-hydrolase domain-encoding genes was associated with clinical severity. To quantify severity, we developed the Purulent Ulcer Skin (PUS) score, which integrates wound size, drainage, and erythema. The α/β-hydrolase and lipoprotein genes were significantly associated with higher PUS scores (higher SSTI severity) and phage-encoded virulence gene products were linked to larger wound size. Machine learning prioritized purL and other metabolic loci as key infection classifiers. NSNVs and unitig-level changes co-localized within nutrient transport, stress resistance, and cytolytic genes, supporting a model of multi-layered genomic selection. Metagenomic assemblies of nasal microbiota were enriched for Staphylococcus, Enterococcus, and Micrococcus species, core metabolic pathways, and taxon-specific virulence determinants. This underscores the roles of metabolic and virulent co-networks within nasal commensals and their adaptive capacity for pathogenic transition. These findings provide a potential genomic blueprint of S. aureus pathoadaptation during SSTI and are a step towards the development of novel therapeutic targets.}, }
@article {pmid41011346, year = {2025}, author = {Wang, S and Li, L and Fu, X and Zhong, H and Zhang, R and Sui, X}, title = {Shrub Expansion Impacts on Carbon, Nitrogen, and Sulfur Cycles and Microorganism Communities in Wetlands in Northeastern China.}, journal = {Microorganisms}, volume = {13}, number = {9}, pages = {}, doi = {10.3390/microorganisms13092014}, pmid = {41011346}, issn = {2076-2607}, support = {CZKYF2021-2-A005//the Research expenses of provincial research institutes in Heilongjiang/ ; CZKYF2025-1-B010//the Research expenses of provincial research institutes in Heilongjiang/ ; PL2024D019//the Natural Sciences Foundation of Heilongjiang Province/ ; ZDYF2024ZR01//the Key Research and Development Program of Heilongjiang Academy of Sciences/ ; CGZH2025ZR02//the special project for the transformation of scientific and technological achievements/ ; }, abstract = {Marsh wetland degradation and shrub expansion, driven by human activities and climate change, can impact carbon, nitrogen, and sulfur cycles by soil microorganisms. There is a paucity of systematic and in-depth research on the impact of shrub expansion in temperate wetlands on soil element cycles, which is a pressing scientific issue that demands resolution. This study used metagenomic sequencing and soil analysis methods to investigate the impact of shrub expansion in the Sanjiang Plain wetlands on carbon, nitrogen, and sulfur cycles in temperate wetland soils, as well as on functional microbial communities. Shrub expansion significantly altered soil carbon, nitrogen, and sulfur cycle processes and the composition (β diversity) of associated functional microbial communities, despite minimal changes in overall α diversity. Significant shifts occurred in the abundance of cycle pathways and related functional genes. Ammonia nitrogen, moisture, and total phosphorus were identified as the primary factors influencing these cycles and the functional microbial communities. Changes in the abundance of specific cycling pathways following shrub expansion are key drivers of functional community structure transformation. These changes may significantly reduce the long-term carbon sequestration potential of wetlands and affect regional climate feedback by altering greenhouse gas fluxes. The findings provide a theoretical basis for managing shrub expansion and assessing wetland function.}, }
@article {pmid41011342, year = {2025}, author = {Li, L and Zhao, J and Liu, C and Deng, Y and Du, Y and Liu, Y and Wu, Y and Wu, W and Pan, X}, title = {Spatial Differentiation of Heavy Metals/Metalloids, Microbial Risk Genes and Soil Microbiota in a Sulfur-Contaminated Landscape.}, journal = {Microorganisms}, volume = {13}, number = {9}, pages = {}, doi = {10.3390/microorganisms13092010}, pmid = {41011342}, issn = {2076-2607}, support = {202203AC100001//Yunnan Province Science and Technology Plan project/ ; }, abstract = {Legacy sulfur smelting has left behind complex contamination landscapes, yet the spatial structuring of microbial risks and adaptation strategies across soil profiles remains insufficiently understood. Microbial risk genes, including those conferring resistance to antibiotic resistance (ARGs), biocide and metal resistance (BRGs/MRGs), and virulence (VFGs), are increasingly recognized as co-selected under heavy metal stress, posing both ecological and public health concerns. In this study, we integrated geochemical analyses with metagenomic sequencing and functional annotation to jointly characterize the vertical (0-7 m) and horizontal (~2 km) distribution of heavy metals/metalloids, microbial communities, and functional risk genes at a historic smelting site in Zhenxiong, Yunnan. Heavy metals and metalloids such as arsenic (As), chromium (Cr), copper (Cu), and lead (Pb) showed clear accumulation with depth, while significantly lower concentrations were observed in both upstream and downstream locations, revealing persistent vertical and horizontal pollution gradients. Correspondingly, resistance and virulence genes were co-enriched at contaminated sites, suggesting potential co-selection under prolonged stress. LEfSe analysis revealed distinct ecological patterns: vertically, upper layers were dominated by nutrient-cycling and mildly stress-tolerant taxa, while deeper layers favored metal-resistant, oligotrophic, and potentially pathogenic microorganisms; horizontally, beneficial and diverse microbes characterized low-contamination zones, whereas heavily polluted areas were dominated by resistant and stress-adapted genera. These findings provide new insights into microbial resilience and ecological risk under long-term smelting stress.}, }
@article {pmid41011328, year = {2025}, author = {Boudreau, PD}, title = {Metagenomic Assembled Genomes of a Pseudanabaena Cyanobacterium and Six Heterotrophic Strains from a Xenic Culture.}, journal = {Microorganisms}, volume = {13}, number = {9}, pages = {}, doi = {10.3390/microorganisms13091996}, pmid = {41011328}, issn = {2076-2607}, support = {5P30GM122733-03/GM/NIGMS NIH HHS/United States ; }, abstract = {Sequencing cyanobacteria from xenic cultures is often challenging when their DNA extracts are confounded by DNA from their heterotrophic microbiome. Using an iterative DNA lysis protocol can fractionate between DNA from the cyanobacterium and the heterotrophic strains. To further demonstrate the utility of this protocol, it was used to sequence another xenic culture of cyanobacteria. This effort led to the assembly of a megabase-length cyanobacterial chromosome; however, repeated ribosomal regions created assembly issues even after adding data from another sequencing run to improve coverage. A separate DNA preparation from a single cell lysis step was also run for comparison but yielded a markedly lower proportion of cyanobacterial reads (<2%). Instead, the circular cyanobacterial chromosome was closed with targeted amplicon sequencing. Phylogenetic analysis assigned this strain to the genus Pseudanabaena. Within the metagenomic assembly were the genomes of six heterotrophic strains, preliminarily assigned as belonging to the genera Acidovorax, Hydrogenophaga, Lysobacter, Novosphingobium, Sediminicoccus, and Tabrizicola. Lysobacter sp. BL-A-41-H3's chromosome was also assembled as a closed circular contig. This study demonstrates that iterative lysis enriches for cyanobacterial DNA and enables concurrent genome assembly of cohabitating heterotrophs alongside the host cyanobacterium.}, }
@article {pmid41011326, year = {2025}, author = {Damiati, LA}, title = {Rhizospheric and Endophytic Microbial Communities Associated with Leptadenia pyrotechnica in Arid Zones.}, journal = {Microorganisms}, volume = {13}, number = {9}, pages = {}, doi = {10.3390/microorganisms13091994}, pmid = {41011326}, issn = {2076-2607}, abstract = {Desert plants host specialized microbiomes that contribute to their survival under extreme conditions; yet, niche and specific microbial dynamics remain poorly understood. In this study, we used 16S rRNA amplicon sequencing to characterize the bacterial communities associated with Leptadenia pyrotechnica, which is a desert-adapted shrub. Five representative sample types were analyzed: rhizospheric soil from a non-arid adjacent location (control; S1); rhizospheric soil from the arid site (S4); and stem endosphere from the arid site (S5, S6, and S7). For each sample type, three biological replicates were collected from different healthy plants to ensure independence. Sequencing yielded high-quality datasets (89,000-134,000 reads/sample) with ASV retention ratios of 68-80%, confirming their sufficient depth for diversity profiling. Alpha diversity indices revealed a markedly greater richness in rhizospheric samples (e.g., S1 Shannon: 3.04; 530 ASVs) than in endosphere samples (Shannon < 1.0; ASVs ≤ 33), consistent with known gradients in desert plant microbiomes. Rarefaction curves confirmed the completeness of sampling. Beta diversity analyses, including PCoA and hierarchical clustering, showed clear segregation between rhizospheric and endophytic communities, indicating strong compartment-specific structuring. The rhizosphere was dominated by Actinobacteria (48%), Proteobacteria (32%), and Firmicutes (10%), whereas the stem endosphere was enriched in Proteobacteria (45%) and Actinobacteria (40%). Taxonomic profiling revealed that Bacillota and Actinomycetota dominated rhizospheric soils, including Bacillus licheniformis, while stem tissues were enriched in Cyanobacteriota and Alphaproteobacteria, suggesting host-driven filtering. Genera such as Cupriavidus, Massilia, and Noviherbaspirillum were exclusive to the rhizosphere, while Paracholeplasma appeared uniquely in stem sample S6. Archaea and rare phyla were nearly absent. The current findings indicate that L. pyrotechnica harbors distinct microbial assemblages in rhizospheric and endophytic niches, reflecting microhabitat-driven selection. These microbial communities may contribute to host resilience by harboring taxa with potential stress-tolerance traits, offering insights for microbiome-informed strategies in arid land restoration.}, }
@article {pmid41011244, year = {2025}, author = {Valencia-Buitrago, M and Oliveira-Carvalho, RD and Cardoso, V and Triviño-Valencia, J and Salamanca-Duque, LM and Martínez-Díaz, V and Zabaleta, J and Galeano-Vanegas, NF and Naranjo-Galvis, CA}, title = {Metagenomic Characterization of Gut Microbiota in Children with Autism Spectrum Disorder: Microbial Signatures and Modulation by Anti-Inflammatory Diet and Probiotics.}, journal = {Pharmaceuticals (Basel, Switzerland)}, volume = {18}, number = {9}, pages = {}, doi = {10.3390/ph18091376}, pmid = {41011244}, issn = {1424-8247}, support = {(Project 121989786084, Contract 765-2021)//Minciencias-Colombia/ ; }, abstract = {Background: Autism Spectrum Disorder (ASD) is increasingly associated with alterations in gut microbiota, intestinal permeability, and immune dysregulation. However, integrative studies exploring these mechanisms in Latin American populations are lacking. Objective: To characterize gut microbiota profiles in Colombian children with ASD and evaluate the effects of two microbiota-targeted interventions, an anti-inflammatory diet and a probiotic formulation, on microbial diversity and taxonomic composition. Methods: In a two-phase study, shotgun metagenomic sequencing was performed on fecal samples from 23 children with ASD and 7 typically developing (TD) controls. In the second phase, 17 children with ASD were randomized to receive a 12-week intervention (anti-inflammatory diet, probiotics, or no intervention). Alpha diversity indices (Shannon, Pielou, and Chao1) and differential abundance analyses were conducted. Results: Compared to TD children, those with ASD showed a higher Firmicutes/Bacteroidetes ratio and a significantly increased abundance of genera such as Clostridioides, Thomasclavelia, Alistipes, and Coprococcus. The presence of functional gastrointestinal disorders (FGIDs) in ASD patients is associated with reduced microbial richness. POST-intervention, the anti-inflammatory diet group showed that no statistically significant changes in alpha diversity were observed, although a slight upward trend was noted and significant enrichment of six bacterial genera, including Moraxella and Eubacterium. The probiotic group exhibited a significant increase in Romboutsia and a decrease in Lachnospira. Cytokine-microbiota networks in ASD were fragmented and dominated by IFN-γ and MCP-1 hubs, indicating systemic immune activation. Interventions induced functional remodeling: The anti-inflammatory diet increased the number of beneficial genera (Eubacterium, Adlercreutzia) and shifted networks toward positive correlations involving IL-8 and MIP-1β. Probiotics increased Romboutsia, reduced Lachnospira, and restructured networks with regulatory cytokines (SDF-1α, Eotaxin) and SCFA-producing taxa (Blautia, Roseburia). Conclusions: Children with ASD in Colombia displayed distinct microbial profiles characterized by pro-inflammatory taxa and altered richness. Both the anti-inflammatory diet and probiotics produced compositional shifts in the gut microbiota, although global changes in diversity were limited. These findings support the potential of microbiota-targeted nutritional strategies for ASD and underscore the need for precision interventions tailored to specific clinical and microbial phenotypes.}, }
@article {pmid41010985, year = {2025}, author = {Petrelli, F and Ghidini, A and Dottorini, L and Ghidini, M and Zaniboni, A and Tomasello, G}, title = {Clinical Evidence for Microbiome-Based Strategies in Cancer Immunotherapy: A State-of-the-Art Review.}, journal = {Medicina (Kaunas, Lithuania)}, volume = {61}, number = {9}, pages = {}, doi = {10.3390/medicina61091595}, pmid = {41010985}, issn = {1648-9144}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/immunology ; *Immunotherapy/methods ; *Neoplasms/therapy ; Immune Checkpoint Inhibitors/therapeutic use ; Probiotics/therapeutic use ; }, abstract = {The gut microbiome has emerged as a critical determinant of immune-checkpoint inhibitor (ICI) efficacy. A narrative review of 95 clinical studies (2015-2025) shows that patients with greater gut microbial diversity and relative enrichment of commensals such as Akkermansia, Ruminococcus, and other short-chain fatty acid producers experience longer progression-free and overall survival, particularly in melanoma and non-small-cell lung cancer. Broad-spectrum antibiotics given within 30 days of ICI initiation and over-the-counter mixed probiotics consistently correlate with poorer outcomes. Early phase I/II trials of responder-derived fecal microbiota transplantation in ICI-refractory melanoma achieved objective response rates of 20-40%, while pilot high-fiber or plant-forward dietary interventions improved immunologic surrogates such as CD8[+] tumor infiltration. Machine-learning classifiers that integrate 16S or metagenomic profiles predict ICI response with an area under the ROC curve of 0.83-0.92. Methodological heterogeneity across sampling, sequencing, and clinical endpoints remains a barrier, underscoring the need for standardization and larger, well-powered trials.}, }
@article {pmid41010668, year = {2025}, author = {Kado, I and Kunimatsu, R and Koizumi, Y and Yoshimi, Y and Ogasawara, T and Abe, F and Ohgashira, S and Tsai, S and Okazaki, K and Tanimoto, K}, title = {Oral Microbiome Analysis and Caries Risk Classification Using the Caries Management by Risk Assessment System in Pre-Orthodontic Patients.}, journal = {Journal of clinical medicine}, volume = {14}, number = {18}, pages = {}, doi = {10.3390/jcm14186464}, pmid = {41010668}, issn = {2077-0383}, support = {23K162040A and 24K20058//Japan Society for the Promotion of Science/ ; }, abstract = {Background/Objectives: This study aimed to classify pre-orthodontic patients using the Caries Management by Risk Assessment (CAMBRA) system and clarify their oral characteristics and microbiome. Methods: At the Department of Orthodontics, Hiroshima University Hospital, 68 patients were included in this study. Clinical parameters, such as plaque control record, DMF index, and number of white spot lesions (WSLs), were obtained. Medical interviews and oral examinations were conducted according to the CAMBRA system, and participants were classified into four risk groups (Low, Moderate, High, and Extreme). The supragingival plaques and stimulated saliva were collected. A saliva test was performed to measure the saliva secretion volume, pH, buffering capacity, and bacterial culture. Microbial DNA was extracted from the stimulated saliva and plaque samples, and 16S rRNA metagenomic analysis was performed. For statistical analysis, the Kruskal-Wallis test was used. Results: Participants were classified into four CAMBRA risk groups, with many classified as the High group. The number of DMF teeth and WSLs were the highest in the Extreme group, which tended to have the worst oral hygiene habits. The saliva test results revealed that the Extreme group had the worst saliva secretion volume, buffering capacity, and Streptococcus mutans score, with statistically significant differences. Bacterial 16S metagenomic sequencing revealed that the genus Fusobacterium had the highest relative abundance in the saliva samples of the Low group, whereas the genus Actinomyces had the highest relative abundance in the Extreme group. Conclusions: In this single-center, cross-sectional study, CAMBRA risk classification accurately reflected the oral condition of pre-orthodontic patients.}, }
@article {pmid41010648, year = {2025}, author = {Jabłońska, A and Sadkowski, A and Richert-Przygońska, M and Styczyński, J}, title = {Next-Generation Sequencing for Infectious Disease Diagnostics in Pediatric Patients with Malignancies or After Hematopoietic Cell Transplantation: A Systematic Review.}, journal = {Journal of clinical medicine}, volume = {14}, number = {18}, pages = {}, doi = {10.3390/jcm14186444}, pmid = {41010648}, issn = {2077-0383}, support = {//Saving Kids with Cancer Foundation/ ; }, abstract = {Background: Immunocompromised children with malignancies or after hematopoietic cell transplantation (HCT) often deteriorate before conventional cultures identify a pathogen. Next-generation sequencing (NGS) promises faster, broader detection, yet its clinical impact in pediatric oncology remains unclear. This review aimed to assess the diagnostic performance and clinical utility of NGS in this population. Methods: We searched PubMed, Embase, and Scopus from January 2010 to April 2025 for studies evaluating NGS (metagenomic, targeted, or whole-genome sequencing) in pediatric oncology or HCT patients meeting predefined eligibility criteria. Duplicate screening, data extraction, and Joanna Briggs Institute risk-of-bias appraisal were performed. Heterogeneity precluded formal meta-analysis; findings were synthesized using narrative synthesis complemented by limited quantitative analyses. The protocol was not registered. Results: Twenty-four studies (≥2700 children; 2019-2025) met inclusion criteria. Metagenomic NGS (mNGS) was the most common approach, applied to blood/plasma (46%), bronchoalveolar fluid (BALF) (21%), and other fluids. In culture-negative sepsis or persistent febrile neutropenia, mNGS detected pathogens in 69-86% of episodes versus 18-56% for culture/polymerase chain reaction (PCR). Described in limited studies, early (<48 h) testing shortened fever by ~1.5 days and cut antimicrobial costs by 25-30%. Across studies, treatment was escalated, de-escalated, or discontinued in a median of 63% of mNGS-positive cases. Whole-genome sequencing (WGS) identified 18 silent transmission clusters and resolved a multidrug-resistant Acinetobacter baumannii outbreak within hours. Conclusions: NGS benefits pediatric hemato-oncology by accelerating pathogen-directed therapy, supporting antimicrobial stewardship, and enhancing outbreak surveillance. Despite cost and standardization barriers, evidence supports its use in selected high-risk patients.}, }
@article {pmid41010544, year = {2025}, author = {Liu, Y and Kuang, W and Li, M and Wang, Z and Liu, Y and Zhao, M and Huan, H and Yang, Y}, title = {Cholesterol-Lowering Mechanism of Lactobacillus Bile Salt Hydrolase Through Regulation of Bifidobacterium pseudolongum in the Gut Microbiota.}, journal = {Nutrients}, volume = {17}, number = {18}, pages = {}, doi = {10.3390/nu17183019}, pmid = {41010544}, issn = {2072-6643}, support = {2024YFF0619500; no. BK20231280; CX(22)2019//National Key Research and Development Program of China; Natural Science Foundation of Jiangsu; Jiangsu Agriculture Science and Technology Innovation Fund/ ; }, mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; *Amidohydrolases/metabolism/pharmacology ; *Cholesterol/blood ; Mice ; Male ; *Bifidobacterium/growth &amp; development/drug effects/metabolism ; *Lactobacillus/enzymology ; *Hypercholesterolemia/blood/microbiology ; Cholesterol 7-alpha-Hydroxylase/metabolism ; Fibroblast Growth Factors/metabolism ; Mice, Inbred C57BL ; *Anticholesteremic Agents/pharmacology ; Bile Acids and Salts/metabolism ; Receptors, Cytoplasmic and Nuclear/metabolism ; Probiotics ; }, abstract = {Background: Cardiovascular diseases (CVDs) represent a major global health burden, and cholesterol reduction is a key strategy for their prevention and management. This study investigated the mechanism by which bile salt hydrolase (BSH) from Lactobacilli reduces cholesterol levels by modulating the growth of Bifidobacterium pseudolongum. Methods: The BSH-recombinant strain YB334 was administered to high-cholesterol-diet mice, and the cholesterol-lowering function of the strain was evaluated by assessing serum cholesterol parameters, including total cholesterol (TC), low-density lipoprotein (LDL) and high-density lipoprotein (HDL). Metagenomic sequencing was used to analyze the gut microbiota, leading to the screening and acquisition of the "responsive" strains affected by BSH. Subsequent investigations were conducted into their cholesterol-lowering effects and mechanisms of action. Results: Oral administration of the BSH-recombinant strain YB334 can effectively reduce serum cholesterol levels in hypercholesterolemic mice while simultaneously leading to a significant increase in the abundance of B. pseudolongum within the gut microbiota. In vitro experiments indicated that this increased abundance might be closely associated with the strain's high tolerance to CA, the catalytic product of the BSH enzyme. The BPL-4 strain, obtained through screening, demonstrated cholesterol-lowering efficacy. Mechanistically, BPL-4 altered bile acid pool composition and modulated the farnesoid X receptor (FXR) signaling axis: it suppressed ileal FXR-fibroblast growth factor 15 (FGF15) expression, thereby de-repressing hepatic cholesterol 7α-hydroxylase (CYP7A1) and accelerating cholesterol catabolism into bile acids. Conclusions: This study provides the first evidence that BSH from lactobacilli can shape the signature gut microbiota by modulating bile acid metabolism via the FXR-CYP7A1 axis, thereby demonstrating a mechanism for its cholesterol-lowering effects.}, }
@article {pmid41010433, year = {2025}, author = {Fernández-Pastrana, VM and González-Reguero, D and Robas-Mora, M and Penalba-Iglesias, D and Pozuelo de Felipe, MJ and Probanza, A and Jiménez-Gómez, P}, title = {Use of Two PGPB Strains for the Valorization of Wastewater Sludge and Formulation of a Biofertilizer for the Recovery of Quercus ilex.}, journal = {Life (Basel, Switzerland)}, volume = {15}, number = {9}, pages = {}, doi = {10.3390/life15091490}, pmid = {41010433}, issn = {2075-1729}, abstract = {In response to the growing demand for agricultural production and the need for more sustainable practices, the use of biofertilizers based on the valorization of agricultural residues is presented as an alternative to traditional chemical fertilizers. This approach seeks to minimize environmental impact and improve soil health in agroforestry systems. The present work studies the effect of two plant growth-promoting bacterial strains (PGPB), Bacillus pretiosus (C1) and Pseudomonas agronomica (C2) on Quercus ilex (holm oak) seedlings. Taxonomic diversity was evaluated by massive sequencing of amplicons of the 16S rRNA gene, as well as the metabolic diversity and antibiotic resistance profile of the bacterial communities. The study also evaluated the impact of PGPB strains on the development of Quercus ilex seedlings. On the other hand, the effect of the biofertilizer on soil bacterial communities was evaluated. The results showed that the addition of biofertilizer significantly improved plant development compared to the addition of traditional irrigation (water) or the addition of fertilizer without the strains. In the same way, it was observed how the addition of the strains reduced the minimum inhibitory concentrations (MIC) in the rhizospheres of the treated individuals compared to traditional irrigation. The metagenomic analysis of the rhizospheric communities revealed the survival of the strains in the soil after their addition in any of the chemical treatments without altering the alpha and beta microbial diversity of the rhizospheric communities.}, }
@article {pmid41010319, year = {2025}, author = {Sakharkar, A and Chen, R and LeRoy, E and Nelson, TM and Proszynski, J and Kim, J and Park, J and Arikatla, MR and Mathyk, B and Mason, CE}, title = {Multi-Omics Profiling of Individuals Sustaining Extreme Physical Stressors.}, journal = {Life (Basel, Switzerland)}, volume = {15}, number = {9}, pages = {}, doi = {10.3390/life15091377}, pmid = {41010319}, issn = {2075-1729}, abstract = {Human engagement in extreme activities, from spaceflight to deep-sea diving and extreme sports, presents unique physiological challenges. Understanding the molecular mechanisms underlying adaptations to these demands is crucial for developing strategies to enhance human performance and resilience in such environments. This review integrates multi-omics data across a range of extreme phenotypes, including astronauts, scuba divers, acute alcohol consumers, long-haul flight passengers, bodybuilders, and simulation racers. We analyze current literature in genomic, transcriptomic, proteomic, metabolomic, and metagenomic studies to identify common and phenotype-specific adaptations, highlighting potential biomarkers and pathways associated with resilience in harsh conditions. This integrated approach offers insights into human adaptability and provides a foundation for developing personalized strategies to mitigate risks and enhance performance in extreme environments, with particular relevance to extended spaceflight.}, }
@article {pmid41009770, year = {2025}, author = {Pita-Galeana, MA and Ruhle, M and López-Vázquez, L and de Anda-Jáuregui, G and Hernández-Lemus, E}, title = {Computational Metagenomics: State of the Art.}, journal = {International journal of molecular sciences}, volume = {26}, number = {18}, pages = {}, doi = {10.3390/ijms26189206}, pmid = {41009770}, issn = {1422-0067}, mesh = {*Metagenomics/methods ; Humans ; *Microbiota/genetics ; *Computational Biology/methods ; Machine Learning ; Metagenome ; }, abstract = {Computational metagenomics has revolutionized our understanding of the human microbiome, enabling the characterization of microbial diversity, the prediction of functional capabilities, and the identification of associations with human health outcomes. This review provides a concise yet comprehensive overview of state-of-the-art computational approaches in metagenomics, alongside widely used methods and tools employed in amplicon-based metagenomics. It is intended as an introductory resource for new researchers, outlining key methodologies, challenges, and future directions in the field. We discuss recent advances in bioinformatics pipelines, machine learning (ML) models, and integrative frameworks that are transforming our understanding of the microbiome's role in health and disease. By addressing current limitations and proposing innovative solutions, this review aims to outline a roadmap for future research and clinical translation in computational metagenomics.}, }
@article {pmid41008211, year = {2025}, author = {Jiang, Y and Lu, Y and Jin, Y and Shen, Y and Liu, N and Bao, S and Peng, K and Gan, L and Wang, C and Zhang, Y and Chen, L and Chen, B and Xiao, Y and He, K and Yi, Z and Zhao, H}, title = {Spatiotemporal Profiling of Starch-Degrading Enzymes in Nong-Flavor Daqu: Molecular Markers for Quantitative Quality Evaluation.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {18}, pages = {}, doi = {10.3390/foods14183239}, pmid = {41008211}, issn = {2304-8158}, support = {2023YFS0505//the 'Unveiling and Commanding' Project of Sichuan Provincial Science and Technology Program/ ; }, abstract = {Nong-flavor (NF) Daqu, a critical fermentation starter for traditional Baijiu, harbors diverse starch-degrading enzymes with poorly characterized functional dynamics. This study transcended traditional quality assessments by developing molecular approaches to dissect starch-hydrolyzing enzyme genes. Specific and degenerate primers targeting glucoamylase, α-amylase, and α-glucosidase genes were designed, and key genes were qualitatively identified with distinct distributions among NF Daqus and unique presences between JXL and HB Daqu. Quantitative PCR revealed six genes with elevated expression in JXL Daqu versus HB Daqu, and which peaked during late fermentation in both Daqus. Metagenomics identified greater enzymatic diversity in HB Daqu. Phylogenetic clustering confirmed evolutionary conservation (GH13/GH15/GH31 families) and specificity of core enzyme genes across both Daqus. Enzymatic assays demonstrated the dominance of saccharification over α-glucosidase activity in both Daqus, with significantly higher α-glucosidase activity in JXL than HB Daqu. Divergent starch degradation strategies emerged: JXL prioritized high enzyme expression/activity, while HB utilized broader gene abundance. Based on Pearson correlation analysis, the saccharification activity showed the highest but weak correlation with α-glucosidase gene_15963 (r = 0.26), and was also positively correlated with the expression of all other enzyme genes except one glucoamylase gene. Meanwhile, α-glucosidase activity was most strongly linked to glucoamylase gene_22243 (r = 0.76), with additional correlations with two α-glucosidase genes being observed. This establishes RNA-based biomarkers for real-time quality control. Our findings decode divergent microbial strategies (JXL: high-expression/high-activity vs. HB: high-diversity) and provide a molecular framework for optimizing starch utilization in Baijiu fermentation. This technology holds potential to enable precision-driven standardization of traditional food production, which would reduce processing waste and enhance resource efficiency.}, }
@article {pmid41008188, year = {2025}, author = {Yao, L and Ma, H and Yao, L and Cao, H and Feng, T and Wang, H and Yu, C and Sun, M}, title = {Initial Sugar Concentration on Sensory Characteristics of Raw Pu-Erh Tea Kombucha and Multi-Omics Analysis of the Fermentation Process Under Optimal Sugar Concentration.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {18}, pages = {}, doi = {10.3390/foods14183216}, pmid = {41008188}, issn = {2304-8158}, support = {No. 32102123//National Natural Science Foundation of China/ ; 2021JQ-956//Natural Science Foundation of Shaanxi Province/ ; CUG170104//Fundamental Research Funds for the Central Universities in China University of Geosciences/ ; }, abstract = {The substrates of kombucha typically consist of tea and sugar. In this study, the effect of initial sugar concentration on volatile compound and sensory characteristics of raw Pu-erh tea (RAPT) kombucha was investigated. Compared to tea free (S1) and sugar free (S2) samples, the sugared tea (39 g/L sucrose in S3 and 78 g/L sucrose in S4) revealed better sensory quality and higher liking scores after the fermentation process. Hence, high-throughput sequencing analysis was performed to determine the variation in microbial composition between S3 and S4. The result showed that S4 exhibited higher abundances of Komagataeibacter and Brettanomyces as compared to S3. In addition, S4 presented the most favorable sensory qualities characterized by higher intensities of fruity, alcoholic, and fatty aromas, and the highest overall liking score. The metagenomic and metabolomic analysis was employed to further explore the metabolic pathways of RAPT kombucha under the optimal sugar concentration. The metagenomic and metabolomic analyses revealed that the pathways related to carbohydrate and amino acid metabolism were highly active under optimal sugar content, with compounds including glucose 6-phosphate, pyruvate and glutamate suggested to be important metabolites in regulating the sensory quality of the kombucha beverage. This paper provides a scientific basis for optimizing sugar addition in kombucha production.}, }
@article {pmid41008047, year = {2025}, author = {Wei, G and Liu, Y}, title = {A Graph Contrastive Learning Method for Enhancing Genome Recovery in Complex Microbial Communities.}, journal = {Entropy (Basel, Switzerland)}, volume = {27}, number = {9}, pages = {}, doi = {10.3390/e27090921}, pmid = {41008047}, issn = {1099-4300}, support = {24KJB520041//the Natural Science Foundation of the Higher Education Institutions of Jiangsu Province of China/ ; }, abstract = {Accurate genome binning is essential for resolving microbial community structure and functional potential from metagenomic data. However, existing approaches-primarily reliant on tetranucleotide frequency (TNF) and abundance profiles-often perform sub-optimally in the face of complex community compositions, low-abundance taxa, and long-read sequencing datasets. To address these limitations, we present MBGCCA, a novel metagenomic binning framework that synergistically integrates graph neural networks (GNNs), contrastive learning, and information-theoretic regularization to enhance binning accuracy, robustness, and biological coherence. MBGCCA operates in two stages: (1) multimodal information integration, where TNF and abundance profiles are fused via a deep neural network trained using a multi-view contrastive loss, and (2) self-supervised graph representation learning, which leverages assembly graph topology to refine contig embeddings. The contrastive learning objective follows the InfoMax principle by maximizing mutual information across augmented views and modalities, encouraging the model to extract globally consistent and high-information representations. By aligning perturbed graph views while preserving topological structure, MBGCCA effectively captures both global genomic characteristics and local contig relationships. Comprehensive evaluations using both synthetic and real-world datasets-including wastewater and soil microbiomes-demonstrate that MBGCCA consistently outperforms state-of-the-art binning methods, particularly in challenging scenarios marked by sparse data and high community complexity. These results highlight the value of entropy-aware, topology-preserving learning for advancing metagenomic genome reconstruction.}, }
@article {pmid41007973, year = {2025}, author = {Sfulcini, M and Lopreiato, V and Piccioli-Cappelli, F and Patrone, V and Bisaschi, M and Yoon, I and Zontini, AM and Barbato, M and Cattaneo, L and Archetti, I and Trevisi, E and Minuti, A}, title = {Saccharomyces cerevisiae Fermentation-Derived Postbiotics Supplementation to Dairy Calves: Effects on Growth, Metabolism, Immune Status and Preliminary First Lactation Outcomes.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {18}, pages = {}, doi = {10.3390/ani15182728}, pmid = {41007973}, issn = {2076-2615}, abstract = {This study evaluated the effects of supplementing dairy calves with Saccharomyces cerevisiae fermentation-derived postbiotics (SCFP) on growth, metabolism, immune status, and first lactation performance. Eighteen Holstein heifer calves were blocked by birth body weight and serum total protein and randomly assigned to control (CTR; n = 9; no supplementation) or SCFP (n = 9; 1 g/d SmartCare[®] in milk replacer until weaning plus 5 g/d NutriTek[®] until 70 d; Diamond V™, USA). Calves were weaned at 60 d and monitored until 160 d. Feed intake did not differ between groups. SCFP calves had greater post-weaning average daily gain from 71 to 100 d (0.93 vs. 0.60 kg/d, SCFP and CTR, respectively) and body weight from 100 to 160 d. They tended to have greater plasma β-hydroxybutyrate at 60 (0.32 vs. 0.27 mmol/L, SCFP and CTR, respectively) and 70 d (0.46 vs. 0.42, SCFP and CTR, respectively) and urea at 70 d (4.89 vs. 4.33 mmol/L, SCFP and CTR, respectively) and had greater acetate (515 vs. 384 μmol/L, SCFP and CTR, respectively) and propionate (33.13 vs. 22.4 ± 4.86 μmol/L, SCFP and CTR, respectively) at 60 d. SCFP calves also had lower nonesterified fatty acids at 21 d (0.23 vs. 0.38 mmol/L, SCFP and CTR, respectively), suggesting reduced energy mobilization during the most critical pre-weaning stage. Plasma myeloperoxidase was greater at 70 d (340 vs. 262 U/L, SCFP and CTR, respectively), as was phagocytosis by polymorphonuclear neutrophils at 60 (+10.4%) and 70 d (+8.2%). Feeding SCFP increased rumen activity and plasma volatile fatty acid concentrations, likely due to enhanced nutrient absorption and reduced weaning stress. SCFP calves exhibited a better immune response to lipopolysaccharide stimulation, as indicated by leukocyte gene expression, MPO, and PMN phagocytosis. Metagenomic analyses showed minor but significant changes in early-life microbiota composition at 7, 21, and 42 d. During first lactation, SCFP cows produced 2.1 kg/d more milk in the first 100 days in milk compared with CTR. In conclusion, early supplementation with SCFP supported rumen development, improved metabolic and immune function, and may enhance future productivity in dairy cows.}, }
@article {pmid41007726, year = {2025}, author = {Zheng, Z and Liu, G and Wang, Y and Li, J and Zhang, C and Zhang, Y and Ye, X and Kang, W}, title = {Perioperative Oral Immunonutrient Regulation of Intestinal Barrier and Gut Microbiota in Patients with Gastric Cancer, a Randomized Controlled Clinical Trial.}, journal = {Biomedicines}, volume = {13}, number = {9}, pages = {}, doi = {10.3390/biomedicines13092163}, pmid = {41007726}, issn = {2227-9059}, support = {Z-2017-24-2403//CIMF-CSPEN Project/ ; Y-NESTLE2022ZD-0105//Beijing Xisike Clinical Oncology Research Foundation/ ; 2022-PUMCH-C-048//the National High Level Hospital Clinical Research Funding/ ; 2022-PUMCH-B-005//the National High Level Hospital Clinical Research Funding/ ; 2023-I2M-C&amp;T-B-016//CAMS Innovation Fund for Medical Sciences/ ; 7232117//Beijing Natural Science Foundation/ ; 320.6750.2022-10-1//Wu Jieping Medical Foundation/ ; 2024ZD0520600//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; }, abstract = {Background and Objectives: Perioperative enteral and parenteral nutrition have been increasingly used to treat malnutrition in patients with gastric cancer. Immunonutrients have been suggested to reduce postoperative inflammatory responses and enhance immune function compared to conventional nutritional formulas. However, the insufficiency of evidence and unclear specific mechanism limit the recommendation level of immunonutrients in clinical guidelines. This study aimed to investigate the effects of immunonutrients on intestinal barrier function and to explore potential mechanisms through gut microbiota modulation. Methods: A total of 58 patients who underwent gastric cancer surgery participated in this randomized controlled trial. The immunonutrients group (n = 29) was additionally supplemented with 282 mg of omega-3 fatty acids, 1.2 g of arginine, and 128 mg of nucleotides per 100 kilocalories compared to the standard nutrients group (n = 29). Perioperative serum immune, nutritional parameters, and intestinal barrier markers (diamine oxidase, D-lactate, endotoxin) were evaluated. Fecal microbiota structure and functional pathways were analyzed via metagenomic sequencing. Results: Postoperative immune and nutritional parameters showed no statistically significant intergroup differences, though mean value curves suggested a protective trend in the immunonutrients group. The immunonutrients group exhibited significantly lower postoperative diamine oxidase (p = 0.043) and endotoxin levels (p = 0.043), alongside a substantial increase in microbiota α-diversity (p = 0.0005). Probiotic genera such as Akkermansia (3.26%) and Bifidobacterium longum (2.31%) were enriched in the immunonutrients group. Functional pathway analysis suggested that immunonutrients enhanced intestinal barrier protection. Conclusions: Immunonutrients may attenuate surgery-induced intestinal barrier damage in gastric cancer patients by modulating gut microbiota diversity, enriching beneficial taxa, and suppressing pathogenic bacteria.}, }
@article {pmid41007466, year = {2025}, author = {Godoy-Vitorino, F}, title = {Strengthening Integrative Microbiome Research Through Regional Leadership.}, journal = {International journal of environmental research and public health}, volume = {22}, number = {9}, pages = {}, doi = {10.3390/ijerph22091322}, pmid = {41007466}, issn = {1660-4601}, support = {1P20GM156713-01/GM/NIGMS NIH HHS/United States ; P20 GM103475/GM/NIGMS NIH HHS/United States ; 2U54MD007600//Center for Collaborative Research in Minority Health and Health Disparities/ ; }, mesh = {*Microbiota ; Puerto Rico ; Leadership ; Humans ; Metagenomics ; Research/organization &amp; administration ; }, abstract = {Microbiome science has revolutionized modern biology, shifting the focus from pathogens to the essential roles of beneficial microbes in health, metabolism, and ecosystems. Advances in genomic technologies like metagenomics have rapidly expanded our understanding of microbial diversity and function. Despite this progress, global microbiome research remains concentrated in high-resource regions, limiting diverse perspectives and opportunities in places like the Caribbean. This communication discusses the establishment of the first Center for Microbiome Sciences in Puerto Rico, which addresses this gap by providing local researchers with access to advanced tools, training, and infrastructure through broader collaboration. Novelty, services, and ideas on the integration of activities among local centers for the scientific improvement of the region are addressed. Additionally, how the center is poised to contribute to improving public and environmental health is also highlighted.}, }
@article {pmid41007378, year = {2025}, author = {da Silva, MB and Medeiros, AB and Dos Anjos, AIM and Ferreira Cavalcante, JV and Santiago, BCF and Monteiro, SS and Vital, AC and Dalmolin, RJS and Lisboa, HM and Pasquali, MAB}, title = {Changes in the Microbiota of the Scale Insect (Diaspis echinocacti, Bouché, 1833) in Opuntia stricta Cladodes: Taxonomic and Metagenomic Analysis as a Function of Infestation Levels.}, journal = {Biology}, volume = {14}, number = {9}, pages = {}, doi = {10.3390/biology14091233}, pmid = {41007378}, issn = {2079-7737}, support = {306165/2023-6//National Council for Scientific and Technological Development/ ; }, abstract = {Drought-tolerant cactus Opuntia stricta sustains livestock in Brazil's semi-arid Northeast but suffers yield losses from the armored scale insect Diaspis echinocacti. Symbiotic bacteria are thought to underpin scale fitness; however, their response to pest pressure remains unexplored. We characterized the bacterial communities of D. echinocacti collected from cladodes displaying low, intermediate, and high infestation (n = 3 replicates per level) using 16S-rRNA amplicon sequencing, processed with nf-core/ampliseq. Shannon diversity declined from low to high density, and Bray-Curtis ordination suggested compositional shifts, although group differences were not significant (Kruskal-Wallis and PERMANOVA, p > 0.05). The obligate endosymbiont "Candidatus Uzinura" dominated all samples (>85% relative abundance) irrespective of density, indicating a resilient core microbiome. PICRUSt2 predicted a contraction of metabolic breadth at higher infestations, with convergence on energy- and amino acid biosynthesis pathways. Taken together, increasing pest density was associated with modest loss of diversity and functional streamlining, rather than wholesale turnover. These baseline data can guide future work on microbiome-based strategies to complement existing scale-insect control in dryland cactus systems.}, }
@article {pmid41007342, year = {2025}, author = {Alfaro, GF and Zhou, Y and Cao, W and Zhang, Y and Rodning, SP and Muntifering, RB and Pacheco, WJ and Moisá, SJ and Wang, X}, title = {Metagenomic Analysis Revealed Significant Changes in the Beef Cattle Rectum Microbiome Under Fescue Toxicosis.}, journal = {Biology}, volume = {14}, number = {9}, pages = {}, doi = {10.3390/biology14091197}, pmid = {41007342}, issn = {2079-7737}, abstract = {Tall fescue toxicosis, caused by ingestion of endophyte-infected tall fescue (Lolium arundinaceum), impairs growth and reproduction in beef cattle and results in over USD 3 billion annual loss to the U.S. livestock industry. While the effects on host metabolism and rumen function have been described, the impact on the rectal microbiome remains poorly understood. In this study, we performed whole-genome shotgun metagenomic sequencing on fecal samples collected before and after a 30-day toxic fescue seed supplementation from eight pregnant Angus × Simmental cows and heifers. We generated 157 Gbp of sequencing data in 16 metagenomes, and assembled 13.1 Gbp de novo microbial contigs, identifying 22 million non-redundant microbial genes from the cattle rectum microbiome. Fescue toxicosis significantly reduced alpha diversity (p < 0.01) and altered beta diversity (PERMANOVA p < 0.01), indicating microbial dysbiosis. We discovered significant enrichment of 31 bacterial species post-treatment, including multiple core rumen taxa. Ruminococcaceae bacterium P7 showed an average of 16-fold increase in fecal abundance (p < 0.01), making it the top-featured species in linear discriminant analysis. Functional pathway analysis revealed a shift from energy metabolism to antimicrobial resistance and DNA replication following toxic seed consumption. Comparative analysis showed increased representation of core rumen taxa in rectal microbiota post-treatment, suggesting disrupted rumen function. These findings demonstrate that fescue toxicosis alters both the composition and functional landscape of the hindgut microbiota. Ruminococcaceae bacterium P7 emerges as a promising biomarker for monitoring fescue toxicosis through non-invasive fecal sampling, with potential applications in herd-level diagnostics and mitigation strategies.}, }
@article {pmid41007335, year = {2025}, author = {Wang, J and Zhao, Y and Wang, P and Yu, Y and Xu, Y and Yang, Y}, title = {Eimeria ovinoidalis Infection Reshapes Gut Microbial Communities and Metabolic Profiles in Tan Sheep.}, journal = {Biology}, volume = {14}, number = {9}, pages = {}, doi = {10.3390/biology14091190}, pmid = {41007335}, issn = {2079-7737}, abstract = {Tan sheep, a valuable indigenous breed in China, are vulnerable to coccidiosis caused by Eimeria ovinoidalis. In this case-control study, four 8-month-old Tan sheep raised under identical conditions were enrolled, including two with confirmed E. ovinoidalis infection (the Eo group) and two healthy controls (the HC group). Integrated metagenomic and untargeted metabolomic analyses were performed to assess gut microbiota and metabolic alterations. Results showed reduced alpha diversity and a distinct microbial composition in the Eo group. LEfSe identified 38 differentially abundant bacterial species, with Prevotella sp. and Fusobacterium necrophorum enriched in the Eo group and Faecalibacterium sp. and Lachnospira sp. enriched in the HC group. KEGG and VFDB analyses revealed significant differences in microbial functional pathways and virulence factor profiles. A total of 543 metabolites were differentially expressed, involving pathways related to inflammation, stress response, and amino acid metabolism. Microbiome-metabolome correlation analysis showed that Eo-associated bacteria were positively linked to pro-inflammatory metabolites, while HC-associated taxa correlated with markers of metabolic homeostasis. These findings provide new insights into the pathogenesis of ovine coccidiosis and may inform targeted interventions.}, }
@article {pmid41006832, year = {2025}, author = {Hug, LA and Hatzenpichler, R and Moraru, C and Soares, AR and Meyer, F and Heyder, A and ,  and Probst, AJ}, title = {A roadmap for equitable reuse of public microbiome data.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {41006832}, issn = {2058-5276}, support = {CTC 1439/2//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; MO3498/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; OCE-2049445//National Science Foundation (NSF)/ ; }, abstract = {Science benefits from rapid open data sharing, but current guidelines for data reuse were established two decades ago, when databases were several million times smaller than they are today. These guidelines are largely unfamiliar to the scientific community, and, owing to the rapid increase in biological data generated in the past decade, they are also outdated. As a result, there is a lack of community standards suited to the current landscape and inconsistent implementation of data sharing policies across institutions. Here we discuss current sequence data sharing policies and their benefits and drawbacks, and present a roadmap to establish guidelines for equitable sequence data reuse, developed in consultation with a data consortium of 167 microbiome scientists. We propose the use of a Data Reuse Information (DRI) tag for public sequence data, which will be associated with at least one Open Researcher and Contributor ID (ORCID) account. The machine-readable DRI tag indicates that the data creators prefer to be contacted before data reuse, and simultaneously provides data consumers with a mechanism to get in touch with the data creators. The DRI aims to facilitate and foster collaborations, and serve as a guideline that can be expanded to other data types.}, }
@article {pmid41006795, year = {2025}, author = {Aoyagi, LN and Wang, Y and Ohbayashi, T and Hirono, Y and Hayatsu, M and Tago, K}, title = {Diversity and characterization of the ammonia-oxidizing bacteria responsible for nitrification in tea field soils.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {33221}, pmid = {41006795}, issn = {2045-2322}, support = {JPNP18016//New Energy and Industrial Technology Development Organization (NEDO)/ ; 16K14874//MEXT KAKENHI/ ; 19H01156//MEXT KAKENHI/ ; 28004A//Science and Technology Research Promotion Program for Agriculture, Forestry, Fisheries, and Food Industry/ ; }, mesh = {*Nitrification ; *Ammonia/metabolism ; *Soil Microbiology ; Oxidation-Reduction ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; Soil/chemistry ; Archaea/metabolism/genetics/classification ; Phylogeny ; *Tea/microbiology ; Biodiversity ; }, abstract = {Ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and comammox Nitrospira have been considered to coexist in acidic soils, oxidizing ammonia within their respective niches. However, their relative contributions to soil nitrification, as well as their properties and ecological roles in acidic soils, remain poorly understood. This study focused on AOB in acidic tea field soils, investigating their ecology and physiology through metagenomic analysis and the genomic and physiological characterization of AOB isolates. β-AOB were significantly more abundant than γ-AOB and AOA in soil layers with the highest potential for nitrification activity, indicating that β-AOB play a key role in acidic tea soil. Diversity analysis of this dominant group identified Nitrosospira as the major genus present in tea fields, and four pure strains representing some of the main operational taxonomic units in this environment were isolated. Physiological and genetic characterization of these isolates revealed some distinct traits compared to other species of the genus and closely related taxa, suggesting adaptations that may contribute to niche differentiation and survival in acidic soils. These findings provide new insights into the ecological role of β-AOB in acidic soils and may inform strategies to manage soil nitrification and reduce nitrogen loss in agricultural ecosystems.}, }
@article {pmid41006325, year = {2025}, author = {Zhang, L and Zhou, DD and Feng, J and Liao, ZJ and Shu, XL and Yang, RM and Gao, YC and Zhou, HH and Zhang, W and Zou, Y and Liu, R}, title = {Intestinal fungal signatures and their impact on immune checkpoint inhibitor efficacy: a multi-cohort meta-analysis.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {188}, pmid = {41006325}, issn = {2055-5008}, support = {2021YFA1301200//the National Key Research and Development Program/ ; No. 82474022, 31801121, 82373961//the National Scientific Foundation of China/ ; 2022RC1022//the Hunan Provincial Science and Technology Innovation Plan Project/ ; }, mesh = {*Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; Humans ; *Gastrointestinal Microbiome/drug effects ; *Fungi/classification/genetics/isolation &amp; purification ; Animals ; Mice ; Feces/microbiology ; Cohort Studies ; *Neoplasms/drug therapy/microbiology ; }, abstract = {Gut microbiota influence on the effectiveness of immune checkpoint inhibitors (ICIs), but research on fungi-an essential component of the microbiome-has been limited. This multi-cohort meta-analysis of 976 fecal metagenomes across 8 cohorts, representing melanoma, non-small cell lung cancer (NSCLC), and renal cell carcinoma (RCC), identified fungal species associated with ICI efficacy. In melanoma, Rhizophagus irregularis and Debaryomyces hansenii were correlated with poor responses, whereas Aspergillus avenaceus was associated with great efficacy. In NSCLC, an increased abundance of Aspergillus pseudonomiae was associated with a favorable prognosis. Stronger bacterial-fungal interactions were observed in responders. The presence of certain fungi in fungal enterotypes, like Aspergillus or Saccharomyces, was linked to better efficacy to ICIs. Mouse models revealed Debaryomyces hansenii impaired ICI efficacy by reducing CD8+ T cells. Our findings highlight specific fungal signatures that may inform strategies to enhance ICI efficacy and encourage further research on microbial impacts on treatment outcomes.}, }
@article {pmid41005935, year = {2026}, author = {Yang, W and Xin, X and Cao, X}, title = {Impacts of trace ofloxacin on autotrophic denitrification process driven by pyrite/sulfur: Performance, microbial community evolution and metagenomic analysis.}, journal = {Journal of environmental sciences (China)}, volume = {159}, number = {}, pages = {775-784}, doi = {10.1016/j.jes.2025.03.062}, pmid = {41005935}, issn = {1001-0742}, mesh = {*Denitrification/drug effects ; Autotrophic Processes ; *Water Pollutants, Chemical/toxicity/analysis ; Sulfides/chemistry ; *Ofloxacin/toxicity/analysis ; Sulfur/chemistry ; Iron/chemistry ; Metagenomics ; *Microbiota/drug effects ; Anti-Bacterial Agents/toxicity ; Bioreactors ; }, abstract = {In this work, ofloxacin (OFL), a kind of frequently detected antibiotic in groundwater, was selected to explore its impact (at ng/L-µg/L-level) on denitrification performance in an autotrophic denitrification system driven by pyrite/sulfur (FeS2/S[0]). Results showed that OFL restrained nitrate removal efficiency, and the inhibition degree was positively related to the concentration of OFL. After being exposed to increased OFL (200 ng/L-100 µg/L) for 69 days, higher inhibition of electron transport activity (ETSA), enzyme activities of nitrate reductase (NAR), and nitrite reductase (NIR) were acquired. Meanwhile, the extracellular protein (PN) content of sludge samples was remarkably stimulated by OFL to resist the augmented toxicity. OFL contributed to increased microbial diversity and sulfur/sulfide oxidation functional genes in ng/L-level bioreactors, whereas led to a decline in µg/L level experiments. With OFL at concentrations of 200 ng/L and 100 µg/L, the whole expression of 10 key denitrification functional genes was depressed, and the higher the OFL concentration, the lower the expression level. However, no significant proliferation of antibiotic resistance genes (ARGs) either in 200 ng/L-OFL or 100 µg/L-OFL groups was observed. Two-factor correlation analysis results indicated that Thiobacillus, Anaerolineae, Anaerolineales, and Nitrospirae might be the main hosts of existing ARGs in this system.}, }
@article {pmid41005808, year = {2025}, author = {Purcell, M and Ackland, J and Staples, KJ and Freeman, A and Wilkinson, TMA}, title = {The respiratory tract virome: unravelling the role of viral dark matter in respiratory health and disease.}, journal = {European respiratory review : an official journal of the European Respiratory Society}, volume = {34}, number = {177}, pages = {}, doi = {10.1183/16000617.0284-2024}, pmid = {41005808}, issn = {1600-0617}, mesh = {Humans ; *Virome ; *Viruses/genetics/pathogenicity/immunology ; Host-Pathogen Interactions ; *Microbiota ; *Respiratory System/virology ; *Respiratory Tract Infections/virology ; Metagenomics ; *Respiratory Tract Diseases/virology/diagnosis ; Animals ; }, abstract = {The human respiratory tract virome is an underexplored component of the microbiome that includes eukaryotic viruses, bacteriophages and archaeal viruses. The respiratory virome represents a dynamic and heterogeneous ecosystem, shaped by host, environmental and microbial factors. Advances in metagenomic sequencing have expanded our understanding of virome composition, dynamics and potential roles in health and disease. Despite increasing interest, virome research remains fragmented and often secondary to bacteriome studies. Challenges in study design, genomic characterisation and interpretation limit consistent conclusions. This review summarises current knowledge of the respiratory virome in health and across acute and chronic respiratory diseases, including acute respiratory infection, asthma, COPD, cystic fibrosis and bronchiectasis. While each condition is distinct, they share features of airway inflammation and immune dysregulation where the virome may act as a modifier or marker. Across these syndromes, emerging evidence highlights the consistent detection of respiratory viruses including potential commensals, such as Anelloviridae, and the often-overlooked role of bacteriophages. We also discuss the concept of viral dark matter, where large proportions of sequence data remain unclassified, potentially representing novel viral taxa. Technical and conceptual challenges are evaluated, alongside recent methodological innovations such as meta-transcriptomics and viral enrichment protocols. We outline how standardised, multi-omic and longitudinal approaches are urgently needed to clarify the virome's functional role, interactions with immunity and microbial communities and its utility as a biomarker or therapeutic target.}, }
@article {pmid41005673, year = {2025}, author = {Zhu, X and Fang, L and Xu, F and Sun, J and Zhang, X and Cai, J}, title = {Deciphering effect of complex organics on Anammox-sulfide autotrophic denitrification coupling system for landfill leachate treatment.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {133388}, doi = {10.1016/j.biortech.2025.133388}, pmid = {41005673}, issn = {1873-2976}, abstract = {The inhibitory effects of complex organics on Anammox-sulfide autotrophic denitrification (SAD) coupled systems are not well understood in full-strength leachate conditions. This research examines the removal of carbon, nitrogen, and sulfur, alongside microbial symbiosis and metabolic alterations, within an Anammox-SAD system that processes raw landfill leachate.. The system attained a total nitrogen removal rate of 98.54 ± 0.42 %, with contributions of 89.47 % from Anammox and 10.53 % from SAD. The system attained a total nitrogen removal rate of 98.54 ± 0.42 %, with contributions of 89.47 % from Anammox and 10.53 % from SAD. GC × GC-TOFMS analysis indicated removal rates of 72.33 %, 51.05 %, and 53.81 % for small-, medium-, and large-molecular-weight organics, respectively, by the Anammox system, thereby reducing stress on SAD. Metagenomics studies revealed that low-molecular-weight organics promoted DNRA, partial denitrification, and Anammox through enhancing electron transfer and functional gene expression. The role of Anammox bacteria in carbon fixation decreased, whereas sulfur metabolism in SAD became increasingly dependent on Sulfurimonas-mediated Sox pathways, indicating metabolic adaptation in response to organic stress and competition between autotrophs and heterotrophs. This study provides novel insights into the application of Anammox-SAD coupled processes for landfill leachate treatment.}, }
@article {pmid41005465, year = {2025}, author = {Wen, W and Zeng, Z and Liang, S and Zhang, Y and Deng, J}, title = {Rapid Diagnosis and Targeted Therapy of Chlamydia psittaci Pneumonia: The Clinical Value of Quantitative Metagenomic Next-Generation Sequencing.}, journal = {Indian journal of medical microbiology}, volume = {}, number = {}, pages = {100984}, doi = {10.1016/j.ijmmb.2025.100984}, pmid = {41005465}, issn = {1998-3646}, abstract = {Chlamydia psittaci (C. psittaci) pneumonia poses significant challenges for early diagnosis due to its non-specific clinical presentation and imaging characteristics. Delayed etiological diagnosis and inappropriate treatment often lead to disease exacerbation. In this case, the patient's initial empirical treatment proved ineffective, and the condition worsened. The diagnosis of C. psittaci infection was ultimately confirmed through quantitative metagenomic next-generation sequencing (Q-mNGS™). Following targeted azithromycin therapy, the patient's symptoms and imaging findings markedly improved. This case underscores the clinical value of metagenomic next-generation sequencing (mNGS) in early diagnosis and targeted treatment of C. psittaci pneumonia in non-immunocompromised individuals.}, }
@article {pmid41005405, year = {2025}, author = {Gomes, BM and de Oliveira, GS and de Melo, VS and de Oliveira Rossini, N and Adriani, PP and Dias, MVB and Chambergo, FS}, title = {Structural and functional characterization of a bifunctional GH43 α-L-arabinofuranosidase/β-xylosidase from the metagenome of Pseudacanthotermes militaris gut.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {147909}, doi = {10.1016/j.ijbiomac.2025.147909}, pmid = {41005405}, issn = {1879-0003}, abstract = {The pursuit of sustainable energy has intensified the search for efficient biocatalysts to convert lignocellulosic biomass. In this context, we characterized a novel bifunctional enzyme, TerARA, identified from the gut metagenome of the termite Pseudacanthotermes militaris. Belonging to the glycoside hydrolase 43 (GH43) family, TerARA was heterologously expressed in E. coli BL21 and purified. The enzyme demonstrated bifunctional activity toward synthetic substrates p-nitrophenyl-α-L-arabinofuranoside (pNP-Araf) (387.22 ± 74.2 U/mg) and p-nitrophenyl-β-D-xylopyranoside (pNP-Xyl) (330.82 ± 31.2 U/mg), with higher catalytic efficiency for pNP-Araf (9.14 s[-1]·mM[-1]), suggesting functional preference as an α-L-arabinofuranosidase. Activity modulation by metal ions revealed that Ca[2+] slightly improved efficiency toward pNP-Araf (to 9.58 s[-1]·mM[-1] at 1 mM), while Zn[2+] reduced efficiency for pNP-Xyl except at 5 mM (6.65 s[-1]·mM[-1]). Zn[2+] also enhanced enzymatic stability, maintaining 80 % activity in pNP-Xyl hydrolysis. Crystallographic analysis at 2.0 Å resolution revealed a 43 Glycosyl Hydrolase catalytic domain with a five-bladed β-propeller fold and two Ca[2+] ions and a Carbohydrate-Binding Module (CBM) domain with a β-sandwich fold likely involved in substrate interaction. Conserved catalytic residues, binding sites, and Ca[2+] stabilizing effects were identified. TerARA's bifunctionality and structural features support its application in hemicellulose degradation and biomass conversion.}, }
@article {pmid41005300, year = {2025}, author = {Zhao, CN and Li, SS and Yau, T and Chen, WQ and Ji, R and Guan, XY and Kong, FS}, title = {Phocaeicola vulgatus induces immunotherapy resistance in hepatocellular carcinoma via reducing indoleacetic acid production.}, journal = {Cell reports. Medicine}, volume = {}, number = {}, pages = {102370}, doi = {10.1016/j.xcrm.2025.102370}, pmid = {41005300}, issn = {2666-3791}, abstract = {Immunotherapy has made remarkable achievements in various cancers, but response rates in hepatocellular carcinoma (HCC) remain highly variable. Understanding mechanisms behind this heterogeneity and identifying responsive patients are urgent clinical challenges. In this study, the metagenomic analysis of 65 HCC patients reveals distinct gut microbiota profiles distinguishing responders (Rs) from non-responders (NRs). These findings are further validated through fecal microbiota transplantation (FMT) in mouse models. Notably, Phocaeicola vulgatus (P. vulgatus) is enriched in NRs and diminishes anti-PD-1 efficacy in both syngeneic and orthotopic tumor models. Mechanistically, P. vulgatus suppresses the production of indoleacetic acid (IAA), thereby weakening interferon (IFN)-γ[+] and granzyme B (GzmB)[+]CD8[+] T cells and impairing the antitumor immune response. Furthermore, supplementation with IAA restores CD8[+] T cell cytotoxicity and counteracts the immune-suppressive effects of P. vulgatus. Our findings establish a causal relationship between P. vulgatus and anti-PD-1 resistance in HCC, highlighting IAA as a potential therapeutic target to enhance immunotherapy outcomes.}, }
@article {pmid41005095, year = {2025}, author = {Liao, H and Sun, X and Duan, CS and Shangguan, H and Yao, HF and Qiao, Z and Cui, HX and Xie, A and O'Connor, P and Su, JQ}, title = {Urbanization homogenized soil viral communities across three climate zones.}, journal = {Journal of hazardous materials}, volume = {498}, number = {}, pages = {139954}, doi = {10.1016/j.jhazmat.2025.139954}, pmid = {41005095}, issn = {1873-3336}, abstract = {Soil viruses play critical roles in shaping microbial communities and propelling the evolution of microorganisms. However, our understanding of how land use and climate factors modulate soil viral communities across broader geographical scales remains limited. Here, we conducted deep metagenomic sequencing and analysis of soil samples from different land use types including forests, farmland, residential areas, and parks across 13 cities spanning three climatic zones in China. Integrating local and global soil virome data (n = 2.1◊10[5] vOTUs (viral Operational Taxonomic Units)) with kmer-based methods has increased our understanding of soil viral diversity in metagenomics by about fortyfold. Our combined results demonstrated that the urban green spaces exhibited remarkably lower heterogeneity compared to those from forests and farmland within China. Parks and residential areas reduced viral species diversity by 19.4 % and 33.5 %, respectively, compared to forests. vOTUs from urban green spaces had significantly higher SNB (social niche breadth) compared to those from forests and farmland, indicating the introduction of generalist vOTUs with high genetic variance, and thus resulting in the homogenization of viral communities in urban green spaces across climate zones. Overall, our study provides a comprehensive understanding of the influence of land use on soil viral communities across climate zones at a national scale.}, }
@article {pmid41005092, year = {2025}, author = {Dou, XX and Mao, BD and Li, A and Gu, JJ and Zhang, XL and Fu, CW and Zhang, XJ and Lan, BJ and Xu, JW and Zhang, BX and Zheng, HJ and Gao, F}, title = {Algal-bacterial symbiosis strengthens the treatment of high-salinity phenolic wastewater and its molecular mechanism.}, journal = {Journal of hazardous materials}, volume = {498}, number = {}, pages = {139957}, doi = {10.1016/j.jhazmat.2025.139957}, pmid = {41005092}, issn = {1873-3336}, abstract = {This study developed algal-bacterial symbiotic flocs (ABSF) for high-salinity phenolic wastewater treatment, showcasing superior performance over activated sludge (AS). ABSF exhibited exceptional structural stability, producing 417.64 mg g[-1] extracellular polymeric substances (EPS) and accumulating 51.2 % lipids. It achieved complete phenol removal and significantly reduced effluent total nitrogen (9.36 vs. 23.59 mg L[-1] in AS) and COD (77.76 vs. 105.34 mg L[-1]), maintaining efficiency even at a 1-day hydraulic retention time. Metagenomic analysis revealed ABSF's diverse microbial community, enriched with functional genera (Candidatus Nitrosocosmicus, Synechocystis, Thauera) linked to nitrogen and aromatic degradation. Enhanced quorum sensing was evidenced by elevated N-acyl-homoserine lactones (C6-HSL: 38.56 ng mL[-1]) and upregulated signal transduction genes (5.4 % abundance). ABSF also showed higher expression of phenol-degrading enzymes and metabolic genes (e.g., succinate dehydrogenase: 0.19 %), accelerating the TCA cycle for efficient pollutant mineralization. Key mechanisms included EPS-mediated stress resistance, microbial synergy, and robust metabolic activity. These findings highlight ABSF as a sustainable solution for refractory industrial wastewater, combining high treatment efficiency with resource recovery potential, offering both environmental and economic benefits.}, }
@article {pmid41005091, year = {2025}, author = {Gou, X and Ji, Y and Zhang, P and Liu, Z and Qiu, J and Song, X and Qin, W and Jiang, J and Liu, X and Wang, B}, title = {Virus-encoded auxiliary metabolic genes fuel the metabolism of organic pollutants in long-term contaminated groundwater.}, journal = {Journal of hazardous materials}, volume = {498}, number = {}, pages = {139940}, doi = {10.1016/j.jhazmat.2025.139940}, pmid = {41005091}, issn = {1873-3336}, abstract = {Virus-encoded auxiliary metabolic genes (AMGs) are important for host metabolism, such as carbon and nitrogen cycling; however, whether and how viral AMGs affect bacterial adaptation to pollution stress in long-term contaminated groundwater remain unclear, significantly limiting our understanding of phage-host interactions on the transformation of organic pollutants in groundwater. Here, by leveraging viromics sequencing for virus-like particles (VLPs) and metagenomic sequencing for host-cell, we profiled comprehensive virome datasets (recovered 16,672 viral contigs) from sites contaminated for over 30 years with chlorinated hydrocarbons and benzene, toluene, ethylbenzene, and xylene (BTEX). We found that contaminated groundwater had higher viral abundance, higher diversity, a broader host spectrum, and more complex virus-host interactions than the control group. Through virus genome functional screening and global multi-habitat mapping analysis, we identified six AMGs involved in alleviating pollutant stress and degradation of xenobiotics, and verified the degradation activity of the AMGs (i.e., L-DEX) through heterologous gene expression experiments, revealing that virus-encoded AMGs have cross-habitat adaptive potential. For site-specific pollutants, further phylogenetic analysis and protein structure prediction of key metabolic genes L-DEX and pcaH were performed. The results showed that they exhibit high evolutionary conservation and functional integrity, suggesting the similar functions as bacterial homologous genes. Overall, these findings enhance our understanding of virus-host interactions in contaminated groundwater and reveal their ecological functions and roles in adaptive evolution.}, }
@article {pmid41005071, year = {2025}, author = {Li, R and Pei, X and Tao, C and Deng, X and Wang, Y and Wang, Y and Wang, J and Shen, Z and Shen, Q and Li, R}, title = {Disrupting manure-to-soil transmission of antibiotic resistance genes with gamma irradiation and hydrogen peroxide.}, journal = {Ecotoxicology and environmental safety}, volume = {304}, number = {}, pages = {119086}, doi = {10.1016/j.ecoenv.2025.119086}, pmid = {41005071}, issn = {1090-2414}, abstract = {The application of untreated livestock manure poses significant risks for the dissemination of antibiotic resistance genes (ARGs) in agricultural ecosystems, yet conventional pretreatments such as composting or single chemical oxidation often fail to control both ARGs and their mobility. In this study, the synergistic effects of gamma irradiation and hydrogen peroxide were evaluated through integrated metagenomic analysis and soil microcosm experiments, showing that the combined treatment achieved the greatest reductions in both the abundance and diversity of ARGs and mobile genetic elements, outperforming individual treatments. Specifically, in the fertilizer treatment, the ARGs and mobile genetic elements in the combined treatment were reduced by 29.47 % and 24.25 %, respectively, compared with those in the control. The intervention selectively depleted ARG-harboring taxa, including Cellvibrio, Alicyclobacillus, and Chitinophaga, while concurrently suppressing microbial functions critical to ARG dissemination, particularly biofilm formation, membrane transport, and SOS stress response pathways. In soil microcosms, pretreated manure maintained ARG suppression via functional reconstruction, with microbial community shifts identified as the primary driver. These findings highlight a novel dual-action mechanism of gamma irradiation/H2O2 co-treatment that not only reduces ARG reservoirs but also disrupts ecological networks underpinning manure-to-soil ARG transmission, offering a mechanistically informed alternative to traditional manure management.}, }
@article {pmid41005055, year = {2025}, author = {Huang, J and Liu, Z and Liu, Y and Liu, X and Tian, Z and Yao, M and Wang, W and Liu, Z}, title = {Butylchlorogenate from Chaenomeles speciosa alleviates ulcerative colitis via suppressing NLRP3 inflammasome activation and remodeling intestinal homeostasis.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {148}, number = {}, pages = {157282}, doi = {10.1016/j.phymed.2025.157282}, pmid = {41005055}, issn = {1618-095X}, abstract = {BACKGROUND: Ulcerative colitis (UC) is a chronic inflammatory disease of the gastrointestinal tract. Despite the availability of traditional clinical treatments, their limitations highlight the need for alternative therapies derived from natural products that offer both strong efficacy and minimal side effects. Chaenomeles speciosa (Sweet) Nakai (CS), edible and medicinal fruit traditionally used to treat gastrointestinal disorders, has shown potential in UC management. However, the specific phytochemicals and mechanisms through which CS exerts its therapeutic effects remain poorly understood.<br><br>PURPOSE: This study aimed to isolate and identify the bioactive compounds in CS, screen for the most potent compounds, especially chlorogenic acid derivatives, and assess their efficacy in treating UC. Additionally, we sought to investigate the underlying mechanisms of action.<br><br>METHODS: The anti-inflammatory components from CS were separated and identified using various chromatographic techniques and nuclear magnetic resonance spectroscopy. Compounds with potential anti-inflammatory activity were screened using the NO release assay and enzyme linked immunosorbent assay (ELISA). Potential therapeutic pathways were explored through network pharmacology. In vivo, the therapeutic effect of the target compound, 3-O-(E)-caffeoylquinic acid n-butylester (BE), on UC was evaluated by monitoring body weight, disease activity index (DAI), colon length, histopathological scores, tight junction protein expression, and inflammatory marker transcript levels. Moreover, surface plasmon resonance (SPR) assay, gene knockdown, molecular docking, molecular dynamics simulations, quantitative Real-Time reverse transcription (qRT-PCR), and western blot (WB) analysis were employed to validate therapeutic mechanisms. The effects of BE on the intestinal microbiota and its associated metabolites in UC mice were further characterized through metagenomic sequencing and Gas Chromatography-Mass Spectrometry (GC-MS).<br><br>RESULTS: After preliminary activity investigation of isolated phenolic compounds based on ELISA, chlorogenic acid and its derivatives (BE and the novel 3-O-(Z)-caffeoylquinic acid n-butylester) were selected for CCK-8 assay and NO release inhibition. Among them, BE exhibited the most potent anti-inflammatory effects and was chosen for further intervention in UC mice. Network pharmacology analysis predicted that the NF-&#x3ba;B signaling pathway is a potential mechanism underlying the therapeutic effects of BE in UC. In vivo, BE effectively restored body weight and colon length, reduced DAI and histopathological scores, preserved the intestinal epithelial barrier, and decreased the expression of inflammatory biomarkers. WB and qRT-PCR experiments validated the BE attenuates inflammation by affecting the NF-&#x3ba;B/NLRP3 signaling pathway. SPR assay, gene knockdown, molecular docking, and molecular dynamics simulations revealed that BE inhibits activation of NLRP3 inflammasome by binding to NLRP3. Additionally, metagenomic sequencing and GC-MS showed that BE significantly reduced the relative abundance of Escherichia coli, while increasing Eubacterium and Roseburia sp. 1XD42-69. BE also restored short-chain fatty acid levels.<br><br>CONCLUSION: Our findings suggest that BE, derived from CS, demonstrates promising therapeutic efficacy against UC. It exerts potent anti-UC effects by targeting NLRP3 and affecting the NF-&#x3ba;B/NLRP3 signaling axis to inhibit activation of NLRP3 inflammasome and remodeling intestinal homeostasis.}, }
@article {pmid41004493, year = {2025}, author = {Cui, Y and Zhao, R and Mi, R and Chen, L and Wang, L and Li, D and Cheng, C and Li, M and Wei, X}, title = {Hematological diseases-related mucormycosis: A retrospective single center study.}, journal = {PLoS neglected tropical diseases}, volume = {19}, number = {9}, pages = {e0013531}, doi = {10.1371/journal.pntd.0013531}, pmid = {41004493}, issn = {1935-2735}, mesh = {Humans ; *Mucormycosis/drug therapy/epidemiology/diagnosis/microbiology/complications ; Middle Aged ; Retrospective Studies ; Female ; Male ; Aged ; Adult ; Young Adult ; Adolescent ; Child ; Mucor/genetics/isolation &amp; purification ; *Hematologic Diseases/complications/microbiology ; *Hematologic Neoplasms/complications ; Risk Factors ; Antifungal Agents/therapeutic use ; High-Throughput Nucleotide Sequencing ; }, abstract = {BACKGROUND AND AIM: Mucormycosis is a life-threatening invasive fungal infection. This study aimed to analyze the clinical characteristics of patients with hematologic malignancies complicated with mucormycosis.<br><br>METHODS: This retrospective study investigated the clinical characteristics, epidemiological features, treatment, and prognosis of 46 patients with hematological diseases and Mucor infection as indicated by mNGS from August 28, 2020 to September 11, 2023. Metagenomic next-generation sequencing (mNGS) refers to the application of high-throughput sequencing technology for the comprehensive analysis of nucleic acid content in patient samples, facilitating the detection and characterization of microbial DNA and/or RNA, and then comparing and analyzing the results with an information database to determine the types of pathogenic microorganisms present in the sample.<br><br>RESULTS: The median age of admission for the included patients was 49 years (9-78). Multivariate analysis identified age over 60 years (p&#x2009;=&#x2009;0.006&#x2009;<&#x2009;0.05), high-dose corticosteroids (p&#x2009;=&#x2009;0.001&#x2009;<&#x2009;0.05), neutropenia lasting more than 10 days (p&#x2009;=&#x2009;0.041&#x2009;<&#x2009;0.05), and two or more Mucor infections (p&#x2009;=&#x2009;0.004&#x2009;<&#x2009;0.05) were independent risk factors for OS in patients with hematological diseases. Moreover, differences between groups were analyzed using the Fisher exact probability method, and no significant difference was observed in the efficacy of various types of antifungal therapies.<br><br>CONCLUSION: Patients with hematologic malignancies benefit greatly from early diagnosis and treatment when suspected of Mucor infection. mNGS is an important supplementary method for early diagnosis of Mucor infection. Moderated use of corticosteroids, reducing the duration of neutropenia, and enhancing autologous immune function are important measures to reduce patient mortality rate.}, }
@article {pmid41004266, year = {2025}, author = {Nasr, E and Henger, A and Grüning, B and Zierep, P and Batut, B}, title = {PathoGFAIR: a collection of FAIR and adaptable (meta)genomics workflows for (foodborne) pathogens detection and tracking.}, journal = {GigaScience}, volume = {14}, number = {}, pages = {}, doi = {10.1093/gigascience/giaf017}, pmid = {41004266}, issn = {2047-217X}, support = {824087//Horizon 2020/ ; 031 A538A//BMBF/ ; }, mesh = {*Metagenomics/methods ; Workflow ; *Foodborne Diseases/microbiology ; *Food Microbiology/methods ; Humans ; Nanopore Sequencing ; *Software ; *Genomics/methods ; }, abstract = {BACKGROUND: Food contamination by pathogens poses a global health threat, affecting an estimated 600 million people annually. During a foodborne outbreak investigation, microbiological analysis of food vehicles detects responsible pathogens and traces contamination sources. Metagenomic approaches offer a comprehensive view of the genomic composition of microbial communities, facilitating the detection of potential pathogens in samples. Combined with sequencing techniques like Oxford Nanopore sequencing, such metagenomic approaches become faster and easier to apply. A key limitation of these approaches is the lack of accessible, easy-to-use, and openly available pipelines for pathogen identification and tracking from (meta)genomic data.<br><br>FINDINGS: PathoGFAIR is a collection of Galaxy-based Findable, Accessible, Interoperable, and Reusable (FAIR) workflows employing state-of-the-art tools to detect and track pathogens from metagenomic Nanopore sequencing. Although initially developed to detect pathogens in food datasets, the workflows can be applied to other metagenomic Nanopore pathogenic data. PathoGFAIR incorporates visualizations and reports for comprehensive results. We tested PathoGFAIR on 130 samples containing different pathogens from multiple hosts under various experimental conditions. For all but 1 sample, workflows have successfully detected expected pathogens at least at the species rank. Further taxonomic ranks are detected for samples with sufficiently high colony-forming unit and low cycle threshold values.<br><br>CONCLUSIONS: PathoGFAIR detects the pathogens at species and subspecies taxonomic ranks in all but 1 tested sample, regardless of whether the pathogen is isolated or the sample is incubated before sequencing. Importantly, PathoGFAIR is easy to use and can be straightforwardly adapted and extended for other types of analysis and sequencing techniques, making it usable in various pathogen detection scenarios.}, }
@article {pmid41003514, year = {2025}, author = {Davis, AB and Evans, M and McKindles, K and Lee, J}, title = {Co-Occurrence of Toxic Bloom-Forming Cyanobacteria Planktothrix, Cyanophage, and Symbiotic Bacteria in Ohio Water Treatment Waste: Implications for Harmful Algal Bloom Management.}, journal = {Toxins}, volume = {17}, number = {9}, pages = {}, doi = {10.3390/toxins17090450}, pmid = {41003514}, issn = {2072-6651}, mesh = {Ohio ; *Bacteriophages/genetics/isolation &amp; purification ; *Cyanobacteria/virology/genetics/growth &amp; development ; Water Purification ; *Harmful Algal Bloom ; Symbiosis ; Lakes/microbiology ; Water Microbiology ; }, abstract = {Cyanobacterial blooms are increasingly becoming more intense and frequent, posing a public health threat globally. Drinking water treatment plants that rely on algal bloom-affected waters may create waste (water treatment residuals, WTRs) that concentrates contaminants. Source waters may contain harmful cyanobacteria, cyanophages (bacteriophages that infect cyanobacteria), and bacteria. Cyanophages are known to affect bloom formation and growth dynamics, so there is a need to understand viral-host dynamics between phage and bacteria in these ecosystems for managing cyanobacteria. This study isolated and characterized lytic cyanophages from WTRs of a HAB-affected lake in Ohio that infect toxic bloom-forming filamentous cyanobacteria Planktothrix agardhii. Phage infections in the Lake Erie cyanobacteria culture were examined visually and via microscopy and fluorometry. Whole genome sequencing and metagenomic analyses were also conducted. Observed changes in Planktothrix included sheared and shriveled filaments, reduced clumping, and buoyancy changes. Photosynthetic pigmentation was unexpectedly more apparent during phage infection. Metagenomic analyses identified nineteen phages and seven other co-existing bacterial genera. Annotated bacterial genomes contained metabolic pathways that may influence phage infection efficiency. Viral genomes were successfully tied to microbial hosts, and annotations identified important viral infection proteins. This study examines cyanobacterial-phage interactions that may have potential for bioremedial applications.}, }
@article {pmid41003209, year = {2025}, author = {Deng, ZL and Yu, FM and Ma, X and Zhao, Q and Liu, JK}, title = {Metagenomic Insights into Disease-Induced Microbial Dysbiosis and Elemental Cycling Alterations in Morchella Cultivation Soils: Evidence from Two Distinct Regions.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {11}, number = {9}, pages = {}, doi = {10.3390/jof11090663}, pmid = {41003209}, issn = {2309-608X}, support = {No.202502AE090044//Major Science and Technology Special Project of Yunnan Province/ ; }, abstract = {Soil-borne diseases represent a major constraint on the sustainable cultivation of morel mushrooms (Morchella spp.), yet the microbial ecological mechanisms driving disease occurrence and progression remain poorly understood. In this study, we conducted comparative metagenomic analyses of rhizosphere and root-adhering soils associated with healthy and diseased Morchella crops from two major production regions in China, aiming to elucidate shifts in microbial community composition, assembly processes, and functional potential. Disease conditions were linked to pronounced microbial dysbiosis, with community assembly shifting from stochastic to deterministic processes, particularly within fungal communities under host selection and pathogen pressure. Co-occurrence network analysis revealed substantial reductions in connectivity, modularity, and clustering coefficients in diseased soils, indicating the loss of ecological stability and keystone taxa. Functional annotations using CAZy, COG, and KEGG databases showed that healthy soils were enriched in genes related to carbohydrate metabolism, aerobic respiration, and ecosystem resilience, whereas diseased soils exhibited higher abundance of genes associated with stress responses, proliferation, and host defense. Furthermore, elemental cycling analysis demonstrated that healthy soils supported pathways involved in aerobic carbon degradation, nitrogen fixation, phosphate transport, and sulfur oxidation, while diseased soils favored fermentation, denitrification, phosphorus limitation responses, and reductive sulfur metabolism. Collectively, these results highlight the importance of microbial functional integrity in maintaining soil health and provide critical insights into microbiome-mediated disease dynamics, offering a foundation for developing microbiome-informed strategies for sustainable fungal crop management.}, }
@article {pmid41003180, year = {2025}, author = {Xu, L and Tao, L}, title = {Pulmonary Verruconis Infection in an Immunocompetent Patient: A Case Report and Literature Review.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {11}, number = {9}, pages = {}, doi = {10.3390/jof11090634}, pmid = {41003180}, issn = {2309-608X}, support = {No//Senior Medical Talents Program of Chongqing for Young and Middle-aged/ ; No. ZQNYXGDRCGZS2021007//Young and Middle-aged Senior Medical Talents Studio/ ; No. 2020-126//Chongqing Clinical Research Centre for Geriatric Diseases Project/ ; cstc2024ycjh-bgzxm00061//Chongqing Talent Contract System Project/ ; }, abstract = {Verruconis species are thermophilic, darkly pigmented fungi commonly found in hot environments. Despite their environmental ubiquity, fewer than fifty human infections have been reported, with V. gallopava responsible for most cases. While infections primarily occur in immunocompromised individuals, only six cases in immunocompetent patients have been documented. We describe a case of pulmonary Verruconis infection in a 75-year-old immunocompetent woman. Despite broad-spectrum antifungal treatments, including liposomal amphotericin B and voriconazole, the patient's condition deteriorated. Bronchoalveolar lavage (BAL) revealed hyphal forms, and fungal culture identified a Verruconis species. Antifungal susceptibility tests showed low minimal inhibitory concentrations (MICs) for amphotericin B (1 μg/mL) and voriconazole (0.5 μg/mL). Clinical manifestations of Verruconis infection in immunocompetent pneumonia patients are non-specific. Structural lung disease was identified as the primary risk factor in such hosts. BAL fungal cultures and metagenomics are valuable tools in diagnosing rare fungal infections. Treatment regimens vary, with amphotericin B and triazoles being the most commonly used antifungal agents. Currently, there are no standardized guidelines for diagnosis or treatment. Further studies are needed to establish clinical protocols.}, }
@article {pmid41002730, year = {2025}, author = {Sakellakis, M and Resta, P and Papagianni, E and Procter, KA and Belouka, I and Gioti, K and Anthouli-Anagnostopoulou, F and Chaniotis, D and Beloukas, A}, title = {Decoding Microbiome's Role in Prostate Cancer Progression and Treatment Response.}, journal = {Diseases (Basel, Switzerland)}, volume = {13}, number = {9}, pages = {}, doi = {10.3390/diseases13090294}, pmid = {41002730}, issn = {2079-9721}, abstract = {Prostate cancer (PCa) is the most common genitourinary malignancy in men, with a multifactorial etiology influenced by genetic, environmental, and microbial determinants. Although the prostate was traditionally considered sterile, advances in microbiome research have challenged this view, revealing potential links between microbial communities and PCa development, progression, and treatment response. This review synthesizes evidence on the gut, urinary, seminal fluid, and prostatic microbiomes, highlighting their potential contributions to PCa pathogenesis and therapeutic outcomes. Key studies utilizing next-generation sequencing (NGS), whole-genome sequencing (WGS), PCR, and metagenomic analyses have identified specific bacterial and fungal taxa associated with Pca; however, findings remain inconsistent across methodologies and cohorts. Microorganisms such as Propionibacterium acnes and Pseudomonas spp. may modulate inflammation, immune responses, and resistance to androgen-deprivation therapy. Further research is required to determine whether microbial signatures can serve as reliable biomarkers for early detection, prognosis, or novel therapeutic strategies in PCa management.}, }
@article {pmid41002272, year = {2025}, author = {Yazhini, A and Söding, J}, title = {Enhancing genome recovery across metagenomic samples using MAGmax.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btaf538}, pmid = {41002272}, issn = {1367-4811}, abstract = {SUMMARY: The number of metagenome-assembled genomes (MAGs) is rapidly increasing with the growing scale of metagenomic studies, driving fast progress in microbiome research. Sample-wise assembly has become the standard due to its computational efficiency and strain-level resolution. It requires dereplication, the removal of near-identical genomes assembled in different metagenomic samples. We present MAGmax, an efficient dereplication tool that enhances both the quantity and quality of MAGs through a strategy of bin merging and reassembly. Unlike dRep, which selects a single representative bin per genome cluster, MAGmax merges multiple bins within a cluster and reassembles them to increase coverage. MAGmax produces more dereplicated, higher-quality MAGs than dRep at 1.6× its speed and using three times less memory.<br><br>The MAGmax open source software, implemented in Rust, is available under the GPLv3 license at https://github.com/soedinglab/MAGmax.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid41002268, year = {2025}, author = {Aminu, S and Ascandari, A and Benhida, R and Daoud, R}, title = {GRUMB: A Genome-Resolved Metagenomic Framework for Monitoring Urban Microbiomes and Diagnosing Pathogen Risk.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btaf548}, pmid = {41002268}, issn = {1367-4811}, abstract = {SUMMARY: Urban infrastructure hosts dynamic microbial communities that complicate biosurveillance and AMR monitoring. Existing tools rarely combine genome-resolved reconstruction with ecological modeling and batch-aware analytics tailored to infrastructure-scale studies. We present GRUMB (Genome-Resolved Urban Microbiome Biosurveillance), an open-source, SLURM-compatible pipeline that reconstructs high-quality metagenome-assembled genomes (MAGs) from shotgun sequencing reads and integrates taxonomic/functional annotation (CARD, VFDB), batch-aware normalization, ecological diagnostics and machine learning classification of environment types with uncertainty and risk scoring. GRUMB accepts either SRA project accessions or paired-end FASTQ files with metadata, and produces assemblies, MAGs, taxonomic and functional profiles, ecological outputs and risk-informed classification. Its modular design enables reproducible, infrastructure-scale biosurveillance across diverse environments.<br><br>.GRUMB is freely available under the MIT License at: https://github.com/SuleimanAminu/genome-resolved-urban-microbiome-biosurveillance; Zenodo DOI: https://doi.org/10.5281/zenodo.15505402. Requirements: Linux (Ubuntu 20.04+), Python 3.11, R 4.2+, SLURM. Issues and feature requests are tracked on GitHub.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid41001537, year = {2025}, author = {Villapol, S and Flinn, H and Marshall, A and Holcomb, M and Burke, M and Cruz-Pineda, L and Soriano, S and Treangen, T}, title = {Gut microbiome remodeling by antibiotics reduces neuroinflammation in traumatic brain injury.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-7411086/v1}, pmid = {41001537}, issn = {2693-5015}, abstract = {Traumatic brain injury (TBI) induces both neuroinflammation and gut microbiome dysbiosis, yet the influence of antibiotics (ABX) on TBI-related neuropathology remains unclear. We administered a broad-spectrum oral ABX regimen to deplete the gut microbiome in single and repeated TBI mouse models. In male mice, ABX treatment significantly reduced neuroinflammation and neurodegeneration post-TBI, with no effects observed in uninjured controls. ABX also altered microbiome composition and decreased serum and fecal short-chain fatty acid levels, while intestinal damage and dysbiosis were further exacerbated by TBI severity. Notably, germ-free male mice exhibited heightened neuroinflammation and larger lesion volumes following TBI, underscoring the microbiome's essential role in recovery. Metagenomic analyses revealed Parasutterella excrementihominis and Lactobacillus johnsonii as potential ABX-resistant taxa post-injury. These findings suggest that short-term ABX treatment may attenuate TBI-induced neuroinflammation by reshaping the gut microbiome, offering directions for microbiome-targeted therapies in TBI.}, }
@article {pmid41001416, year = {2025}, author = {Wang, Q and Zhao, M and Liu, A and Zhao, Y and Fan, Z and Huang, Y and Gao, Z and He, M}, title = {Investigation of co-existing bacteria in platelets by employing long-term culturomics and metagenomics.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1607554}, pmid = {41001416}, issn = {2235-2988}, mesh = {Humans ; *Metagenomics/methods ; *Blood Platelets/microbiology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation &amp; purification/growth &amp; development ; DNA, Bacterial/genetics/chemistry ; DNA, Ribosomal/chemistry/genetics ; Sequence Analysis, DNA ; Phylogeny ; Bacteriological Techniques/methods ; }, abstract = {INTRODUCTION: Bacterial contamination of platelets presents a substantial risk in transfusion medicine. Conventional detection approaches have limitations in sensitivity and bacterial coverage. In this study we employed culturomics and metagenomics to investigate co-existent bacteria in platelets, aiming to enhance transfusion safety and explore healthy bacteremia.<br><br>METHODS: Platelet from 6 healthy donors underwent a 30-days extensive cultivation and isolation procedure using in-house culturomics.<br><br>RESULTS: 16S rRNA sequencing identified 90 bacterial strains across 3 phyla, 5 classes, 5orders, 7 families, 9 genera, and 23 species. Metagenomics sequencing revealed greater microbial diversity, detecting an average of 3018 microbial species per sample. The bacteria concurrently detected by both culturomics and metagenomics included species from Firmicutes, Actinobacteria, and Proteobacteria.<br><br>DISCUSSION: This combined approach validates the presence of bacteria in platelets, likely originating from the skin, gut, oral cavity, environment, or bloodstream, providing a comprehensive strategy for bacterial identification in transfusion products.}, }
@article {pmid41001381, year = {2025}, author = {Xu, Y and Liang, G and Huang, C and Wang, Y and Liang, Z and Jiang, Y and Huang, C and Liu, J}, title = {Mediastinal infections: diagnostic and therapeutic advances from traditional surgery to novel minimally invasive techniques.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1653443}, pmid = {41001381}, issn = {2296-858X}, abstract = {Mediastinal infections present significant diagnostic and therapeutic challenges, contributing to highly variable mortality. Diagnostic dilemmas arise from complex anatomy and radiographic similarities to malignancies. Endobronchial Ultrasound-guided Transbronchial Needle Aspiration (EBUS-TBNA) and cultures are constrained by small samples, architectural distortion, low sensitivity, and slow results in special circumstances. Therapeutic obstacles include antibiotic resistance, poor antimicrobial penetration due to altered vascularity, and high surgical morbidity. Endobronchial ultrasound-guided transbronchial mediastinal cryobiopsy (EBUS-TMC) provides larger histologically preserved specimens; metagenomic next-generation sequencing (mNGS) achieves rapid sensitive pathogen detection; advanced imaging (Dual Energy Computed Tomography, DECT; Positron Emission Tomography/Computed Tomography, PET/CT) enhances lesion differentiation and intervention planning; while minimally invasive drainage, nanocarrier-based targeted antimicrobial delivery, and reconstructive techniques collectively reduce complications and improve therapeutic efficacy. Multidisciplinary integration of these innovations is advancing precision medicine approaches.}, }
@article {pmid41000747, year = {2025}, author = {Tripp, AD and Qu, EB and Balogun, I and Brodsky, J and Baker, JS and Mancuso, CP and Roux, S and Hussain, FA and Lieberman, TD}, title = {Phage-mediated lysis does not determine Cutibacterium acnes colonization on human skin.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.09.09.675206}, pmid = {41000747}, issn = {2692-8205}, abstract = {Despite Cutibacterium acnes being the most abundant and prevalent bacteria on human skin, only a single type of phage has been identified that infects this host. Here, we leverage this one-to-one system to systematically characterize how the phage-bacteria arms race shapes C. acnes evolution and community composition on individual people. Our analysis reveals a surprising lack of phage-mediated selection despite global prevalence of C. acnes phages. Analysis of anti-phage defense systems across 3,205 bacterial genomes revealed a limited, phylogenetically restricted defense repertoire under weak selective pressure to diversify or be maintained. Functional assays did not reveal alternative phage resistance mechanisms or fitness costs associated with defense gene carriage that could explain this limited immune arsenal. This lack of pressure to maintain phage resistance could not be explained by lack of phage colonization, as examination of 471 global human facial skin metagenomes demonstrated that even in samples with high virus-to-microbe ratio, phage-sensitive clades dominate on-person populations. Together, these findings indicate that phage pressure, while present, does not play a critical role in determining strain fitness and success within C. acnes populations on human skin. We propose that this observed weak phage-mediated selective pressure can be explained by the anatomy of skin: C. acnes growth is thought to occur at the bottom of pores, where exposure to phage may be limited by physical barriers. Together, this portrait of a static arms race provides a strong contrast with other microbial species in different ecosystems and expands understanding of phage-bacteria interactions in the human microbiome.}, }
@article {pmid41000239, year = {2025}, author = {Ajrithirong, P and Krasaesin, A and Sriarj, W and Gavila, P and Chetruengchai, W and Sriwattanapong, K and Manaspon, C and Samaranayake, L and Porntaveetus, T}, title = {The metagenome and metabolome signatures of dental biofilms associated with severe dental fluorosis.}, journal = {Journal of oral microbiology}, volume = {17}, number = {1}, pages = {2560591}, pmid = {41000239}, issn = {2000-2297}, abstract = {OBJECTIVE: To explore the plaque biofilm microbiome associated with severe dental fluorosis (SF), and to describe its metagenome and metabolome.<br><br>METHODS: Sixteen plaque biofilm samples were collected from eight 6- to 15-year-old Thai children with SF and eight age-matched, caries-free and controls. Biofilms were analyzed using shotgun metagenomic sequencing, followed by bioinformatics evaluation.<br><br>RESULTS: Taxonomic profiling of biofilms from SF and controls identified a total of 12 phyla and 354 species. While alpha diversity was similar between the groups, beta diversity analysis (P&#x2009;=&#x2009;0.0010) indicated distinct microbial community structures. LEfSe highlighted key discriminatory taxa: five health-associated species (Actinomyces dentalis, Tannerella sp. HOT 286, Candidatus Nanosynbacter sp, Selenomonas noxia and Treponema sp OMZ 804) were enriched in controls, while Neisseria sicca, known for fluoride-sensitive esterase production, was significantly elevated in SF. Functionally, eight metabolic pathways were altered; three of these (phosphatidylcholine acyl editing, anhydromuropeptides recycling II, ubiquinol-7 biosynthesis), hypothesized to support N. sicca activity, were upregulated in the SF group.<br><br>CONCLUSION: SF is associated with a significant shift in the biofilm microbiota, characterized by enrichment of N. sicca and a reduction in health-associated taxa. Altered metabolic pathways supporting N. sicca provide mechanistic insights into its role as a candidate biomarker for fluorosis, warranting further investigation.}, }
@article {pmid41000214, year = {2025}, author = {Pellizzari Wielewski, L and Lujan Ferreira, M and Alnoch, RC and Mitchell, DA and Krieger, N}, title = {Evaluating Pre-Immobilization and Post-Immobilization Bioimprinting Strategies for the Activation of Lipases: A Case Study of LipC12.}, journal = {Food technology and biotechnology}, volume = {63}, number = {3}, pages = {351-361}, pmid = {41000214}, issn = {1330-9862}, abstract = {RESEARCH BACKGROUND: Although there are many studies of the bioimprinting of lipases, there is no study comparing the strategies of bioimprinting prior to immobilization (pre-immobilization) and bioimprinting after immobilization (post-immobilization). Likewise, there is no study that compares bioimprinting of lipases immobilized from a pure lipase preparation and lipases immobilized from a crude extract. We therefore investigated these strategies, using the metagenomic lipase LipC12.<br><br>EXPERIMENTAL APPROACH: We immobilized LipC12 covalently on the commercial support Immobead 150P and treated it with various bioimprinting agents, either pre-immobilization or post-immobilization. We also compared immobilization from a pure LipC12 preparation and immobilization from a crude cell-free extract.<br><br>RESULTS AND CONCLUSIONS: The best improvements in triolein-hydrolyzing activity in n-hexane, compared to a non-bioimprinted control, were obtained with post-immobilization bioimprinting, using oleic acid dissolved in t-butanol: a 12-fold improvement for immobilization from a pure LipC12 preparation and an almost 14-fold improvement for immobilization from the crude cell-free extract. This bioimprinting agent also gave a 3.5-fold increase in activity for the synthesis of ethyl oleate in n-hexane, this result being obtained for pre-immobilization bioimprinting and immobilization from the cell-free extract.<br><br>This study is the first to compare pre-immobilization and post-immobilization bioimprinting strategies, as well as bioimprinting of enzymes immobilized from both pure enzyme preparations and crude cell-free extracts. These results encourage further investigation into bioimprinting strategies.}, }
@article {pmid41000028, year = {2025}, author = {Karatas, M and Geenen, C and Keyaerts, E and Budts, L and Raymenants, J and Eggers, C and Craessaerts, B and André, E and Matthijnssens, J}, title = {Shotgun metagenomics on indoor air for surveillance of respiratory, enteric, and skin viruses in a Belgian daycare setting, January to December 2022.}, journal = {Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin}, volume = {30}, number = {38}, pages = {}, doi = {10.2807/1560-7917.ES.2025.30.38.2400711}, pmid = {41000028}, issn = {1560-7917}, mesh = {Humans ; *Metagenomics/methods ; Belgium/epidemiology ; *Viruses/isolation &amp; purification/genetics/classification ; *Environmental Monitoring/methods ; *Air Microbiology ; *Child Day Care Centers ; *Air Pollution, Indoor/analysis ; *Respiratory Tract Infections/virology/epidemiology ; *Virus Diseases/epidemiology/virology ; }, abstract = {BACKGROUNDHospital-based communicable disease surveillance may be costly during large outbreaks and often misses mild or asymptomatic infections. It can be enhanced by environmental surveillance, which monitors circulating pathogens, even from asymptomatic carriers.AIMWe investigated if tracking viruses in indoor air could be used for their surveillance in a community setting. We also tested the value of untargeted metagenomics to identify viruses in air samples.METHODSWeekly indoor air samples were collected with active air samplers from January until December 2022 from a daycare centre in Leuven, Belgium. Samples were analysed using respiratory and enteric quantitative (q)PCR panels, as well as with untargeted metagenomics, enabling both targeted and agnostic viral detections.RESULTSHuman-associated viruses were detected in 40 of 42 samples across the study period, with MW polyomavirus being most prevalent (33 samples). Respiratory agents such as rhinoviruses and RSV-B and enteric viruses including rotavirus A, astrovirus, and adenovirus appeared at epidemiologically expected times. Skin-associated viruses were also observed, notably Merkel cell polyomavirus and STL polyomavirus. Metagenomics enabled reconstructing multiple complete genomes, distinguishing viral subtypes and detecting copresence of closely related variants. Additionally, several animal, insect, fungal, and plant viruses were found, reflecting both indoor and outdoor environmental exposure.CONCLUSIONIndoor air monitoring, combined with untargeted metagenomics, demonstrates a potential to support virus surveillance. This approach can allow monitoring circulation of viruses in community settings, including those causing asymptomatic or mild infections. By enabling to reconstruct complete viral genomes, it allows detailed variant tracking, facilitating adapted public health responses.}, }
@article {pmid41000006, year = {2025}, author = {Hodgson, RJ and Cando-Dumancela, C and Davies, T and Dinsdale, EA and Doane, MP and Edwards, RA and Liddicoat, C and Peddle, SD and Ramesh, SA and Robinson, JM and Breed, MF}, title = {Contrasting Microbial Taxonomic and Functional Colonisation Patterns in Wild Populations of the Pan-Palaeotropical C4 Grass, Themeda triandra.}, journal = {Plant, cell &amp; environment}, volume = {}, number = {}, pages = {}, doi = {10.1111/pce.70205}, pmid = {41000006}, issn = {1365-3040}, support = {//This metagenomics sequencing for this project was supported by the Flinders University Accelerator for Microbiome Exploration. We also received funding from the Holsworth Wildlife Research Endowment with the Ecological Society of Australia, the Conservation Biology Grant 2022 with the Biological Society of South Australia and Nature Conservation Society of South Australia and the Lirabenda Wildlife Research Fund from the Field Naturalists Society of South Australia. We also received support from the Australian Research Council (grant numbers LP190100051 and LP190100484) and the New Zealand Ministry of Business Innovation and Employment (grant UOWX2101)./ ; }, abstract = {The interactions between native plants and soil microbiota are not well characterised, despite growing recognition of their importance for host plant fitness and ecological functioning. We used shotgun metagenomics to examine microbial taxonomic and functional colonisation patterns in wild populations of the pan-palaeotropical C4 grass, Themeda triandra, across a globally representative aridity gradient (aridity index 0.318-0.903). We investigated these patterns through the two-step selection process whereby microbes are recruited from bulk soils into rhizospheres (soil on the root surface), and root interiors (endospheres). We provide clear evidence of this process through decreasing microbial taxonomic diversity from bulk soil to T. triandra roots. Surprisingly, microbial functional potential showed the opposite trend: the diversity of potential functions (exponent of Shannon's diversity) increased from bulk soil to the rhizosphere and endosphere, but functional richness did not. Finally, we found that increasing aridity was associated with rhizospheres that were more compositionally similar, yet remained highly diverse in functional potential. Overall, aridity is strongly associated with the root-associated microbiome of T. triandra, selecting for microbiota that likely support plant resilience under dry conditions. Furthermore, microbial functional potential closely tracks taxonomic composition and aridity trends, highlighting how native plants can shape their microbial communities.}, }
@article {pmid40999698, year = {2025}, author = {Elliott, L and Coissac, E}, title = {Can Amplicon Sequencing Be Replaced by Metagenomics for Biodiversity Inventories?.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e70047}, doi = {10.1111/1755-0998.70047}, pmid = {40999698}, issn = {1755-0998}, support = {819192//European Research Council (ERC)/ ; }, }
@article {pmid40999305, year = {2025}, author = {Yang, S and Ma, B and Gao, M and Wu, J and Pilling, D and Zhu, L and Wang, X and Dong, Q and Wang, Y and Pool, K and Maloney, S and Li, P and Blache, D and Ding, L and Chen, L}, title = {Gut microbial genetic variations are associated with exploratory behavior via SNV-driven metabolic regulation in a sheep model.}, journal = {Science China. Life sciences}, volume = {}, number = {}, pages = {}, pmid = {40999305}, issn = {1869-1889}, abstract = {Host neurocognitive functions are influenced by the gut microbiome, but the role of microbial genetic variation in shaping host neural behavior remains unexplored. Here, we profiled multi-omics data and neurobehavioral phenotypes in a model of 200 Merino sheep. Genomic reconstruction of deeply sequenced fecal and ruminal samples generated 5,253 species-level metagenomic-assembled genomes, of which 3,548 were identified as novel species when compared with existing databases of sheep. Association between strain-level genetic dissimilarities and host neurobehavioral traits showed that phylogenetic differences in 85% of species were associated with exploratory behavior (FDR<0.05). We further associated 146 million microbial single nucleotide variations (SNVs) with 953 plasma metabolites and identified 34 study-wide significant associations (P<2.9×10[-8]), which involve potential microbial genetic regulation of host neuroactivity and oxidative stress-related metabolites, including 4-Anisic acid and D-galacturonate. Integrated analysis revealed that microbial SNVs may regulate host cognitive exploration through regulating metabolites via structural modulation of encoded proteins. For instance, we found that novel time- zone entry was associated with 4-Anisic acid, which was determined by SNV via structural regulation of membrane transporters. Our findings suggest that microbial genetic variation plays a critical role in modulating host neurocognition, possibly through metabolite regulation, which provides novel insights for targeted interventions in neurometabolic disorders.}, }
@article {pmid40999078, year = {2025}, author = {Zhang, C and Zhou, J and Mai, BK and Qin, Z and Finnigan, J and Gittings, S and Liu, P and Yang, Y}, title = {A pyridoxal radical carboligase and imine reductase photobiocatalytic cascade for stereoselective synthesis of unnatural prolines.}, journal = {Nature chemistry}, volume = {}, number = {}, pages = {}, pmid = {40999078}, issn = {1755-4349}, support = {W911NF-24-2-0246//United States Department of Defense | United States Army | U.S. Army Research, Development and Engineering Command | Army Research Office (ARO)/ ; CHE-2400087//National Science Foundation (NSF)/ ; }, abstract = {Cooperative photobiocatalysis is a useful strategy for achieving stereoselective intermolecular radical reactions that are not known in either biology or chemistry. The diastereoselective and enantioselective synthesis of cyclic non-canonical amino acids remains challenging using established methods. Here we report a multienzyme photobiocatalytic cascade to stereoselectively prepare polysubstituted unnatural prolines. We engineered an underexploited class of pyridoxal 5'-phosphate aldolases as new-to-nature radical carboligases to catalyse the decarboxylative C-C coupling of aspartic acid, furnishing imine-containing azacyclic non-canonical amino acids. High-throughput screening of metagenomic imine reductases led to the development of diastereoselective biocatalytic reduction and dynamic kinetic asymmetric transformation of cyclic imines, providing optically pure unnatural prolines featuring an elusive 2,5-anti stereochemistry with up to three stereocentres. Beyond its synthetic utility, this study established a new mode of radical pyridoxal enzymology by leveraging open-shell enamine catalysis, opening up avenues for developing new free radical reactions.}, }
@article {pmid40998909, year = {2025}, author = {Wang, LJ and Huang, M and Hu, CQ and Yuan, N and Wang, R and Li, M and Guo, XC and Lv, ZH and Xie, KQ and Yang, ZF and Zhu, D and Yang, LQ and Yin, YR}, title = {Characterization of a novel halophilic and thermostable multifunctional cellulase from Ebinur Salt Lake.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {32877}, pmid = {40998909}, issn = {2045-2322}, support = {230212528080//Xingdian Talent Support Program of Yunnan Province&#xff0c;China/ ; 202401AT071166//Yunnan Applied Basic Research Project&#xff0c;China/ ; }, mesh = {*Cellulase/genetics/metabolism/chemistry/isolation &amp; purification ; *Lakes/microbiology ; Enzyme Stability ; China ; Hydrogen-Ion Concentration ; Cellulose/metabolism ; Recombinant Proteins/metabolism/genetics/chemistry/isolation &amp; purification ; Amino Acid Sequence ; Temperature ; Hydrolysis ; Substrate Specificity ; Escherichia coli/genetics ; }, abstract = {Cellulase is essential for cellulose hydrolysis and is used across industries such as food, feed, textiles, biofuel, and biomass pretreatment. However, its utility is restricted by high temperatures and salt concentrations. This study identified a novel cellulase gene (named c5-cel4) from Ebinur Salt Lake in Xinjiang, China using metagenomic technology. Its amino acid sequence has a 90.97% similarity to the GH5 family cellulase of Microbulbifer litoralis (WP_250463697.1). The gene was expressed in Escherichia coli, and the recombinant protein, C5-CEL4, was purified via Ni-NTA affinity chromatography. C5-CEL4, secreted extracellularly (0.886 U/mL), revealed a protein size 14 KDa smaller than predicted, with mass spectrometry indicating a truncated C-terminal of 135 amino acid residues. Optimal activity was observed at 50 °C and pH 7.0, maintaining over 80% activity at 40-65 °C and 45-50 °C for 2 h. The enzyme's half-life was 60 min at 55-60 °C, retaining over 90% activity after 24 h in pH 5.0-12.0 buffers. C5-CEL4 showed activity against CMC-Na, bagasse xylan, and beech xylan, with Kcat values of 98.20 s[- 1] and 12.32 s[- 1] for CMC-Na and bagasse xylan, respectively. It also hydrolyzed wheat bran and maize stalks into reducing sugars. Remarkably, C5-CEL4 exhibited high salt tolerance, maintaining 100% activity in 0.5 M-5.0 M NaCl and after 9 months in 5.0 M NaCl. It retained over 90% activity in ionic liquids (BMIM-Ac, EMIM-Cl, BMIM-BF4) at 50% concentration and showed resistance to heavy metal ions (Co[2+], Cu[2+], Ag[+], Mn[2+], Pb[2+], and Ni[2+]) and inhibitors (PMSF, DTT, Tween80, and SDS). In conclusion, C5-CEL4 is a robust cellulase with heat, alkali, salt, ionic liquid, and inhibitor resistance, alongside cellulase and xylanase activity, presenting significant potential for feed, food, and bioenergy applications.}, }
@article {pmid40998902, year = {2025}, author = {Satpathy, SS and Pradhan, D}, title = {Unveiling community structure, antimicrobial resistance, and virulence factor of a wastewater sample of dairy farm located in mayurbhanj, odisha, India.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {32919}, pmid = {40998902}, issn = {2045-2322}, mesh = {*Wastewater/microbiology ; India ; *Virulence Factors/genetics ; *Dairying ; *Bacteria/genetics/drug effects/pathogenicity/isolation &amp; purification ; *Drug Resistance, Bacterial/genetics ; Farms ; Animals ; Anti-Bacterial Agents/pharmacology ; *Microbiota ; Water Microbiology ; }, abstract = {Nutrient-rich dairy wastewater (DWW) is an excellent growing medium for microbes. Their antimicrobial resistance (AMR) genes and pathogenic roles remain in the DWW and even multiply in environmental settings, in contrast to many chemical toxins that break down over time. Necessary steps and standardized techniques for tracking AMR in DWW samples are desperately needed. In this context, a DWW sample was evaluated to assess the necessity of remediation and develop a suitable treatment technique. Physicochemical characterizations of the sample showed an elevated level of pollutants like proteins, fats, and carbohydrates that led to the water pollution and microbial diversity (e.g., 36 phyla, 72 classes, 111 orders, 168 families, 275 genera, and 347 species). The Shannon and Simpson indices showed that the DWW sample had a high level of microbial diversity of a few species. The gene ontology (GO) analysis revealed the functional categories with 2795 genes belonging to 11 virulence categories. Most of the identified AMR genes belonged to beta-lactamase, and the majority of them were linked to Escherichia coli, Mycobacterium tuberculosis, Staphylococcus aureus, Klebsiella pneumoniae, Pseudomonas aeruginosa, Enterobacter cloacae, etc. The major bacterial phyla carrying AMR genes included Firmicutes (36%), Proteobacteria (31%), Actinobacteria (21%), and Bacteroidetes (5%).}, }
@article {pmid40998209, year = {2025}, author = {Olsen, IA and Eggesbø, M and Trivedi, U and Timmermann, A}, title = {Per- and polyfluoroalkyl substances and the gut microbiota in infants: A scoping review.}, journal = {Environmental research}, volume = {}, number = {}, pages = {122937}, doi = {10.1016/j.envres.2025.122937}, pmid = {40998209}, issn = {1096-0953}, abstract = {PER: and polyfluoroalkyl substances (PFASs) are persistent environmental chemicals associated with adverse health effects. Emerging evidence suggests PFAS exposure may influence gut microbiota composition, which is a critical determinant of health particularly during infancy. A systematic search was conducted in PubMed to identify epidemiological studies investigating PFAS exposure and infant gut microbiota. Seven studies met the inclusion criteria, examining a range of PFASs derived from either breast milk, maternal blood, or umbilical cord blood and including from 30 to 789 subjects. These studies used either 16S rRNA sequencing or shotgun metagenomics to assess microbiota changes. Perfluorooctane sulfonic acid (PFOS) and perfluorooctanoic acid (PFOA) were the most frequently examined PFASs. Across studies, exposure to PFASs was associated with both increased and decreased α-diversity. β-diversity shifts were also observed in some studies, suggesting altered microbial structures. PFAS exposure was associated with changes in the abundance of specific taxa, such as increased Enterococcus and decreased Faecalibacterium and Phocaeicola vulgatus. Functional pathway alterations were also reported, including disrupted bile acid metabolism. Variation in study design, covariate adjustment, and methodological approaches likely contribute to the inconsistencies in the observed associations between PFAS exposure and the infant gut microbiota. In conclusion, current evidence suggests that PFAS exposure may influence infant gut microbiota, but more and larger longitudinal studies are needed to better understand whether PFAS exposure is associated with altered gut microbiota composition in infants. This review synthesizes existing evidence on associations between PFAS exposure and gut microbiota composition in infants.}, }
@article {pmid40997705, year = {2025}, author = {Sheng, B and Liu, S and Xiong, K and Liu, J and Zhu, S and Zhang, H and Zhang, R}, title = {Response of bacterial pathogens to process upgrades and floc sizes in a full-scale landfill leachate treatment plant.}, journal = {Journal of environmental management}, volume = {394}, number = {}, pages = {127377}, doi = {10.1016/j.jenvman.2025.127377}, pmid = {40997705}, issn = {1095-8630}, abstract = {Bacterial pathogens in wastewater environments pose serious public health risks, serving as reservoirs for antibiotic resistance genes (ARGs) and contributing to the global antimicrobial resistance (AMR) crisis. This study investigated how process upgrades and sludge aggregate sizes influence the distribution of bacterial pathogens and ARGs in a full-scale landfill leachate treatment plant (LLTP). Using 16S rRNA and metagenomic sequencing, we analyzed potential pathogens and ARG profiles during the progression from conventional nitrification-denitrification (CND) to partial nitrification-denitrification (PND). Results showed a notable increase in the relative abundance of potential pathogenic genera in large aggregates following the process upgrade, indicating structural and functional shifts in microbial communities. The average abundance of WHO-priority ARGs, including baeR, smeR, and adeL, was significantly higher at the PND phase, likely linked to the process upgrade. Additionally, the activity of mobile genetic elements (MGEs), particularly those involved in horizontal gene transfer and DNA repair, was enhanced at the PND phase, accelerating ARG dissemination. Importantly, the process upgrade reduced the relative abundance of Streptococcus pyogenes, a high-risk pathogen, suggesting improved pathogen control. This study provides critical insights into optimizing LLTP processes to mitigate AMR risks and improve public health safety.}, }
@article {pmid40997694, year = {2025}, author = {Sun, J and Zhao, X and Liu, JJ and Zhang, Z and Yan, WJ and Zhang, PD}, title = {Functional specialization of the eelgrass rhizosphere microbiome: Root exudate-mediated assembly and implications for degraded meadow rehabilitation.}, journal = {Marine environmental research}, volume = {212}, number = {}, pages = {107577}, doi = {10.1016/j.marenvres.2025.107577}, pmid = {40997694}, issn = {1879-0291}, abstract = {Seagrass meadows provide vital coastal ecosystem services but face accelerated degradation due to anthropogenic stressors. While rhizosphere microbes are recognized for enhancing nutrient cycling and supporting meadow resilience, the mechanisms by which seagrasses recruit functional groups critical for stress mitigation from bulk sediment via root exudates remain poorly understood. This study employed metagenomics and metabolomics to characterize Zostera marina root exudates and compare microbial (bacterial, fungal, archaeal) composition, diversity, and metabolic functions between bulk sediment and rhizosphere. We demonstrate that root exudates--enriched in organic acids and phenolic compounds--act as ecological filters, selectively enriching rhizosphere taxa with specialized functions relevant to habitat recovery, such as nitrogen/sulfur cycling (key processes for mitigating eutrophication impacts). Rhizosphere communities exhibited reduced diversity but heightened functional specialization aligned with host nutrition and stress tolerance, contrasting sharply with bulk sediment communities dominated by methane production and carbon degradation pathways. Critically, bulk sediment serves as a reservoir of pre-adapted genetic potential for environmental adaptation, supplying niche-adaptive genes to the rhizosphere microbiome. Strong metabolite-microbe correlations confirm host exudates as primary drivers of microbial assembly, synchronizing functional traits with host demands. These findings elucidate host-mediated recruitment strategies underpinning seagrass resilience and provide mechanistic insights for designing microbiome-assisted rehabilitation of degraded seagrass habitats. (Images were created with BioRender).}, }
@article {pmid40997562, year = {2025}, author = {Duan, Y and Zhang, J and Petropoulos, E and Zhao, J and Chen, Y and Wang, L and Wang, X and Jia, R and Wu, F and Li, Y}, title = {Metagenomic profiling of antibiotic resistance genes in terrestrial ecosystems across China.}, journal = {Ecotoxicology and environmental safety}, volume = {304}, number = {}, pages = {119096}, doi = {10.1016/j.ecoenv.2025.119096}, pmid = {40997562}, issn = {1090-2414}, abstract = {Soil represents a significant reservoir of antibiotic resistance genes (ARGs), yet their distribution across diverse terrestrial ecosystems remains poorly characterized. To address this knowledge gap, we conducted a large-scale, cross-regional soil survey spanning 4300 km in China, collecting samples at 42 intervals across six distinct terrestrial ecosystems. High diversity (18 ARG types and 129 ARG subtypes) and abundance (mean value: 724.9 [coverage, ×/Gb]) of ARGs were observed in the topsoil (0-20 cm depth) across the six terrestrial ecosystems, with tetracycline resistance and efflux pump being the prevailing class and resistance mechanism respectively. Notably, only aac (6')-I ranked among the highest-risk ARGs (Rank I), indicating that merely 0.78 % of detected ARGs pose a severe pathogenic threat. Meanwhile, horizontal gene transfer (HGT) is likely the primary transmission mechanism for ARGs in these soils. While most ARGs currently present minimal direct public health risks, their high transmission potential warrants attention. Furthermore, stochastic processes dominate the spread of soil ARGs, though both stochastic and deterministic processes contribute to the spread of their hosts. Collectively, these results provide timely insights into the resistance mode of soil ARGs in terrestrial ecosystems.}, }
@article {pmid40997471, year = {2025}, author = {Wei, T and Zhen, Z and Luo, S and Chen, Y and Li, J and Liang, YQ and Song, M and Li, J and Lin, Z and Zhang, D}, title = {Earthworm-assisted shift and enrichment of the active di(2-ethylhexyl) phthalate degraders in farmland soils by DNA-stable isotope probing.}, journal = {Journal of hazardous materials}, volume = {498}, number = {}, pages = {139916}, doi = {10.1016/j.jhazmat.2025.139916}, pmid = {40997471}, issn = {1873-3336}, abstract = {Di(2-ethylhexyl) phthalate (DEHP) is a widely used plasticizer that poses significant environmental and health risks due to its accumulation in agricultural soils and endocrine-disrupting effects. This study investigated the roles of earthworm-assisted bioremediation of DEHP by using DNA stable isotope probing (DNA-SIP) and metagenomic sequencing, and identified the shift of the active microbes involved in DEHP degradation. DEHP degradation efficiency increased from 41.72 % in natural soil to 79.90 % in earthworm-amended soil, 47.31 % and 9.48 % of which attributed to gut microbiota and improved soil microenvironment. We identified 15 active DEHP-degrading OTUs, including five newly reported genera (Romboutsia, Deinococcus, Paeniglutamicibacter, Intrasporangium, and Methylotenera). Functional pathway analysis revealed microenvironment-specific degradation routes. The 2,3-epoxy-2,3-dihydrobenzoyl-CoA and 4,5-dihydroxyphthalate pathways were exclusively active in soil, while cis,cis-muconate and 2-oxopent-4-enoate pathways were unique in earthworm gut. Notably, both soil and gut shared 4-hydroxyphthalate and glutaryl-CoA pathways, and the latter one was highly promoted in gut (1.11 %) and strongly associated with key degraders such as Pseudomonas, Ensifer, and Acinetobacter. All gut-associated degradation routes converged into the citrate cycle, indicating enhanced potential for complete mineralization under microaerobic conditions. This work provides valuable strategies for optimizing earthworm-assisted bioremediation to mitigate DEHP pollution in agricultural soils.}, }
@article {pmid40997464, year = {2025}, author = {Xie, S and Peng, L and Zhou, Z and Xu, N and Li, S and Feng, Y}, title = {Biodegradable microplastics amplify antibiotic resistance in aquaculture: A potential One Health crisis from environment to seafood.}, journal = {Journal of hazardous materials}, volume = {498}, number = {}, pages = {139932}, doi = {10.1016/j.jhazmat.2025.139932}, pmid = {40997464}, issn = {1873-3336}, abstract = {Aquaculture has become a reservoir for antibiotic resistance genes (ARGs) and microplastics (MPs), threatening food security and human health. However, the role of MPs, in ARGs dissemination remains unclear. Here, we tracked ARGs dynamics in tilapia aquaculture systems via a 90-day in situ MPs-exposure experiment, and compared the impacts of conventional polypropylene MPs (PP-MPs) and biodegradable poly (butylene adipate-co-terephthalate) MPs (PBAT-MPs) on resistome distribution, ecological risks, and microbial assembly across water, sediment, plastisphere, and fish guts via metagenomics. Results revealed the MPs served as microbial scaffolds, enriching microbiome and resistome. Species turnover (>80 %) and deterministic process induced by MPs dominated the microbial community assembly. Astonishingly, PBAT-MPs posed higher risks compared to PP-MPs based on risks ranking (Rank I ARGs and risk index) and pathogen identification (37 % and 34 % of clinical ARGs, respectively). Stronger correlations were built in plastisphere between the microbial communities and ARGs (r > 0.8 and p < 0.05). Microbes (path coefficient = 0.632, p < 0.01) and MGEs (path coefficient = 0.344, p < 0.01) jointly exerted positive correlations with the ARGs profile. With sediments and MPs functioning ARGs reservoir and vectors, resistome dissemination mediated by plastisphere biofilm evolution were potentially exacerbated through trophic accumulation. By integrating multi-compartment resistome mapping (sediment reservoir-MPs vector-fish exposure), we established MPs as amplifiers of ARGs across trophic chains, directly linking environmental dynamics to human dietary exposure risks, thereby advancing environmental sustainability, food safety and antimicrobial resistance governance under One Health Perspective.}, }
@article {pmid40996787, year = {2025}, author = {Bergner, L and Catalano, S and Nichols, J and Da Silva Felipe, A and Cao, X and Mair, D and Nankasi, A and Arinaitwe, M and Mubangizi, A and Pybus, OG and Standley, C and Faust, CL and Raghwani, J}, title = {Quantifying viral load and characterizing virus diversity in wildlife samples with target enrichment sequencing.}, journal = {Microbial genomics}, volume = {11}, number = {9}, pages = {}, doi = {10.1099/mgen.0.001513}, pmid = {40996787}, issn = {2057-5858}, mesh = {Animals ; *Viral Load ; *Metagenomics/methods ; Feces/virology ; *Animals, Wild/virology ; Genome, Viral ; High-Throughput Nucleotide Sequencing/methods ; *Viruses/genetics/classification/isolation &amp; purification ; RNA Viruses/genetics/isolation &amp; purification ; DNA Viruses/genetics/isolation &amp; purification ; Rodentia/virology ; }, abstract = {Metagenomics is a powerful tool for characterizing viruses, with broad applications across diverse disciplines, from understanding the ecology and evolutionary history of viruses to identifying causative agents of emerging outbreaks with unknown aetiology. Additionally, metagenomic data contain valuable information about the amount of virus present within samples (i.e. viral load), which can provide insights into transmission potential, time since infection and, in turn, epidemic trajectories. However, before we can effectively use metagenomic data to inform transmission, we need to understand the general relationship between sequencing outputs and viral load. Here, using a commercially available probe panel targeting a wide diversity of viruses, we investigated the detection and recovery of virus genomes by spiking known concentrations of DNA and RNA viruses into wild rodent faecal samples. In total, 15 experimental replicates were sequenced with target enrichment sequencing and compared to shotgun sequencing of the same background samples. Target-enriched sequencing recovered all spike-in viruses at every concentration (10[2], 10[3] and 10[5]±1 log genome copies) and showed a log-linear relationship between spike-in concentration and mean read depth. Background viruses (including Kobuvirus and Cardiovirus) were recovered consistently across all biological and technical replicates and by shotgun sequencing, but genome coverage was variable between virus genera and likely reflected the composition of the target enrichment probe panel. Overall, our study highlights the strengths and weaknesses of using commercially available panels to quantify and characterize wildlife viromes and underscores the importance of probe panel design for accurately interpreting coverage and read depth. To advance the use of metagenomics for understanding virus transmission, further research will be needed to elucidate how sequencing strategy (e.g. library depth and pooling), virome composition and probe design influence viral read counts and genome coverage.}, }
@article {pmid40996703, year = {2025}, author = {Sierra, MA and Ryon, K and Arikatla, MR and Elshafey, R and Bhaskar, H and Proszynski, J and Bhattacharya, C and Shaaban, H and Danko, DC and Ambrose, P and Spaulding, SA and Zambrano, MM and Consortium, TMD and Mason, CE}, title = {The Microbe Directory: a centralized database for biological interpretation of microbiome data.}, journal = {Database : the journal of biological databases and curation}, volume = {2025}, number = {}, pages = {}, doi = {10.1093/database/baaf060}, pmid = {40996703}, issn = {1758-0463}, support = {U01DA053941/NH/NIH HHS/United States ; U54AG089334/NH/NIH HHS/United States ; R01AI151059/NH/NIH HHS/United States ; 80NSSC24K0728/NASA/NASA/United States ; 80NSSC24K1052/NASA/NASA/United States ; //WorldQuant Foundation/ ; }, mesh = {*Microbiota/genetics ; Humans ; *Databases, Genetic ; Data Curation ; Metadata ; Animals ; Metagenomics ; }, abstract = {The Microbe Directory (TMD) is a centralized database of metadata for microbes from all domains that helps with the biological interpretation of metagenomic data. The database comprises phenotypical and ecological traits of microorganisms, which have been verified by independent manual annotations. This effort has been possible by the help of a community of volunteer students worldwide who were trained in manual curation of microbiology data. To summarize this information, we have built an interactive browser that makes the database accessible to everyone, including non-bioinformaticians. We used the TMD data to analyse microbiome samples from different projects such as MetaSUB, TARA Oceans, Human Microbiome Project, and Sponge Microbiome Project, showcasing the utility of TMD. Furthermore, we compare our microbial annotations with annotations collected by artificial intelligence (AI) and demonstrate that despite the high speed of AI in reviewing and collecting microbial data, annotation requires domain knowledge and therefore manual curation. Collectively, TMD provides a unique source of information that can help to interpret microbiome data and uncover biological associations. Database URL: www.themicrobedirectory.com/.}, }
@article {pmid40996674, year = {2025}, author = {Waheed, A and Wazir, H and Ram, M and Irshad, NUN}, title = {Letter to the editor: The added value of metagenomic next-generation sequencing in central nervous system infections: a systematic review of case reports.}, journal = {Infection}, volume = {}, number = {}, pages = {}, pmid = {40996674}, issn = {1439-0973}, }
@article {pmid40996452, year = {2025}, author = {Ma, B and Bu, Y and Huang, J and Liu, Y and Guo, Z and Yu, H and Liang, T and Wang, D}, title = {Bioactive compounds from deep-sea extremophiles: emerging potential in cosmeceuticals and nutraceuticals.}, journal = {FEMS microbiology letters}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsle/fnaf102}, pmid = {40996452}, issn = {1574-6968}, abstract = {The deep sea contains a varied range of extremophilic bacteria that have adapted to harsh environments by producing bioactive substances with remarkable properties. These molecules, including enzymes, peptides, and secondary metabolites, demonstrate exceptional stability, strong antioxidant properties, and advantageous biocompatibility, making them viable candidates for use in cosmeceuticals and nutraceuticals. This paper offers a thorough examination of the biotechnological potential of deep-sea extremophiles as a largely underutilised source of functional agents for cosmetics, anti-ageing products, and health-enhancing dietary ingredients. Key bioactive molecules, such as extremozymes, exopolysaccharides, and microbial pigments, along with their bioactivities, including ultraviolet protection, collagen stimulation, and oxidative stress attenuation, are examined, with an elucidation of their methods of action. Recent advancements in biotechnological instruments, particularly metagenomics and high-throughput screening, are analysed for their contributions to addressing the difficulties of producing extremophiles and aiding in the identification of new bioactive compounds. The paper examines existing limits in scalable bioprocessing and regulatory compliance, investigates solutions like synthetic biology and fermentation optimisation to enhance the viability of commercial utilisation. This study highlights the capacity of deep-sea extremophiles to considerably aid in the creation of sustainable, high-value goods in the health and wellness sectors.}, }
@article {pmid40996449, year = {2025}, author = {Mimpen, IL and Battaglia, TW and Parra Martinez, M and Toner-Bartelds, C and Zeverijn, LJ and Geurts, BS and Verkerk, K and Hoes, LR and van Renterghem, AWJ and Noe, M and Hofland, I and Broeks, A and van der Noort, V and Stigter, ECA and Gulersonmez, CMC and Burgering, BMT and van Gogh, M and de Zoete, MR and Gelderblom, H and Dijkstra, KK and Wessels, LFA and Voest, EE}, title = {Microbial metabolic pathways guide response to immune checkpoint blockade therapy.}, journal = {Cancer discovery}, volume = {}, number = {}, pages = {}, doi = {10.1158/2159-8290.CD-24-1669}, pmid = {40996449}, issn = {2159-8290}, abstract = {Studies have identified a link between specific microbiome-derived bacteria and immune checkpoint blockade (ICB) efficacy. However, these species lack consistency across studies and their immunomodulatory mechanisms remain elusive. To understand the influence of the microbiome on ICB response we studied its functional capacity. Using pan-cancer metagenomics data of ICB-treated patients, we showed that community-level metabolic pathways are stable across individuals, making them suitable to predict ICB response. We identified several microbial metabolic processes significantly associated with response, including the methylerythritol phosphate (MEP) pathway, which was associated with response and induced Vδ2 T cell-mediated anti-tumor responses in patient-derived tumor organoids. In contrast, riboflavin synthesis was associated with ICB resistance, and its intermediates induced mucosal-associated invariant T (MAIT) cell-mediated immune suppression. Moreover, gut metabolomics revealed that high riboflavin levels were linked to worse survival in patients with abundant intratumoral MAIT cells. Collectively, our results highlight the relevance of metabolite-mediated microbiome-immune cell crosstalk.}, }
@article {pmid40996271, year = {2025}, author = {Wong, MK and Armstrong, E and Heirali, AA and Schneeberger, PHH and Chen, H and Cochrane, K and Sherriff, K and Allen-Vercoe, E and Siu, LL and Spreafico, A and Coburn, B}, title = {Assessment of ecological fidelity of human microbiome-associated mice in observational studies and an interventional trial.}, journal = {mBio}, volume = {}, number = {}, pages = {e0190425}, doi = {10.1128/mbio.01904-25}, pmid = {40996271}, issn = {2150-7511}, abstract = {Composition and function of the gut microbiome are associated with diverse health conditions and treatment responses. Human microbiota-associated (HMA) mouse models are used to establish causal links for these associations but have important limitations. We assessed the fidelity of HMA mouse models in recapitulating ecological responses to a microbial consortium using stools collected from a human clinical trial. HMA mice were generated using different routes of consortium exposure, and their ecological features were compared to human donors by metagenomic sequencing. HMA mice resembled other mice more than their respective human donors in gut microbial composition and function, with taxa including Akkermansia muciniphila and Bacteroides spp. enriched in mouse recipients. A limited repertoire of microbes was able to engraft into HMA mice regardless of route of consortium exposure. In publicly available HMA mouse data sets from four distinct health conditions, we confirmed our observation that a taxonomically restricted set of microbes reproducibly engrafts in HMA mice and observed that stool microbiome composition of HMA mice was more like other mice than their human donor. Our data suggest that HMA mice are limited models for assessing the ecological impact of microbial consortia, with ecological effects in HMA mice being more strongly associated with host species than donor stool ecology or ecological responses to treatment in humans. Comparisons to published studies suggest this may be due to comparatively large host-species effects that overshadow ecological effects of treatments in humans that HMA models aim to recapitulate.IMPORTANCEHMA mice are models that better represent human gut ecology compared to conventional laboratory mice and are commonly used to test the effects of the gut microbiome on disease or treatment response. We evaluated the fidelity of using HMA mice as avatars of ecological response to a human microbial consortium, Microbial Ecosystem Therapeutic 4. Our results show that HMA mice in our cohort and across other published studies are more similar to each other than the human donors or inoculum they are derived from and harbor a taxonomically restricted gut microbiome. These findings highlight the limitations of HMA mice in evaluating the ecological effects of complex human microbiome-targeting interventions, such as microbial consortia.}, }
@article {pmid40996249, year = {2025}, author = {Luo, Y and Xu, X and Qiao, R and Zhao, R-P and Zhou, Z-W and Li, D-A and Wen, Y and Song, J-M and Chen, L-L}, title = {Comparative analysis of rhizosphere microbiomes of cultivated and wild rice under contrasting field water regimes.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0026325}, doi = {10.1128/spectrum.00263-25}, pmid = {40996249}, issn = {2165-0497}, abstract = {UNLABELLED: Asian cultivated rice (Oryza sativa L.) is domesticated from the common wild rice (Oryza rufipogon Griff.). However, the increasing water stress caused by climate change in recent years has become a major threat to rice growth and yield. To explore the adaptive changes of rhizosphere microbiomes in annual cultivated and perennial wild rice under different water limitation conditions, we conducted metagenomic sequencing analysis on rice rhizosphere soil samples from natural environments with varying water conditions. In particular, the genus Pseudomonas plays a dominant role in the rhizosphere microbiome of wild rice under non-irrigated condition. For archaea, we found that, compared to non-irrigated condition, submergence condition enriched methanogenic Methanosarcina. In comparison to cultivated rice, wild rice showed significant enrichment of Nitrosarchaeum, as ammonia-oxidizing archaea play a key role in the nitrogen cycle, whereas cultivated rice tends to enrich methanogenic archaea (Methanosarcina), which may increase methane emissions and have adverse environmental impacts. The rhizosphere metabolites of wild rice also enriched DL-Norleucine, L-Phenylalanine, and Palmitic acid, which may enhance root water absorption and provide essential nutrients to help rice resist water-limiting stress. In terms of rhizosphere microbiome function, asnB and nirK were particularly enriched in wild rice under non-irrigated condition, suggesting that wild rice may exhibit higher ecological adaptability to water stress by enhancing nitrogen assimilation and denitrification processes. Excavating these microbiome communities and functional changes in rice rhizospheres is crucial for optimizing water-limiting resistance, protecting the environment, and improving rice yield.<br><br>IMPORTANCE: This study highlights the differences in rhizosphere microbiomes and metabolites between wild and cultivated rice, providing new insights into how water limitation impacts their interaction with the rhizosphere microbiome. These findings are crucial for advancing rice cultivation under submergence and non-irrigated conditions, offering strategies to optimize farming practices, manage water scarcity, and reduce methane emissions. In contrast to cultivated rice, wild rice may regulate its rhizosphere microbial community to enhance resistance to water stress. This discovery offers valuable theoretical support for improving rice growth and adaptation across diverse ecological environments.}, }
@article {pmid40996044, year = {2025}, author = {Kwon, J and Correa, MA and Kong, Y and Pelletiers, W and Wade, M and Olson, D and Pettigrew, MM}, title = {Microbiome signatures of Clostridioides difficile toxin production and toxin gene presence: a shotgun metagenomic approach.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0043525}, doi = {10.1128/msphere.00435-25}, pmid = {40996044}, issn = {2379-5042}, abstract = {Clostridioides difficile is an opportunistic gastrointestinal pathogen capable of asymptomatic colonization and causes diseases ranging from diarrhea to pseudomembranous colitis. Accurate diagnosis of C. difficile infection (CDI) is challenging and critical for treatment and control. We hypothesized that gut microbiome profiles could help distinguish C. difficile colonized patients with diarrhea from those with true CDI. We analyzed 172 stool samples from individuals who tested glutamate dehydrogenase positive for C. difficile. Participants were categorized by toxin status (i.e., toxin positive or negative) and then further classified into three toxin groups based on the production of toxin, and if not produced, whether the C. difficile strain carried toxin-encoding genes. We examined associations between patient characteristics, prior antibiotics exposure, microbiome community structure and function, and toxin categories. Thirty-five percent of toxin-negative participants received antibiotics despite not meeting the criteria for true CDI. Enterococcus species were abundant in all groups. The relative abundance of E. faecalis was higher among individuals with prior antibiotics exposure. Alpha and beta diversity did not differ by toxin group. After controlling for prior antibiotics exposure and previous CDI episode, the abundance of Akkermansia muciniphila, Flavonifractor plautii, and Bifidobacterium adolescentis distinguished individuals with toxin-positive C. difficile. C. difficile abundance did not differentiate participants with true CDI from those who were colonized. We identified associations between the gut microbiome and C. difficile toxin gene presence and toxin production. These results highlight the potential for microbiome-informed diagnostics to improve CDI accuracy and guide treatment decisions.IMPORTANCEClostridioides difficile colonizes humans and causes diarrhea in community and hospital settings. C. difficile infection (CDI) is a toxin-mediated disease, and its diagnosis is challenging. The goal of this study was to determine whether differences in the gut microbiome could help distinguish between colonized individuals and those with CDI. We examined stool samples and data from 172 individuals categorized into three groups based on the detection of toxin and, if not detected, whether toxin-encoding genes were present in the C. difficile strain. We identified bacteria, such as Enterococcus faecalis, that were more abundant in people who had used antibiotics. While the diversity of the gut microbiome did not differ by toxin group, specific gut bacteria, antibiotic resistance genes, and metabolic pathways were associated with toxin group. Our findings suggest that considering the full gut microbiome and factors like past antibiotic use could help improve the diagnosis and treatment of CDI.}, }
@article {pmid40995781, year = {2025}, author = {Hensen, T and Thiele, I}, title = {Metabolic modeling links gut microbiota to metabolic markers of Parkinson's disease.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2554195}, doi = {10.1080/19490976.2025.2554195}, pmid = {40995781}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Parkinson Disease/microbiology/metabolism/blood ; Male ; Female ; Biomarkers/blood/metabolism ; Middle Aged ; Aged ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Metagenomics ; Leucine/metabolism/blood ; }, abstract = {Human gut microbiota have been implicated in metabolic disruptions in Parkinson's disease (PD). However, the underlying mechanisms linking gut microbiota to these disease-related metabolic changes remain largely unknown. In this study, we applied constraint-based metabolic modeling to identify potential causal links between compositional shifts in gut microbiota in PD and metabolic blood markers of PD. We personalized in silico whole-body metabolic models with gut metagenomics of 435 PD patients and 219 healthy controls and profiled in silico gut microbiome influences on 116 blood metabolites with replicated associations with PD diagnosis. Our analysis identified a reduced capacity of the PD host-microbiome co-metabolism to produce L-leucine and leucylleucine in blood. These metabolic predictions were traced back to lower L-leucine production of Roseburia intestinalis and higher L-leucine consumption by Methanobrevibacter smithii in PD microbiomes. We further predicted reduced host-microbiome production capacities of butyrate, myristic acid, and pantothenate in the blood of PD patients and linked these associations to reduced relative abundances of Faecalibacterium prausnitzii. Finally, lower nicotinic acid production capacities were predicted in PD patients, which were associated with increased relative abundances and increased nicotinic acid consumption of Ruthenibacterium lactatiformans in PD. In conclusion, we predicted that the gut microbiome can drive altered blood levels of six metabolites in PD and identified candidate microbial species that may influence these metabolic alterations. These findings may facilitate the development of novel therapies targeting the gut-brain axis in PD.}, }
@article {pmid40995566, year = {2025}, author = {Seidel, J and Kaipf, C and Straub, D and Nahnsen, S}, title = {nf-core/detaxizer: a benchmarking study for decontamination from human sequences.}, journal = {NAR genomics and bioinformatics}, volume = {7}, number = {3}, pages = {lqaf125}, pmid = {40995566}, issn = {2631-9268}, mesh = {Humans ; Benchmarking ; *Software ; *Metagenomics/methods ; *Decontamination/methods ; }, abstract = {Privacy is paramount in health data, particularly in human genetics, where information extends beyond individuals to their relatives. Metagenomic datasets contain substantial human genetic material, necessitating careful handling to mitigate data leakage risks when sharing or publishing. The same applies to genetic datasets from the environment or datasets from contaminated laboratory samples, although to a lesser extent. Completely removing human sequence data while retaining unbiased nonhuman reads is not achievable currently, but several tools exist. To address these topics, we developed nf-core/detaxizer, a nextflow-based pipeline that employs Kraken2 and bbmap/bbduk for taxonomic classification, identifying and optionally filtering Homo sapiens reads. Due to its generalized design, other taxa can also be classified and filtered. We benchmark its filtering efficacy for human reads against Hostile and CLEAN, demonstrating its utility for secure data preprocessing. The comparison showed that the choice of tool and database can result in differences of up to an order of magnitude in both the amount of human data not removed and the amount of microbial data mistakenly removed. As part of the nf-core initiative, nf-core/detaxizer adheres to best practices, leveraging containerized dependencies for streamlined installation. The source code is openly available under the MIT license: https://github.com/nf-core/detaxizer.}, }
@article {pmid40995227, year = {2025}, author = {Lee, SH and Kim, EB and Park, SC and Nam, SJ and Cho, H and Jeon, HJ and Lee, SP}, title = {Evaluation of the gastric microbiota based on body mass index using 16S rRNA gene sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1651316}, pmid = {40995227}, issn = {2235-2988}, mesh = {Humans ; *RNA, Ribosomal, 16S/genetics ; *Body Mass Index ; Female ; Male ; Middle Aged ; Obesity/microbiology ; *Gastrointestinal Microbiome/genetics ; Adult ; DNA, Bacterial/genetics/chemistry ; Sequence Analysis, DNA ; DNA, Ribosomal/chemistry/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; *Stomach/microbiology ; Overweight/microbiology ; Metagenomics ; Phylogeny ; }, abstract = {INTRODUCTION: Obesity is a multifactorial condition influenced by various factors, including the gut microbiota. However, the relationship between the gastric microbiota and obesity remains poorly understood. This study aimed to investigate the composition of gastric microbiota, excluding Helicobacter pylori, in relation to body mass index (BMI) and metabolic indicators.<br><br>METHODS: Thirty participants undergoing health checkups were classified into three groups-normal weight (BMI 18.5-22.9), overweight (BMI 23.0-24.9), and obese (BMI &#x2265;25.0)-with ten individuals per group. Those with H. pylori infection, atrophic gastritis, or intestinal metaplasia were excluded. Gastric microbiota from four antral biopsies per subject were analyzed using 16S rRNA sequencing and functional profiling by metagenomic prediction.<br><br>RESULTS AND DISCUSSION: Alpha diversity (Gini-Simpson index) was significantly lower in the combined overweight/obese group than that in the normal group (P=0.049). Beta diversity analysis revealed clear group separation (Bray-Curtis, P=0.005; unweighted UniFrac, P=0.004). Significant species differences between the groups were observed; specifically, the abundances of Muribaculum gordoncarteri, Turicibacter bilis, and Duncaniella dubosii, were significantly reduced in the overweight/obese group. Functional predictions showed differential enrichment of pathways related to fatty acid, amino acid, vitamin, and carbohydrate metabolism across BMI categories. These findings suggest that alterations in the gastric microbiota may be linked to obesity and metabolic dysregulation.}, }
@article {pmid40995224, year = {2025}, author = {Duan, Y and Li, Q and Fei, H and Song, J and Xu, C}, title = {The diagnostic value of RNA-mNGS and DNA-mNGS in differentiating bacterial infection from colonization in the lower respiratory tract.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1639148}, pmid = {40995224}, issn = {2235-2988}, mesh = {Humans ; Male ; Female ; Middle Aged ; *High-Throughput Nucleotide Sequencing/methods ; *Respiratory Tract Infections/diagnosis/microbiology ; DNA, Bacterial/genetics ; Aged ; *Bacteria/genetics/classification/isolation &amp; purification ; *Bacterial Infections/diagnosis/microbiology ; ROC Curve ; *Metagenomics/methods ; Adult ; Diagnosis, Differential ; RNA, Bacterial/genetics ; Sensitivity and Specificity ; Acinetobacter baumannii/genetics/isolation &amp; purification ; Aged, 80 and over ; }, abstract = {BACKGROUND: Metagenomic next-generation sequencing(mNGS) has been widely used in the pathogenetic diagnosis of lower respiratory tract infections. However, the interpretation of pathogens detected by mNGS remains inconclusive.<br><br>OBJECTIVE: Our study aimed to compare the differential diagnostic value of sequencing reads and the relative abundance of bacteria detected by RNA-mNGS versus DNA-mNGS in distinguishing between bacterial infection and colonization in the lower respiratory tract.<br><br>METHODS: The hospitalized patients with suspected lower respiratory tract infections who had completed RNA-mNGS and DNA-mNGS testing at our hospital from June 2021 to December 2023 were reviewed and divided into two groups: the infected group and the colonized group, based on their final diagnoses. The Mann-Whitney U test was used to analyze differences in the number of bacterial sequencing reads and relative abundance between the two groups; the predictive capability of bacterial sequencing reads and relative abundance for identifying bacterial infections was evaluated using receiver operating characteristic (ROC) curves.<br><br>RESULTS: A total of 69 eligible patients were enrolled, with 85 detections of the four target bacterial species (Pseudomonas aeruginosa, Acinetobacter baumannii, Klebsiella pneumoniae, and Corynebacterium striatum) identified: 46 in infected patients and 39 in colonized patients. The number of sequencing reads and relative abundance of bacterial RNA and DNA in the pathogenic bacteria were significantly higher than those in the non-pathogenic bacteria (all P-values <0.01). ROC curves were used to evaluate the performance of the sequencing reads and relative abundance of bacterial species in predicting the responsible pathogens. The AUC value for RNA relative abundance was the highest at 0.991 (95% CI: 0.977-1.000, P < 0.001), with a cutoff value of 26.28%, a sensitivity of 0.957, and a specificity of 0.974. In the DNA-mNGS results, the AUC value for the ratio of the sequencing reads between the first and the second ranked bacterial sequences in predicting bacterial infection was [0.835 (95% CI: 0.742-0.928), P < 0.001], and the AUC value for the ratio of relative abundance in predicting bacterial infection was [0.839 (95% CI: 0.749-0.929), P < 0.001)], both having a cutoff value of 47.26, a sensitivity of 0.644 and a specificity of 0.929.<br><br>CONCLUSIONS: Bacterial relative abundance and sequencing reads can serve as indicators to distinguish between infection and colonization, and the relative abundance based on RNA-mNGS exhibits the best differential diagnostic performance; when DNA-mNGS results stand alone, the relative abundance of the detected bacteria and the ratio of relative abundance between the first-ranked and the second-ranked detected bacteria can be utilized for a comprehensive assessment of infection versus colonization.}, }
@article {pmid40994895, year = {2025}, author = {Rathinavelu, S and Beck, K and Wälchli, DL and Bürgmann, H}, title = {Optimization and validation of a consolidated Set of TaqMan qPCR assays for the surveillance of clinically relevant antibiotic resistance genes in environmental matrices.}, journal = {MethodsX}, volume = {15}, number = {}, pages = {103600}, pmid = {40994895}, issn = {2215-0161}, abstract = {The continued rise of antibiotic resistance and adoption of the One Health approach necessitates reliable methods for detection and quantification of antibiotic resistance genes (ARGs) in complex environmental matrices. Here we present a consolidated set of TaqMan quantitative PCR assays for quantification of clinically relevant and emerging ARGs in complex environmental matrices.•We systematically designed five new primer sets, six TaqMan probes and verified and adapted four previously published relevant primer/probe sets from literature and evaluated their specificity in silico against current database.•For external quantification, two sets of gBlock standard libraries were designed. We experimentally validated the specificity, sensitivity, and efficiency of the assays with positive strain control DNA, negative strain control DNA, general no target controls, extraction blank controls, negative controls, and environmental test samples (i.e., metagenomic DNA from complex environmental matrices) to comprehensively assess each assays' performance.•Optimization included iterative testing of both primer and probe concentration, annealing temperature, and annealing time. Results demonstrated robust and reliable detection and quantification of ARGs in clinical isolates and wastewater effluents with high sensitivity, specificity, and efficiency.This makes the assays suitable for surveillance in wastewater or various environmental matrices, in support of efforts to mitigate dissemination of antibiotic resistance.}, }
@article {pmid40993967, year = {2025}, author = {Bibbò, S and Ahlström, G and Pes, GM and Graham, DY and Engstrand, L and Merola, E and Dore, MP}, title = {Resilience of the Gut Microbiome to Short Proton Pump Inhibitor Therapy With or Without High-Dosage L. reuteri in H. pylori-Infected Adults.}, journal = {Helicobacter}, volume = {30}, number = {5}, pages = {e70064}, doi = {10.1111/hel.70064}, pmid = {40993967}, issn = {1523-5378}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Limosilactobacillus reuteri/physiology/growth &amp; development ; *Helicobacter Infections/drug therapy/microbiology ; *Proton Pump Inhibitors/therapeutic use/administration &amp; dosage ; Female ; Male ; Middle Aged ; Double-Blind Method ; Adult ; Pantoprazole/therapeutic use ; *Probiotics/administration &amp; dosage ; Helicobacter pylori/drug effects ; Feces/microbiology ; Aged ; }, abstract = {BACKGROUND: Helicobacter pylori eradication therapy typically consists of a combination of antibiotics and an antisecretory drug. Probiotics may be added to reduce side effects and possibly improve outcomes.<br><br>MATERIALS AND METHODS: We conducted a double-blind, randomized trial of pantoprazole plus either Lactobacillus reuteri (Gastrus) (high dose) or a matching placebo to assess the impact on the gut microbiota of H. pylori-positive adults. Fecal samples were collected at baseline and after one and 2&#x2009;months for shotgun metagenomic sequencing.<br><br>RESULTS: A total of 26 patients were recruited and completed therapy. L. reuteri was only detected in the group that received supplemental L. reuteri and only at the 1-month post-treatment interval. L. reuteri failed to colonize for long-term&#xa0;the gut, and challenge with L. reuteri failed to alter alpha-diversity (Shannon index) or beta-diversity (community ordination) metrics at any time point. Machine learning (PLS-DA) analysis identified the presence of L. reuteri as the most distinguishing feature at 1 month. No other taxa showed a significant difference between groups.<br><br>CONCLUSION: Short-term administration of pantoprazole and L. reuteri had no lasting effects on gut microbial composition. While L. reuteri transiently bloomed during supplementation, the overall gut microbiota showed resilience, returning to baseline shortly after therapy.<br><br>TRIAL REGISTRATION: Identifier: NCT03404440.}, }
@article {pmid40993650, year = {2025}, author = {Li, C and Wang, H and Liu, S and Shen, X and Jiang, X and Liu, F and Zhang, B}, title = {Successful treatment of HIV-related progressive multifocal leukoencephalopathy and immunological reconstitution inflammatory syndrome with intravenous human immunoglobulin: a case report.}, journal = {AIDS research and therapy}, volume = {22}, number = {1}, pages = {89}, pmid = {40993650}, issn = {1742-6405}, support = {No. [2024]FY006//Key Laboratory of Infectious Diseases and Liver Diseases (University-Level Key Laboratory)/ ; No. [2024]FY006//Key Laboratory of Infectious Diseases and Liver Diseases (University-Level Key Laboratory)/ ; No. [2024]FY006//Key Laboratory of Infectious Diseases and Liver Diseases (University-Level Key Laboratory)/ ; No. [2024]FY006//Key Laboratory of Infectious Diseases and Liver Diseases (University-Level Key Laboratory)/ ; No. [2024]FY006//Key Laboratory of Infectious Diseases and Liver Diseases (University-Level Key Laboratory)/ ; No. [2024]FY006//Key Laboratory of Infectious Diseases and Liver Diseases (University-Level Key Laboratory)/ ; No. [2024]FY006//Key Laboratory of Infectious Diseases and Liver Diseases (University-Level Key Laboratory)/ ; Qian Cai She [2022] No. 162//2023 Major Infectious Disease Prevention and Control - HIV/AIDS Comprehensive Prevention and Treatment Project/ ; Qian Cai She [2022] No. 162//2023 Major Infectious Disease Prevention and Control - HIV/AIDS Comprehensive Prevention and Treatment Project/ ; Qian Cai She [2022] No. 162//2023 Major Infectious Disease Prevention and Control - HIV/AIDS Comprehensive Prevention and Treatment Project/ ; Qian Cai She [2022] No. 162//2023 Major Infectious Disease Prevention and Control - HIV/AIDS Comprehensive Prevention and Treatment Project/ ; Qian Cai She [2022] No. 162//2023 Major Infectious Disease Prevention and Control - HIV/AIDS Comprehensive Prevention and Treatment Project/ ; Qian Cai She [2022] No. 162//2023 Major Infectious Disease Prevention and Control - HIV/AIDS Comprehensive Prevention and Treatment Project/ ; Qian Cai She [2022] No. 162//2023 Major Infectious Disease Prevention and Control - HIV/AIDS Comprehensive Prevention and Treatment Project/ ; }, mesh = {Humans ; Male ; *Leukoencephalopathy, Progressive Multifocal/drug therapy/diagnostic imaging/virology ; Adult ; *Immune Reconstitution Inflammatory Syndrome/drug therapy ; *Immunoglobulins, Intravenous/therapeutic use/administration &amp; dosage ; *HIV Infections/complications/drug therapy ; JC Virus/genetics ; Treatment Outcome ; Magnetic Resonance Imaging ; Brain/diagnostic imaging ; }, abstract = {BACKGROUND: Progressive multifocal leukoencephalopathy-immune reconstitution inflammatory syndrome (PML-IRIS) is a high-mortality disease among patients with AIDS. It is caused by infection with the John Cunningham virus (JCV). Currently, there are no specific antiviral treatments targeting JCV. Thus, immune reconstitution remains the primary therapeutic approach.<br><br>CASE PRESENTATION: A 29-year-old male patient diagnosed with AIDS presented for medical evaluation after two months of antiretroviral therapy (ART), reporting symptoms of dizziness and headache. The detection of JC virus was confirmed in cerebrospinal fluid (CSF) through metagenomic next-generation sequencing (mNGS) analysis. Plain and enhanced cranial MRI scans revealed diffusely distributed nodular and patchy enhancement shadows within the brain parenchyma, consistent with a diagnosis of PML-IRIS. Given that glucocorticoids and PD-1 inhibitors may possess higher toxicity profiles and side effects compared to intravenous immunoglobulin (IVIG), which has been shown to restore immune function while causing fewer adverse reactions rapidly, a five-day regimen of intravenous IVIG infusion was administered in conjunction with continuous ART. Following this intervention, the patient showed significant clinical improvement, including reduced dizziness and headache, and improved neurological function.<br><br>CONCLUSIONS: The administration of IVIG alone may be considered an effective immunologic reconstitution strategy in treating early stages of PML-IRIS associated with AIDS, despite the complexity of the disease. This approach could be attributed to direct anti-JCV effects, neutralization of toxins, inhibition of inflammatory cytokine release, and its relatively tolerable safety profile. This case report aims to serve as a reference for clinical practitioners regarding the use of standalone IVIG therapy for HIV-related early PML-IRIS management; however, further investigation is warranted to determine its efficacy in cases where PML-IRIS has been detected at later stages.}, }
@article {pmid40674381, year = {2025}, author = {Miesbach, W and Boban, A and Chowdary, P and Coppens, M and Jimenez-Yuste, V and Klamroth, R and Mulders, G and Crato, M and Peyvandi, F}, title = {Qualification Criteria of Gene Therapy for Haemophilia-Opinion of the EAHAD Gene Therapy Working Group.}, journal = {Haemophilia : the official journal of the World Federation of Hemophilia}, volume = {31}, number = {5}, pages = {966-972}, pmid = {40674381}, issn = {1365-2516}, mesh = {Humans ; *Hemophilia A/therapy/genetics ; *Genetic Therapy/standards/methods ; Surveys and Questionnaires ; }, abstract = {BACKGROUND: Following the approval of the first gene therapies for haemophilia, it is essential to develop an optimal infrastructure for the administration of gene therapy. This can be ensured by identifying the criteria for the definition of treatment centres (hub centres) and follow-up centres (spoke centres), as well as establishing effective cooperation between them.<br><br>METHODS: The interdisciplinary members of the EAHAD Gene Therapy Working Group answered a survey to define requirements for centres participating in gene therapy care, addressing aspects such as product administration, coagulation parameter monitoring, and long-term safety surveillance.<br><br>RESULTS: The majority support the implementation of standardised protocols. Hub centres are expected to maintain high standards of quality and flexibility, possess pharmacist expertise, ensure regulatory compliance, and have experience in gene therapy Spoke centres should be certified haemophilia centres, access to hepatologists and providing 24-h support. Prior to gene therapy, spoke centres manage initial patient interactions, while hub centres handle complex care needs. Post-therapy, both centres can monitor factor levels and liver health. However, hub centres are responsible for managing immunosuppression and facilitating specialist consultations. Collaboration between both centres is crucial for data sharing and the assessment and resolution of adverse events, emphasising the importance of timely test results and regular liver imaging.<br><br>CONCLUSION: The survey results highlight essential criteria for the safe and effective delivery of gene therapy through a structured hub-and-spoke model. These include accreditation, clinical trial experience, access to specialized healthcare professionals, and the establishment of standard operating procedures for monitoring and managing adverse events.}, }
@article {pmid40993109, year = {2025}, author = {Zeng, Y and Zhong, X and Chai, L and Zhang, X and Lu, Z and Liu, G and Tu, T and Lu, L and Zhang, R and Yu, H and Zhang, S and Wang, S and Shen, C and Shi, J and Xu, Z}, title = {Prokaryotic evolution shapes specialized communities in long term engineered pit mud ecosystem.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {186}, pmid = {40993109}, issn = {2055-5008}, support = {32201993//National Natural Science Foundation of China/ ; 31901658//National Natural Science Foundation of China/ ; 2024T170375//China Postdoctoral Science Foundation/ ; }, mesh = {*Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Microbial Consortia ; Ecosystem ; *Microbiota ; *Archaea/classification/genetics/metabolism ; Metagenomics ; Fermentation ; Phylogeny ; }, abstract = {Elucidating the temporal dynamics of complex microbial consortia is crucial for engineering robust microbiome. We investigated prokaryotic evolution in pit mud, a centuries-old engineered environment used in Chinese liquor fermentation. Metagenomic analysis of 120 pit mud samples across different ages revealed a transition from generalist-dominated to specialist-enriched communities. This shift was characterized by decreased hydrolytic potential and increased organic acid metabolism, with key taxonomic changes including declines in Proteiniphilum and Petrimonas, and increases in Methanobacterium and Caproicibacter. The mature specialist community accelerates the short-chain organic acids turnover through syntrophic fatty acid oxidation, methanogenesis, and carbon chain elongation, maintaining ecosystem stability. While nutrient availability primarily shapes early stages community interactions, environmental stress becomes a dominant factor in mature systems. These insights into long-term prokaryotic adaptation provide a foundation for the rational design of resilient, functionally optimized microbial communities for biotechnological applications.}, }
@article {pmid40992856, year = {2025}, author = {Dolkar, P and Modeel, S and Siwach, S and Yadav, P and Chaurasia, M and Themchurin, L and Yadav, A and Atri, A and Kapoor, S and Negi, RK and Negi, T and Negi, RK}, title = {Metagenomic analysis of metal(loid)s resistance genes and its environmental applications.}, journal = {Advances in applied microbiology}, volume = {132}, number = {}, pages = {123-168}, doi = {10.1016/bs.aambs.2025.08.001}, pmid = {40992856}, issn = {0065-2164}, mesh = {*Metagenomics/methods ; *Metals, Heavy/metabolism/toxicity ; *Bacteria/genetics/drug effects/metabolism ; *Drug Resistance, Bacterial/genetics ; Biodegradation, Environmental ; *Environmental Pollutants/metabolism ; }, abstract = {Heavy metals are widely used to satiate the demands of growing industrialization and modern life. However, the presence of metal in large quantities in the ecosystem significantly impacts all life forms, particularly microorganisms. Many bacterial strains have developed metal resistance genes (MRG) to survive in extreme conditions through various mechanisms, such as active efflux, sequestration, permeability barriers, or co-resistance with antibiotic resistance genes. Metagenomic analysis is a powerful approach that enables the exploration of the functional repertoire and diversity of microorganisms, providing deeper insights into the mechanisms underlying the development of MRGs, and the active metabolites they produce to adapt to the polluted environments. With the advancement of these techniques, the knowledge can be further applied to environmental applications, such as bioremediation, biomonitoring, and synthetic biology. Bacteria with metal toxicity tolerance can be employed to enhance environmental sustainability and mitigate potential hazards.}, }
@article {pmid40992653, year = {2025}, author = {Sharma, SP and Kwon, GH and Song, SH and Park, JH and Kim, MJ and Eom, JA and Lee, KJ and Yoon, SJ and Park, H and Won, SM and Oh, KK and Ham, YL and Baik, GH and Kim, DJ and Suk, KT}, title = {Phocaeicola plebeius oral treatment improve fibrosis by reversing cirrhosis-related hepatic gene dysregulation.}, journal = {Life sciences}, volume = {}, number = {}, pages = {123979}, doi = {10.1016/j.lfs.2025.123979}, pmid = {40992653}, issn = {1879-0631}, abstract = {BACKGROUND: Bacteroides-centric gut dysbiosis reported to exacerbates liver cirrhosis via inflammation and fibrosis, therefore utilizing Bacteroides species as microbiome-based therapeutic logical to mitigate disease progression.<br><br>MATERIALS AND METHODS: Feces were collected from 52 Healthy and 144 Liver cirrhosis individuals for V3-V4 dependent 16rRNA-bsed comparative metagenomics analysis, followed a by microbiome depleted and non-depleted DDC mice model to explain the role of Bacteroidetes phylum classified microbial species P. plebeius in liver fibrosis pathophysiological pathways.<br><br>RESULTS: Bacteroides presented cirrhosis-dependent decrease in human and animal microbiome, and negatively correlated to key molecular pattern associated with cirrhosis. P. plebeius significantly reduced in abundance and identified as a microbial biomarker for cirrhosis (AUC&#x202f;=&#x202f;0.73) and treatment with P. plebeius significantly improved the levels of cirrhosis-related phenotypical and biochemical markers in the microbiome-depleted cirrhosis group. P. plebeius decrease the expression of S100a9, CCR1, ADAM8, TREM2, ITGAM, and MYO5A which are primarily responsible for inducing inflammation in liver cirrhosis. P. plebeius downregulated the fibrosis related genes expression including CD51, PLAT, ITGA3, CXCR4, and TGFBR1 and gene related to extracellular matrix formation including COL1A1, LTBP2, S100A6, and SMCO2. Additionally, P. plebeius treatment decreased the expression of hepatotoxicity-related genes including LPL, KRT18, ALDOA, and MCM10, and increased the expression of FABP1 and RDX. Additionally, P. plebeius normalized the expression of genes connected to two pathophysiological process including TIMP4, TGFB3, S100A8, PLSCR1, MMP8, CXCL4, and BMP.<br><br>CONCLUSIONS: Our study revealed P. plebeius as a multifaceted bio-therapeutic candidate that normalized dysregulated gene expression and reversed hepatic inflammation, fibrogenesis, and hepatotoxicity.}, }
@article {pmid40992306, year = {2025}, author = {Wang, J and Jin, T and Zhao, Y and Wang, L and Le, T}, title = {Effect of quorum quenching on toluene biodegradation in fungal-bacterial biotrickling filters: Insights from long-term performance and microbial mechanism.}, journal = {Journal of environmental management}, volume = {394}, number = {}, pages = {127408}, doi = {10.1016/j.jenvman.2025.127408}, pmid = {40992306}, issn = {1095-8630}, abstract = {The long-term efficiency of fungal-bacterial biotrickling filters (FB-BTFs) is frequently limited by biofilm clogging. Quorum quenching (QQ) bacteria, by interfering with quorum sensing, can attenuate excessive biofilm formation, thereby providing a viable solution to this challenge. This study operated two lab-scale FB-BTFs (FB-BTF1: control group; FB-BTF2: QQ bacteria Pseudomonas sp. WX14 addition) for 135 days to elucidate the effects of QQ on biofilm formation, pollutant removal, and microbial regulation. Compared with FB-BTF1, FB-BTF2 achieved 1.21 times higher removal efficiency and 1.32 times higher elimination capacity, while reducing pressure drop and biomass accumulation by 77.38 Pa/m and 217.14 mg/L, respectively. QQ bacteria suppressed extracellular polymeric substances secretion, lowering protein and polysaccharide content by 14.12 mg/L and 20.41 mg/L, which reduced biofilm hydrophobicity and adhesion. Meanwhile, the activities of toluene monooxygenase and catechol 2,3-dioxygenase were enhanced by 0.21 U/mL and 0.43 U/mL, accelerating aromatic ring cleavage. Microbial community analysis indicated an elevated abundance of QQ-related genera (e.g., Pseudomonas). Metagenomic sequencing further confirmed that QQ regulation occurred via downregulation of autoinducer-2 synthesis genes (e.g., luxS) and c-di-GMP synthesis genes (e.g., dge1, tpbB), accompanied by upregulation of c-di-GMP degradation genes (e.g., gmr, adrB). These results indicated that inoculating QQ bacteria effectively mitigate biofilm clogging and maintained high microbial activity, offering a viable strategy to ensure the long-term stability and efficiency of FB-BTFs for volatile organic compound removal.}, }
@article {pmid40992198, year = {2025}, author = {Ma, Y and Sun, S and Gu, X and Fan, Y and He, S}, title = {Mechanistic insights into microplastic-mediated shifts in nitrogen metabolism and sensory quality across emergent and submerged-plant wetlands: Evidence from metagenomics and physiological indicators.}, journal = {Journal of hazardous materials}, volume = {498}, number = {}, pages = {139937}, doi = {10.1016/j.jhazmat.2025.139937}, pmid = {40992198}, issn = {1873-3336}, abstract = {Polystyrene microplastics (PS-MPs), increasingly present in aquatic environments, pose potential threats to constructed wetlands (CWs) potentially altering both nitrogen removal and sensory water quality. This study investigated the response of PS-MPs on surface flow constructed wetlands (SFCWs) planted with emergent (Iris pseudacorus) and submerged (Vallisneria natans) macrophytes. The results showed that PS-MPs significantly reduced total nitrogen removal by 12.64 % in emergent macrophyte systems (EM-CW) compared to the control, mainly due to a 45.23 % decrease in NO3[-]-N removal. Conversely, submerged macrophyte systems (SM-CW) showed a 29.98 % increase in denitrification efficiency but experienced a 7.16 % reduction in NH4[+]-N removal compared to controls (SU-CW). Sensory indicators, including surface chroma and turbidity, increased by 18.88 % and 20.60 %, respectively, in SM-CW, while EM-CW maintained stable sensory indicators, suggesting different tolerance based on macrophyte life form. Metagenomic analysis revealed a 45.6-70.7 % decline in denitrification genes (e.g., norC, nosZ) in EM-CW, whereas the nitrification gene hao was suppressed by 79.8 % in SM-CW. These findings demonstrate that macrophytes life form governs the impacts of PS-MPs on nitrogen removal and sensory quality, highlighting a life-form-dependent tolerance mechanism. This study also emphasizes the need to consider types of macrophytes when designing CWs under PS-MPs stress.}, }
@article {pmid40992048, year = {2025}, author = {Liang, SM and Zhou, JQ and Xu, HT and Fang, SY and Zhang, Y and Zhang, ZZ and Jin, RC}, title = {Intermittent glycerol feeding shapes a glycogen-storing phenotype for enhanced nitrite accumulation via sequential denitrification.}, journal = {Water research}, volume = {288}, number = {Pt A}, pages = {124646}, doi = {10.1016/j.watres.2025.124646}, pmid = {40992048}, issn = {1879-2448}, abstract = {Achieving stable and efficient denitratation is a promising strategy to supply nitrite for mainstream anammox processes, yet the underlying microbial mechanisms remain poorly understood, especially with alternative carbon sources like glycerol. Here, we hypothesized that intermittent feeding regimes could drive higher nitrite accumulation by selecting for specific metabolic phenotypes. To test this, an intermittently-fed sequencing batch reactor (SBR) and a continuously-fed up-flow anaerobic sludge blanket (UASB) reactor were operated under identical carbon-restricted conditions (COD/NO3[-]-N = 3.5). The SBR achieved a significantly higher and stable nitrite accumulation efficiency (NiAE) of 43.0 ± 4.1 % compared to the UASB (18.9 ± 5.4 %). Genome-resolved metagenomics revealed that the SBR community was enriched in species with glycogen-storing potential, leading to a 45.8 % greater overall abundance of genes related to glycogen metabolism compared to the UASB. Phenotypic analyses confirmed that the SBR sludge contained significantly more intracellular glycogen and displayed a nitrate reductase (NAR) to nitrite reductase (NIR) activity ratio that was an order of magnitude higher than the UASB sludge. This kinetic imbalance underpinned a "sequential denitrification" phenotype, where nitrate was preferentially reduced to nitrite. Critically, the UASB-enriched community, when subjected to batch-fed conditions, also exhibited a high denitratation potential close to the SBR culture, demonstrating that this phenotype is a plastic trait regulated by the glycerol feeding strategy rather than a fixed attribute of the community structure. This study uncovers a fundamental mechanism where intermittent glycerol availability directs metabolic flux towards glycogen storage, which in turn regulates electron partitioning between NAR and NIR. This highlights a significant divergence between genotypic potential and realized phenotype, offering a new paradigm for controlling nitrogen transformation pathways in engineered ecosystems.}, }
@article {pmid40990924, year = {2025}, author = {Street, TL and Bejon, P and Leach, L and Oakley, S and Young, BC and Sanderson, ND}, title = {Nanopore adaptive sampling for bacterial identification from periprosthetic joint replacement tissue.}, journal = {Microbial genomics}, volume = {11}, number = {9}, pages = {}, doi = {10.1099/mgen.0.001507}, pmid = {40990924}, issn = {2057-5858}, mesh = {Humans ; *Prosthesis-Related Infections/microbiology/diagnosis ; *Nanopores ; *Bacteria/genetics/isolation &amp; purification/classification ; DNA, Bacterial/genetics ; *Metagenomics/methods ; *Joint Prosthesis/microbiology ; }, abstract = {Metagenomic approaches to the diagnosis of prosthetic joint infections promise more accurate and more rapid diagnosis. However, the high host DNA to bacterial DNA ratio is a challenge. Nanopore adaptive sampling (AS) can be used to preferentially sequence more of the infecting organism. Here, we evaluate AS using clinical samples from infected prosthetic joints to determine the absolute fold enrichment achieved. We found that AS achieved a range of 1.61- to 1.96-fold higher absolute fold enrichment for bacterial sequenced bases using AS over control pores. In this limited sample set, AS did not impact bacterial diagnosis overall but led to a modest increase in the bacterial sequence available without any obvious cost.}, }
@article {pmid40990897, year = {2025}, author = {Xu, T and Yuan, Q and Wang, J and Wu, Z and Chen, Z and Wang, Z and Sun, W and Zhang, M and Ji, N and Huang, M}, title = {Clinical characteristics and risk factors associated with severe community-acquired pneumonia infected by Chlamydia psittaci.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0047725}, doi = {10.1128/spectrum.00477-25}, pmid = {40990897}, issn = {2165-0497}, abstract = {UNLABELLED: The study aimed to describe the clinical features of psittacosis pneumonia and identify risk factors associated with severe psittacosis pneumonia. We retrospectively collected data from patients with psittacosis pneumonia, confirmed by metagenomic next-generation sequencing (mNGS) from January 2022 to June 2024 and analyzed differences between severe and non-severe groups. A total of 24 patients (eight severe/16 non-severe) were diagnosed with psittacosis, and 33.3% had severe psittacosis pneumonia. The levels of white blood cells (WBCs), neutrophils, neutrophil-to-lymphocyte ratio (NLR), hypersensitive C-reactive protein (hs-CRP), and procalcitonin (PCT) and the detection rate of fungi by mNGS were significantly higher in the severe group than in the non-severe group. The length of stay and omadacycline use were longer in patients of the severe group when compared to the non-severe group. Receiver operating characteristic (ROC) curves indicated that NLR had a better predictive value of severe conditions than PCT and hs-CRP. Patients with psittacosis pneumonia have a high rate of severe disease, and NLR may be a useful tool to promptly ascertain the severity of the disease and optimal therapies for better outcomes.<br><br>IMPORTANCE: This study explores the clinical features of psittacosis pneumonia and identifies key factors that may predict the severity of the disease. By analyzing data from 24 patients diagnosed using metagenomic next-generation sequencing (mNGS), the research uncovers important differences between severe and non-severe cases. The study finds that patients with severe psittacosis pneumonia have elevated levels of white blood cells (WBCs), neutrophils, neutrophil-to-lymphocyte ratio (NLR), C-reactive protein (hs-CRP), and procalcitonin (PCT), as well as a higher detection rate of fungi. Notably, the NLR emerges as a strong predictor of severe disease, suggesting its potential as an early diagnostic tool. These findings provide valuable insights that can help healthcare providers identify high-risk patients more quickly, allowing for timely interventions and improved management of the disease. Ultimately, this research could lead to better outcomes by guiding treatment decisions and enhancing our understanding of psittacosis pneumonia.}, }
@article {pmid40990729, year = {2025}, author = {López, N and Cuesta, G and Puerta-Alcalde, P}, title = {Viral meningoencephalitis: a focus on diagnostics.}, journal = {Current opinion in infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1097/QCO.0000000000001153}, pmid = {40990729}, issn = {1473-6527}, abstract = {PURPOSE OF REVIEW: This review provides an updated overview of diagnostic strategies for viral meningoencephalitis, with a focus on molecular techniques currently used in clinical practice and the emerging role of next-generation sequencing technologies.<br><br>RECENT FINDINGS: The clinical and laboratory presentation of viral meningoencephalitis is often nonspecific, making timely and accurate diagnosis challenging. While PCR and multiplex RT-PCR assays have become widely used, they have notable limitations, including reduced sensitivity in low-viral-load cases and the requirement for prior pathogen suspicion. Newer platforms like QIAstat-Dx allow interpretation through cycle threshold values, but false positives and false negatives remain concerns. mNGS offers a hypothesis-free approach with improved diagnostic yield - especially in immunocompromised hosts and atypical presentations - and has proven valuable for detecting rare, emerging, or unexpected pathogens. However, practical limitations such as cost, long turnaround times, and the need for expert interpretation currently restrict its routine use.<br><br>SUMMARY: The integration of mNGS into routine diagnostic workflows could significantly improve the diagnostic yield for viral meningoencephalitis, especially in cases with negative or inconclusive results from traditional methods. However, further studies are necessary to refine its clinical application, optimize cost-effectiveness, and establish guidelines for its use in the diagnostic management of meningoencephalitis.}, }
@article {pmid40990684, year = {2025}, author = {Schneggenburger, T and Zola, J}, title = {SKiM: Accurately Classifying Metagenomic ONT Reads in Limited Memory.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btaf537}, pmid = {40990684}, issn = {1367-4811}, abstract = {MOTIVATION: Oxford Nanopore Technologies' devices, such as MinION, permit affordable, real-time DNA sequencing, and come with targeted sequencing capabilities. Such capabilities create new challenges for metagenomic classifiers that must be computationally efficient yet robust enough to handle potentially erroneous DNA reads, while ideally inspecting only a few hundred bases of a read. Currently available DNA classifiers leave room for improvement with respect to classification accuracy, memory usage, and the ability to operate in targeted sequencing scenarios.<br><br>RESULTS: We present SKiM: Short K-mers in Metagenomics, a new lightweight metagenomic classifier designed for ONT reads. Compared to state-of-the-art classifiers, SKiM requires only a fraction of memory to run, and can classify DNA reads with higher accuracy after inspecting only their first few hundred bases. To achieve this, SKiM introduces new data compression techniques to maintain a reference database built from short k-mers, and treats classification as a statistical testing problem.<br><br>AVAILABILITY: SKiM source code, documentation, and test data are available from: https://gitlab.com/SCoRe-Group/skim.<br><br>CONTACT: tcschneg@buffalo.edu.}, }
@article {pmid40990531, year = {2025}, author = {Del Carratore, F and Breitling, R}, title = {Engineering microbiomes for natural product discovery and production.}, journal = {Natural product reports}, volume = {}, number = {}, pages = {}, doi = {10.1039/d5np00038f}, pmid = {40990531}, issn = {1460-4752}, abstract = {Covering: 2021 to 2025Microbial communities represent a vast and largely untapped source of natural products with potential applications in various fields, including medicine, agriculture, and the biomanufacturing industry. Secondary metabolites play a crucial role in mediating interspecies interactions within these communities, influencing their structure and function. Recent advances in microbial genetic engineering and multi-omics technologies have enabled the harnessing of these interactions for enhanced natural product discovery and production. These techniques, coupled with systems biology and mathematical modelling, allow for the rational design and manipulation of microbial consortia to elicit the expression of cryptic biosynthetic gene clusters and to optimize the production of desired compounds. Additionally, direct mining of microbiomes using metagenomics, metatranscriptomics, and metabolomics has revealed a wealth of novel biosynthetic gene clusters and secondary metabolites with potential therapeutic and industrial value. Despite the challenges associated with cultivating and characterizing diverse microbial species, ongoing advancements in computational tools and data analysis are rapidly expanding our ability to explore and exploit the seemingly inexhaustible reservoir of natural products hidden within microbial communities.}, }
@article {pmid40990483, year = {2025}, author = {Poretsky, RS and Gonzalez, DS and Horton, A and Schoeny, M and Lin, CY and Jarju, ML and Secreto, M and Chau, C and Gough, E and Newcomer, E and Chaudhary, A and Duffner, L and Undevia, N and Coulliette-Salmond, A and Lyons, AK and Whitehill, F and Hayden, MK and Green, SJ and Lin, MY}, title = {Establishing a Practical Approach to Sewer Monitoring for Antimicrobial Resistance Genes and Organisms at Healthcare Facilities.}, journal = {The Journal of infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/infdis/jiaf434}, pmid = {40990483}, issn = {1537-6613}, support = {200-2021-12772/CC/CDC HHS/United States ; Domain 1-A004//Safety and Healthcare Epidemiology Prevention Research Development/ ; }, abstract = {BACKGROUND: Surveillance of wastewater from healthcare facilities has the potential to identify the emergence of multidrug-resistance (MDR) genes of public health importance. Specifically, wastewater surveillance (WWS) can provide sentinel surveillance of novel MDR genes or organisms in healthcare facilities, helping to direct targeted prevention efforts and monitor longitudinal effects. Several knowledge gaps need to be addressed before WWS can be used routinely for MDR surveillance, including determining optimal approaches to sampling, processing, and testing wastewater.<br><br>METHODS: To this end, we evaluated multiple methods for wastewater collection (passive, composite, and grab), concentration (nanoparticles, filtration, and centrifugation), and PCR quantification (real-time quantitative PCR vs. digital PCR) for Candida auris and 5 carbapenemase genes (blaKPC, blaNDM, blaVIM, blaIMP, and blaOXA-48-like) twice weekly for 6&#x2005;months at a long-term acute care hospital in Chicago, IL. We also tested the effects of different transport and sample storage conditions on PCR quantification.<br><br>RESULTS: All genes were detected in facility wastewater, with blaKPC being the most consistently abundant. Experiments were done in triplicate with gene copy, variance, and number of detections between triplicates used to determine method efficacy. We found that passive samples processed immediately by centrifugation followed by bead-beating and dPCR provided the most reliable results for detecting MDR genes and C. auris. We also present the tradeoffs of different approaches and use culture and metagenomics to elucidate clinical relevance.<br><br>CONCLUSIONS: This study establishes a practical approach for WWS as a potential tool for public health monitoring of MDR burden in healthcare facilities.}, }
@article {pmid40990482, year = {2025}, author = {Wang, M and Song, W and Zhou, J and Ji, M and Ma, K and Li, Y and Tu, Q}, title = {Targeted assembly recovers high ammonia monooxygenase diversity in mudflat intertides.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0062025}, doi = {10.1128/msystems.00620-25}, pmid = {40990482}, issn = {2379-5077}, abstract = {Microbial communities in the Earth's biosphere mediate various biogeochemical cycling processes that are essential to maintain ecosystem multi-functioning and stability via the functional genes they carry. Although progress is being made, obtaining high-quality sequence data sets for microbial functional genes in complex environments remains challenging, both technically and in terms of computational resources required. In this study, using the amo gene family encoding ammonia monooxygenase as an example, we aimed to recover important microbial functional genes from shotgun metagenomes via targeted assembly. Comparing to conventional assembly approaches such as single-sample and multi-sample assembly, targeted assembly recovered much higher amo gene diversity while requiring substantially less computational resource and shorter running time. In addition, amo genes recovered by targeted assembly were found with fewer chimeras. Meanwhile, more amo operons were recovered. Not only were the commonly known amoABC subunits observed, but also the less commonly found subunits, like amoX and amoE. Notably, the archaeal amoA subunits recovered by targeted assembly represented the most "super-clades" for ammonia monooxygenase, including NT-α, NT-γ, NP-γ, NP-ζ, and NP-η, demonstrating the advantage of targeted assembly over conventional approaches. Comparable spatial patterns, such as taxa-area and distance-decay relationships, were also observed for the recovered amo assemblages. This study demonstrated an efficient route to recover microbial functional genes from shotgun metagenomes with minimal computational resource and running time.IMPORTANCEMicrobial communities play critical roles in the Earth's biosphere by mediating various biogeochemical cycles of essential elements and maintaining ecosystem stability and multi-functioning through the functional genes they carry. However, recovering the key functional genes from such complex communities remains challenging. Both advantages and limitations exist for different technologies. In this study, using the amo gene family as an example, we show that targeted assembly enables accurate and rapid recovery of high-quality amo sequences from shotgun metagenomes, consuming minimal computational resources and running time. Compared to conventional full-assembly approaches, the amo sequences recovered by targeted assembly are found with more operons, higher (phylo)genetic diversity, and fewer chimeras. This study provides an efficient alternative route for recovering microbial functional genes, particularly when computational resources are limited.}, }
@article {pmid40990171, year = {2025}, author = {Sehgal, N and Pajuelo, MJ and Gilman, RH and Pickering, AJ and Earl, AM and Worby, CJ and Nadimpalli, ML}, title = {Effects of commonly used antibiotics on children's developing gut microbiomes and resistomes in peri-urban Lima, Peru.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {}, number = {}, pages = {}, doi = {10.1093/jac/dkaf358}, pmid = {40990171}, issn = {1460-2091}, support = {R01AI108695-01A/GF/NIH HHS/United States ; KL2TR002545/GF/NIH HHS/United States ; U19AI110818/GF/NIH HHS/United States ; 5T32ES012870/GF/NIH HHS/United States ; //Emory University/ ; //MP3 Initiative/ ; }, abstract = {BACKGROUND: The effects of antibiotic use on children's gut microbiomes and resistomes are not well characterized in middle-income countries, where antibiotic consumption is exceptionally common.<br><br>OBJECTIVES: We characterized the effects of antibiotics commonly used by Peruvian children (i.e. amoxicillin, azithromycin, cefalexin, trimethoprim/sulfamethoxazole) on the &#x3b1;-diversity, &#x3b2;-diversity and abundance of gut genera and antibiotic resistance genes (ARGs) from 3 to 16&#x2005;months.<br><br>METHODS: This study included 54 children from a prospective cohort of enteric infections in peri-urban Lima, 2016-19. Stools collected at 3, 6, 7, 9, 12 and 16&#x2005;months underwent DNA extraction and short-read metagenomic sequencing. We profiled the taxonomy of stool metagenomes and assessed ARG abundance by aligning reads to the ResFinder database. We used daily surveillance data (40&#x200a;662 observations) to tabulate the number of antibiotic courses consumed in the 30&#x2005;days prior to stool sampling. Using linear mixed models, we examined associations of recent antibiotic use with richness, diversity and abundance of gut genera and ARGs over time.<br><br>RESULTS: Each additional recent antibiotic course decreased Bifidobacterium and Dialister abundance and increased Veillonella abundance, although gut richness and diversity were not affected. Recent use of amoxicillin, azithromycin, cefalexin or trimethoprim/sulfamethoxazole, specifically, did not impact gut microbiome measures. Amoxicillin, azithromycin and trimethoprim/sulfamethoxazole significantly enriched multiple ARGs and amoxicillin use significantly increased total ARGs.<br><br>CONCLUSIONS: Common antibiotics like amoxicillin and azithromycin appear to be key drivers of the paediatric gut resistome. Resistome perturbations appeared to be stronger, or persist for longer, than gut microbiome effects in this middle-income country setting.}, }
@article {pmid40989951, year = {2025}, author = {Li, X and Yang, X and Liu, S and Liang, X and Chen, H and Liu, D}, title = {Yeast culture improves growth, antioxidant status, immunity, and gut microbiota homeostasis in preweaning Holstein calves.}, journal = {Frontiers in veterinary science}, volume = {12}, number = {}, pages = {1670912}, pmid = {40989951}, issn = {2297-1769}, abstract = {INTRODUCTION: Calves in the lactation period exhibit limited disease resistance and stress tolerance, making them particularly vulnerable to health challenges such as diarrhoea. Yeast culture (YC) supplementation has emerged as a promising strategy to enhance health and growth in young ruminants. This study aimed to investigate the effects of YC supplementation on growth performance, antioxidant capacity, immune function, and intestinal microbiota composition in lactating Holstein calves.<br><br>METHODS: A total of 40 lactating Holstein calves were randomly assigned to either a control group or a YC-supplemented group, with the feeding trial lasting 60 days. Growth performance parameters were recorded, serum antioxidant and immune markers were evaluated, and gut microbial diversity and composition were analysed using metagenomic sequencing. Furthermore, correlations between microbial taxa and serum markers were assessed.<br><br>RESULTS: The results showed that YC supplementation significantly increased average daily gain (ADG) and feed intake, and reduced the incidence of diarrhoea (p < 0.05). Serum levels of total antioxidant capacity (T-AOC), total superoxide dismutase (T-SOD), and glutathione peroxidase (GSH-Px) were significantly elevated, while malondialdehyde (MDA) content was significantly decreased (p < 0.05), indicating improved antioxidant status. Immunoglobulin and cytokine levels were also significantly higher in the YC group (p < 0.05). Metagenomic analysis revealed a significant increase in the Chao index and a trend toward higher Shannon diversity in the YC group. YC supplementation notably increased the relative abundance of beneficial bacteria such as Phocaeicola plebeius, Ruminococcus sp., Segatella copri, and Candidatus Scatovivens faecipullorum, while reducing potentially pathogenic bacteria like Candidatus Cryptobacteroides sp. and Dorea sp. Correlation analysis showed that T-AOC was positively associated with P. plebeius and S. copri, while MDA was positively correlated with Candidatus Cryptobacteroides sp. and negatively correlated with Ruminococcus sp. and other beneficial taxa. Similarly, several immune markers exhibited positive correlations with beneficial bacteria and negative correlations with harmful bacteria. Functional pathway analysis suggests that YC may enhance immune responses and antioxidant capacity through activation of the T cell receptor and B cell receptor signalling pathways.<br><br>DISCUSSION: In conclusion, YC supplementation improved growth performance, enhanced antioxidant and immune functions, and favourably modulated gut microbiota in lactating Holstein calves. These changes collectively contributed to reduced diarrhoea incidence and improved overall health, highlighting yeast culture as a valuable nutritional strategy for calf health management.}, }
@article {pmid40989903, year = {2025}, author = {Malygina, EV and Potapova, NA and Imidoeva, NA and Vavilina, TN and Belyshenko, AY and Morgunova, MM and Dmitrieva, ME and Shelkovnikova, VN and Vlasova, AA and Lipatova, OE and Zhilenkov, VM and Batalova, AA and Stoyanova, EE and Axenov-Gribanov, DV}, title = {Microbial communities inhabiting the surface and gleba of white (Tuber magnatum) and black (Tuber macrosporum) truffles from Russia.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e20037}, pmid = {40989903}, issn = {2167-8359}, mesh = {Russia ; *Microbiota ; *Ascomycota/genetics/classification/isolation &amp; purification ; Symbiosis ; Soil Microbiology ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Phylogeny ; Mycorrhizae/genetics ; }, abstract = {The complex symbiotic relationships between truffles and their microbiota, coupled with their obligate mycorrhizal lifestyle, present significant challenges for obtaining axenic mycelium and achieving controlled cultivation. This study aimed to characterize the microbial communities within the surface and gleba of truffle ascomata using 16S and 18S rRNA gene sequencing and identify the taxonomic composition and ecological roles of these microbiota. Specimens of Tuber magnatum (white truffle) and Tuber macrosporum (smooth black truffle) were collected, with T. magnatum representing the first documented discovery of this species in Russia. Metabarcoding profiling identified both species-specific and shared microbial taxa, with the yeast-like fungus Geotrichum spp. emerging as a core symbiont in both truffle species. Its consistent detection in surface and gleba tissues suggests a critical role in mycorrhizal establishment and spore dispersal, potentially mediated by sulfur volatiles that attract mycophagous fauna. In T. magnatum, the bacterial community was dominated by Proteobacteria, particularly Alphaproteobacteria and Gammaproteobacteria, with the nitrogen-fixing genus Bradyrhizobium being especially abundant. The truffle microbiota predominantly comprised soil-derived microorganisms (e.g., nitrogen-fixing Rhizobiaceae spp., phenol-degrading Mycoplana spp.) and plant-associated symbionts (e.g., ectomycorrhizal Sebacina spp.), implicating these communities in nutrient cycling, xenobiotic degradation, and host plant interactions. By elucidating the taxonomic and functional profiles of truffle-associated microbiota, this study provides foundational insights into their ecological contributions. Chemical differences align with tissue-specific microbial communities, suggesting microenvironmental specialization in bioactive compound synthesis. These findings advance efforts to replicate critical symbiotic interactions in vitro, a prerequisite for developing sustainable cultivation protocols for T. magnatum and T. macrosporum under controlled conditions.}, }
@article {pmid40989756, year = {2025}, author = {Teng, P and Peng, J and Zhang, X and Wang, Y and Jiang, C and Wang, S and Wang, M and Han, X and Liu, X}, title = {Severe Community-Acquired Pneumonia with Disseminated Infection Caused by Highly Virulent Pseudomonas aeruginosa: Successful Treatment of a Case.}, journal = {Journal of inflammation research}, volume = {18}, number = {}, pages = {12817-12824}, pmid = {40989756}, issn = {1178-7031}, abstract = {PURPOSE: Pseudomonas aeruginosa (P. aeruginosa) is a Gram-negative pathogen with strong colonization ability and multidrug resistance. Disseminated infection complicated by secondary organizing pneumonia is extremely uncommon.<br><br>PATIENTS AND METHODS: We describe a rare case of severe community-acquired pneumonia due to highly virulent P. aeruginosa, complicated by endophthalmitis, ecthyma gangrenosum, and secondary organizing pneumonia. Clinical features, microbiological results, histopathology, and treatment were analyzed.<br><br>RESULTS: A 61-year-old woman developed a disseminated infection caused by highly virulent P. aeruginosa, presenting with persistent high fever, impaired consciousness, ocular involvement, mucocutaneous erosions, and widespread erythematous papules. The diagnosis was confirmed by consistent isolation of P. aeruginosa from sputum, blood, and ocular pus, and detection in bronchoalveolar lavage fluid by metagenomic sequencing. Whole-genome sequencing of the ocular isolate identified multiple virulence factors, including Type III secretion system effectors ExoS, ExoT, and ExoY, reflecting the pathogen's capacity for systemic dissemination. Lung biopsy revealed extensive necrosis with fibrinoid exudation and granulation tissue, consistent with secondary organizing pneumonia. The patient received combined antimicrobial and anti-inflammatory therapy targeting both the disseminated infection and the organizing pneumonia, resulting in rapid defervescence, restoration of consciousness and oral intake, and clinical improvement. She was subsequently discharged in stable condition.<br><br>CONCLUSION: This case highlights the disseminated potential of highly virulent P. aeruginosa and underscores the need for vigilance regarding secondary organizing pneumonia in such infections. Timely recognition, together with a treatment strategy combining appropriate antimicrobial and anti-inflammatory therapy, is crucial to improving patient outcomes.}, }
@article {pmid40989626, year = {2025}, author = {Herlina, N and Safika,  and Handharyani, E and Setiyono, A}, title = {Pathogen-driven pregnancy loss in dairy cattle: An overview of diagnostic advances and innovations.}, journal = {Open veterinary journal}, volume = {15}, number = {6}, pages = {2286-2297}, pmid = {40989626}, issn = {2218-6050}, mesh = {Animals ; Cattle ; Female ; Pregnancy ; *Abortion, Veterinary/microbiology/diagnosis/parasitology/virology ; *Cattle Diseases/diagnosis/microbiology/parasitology/virology ; Dairying ; Enzyme-Linked Immunosorbent Assay/veterinary ; Polymerase Chain Reaction/veterinary ; }, abstract = {Pregnancy failure or abortion in dairy cattle is a major reproductive concern that affects animal welfare and the dairy industry's economic stability. Pathogens are a key factor contributing to this issue. Accurate diagnosis is essential for effective management and preventive measures. This review discusses various pathogens responsible for abortion in dairy cattle, including bacteria, viruses, and protozoa. Conventional diagnostic methods, which are important, may not always comprehensively detect all pathogens involved in abortion. This study focuses on current advances in diagnostic technology, particularly molecular approaches such as polymerase chain reaction and enzyme-linked immunosorbent assays, as well as the promise of metagenomic techniques for increased accuracy. By integrating recent research findings, this review emphasizes the significance of these advancements in enhancing disease management, prevention measures, and overall herd health.}, }
@article {pmid40989193, year = {2025}, author = {Jonas, LC and Schmitz-Esser, S and Youngs, CR}, title = {Analysis of the sheep (Ovis aries) vaginal microbiota preceding spontaneous abortion: a pilot study.}, journal = {Access microbiology}, volume = {7}, number = {7}, pages = {}, pmid = {40989193}, issn = {2516-8290}, abstract = {Little is known regarding the vaginal microbiota of sheep that undergo spontaneous abortions. The aim of this pilot study was to characterize, using 16S rRNA gene sequencing and shotgun metagenomics, the vaginal microbiota throughout the gestation of two ewes (Ewe1 and Ewe2) that spontaneously aborted. To achieve this, weekly vaginal swabs were collected from the ewes prior to breeding until pregnancy testing; thereafter, biweekly swabs were collected until the spontaneous abortion occurred. Based on the 16S rRNA sequencing data, Ewe1's vaginal microbiota, overall, contained high abundances of Histophilus (12.9% relative abundance), Staphylococcus (10.8% relative abundance) and Unclassified Pasteurellaceae (8.7% relative abundance). Most notable was the high abundance of Campylobacter following the abortion in Ewe1's vaginal microbiota. Ewe2's vaginal microbiota was characterized by high abundances of Pasteurella (41.7% relative abundance) throughout gestation. Shotgun metagenomic sequencing produced two high-quality metagenome-assembled genomes (MAGs), identified as Campylobacter jejuni and Histophilus somni. The C. jejuni MAG had 99.95% average nucleotide identity to the most abundant sheep abortive C. jejuni clone in the USA. The H. somni MAG was most similar to a pathogenic H. somni strain and contained genes that contribute to serum resistance and sialic acid utilization. The results presented here demonstrate the need for continued research into the vaginal microbiota, specifically to identify potential predictors of spontaneous abortion.}, }
@article {pmid40989186, year = {2025}, author = {Yang, P and Zhang, H and Yin, L and Chen, J and Chen, Y and Yang, H and Liu, Q and Zhang, W}, title = {Genetic diversity of Microviridae phages in the human respiratory tract.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1629120}, pmid = {40989186}, issn = {2235-2988}, mesh = {Humans ; *Genetic Variation ; Phylogeny ; Genome, Viral ; *Microviridae/genetics/classification/isolation &amp; purification ; Metagenomics ; Nasopharynx/virology ; *Respiratory System/virology ; *Bacteriophages/genetics/classification ; Capsid Proteins/genetics ; }, abstract = {Recent studies have revealed that Microviridae, a family of ssDNA viruses, are widely distributed in natural environments and play significant roles in various ecosystems. While Microviridae members dominate the human gut microbiome, their genetic diversity in the human respiratory ecosystem remains unclear. The distribution, genetic characteristics, and ecological roles of Microviridae are still poorly understood. This study identified 327 Microviridae-associated contigs from nasopharyngeal swab samples of healthy individuals through metagenomic sequencing and comparative genomics analysis, including 15 near-complete Microviridae-related genomes. These genomes exhibited high sequence divergence from each other, revealing their high genetic diversity. Phylogenetic analysis based on VP1 (major capsid protein; F protein) demonstrated that the 15 genomes could be classified into seven distinct Microviridae groups. CRISPR spacer matching predicted the host of the 15 genomes. The total read counts of Microviridae across all 12 libraries were quantified and compared using the Kruskal-Wallis test. This work significantly expands the understanding of the diversity, genomic architecture, and evolutionary dynamics of Microviridae within the human respiratory tract.}, }
@article {pmid40989178, year = {2025}, author = {Xu, W and Wang, W and Sui, L and Liu, N and Zhao, Y and Liu, Q}, title = {A novel genotype of Hepacivirus bovis identified in reindeer (Rangifer tarandus) in northeastern China.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1646191}, pmid = {40989178}, issn = {2235-2988}, mesh = {Animals ; Phylogeny ; *Reindeer/virology ; China ; *Genotype ; *Hepacivirus/genetics/classification/isolation &amp; purification ; Genome, Viral ; *Hepatitis C/veterinary/virology ; Cattle ; Recombination, Genetic ; Host Specificity ; Metagenomics ; }, abstract = {BACKGROUND: Hepaciviruses (family Flaviviridae) are significant pathogens affecting both human and animal health. While the hepatitis C virus (Hepacivirus hominis) is extensively studies in humans, related viruses have been identified across various animal species. Bovine hepacivirus (BovHepV) is capable of persistent infection in cattle, facilitating mutation accumulation and recombination events that may generate novel variants. BovHepV has also been found in wild boars and sheep, suggesting a broader host range than previously recognized.<br><br>METHODS: In this study, metagenomic sequencing was performed on 21 serum samples collected from reindeer (Rangifer tarandus) in Inner Mongolia, China. Two near-complete hepacivirus genomes were identified and designated as Rangifer tarandus hepacivirus (RtHepV) isolates GH01 and GH02. Phylogenetic and p-distance analyses were used to assess genetic relatedness to known hepaciviruses. Recombination detection and host-virus co-evolutionary analyses were also conducted.<br><br>RESULTS: Among 21 reindeer serum samples, the positivity rates of RtHepV GH01 and GH02 were 42.9% (9/21) and 4.8% (1/21), respectively. These isolates shared the highest sequence identities with the BovHepV Bulgaria 9 strain, with nucleotide identities of 68.2% (GH01) and 67.9% (GH02), and amino acid identities of 75.0% (GH01) and 74.8% (GH02). Phylogenetic analysis clustered RtHepV within the Hepacivirus bovis lineage, but in a distinct clade separate from previously reported BovHepV strains. P-distance calculations indicated that RtHepV does not constitute a novel species; instead, it qualifies as a novel genotype within Hepacivirus bovis, as its amino acid identity with other subtypes falls below the 77% threshold. Recombination analyses revealed evidence of genetic exchange between RtHepV and BovHepV strains. Co-evolutionary analyses further highlighted frequent host-switching events within the genus Hepacivirus.<br><br>CONCLUSION: This study reports the identification of two novel hepacivirus variants in reindeer from northeastern China, closely related to bovine hepaciviruses. These findings expand the known host range and geographic distribution of Hepacivirus, highlighting its ecological adaptability and the risk of cross-species transmission. The results underscore the potential public and veterinary health implications of hepaciviruses, warranting further investigation into the epidemiology of hepaciviruses.}, }
@article {pmid40989092, year = {2025}, author = {Liu, Y and Zhang, P and Tang, Y and Huang, R and Han, S and Hou, J and Pan, C}, title = {Combined metagenomics and metabolomics to analyse the fermentation process of Taorong-type Baijiu and its response mechanism with amino acids.}, journal = {Food chemistry: X}, volume = {30}, number = {}, pages = {102987}, pmid = {40989092}, issn = {2590-1575}, abstract = {Taorong-type Baijiu is an innovative flavour of Baijiu, its fermentation pattern and its response mechanism with amino acids are not clear. Therefore, shotgun metagenomics and metabolomics were combined to analyse this issues. The results showed that the fermentation process could be divided into three phases, the microbial diversity exhibited an initial increase, followed by a subsequent decrease, reaching a peak at 7 d. Pichia kudriavzevii, Paecilomyces variotii and Ligilactobacillus acidipiscis were the dominant microorganisms in the pre-fermentation phase, while in the middle and late-fermentation the dominant microorganisms shifted to Acetilactobacillus jinshanensis and Lactobacillus acetotolerans. Correlation analysis showed that pH, starch and reducing sugars were the main drivers in the pre-fermentation phase. Concurrently, Various amino acids, such as Val and Glu, accumulate while also promoting the succession of Baijiu microbiota and the production of flavouring substances. This results will provide a certain theoretical basis for the standardised production of Baijiu.}, }
@article {pmid40988890, year = {2025}, author = {Kwack, DW and Praveen, Z and Kim, YH and Yoo, CW and Ko, JH and Youn, SM and Park, JY and Lee, JH and Choi, SW and Kim, MK}, title = {Oral microbial signatures underlying recurrence via PI3K/AKT/mTOR pathway modulation in oral squamous cell carcinoma.}, journal = {Journal of oral microbiology}, volume = {17}, number = {1}, pages = {2560020}, pmid = {40988890}, issn = {2000-2297}, abstract = {BACKGROUND: Oral squamous cell carcinoma (OSCC) often recurs locally, reducing survival. The oral microbiome may influence tumor recurrence, but its prognostic role is unclear. This study investigated oral microbiomes associated with OSCC recurrence and their prognostic merit.<br><br>MATERIALS AND METHODS: Saliva samples were collected from 133 patients with OSCC. 16S rRNA gene sequencing was performed, and microbial signatures were predicted via XGBoost. Functional metagenomic prediction was conducted using PICRUSt2.<br><br>RESULTS: XGBoost identified Eubacterium, Lactobacillus, Kingella, Paludibacter, Parvimonas, Staphylococcus, and Veillonella as predictive for OSCC recurrence. Eubacterium and Lactobacillus were significantly enriched in recurrent disease and associated with poor survival. Staphylococcus and Veillonella were abundant in non-recurrent disease, correlating with a favorable prognosis. The microbiome-based model achieved superior predictive performance (AUC&#x2009;=&#x2009;0.741) compared with the clinical N-stage model (AUC&#x2009;=&#x2009;0.66). Eubacterium and Lactobacillus showed positive correlations with key genes, such as protein kinase B (AKT), fibroblast growth factor receptor 1 and guanine nucleotide-binding protein G subunit beta-2, within the phosphoinositide 3-kinase (PI3K)/AKT/mammalian target of rapamycin (mTOR) pathway. In contrast, Veillonella was negatively correlated with these genes.<br><br>CONCLUSIONS: Oral saliva microbiome profiling reveals distinct microbial patterns associated with OSCC recurrence. Our correlation-based functional predictions indicated that the enrichment of Eubacterium and Lactobacillus along with a lower abundance of Veillonella may influence recurrence through oncogenic PI3K/AKT/mTOR, underscoring the prognostic potential of saliva-based microbial biomarkers.}, }
@article {pmid40988851, year = {2025}, author = {Bitencourt, JAP and Bandeira, DM and Gonçalves, AC and Snak, A and de Castro, DCM and de Lima Ribeiro, R and Argolo, LA and Dos Santos Scherer, R and Lima, BA and Albino, UB and Pinto, FGDS}, title = {Exploring microbial dynamics in ferruginous caves: taxonomic and functional diversity across seasons and cave zones.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1619203}, pmid = {40988851}, issn = {1664-302X}, abstract = {Bacterial communities in ferruginous caves are known for their high diversity and functional adaptability to environmental conditions. In this study, we characterized the taxonomic and potential functional profiles of two iron-rich caves, GEM-1423 and GEM-1462, across photic, dysphotic, and aphotic zones during both rainy and dry seasons. High-throughput sequencing revealed distinct microbial community structures. GEM-1423 showed strong dominance of specific taxa, while GEM-1462 exhibited lower dominance of iron-metabolizing groups and higher beta diversity, particularly in the dry season-indicating a greater degree of species replacement. Notably, iron availability emerged as a key factor influencing microbial dynamics in both caves, affecting community composition and functional pathways. Core genera, such as Bacillus, Acidothermus, Mycobacterium, and Acidisphaera, were associated with nitrogen and carbon cycling, as well as indirect iron solubilization through production of organic acids. Potential functional profiles varied seasonally: energy metabolism was enriched during the dry season, while nutrient cycling pathways were more abundant in the rainy season. We also detected taxa involved in manganese oxidation, urea degradation, and functions with biotechnological relevance, including antimicrobial compound production and metal resistance. These findings highlight the complex interactions between environmental factors, microbial diversity, and ecosystem function in ferruginous caves, and underscore the biotechnological potential of microbial communities from extreme environments.}, }
@article {pmid40988762, year = {2025}, author = {Hu, H and Yang, Y and Lu, W and Huang, XE}, title = {Analysis of Risk Factors for Severe Pneumonia Progression in Chlamydia psittaci Infections: A Retrospective Study.}, journal = {International journal of general medicine}, volume = {18}, number = {}, pages = {5605-5615}, pmid = {40988762}, issn = {1178-7074}, abstract = {INTRODUCTION: Psittacosis pneumonia, caused by Chlamydia psittaci, is a zoonotic infection with a severe-case mortality rate of 15-20%. This study aimed to identify risk factors for severe pneumonia and evaluate the discriminative performance of corresponding predictive models.<br><br>METHODS: In this retrospective study, 51 patients with metagenomic next-generation sequencing (mNGS)-confirmed psittacosis pneumonia were classified into severe (n=20) and non-severe (n=31) groups. Demographic characteristics, clinical manifestations, laboratory parameters, and imaging features were collected. Variables were analyzed using univariate screening, variance inflation factor (VIF)-based multicollinearity control, least absolute shrinkage and selection operator (LASSO) regression, and Firth-penalized logistic regression. Receiver operating characteristic (ROC) analysis evaluated predictive performance.<br><br>RESULTS: Patients with severe pneumonia were significantly older (p = 0.043) and showed a higher prevalence of underlying diseases (p = 0.025) and cardiovascular diseases (CVD, p = 0.028). They also exhibited persistent lymphocytopenia, progressive decreases in hemoglobin (Hb) levels, and a higher rate of bilateral lung involvement. LASSO regression identified four key predictors: history of CVD, first lymphocyte count (LYM), second Hb measurement, and lactate dehydrogenase (LDH) level. Firth-penalized logistic regression confirmed that a history of CVD (OR = 4.874, 95% CI: 1.270-22.763) and a decreased second Hb measurement (OR = 0.415, 95% CI: 0.169-0.844) were independent risk factors for severe pneumonia. ROC analysis demonstrated that the combination of CVD history and the second Hb measurement achieved a specificity of 90.32%, while the combination of CVD history and LDH exhibited a sensitivity of 90%. The final multivariable model showed good discriminatory performance, with an area under the curve (AUC) of 0.885, sensitivity of 75%, and specificity of 93.50%.<br><br>CONCLUSION: CVD history and progressive Hb decrease are independent risk factors for severe psittacosis pneumonia. Dynamic monitoring of LYM, Hb, LDH, and CVD history facilitates early risk stratification. The multivariate model demonstrates high predictive accuracy and clinical utility.}, }
@article {pmid40988537, year = {2025}, author = {Tsamadou, V and Ohlsson, JA and Schnürer, A}, title = {Converge or Diverge? Exploring the Fate of Taxonomically Different Anaerobic Digestion Communities Under Uniform Growth Conditions.}, journal = {Microbial biotechnology}, volume = {18}, number = {9}, pages = {e70233}, doi = {10.1111/1751-7915.70233}, pmid = {40988537}, issn = {1751-7915}, support = {310432//Energimyndigheten/ ; //Swedish Research Council (VR). The grant agreement corresponds to the Swedish Research Council./ ; //Sveriges Lantbruksuniversitet/Swedish University of Agricultural Sciencesarch Council through grant agreement no. 2022-06725/ ; }, mesh = {Anaerobiosis ; Culture Media/chemistry ; *Bacteria/classification/genetics/metabolism/growth &amp; development ; Sewage/microbiology ; Ammonia/metabolism ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Bioreactors/microbiology ; Biofuels ; DNA, Ribosomal/chemistry/genetics ; *Biota ; Sequence Analysis, DNA ; Metagenomics ; }, abstract = {Biogas inocula with distinct taxonomic compositions often converge to similar communities when fed the same substrate, indicating strong substrate-driven deterministic assembly. Nevertheless, stochastic processes have also been suggested as a critical element for microbial assembly in biogas systems. To date, assembly processes have mainly been investigated with undefined, non-sterile substrates, making it difficult to exclude the influence of external microorganisms. The aim of the present study was to investigate whether three taxonomically distinct anaerobic digestion (AD) communities would converge when exposed to uniform growth conditions during semi-continuous operation with a sterilised defined medium. The inocula originated from mesophilic processes using different substrates (food waste, sludge, and manure) and total ammonia levels (0.5-7.2 g/L). The medium was formulated to support all four main metabolic steps of AD: hydrolysis, fermentation, anaerobic oxidation, and methanogenesis. Taxonomic, phylogenetic, and functional analyses conducted via 16S and metagenomic sequencing showed that the substrate had no deterministic effect on microbial community taxonomic composition. Instead, the final community structure was dictated primarily by the initial inoculum, regardless of changes in substrate composition or ammonia levels. Despite taxonomic divergence, broad-level functionality and operational performance remained similar between communities.}, }
@article {pmid40988166, year = {2025}, author = {Xu, L and Li, D}, title = {Lymphoma combined with Tropheryma whipplei infection: A case report and literature review.}, journal = {Medicine}, volume = {104}, number = {38}, pages = {e44611}, doi = {10.1097/MD.0000000000044611}, pmid = {40988166}, issn = {1536-5964}, mesh = {Humans ; Adult ; *Whipple Disease/diagnosis/complications/drug therapy ; *Tropheryma/isolation &amp; purification ; Male ; *Lymphoma/complications/diagnosis ; Anti-Bacterial Agents/therapeutic use ; Bronchoalveolar Lavage Fluid/microbiology ; }, abstract = {RATIONALE: Whipple disease is exceptionally rare in patients with lymphoma in China, particularly when presenting with pulmonary symptoms as the initial manifestation. Respiratory involvement is atypical for Whipple disease and may easily be overlooked, especially in patients receiving targeted drug therapy for lymphoma. In such cases, it can be challenging to distinguish between disease progression, drug-induced pneumonia, and infectious etiologies, as the clinical and radiological findings often overlap.<br><br>PATIENT CONCERNS: A 39-year-old patient with lymphoma and persistent fever did not respond well to the broad-spectrum antibiotics.<br><br>DIAGNOSES: In contrast to traditional pathological examination or tissue periodic acid-Schiff staining, the patient was diagnosed using metagenomic next-generation sequencing of pulmonary alveolar lavage fluid.<br><br>INTERVENTIONS: Symptomatic treatment, including anti-infective agents, cough relief, and expectorants, was administered. Bronchoscopy and lung puncture were performed to determine the cause of the disease.<br><br>OUTCOMES: Following the confirmation of Tropheryma whipplei by metagenomic next-generation sequencing, targeted antimicrobial therapy was likely initiated. The patient's symptoms, including the persistent fever, subsequently resolved, indicating a positive response to the appropriate treatment.<br><br>LESSONS: Whipple trophic pneumonia is an opportunistic infection with low incidence. It typically presents with atypical clinical signs and symptoms, making diagnosis challenging based on the imaging findings. It is often misdiagnosed, particularly in patients receiving immunosuppressants. Gene detection in the lung lavage fluid can aid in diagnosis. This case report discusses a patient with lymphoma and Whipple disease, while also reviewing current literature on the bacterium to enhance clinician awareness of its complexities.}, }
@article {pmid40987851, year = {2025}, author = {Du, LF and Shi, W and Cui, XM and Fan, H and Jiang, JF and Bian, C and Ye, RZ and Wang, Q and Zhang, MZ and Yuan, TT and Xia, LY and Ruan, XD and Chang, QC and Du, CH and Que, TC and Wang, X and Han, XH and Yang, TC and Jiang, BG and Chen, JY and Wang, XR and Tan, LF and Liu, YW and Deng, LL and Liu, Y and Zhu, Y and Pan, YS and Wang, N and Lin, ZT and Li, LF and Li, C and Shen, SJ and Liu, YT and Tian, D and Han, XY and Wang, J and Wang, YF and Gao, WY and Li, YY and Xiong, T and Wang, TH and Shi, XY and Zhu, DY and Zhu, JG and Wang, CC and Shi, WQ and Zhan, L and Liu, ZH and Feng, D and Zhao, L and Sun, Y and ,  and Wang, J and Jia, N and Zhao, F and Cao, WC}, title = {Genome-resolved metagenomics reveals microbiome diversity across 48 tick species.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {40987851}, issn = {2058-5276}, support = {2019YFC1200501//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32025009//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Ticks are arthropod vectors capable of transmitting a wide spectrum of pathogens affecting humans and animals. However, we have relatively limited information of their genomic characteristics and the diversity of associated microbiomes. Here we used long- and short-read sequencing on 1,479 samples from 48 tick species across eight genera from China to determine their genome and associated pathogens and microbiome. Through de novo assembly, we reconstructed 7,783 bacterial genomes representing 1,373 bacterial species, of which, 712 genomes represented 32 potentially pathogenic species. Computational analysis found nutritional endosymbionts to be prevalent and highly specific to tick genera. The microbiome genome-wide association study revealed host genetic variants linked to pathogen diversity, abundance and key biological pathways essential to tick biology, including blood-feeding and pathogen invasion. These findings provide a resource for studying the host-microbe interactions within ticks, paving the way for strategies to control tick populations and tick-borne diseases.}, }
@article {pmid40987526, year = {2025}, author = {Shaw, J and Boucher, C and Yu, YW and Noyes, N and Li, H}, title = {Long-read reconstruction of many diverse haplotypes with devider.}, journal = {Genome research}, volume = {}, number = {}, pages = {}, doi = {10.1101/gr.280510.125}, pmid = {40987526}, issn = {1549-5469}, abstract = {Reconstructing exact haplotypes is important when sequencing a mixture of similar sequences. Long-read sequencing can connect distant alleles to disentangle similar haplotypes, but handling sequencing errors requires specialized techniques. We present devider, an algorithm for haplotyping small sequences - such as viruses or genes - from long-read sequencing. devider uses a positional de Bruijn graph with sequence-to-graph alignment on an alphabet of informative alleles to provide a fast assembly-inspired approach compatible with various long-read sequencing technologies. On a synthetic Nanopore dataset containing seven HIV strains, devider recovered 97% of the haplotype content and had the most accurate abundance estimates while taking < 4 minutes and 1 GB of memory for > 8000× coverage. Benchmarking on synthetic mixtures of antimicrobial resistance (AMR) genes showed that devider recovered 83% of haplotypes, 23 percentage points higher than the next best method. On real PacBio and Nanopore datasets, devider recapitulates previously known results in seconds, disentangling a bacterial community with > 10 strains and an HIV-1 co-infection dataset. We used devider to investigate the within-host diversity of a long-read bovine gut metagenome enriched for AMR genes, discovering 13 distinct haplotypes for a tet(Q) tetracycline resistance gene with > 18,000× coverage and 6 haplotypes for a CfxA2 beta-lactamase gene. We found clear recombination blocks for these AMR gene haplotypes, showcasing devider's ability to unveil evolutionary signals for heterogeneous mixtures.}, }
@article {pmid40987432, year = {2025}, author = {Sayeli, FG and Pirmoradian, M and Zanjaniha, S and Moradi, H and Khorrami, Y and Saedi, M and Bayat, Z and Zahedi, P and Jafari, D}, title = {Molecular diagnostics for infectious disease.}, journal = {Clinica chimica acta; international journal of clinical chemistry}, volume = {}, number = {}, pages = {120619}, doi = {10.1016/j.cca.2025.120619}, pmid = {40987432}, issn = {1873-3492}, abstract = {Molecular diagnostic methods have been used in clinical and environmental settings for over three decades. Conventional approaches, which often involve long processing times and limited sensitivity, are gradually being replaced by molecular tests that offer improved analytical performance. Nucleic acid testing (NAT), particularly PCR-based methods and their variants such as quantitative PCR (qPCR) and reverse transcription PCR (RT-PCR), have demonstrated higher sensitivity and specificity than conventional assays. Recent developments in next-generation sequencing (NGS), including metagenomic and whole-genome sequencing, have also enhanced the identification of complex pathogens and resistance mechanisms. Point-of-care testing (POCT) is another advancement, supported by newly developed isothermal amplification (IA) techniques such as loop-mediated isothermal amplification (LAMP) and recombinase polymerase amplification (RPA), which allow rapid detection in decentralized settings. In addition, newer approaches such as droplet digital PCR (ddPCR) and CRISPR-based diagnostics are very promising due to their potential to provide accurate nucleic acid detection in low amounts of target. Aptamer-based sensors are also under extensive research and development for their application in diagnosis of infection. This review outlines both traditional and recent advanced molecular diagnostic tools, with a focus on their application to infectious disease detection.}, }
@article {pmid40987427, year = {2025}, author = {Hsu, BM and Chen, JS and Wang, WY and Chen, CJ and Fan, CW and Wu, CC and Hussain, B and Tsai, HC}, title = {An integral view of gut microbiome diversity and functional metabolic changes of a gut-brain axis associated with dementia based on metagenomic analysis.}, journal = {Physiology &amp; behavior}, volume = {}, number = {}, pages = {115112}, doi = {10.1016/j.physbeh.2025.115112}, pmid = {40987427}, issn = {1873-507X}, abstract = {BACKGROUND: Growing evidence highlights the vital role by gut microbiota in brain health through the gut-brain axis, which involves neural, immune, endocrine, and metabolic signaling pathways. Disruption of this axis through microbial dysbiosis is increasingly linked to cognitive disorders, including dementia. However, the specific taxa and pathways involved remain poorly characterized. This study investigates taxonomic and functional shifts in the gut microbiome across healthy individuals, mild dementia, and dementia patients, aiming to identify microbial signatures and metabolic alterations associated with cognitive decline.<br><br>METHODS: A total of 184 participants (aged 60-98) were recruited and grouped into healthy, mild dementia, and dementia categories based on Clinical Dementia Rating scores. Demographic and clinical data were collected through structured interviews. Fecal samples were collected from participants and DNA was extracted and subjected to 16S rRNA gene sequencing. Sequencing data were processed using QIIME2 and classified using the SILVA database. Alpha (Shannon, Inverse Simpson) and beta diversity (Bray-Curtis PCoA) were analyzed between participant groups. Functional prediction was performed with PICRUSt2 to estimate KEGG orthologs from normalized ASVs. Statistical analyses were conducted in R using Kruskal-Wallis and PERMANOVA tests to assess group-level differences.<br><br>RESULTS: Dementia patients exhibited the highest proportion of unique ASVs (32.1%) but showed reduced alpha diversity compared to mild dementia and healthy controls. PCoA revealed distinct microbial clustering across groups, explaining 19.3% of total variance, with dementia samples forming a unique cluster. Taxonomically, dementia samples were enriched in Firmicutes and pro-inflammatory genera such as Peptoclostridium and Scardovia, while healthy controls harbored more SCFA-producing taxa like Lachnospiraceae_UCG-001. Co-occurrence networks in dementia were more complex, with increased inter-species connectivity and key drivers including Dorea and Clostridium innocuum. Functionally, dementia samples showed enrichment of vanillate degradation pathways and depletion of neuroprotective pathways like ergothioneine and vitamin E biosynthesis, correlating with specific microbial signatures.<br><br>CONCLUSIONS: Cognitive decline was associated with reduced microbial diversity and selective enrichment of pro-inflammatory taxa, reflecting gut ecological instability due to dementia. Microbial composition shifted progressively with dementia severity, indicating disease-specific gut microbial restructuring. Moreover, the loss of key functional microbial metabolites such as neuroprotective and anti-inflammatory metabolites supports targeting such metabolites and their producing gut microbiota as a therapeutic strategy for dementia. Future studies should ensure generalization by recruiting multi-center participants with strict guidelines for monitoring confounders.}, }
@article {pmid40986950, year = {2025}, author = {Peng, Y and Huang, Z and Bian, F and Wu, Z and Zhong, Z and Zhang, X}, title = {Characteristics of microbial phosphorus cycling in Phyllostachys praecox forest soils supplemented with the phosphate-solubilizing bacterium Pseudomonas sp. OP1 revealed by metagenomics.}, journal = {Journal of environmental management}, volume = {394}, number = {}, pages = {127363}, doi = {10.1016/j.jenvman.2025.127363}, pmid = {40986950}, issn = {1095-8630}, abstract = {Soil phosphorus (P) is an essential nutrient for plants and a limiting factor in bamboo forest productivity. Plant endophytic phosphate-solubilizing bacteria (PSB) play a crucial role in soil P cycling. However, the mechanisms by which they influence soil P cycling in bamboo forests remain unclear. Here, we employed a metagenomics approach to evaluate the effects of the endophytic PSB Pseudomonas sp. OP1 on microbial P cycling in Phyllostachys. praecox forest soils. OP1 treatment significantly increased labile phosphorus (LP), moderately labile phosphorus (MLP), and nonlabile phosphorus (NLP) by 23.7, 40.37, and 18.98 % compared with the control (CK), respectively (p < 0.05). OP1 further significantly increased the abundance of functional genes associated with inorganic P solubilization and P transport. OP1-treated soils were enriched in ppx, gcd, ugpC, phnW, and phoN, whereas CK was characterized by phnC, phnP, ppa, and phnO. OP1 application altered the community structure of P-cycling microorganisms, enriching Chloroflexi and Bradyrhizobium while reducing Firmicutes and Streptomyces. Mantel tests revealed significant relation of soil P fractions to alkali-hydrolyzed nitrogen (AN), P-cycling genes, and the related microbial communities. Specifically, AN, ppx, phnW, phoN, and Nitrospirae (complete ammonia oxidizers) were significantly positively correlated with LP, MLP, and NLP, while Planctomycetota (anaerobic ammonia oxidizers) exhibited negative correlations with these P fractions, highlighting nitrogen-P co-regulation and microbial-mediated P transformation. These findings highlight the potential of PSB in enhancing soil P-use efficiency and reducing chemical phosphate fertilizer use, providing insights into the microbial mechanisms underlying P cycling in bamboo forests and supporting sustainable bamboo plantation management.}, }
@article {pmid40985734, year = {2025}, author = {Hribovšek, P and Olesin Denny, E and Mall, A and Dahle, H and Steen, IH and Stokke, R}, title = {Adaptation strategies of iron-oxidizing bacteria Gallionella and Zetaproteobacteria crossing the marine-freshwater barrier.}, journal = {mBio}, volume = {}, number = {}, pages = {e0257224}, doi = {10.1128/mbio.02572-24}, pmid = {40985734}, issn = {2150-7511}, abstract = {Iron-oxidizing Betaproteobacteria and Zetaproteobacteria are generally associated with freshwater and marine environments, respectively. Despite repeated cross-environment observations of these taxa, there has been no focused exploration of the genomes of marine Gallionella (Betaproteobacteria) to understand transitions between freshwater and marine habitats. Consequently, their roles in these environments remain uncertain. Here, we present strong evidence for the co-occurrence of Gallionella and Zetaproteobacteria at deep-sea hydrothermal vents at the Arctic Mid-Ocean Ridges through metagenomic analyses. Phylogenomic analysis of Gallionella metagenome-assembled genomes (MAGs) suggests that seawater adaptation is an evolutionary event that occurred multiple times in distinct lineages. Similarly, several distinct evolutionary events for freshwater and terrestrial Mariprofundus and other Zetaproteobacteria are predicted. The presence of c-type cytochrome cyc2 iron oxidation genes in co-occurring marine Betaproteobacteria and Zetaproteobacteria implies an overlap in niches of these iron-oxidizers. Functional enrichment analyses reveal genetic differences between marine MAGs of both iron-oxidizing groups and their terrestrial aquatic counterparts linked to salinity adaptation. Though scanning electron microscopy confirms the presence of Fe(III) oxyhydroxide stalks where Gallionella and Mariprofundus co-occur, Gallionella MAGs from hydrothermal vents lack evidence of putative stalk formation genes. Mariprofundus is therefore the likely sole stalk-producing iron-oxidizer in this environment. Conversely, the discovery of putative stalk formation genes in Mariprofundus MAGs across the marine-freshwater barrier suggests that Fe(III) oxyhydroxide stalks might not be an exclusive signature for single iron-oxidizing taxa in marine and freshwater environments. Our research provides novel insights into the iron-oxidizing capacities, stalk production, environmental adaptation, and evolutionary transitions between marine and freshwater habitats for Gallionella and Zetaproteobacteria.IMPORTANCEIron-oxidizing bacteria (FeOB) play an important role in the global cycling of iron, carbon, and other metals. While it has previously been assumed that bacterial evolution does not frequently involve crossing the salinity barrier, recent studies indicate that such occurrences are more common than previously thought. Our study offers strong evidence that this also happens among FeOB, with new insights into how these bacteria adapt to the new environment, including hydrothermal vents and freshwater habitats. In addition, we emphasize the importance of accurate iron-oxidizing taxa identification through sequencing, rather than relying solely on the morphology of Fe(III) oxyhydroxides and environment. On a larger scale, microorganisms within established communities need to respond to changes in salinity due to events like seawater intrusion in coastal aquifers, and thus, our findings underscore the importance of knowledge of transitions across habitat types with different salt concentrations.}, }
@article {pmid40985733, year = {2025}, author = {Romero, JL and Ratliff, JH and Carlson, CJ and Griffiths, DR and Miller, CS and Mosier, AC and Roane, TM}, title = {Community and functional stability in a working bioreactor degrading 1,4-dioxane at the Lowry Landfill Superfund Site.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0057425}, doi = {10.1128/aem.00574-25}, pmid = {40985733}, issn = {1098-5336}, abstract = {UNLABELLED: 1,4-dioxane (dioxane) is an emerging contaminant that poses risks to human and environmental health. Bacterial dioxane degradation is increasingly being studied as a method to remove dioxane from contaminated water. However, there is a lack of studies on microbial community structures and functions within efficient, large-scale, biodegradation-based remediation technologies. The Lowry Landfill Superfund Site (Colorado, USA) uses an on-site, pump-and-treat facility to remove dioxane from contaminated groundwater by biodegradation. Here, 16S rRNA gene and shotgun metagenomic sequencing were used to describe microbial community composition, soluble di-iron monooxygenase (SDIMO) alpha hydroxylases, and potential for dioxane degradation and horizontal gene transfer in bioreactor support media from the facility. Support media showed diverse microbial communities dominated by Nitrospiraceae, Nitrososphaeraceae, and Nitrosomonadaceae. Pseudonocardia was also detected, suggesting a potential presence of known dioxane-degraders. Candidate SDIMOs belonged mostly to Group V, followed by Groups IV, II, and I (based on read depth). The most abundant Group V clade contained 38 proteins that were phylogenetically related to DxmA-like proteins, including that of Pseudonocardia dioxanivorans CB1190 (a known dioxane degrader). Seventeen Lowry contigs containing DxmA-like proteins contained protein-coding genes potentially involved in chemical degradation, transcriptional regulation, and chemical transport. Interestingly, these contigs also included evidence of potential horizontal gene transfer, including toxin-antitoxin proteins, phage integrase proteins, putative transposases, and putative miniature inverted-repeat transposable elements. These findings improve our understanding of potential dioxane biodegradation mechanisms in a functioning remediation system. Further studies are needed to definitively confirm microbial activity and enzymatic activity toward dioxane removal in this site.<br><br>IMPORTANCE: As an environmental contaminant, 1,4-dioxane poses risks for water quality and human health. Used as a solvent and chemical stabilizer in a variety of manufacturing and industrial applications, microbiological methods of detoxification and mitigation are of interest. The degradation of 1,4-dioxane by the bacterium Pseudonocardia spp. is the best understood example; however, these studies are largely based on single isolate, bench-scale, or in silico experiments. Consequently, a knowledge gap exists on bacterial degradation of 1,4-dioxane at environmentally relevant concentrations using functioning remediation technologies at scale. This study addresses this gap directly by describing microbial taxa, enzymes, and potential horizontal gene transfer mechanisms associated with an active treatment plant located on a 1,4-dioxane-impacted U.S. Environmental Protection Agency (EPA) superfund site. As 1,4-dioxane contamination gains more attention, these findings may prove useful for future facilities aiming to promote and optimize removal by biodegradation.}, }
@article {pmid40985699, year = {2025}, author = {Seitz, VA and McGivern, BB and Shaffer, M and Borton, MA and Belk, AD and Ghadermazi, P and Martino, C and Shenhav, L and Zhang, AR and Shi, P and Emmons, A and Deel, H and Xu, ZZ and Nieciecki, V and Zhu, Q and Cantrell, K and Ben-Hur, A and Reed, SC and Humphry, GC and Ackermann, G and McDonald, D and Joshua Chan, SH and Connor, M and Boyd, DA and Smith, J and Watson, JMS and Vidoli, G and Steadman, D and Lynne, AM and Bucheli, S and Carter, DO and Burcham, ZM and Knight, R and Wrighton, KC and Metcalf, JL}, title = {CaDAVEr: a metagenome-assembled genome catalog of microbial decomposers across vertebrate environments.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0132324}, doi = {10.1128/mra.01323-24}, pmid = {40985699}, issn = {2576-098X}, abstract = {Microbial degradation of organic matter is a fundamental Earth process, yet a mechanistic understanding of microbial metabolisms and successional ecology involved in decomposition remains poorly understood. Here, we announce the recovery of 277 cadaver-associated soil metagenome-assembled genomes to enhance our understanding of vertebrate decomposition microbial processes.}, }
@article {pmid40985644, year = {2025}, author = {Mobanga, M and Fadiji, AE and Tshisekedi, KA and Kawadza, TD and Babalola, OO}, title = {A collection of metagenome-assembled genomes from platinum mine tailings in South Africa.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0056925}, doi = {10.1128/mra.00569-25}, pmid = {40985644}, issn = {2576-098X}, abstract = {This study presents 84 metagenome-assembled genomes from platinum mine tailings and non-mined soil. The analysis reveals diverse Proteobacteria. This work offers insights into pollutant degradation, resource recovery, and potential strategies for ecological restoration in mining-impacted environments.}, }
@article {pmid40985583, year = {2025}, author = {Liu, H and Hu, L and Wang, X and You, X and Jiang, H and Hou, S and Li, J and Liu, K}, title = {High-throughput cultivation and screening of plant-promoting bacteria with nitrogen fixation from mangrove sediments.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxaf235}, pmid = {40985583}, issn = {1365-2672}, abstract = {AIMS: The present study was to isolate, cultivate, and screen plant growth-promoting bacteria (PGPB) from mangrove sediments at high throughput, and compare the differences in microbial diversity and PGPB screening efficiency between the high-throughput and traditional agar plate methods.<br><br>METHODS AND RESULTS: A high-throughput method combining limiting dilution and two-sided barcode PCR was developed to effectively isolate and identify bacteria from mangrove sediments. Moreover, the metagenome and 16S rRNA amplicon sequencing were used for identification of potential PGPB genera and investigation of microbial diversity in different pooled cultures. The results showed that the microbial communities of the bacteria cultured by the high-throughput method had a significantly lower Simpson index (p&#xa0;<&#xa0;0.05) and a higher proportion of rare species than that by the agar plate method. A diverse bacterial consortium encompassing 79 species of 39 genera and 6 phyla were successfully isolated by the high-throughput method. Furthermore, three species of Bacillus and four species of Pseudomonas exhibiting plant growth-promoting properties were isolated and purified from a series of Bacillus and Pseudomonas genera, including a previously uncultured Pseudomonas strain. In contrast, all the PGPB screened by the agar plate method belonged to the Vibrio genus, which has been reported to be pathogenic to humans.<br><br>CONCLUSIONS: The study demonstrated that the high-throughput method was superior to traditional plate methods for isolating a broader spectrum of microbial diversity from mangrove sediments, particularly rare species. When combined with metagenome sequencing, this approach enables a more efficient screening for PGPB potentially applicable for agriculture or environmental protection.}, }
@article {pmid40985550, year = {2025}, author = {He, Y and Baltar, F and Wang, Y}, title = {Seasonal variability in community structure and metabolism of active deep-sea microorganisms.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf214}, pmid = {40985550}, issn = {1751-7370}, abstract = {Learning about the metabolic activities and adaptations of deep-sea microbes is challenging, as sample collection and retrieval often cause RNA degradation and microbial community shifts. Here, we employed an in situ DNA/RNA co-extraction device to collect 18 time-series nucleic acid samples during winter and summer in the South China Sea, minimizing sampling perturbation for metatranscriptome and metagenome analyses. Between the two seasons, the prokaryotic microbiota showed seasonal variations in species composition. Burkholderiales dominated in summer, whereas Pseudomonadales, Bacillales, and Rhodobacterales were enriched in winter. However, the dominant transcriptionally active taxa affiliated with Nitrososphaerales, MGIII, SAR324, UBA11654, Marinisomatales and Poseidoniales remained largely stable across seasons. Among eukaryotes, Ciliophora were the most active, whereas Retaria were abundant but inactive. Despite the stable active prokaryotic community, metabolic profiles differed significantly between seasons. In the winter, autotrophic microorganisms, particularly Nitrososphaerales, exhibited higher CO2 fixation activity via the 3HP/4HB cycle, accompanied by enhanced ammonia oxidation for energy generation. In addition, CO oxidation activity was also elevated. In the summer, the primary source of energy originated from heterotrophic microorganisms capable of utilizing fatty acids, benzoate, and H2, likely relying on anaerobic respiration within organic particles. This may relate with nutrient source variations as reflected by the different levels of microbial network complexity between two seasons. Altogether, our in situ metatranscriptomes revealed the metabolic activities and adaptations of active microbial groups across seasons, providing a basis for identifying the microbial contributors to elemental cycles in the deep ocean.}, }
@article {pmid40985439, year = {2025}, author = {Derksen, K and Brimblecombe, P and Piñar, G and Waldherr, M and Graf, AB and Querner, P and Sterflinger, K}, title = {Monitoring of Fungal Diversity and Microclimate in Nine Different Museum Depots.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {11}, number = {7}, pages = {}, doi = {10.3390/jof11070478}, pmid = {40985439}, issn = {2309-608X}, support = {Heritage_2020-043_Modeling-Museum//Austrian Academy of Sciences (&#xd6;AW)/ ; }, abstract = {Within museum depots, the largest part of all heritage collections is stored. Often, the preservation of highly sensitive objects is an ongoing challenge, as the materials are constantly subjected to and influenced by ever-present environmental factors-above all the surrounding climate and other physicochemical processes. Biological degradation is also a major risk for collections. Fungal infestation poses a particular threat, in many regions increasingly the result of climate change. Models for damage prediction and risk assessment are still underdeveloped and require a more substantial database. Approaching this need, nine museum depots and archives were selected in this study. Two years of monitoring the indoor microclimate with thermohygrometric sensors, investigating fungal abundance and diversity through culture-dependent and -independent (metagenomics) approaches, and the collection of relevant additional information resulted in a vast amount of diverse data. The main fungal genera identified through cultivation were Cladosporium, Penicillium, Aspergillus, Alternaria and Epicoccum. The cultivation-independent approach identified Aspergillus, Pyronema, Penicillium, Xenodidymella and Blumeria as the main taxa. Data analyses indicated that key drivers involved in similarities, patterns and differences between the locations were their geographic location, immediate outdoor surroundings and indoor (micro)climatic fluctuations. The study also sheds light on a possible shift in focus when developing strategies for preventing mold growth in collection depots beyond the prevailing path of tightest possible climate control.}, }
@article {pmid40985325, year = {2025}, author = {He, J and Xiao, J and Shen, X and Zhao, K and Lei, X and Zhang, H and Sun, C and Lu, H and Shao, Y}, title = {Multi-Habitat Landscape Promotes Microbial Diversity: Insights from the Traditional Agricultural Heritage and the Global Trend.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e06402}, doi = {10.1002/advs.202506402}, pmid = {40985325}, issn = {2198-3844}, support = {518000-523500922002//Scientific Pre-research Fund of Zhejiang University/ ; CARS-18//Agriculture Research System of China/ ; 32022081//National Outstanding Youth Science Fund Project of National Natural Science Foundation of China/ ; 31970483//National Outstanding Youth Science Fund Project of National Natural Science Foundation of China/ ; }, abstract = {Ecosystems are interconnected networks of diverse habitat types, rather than isolated patches. However, the role of the multi-habitat landscape in influencing microbial diversity remains poorly understood. This study investigates bacterial and fungal communities within a 2500-year agricultural heritage system, the Mulberry-dyke and Fish-pond (MF), which integrates various terrestrial and aquatic habitats. Using amplicon sequencing, metagenomics, metatranscriptomics, and genomic analyses, these findings reveal a significant proportion of unclassified microbial taxa, underscoring the importance of MF systems as an untapped reservoir of microbial genetic resources. Moreover, single-nucleotide-level analyses demonstrate that a multi-habitat landscape enhances microbial diversity through ecosystem-wide assembly, facilitated by cross-habitat microbial dispersal. Taxa found across multiple habitats exhibit convergence in microdiversity and adaptive genetic traits, indicating both ecological and functional mechanisms underlying their adaptability. A global analysis of public microbiome datasets furthermore confirms that regions with higher habitat heterogeneity support significantly higher taxonomic and functional diversity of microbiomes. Overall, this study sheds new light on the overlooked microbial diversity in traditional agricultural heritages and emphasizes the value of ancestral ecological wisdom underlying multi-habitat integration for ecosystem management. These insights offer valuable guidance for developing sustainable agricultural strategies, enhancing microbial diversity, and reinforcing ecosystem resilience in the face of global change.}, }
@article {pmid40984062, year = {2025}, author = {Li, T and Conte, MA and Gandhi, J and Panciera, M and Shah, N and Emma, D and Maswai, J and Friberg, HL and Collins, ND and Ake, J and Hang, J}, title = {Discovery of Respiratory Pathogens in People Living With HIV in the African Cohort Study.}, journal = {Military medicine}, volume = {190}, number = {Supplement_2}, pages = {327-332}, doi = {10.1093/milmed/usaf180}, pmid = {40984062}, issn = {1930-613X}, support = {RF1 MH133442/NH/NIH HHS/United States ; W81XWH-18-2-0040/NH/NIH HHS/United States ; //Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc./ ; /PEPFAR/PEPFAR/United States ; }, mesh = {Humans ; Adult ; *HIV Infections/epidemiology/complications ; Male ; Female ; Prospective Studies ; Cohort Studies ; *Respiratory Tract Infections/epidemiology/virology ; Kenya/epidemiology ; Middle Aged ; COVID-19/epidemiology ; SARS-CoV-2/pathogenicity ; Prevalence ; Uganda/epidemiology ; United States/epidemiology ; Adolescent ; Tanzania/epidemiology ; Nigeria/epidemiology ; }, abstract = {INTRODUCTION: Respiratory infection outbreaks pose a threat to the readiness of the United States and allied armed forces. Predicting and preventing such outbreaks requires understanding of the epidemiology of potential respiratory pathogens in communities where service members live and work. We conducted pan-viral surveillance of respiratory specimens from people living with HIV or without HIV but under the risk enrolled in the U.S. Military HIV Research Program's African Cohort Study to determine the prevalence and possible clinical presentation of viruses in this population.<br><br>METHODS: The African Cohort Study is an open-ended prospective cohort study that enrolls people with and without HIV aged &#x2265;15&#x2009;years at 12 clinical sites in Kenya, Tanzania, Uganda, and Nigeria. The study follows participants every 6 months and collects social, demographic, clinical, and laboratory data. A total of 131 respiratory samples, collected from March 2022 to February 2023 from participants in South Rift Valley Province, Kenya, who had symptoms of respiratory illness or a positive COVID-19 test, were analyzed using a pan-viral hybridization metagenomic next-generation sequencing approach. Libraries were sequenced on the Illumina Next-generation Sequencing System NovaSeq 6000. Sample data were run through several pathogen discovery pipelines.<br><br>RESULTS: Full genome and partial genome sequences were assembled for several respiratory viruses including SARS-CoV-2, human coronavirus HKU1, human adenovirus 62, human metapneumovirus, human mastadenovirus B (coinfection with SARS-CoV-2), human mastadenovirus C (coinfection with SARS-CoV-2), and human parechovirus 3 (coinfection with adenovirus 62). The results showed that SARS-CoV-2 lineages correspond with lineages circulating during March 2022 to February 2023 and revealed additional viral respiratory pathogens and viruses known to be associated with HIV.<br><br>CONCLUSIONS: These preliminary results suggest that continued genomic surveillance efforts are needed for data-driven decisions on force health protection, prevention of emerging respiratory infections, and mitigation of impacts on military readiness caused by infectious diseases.}, }
@article {pmid40983948, year = {2025}, author = {Zafeiropoulos, H and Delopoulos, EIM and Erega, A and Schneider, A and Geirnaert, A and Morris, J and Faust, K}, title = {microbetag: simplifying microbial network interpretation through annotation, enrichment tests, and metabolic complementarity analysis.}, journal = {Genome biology}, volume = {26}, number = {1}, pages = {292}, pmid = {40983948}, issn = {1474-760X}, support = {101000309//Horizon 2020/ ; 101000309//Horizon 2020/ ; 9017//EMBO Scientific Exchange Grant/ ; }, mesh = {*Software ; *Metabolic Networks and Pathways ; Molecular Sequence Annotation ; Metagenome ; Databases, Genetic ; *Microbiota ; }, abstract = {Microbial co-occurrence network inference is often hindered by low accuracy and tool dependency. We introduce microbetag, a comprehensive software ecosystem designed to annotate microbial networks. Nodes, representing taxa, are enriched with phenotypic traits, while edges are enhanced with metabolic complementarities, highlighting potential cross-feeding relationships. microbetag's online version relies on microbetagDB, a database of 34,608 annotated representative genomes. microbetag can be applied to custom (metagenome-assembled) genomes via its stand-alone version. MGG, a Cytoscape app designed to support microbetag, offers a streamlined, user-friendly interface for network retrieval and visualization. microbetag effectively identified known metabolic interactions and serves as a robust hypothesis-generating tool.}, }
@article {pmid40983296, year = {2025}, author = {Yang, T and Han, Y and Zhang, M and Li, L and Chen, M and Li, N and Wang, X}, title = {Quorum sensing enhances extracellular electron uptake of electrotrophic biofilm via metabolic cascade for aerobic biochemical oxygen demand sensing.}, journal = {Bioresource technology}, volume = {439}, number = {}, pages = {133363}, doi = {10.1016/j.biortech.2025.133363}, pmid = {40983296}, issn = {1873-2976}, abstract = {Electrotrophic biocathodes enable rapid biochemical oxygen demand (BOD) sensing but face challenges like slow colonization, low current, and poorly understood microbial interactions. This study employed exogenous quorum sensing signals (C6-HSL and 3O-C12-HSL) to enhance biofilm development on oxygen-reducing biocathodes. These two N-acyl-homoserine lactones (AHLs) accelerated formation and boosted current density 5-6 times. Candidatus Tenderia served as key electrotrophs, while non-electroactive Moheibacter promoted early adhesion and extracellular polymeric substance (EPS) production. Metagenomics showed upregulation of genes related to iron metabolism, adhesion, and electron transfer, alongside increased fulvic-like shuttle secretion. A cascade model was proposed: AHLs initiate non-electrotrophic EPS production, facilitating electrotrophs colonization and electron transfer. AHL-enhanced biofilm showed improved BOD sensing sensitivity and linearity, providing a new strategy and mechanistic basis for developing efficient biocathode biosensors.}, }
@article {pmid40983295, year = {2025}, author = {Shi, X and Yasuda, S and Tuohy, M and Wang, Z and Hu, Y and Trably, E and Lens, PNL and Zhan, X}, title = {Decoding butyrate fermentation with glucose as a model substrate: Parameter optimization and metagenomic insights.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {133365}, doi = {10.1016/j.biortech.2025.133365}, pmid = {40983295}, issn = {1873-2976}, abstract = {Selective butyrate production via anaerobic fermentation holds promise for sustainable biochemicals. Despite butyrate frequently accumulate in anaerobic systems, its mechanisms and optimal conditions remain unclear. To address this gap, batch experiments with glucose were conducted to explore the effect of pH (4.5-7.0 and 8.5-11.0), temperature (37 °C and 55 °C) and inoculum-to-substrate ratio (ISR; 3:1, 2:1, 1:1, 1:2, and 1:3) on butyrate production. The results indicated that the optimal conditions were pH 5.5, 37 °C, and an ISR of 1:3, refining previously inconsistent reports. Metagenomic analysis demonstrated that temperature and ISR significantly influenced microbial communities, identifying key butyrate producers: Clostridium, Caproicibacter, Caproicibacterium, Sporolactobacillus, and Ethanoligenens. The functional gene analysis revealed enriched reverse β-oxidation genes under optimal conditions, highlighting the key role of carbon chain elongation in butyrate production. These findings provide mechanistic insights into butyrate biosynthesis and practical strategies for improving selective butyrate production in anaerobic fermentation.}, }
@article {pmid40982389, year = {2025}, author = {Pizzini, JD and Midani, FS and Britton, RA}, title = {Updated Protocol for the Assembly and Use of the Minibioreactor Array (MBRA).}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {223}, pages = {}, doi = {10.3791/68788}, pmid = {40982389}, issn = {1940-087X}, mesh = {*Bioreactors/microbiology ; *Microbiota/physiology ; Humans ; }, abstract = {The human microbiome comprises diverse and dynamic microbial communities that play essential roles in host health. Understanding these communities and their responses to environmental factors is critical for advancing microbiome-based therapeutics. Traditional in vitro models for cultivating human-derived microbiota often lack scalability and require extensive technical expertise, limiting their accessibility and throughput. To address these limitations, we developed the Minibioreactor Array (MBRA) system -- a modular, single-stage, continuous-flow platform for high-throughput cultivation of microbial communities. This system enables parallel cultivation of up to 48 distinct microbial communities, supporting experimental flexibility while maintaining the stable growth of complex ecosystems. This protocol provides detailed guidance on MBRA fabrication, assembly, sterilization, and operation. The system's modular design allows for easy integration into anaerobic chambers and supports customization for a wide range of experimental applications. It has been used to study microbial responses to antibiotics, dietary compounds, and pathogen invasion, and to screen for pathogen-resistant communities. With its accessibility, scalability, and reproducibility, the MBRA represents a powerful model system for investigating microbial interactions and advancing microbiome research.}, }
@article {pmid40982108, year = {2025}, author = {Saini, K and Kumar, SS and Kumar, V and Bajar, S}, title = {Demonstrated role of sulfate-reducing bacterial consortia in anaerobic paracetamol biodegradation.}, journal = {Biodegradation}, volume = {36}, number = {5}, pages = {91}, pmid = {40982108}, issn = {1572-9729}, support = {SR/PURSE/2022/126(G)//Department of Science and Technology (DST) PURSE Grant, New Delhi, India/ ; }, mesh = {*Acetaminophen/metabolism ; Biodegradation, Environmental ; *Microbial Consortia ; *Sulfates/metabolism ; Anaerobiosis ; *Bacteria/metabolism/genetics/classification ; *Water Pollutants, Chemical/metabolism ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The escalating global production and usage of paracetamol (C8H9NO2), a widely administered analgesic and antipyretic pharmaceutical, has led to its ubiquitous presence in environmental matrices, including surface waters, municipal wastewater, and even potable water sources. Owing to its persistence and bioaccumulative potential, paracetamol poses a significant ecotoxicological threat, particularly through trophic transfer in aquatic ecosystems. Conventional wastewater treatment methods often fall short in completely eliminating such micropollutants. In this context, bioremediation offers a promising, sustainable, and cost-effective alternative for pharmaceutical remediation. This study investigates the anaerobic degradation potential of two sulfate-reducing bacterial consortia, designated Consortium I and Consortium II, isolated from Okhla landfill leachate and enriched with distinct Postgate media formulations. Paracetamol was introduced at varying concentrations (50-500 mg/L), with and without supplementation of an auxiliary carbon source, sodium lactate. Metagenomic profiling via 16S rRNA sequencing revealed that Consortium I was primarily composed of Clostridium (40.1%) and Acidipropionibacterium (31.2%), whereas Consortium II exhibited a dominant presence of Clostridium (80.3%) and Bacillus (7.99%). Consortium II exhibited superior degradation kinetics, achieving complete removal of 500 mg/L paracetamol in 48 h under lactate-free conditions. Conversely, the presence of sodium lactate significantly attenuated degradation efficiency, suggesting substrate competition and metabolic preference. Gas chromatography-mass spectrometry (GC-MS) identified 4-aminophenol and hydroquinone as transient intermediates, supporting a proposed anaerobic degradation pathway for paracetamol. These findings underscore the potential of native sulfate reducing bacterial consortia in the bioremediation of contaminants and provide mechanistic insight into anaerobic paracetamol degradation, offering a viable strategy for enhanced treatment efficacy of contaminated waste streams.}, }
@article {pmid40981677, year = {2025}, author = {Liu, X and Li, P and Bao, K and Wang, Y and Wang, H and Wang, Y and Jiang, Z and Yang, Y and Yuan, S and Kappler, A and Wang, Y}, title = {Synergistic interaction between microbial nitrogen fixation and iron reduction in the environment.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf212}, pmid = {40981677}, issn = {1751-7370}, abstract = {Nitrogen and iron are essential yet often limiting nutrients in many ecosystems. Microbial nitrogen fixation by diazotrophs and dissimilatory ferric iron reduction are key processes that sustain nitrogen and iron availability. However, their interactions are not well understood. Here, we demonstrate a synergistic relationship between microbial nitrogen fixation and ferric iron reduction, observed in both laboratory cultures and environmental samples. In diazotrophic ferric iron-reducing bacteria, including Klebsiella grimontii N7 and Geobacter sulfurreducens PCA, nitrogen fixation enhanced heterotrophic ferric iron-reducing rates by 14.7- and 2.69-fold, respectively, and ferric iron reduction concurrently increased 15N2 fixation by up to 100%. A similar synergy was observed in an interspecies system comprising the diazotroph Azospirillum humicireducens SgZ-5 T and the dissimilatory ferric iron-reducing bacterium Shewanella oneidensis MR-1. Transcriptomic analysis revealed that nitrogen fixation upregulated pathways involved in carbon and nitrogen metabolism, including amino acid biosynthesis, glycolysis, and the tricarboxylic acid cycle (P < 0.01), thereby accelerating ferric iron reduction through nitrogen supply. In turn, ferric iron reduction stimulated organic carbon oxidation, generating the energy and reducing equivalents needed for microbial nitrogen fixation. These findings were further validated through microcosm experiments and meta-omics analyses of environmental samples from aquifers, marine sediments, hot springs, and soils, providing new insights into the coupled nitrogen, iron, and carbon cycles in natural ecosystems.}, }
@article {pmid40981431, year = {2025}, author = {Schwarzer, S and Bäcker, LE and Nijland, JG and Hayani Aji, I and de Jong, A and Moraru, C and Steglich, C and Quax, TEF}, title = {The infection cycle of the haloarchaeal virus HFTV1 is tightly regulated and strongly inhibits motility of its host.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0070425}, doi = {10.1128/msystems.00704-25}, pmid = {40981431}, issn = {2379-5077}, abstract = {Although viruses have been shown to infect all domains of life, our understanding of the genetic program behind the exploitation of host resources to produce progeny virions is thus far limited to several bacterial viruses. Therefore, to elucidate the transcriptome of euryarchaeal viruses and their hosts, we employed RNAseq analysis of samples taken at different time points from Haloferax gibbonsii LR2-5 cultures infected with the lytic model virus Haloferax tailed virus 1 (HFTV1). While following the transcription of viral genes throughout the infective life cycle, we observed a tight temporal regulation of viral transcripts and differential expression from within viral gene clusters. Furthermore, antisense RNAs (asRNAs) appear to play an important role in support of the timing of late-expressed viral genes. Therefore, with many differentially expressed transcripts, including intragenic transcripts and asRNAs, the regulatory machinery employed by HFTV1 contrasts with that of viral model systems (based on phages), in which antitermination and/or alternative polymerases (seemingly lacking in HFTV1) are more widespread. When examining differentially expressed host genes, we observed a strong downregulation of genes involved in motility, such as those encoding the archaellum and chemotaxis machinery, which was confirmed by swimming assays of HFTV1 infected cells. This might be a strategy of the virus to redirect energy flowing into movement toward the production of virions. In conclusion, this work provides a stepping stone for further exploration of the intriguing strategies of viral transcriptional regulation throughout their infection cycle across the domains of life.IMPORTANCEViruses infect members of all three domains of life, including Archaea. Euryarchaea are widespread microorganisms found in various environments, such as the human gut and solar salterns. Due to the exceptional availability of cell biology and genetic tools for some salt-loving archaea, they serve as a model system from which insights can be extrapolated. Insights into the regulation of viral infections are of particular importance, especially since HFTV1 has been adopted as a model virus by the archaeal viral community. We found that, while harboring parallels with bacterial viruses, such as tight temporal regulation, HFTV1 harbors an impressive number of differentially expressed transcriptional units. Furthermore, antisense RNAs and intragenic regulatory elements seem to play a much more prominent role in HFTV1 gene expression. Thus, this work challenges current models and provides valuable new insights into the gene regulation of viral infection of archaea, which mark similarities and differences with viruses from other domains of life.}, }
@article {pmid40981429, year = {2025}, author = {Ferretti, P}, title = {The gut remembers: the long-lasting effect of medication use on the gut microbiome.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0107625}, doi = {10.1128/msystems.01076-25}, pmid = {40981429}, issn = {2379-5077}, abstract = {Growing evidence suggests that antibiotics and many human-targeted medications can alter the gut microbiome composition, but the persistence of these effects remains unclear. In their article, Aasmets and colleagues (O. Aasmets, N. Taba, K. L. Krigu, R. Andreson, et al., mSystems e00541-25, 2025, https://doi.org/10.1128/msystems.00541-25) leveraged electronic health records (EHR) and stool metagenomic data from 2,509 individuals to assess the impact of past medication use (up to 5 years prior to sampling) on the gut microbiome composition. They found that nearly half of the 186 tested drugs had long-term effects, with antibiotics, beta-blockers, benzodiazepine derivatives, proton-pump inhibitors, and antidepressants associated with microbiome changes that persisted for years after intake. For some medications, the effects were additive, with greater impact observed after repeated use. Overall, the authors highlight how medication use in the years preceding sample collection represents an often overlooked confounding factor in microbiome studies and emphasize the utility of combining EHR with microbiome data to assess the impact of past medication use.}, }
@article {pmid40981420, year = {2025}, author = {Wing, AJ and Hegarty, B and Bastien, GE and Denef, VJ and Evans, J and Dick, GJ and Duhaime, MB}, title = {Tracking putative Microcystis viruses and virus-host associations across distinct phases of a Microcystis-dominated bloom.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0057525}, doi = {10.1128/msystems.00575-25}, pmid = {40981420}, issn = {2379-5077}, abstract = {Viruses significantly impact microbial community composition and function. Yet their role in the fate of freshwater cyanobacterial harmful algal blooms (cHABs), an increasing threat to freshwater systems, remains poorly understood. Here, we address this with a metagenomic analysis of viruses of bloom-forming Microcystis aeruginosa through a seasonal cHAB in the western basin of Lake Erie. We identified globally distributed Microcystis viruses in Lake Erie based on sequence homology to well-studied isolates. A machine-learning model was then used to predict associations between uncharacterized viral populations and the Microcystis and non-Microcystis hosts of the cHAB. Size fractionation of water samples allowed us to identify significant fraction-specific trends in Microcystis viral diversity that corresponded with Microcystis genetic diversity. Viral diversity was highest in the non-colony-associated fraction and lowest in the colony-associated fraction, suggesting that colony formation may lead to bottlenecks in viral diversity in cHABs. Significant turnover of predicted Microcystis virus populations was observed through time, but not between stations miles apart. The virus-host networks revealed extensive interconnectivity and the potential for virus-mediated cross-species genetic exchange. The networks predicted that Lake Erie Microcystis viruses infect hosts spanning phyla, in agreement with lab studies in other systems but challenging previous notions of "narrow" host-virus associations in this genus. Abundant Microcystis virus genes revealed a potential role in key metabolic pathways and host adaptation. These findings advance our understanding of Microcystis viruses and their potential influence on host metabolism, species interactions, and coevolution in Microcystis-dominated cHABs.IMPORTANCEUnderstanding associations between viruses, their hosts, and environmental factors is key for identifying the mechanisms behind the rise and fall of cyanobacterial harmful algal blooms. This study explores the diversity and host ranges of viruses predicted to infect Microcystis, reporting how these properties vary over time, across sample stations in western Lake Erie, and among different filter size fractions. We found that Microcystis virus diversity is highest in non-colony-associated fractions and the lowest in colony-associated fractions, suggesting a link between Microcystis colony formation and reduced viral diversity. We identify abundant genes belonging to predicted Microcystis viruses and their potential roles in key metabolic pathways and adaptation to environmental changes. These findings enhance our understanding of the interplay among viruses, Microcystis, and co-occurring bacteria in cHABs, offering insights into the mechanisms driving bloom dynamics, species interactions, and coevolutionary processes.}, }
@article {pmid40981185, year = {2025}, author = {Ardila, CM and Pineda-Vélez, E and Vivares-Builes, AM}, title = {Transcriptomic and Metagenomic Biomarkers in Peri-Implantitis: A Systematic Review, Diagnostic Meta-Analysis, and Functional Meta-Synthesis.}, journal = {Medical sciences (Basel, Switzerland)}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/medsci13030187}, pmid = {40981185}, issn = {2076-3271}, mesh = {*Peri-Implantitis/genetics/diagnosis/metabolism ; Humans ; *Biomarkers/metabolism ; *Metagenomics/methods ; *Transcriptome/genetics ; Machine Learning ; Computational Biology ; }, abstract = {Background/Objectives: Evidence from transcriptomic and histopathologic studies has revealed that peri-implantitis lesions are characterized by deeper inflammatory infiltration, increased immune cell accumulation, and distinctive molecular signatures. This systematic review aimed to evaluate the diagnostic and pathophysiological potential of transcriptomic, metagenomic, and bioinformatic biomarkers in peri-implantitis by integrating findings from bioinformatics and machine learning-based studies. The dual objective was to identify biologically relevant markers and assess the accuracy of predictive models, addressing diagnostic gaps in peri-implant disease management. Methods: Eligible designs included cross-sectional, case-control, and cohort studies. Literature searches were conducted across PubMed, EMBASE, Scielo, and Scopus, with independent screening, data extraction, and quality assessment. Functional meta-synthesis was used to thematically organize biomarkers and pathways, while diagnostic meta-analysis pooled ROC-AUC values to assess model performance. Results: Eleven studies met the inclusion criteria. Functional synthesis revealed five recurring biomarker themes: innate and adaptive immune responses, immune cell infiltration, fibroblast activation, and ceRNA regulation. A meta-analysis of six studies reported a pooled AUC of 0.91 (95% CI: 0.88-0.93) with I[2] = 0%, indicating no heterogeneity, supporting the reliability of ML-based models in distinguishing peri-implantitis from healthy conditions. Sources of variation included differences in validation strategies and data preprocessing. Conclusions: Integrating transcriptomic, metagenomic, and bioinformatic biomarkers with machine learning may enable earlier and more accurate diagnosis of peri-implantitis. The identified biomarkers highlight molecular and microbial pathways linked to inflammation and tissue remodeling, underscoring their potential as diagnostic indicators and therapeutic targets with translational relevance.}, }
@article {pmid40981149, year = {2025}, author = {Medina-Martínez, I and Gil-Gutiérrez, R and García-García, J and de la Hera-Fernández, FJ and Navarrete-Navarrete, N and Zamora-Pasadas, M and Ortego-Centeno, N and Callejas-Rubio, JL and García-García, F and Gálvez-Peralta, J and Rodríguez-Nogales, A and Correa-Rodríguez, M and Rueda-Medina, B}, title = {Association of Gut Dysbiosis with Disease Phenotype and Treatment in Systemic Lupus Erythematosus.}, journal = {Medical sciences (Basel, Switzerland)}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/medsci13030151}, pmid = {40981149}, issn = {2076-3271}, support = {20.000 &#x20ac;//B-CTS-100-UGR20, Consejer&#xed;a de Econom&#xed;a, Innovaci&#xf3;n y Ciencia de la Junta de Andaluc&#xed;a I+D+i Programa operativo FEDER Andaluc&#xed;a 2014-2020/ ; }, mesh = {Humans ; *Lupus Erythematosus, Systemic/microbiology/drug therapy/complications ; *Dysbiosis/microbiology/complications ; Female ; *Gastrointestinal Microbiome/genetics ; Male ; Adult ; Middle Aged ; Phenotype ; Feces/microbiology ; Case-Control Studies ; }, abstract = {Introduction: Gut dysbiosis has been associated with the development of autoimmune diseases, including systemic lupus erythematosus (SLE). Although previous studies suggest microbial alterations in SLE, evidence at the species level and its clinical relevance remain limited. This study aimed to characterise the gut microbiota at species level in SLE patients and evaluate its association with clinical features. Materials and methods: A total of 57 SLE patients and 57 matched controls were included. Faecal samples were collected using the OMNIgene-GUT kit, and microbial DNA was extracted with the Maxwell RSC PureFood GMO kit. Metagenomic sequencing was performed using the Illumina MiSeq platform, and the data was analysed with QIIME2. Microbial diversity and relative abundance were assessed using the phyloseq package, and differentially abundant taxa were identified using DESeq2. Clinical subgroups among SLE patients were identified via k-means clustering. Results: SLE patients exhibited significantly different beta diversity compared to controls (p = 0.001), with increased abundance of Pseudomonadota (3.81% vs. 6.80%, p < 0.05) and decreased Bacteroidota (53.42% vs. 38.04%, p < 0.05). Only 10 bacterial species were consistently present across all SLE samples, including Akkermansia muciniphila, Bacteroides dorei, and Lactobacillus gasseri. Hypertensive patients and those treated with corticosteroids presented a marked depletion of key microbial taxa. Conversely, Belimumab-treated patients displayed a distinct microbiota enriched in species such as Alistipes shahii and Prevotella corporis. Conclusions: This study confirms significant gut microbiota alterations in SLE and pinpoints microbial profiles associated with clinical subgroups. These findings suggest gut dysbiosis may contribute to SLE pathogenesis and indicate biomarkers for disease stratification.}, }
@article {pmid40981112, year = {2025}, author = {Sandu, EC and Cirstoiu, C and Iordache, S and Costache, MA and Iacobescu, GL and Cursaru, A}, title = {The Ongoing Struggle to Find a Gold Standard for PJI Diagnosis.}, journal = {Reports (MDPI)}, volume = {8}, number = {3}, pages = {}, doi = {10.3390/reports8030155}, pmid = {40981112}, issn = {2571-841X}, abstract = {Periprosthetic joint infection (PJI) is a devastating complication of joint arthroplasty surgery that is difficult to both diagnose and treat. Misdiagnosing a prosthetic infection has terrible consequences for both the patient and healthcare system. No currently used diagnostic test fulfills the requirements to be considered a gold standard. This shortcoming has been overcome through the implementation of multi-criteria diagnostic protocols elaborated by societies including the Infectious Diseases Society of America, International Consensus Meeting and European Bone and Joint Infection Society, using a combination of clinical, paraclinical and molecular findings in order to achieve the best accuracy in diagnosing PJI. This review aims to survey the current state of the techniques and technologies used for the diagnosis of PJI, investigating the accuracies of serum biomarkers (e.g., C-reactive protein, Interleukin-6, procalcitonin, D-dimers, Serum Intercellular Adhesion Molecule-1), synovial biomarkers (e.g., Antimicrobial peptides, lipocalin-2, leukocyte esterase, calprotectin), tissue biomarkers (e.g., Toll-like receptors, CD15) and advanced molecular techniques (e.g., Polymerase chain reaction, Metagenomic next-generation sequencing), as well as describing their ongoing limitations. In the search for an accurate, inexpensive and fast diagnostic test for PJI, we conclude that the accuracies of the currently studied biomarkers could be further enhanced through the development of novel detection technologies.}, }
@article {pmid40980884, year = {2025}, author = {Robinson, CRP and Dolezal, AG and Liachko, I and Newton, ILG}, title = {Hi-C-resolved metagenomics reveals host range variation among mobile genetic elements within the European honey bee.}, journal = {mBio}, volume = {}, number = {}, pages = {e0224325}, doi = {10.1128/mbio.02243-25}, pmid = {40980884}, issn = {2150-7511}, abstract = {Mobile genetic elements (MGEs), such as plasmids and bacteriophages, are major contributors to the ecology and evolution of host-associated microbes due to symbiotic interactions and gene flow via horizontal gene transmission. Antibiotic resistance genes (ARGs), which are frequently trafficked via MGEs, are known to be enriched within North American honey bee microbiomes due to decades of antibiotic exposure. While previous studies have identified nearly identical MGE-associated ARGs across geographically disparate honey bee colonies, our understanding of how ARGs are distributed and mobilized within and between individual microbiomes is limited. To address this limitation, we leverage Hi-C-resolved metagenomics with the honey bee worker gut microbiome and show that the worker gut contains dense, nested, and highly distinct MGE communities. We show that phage-microbe networks exhibit high variation among individual metagenomes and that phages show broad host range with respect to both the number and phylogenetic distance of their hosts. Comparisons of individual microbiomes reveal highly individualized plasmid communities that exhibit broad host range variation within microbiomes. Finally, we provide specific evidence that antibiotic resistance cassettes are being actively shuttled between honey bee microbes via plasmids and that these broad host range plasmids frequently recombine to share gene content. Our work corroborates early observations of ARG dispersal in honey bee colonies and provides evidence for how these genes are mobilized within and across honey bee-associated microbial communities.IMPORTANCEMobile genetic elements (MGEs) are found in every microbial community and often encode genes conferring antibiotic resistance (ARGs). Within the honey bee worker gut microbiome, ARGs are particularly frequent due to decades of antibiotic exposure. Previous studies have identified nearly identical ARGs in geographically disparate honey bee colonies, which suggests recent mobilization by MGEs into these colonies, but identifying how these ARGs are mobilized and distributed within honey bee colonies remains a challenging task, as most techniques rely on microbial culture. Applying metagenomic Hi-C, we describe how these ARGs are distributed among individual plasmid backbones and how those plasmids are distributed among host microbial populations. Remarkably, we find plasmids exhibit broad host range variation, although they encode nearly identical ARGs. Our work corroborates earlier observations of ARG dispersal in honey bee colonies and provides further evidence for how these ARGs are mobilized across vast geographic distance.}, }
@article {pmid40980873, year = {2025}, author = {Lai, W and Alberdi, A and Leu, A and de Leon, AVP and Kobel, CM and Aho, VTE and Roehe, R and Pope, PB and Hvidsten, TR}, title = {Metabolic capabilities of key rumen microbiota drive methane emissions in cattle.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0060125}, doi = {10.1128/msystems.00601-25}, pmid = {40980873}, issn = {2379-5077}, abstract = {UNLABELLED: The rumen microbiome plays a critical role in determining feed conversion and methane emissions in cattle, with significant implications for both agricultural productivity and environmental sustainability. In this study, we applied a hierarchical joint species distribution model to predict directional associations between biotic factors and abundances of microbial populations determined via metagenome-assembled genomes (MAGs). Our analysis revealed distinct microbial differences, including 191 MAGs significantly more abundant in animals with a higher methane yield (above 24 g/kg dry matter intake [DMI]; high-emission cattle), and 220 MAGs more abundant in low-emission cattle. Interestingly, the microbiome community of the low-methane-emission rumen exhibited higher metabolic capacity but with lower functional redundancy compared to that of high-methane-emission cattle. Our findings also suggest that microbiomes associated with low methane yields are prevalent in specific functionalities such as active fiber hydrolysis and succinate production, which may enhance their contributions to feed conversion in the host animal. This study provides an alternate genome-centric means to investigate the microbial ecology of the rumen and identify microbial and metabolic intervention targets that aim to reduce greenhouse gas emissions in livestock production systems.<br><br>IMPORTANCE: Ruminant livestock are major contributors to global methane emissions, largely through microbial fermentation in the rumen. Understanding how microbial communities vary between high- and low-methane-emitting animals is critical for identifying mitigation strategies. This study leverages a genome-centric approach to link microbial metabolic traits to methane output in cattle. By reconstructing and functionally characterizing hundreds of microbial genomes, we observe that a low-methane-emission rumen harbors well-balanced, "streamlined" microbial communities characterized by high metabolic capacity and minimal metabolic overlap across populations (low functional redundancy). Our results demonstrate the utility of genome-level functional profiling in uncovering microbial community traits tied to climate-relevant phenotypes.}, }
@article {pmid40980872, year = {2025}, author = {Prokofeva, MI and Karaseva, AI and Tulenkov, AS and Klyukina, AA and Suzina, NE and Bale, NJ and Mets, A and Schleper, C and Elcheninov, AG and Kochetkova, TV}, title = {Polysaccharide-degrading archaea dominate acidic hot springs: genomic and cultivation insights into a novel Thermoproteota lineage.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0071025}, doi = {10.1128/msystems.00710-25}, pmid = {40980872}, issn = {2379-5077}, abstract = {The expansion of sequencing technologies and bioinformatics has greatly advanced our understanding of microbial "dark matter," yet the isolation of pure cultures, especially among Archaea, remains rare and challenging. Cultivation is still essential for the reliable characterization of microbial metabolism, which cannot be fully replaced by metagenomics and other omics-based approaches. Here, we report the first cultivated representatives of a deep-branching archaeal lineage previously known as Candidatus Marsarchaeota. Our phylogenomic analyses place these isolates within the phylum Thermoproteota as a novel order, Tardisphaerales. Members of Tardisphaerales dominate the prokaryotic communities in acidic hot springs below 70°C, comprising up to 40% of the total microbial population, underscoring their ecological significance. Functional genomics and culture experiments reveal a thermoacidophilic, anaerobic lifestyle, with energy metabolism based on carbohydrate fermentation, particularly of polysaccharides. This metabolic capability is supported by numerous glycosidase-encoding genes and by unprecedented metabolic versatility among thermoacidophiles. The isolates possess complete glycolysis, Entner-Doudoroff, and pentose-phosphate pathways, allowing them to utilize different sugars. Specialization in polysaccharide hydrolysis presumably provides an adaptive advantage for these slow-growing archaea, as most other heterotrophic thermoacidophiles prefer peptides or simple sugars. Furthermore, robust defense mechanisms against reactive oxygen species and persistence in acidic conditions enable Tardisphaerales to outcompete other heterotrophs and maintain dominance in these extreme habitats. The discovery and cultivation of this new order expand prokaryotic taxonomy and reveal the key players in carbon cycling in acidic geothermal ecosystems.IMPORTANCEMost of the dominant prokaryotes in natural environments remain uncultivated, and their metabolic potential and ecological role can be inferred solely from metagenomics. However, cultivation is essential for comprehensive functional characterization and identification of novel traits. Here, we describe the first cultivated representatives of the new archaeal order Tardisphaerales within the novel class Tardisphaeria (phylum Thermoproteota), a lineage abundant in acidic hot springs. Through the whole-genome reconstruction and microbiological experiments in pure cultures, we demonstrate that these archaea are metabolically distinct from the known thermoacidophiles, making them the key degraders of the complex organic matter in hot, acidic environments. Their genomes encode a diverse set of glycosidases that allow efficient polysaccharide breakdown at high temperatures and low pH, a trait with promising biotechnological applications.}, }
@article {pmid40980765, year = {2025}, author = {Xiong, R}, title = {Advancing Digital Precision Medicine for Chronic Fatigue Syndrome through Longitudinal Large-Scale Multi-Modal Biological Omics Modeling with Machine Learning and Artificial Intelligence.}, journal = {ArXiv}, volume = {}, number = {}, pages = {}, pmid = {40980765}, issn = {2331-8422}, abstract = {We studied a generalized question: chronic diseases like ME/CFS and long COVID exhibit high heterogeneity with multifactorial etiology and progression, complicating diagnosis and treatment. To address this, we developed BioMapAI, an explainable Deep Learning framework using the richest longitudinal multi-omics dataset for ME/CFS to date. This dataset includes gut metagenomics, plasma metabolome, immune profiling, blood labs, and clinical symptoms. By connecting multi-omics to a symptom matrix, BioMapAI identified both disease- and symptom-specific biomarkers, reconstructed symptoms, and achieved state-of-the-art precision in disease classification. We also created the first connectivity map of these omics in both healthy and disease states and revealed how microbiome-immune-metabolome crosstalk shifted from healthy to ME/CFS.}, }
@article {pmid40980756, year = {2025}, author = {Kosmopoulos, JC and Anantharaman, K}, title = {Viral Dark Matter: Illuminating Protein Function, Ecology, and Biotechnological Promises.}, journal = {ArXiv}, volume = {}, number = {}, pages = {}, pmid = {40980756}, issn = {2331-8422}, abstract = {Viruses are the most abundant biological entities on Earth and play central roles in shaping microbiomes and influencing ecosystem functions. Yet, most viral genes remain uncharacterized, comprising what is commonly referred to as "viral dark matter." Metagenomic studies across diverse environments consistently show that 40-90% of viral genes lack known homologs or annotated functions. This persistent knowledge gap limits our ability to interpret viral sequence data, understand virus-host interactions, and assess the ecological or applied significance of viral genes. Among the most intriguing components of viral dark matter are auxiliary viral genes (AVGs), including auxiliary metabolic genes (AMGs), regulatory genes (AReGs), and host physiology-modifying genes (APGs), which may alter host function during infection and contribute to microbial metabolism, stress tolerance, or resistance. In this review, we explore recent advances in the discovery and functional characterization of viral dark matter. We highlight representative examples of novel viral proteins across diverse ecosystems including human microbiomes, soil, oceans, and extreme environments, and discuss what is known, and still unknown, about their roles. We then examine the bioinformatic and experimental challenges that hinder functional characterization, and present emerging strategies to overcome these barriers. Finally, we highlight both the fundamental and applied benefits that multidisciplinary efforts to characterize viral proteins can bring. By integrating computational predictions with experimental validation, and fostering collaboration across disciplines, we emphasize that illuminating viral dark matter is both feasible and essential for advancing microbial ecology and unlocking new tools for biotechnology.}, }
@article {pmid40980733, year = {2025}, author = {Thoppil, R and Blain, S and Zhang, R and Guéneuguès, A and Crispi, O and Catala, P and Marie, B and Obernosterer, I}, title = {Response of marine microbes to iron contained in colloids of glacial origin: a Kerguelen Island case study.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf093}, pmid = {40980733}, issn = {2730-6151}, abstract = {The trace element iron (Fe) is a major constraint for microbially mediated processes in the Southern Ocean. The accelerated melting of glaciers could present a novel source of Fe, but whether glacial Fe is bioavailable to marine microbes is not known. We investigated the response of marine heterotrophic prokaryotes to Fe contained in colloids (20-200 nm) of glacial origin collected on Kerguelen Island (Southern Ocean). We followed prokaryotic growth in incubation experiments amended with colloids of either glacial or nonglacial origin and determined community composition and the abundance of genes involved in Fe-related processes in metagenomes and metagenome-assembled genomes (MAGs) at the final time point. Prokaryotic taxa belonging to Vibrionaceae and Pseudomonadaceae accounted together for 32% to 67% of the relative abundances in the glacial colloid-amended treatments, while Rhodobacteraceae, Flavobacteriaceae, and Alteromonadaceae were the dominant contributors to the communities in the incubations amended with nonglacial colloids. Metagenomic analysis revealed a higher abundance of genes involved in the biosynthesis of the siderophores pyoverdine and vibrioferrin as well as their respective transporters in the presence of glacial colloids compared to nonglacial colloids. Genes for the transport of both siderophores were present in diverse MAGs, while biosynthesis genes were detected in fewer MAGs. Our results suggest that the utilization of siderophores facilitates access to Fe from glacial colloids and points to the key role of specific prokaryotes in rendering this source of Fe available to Southern Ocean microbial communities.}, }
@article {pmid40980728, year = {2025}, author = {Wang, P and Peng, X and Jing, H}, title = {Diversity and ecological potentials of viruses inhabiting in the Kermadec and Diamantina trench sediments.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf147}, pmid = {40980728}, issn = {2730-6151}, abstract = {Viruses are the most abundant biological entities in marine ecosystems, playing an important role in biogeochemical cycling and the regulation of microbial dynamics. However, their assembly driving force, genomic evolution, and potential ecological functions in the hadal trench remain largely unknown. Here, 32 359 viral operational taxonomic units were derived from metagenomes of 40 sediment samples in the Kermadec and Diamantina trenches. High novelty and habitat-specific endemism of viruses based on the protein-sharing network analysis were demonstrated. Their auxiliary metabolic genes were involved in the biogeochemical cycles and compensatory metabolic process of the host inferring from the virus-host linkage prediction. Distinct viral community assembly in the two trenches and among different sampling depths was mainly driven by the stochastic processes, especially dispersal limitation. This was further proved by the low genomic mutation rates at deeper depths with potentially high hydrostatic pressures. These niche-dependent distribution patterns and genomic features together reflected the survival and adaptative strategy of viruses. This study provided new insights into the high diversity, ecological potentials, evolution, and adaptive mechanism of viruses in the deep biosphere.}, }
@article {pmid40980320, year = {2025}, author = {Wang, YL and Xu, XQ and Long, YY and Cheng, YL}, title = {Characterization of gut microbiota and metabolites in individuals with constipation-predominant irritable bowel syndrome.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1617288}, pmid = {40980320}, issn = {1664-302X}, abstract = {OBJECTIVE: Constipation-predominant irritable bowel syndrome (IBS-C) is a prevalent functional gastrointestinal disorder with an incompletely understood pathogenesis. Recent studies have found that gut microbiota may contribute to its development. This study aimed to characterize the gut microbiota and associated metabolites in individuals with IBS-C to investigate potential pathogenic mechanisms.<br><br>METHODS: A total of 22 individuals diagnosed with IBS-C and 22 healthy controls were recruited at the First Hospital of Tsinghua University between January and December 2023. Stool samples were collected and subjected to metagenomic and metabolomic analyses to assess microbial composition and metabolic profiles. Bioinformatic analyses were employed to integrate and interpret the data.<br><br>RESULTS: Metagenomic sequencing results indicated no significant differences in overall gut microbial diversity between the IBS-C group and healthy individuals (p > 0.05). However, six bacterial species exhibited differential abundance. Notably, the relative abundance of beneficial taxa such as Megasphaera elsdenii, Bifidobacterium bifidum, and Alistipes inops was significantly reduced in the IBS-C group (p < 0.05). Metabolomic profiling demonstrated that differential metabolites were primarily enriched in pathways related to 3 short-chain fatty acids (SCFA) metabolism. SCFA levels were significantly downregulated in individuals with IBS-C, and a trend toward increased levels of the pro-inflammatory metabolite leukotriene D5 was observed.<br><br>CONCLUSION: Individuals with IBS-C demonstrate gut microbiota dysbiosis, characterized by reduced abundance of specific probiotic species and altered SCFA metabolism, along with potential low-grade inflammatory activity. These findings offer insights into the pathophysiological mechanisms of IBS-C and may inform the development of new therapeutic strategies.}, }
@article {pmid40980315, year = {2025}, author = {Jiang, Y and Zhang, X and Li, M and Yang, J and Zhang, Y and Qin, S and Feng, W}, title = {Microbial network properties and functional gene diversity drive soil multifunctionality during biocrust succession.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1656706}, pmid = {40980315}, issn = {1664-302X}, abstract = {INTRODUCTION: Biocrusts are critical components of desert ecosystems, performing vital functions including soil stabilization, nutrient enrichment, and regulation of carbon (C) and nitrogen (N) cycles. This study investigated the microbial mechanisms underlying biocrust-mediated soil multifunctionality (SMF) in the Mu Us Desert by comparing algal-, lichen-, and moss-dominated crusts.<br><br>METHODS: We systematically sampled biocrust layers and underlying subcrust soils (0-5 cm depth), employing metagenomic sequencing and co-occurrence network analysis to characterize microbial community structures and functional properties. SMF was quantified using an integrative index based on ten parameters associated with C, N, and phosphorus (P) cycling processes.<br><br>RESULTS: Results revealed significant variation in SMF among biocrust types, with moss crusts exhibiting the highest level, followed by lichen and algal crusts. Microbial community characteristics indicated that although lichen crusts showed the highest taxonomic diversity and network complexity, moss crusts showed a significant positive correlation with SMF. Network topological parameters, particularly network density within the biocrust layers, correlated significantly positively with SMF (p < 0.05), contrasting with the non-significant relationship observed for taxonomic diversity. Functional gene analysis revealed that the diversity of C degradation and N cycling genes exhibited a significant positive correlation with SMF.<br><br>DISCUSSION: Our findings demonstrate that biocrusts enhance SMF primarily by mediating both direct and indirect effects on N cycling functional gene diversity and microbial network complexity. This study underscores the critical role of functional gene diversity in driving biocrust-mediated ecological functions in desert ecosystems and provides a theoretical framework for developing sustainable land management and ecological restoration strategies in drylands.}, }
@article {pmid40979678, year = {2025}, author = {Farkas, C and Guerra, M and Heredia, AA and Castro, JF}, title = {Comparative metagenomics of wild and cultivated Fragaria chiloensis reveals major rhizosphere microbiome shifts linked to stress adaptation.}, journal = {Current research in microbial sciences}, volume = {9}, number = {}, pages = {100460}, pmid = {40979678}, issn = {2666-5174}, abstract = {Fragaria chiloensis ssp. chiloensis, endemic to Chile, includes a wild form (f. patagonica) and a cultivated "white strawberry" (f. chiloensis) historically grown in central-south Chile. In this study high throughput metagenomic sequencing was employed to examine the rhizosphere microbial communities of wild and cultivated plants were examined to explore how domestication has shaped microbial structure and function. This enabled binning and functional annotations indicating that wild rhizospheres were dominated by Frankia and Bradyrhizobium, whereas cultivated samples exhibited broader genus-level diversity yet preserving a core ecological function through functional redundancy. Metabolic reconstructions further spotlight high-biomass taxa, with Frankia in wild plants and Nocardia in cultivated plants, that harbored extensive biosynthetic gene clusters, linking robust growth to specialized metabolite production and putative osmoprotection. Collectively, these findings illustrated how domestication reshapes the rhizosphere microbiome and contributes to One Health-aligned strategies for sustainable agriculture.}, }
@article {pmid40979368, year = {2025}, author = {Wang, W and Chen, X and Fang, D and Li, L and Yueda, AG and Gan, J and Deng, X and Ma, X and Chen, Y and Shi, Y and He, F and Wu, C and Yi, Z and Fu, M and Yi, J}, title = {Partial Treponema spp. as candidate probiotics for rumen methane mitigation revealed by a module-based activity index.}, journal = {Frontiers in veterinary science}, volume = {12}, number = {}, pages = {1654829}, pmid = {40979368}, issn = {2297-1769}, abstract = {INTRODUCTION: Methane emissions from ruminants, driven by methanogenic archaea, are a major source of greenhouse gases. Current strategies often rely on metagenomic (MG) abundance as a proxy for methanogenic potential, despite evidence of a disconnect with in-situ activity.<br><br>METHODS: We analyzed paired MG and meta-transcriptomic (MT) datasets from 48 bovine rumen samples. Comparative analyses were performed to assess microbial taxonomic abundance versus transcriptional activity. A Methanogenesis Pathway Expression Activity Index (MPEAI) was developed by integrating expression of four KEGG modules, and Random Forest modeling was applied to identify microbial taxa associated with MPEAI.<br><br>RESULTS: MG and MT profiles showed incongruence in both microbial community composition and diversity, with MT revealing reduced archaeal transcriptional activity. Dominant archaeal genera (Methanobrevibacter, Methanocaldococcus) were transcriptionally suppressed relative to MG abundance (p&#x202f;<&#x202f;0.001). In contrast, methanogenesis modules (M00356, M00567, M00357, M00563) exhibited higher expression in MT than MG (p&#x202f;<&#x202f;0.0001), indicating pathway-level hyperactivity despite archaeal suppression. Random Forest analysis linked MPEAI variation to several Treponema species, which showed significant negative correlations with methanogenic pathway activity (r&#x202f;= -0.36 to -0.57, p&#x202f;<&#x202f;0.01).<br><br>CONCLUSION: Rumen methanogenesis is regulated by functional pathway activity rather than archaeal abundance. The consistent negative associations of Treponema species with methanogenesis highlight their potential as probiotic candidates for methane mitigation and underscore bacterial-archaeal interactions in shaping rumen methane production.}, }
@article {pmid40979367, year = {2025}, author = {Cojkic, A and Niazi, A and Hansson, I and Morrell, JM}, title = {Variations in bacterial profiles associated with semen collection timing and bull breed, analyzed using 16S rRNA sequencing and MALDI-TOF MS.}, journal = {Frontiers in veterinary science}, volume = {12}, number = {}, pages = {1583136}, pmid = {40979367}, issn = {2297-1769}, abstract = {INTRODUCTION: Bacterial contamination can occur at multiple stages of semen processing, necessitating the use of antibiotics in bull semen preservation, mandated by regulatory guidelines. To manage antimicrobial resistance (AMR), targeted antibiotic use based on bacterial identification is essential. This study aimed to characterize bacterial communities in bull semen using metagenomic analysis and MALDI-TOF MS across different semen collection times from the same bulls and between two breeds.<br><br>METHODS: Semen samples were collected from 20 dairy bulls (8 Viking Holstein and 12 Viking Red). Each bull provided three ejaculates within a week: the first after a 96 h since previous collection (T1), the second 48&#x202f;h later (T2), and the third 24&#x202f;h after the second (T3). Bacterial species were identified through culturing on cattle blood agar, followed by MALDI-TOF MS identification. Additionally, 16S rRNA sequencing was performed to determine bacterial diversity after DNA extraction.<br><br>RESULTS: MALDI-TOF analysis identified 33 bacterial species across 60 semen samples. Six species were exclusive to Viking Holstein (VH) bulls, while 12 were specific to Viking Red (VR) bulls. Certain bacterial species were present only at specific time points: three in the first ejaculate, seven in the second, and five in the third. Across individual bulls, Bacillus spp., Proteus spp., and Staphylococcus spp. were the most consistently detected. Metagenomic analysis revealed 23 phyla and 402 genera in semen samples. Alpha diversity (Shannon index) showed a trend toward p&#x202f;=&#x202f;0.07 across the bull samples, while beta diversity significantly differed between breeds, with VH samples forming a distinct cluster and VR samples displaying greater microbiome variability. Additionally, specific genera appeared only at one collection time point: Bacteroides, Serratia, Pantoea at T1, Wolbachia, Prevotella, Peptococcus, Alloprevotella at T2, and Streptococcus, Staphylococcus, and Mycoplasma at T3. Specific genera, Acidocella and Escherichia, exhibited negative correlations with most bacterial taxa but showed a slight positive correlation with each other; while Acidocella was detected in nearly all semen samples, except for two samples.<br><br>DISCUSSION: The seminal microbiota of bulls varies over time and differs between breeds, indicating that it is influenced by a complex interaction of environmental, physiological, and host-related factors.}, }
@article {pmid40978735, year = {2025}, author = {Li, H and Cheng, Z and Li, K}, title = {Case Report: Disseminated actinomycosis-induced splenic rupture with spleen and liver abscesses.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1654793}, pmid = {40978735}, issn = {2296-858X}, abstract = {Disseminated actinomycosis is a rare, slowly progressing infection caused by Actinomyces species and can manifest as the formation of multiple abscesses and sulfur granules in infected tissues. In this report of this rare disease, the pathogens were not traced at the initial stage, and extremely rare but dangerous complications occurred, resulting in a new research perspective for the early identification of this rare disease. This study reports a case of disseminated actinomycosis in a 59-year-old Asian female with a history of lung infection. She experienced splenic rupture after mild percussion performed due to abdominal pain, accompanied by fever and sepsis; the rupture was effectively managed with conservative treatment; however, she experienced delayed splenic rupture later. Pathological examination of spleen and liver biopsy samples revealed chronic suppurative inflammation with abscesses, and the surrounding hyphae were arranged radially, the metagenome next-generation sequencing of pus shows that it belongs to Actinomyces israelii. The patient was cured with splenectomy and comprehensive treatment, including anti-infective therapy combined with imipenem/cilastatin, penicillin and antishock therapy. The results of this study emphasize the importance of etiology tracing and accurate, early treatment for the disease. Moreover, if minor trauma leads to unexpected damage to internal organs, the possibility of the coexistence of other etiologies should be considered.}, }
@article {pmid40977701, year = {2025}, author = {Ren, P and Zhao, Y and Li, X and Xie, J and Liao, X and Luo, Q and Liu, X and Li, J and Fan, Y and Cheng, X and Fu, X and Zhou, J and Wu, X}, title = {Comprehensive metagenomic and lipidomic analysis showed that baicalin could improve depressive behaviour in atherosclerotic mice by inhibiting nerve cell ferroptosis.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1599570}, pmid = {40977701}, issn = {1664-3224}, mesh = {Animals ; *Flavonoids/pharmacology/therapeutic use ; *Ferroptosis/drug effects ; *Atherosclerosis/drug therapy/metabolism/complications ; Mice ; *Depression/drug therapy/metabolism/etiology ; *Neurons/drug effects/metabolism ; Metagenomics/methods ; Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; Lipidomics/methods ; Disease Models, Animal ; Male ; Lipid Metabolism/drug effects ; Behavior, Animal/drug effects ; }, abstract = {BACKGROUND: Atherosclerosis (AS) concomitant depression is a serious clinical problem with unclear mechanisms of co-morbidity. Baicalin (BA) can resist atherosclerosis and depression by regulating intestinal flora and host lipid metabolism. Therefore, based on intestinal microorganisms and lipid metabolism, this study explored the mechanism of baicalin against AS concomitant depression.<br><br>METHODS: 16 C57BL/6 mice were fed with normal diet as blank control group. 48 ApoE[-/-]mice were randomly divided into 3 groups (model group and BAL, BAH two treatment groups). The mouse model of atherosclerosis concomitant depression was established by high-fat feeding combined with restraint stimulation for 16 weeks. Behavioural experiments and biochemical indexes were used to detect the antidepressant effect and anti-atherosclerosis effect of baicalin. Metagenomic sequencing technology combined with metabolomics analysis was used to detect the effects of BA on intestinal microflora structure and brain lipids in AS co-depressed mice. Erastin was used to induce HT-22 hippocampal neurons to construct a model of ferroptosis. The inhibition of baicalin on ferrotosis was verified by detecting the cell viability, ROS production, and expression levels of glutathione, SLC7A11, GPX4 and ACSL4 in each group.<br><br>RESULTS: Baicalin could effectively improve the indexes of AS co-depressed mice, and the results of metagenomics and lipidomics showed that there were disorders of intestinal flora represented by Helicobacter_typhlonius and Escherichia_coli and disorders of lipid metabolism represented by PE in the AS co-depressed model mice. The correlation analysis showed that the lipid metabolism disorders in the model mice were closely related to the intestinal flora disorders, and baicalin intervention could effectively improve the intestinal flora and lipid metabolism disorders in the AS co-depressed mice. Metabolic pathway enrichment analysis showed that differential lipid PEs were significantly enriched in the iron death pathway, and our further in vitro cellular experiments showed that baicalin could inhibit Erastin-induced Ferroptosis in the hippocampal neuronal cell line HT-22 by promoting the expression of SLC7A11, GSH, and GPX4, inhibiting the expression of ACSL4, and decreasing the cellular ROS.<br><br>CONCLUSION: Baicalin improves intestinal microbiota and brain lipid metabolism and inhibits ferroptosis of nerve cells, which possesses the application value of anti-atherosclerotic concomitant depression.}, }
@article {pmid40977416, year = {2025}, author = {Liu, C and Song, Y and Niu, S and Jiang, Y and Zhu, T and Li, X and Cui, R and Deng, Q}, title = {COVID-19 Infection Confirmed by Bronchoalveolar Lavage Fluid Metagenomics -Next-Generation Sequencing Instead of Pharyngeal Swabs in Follicular Lymphoma: Three-Case Report and Literature Review.}, journal = {Journal of clinical laboratory analysis}, volume = {}, number = {}, pages = {e70103}, doi = {10.1002/jcla.70103}, pmid = {40977416}, issn = {1098-2825}, support = {TJWJ2023ZD003//Tianjin Municipal Health Commission/ ; Y-NCJH202201-0027//Beijing Xisike Clinical Oncology Research Foundation/ ; Y-2022YMJN/MS-0001//Beijing Xisike Clinical Oncology Research Foundation/ ; }, abstract = {BACKGROUND: Hematologic malignancy patients with B lymphocytopenia after anti-CD20 monoclonal antibody or anti-CD19 chimeric antigen receptor (CAR) T cell therapy often face prolonged SARS-CoV-2 positivity on pharyngeal swabs and persistent or recurrent COVID-19 infection, resulting in high mortality.<br><br>METHODS: Here, we describe three follicular lymphoma (FL) patients with persistent fever, cough, and hypoxemia, but they were ruled out for bacterial, viral, fungal, and other pathogen infections, and the throat swabs were consistently SARS-CoV-2 negative. These FL patients with B lymphocyte deficiency who were diagnosed with COVID-19 infection confirmed by bronchoalveolar lavage fluid (BALF) metagenomics next-generation sequencing (mNGS). Their COVID-19 infection was characterized by differences in viral load in the upper and lower respiratory tracts. When this particular COVID-19 infection occurred, although their percentages and absolute values of CD8[+] T cells and CD4[+] T cells were normal, they all had B lymphocyte deficiency and hypogammaglobulinemia. They all had low expression of interleukin (IL)-6 in peripheral blood inconsistent with clinical infection symptoms.<br><br>RESULTS: The patients received a combination therapy of molnupiravir and methylprednisolone; then their symptoms were relieved over the next 2&#x2009;weeks-2&#x2009;months.<br><br>CONCLUSION: Therefore, for immunocompromised patients, especially those with B lymphocyte deficiency, hypogammaglobulinemia, and low expression of IL-6 in peripheral blood inconsistent with clinical infection symptoms, mNGS for BALF should be performed as soon as possible in this particular condition to confirm the diagnosis of COVID-19 infection.}, }
@article {pmid40976023, year = {2025}, author = {Wang, Y and Zhang, S and Jia, R and He, X and Li, A and Yuan, D}, title = {Higher ammonia oxidizing activity of comammox cooperates with ammonia-oxidizing bacteria to release N2O in river ecological restoration areas.}, journal = {Journal of environmental management}, volume = {394}, number = {}, pages = {127360}, doi = {10.1016/j.jenvman.2025.127360}, pmid = {40976023}, issn = {1095-8630}, abstract = {Ecological restoration techniques play a crucial role in mitigating eutrophication of urban rivers. However, it remains unclear whether and how complete ammonia oxidation (comammox) responds to nitrous oxide (N2O) emissions in the sediments of ecologically and non-ecologically restored rivers. This study investigated the occurrence and activity of comammox as well as the microbial composition and factors influencing N2O-producing pathways in rivers undergoing ecological and non-ecological restoration. The results demonstrated that comammox clade A and B bacteria were widely distributed in the habitats of ecological restoration areas, with ecological niche differences observed in the overlying water and surface sediments. Compared to the sediments from non-ecological restoration areas (0.62 ± 0.14 mg N kg[-1] day[-1]), comammox exhibited the higher activity in ecological restoration sediments, with its activity and contribution to nitrification (1.63 ± 0.35 mg N kg[-1] day[-1], 26.1 ± 5.65 %) exceeding those of ammonia-oxidizing archaea (AOA) (0.75 ± 0.17 mg N kg[-1] day[-1]; 11.85 ± 2.23 %) but lower than ammonia-oxidizing bacteria (AOB) (3.88 ± 0.34 mg N kg[-1] day[-1]; 62.05 ± 5.11 %). Although AOB in sediments of ecological restoration rivers dominated N2O production via the ammonia-driven pathway, the comammox coupled with nitrifier denitrification produced notable N2O activity (1.68 ± 0.57 μg N kg[-1] day[-1]). Metagenomic analysis revealed that key functional genes (amoA, hao, and nirK) of comammox bacteria in the sediments of ecologically restored river habitats were involved in the nitrifier denitrification process. The keystone species Ca. Nitrospira nitrificans from comammox supplied nitric oxide (NO) to Nitrosomonas europaea from AOB to produce N2O. Furthermore, cooperative production of N2O by Ca. Nitrospira nitrificans was influenced by environmental factors such as total organic matter and moisture content. This study provides new insights into the mechanisms of N2O emissions from comammox in river habitats of the ecological restoration areas.}, }
@article {pmid40975788, year = {2025}, author = {Hutton, ALK and Grigson, S and Bartle, L and Papudeshi, B and Mallawaarachchi, V and Tarasenko, A and Mitchell, JG and Edwards, RA}, title = {Picobirnavirus: how do you find where it's hiding?.}, journal = {Critical reviews in microbiology}, volume = {}, number = {}, pages = {1-11}, doi = {10.1080/1040841X.2025.2560918}, pmid = {40975788}, issn = {1549-7828}, abstract = {Picobirnaviruses (PBVs) are double-stranded RNA viruses detected in various environments and host-associated samples, including those from humans, non-human animals, invertebrates and birds. First described in human fecal material, PBVs were initially hypothesized to be human enteric pathogens. However, no definitive association with disease has been established. Their pathogenic potential remains unclear, therefore, their presence in clinical or environmental samples may reflect asymptomatic colonization, indirect association or infection of a non-human host. The PBV genome exhibits remarkably high genetic diversity both within and across its genomic segments, as well as notable variability in genetic code usage. Some PBV genomes use alternative codon assignments, raising the possibility that they infect prokaryotic or otherwise unconventional hosts. This review critically examines the experimental and bioinformatic methods used to detect PBVs and infer their host range. We distinguish between methods used for PBV genome identification (e.g. PCR, metagenomic sequencing) and those aimed at host determination (e.g. culturing attempts, codon usage bias, cloning into model systems). We also evaluate the challenges and limitations associated with each approach. Elucidating PBVs' host range is essential to understanding their biological roles and ecological significance, including potential implications for human and animal health and microbial community dynamics across ecosystems.}, }
@article {pmid40975419, year = {2025}, author = {Liu, D and Liu, Y and Wang, C and Song, M and Dou, X and Liu, X}, title = {Urbanization weakens soil carbon stocks but enhances carbon stability through coupled physicochemical and microbial mechanisms in Beijing urban-rural forests.}, journal = {Environmental research}, volume = {}, number = {}, pages = {122901}, doi = {10.1016/j.envres.2025.122901}, pmid = {40975419}, issn = {1096-0953}, abstract = {Urban forest soils are important carbon (C) pools, and their C transformation processes are influenced by environmental changes driven by rapid urbanization. However, the mechanisms underlying soil organic C (SOC) storage and stability remain unclear. In this study, we investigated forest soils along an urban-rural gradient in Beijing from the physical (soil aggregates), chemical ([13]C NMR), and microbial (metagenomic sequencing) perspectives to elucidate SOC stabilization mechanisms. We found SOC content in urban soils was 20.97% lower than in suburban forests and 31.21% in rural forests, primarily due to reduced litter input and altered C turnover. The proportion of SOC within the silt-clay fraction was increased by 23.76%, indicating greater physical protection. The relative abundance of aromatic C and alkyl C were increased by 2.27% and 2.34%, respectively, suggesting enhanced chemical recalcitrance. Microbial analysis showed a 36.48% reduction in ectomycorrhizal fungi, a 36.28% decline in oxidative enzyme activities, and a 47.36% decrease in genes related to recalcitrant degradation, while genes and enzymes targeting labile C were enriched. These shifts constrained decomposition of recalcitrant compounds, reinforcing SOC persistence. Overall, urbanization reduces SOC storage but enhances SOC stability due to promoting fine-fraction association, chemical recalcitrance, and optimizing microbial community composition. These findings provide new insights into urban soil C sequestration and feedbacks to climate change.}, }
@article {pmid40974832, year = {2025}, author = {Yuan, X and Zuo, Z and Yang, Y and Zhang, Y and Xin, X and Zuo, J}, title = {Enrichment and application of sewer-derived aerobic methanotrophs to enhance gaseous methane removal in sewers.}, journal = {Environment international}, volume = {204}, number = {}, pages = {109798}, doi = {10.1016/j.envint.2025.109798}, pmid = {40974832}, issn = {1873-6750}, abstract = {Methane emission from sewer systems persists as a dual environmental threat, combining explosion risks with potent greenhouse gas impacts. Current methane removal strategies have primarily targeted biofilm and wastewater phases by chemical dosing; however, microbial adaptation and fluctuating water quality often reduce the control efficiency, incurring high chemical costs. Here we propose and demonstrate a novel microbial approach that utilizes aerobic methanotrophs for direct gaseous methane oxidation. Sewer-derived microbes was discovered to exhibit a high methane oxidation capacity of 0.30 μmol/(h·g). The sewer-derived methanotrophs were then successfully enriched, with a high methane oxidation rate of more than 200 mg CH4/(g DCW·d). Leveraging the enriched aerobic methanotrophs, an innovative in-situ gaseous methane control strategy was developed. Methane emission reduction reached 85.6 % in a sewer reactor under prolonged operation, and microbial activity could be restored following easy and flexible reactivation treatment. Notably, hydrogen sulfide could be eliminated in this reactor, attributed to biochar-mediated adsorption and subsequent chemolithotrophic oxidation, which demonstrates the multifunctionality of the hybrid system. High-throughput sequencing and metagenomic sequencing further revealed Methylocystis (15 %-20 % relative abundance) and Methylophilus (17 %-46 % relative abundance) as core functional species that exhibit significant potential for carbon emission reduction in sewer systems. These results can demonstrate an economical and environmentally friendly solution to both gaseous methane and hydrogen sulfide removal in sewers.}, }
@article {pmid40974593, year = {2025}, author = {Xu, X and Zhang, Q and Cui, X and Liu, Y and Xu, Y and Wang, X and Wei, L and Cheng, R and Wang, W and Zhang, X and Li, F}, title = {A Novel Marine Bacterium-Derived Heparinase with High Potential for the Structure-Function Studies of Heparin/Heparan Sulfate.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.5c08686}, pmid = {40974593}, issn = {1520-5118}, abstract = {Heparinases are crucial for deciphering heparin/heparan sulfate (HP/HS) structures; yet most known heparinases from terrestrial sources share similar properties. Here, we identify a novel heparinase, HD1492, from HP-cultured marine bacterial metagenomes. Although phylogenetically classified as heparinase II, its exhibits unique enzymatic properties by preferentially cleaving sulfated regions in HP/HS and generating resistant oligosaccharides from low-sulfated HS. These oligosaccharides have a signature feature: one or several nonsulfated disaccharides linked to an N-sulfated disaccharide at the reducing end. This property enables HD1492 to reveal the distribution and composition of nonsulfated domains in HP/HS─overcoming the limitation of conventional disaccharide analysis─as validated in mouse organ-derived GAGs and the drug sulodexide. Overall, the unique enzymatic properties of HD1492 confer innovative value that distinguishes it from terrestrial heparinases, providing a much-needed tool for the resolution of HP/HS structural and functional domains and the development and quality control of related products.}, }
@article {pmid40974529, year = {2025}, author = {Tian, C and Tang, Z and Zhang, X and Yao, X and Li, Y and Zhuang, D and Luo, Y and Li, T and Bai, L and Zhao, F and Zhu, L and Shi, G and Jiang, P and Gong, Q and Zhou, H and Gao, H and Wu, Q and Sang, J and Liu, X and Li, X and Yu, L and Zhang, Z}, title = {Uncovering the gut microbiome and antibiotic resistome of mammals on the Tibetan Plateau.}, journal = {Science China. Life sciences}, volume = {}, number = {}, pages = {}, pmid = {40974529}, issn = {1869-1889}, abstract = {The mammalian species on the Tibetan Plateau are diverse and abundant, yet our understanding of their gut microbiome and antibiotic resistome remains limited. Here, we used metagenomics to analyse the gut microbiota of 2,561 mammals from the Tibetan Plateau, covering 14 species across six orders. Using de novo metagenome assembly, we reconstructed a total of 112,313 high- to medium-quality metagenomic assembly genomes (MAGs), representing 21,902 microbial species, 86% of which were unclassified. More than 8,000 nonredundant antibiotic resistance genes (ARGs) encompassing 28 types were identified in the gut microbiome of Tibetan Plateau mammals. We further conducted a risk assessment of these ARGs, identifying 334 nonredundant ARGs with high-risk characteristics related to human health. Importantly, seven cross-species horizontal gene transfer events involving high-risk ARGs were identified, three of which occurred between human and nonhuman mammalian gut microbiota. Additionally, we found that the abundance of ARGs in human gut microbiomes on the Tibetan Plateau was greater than that in those from eastern China, Europe, and the United States, whereas the abundance of ARGs in livestock gut microbiomes from the Tibetan Plateau was lower than that in livestock gut microbiomes from those regions. This study reveals that the gut microbiota of Tibetan Plateau mammals is a largely unexplored resource and a significant reservoir of ARGs, offering crucial insights into microbiome research and demonstrating potential public health implications.}, }
@article {pmid40974459, year = {2025}, author = {Guo, Y and Zhu, Y and Jiang, L}, title = {Treponema denticola as a potential pathogen of pneumonia in individuals with poor oral hygiene: a case report.}, journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {}, number = {}, pages = {}, pmid = {40974459}, issn = {1435-4373}, abstract = {Treponema denticola is an oral spirochete closely related to periodontal disease. However, the association between Treponema denticola and pneumonia has seldom been reported. In this report, we present a case wherein pneumonia attributable to Treponema denticola was identified through the application of metagenomic next-generation sequencing analysis. The patient had a history of oral operation and poor oral hygiene, which were likely the risk factors of the infection. The results indicated the association between oral microbes and pneumonia and highlighted the importance of maintaining optimal oral health.}, }
@article {pmid40974374, year = {2025}, author = {Hemnani, M and Karatas, M and Cruz, AVS and da Silva, PG and Thompson, G and Poeta, P and Rebelo, H and Matthijnssens, J and Mesquita, JR}, title = {Metagenomic analysis of viral diversity in Portuguese bats.}, journal = {Veterinary research communications}, volume = {49}, number = {6}, pages = {319}, pmid = {40974374}, issn = {1573-7446}, mesh = {Animals ; *Chiroptera/virology ; Metagenomics ; Portugal/epidemiology ; Feces/virology ; *Coronavirus/genetics/isolation &amp; purification/classification ; Spike Glycoprotein, Coronavirus/metabolism/genetics ; *Coronavirus Infections/veterinary/virology/epidemiology ; Phylogeny ; }, abstract = {Bats are highly diverse mammals and known reservoirs of numerous zoonotic viruses. Their role in the ecology of emerging infectious diseases continues to be of significant interest. This study aimed to evaluate the occurrence of coronaviruses (CoVs) in Portuguese bats and predict the affinity of their spike proteins with the aminopeptidase N (APN) receptor of several host species. The study also explored the viral diversity in bat samples using metagenomic sequencing. Ten bats (five Myotis myotis and five Miniopterus schreibersii) were captured at an underground roost in 2022 (Central Portugal), and fecal samples, oral, and anal swabs were collected (n = 27). A Pan-CoV nested RT-PCR was used for initial screening, followed by viral metagenomic sequencing of all fecal samples and one CoV-positive buccal swab. In silico protein docking studies were performed between a Portuguese bat CoV spike protein and APNs of bats, pigs, and humans. Pan-CoV nested RT-PCR identified three positive samples: two fecal samples and one buccal sample. Metagenomic sequencing allowed us to determine two near complete CoV genomes. Protein docking predicted strong binding of this spike protein to bat, porcine, and human APN receptors. Metagenomics also identified picornaviruses, adenovirus, and dependoparvovirus in fecal samples. This study reports the first near complete genome sequences of two members of the Alphacoronavirus genus from a Portuguese bat The identification of other viral families highlights the diverse virome of these cave-dwelling bat species. Protein docking studies suggest a potential for cross-species transmission of this bat CoV between bats, porcines and humans, though further research is needed to confirm these interactions.}, }
@article {pmid40974275, year = {2025}, author = {Casey, KM and Barouch-Bentov, R and Reineking, W and Alonso, FH and Moorhead, R and Fazel, M and Armien, AG and Uzal, FA and Chanin, RB and Bhatt, AS and Green, SL and Felt, SA and Nagamine, CM}, title = {Clostridium cuniculi is associated with chronic high-morbidity low-mortality diarrhea in NSG and NSG-related mouse strains.}, journal = {Veterinary pathology}, volume = {}, number = {}, pages = {3009858251372565}, doi = {10.1177/03009858251372565}, pmid = {40974275}, issn = {1544-2217}, abstract = {In October 2020, adult male and female NSG (NOD. Cg-Prkdc[scid] Il2rg[tm1Wjl]/Sz) mice were reported for diarrhea within a mouse barrier facility. Other immunodeficient strains harboring the SCID (Prkdc[scid]) or Rag (Rag[null]) mutations together with the IL2rg (Il2rg[null]) mutation were affected. At its peak, over 20 laboratories in 10/16 (62.5%) barrier rooms were affected. Mortality was rare except in lactating females (≥ P11). Grossly, nonlactating adult female and male mice (n = 16) had mild to moderate, small and large intestinal distension with corresponding individual cell death and sloughing of superficial enterocytes in the cecocolonic mucosa. Lactating NSG dams (n=6) had moderate to severe gastrointestinal distension and/or segmental, dark red to gray, small intestinal discoloration. In addition to the same histologic lesions seen in nonlactating female NSG mice, lactating NSG dams often had severe ulcerative inflammation affecting the jejunum, ileum, cecum, and colon. Traditional ancillary diagnostic tests including aerobic and anaerobic cultures (blood, liver, spleen, and intestines), fecal PCR, and fecal floatation failed to yield a causative organism. Further cohousing and oral gavage studies determined neither immunocompetent CD1 (Crl:CD1 [ICR]) mice nor immunodeficient NOD scid (NOD.Cg-Prkdc[scid]/J) and Rag2 KO (C57BL/6. Cg-Rag2[tm1.1Cgn]/J) mice were susceptible to clinical disease. Extensive control barriers were implemented including a veterinary-managed NSG breeding barrier, alterations in husbandry practices, and strategic environmental disinfection, allowing for continuity of experimental studies while avoiding widespread depopulation of the barrier. Subsequent strain-resolved metagenomics and qPCR assay development identified Clostridium cuniculi and its enterotoxin exclusively within diarrheic mice.}, }
@article {pmid40974247, year = {2025}, author = {Barouch-Bentov, R and Merrill, BD and Reineking, W and Moorhead, R and Herberg de Alonso, F and Fazel, M and Uzal, FA and Felt, SA and Sonnenburg, JL and Casey, KM and Nagamine, CM}, title = {Strain-resolved metagenomic analysis and qPCR validation suggest Clostridium cuniculi is the etiologic agent for infectious diarrhea in severely immunodeficient mice.}, journal = {Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc}, volume = {}, number = {}, pages = {10406387251378688}, doi = {10.1177/10406387251378688}, pmid = {40974247}, issn = {1943-4936}, abstract = {In late 2020, the mouse barrier facility at Stanford University experienced an outbreak of diarrhea in adult mice and sudden deaths in mid-lactation females. Affected strains were immunodeficient, carrying either the Prkdc[scid] or Rag[null] mutations and the Il2rγ[null] mutation, predominantly NOD.Cg-Prkdc[scid] Il2rγ[tm1Wjl]/SzJ (NSG) mice. The diarrhea was transmissible to naïve NSG mice by co-housing or gavage of intestinal homogenates from diarrheic mice, suggesting the involvement of an infectious agent and thus was given the name "infectious diarrhea." Conventional testing failed to identify an etiology. Strain-resolved metagenomic analyses using DNA from diarrheic and control fecal samples yielded the genome sequence of an enterotoxin-encoding Clostridium cuniculi strain, a candidate factor underlying the diarrhea outbreak. We hypothesized that the presence of C. cuniculi and its enterotoxin in fecal samples could serve as biomarkers. Quantitative real-time PCR (qPCR) assays using specific primers for C. cuniculi and its enterotoxin were generated and validated. We analyzed fecal samples from 111 NSG or NSG-related mice that were healthy, 37 that had clinical signs of infectious diarrhea, and 28 that had diarrhea attributable to known causes. Positive qPCR results for C. cuniculi and its enterotoxin only occurred in feces from mice with infectious diarrhea. All positive samples contained both C. cuniculi and its enterotoxin. Our data suggest that infectious diarrhea in these cases is mediated, at least in part, by the transmission of C. cuniculi and its enterotoxin. Our novel qPCR assays for C. cuniculi and its enterotoxin are effective tools for the detection of infectious diarrhea in NSG mice.}, }
@article {pmid40973961, year = {2025}, author = {Lin, PT and Wu, YW}, title = {Highly-accurate prediction of colorectal cancer through low abundance uncultivated genomes recovered using metagenomic co-assembly and binning approach.}, journal = {BMC cancer}, volume = {25}, number = {Suppl 2}, pages = {1418}, pmid = {40973961}, issn = {1471-2407}, support = {MOST110-2221-E-038-019-MY3//Ministry of Science and Technology, Taiwan/ ; MOST111-2221-E-038-023-MY3//Ministry of Science and Technology, Taiwan/ ; grant TMU-NTUST-108-08//Taipei Medical University-National Taiwan University of Science and Technology Joint Research Program/ ; }, mesh = {*Colorectal Neoplasms/microbiology/genetics/diagnosis ; Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Metagenome ; RNA, Ribosomal, 16S/genetics ; Asian People/genetics ; White People/genetics ; Male ; Female ; }, abstract = {BACKGROUND: Recent microbiome studies have established the association between the composition of gut microbiota and various diseases. Since 16S ribosomal RNA sequencing may suffer from problems such as lower taxonomic resolution or limited sensitivity, more and more studies embraced whole-metagenome approach, which has the potential of sequencing everything in the target microbiome, to conduct microbial association analysis. However, species profiling, which is the most popular analysis technique for whole-metagenome analysis, cannot detect uncultivated species. Since uncultivated species may also be indispensable in the gut environments, it is crucial to identify those uncultivated species and evaluate their importance in discerning disease samples from healthy ones.<br><br>RESULTS: After conducting de novo co-assembly and genome binning procedures on two colorectal cancer (CRC) cohorts, in which one of them was from the Asian population while the other was from the Caucasian population, we identified that the Asian and Caucasian cohorts shared a significant amount of microbial species in their microbiota. In addition we found that low abundance genomes may be more important in classifying disease and healthy metagenomes. By sorting the genomes based on their random forest importance scores in differentiating disease and healthy samples and cumulatively evaluating the genome subsets in predicting CRC status, we identified dozens of "important" genomes for each of the cohorts that were able to predict CRC with very high accuracy (0.90 and 0.98 AUROC for the Asian and Caucasian cohorts respectively). Uncultivated species were also identified among the selected genomes, highlighting the importance of including the uncultivated species in order to build better disease prediction models and evaluate the roles of the uncultivated species in the disease formation or progression. Finally we found that the "important" species for both cohorts did not overlap with each other, hinting that the species highly associated with CRC disease may be different between the Eastern and Western populations.<br><br>CONCLUSION: In this study we demonstrated the importance of recovering and analyzing low abundance uncultivated species to identify their associations with colorectal cancer. We hope this work shed new light on a more comprehensive understanding of how our gut microbes are correlated with diseases.}, }
@article {pmid40973790, year = {2025}, author = {Bignaud, A and Conti, DE and Thierry, A and Serizay, J and Labadie, K and Poulain, J and Cheny, O and Colón-González, M and Debarbieux, L and Guerrero-Osornio, M and Helaine, S and Hill, P and Le Tinier, G and Millot, GA and Morales, L and Parada, A and Riera, N and Iraola, G and Koszul, R and Marbouty, M}, title = {Phages with a broad host range are common across ecosystems.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {40973790}, issn = {2058-5276}, support = {ANR-20-CE92-0048//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-20-CE92-0048//Agence Nationale de la Recherche (French National Research Agency)/ ; 16-JPEC-0003-05//Agence Nationale de la Recherche (French National Research Agency)/ ; FSGSK_1_2019_1_159735//Agencia Nacional de Investigaci&#xf3;n e Innovaci&#xf3;n (National Agency for Research and Innovation)/ ; FSGSK_1_2019_1_159735//Agencia Nacional de Investigaci&#xf3;n e Innovaci&#xf3;n (National Agency for Research and Innovation)/ ; FSGSK_1_2019_1_159735//Agencia Nacional de Investigaci&#xf3;n e Innovaci&#xf3;n (National Agency for Research and Innovation)/ ; }, abstract = {Phages are diverse and abundant within microbial communities, where they play major roles in their evolution and adaptation. Phage replication, and multiplication, is generally thought to be restricted within a single or narrow host range. Here we use published and newly generated proximity-ligation-based metagenomic Hi-C (metaHiC) data from various environments to explore virus-host interactions. We reconstructed 4,975 microbial and 6,572 phage genomes of medium quality or higher. MetaHiC yielded a contact network between genomes and enabled assignment of approximately half of phage genomes to their hosts, revealing that a substantial proportion of these phages interact with multiple species in environments as diverse as the oceanic water column or the human gut. This observation challenges the traditional view of a narrow host spectrum of phages by unveiling that multihost associations are common across ecosystems, with implications for how they might impact ecology and evolution and phage therapy approaches.}, }
@article {pmid40973705, year = {2025}, author = {Boodman, C and Cimen, C and Yansouni, CP and Cheng, MP}, title = {Culture Clash: Dual-Pathogen Endocarditis and the Metagenomic Next Generation Sequencing Studies We Need.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {}, number = {}, pages = {}, doi = {10.1093/cid/ciaf518}, pmid = {40973705}, issn = {1537-6591}, }
@article {pmid40973697, year = {2025}, author = {Khalil, S and Sohail, MR}, title = {Metagenomic Next Generation Sequencing and Cardiovascular Infections: Promise and Pitfalls of Polymicrobial Detection.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {}, number = {}, pages = {}, doi = {10.1093/cid/ciaf519}, pmid = {40973697}, issn = {1537-6591}, }
@article {pmid40972887, year = {2025}, author = {Hitch, TCA and Bosch, J and Bolsega, S and Deschamps, C and Etienne-Mesmin, L and Treichel, N and Blanquet-Diot, S and Ocvirk, S and Basic, M and Clavel, T}, title = {Function-Based Selection of Synthetic Communities Enables Mechanistic Microbiome Studies.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf209}, pmid = {40972887}, issn = {1751-7370}, abstract = {Understanding the complex interactions between microbes and their environment requires robust model systems such as synthetic communities (SynComs). We developed a functionally directed approach to generate SynComs by selecting strains that encode key functions identified in metagenomes. This approach enables the rapid construction of SynComs tailored to any ecosystem. To optimize community design, we implemented genome-scale metabolic models, providing in silico evidence for cooperative strain coexistence prior to experimental validation. Using this strategy, we designed multiple host-specific SynComs, including those for the rumen, mouse, and human microbiomes. By weighting functions differentially enriched in diseased versus healthy individuals, we constructed SynComs that capture complex host-microbe interactions. We designed an inflammatory bowel disease SynCom of 10 members that successfully induced colitis in gnotobiotic IL10-/- mice, demonstrating the potential of this method to model disease-associated microbiomes. Our study establishes a framework for designing functionally representative SynComs of any microbial ecosystem, facilitating mechanistic study.}, }
@article {pmid40972811, year = {2025}, author = {Teng, Z and Li, L and Che, T and Liang, J and Yao, X and Zhao, N and Zhao, F and Sun, H and Wang, L and Wang, Q and Liu, G and Qin, T}, title = {A Novel Balamuthia Lineage Causing Fatal Granulomatous Amoebic Encephalitis in an Immunocompetent Infant.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {}, number = {}, pages = {108063}, doi = {10.1016/j.ijid.2025.108063}, pmid = {40972811}, issn = {1878-3511}, abstract = {OBJECTIVES: To characterize a genetically distinct Balamuthia lineage causing fatal granulomatous amoebic encephalitis (GAE) in a 10-month-old infant and highlight diagnostic challenges compounded by SARS-COV-2 infection comorbidity.<br><br>METHODS: Case report of a 10-month-old male with GAE. Metagenomic next-generation sequencing (mNGS) and PCR sequencing of 18S/12S rRNA genes from brain biopsy tissue were performed. Phylogenetic analysis was conducted to identify the genetic characteristics of the pathogen.<br><br>RESULTS: The patient presented with recurrent fever, seizures, and rapidly progressive neurological deterioration. He had documented SARS-CoV-2 infection two weeks prior to symptom onset. The mNGS of biopsy tissue identified Balamuthia infection. Genetic analysis revealed 18S rRNA similarity of 95.33% and mitochondrial 12S rRNA similarity of 85.49% versus known species. Phylogenetic trees confirmed a distinct clade, suggesting a potential novel species. Despite aggressive treatment, the patient died after 13 days of hospitalization.<br><br>CONCLUSIONS: This case highlights the challenges in diagnosing and managing GAE, particularly in pediatric patients with atypical presentations. The discovery of a genetically distinct Balamuthia strain indicates the importance of global surveillance for emerging pathogens. Clinicians should consider Balamuthia as a potential cause of encephalitis in children with unexplained neurological symptoms, even in non-endemic regions.}, }
@article {pmid40972730, year = {2025}, author = {Wang, X and Chen, M and Su, Y and Zhang, X and Chen, J and Huang, Z and Xie, J and Xie, Q and He, L and Su, L and Su, Z and Wang, H and Li, Y}, title = {A Novel Cholesterol-Reducing Mechanism of Polygonati Rhizoma: Dual Action via Bacteroides-Mediated Cholesterol Sulfonation and Feedback Inhibition of ACAT2 by Sulfated Metabolite.}, journal = {Journal of ethnopharmacology}, volume = {}, number = {}, pages = {120619}, doi = {10.1016/j.jep.2025.120619}, pmid = {40972730}, issn = {1872-7573}, abstract = {Polygonati Rhizoma (PR) has the function of "invigorating spleen and tonifying kidney", and is historically applied as a homology of medicine and food to prevent and treat dyslipidemia in China. However, there is limited experimental evidence to buttress this application, and the underlying mechanism has not been fully deciphered.<br><br>AIM OF THE STUDY: To analyze the composition and illuminate the cholesterol-lowering potential and molecular mechanism of PR's aqueous extract (PRE) in high-fat emulsion (HFE)-induced hypercholesterolemia mouse model.<br><br>MATERIALS AND METHODS: Ion chromatograph was employed to determine the monosaccharide composition of PRE. HFE-induced Kunming mouse model was constructed to unravel the anti-hypercholesterolemia effect of PRE. Metagenomic sequences and liquid chromatography-mass spectrometry (LC-MS) analysis were performed to elucidate the mechanism through which PR regulated cholesterol metabolism. Antibiotic cocktail (ABX) intervention and fecal microbiota transplantation (FMT) were used to validate whether PRE regulated cholesterol metabolism through the intestinal microbiota. The cholesterol-reducing effect of cholesterol sulfate (CS) was explored in poloxamer 407 (P407)-induced mouse model of dyslipidemia. Molecular docking and molecular dynamics (MD) simulation were also employed to elucidate the underlying mechanisms. Furthermore, a combination of qRT-PCR, Western blot, and surface plasmon resonance (SPR) were employed to delineate its mechanism.<br><br>RESULTS: Our study indicated that the polysaccharides of PRE were mainly composed of fructose (92.33%) and glucose (5.25%). PRE treatment effectively blocked body weight gain, significantly decreased serum and hepatic levels of triglycerides (TG), total cholesterol (TC), and low-density lipoprotein cholesterol (LDL-C), and increased high-density lipoprotein cholesterol (HDL-C) level. Additionally, PRE ameliorated hepatic lipid accumulation in mice with HFE-elicited hypercholesterolemia. Notably, metagenomic sequencing and LC-MS analysis indicated that PRE markedly increased the abundance of intestinal genera Bacteroides and significantly elevated the fecal CS concentration in HFE mice. Genome-based functional analysis further indicated that cofactors of sulfonation (ATP sulfurylase CysD and CysN, BT0414-BT0415) were significantly upregulated after treatment with PRE. The cholesterol-lowering effect of PRE was largely contingent upon microbial conversion of cholesterol-to-CS mediated by Bacteroides, as validated by antibiotics-induced intestinal microbiota depletion in pseudo-germ-free model and restoration of gut microbiota through FMT. In vitro study also showed that PRE promoted the growth of Bacteroides thetaiotaomicron. Furthermore, CS markedly alleviated serum, hepatic, bile, and fecal levels of TG, TC, LDL-C, HDL-C and TBA, indicative of appreciable lipid-lowering effect. MD simulation and SPR result indicated that CS directly bound to ACAT2. Consistent with this interaction, CS greatly downregulated the mRNA and protein expression of ACAT2 in small intestinal tissue.<br><br>CONCLUSION: These findings for the first time suggested that PR acted as a prebiotic agent to ameliorate hypercholesterolemia, at least in part, via dual mechanism involving modulation of Bacteroides-mediated sulfonation metabolic pathway and feedback inhibition of ACAT2 by CS, highlighting its therapeutic potential for cholesterol-related disorders. This work might also offer novel mechanistic insight and further buttressed the ethnopharmacological application of PR in the therapy of hypercholesterolemia.}, }
@article {pmid40972462, year = {2025}, author = {Wang, X and Luo, Y and Gu, Y and Ren, T and Liu, Y and Wang, X and Zhao, N and Nie, X and Liu, D and Zhao, Z}, title = {Physicochemical properties, microbial diversity, metabolites and their potential relationships of traditional Chinese Zhacai fermented for different periods.}, journal = {International journal of food microbiology}, volume = {444}, number = {}, pages = {111447}, doi = {10.1016/j.ijfoodmicro.2025.111447}, pmid = {40972462}, issn = {1879-3460}, abstract = {In this study, we investigated the physicochemical properties, dominant microorganisms, non-volatile metabolites and their relationships of traditional Chinese Zhacai (TCZ) at the "second-time pickling and pressing" stage fermentation. pH and amino acid nitrogen contents exhibited an increasing and then decreasing trend. Metagenomics analysis revealed the dominant bacterial species Lactiplantibacillus (Lpb.) plantarum and Latilactobacillus (Lat.) sakei, and fungal species Debaryomyces (D.) hansenii. LEfSe analysis identified a total of 47 differentially abundant bacteria, including Lpb. plantarum and Lat. Sakei. Metabolomics analysis indicated organic acids and their derivatives, organic heterocyclic compounds, lipids and lipid-like molecules as the major differential metabolites. Spearman's correlation results showed significant correlations among differential bacteria, non-volatile metabolites and physicochemical properties. Unexpectedly, differential fungi were not observed in TCZ at this fermentation period. Pathway enrichment identified phenylpropanoid biosynthesis and tryptophan metabolism as dominant metabolic pathways, both influencing the TCZ flavor development. This study contributes to further understanding of quality formation of TCZ, providing a foundational resource for future optimization and industrial application.}, }
@article {pmid40972367, year = {2025}, author = {Rattanapitoon, NK and Thanchonnang, C and Arunsarn, P and Rattanapitoon, SK}, title = {Re: "Severe angiostrongyliasis with neuropsychiatric symptoms in vulnerable adults: Early diagnosis via next-generation sequencing and successful treatment".}, journal = {Journal of infection and public health}, volume = {18}, number = {12}, pages = {102973}, doi = {10.1016/j.jiph.2025.102973}, pmid = {40972367}, issn = {1876-035X}, abstract = {Tang et al. (2025) report on two cases of neuroangiostrongyliasis in vulnerable adults, diagnosed via metagenomic next-generation sequencing (mNGS). We highlight the clinical value of mNGS in detecting atypical presentations, particularly in patients without eosinophilia or classic meningitic signs. While mNGS demonstrates diagnostic potential, its limitations and feasibility in low-resource settings must be acknowledged. We propose a contextualized approach integrating mNGS with cost-effective tools like LAMP and rapid antigen tests, especially for underserved populations.The commentary also calls attention to the risk of underdiagnosed parasitic CNS infections in socioeconomically vulnerable groups and urges broader diagnostic preparedness and targeted surveillance.}, }
@article {pmid40972220, year = {2025}, author = {Saha, S and Mondal, A and Bag, S and Ghosh, S and Mandal, AH and Saha, NC and Chatterjee, S and Sopjiani, M and Multisanti, CR and Faggio, C}, title = {Are biopesticides really safe? Impacts on gut microbiota and intestinal health in freshwater fish.}, journal = {Journal of contaminant hydrology}, volume = {276}, number = {}, pages = {104727}, doi = {10.1016/j.jconhyd.2025.104727}, pmid = {40972220}, issn = {1873-6009}, abstract = {The growing use of biopesticides as eco-friendly alternatives to chemical pesticides is reshaping pest control in agriculture and aquaculture. However, their potential effects on non-target aquatic species, particularly freshwater fish, remain underexplored. This review investigates how different biopesticides, such as microbial agents, biochemical compounds, and plant-incorporated protectants, affect the gut microbiota and intestinal health of freshwater fish. The gut microbiome plays a vital role in digestion, nutrient absorption, immunity, and overall fish health. Biopesticide exposure may disrupt microbial balance, leading to reduced diversity, changes in community composition, inflammation, and dysbiosis. These alterations can impair digestive efficiency, immune function, growth, and reproduction. Promising mitigation strategies include the use of probiotics, prebiotics, symbiotics, insect-based feeds and other non-bacterial dietary interventions to restore gut homeostasis and improve fish resilience. In addition, advanced techniques like metagenomics and metabolomics are enhancing our understanding of host-microbiome interactions under biopesticide exposure. This review emphasizes the importance of including gut microbiota health in environmental risk assessments for biopesticide use in aquaculture. Future studies should adopt a multidisciplinary approach combining toxicology, microbiology, nutrition, and environmental science to develop species-specific, long-term strategies that safeguard fish health in increasingly pesticide-influenced aquatic environments.}, }
@article {pmid40972162, year = {2025}, author = {Zhang, L and Mao, Y and Wang, Z}, title = {Quantitative comparison of HT-qPCR/16S rRNA sequencing and metagenomics for antibiotic resistance gene profiling: A novel risk assessment approach.}, journal = {Journal of hazardous materials}, volume = {498}, number = {}, pages = {139904}, doi = {10.1016/j.jhazmat.2025.139904}, pmid = {40972162}, issn = {1873-3336}, abstract = {Antibiotic resistance genes (ARGs) threaten environmental and public health, but risk assessment limitations hinder targeted control. This study compared high-throughput qPCR (HT-qPCR) and metagenomic sequencing for ARG monitoring in the aquaculture environment, and developed a novel ARG risk assessment model based on HT-qPCR/16S rRNA. The results showed that 28 out of the 31 targeted ARGs based on HT-qPCR were detected, 18 of which were also identified by the metagenomic method. Despite these methodological differences-with metagenomics excelling in comprehensive diversity profiling and HT-qPCR demonstrating its strength in absolute quantification-both approaches effectively captured the variations in ARG profiles across different environments. Co-occurrence analysis with HT-qPCR and 16S rRNA identified dominant potential ARG-hosts (e.g., Pseudomonas, Acinetobacter) overlapping with metagenomic results. Both methods consistently revealed key environmental drivers of ARGs in water. The novel ARG risk assessment model based on HT-qPCR/16S rRNA, by integrating absolute abundance, detection frequency, mobility and host pathogenicity, identified high-risk ARGs (mexF, ereA, sul2, aadA and floR), which were consistent with those identified by the metagenomic method, and revealed that ARGs in aquaculture water pose a higher potential risk than those in sediment. This study aids in selecting ARG monitoring methods and offers technical support for ARG risk assessment.}, }
@article {pmid40971838, year = {2025}, author = {Guo, X and Liang, A}, title = {Biological and Microbial ControlRhizosphere-derived microbiome of Ailanthus altissima drives gut microbiome composition in Lycorma delicatula (Hemiptera: Fulgoridae).}, journal = {Journal of economic entomology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jee/toaf217}, pmid = {40971838}, issn = {1938-291X}, support = {32470469//National Natural Science Foundation of China/ ; 32070470//National Natural Science Foundation of China/ ; 31561163003//National Natural Science Foundation of China/ ; }, abstract = {The spotted lanternfly (SLF), Lycorma delicatula (White) (Hemiptera: Fulgoridae), a highly polyphagous invasive pest, preferentially feeds on tree-of-heaven (TOH), Ailanthus altissima (Mill.) Swingle (Sapindales: Simaroubaceae). However, the bacterial interactions between this pest and its host plant remain poorly understood. In this study, we investigated the bacterial community composition and functional profiles in the SLF gut, TOH leaves, and TOH rhizosphere soil using amplicon and metagenomic sequencing. This study showed that the bacterial alpha-diversity differed significantly among the 3 sample types (P < 0.05). Venn analysis identified 4 shared amplicon sequence variants (ASVs) between the TOH rhizosphere soil and SLF gut, suggesting potential bacterial interactions or transfer. Further source-tracking analysis indicated that most gut bacteria originated from the rhizosphere soil. However, the dominant taxa varied across compartments: Proteobacteria dominated both the SLF gut and TOH leaves, while Acidobacteria predominated in the TOH rhizosphere soil. Network analysis revealed significant correlations between gut and rhizosphere microbes, notably Candidatus Vidania and Fastidiosipila (P < 0.05, r = 1). Functional profiling showed that the rhizosphere microbiome was enriched in nitrogen cycling and carbon fixation pathways, whereas the gut microbiome was associated with carbohydrate metabolism and nutrient assimilation. These results provide new insights into the potential roles of microbiomes in mediating plant-insect interactions and underscore the rhizosphere as a critical microbial source for SLF. Understanding these microbial connections may support the development of innovative and sustainable pest management strategies.}, }
@article {pmid40971807, year = {2025}, author = {Kobel, CM and Aho, VTE and Øyås, O and Nørskov-Lauritsen, N and Woodcroft, BJ and Pope, PB}, title = {CompareM2 is a genomes-to-report pipeline for comparing microbial genomes.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btaf517}, pmid = {40971807}, issn = {1367-4811}, abstract = {SUMMARY: Here, we present CompareM2, a genomes-to-report pipeline for comparative analysis of bacterial and archaeal genomes derived from isolates and metagenomic assemblies. CompareM2 is easy to install and operate, designed in such a way that the user can install the complete software in one step and launch all analyses on a set of microbial genomes (bacterial and archaeal) in a single action. The central results generated via the CompareM2 workflow are emphasized in a portable dynamic report document.<br><br>CompareM2 is a free software that is scalable to a range of project sizes, and welcomes modifications and pull requests from the community on its Git repository at https://github.com/cmkobel/comparem2.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid40971779, year = {2025}, author = {Zhang, M and Wang, C and Huang, Y and Li, Q and Hu, J and Pan, K and Zhu, Q and Jiang, W and Qiu, J and Yan, X and Hong, Q}, title = {Widespread distribution of BpfA-mediated bisphenol F degradation among members of the Pseudomonadota and Actinomycetota.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf206}, pmid = {40971779}, issn = {1751-7370}, abstract = {Bisphenol F, a widely used primary raw material in the production of polycarbonate and epoxy resins, is frequently detected in the environment and poses significant risks to ecosystems and human health. Microorganisms play an important role in bisphenol F degradation in the natural environment; however, the genetic determinants involved remain unknown. A flavoprotein oxidase BpfA from Microbacterium sp. strain F2 was identified in this study, which is responsible for the crucial steps of bisphenol F degradation involving its conversion to 4,4'-dihydroxybenzophenone through three consecutive reactions. BpfA phylogenetically clusters within the 4-phenol oxidizing subfamily of the vanillyl alcohol oxidase/para-cresol methylhydroxylase flavoprotein family. Three homologs in this subfamily-vanillyl alcohol oxidase, eugenol oxidase, and flavoprotein oxidase-shared over 35.0% identity with BpfA and demonstrated bisphenol F-degrading activity, yet the catalytic efficiency of BpfA against bisphenol F (508.1 mM-1 s-1) was significantly higher than that of vanillyl alcohol oxidase (0.2 mM-1 s-1), eugenol oxidase (0.2 mM-1 s-1), and flavoprotein oxidase (0.3 mM-1 s-1). Structural analysis indicated that strong active site hydrophobicity was likely the reason for this high catalytic efficiency. Bioinformatics-based taxonomic profiling revealed that candidate bisphenol F degraders carrying bpfA mainly belonged to the Pseudomonadota and Actinomycetota phyla, and were predominantly found in metagenomes from cultivated land and forests. This study elucidated the function and distribution pattern of bpfA, enhancing our understanding of microbial bisphenol F degradation in the environment.}, }
@article {pmid40971415, year = {2025}, author = {Vermeer, E and Prins, FM and Hidding, IJ and Jagt, JZ and de Jonge, R and Benninga, MA and Gacesa, R and Weersma, RK and de Boer, NKH and de Meij, TGJ}, title = {Metagenomic Sequencing Reveals Distinct Gut Microbiome Profiles in Therapy-Naïve de Novo Pediatric Inflammatory Bowel Disease.}, journal = {Inflammatory bowel diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/ibd/izaf184}, pmid = {40971415}, issn = {1536-4844}, support = {WO 19-25//The Dutch Digestive Foundation (MLDS)/ ; }, abstract = {BACKGROUND AND AIMS: Microbiome studies reveal distinct microbial differences in inflammatory bowel disease (IBD), indicating its potential role in pathophysiology and as a noninvasive diagnostic biomarker. This study aims to profile the gut microbiome in children with IBD, compared to both healthy controls (HC) and controls with gastrointestinal symptoms (CGI), and to assess the potential of microbiome profiles as noninvasive diagnostic markers for de novo treatment-naïve pediatric IBD, and as early predictive markers for therapy response.<br><br>METHODS: We analyzed baseline fecal samples and clinical data from 103 therapy-na&#xef;ve children with IBD, 75 CGI, and 356 age and sex matched HC. Metagenomic sequencing was performed, and prediction models assessed diagnostic potential and prediction of induction therapy response at 3 months.<br><br>RESULTS: Alpha diversity progressively decreased from HC to CGI (P&#x2009;<&#x2009;.001) and decreased even further in IBD patients (P&#x2009;=&#x2009;.0056). Beta diversity analysis showed significant clustering differences (P&#x2009;<&#x2009;.001, R2 = 0.045). Differential abundance analysis revealed 116 species differing between HC and IBD, and 30 species between CGI and IBD. Prediction models based on microbiome features accurately distinguished IBD from HC (area under the curve [AUC]&#x2009;=&#x2009;0.96) and from CGI (AUC&#x2009;=&#x2009;0.71). However, these models were outperformed by clinical features, such as fecal calprotectin. Microbiome-based prediction of response to induction therapy in general showed limited accuracy (AUC&#x2009;=&#x2009;0.63), as well as for response to nutritional induction therapy (AUC&#x2009;=&#x2009;0.67).<br><br>CONCLUSIONS: We observed profound gut microbiome differences between de novo, therapy-na&#xef;ve pediatric IBD patients and controls. While microbiome profiles hold promise for improving diagnostic precision, their predictive value for therapy response seems limited.}, }
@article {pmid40970740, year = {2025}, author = {Briand, M and Jacques, M-A and Dittmer, J}, title = {The hidden life of Xylella: mining the NCBI Sequence Read Archive reveals potential new species, host plants, and infected areas for this elusive bacterial plant pathogen.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0091325}, doi = {10.1128/aem.00913-25}, pmid = {40970740}, issn = {1098-5336}, abstract = {New crop disease outbreaks can occur when phytopathogenic bacterial pathogens acquire new traits, switch to a new host plant, or are introduced into new geographic areas. Therefore, the rapid detection of a pathogen in a new environment and/or in a new host plant is essential to mitigate disease outbreaks. However, bacteria with a wide plant host range, many asymptomatic hosts, and slow symptom development can sometimes remain unnoticed for years. This is the case for the vector-borne xylem-inhabiting bacterium Xylella fastidiosa known to infect hundreds of plant species worldwide and its sister species X. taiwanensis, currently thought to be restricted to Taiwan. To investigate whether the two Xylella species are already present in other parts of the world, potentially in unrecognized host species, we performed an in-depth data mining of raw sequence data available in the NCBI Sequence Read Archive. This led to the identification of 62 datasets from diverse plant and insect samples from around the world. Furthermore, nine draft and one circular Xylella genome could be assembled from these datasets. Our results reveal several potential new host plants and previously unrecognized infected areas in the Americas, Africa, and Southeast Asia. Moreover, the newly assembled genomes represent several new strains of both X. fastidiosa and X. taiwanensis as well as an additional Xylella species infecting wild rice. Taken together, our work extends our knowledge on the genetic diversity, host range, and global distribution of the genus Xylella and can orient surveillance programs towards new regions and host plants.IMPORTANCEThe rapid detection of a pathogen in a new environment and/or in a new host plant is essential to mitigate disease outbreaks. However, bacteria with a wide plant host range, many asymptomatic hosts, and slow symptom development can sometimes remain unnoticed for years. In this work, we used an in-depth screening of publicly available raw sequencing data as an alternative approach to investigate the distribution of the xylem-inhabiting bacteria Xylella fastidiosa and X. taiwanensis across the world. Our results reveal several potential new host plants and previously unrecognized infected areas in the Americas, Africa, and Southeast Asia. Moreover, we provide evidence, including a complete genome sequence, for a third Xylella species infecting wild rice. This work extends our knowledge of the genetic diversity, plant host range, and global distribution of the genus Xylella in natural environments and motivates surveillance programs in so-far-neglected biomes, regions, and host plants.}, }
@article {pmid40970702, year = {2025}, author = {Hu, J and Blazier, JC and Gitter, A and Gregory, LF and Gentry, TJ}, title = {How sequencing technology shapes our understanding of river water microbiomes and resistomes: a comparative study.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0172325}, doi = {10.1128/aem.01723-25}, pmid = {40970702}, issn = {1098-5336}, abstract = {UNLABELLED: River ecosystems are vital for supporting biodiversity and supplying freshwater, but are increasingly impacted by microbial pollution, including the spread of antibiotic resistance genes (ARGs), which poses growing public health concerns. While high-throughput sequencing technologies have advanced our ability to study microbial communities and resistomes, their varying capabilities and biases require comparative analysis. In this study, we compared three sequencing approaches-Illumina 16S rRNA amplicon, Illumina shotgun metagenomics, and Oxford Nanopore-based long-read metagenomics-to profile microbial communities, ARGs, and virulence factors (VFs) in 48 river water samples. All methods identified Proteobacteria and Actinobacteria as dominant phyla, but substantial differences emerged at finer taxonomic levels. Long-read metagenomics and 16S data showed greater consistency at the genus level, while Illumina metagenomics differed, detecting more potential pathogens and fewer native freshwater taxa. For ARG and VF profiling, unassembled Illumina data yielded higher diversity and abundance, but assembled Illumina data showed comparable results to long-read metagenomics data in terms of dominant genes and host associations. Although Illumina provides high sensitivity, the use of short reads and associated assembly limitations can compromise functional accuracy. In contrast, long-read metagenomics facilitates gene-level resolution and direct host linkage, providing a more comprehensive understanding of environmental microbiomes. Our findings highlight the strengths and limitations of each method and support Oxford Nanopore technology (ONT)-based long-read metagenomic sequencing as a cost-effective and informative tool for high-resolution taxonomic and functional analysis of complex environmental samples.<br><br>IMPORTANCE: Accurate characterization of microbial communities and their functional traits, such as antibiotic resistance, is essential for evaluating water quality and associated public health risks. However, the selection of sequencing methods can substantially influence the detection and interpretation of microbial community composition and functional potential in environmental samples. By directly comparing amplicon, short-read metagenomic, and long-read metagenomic sequencing across 48 freshwater samples collected across different sites and time points, this study builds upon earlier work that typically focused on only two methods or less complex communities. It provides a comparative evaluation of three widely used sequencing approaches, demonstrating how methodological differences affect the resolution and reliability of taxonomic and functional profiling in complex environmental microbiomes. By highlighting the strengths and limitations of each platform, these findings enhance our understanding of how sequencing strategy shapes environmental microbiome analyses and contributes to evidence-based method selection in environmental microbiology and antimicrobial resistance monitoring.}, }
@article {pmid40970697, year = {2025}, author = {Chen, Y and Tang, H and Zheng, J and Yang, Q and Han, D}, title = {Transforming tuberculosis diagnosis with clinical metagenomics: progress and roadblocks.}, journal = {Journal of clinical microbiology}, volume = {}, number = {}, pages = {e0053725}, doi = {10.1128/jcm.00537-25}, pmid = {40970697}, issn = {1098-660X}, abstract = {Tuberculosis (TB) remains a leading global infectious killer, yet traditional diagnostic methods are inadequate. Acid-fast staining suffers from low sensitivity, and mycobacterial culture requires prolonged incubation because of the slow growth of Mycobacterium tuberculosis. PCR-based molecular assays allow rapid detection, but their capacity for resistance profiling is limited to a narrow set of mutations. Metagenomic next-generation sequencing (mNGS) has emerged as a promising culture-independent tool for TB detection, enabling broad-spectrum pathogen identification and offering added value in complex scenarios including extra-pulmonary disease, mixed infections, and infections in immunocompromised or pediatric populations. Clinical studies indicate that mNGS achieves moderate to high sensitivity and excellent specificity in the diagnosis of tuberculosis. However, its diagnostic performance is often constrained by low mycobacterial read counts, interference from abundant host nucleic acids, and the inability to distinguish active from latent infection. In addition, the accuracy of drug resistance prediction using mNGS remains limited, and the World Health Organization currently endorses targeted NGS as the preferred sequencing-based approach for resistance profiling. Despite these challenges, mNGS has facilitated novel diagnostic strategies that combine pathogen detection with host-response data, thereby broadening its potential clinical utility. Nevertheless, practical barriers such as high cost, complex laboratory workflows, and difficulties in data interpretation continue to restrict widespread adoption in routine practice. Future efforts should prioritize technical optimization, standardized protocols, and integration with conventional diagnostics to establish cost-effective and clinically meaningful roles for mNGS in TB diagnosis and management.}, }
@article {pmid40970218, year = {2024}, author = {Finn, RD and Balech, B and Burgin, J and Chua, P and Corre, E and Cox, CJ and Donati, C and Dos Santos, VM and Fosso, B and Hancock, J and Heil, KF and Ishaque, N and Kale, V and Kunath, BJ and Médigue, C and Nogueira, T and Pafilis, E and Pesole, G and Richardson, L and Santamaria, M and Strepis, N and Van Den Bossche, T and Vizcaíno, JA and Zafeiropoulos, H and Willassen, NP and Pelletier, E and Batut, B}, title = {Establishing the ELIXIR Microbiome Community.}, journal = {F1000Research}, volume = {13}, number = {}, pages = {}, doi = {10.12688/f1000research.144515.2}, pmid = {40970218}, issn = {2046-1402}, mesh = {*Microbiota ; *Metagenomics/methods ; Computational Biology ; }, abstract = {Microbiome research has grown substantially over the past decade in terms of the range of biomes sampled, identified taxa, and the volume of data derived from the samples. In particular, experimental approaches such as metagenomics, metabarcoding, metatranscriptomics and metaproteomics have provided profound insights into the vast, hitherto unknown, microbial biodiversity. The ELIXIR Marine Metagenomics Community, initiated amongst researchers focusing on marine microbiomes, has concentrated on promoting standards around microbiome-derived sequence analysis, as well as understanding the gaps in methods and reference databases, and identifying solutions to the computational overheads of performing such analyses. Nevertheless, the methods used and the challenges faced are not confined to marine microbiome studies, but are broadly applicable to other biomes. Thus, expanding this Marine Metagenomics Community to a more inclusive ELIXIR Microbiome Community will enable it to encompass a broader range of biomes and link expertise across 'omics technologies. Furthermore, engaging with a large number of researchers will improve the efficiency and sustainability of bioinformatics infrastructure and resources for microbiome research (standards, data, tools, workflows, training), which will enable a deeper understanding of the function and taxonomic composition of the different microbial communities.}, }
@article {pmid40970131, year = {2025}, author = {Urayama, SI and Fukudome, A and Mutz, P and Matsushita, Y and Takaki, Y and Nishimura, Y and Medvedeva, S and Krupovic, M and Koonin, EV and Nunoura, T}, title = {Identification of Obelisk-like covalently closed circular RNA replicon in hot springs by double-stranded RNA sequencing and expansion of the diversity of the Obelisk superfamily.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.09.03.673927}, pmid = {40970131}, issn = {2692-8205}, abstract = {Extensive metatranscriptome mining has recently vastly expanded the range of covalently closed circular (ccc) RNA replicons. A notable group of such replicons are Obelisks, cccRNAs of about 1 kilobase (kb) encoding a protein with a unique fold, Oblin-1, and detected in a broad variety of metatranscriptomes, in particular, those from the human gastrointestinal tract. We adopted Fragmented and primer-Ligated DsRNA Sequencing (FLDS) method to selectively sequence double-stranded (ds) RNAs, the replicative intermediates of RNA replicons, and to identify cccRNAs among the resulting sequences. From these data, we selected cccRNAs with predicted extensive intramolecular base-pairing, a hallmark of viroid-like elements. ch We employed FLDS to explore metatranscriptomes from acidic hot springs in Japan and discovered a distinct family of Obelisks probably associated with thermoacidophilic bacteria (Hot spring Obelisks, HsObs). The proteins encoded by HsObs, HsOblins, show no significant sequence similarity to previously identified Oblin-1 proteins, but are predicted to adopt a closely similar structure. A comprehensive search of metagenomes for Oblin-1 and HsOblin homologs substantially expanded this family of Obelisk-encoded proteins revealing several distinct subfamilies that share the same core fold. A cccRNA encoding an HsOblin homolog was also detected in a Yellowstone hot spring metatranscriptome. Apart from Oblin-1, some subfamilies of Obelisks were predicted to encode additional small proteins with simple alpha-helical folds.}, }
@article {pmid40969704, year = {2025}, author = {Onohuean, H and Onohuean, FE and Omara, C and Saleem, H}, title = {Prevalence and epidemiological distribution of substance use among people living with HIV in the East African region: a meta-analysis.}, journal = {Frontiers in psychiatry}, volume = {16}, number = {}, pages = {1494469}, pmid = {40969704}, issn = {1664-0640}, abstract = {BACKGROUND: The East African region lacks synthesised scientific evidence on the impact of different substances used on HIV management and treatment outcomes in this population. We meta-analysed epidemiological data on substance use among people living with HIV to determine the regional estimate of the prevalence, associated factors, and changes over time for each gender, per year or age.<br><br>METHOD: The documents were obtained via electronic databases following Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines.<br><br>RESULTS: The 53 studies from the East African region showed a pool estimate proportion of 60.36%, 95% confidence interval (CI) (0.5301-0.6728) with an I [2] = 98.88% using the random-effects model, and Q-statistic (df = 52) = 4,662.95, p < 0.0001. The publication bias is revealed by funnel plots, 55.15%, CI (0.4637-0.6362); Egger's linear regression test indicates z = 12.6415, p < 0.0001; and the rank correlation test of Kendall's tau = 0.1011, p = 0.2955. The subgroup analysis showed an estimate of the study type: cohort, 66.10%, CI (0.5672-0.7437), I [2] = 98.60%, and cross-sectional, 58.98%, CI (0.4009-0.7555), I [2] = 99.06%. The variables of the subgroup analysis by study size indicate the following: >1,000 sample size, 76.05%, CI (0.4661-0.9203), I [2] = 99.75%, and <1,000 sample size, 62.85%, CI (0.5396-0.7095) I [2] = 100%. The meta-regression analysis of heterogeneity indicates that the covariate of countries (R [2] = 0.00%, p < 0.0001), types of substance use (R [2] = 0.00%, p < 0.0001), and study period (R [2] = 16.95%, p = 0.0013) significantly moderate the observed heterogeneity.<br><br>CONCLUSION: The East African region has a high prevalence of substance use among people living with HIV, which may further increase the risk of spread of infections and signs of deteriorating physical and mental health. Comprehensive treatment and establishing interventions for substance abuse/misuse among people living with HIV could be a top health priority in the region.}, }
@article {pmid40969555, year = {2025}, author = {Zhang, Y and Zhang, Y and Xing, G and Mei, T and Wang, M and Huang, C and Yi, H and Zhan, Y and Yang, S and Yan, Q and Li, S and Chen, C}, title = {Characterization of the oral virome in patients with diabetes mellitus.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1607798}, pmid = {40969555}, issn = {2235-2988}, mesh = {Humans ; *Virome ; *Mouth/virology/microbiology ; Male ; Female ; *Diabetes Mellitus/virology/microbiology ; Middle Aged ; *Viruses/classification/genetics/isolation &amp; purification ; Metagenomics ; Microbiota ; Bacteria/classification/genetics ; Adult ; Aged ; Dysbiosis ; Metagenome ; }, abstract = {INTRODUCTION: Diabetes mellitus (DM), a globally prevalent chronic metabolic disorder characterized by persistent hyperglycemia, has been increasingly linked to dysbiosis of the oral microbiome. However, the relationship between the virome, a crucial component of the oral microbiome, and DM remains poorly understood.<br><br>METHODS: To explore the characteristics of the oral virome in DM patients, we analyze the oral viral communities of 45 DM patients and 40 healthy controls (HC) using a publicly available metagenomic dataset.<br><br>RESULTS: Our analysis revealed no significant differences in a-diversity between DM patients and HC. However, Podovirus was enriched in DM patients, whereas Microviridae was more prevalent in HC. A total of 1,131 virus signal was identified, primarily belonging to the Siphovirus and Myovirus taxa. Notably, HC-enriched vOTUs exhibited broader host tropism, predominantly infecting Prevotella, Fusobacterium, and Gemella, whereas DM-enriched vOTUs showed narrower specificity for Pauljensenia and Veillonella. Cross-kingdom network analysis suggested that certain viruses (HMP_1157.k81_309051) may have potential links to the development of DM, and the bacteria genus F0040 might play a significant role in maintaining oral health. Additionally, the random forest model based on viral markers effectively distinguished between HC and DM patients (AUC =90.8%), significantly outperforming the bacterial model.<br><br>DISCUSSION: This indicates that these unique viral markers could serve as potential targets for DM intervention. Taken together, our findings reveal distinct alterations in the oral virome of DM patients and highlight its promise as a novel diagnostic and therapeutic target in metabolic disease research.}, }
@article {pmid40969552, year = {2025}, author = {Wang, J and Ren, W and Liu, S and Li, Z and Zeng, Y and Meng, J and Yao, X}, title = {Changes in antioxidant capacity and gut microbiota in mice after intake of camel milk.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1621031}, pmid = {40969552}, issn = {2235-2988}, mesh = {Animals ; Camelus ; *Gastrointestinal Microbiome ; *Antioxidants/metabolism/analysis ; *Milk/chemistry ; Mice ; Mice, Inbred ICR ; Liver/metabolism ; Bacteria/classification/genetics/isolation &amp; purification ; Colon/microbiology ; Metagenomics ; Male ; Fermentation ; Probiotics/administration &amp; dosage ; }, abstract = {Fermented camel milk offers significant nutritional benefits, enriched with probiotics that generate bioactive compounds advantageous to human health. In order to investigate the effects of camel milk with different treatments on Antioxidant Capacity and Gut Microbiota in mice, 32 ICR mice were selected and randomly divided into 4 groups, including gavage with 10 mL/kg body weight of distilled water (DW Group), camel milk (CM Group), fermented camel milk (FCM Group), and pasteurized fermented camel milk (PFCM Group) every morning, respectively. After 28 days, liver and colon samples were collected to assess liver antioxidant capacity, and metagenomic analysis was performed on alterations in microbial community structures. Results demonstrated that all camel milk treatments elevated liver total protein levels while reducing MDA and SOD activity. In addition, the PFCM group had the highest total antioxidant capacity and the lowest SOD content. In addition, the intestinal microorganisms of mice changed at the phylum, genus and species levels after being gavaged with camel milk of different treatments. A total of 4732 microorganisms were identified, of which 259, 222, 116 and 164 were unique to the DW, CM, FCM and PFCM groups, respectively. The relative abundances of Adlercreutzia caecimuris, Adlercreutzia mucosicola and Enterorhabdus sp. P55 were significantly higher in the CM, FCM and PFCM groups than in the DW group, and the relative abundances of Parvibacter caecicola, Adlercreutzia muris and Roseburia sp. 1XD42-69 were significantly higher in the CM and PFCM groups than in the DW group. In addition, the relative abundances of Faecalibaculum rodentium, Alistipes muris and Limosilactobacillus reuteri were different between the CM and FCM groups. The results of the correlation analysis between the relative abundance of microbial species and antioxidant indices showed that Adlercreutzia mucosicola, Adlercreutzia muris, Lactobacillus acidophilus, and Enterorhabdus sp. P55 were significantly correlated with the antioxidant indices of mice. Further functional annotations indicated that these microorganisms might modulate antioxidant activity via metabolic and organismal systems. In summary, camel milk and fermented camel milk can play a positive role in regulating the intestinal flora of mice, thereby regulating the antioxidant capacity of mice and alleviating the effects of oxidative stress on the body. This study provides a scientific foundation for the further exploration and utilization of camel milk.}, }
@article {pmid40969435, year = {2025}, author = {Murthy, MK and Gupta, VK and Maurya, AP}, title = {Diagnosis of nontuberculous mycobacterial infections using genomics and artificial intelligence-machine learning approaches: scope, progress and challenges.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1665685}, pmid = {40969435}, issn = {1664-302X}, abstract = {The nontuberculous mycobacterial (NTM) infections cause morbidity and mortality in individuals who are immunocompromised and those with lung conditions. The timely diagnosis of NTM infections is thus the need of the hour for appropriate management of the disease. In this context, genomics has played a pivotal role in diagnosis of NTM by targeting various conserved regions which are useful for species identification and diagnosis. Also, the exploring of whole genome of nontuberculous mycobacteria has made species identification easier and has revolutionized the diagnostic landscape of NTM. The refinement of Whole Genome Sequencing (WGS) and the advent of targeted Next Generation Sequencing (tNGS) and metagenomic NGS (mNGS) has helped in bringing down the cost without compromising the quality in NTM diagnostics. The advent of artificial intelligence (AI) technologies has made NTM diagnosis even easier by analyzing complex genomic data and providing faster results. Thus, this comprehensive review discusses the strides made in genomics and AI based approaches in the diagnosis of NTM infections and the way forward for harnessing this potential to the maximum for the benefit of mankind.}, }
@article {pmid40969426, year = {2025}, author = {Zhou, S and Liu, H and Bai, X and Li, D and Wang, T and Zhong, H and Gao, W and Sun, J}, title = {Geographic patterns of antibiotic resistance in the human gut microbiome: insights from metagenome-assembled genomes across four Chinese provinces.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1652757}, pmid = {40969426}, issn = {1664-302X}, abstract = {Next-generation metagenomic sequencing has substantially advanced our understanding of the human intestinal microbiome. Many commensal microbes in the human gut carry a wide array of antibiotic resistance genes (ARGs), collectively forming the gut-associated resistome. In this study, we investigated the gut resistome using metagenomic sequencing. We collected 119 fecal samples from individuals in four Chinese provinces: Yunnan, Guizhou, Sichuan, and Jiangsu. By constructing metagenome-assembled genomes (MAGs) and comprehensive gene catalogs, we aimed to characterize the microbial community structure and assess the distribution of ARGs and mobile genetic elements (MGEs). Our results revealed significant regional differences in gut microbial composition. While Bacillota_A and Actinomycetota were the dominant phyla across all samples, their relative abundances and species-level profiles varied markedly among provinces. Our analysis of ARGs revealed a wide range of antibiotic resistance genes present in the gut microbiota. These ARGs showed uneven distribution across bacterial taxa and among individuals from different regions. For example, ARGs conferring resistance to commonly used antibiotics, such as multidrug agents, peptides, tetracyclines, glycopeptides, and aminoglycosides, were more prevalent in Jiangsu samples than in Sichuan and Yunnan samples, likely reflecting regional differences in antibiotic usage. In MAGs unique to Jiangsu samples, we identified five types of MGEs encompassing 24 subtypes. Among these, transposases (7 subtypes) and recombinases (10 subtypes) were the most abundant. This study offers critical insights into gut resistome compositions and distributions across different populations. Our findings have important implications for public health, microbiota-host interactions, and the development of targeted strategies to mitigate antibiotic resistance.}, }
@article {pmid40969225, year = {2025}, author = {Yao, L and Shan, Y and Chen, G and Wang, J and Yang, J and Yu, J and Yang, C and Chen, X}, title = {Influence of tobacco Flower bud extract on microbial community and aroma quality during cigar leaves fermentation.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {13}, number = {}, pages = {1647801}, pmid = {40969225}, issn = {2296-4185}, abstract = {INTRODUCTION: Tobacco flower buds play a crucial role in enhancing the aroma quality of cigar tobacco leaves (CTLs). By incorporating tobacco flower bud extract into the fermentation process, this study investigates its effects on microbial community dynamics and the volatile aroma compounds in CTLs, aiming to improve cigar flavor and quality during fermentation.<br><br>METHODS: To investigate the effects of tobacco flower bud extract on microbial communities and aroma quality during the fermentation of cigar tobacco leaves, volatile aroma components were evaluated using gas chromatography-mass spectrometry (GC-MS). The microbial community dynamics across different fermentation stages were analyzed using metagenomic sequencing.<br><br>RESULTS AND DISCUSSION: Results revealed that tobacco flower buds contain 23 characteristic aroma compounds, including &#x3b2;-ionone and phenylethanal. Notably, the extract induced a pronounced microbial shift, enriching Aspergillus in unfermented leaves and promoting Staphylococcus dominance (97%-98%) during fermentation. This shift facilitated carbohydrate and protein degradation, significantly reducing nicotine content (P < 0.001), increased total sugar (12.5%-18.75%) and reducing sugar levels (13.04%-27.27%), and optimized the potassium-to-chloride ratio. Aroma analysis demonstrated significant enrichment of carotenoid degradation products (farnesyl acetone, citronellal) and Maillard reaction products (5-methyl-2-furaldehyde) in the FE group, with total aroma content increasing by 11.9% compared to control (FW). Metagenomic functional analysis further indicated that the extract inhibited pathways related to harmful metabolite synthesis (47.0% reduction) and enhanced carbohydrate metabolism (30.6% increasing). This study confirms that tobacco flower bud extract reshapes microbial communities and metabolic networks by simultaneously suppressing harmful microbes and enhancing aroma, providing theoretical support for optimizing cigar fermentation and agricultural waste utilization.}, }
@article {pmid40968678, year = {2025}, author = {Betrains, A and Vanderschueren, S and Rovers, CP and Mulders-Manders, CM}, title = {How to deal with the major diagnostic challenges in fever of unknown origin: an expert opinion.}, journal = {The quarterly journal of nuclear medicine and molecular imaging : official publication of the Italian Association of Nuclear Medicine (AIMN) [and] the International Association of Radiopharmacology (IAR), [and] Section of the Society of...}, volume = {}, number = {}, pages = {}, doi = {10.23736/S1824-4785.25.03651-9}, pmid = {40968678}, issn = {1827-1936}, abstract = {In this review we summarize the current knowledge on fever of unknown origin (FUO). Fever of unknown origin remains a diagnostic challenge even despite increasing diagnostic possibilities since its first definition. Uniform definition of FUO is pivotal to correctly select patients that benefit from the extensive workup that may be needed. The number of conditions associated with FUO is still increasing. Epidemiologic differences and differences in diagnostic possibilities are a challenge when comparing outcomes from cohorts with different epidemiologic backgrounds. The diagnostic protocol that was proposed as early as 2007, with a central role for [18]F-FDG-PET/CT, still remains the golden standard for the workup of FUO. Early use of new diagnostic modalities, including the use of metagenomic next generation sequencing and artificial intelligence, may shorten the diagnostic delay. In patients remaining undiagnosed, second opinion in an expert center can be considered, especially when therapeutic trials are considered. An increasing subset of patients presents with absent inflammatory parameters. Correct evaluation within a febrile episode is important in patients with intermittent disease, but these patients may also suffer from habitual or functional hyperthermia. We advise to let go of these terms and introduce the criteria for temperature elevation with missing inflammatory parameters (TEMP) syndrome.}, }
@article {pmid40968586, year = {2025}, author = {Gundelly, P and Ransom, E and Stewart, Z and Ruch, B and Jittirat, A and Denny, L and Kasten, J and Taylor, ML and Salzer, JS and Basavaraju, SV and Annambhotla, P and McCormick, DW and Gleaton, AN and Karpathy, SE and Singleton, J and Ramos, C and Paddock, CD and Rothfeldt, LK and Baker, M and Villalba, JA}, title = {Transmission of Ehrlichia chaffeensis From an Organ Donor to a Kidney-Pancreas Transplant Recipient.}, journal = {Transplant infectious disease : an official journal of the Transplantation Society}, volume = {}, number = {}, pages = {e70107}, doi = {10.1111/tid.70107}, pmid = {40968586}, issn = {1399-3062}, }
@article {pmid40968530, year = {2025}, author = {Popov, IV and Chikindas, ML and Venema, K and Ermakov, AM and Popov, IV}, title = {KEGGaNOG: A Lightweight Tool for KEGG Module Profiling From Orthology-Based Annotations.}, journal = {Molecular nutrition &amp; food research}, volume = {}, number = {}, pages = {e70269}, doi = {10.1002/mnfr.70269}, pmid = {40968530}, issn = {1613-4133}, support = {23-14-00316//Russian Science Foundation/ ; }, abstract = {Functional interpretation of bacterial genomes and metagenomes is essential for applications ranging from microbial ecology to probiotic development. KEGGaNOG is a lightweight and scalable Python tool that enables pathway-level profiling by translating orthology-based annotations into KEGG module completeness scores. KEGGaNOG accepts input from eggNOG-mapper annotations and supports both individual genome and multi-sample analyses. It calculates completeness scores for KEGG modules using internally integrated KEGG-Decoder logic and offers a suite of visualization options, including heatmaps, grouped summaries, barplots, radar plots, and correlation networks. We demonstrate its use on 11 well-characterized bacterial genomes, including several probiotic strains. KEGGaNOG accurately captured core biosynthetic capabilities and highlighted functionally informative differences across samples, such as vitamin biosynthesis, stress-response pathways, and transport systems. KEGGaNOG provides a practical framework for high-throughput functional annotation and comparative metabolic profiling in bacterial genomics and microbiome research. It is particularly well suited for preliminary analysis of novel or uncharacterized strains and is applicable to both isolate and metagenome-derived data. In the context of probiotic research, KEGGaNOG supports mechanistic exploration and strain selection by linking genomic content to functional capacity in a reproducible and interpretable manner.}, }
@article {pmid40968486, year = {2025}, author = {Hsu, PS and Lin, JA and Hung, YT and Wu, TH and Chen, YH and Wu, MC}, title = {Pollen beebreads as a source of probiotics: a metagenomic and biochemical characterization.}, journal = {Journal of the science of food and agriculture}, volume = {}, number = {}, pages = {}, doi = {10.1002/jsfa.70209}, pmid = {40968486}, issn = {1097-0010}, support = {//National Scienece and Technology Council/ ; //Ministry of Agriculture/ ; }, abstract = {BACKGROUND: Pollen beebread, a fermented pollen stored in honeycombs, is a crucial food source for honey bees and holds promise as a nutraceutical for humans. This study investigated the nutritional composition, antioxidant properties, and microbiota of beebread derived from three major floral sources in Taiwan: rapeseed (Brassica napus, Bn), beggartick (Bidens pilosa var. radiata, Bp), and tea tree (Camellia sinensis, Cs).<br><br>RESULTS: Beebread from different floral sources exhibited significant differences in protein content (up to ~140&#x2009;mg bovine serum albumin equivalents (BSAE) g[-1] in Bn beebread vs. ~105&#x2009;mg BSAE g[-1] in Bp and Cs beebread), phenolic content (up to ~30&#x2009;mg gallic acid equivalents g[-1] in Bn beebread), flavonoid content (up to ~45&#x2009;mg quercetin equivalents g[-1] in Bn beebread), and antioxidant activity (up to ~130 &#x3bc;mol Trolox equivalents g[-1] in Bn beebread). A metagenomic analysis revealed distinct microbiota across samples, with differences in alpha diversity: Bn beebread exhibited higher species richness, whereas Cs beebread exhibited greater evenness. Firmicutes were the dominant phylum in Bn and Bp beebread (average relative abundances of 57.5% and 57.7%, respectively), whereas Proteobacteria predominated in Cs beebread (58.5%). Lactobacillus was the most abundant genus, with average relative abundances of 52.8% and 51.5%, respectively, in Bp and Bn beebread samples.<br><br>CONCLUSION: These findings highlight the influence of floral origin on the nutritional and microbial profiles of beebread and support its potential as a source of beneficial microbes and nutrients. &#xa9; 2025 Society of Chemical Industry.}, }
@article {pmid40968405, year = {2025}, author = {Trubl, G and Probst, AJ}, title = {Clarifying Terminology in Microbial Ecology: A Call for Precision in Scientific Communication.}, journal = {Environmental microbiology}, volume = {27}, number = {9}, pages = {e70177}, doi = {10.1111/1462-2920.70177}, pmid = {40968405}, issn = {1462-2920}, support = {SCW1632//U.S. Department of Energy Office of Biological and Environmental Research through the Genomic Science Program and the Lawrence Livermore National Laboratory/ ; CRC 1439/1//Deutsche Forschungsgemeinschaft/ ; CRC 1439/2//Deutsche Forschungsgemeinschaft/ ; 426547801//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Terminology as Topic ; *Ecology ; *Microbiota ; *Microbiology ; Communication ; }, abstract = {The rapid evolution of microbiology as a field of research has led to the introduction of new terminology and the adaptation of existing terms. However, inconsistencies in the use of these terms, including variations across different scientific disciplines, can lead to confusion and miscommunication within the scientific community. This article discusses the importance of precise terminology in microbiome research, highlighting examples where terms have been misused or redefined without clear justification. We also present a list of frequently used terms in microbial ecology along with their specific definitions. We argue that the misuse of terminology can hinder scientific progress by creating ambiguity and misunderstanding. To address this, we propose a set of guidelines for the consistent use of key terms and provide clear definitions for some of the most commonly misused or newly introduced terms in the field. The definitions provided herein will also function as a guide for young researchers new to the field of microbial ecology. Accurate and consistent use of terminology is crucial for effective communication and collaboration in microbiology research. By adhering to standardised definitions, researchers can ensure that their work is clearly communicated and contributes meaningfully to the progress of science.}, }
@article {pmid40968314, year = {2025}, author = {Margaryan, A and Nikolyan, S and Ayvazyan, I and Panosyan, H and Birkeland, NK}, title = {Heavy Metal-Resistant Bacterial Communities in the Artsvanik Tailing Dump, Armenia.}, journal = {Current microbiology}, volume = {82}, number = {11}, pages = {511}, pmid = {40968314}, issn = {1432-0991}, support = {21SCG-1F016//Higher Education and Science Committee, Ministry of Education, Science, Culture and Sports, Republic of Armenia/ ; 23AA-1F036//Higher Education and Science Committee, Ministry of Education, Science, Culture and Sports, Republic of Armenia/ ; Microbio-4619//Armenian National Science and Education Fund/ ; Microbio-3869//Armenian National Science and Education Fund/ ; }, mesh = {*Metals, Heavy/pharmacology/toxicity/metabolism ; *Bacteria/drug effects/classification/genetics/isolation &amp; purification/metabolism ; *Soil Microbiology ; Mining ; Armenia ; *Soil Pollutants/metabolism ; Phylogeny ; Drug Resistance, Bacterial ; }, abstract = {Mining tailings contain high concentrations of toxic elements that can damage soil or aquatic ecosystems, reducing microbial diversity. To elucidate the bacterial community in tailings, we analyzed bacterial abundance in Cu and Mo mine tailing dump at the Artsvanik, via metagenomic and culturing. In terms of community structure, Illumina shotgun sequencing revealed that Actinomycetota exhibited the highest abundance (40.7%), followed by Pseudomonadota (22%), and Bacteroidota (10.75%). Acidobacteriota (5%), Chloroflexota (5%), Verrucomicrobia (4.25%), Planctomycetota (3.88%), Bacillota (2.8%), Gemmatimonadota (2%), and other phyla were present at low abundances. Metal-resistant bacteria in the genera Inquilinus, Methylobacterium, Sinorhizobium, Noviherbaspirillum, Variovorax, Pseudarthrobacter, Rheinheimera, Pseudomonas, Algoriphagus, Bacillus, and Niallia, were isolated from the soil and sludge samples and from weed plants in the surrounding area. For the isolated strains, the maximum tolerable concentrations of Ni(II), Cu(II), Zn(II), Cd(II), Co(II), Mo(VI), and Cr(VI) were 1-2, 1-4, 2-5, 0.3-0.6, 0.5-2, 60-68 and 0.2-0.6 mM, respectively. The strains grew in the presence of a combination of Ni(II), Cd(II), Zn(II), and Co(II) at 0.75 mM in growth medium. Owing to their high levels of resistance toward heavy metals, these isolated strains hold potential for use in bioremediation to reduce heavy-metal toxicity in contaminated environments.}, }
@article {pmid40967861, year = {2025}, author = {Ma, Y and Si, JH and Sun, DJY and Yu, CQ and Pang, YJ and Lyu, J and Li, LM}, title = {[Progress in population-based research of human microbiome and cardiovascular diseases].}, journal = {Zhonghua liu xing bing xue za zhi = Zhonghua liuxingbingxue zazhi}, volume = {46}, number = {9}, pages = {1680-1687}, doi = {10.3760/cma.j.cn112338-20241219-00816}, pmid = {40967861}, issn = {0254-6450}, support = {2023ZD0510101, 2023ZD0510100//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; }, mesh = {Humans ; *Cardiovascular Diseases/microbiology ; *Microbiota ; Metagenomics ; }, abstract = {The human microbiome encompasses a diverse array of microorganisms and their functional interactions within the human body. It exhibits a vast diversity of species and complex roles across various body environments. Advanced sequencing technologies, such as 16S amplicon sequencing and metagenomic sequencing, facilitate in-depth analysis on this microbial community. Recent researches have suggested that characteristics of the human microbiome (such as diversity and composition of microbiome, involving metabolic pathways and metabolites) might be associated with the onset and progression of cardiovascular diseases. These findings provide valuable insights into the etiology of chronic diseases and might aid in the development of novel disease biomarkers and intervention strategies. This paper summarizes the designs, current status and key findings of current population-based research in this field, and introduce the future development and analyze the existing critical problems that need further investigations.}, }
@article {pmid40967455, year = {2025}, author = {Arffman, RK and Folch, BA and Leonés-Baños, I and Altmäe, S}, title = {Gut Feelings - The gut microbiome as a regulator of mental health in polycystic ovary syndrome.}, journal = {Fertility and sterility}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.fertnstert.2025.09.014}, pmid = {40967455}, issn = {1556-5653}, abstract = {IMPORTANCE: Polycystic ovary syndrome (PCOS) is a common endocrine disorder associated with reproductive, metabolic, and mental health comorbidities. The exact mechanisms of PCOS-related psychological distress and the role of the microbiome in the process remain unclear.<br><br>OBJECTIVE: To systematically review the current literature on the gut microbiome's association with mental health in women with PCOS and to review the possible mechanisms.<br><br>EVIDENCE REVIEW: A comprehensive literature search across the PubMed database until July 2025. Studies were included if they met the following criteria: 1) observational / intervention studies, 2) assessing microbiome through 16S rRNA amplicon / 16S rRNA gene sequencing / metagenomics, 3) comparing microbiome between women with and without PCOS, 4) published from 2007 until 2025, and 5) articles available online. The exclusion criteria were: 1) language other than English or Spanish, 2) reviews, 3) abstracts/posters, 4) case reports, 5) full text not available, and 6) duplicates. Two independent reviewers screened all titles and abstracts to determine eligibility, and discrepancies were resolved through discussion. The methodological quality and the potential risk of bias were assessed following the Joanna Briggs Institute Critical Appraisal Checklist for Case-Control Studies.<br><br>FINDINGS: A total of 159 studies were identified and screened for title, abstract, and full text. Eight studies met the criteria (2 rodent; 6 human studies). The quality assessment indicated that half of the studies (4/8) presented a high risk of bias. Regardless of the limited number of studies and the low quality scores, all the studies highlighted the association of the gut microbiome in PCOS with mental health problems.<br><br>CONCLUSIONS AND RELEVANCE: Our review provides the first summary of the studies performed today on the Gut-Brain axis in PCOS. Our review highlights that the current state of the research is rather preliminary, and the existing studies possess various limitations and often lack rigorous study design. Nevertheless, all the studies indicated an association between changes in gut microbiome and mental health indicators in PCOS. We also noted a consistent increase in Gram-negative bacteria in women with PCOS and mental health issues. More research is needed on humans with a bigger sample size, different ethnicities, and wider age groups to clarify the microbial patterns involved, and in parallel, the field should move from descriptive studies to mechanistic approaches. Polycystic ovary syndrome (PCOS) is a common endocrine disorder associated with reproductive, metabolic, and mental health comorbidities. The exact mechanisms of PCOS-related psychological distress and the role of the microbiome in the process remain unclear. In this review, we systematically screen the current literature on the gut microbiome's association with mental health in women with PCOS and describe possible mechanisms. We did a comprehensive literature search across the PubMed database until July 2025. A total of 159 studies were identified and screened for title, abstract, and full text. Eight studies met the inclusion criteria (2 rodent; 6 human studies). The quality assessment showed that half of the studies presented a high risk of bias. Regardless of the limited number of studies and the low quality scores, all the studies indicated an association between the gut microbiome, PCOS, and mental health problems. The studies also consistently reported an increase in Gram-negative bacteria in women with PCOS and mental health issues. The review also describes the possible contributors in gut-brain-PCOS crosstalk, such as gut permeability, inflammation, short-chain fatty acids, neurotransmitters, gastrointestinal hormones, bile acids, and the sex hormone-gut microbiota axis. Our review highlights that the current state of the research on the Gut-Brain-PCOS axis is rather preliminary, and the existing studies possess various limitations and often lack rigorous study design. Therefore, more research is needed on humans with a bigger sample size, different ethnicities, and wider age groups to clarify the microbial patterns involved, and in parallel, the field should move from descriptive studies to mechanistic approaches.}, }
@article {pmid40967406, year = {2025}, author = {Harwood, M and South, J and Dunn, AM and Stebbing, PD and Burgess, A and Bojko, J}, title = {Pathogen diversity of the non-native narrow-clawed crayfish (Pontastacus leptodactylus) in a UK water body.}, journal = {Journal of invertebrate pathology}, volume = {}, number = {}, pages = {108458}, doi = {10.1016/j.jip.2025.108458}, pmid = {40967406}, issn = {1096-0805}, abstract = {Biological invasions are intrinsically linked to introducing associated symbiotic organisms, some of which can be parasitic or pathogenic. The pathogenic risk of an 'invasive parasite' (aka. exotic pathogen) stems from its potential to infect native hosts and induce behavioural change or mortality, with the pathogen potentially presenting a greater risk than the host. Conversely, parasites translocated by invasive hosts may also reduce the impact of their host, indirectly curbing the hosts impact on the invaded ecosystem. In this study, we develop a pathogen profile for the narrow-clawed crayfish, Pontastacus leptodactylus. This is a non-native species in the United Kingdom, and poses a possible risk as a sink for invasive parasites. We use histopathology, metagenomics and metratranscriptomics to outline the symbiotic diversity harboured by a P. leptodactylus population from West Yorkshire, England. We discovered several protozoan and bacterial species that appear to be putatively commensal with this invader, as well as several RNA viruses (Hepelivirales; Picornavirales; Nodaviridae, and others) that may be more pathogenic in nature. Microsporidia and Nudiviridae were absent in our population sample set, as were all metazoan obligate parasites, such as trematodes and acanthocephalans. Using the novel genomic and pathological data available to us, we have explored the evolutionary history of each symbiotic species and provided an initial assessment on the putative risk to native species.}, }
@article {pmid40967080, year = {2025}, author = {Chen, J and Li, W and Yang, L and Li, J and Wang, S and Chen, Z and Xu, S and Wen, M and Liang, J and Hu, Z and Pan, F and He, L and Gu, L and Wang, Z and Chen, H and Guo, Z}, title = {Microbiota-derived butyrate potentiates MSLN CAR-T cell therapy by metabolic reprogramming and extracellular matrix remodeling.}, journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie}, volume = {192}, number = {}, pages = {118560}, doi = {10.1016/j.biopha.2025.118560}, pmid = {40967080}, issn = {1950-6007}, abstract = {Despite the success of chimeric antigen receptor (CAR)-T cell therapy in hematologic malignancies, its efficacy in solid tumors remains limited due to T cell dysfunction and immunosuppressive microenvironments. Emerging evidence suggests that gut microbiota-derived metabolites, particularly short-chain fatty acids (SCFAs), may enhance T cell function, but their role in CAR-T therapy is unexplored. Here, in a small patient cohort (n = 4), preliminary metagenomic and metabolomics data suggested an association between higher butyrate levels and improved CAR-T responses, motivating our investigation of sodium butyrate (NaB), a microbiota-derived short-chain fatty acid, as a potential enhancer of CAR-T cell function through integrated metabolic and transcriptional reprogramming. Functional screening showed that NaB treatment augmented CAR-T cell antitumor activity while promoting a memory-like phenotype and reducing exhaustion markers. Mechanistically, NaB amplified antigen-driven phosphorylation of signaling effectors (p-ERK1/2, p-ZAP-70, p-AKT), inducing dual activation of glycolytic and oxidative phosphorylation pathways, coupled with upregulation of extracellular matrix (ECM)-remodeling genes (MMPs, Collagens), thereby improving tumor homing capacity. These preliminary findings suggest NaB as a potential link between microbial metabolism and CAR-T cell efficacy, offering a promising yet exploratory strategy to optimize adoptive immunotherapy through signaling-metabolic-ECM crosstalk, pending validation in larger cohorts.}, }
@article {pmid40966918, year = {2025}, author = {Sun, H and Hu, J and Wang, B and Wang, G and Liu, Y and Yang, X and Wang, G and Zhang, Y and Ding, J and Lv, X and Qu, Z and Zhang, S}, title = {Short-chain PFAS in coastal sediments: PFBS-driven antimicrobial resistance and pathogen risks.}, journal = {Water research}, volume = {288}, number = {Pt A}, pages = {124579}, doi = {10.1016/j.watres.2025.124579}, pmid = {40966918}, issn = {1879-2448}, abstract = {Coastal sediments serve as reservoirs for emerging contaminants, like perfluorobutane sulfonic acid (PFBS), antibiotic resistomes, and pathogens, posing risks to marine ecosystems and public health. Here, we investigate the effects of PFBS on antimicrobial resistance and pathogen dynamics in sediments through metagenomics. Our findings show that coastal sediments contain various antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and bacterial pathogens, with PFBS exposure significantly altering their abundance and composition. PFBS exposure increased ARGs (34.44 %-51.11 %) and MGEs (42.96 %-52.96 %). Importantly, high-risk vanY (vanB culuster) (1.37-fold) and vanYG1 (1.21-fold), were considerably enriched. Additionally, among 1190 detected pathogens, 67 emerging pathogens were extensively shared across all 28 samples. Notably, prevalent T. pallidum (9.69-fold) and S. pneumoniae (3.82-fold) exhibited the most pronounce increases in PFBS-exposed sediments. Further analysis revealed that 24.67 % of the pathogens co-harbored both ARGs and MGEs, amplifying resistance dissemination and pathogen virulence. Remarkably, emerging M. smegmatis and Y. pseudotuberculosis, harboring the predominant high-risk vanY (vanM cluster), pose a critical antimicrobial threat to coastal ecosystems. These results underscore PFBS as a key driver of antimicrobial resistance and pathogenic proliferation in coastal sediments, highlighting the urgent need for further insight into the effects of short-chain PFAS on marine ecological security.}, }
@article {pmid40966609, year = {2025}, author = {Wu, L and Bao, D and Liao, H and Yan, M and Ge, Y and Han, Z and Xia, X}, title = {Pore-Scale Mass Transfer Heterogeneity Shapes Nutrient Accessibility and Functional Assembly in Porous Microbial Ecosystems.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf205}, pmid = {40966609}, issn = {1751-7370}, abstract = {Porous ecosystems represent ubiquitous microbial habitats across natural settings including soil, gut tract, and food matrices, where microscale spatial architecture critically shapes microbial colonization and interactions. Yet, the mechanisms of how pore-scale physical constraints influence microbial community assembly and metabolic performance remain poorly understood. Here, we employed a microfluidic platform with tunable inter-pillar spacings, coupled with a multi-omics approach including in situ imaging, exometabolomics, metagenomics, and metatranscriptomics, to investigate how pore-size modulates microbial community dynamics. Comparing representative small (50 μm) and large (150 μm) pore-sizes, we found that larger pore-sizes promoted greater biomass accumulation and significantly enhanced exometabolite production, particularly of amino acids. Microscopy and quantitative assays revealed that 150 μm pores facilitated more efficient substrate degradation, especially of carbohydrates. Taxonomic profiling showed that increasing pore-size reduced community evenness while enhancing richness, selectively enriching carbohydrate-degrading and amino acid-producing taxa, and promoting more complex, positively correlated co-occurrence networks. Metatranscriptomic analysis further demonstrated that larger pore-size significantly upregulated key functional genes involved in substrate degradation, amino acid biosynthesis, and stress response pathways. Fluorescent tracer assays revealed pronounced mass transfer heterogeneity, where smaller pores exhibited prolonged solute persistence and steeper chemical gradients, ultimately restricting substrate availability and microbial activity. Collectively, our results reveal that alleviation of microscale spatial constraints enhances nutrient accessibility, metabolic function, and community organization in porous ecosystems, underscoring the pivotal role of physical microstructure in regulating both the taxonomic composition and functional capacity of microbial ecosystems.}, }
@article {pmid40966389, year = {2025}, author = {Yan, Y and Zhou, X and Liu, L and Cai, Z and Penuelas, J and Huang, X}, title = {Soil Nutrient Enrichment Induces Trade-Offs in Bacterial Life-History Strategies Promoting Plant Productivity.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e10066}, doi = {10.1002/advs.202510066}, pmid = {40966389}, issn = {2198-3844}, support = {U21A20226//National Natural Science Foundation of China/ ; 42430701//National Natural Science Foundation of China/ ; KYCX24_1825//Graduate Research and Innovation Projects of Jiangsu Province/ ; CX(23)1038//Jiangsu Provincial Agricultural Science and Technology Independent Innovation Fund/ ; 2023YFD1902000//Key Technologies Research and Development Program/ ; }, abstract = {Despite the global prevalence of anthropogenic soil nutrient enrichment, its impacts on the trade-offs in microbial life-history strategies remain poorly understood, which is critical for agroecosystem productivity. Here, large-scale observational studies are integrated with controlled experiments to systematically evaluate how soil nutrient enrichment affects bacterial functional potential and growth-rate potential, ultimately determining microbial functions and plant productivity. These findings reveal stark contrasts between nutrient-poor open field (OF) and nutrient-rich greenhouse (GH) soils across multiple paired sites using 16S rRNA gene amplicon and metagenomic sequencing. OF microbial communities dominated by oligotrophs have higher taxonomic diversity, larger average genome sizes with abundant nutrient-cycling genes, but lower 16S ribosomal RNA gene operon copy numbers and predicted maximum growth rates. Conversely, GH communities dominated by copiotrophs have higher growth-rate potential, more plant-beneficial bacteria, and higher diversity of functional genes (e.g., biofilm formation, secondary metabolism, and bacterial chemotaxis), but lower bacterial functional potential. Controlled pot experiments demonstrate that GH-enriched microbial functions strongly promote plant growth, particularly under sufficient nutrients and abiotic stress. These findings reveal a nutrient-driven trade-off between bacterial functional potential and growth rate, with implications for optimizing nutrient management strategies in precision agriculture to enhance specific microbial functions and plant productivity.}, }
@article {pmid40966281, year = {2025}, author = {Dai, J and Chen, C and Zhai, ZQ and Gao, AX and Johnson, DR and Kopittke, PM and Zhao, FJ and Wang, P}, title = {The balance between microbial arsenic methylation and demethylation in paddy soils underpins global arsenic risk and straighthead disease in rice.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {38}, pages = {e2508311122}, doi = {10.1073/pnas.2508311122}, pmid = {40966281}, issn = {1091-6490}, support = {42325701 W2411035//National natural science foundation of china/ ; }, mesh = {*Oryza/microbiology/metabolism ; *Arsenic/metabolism/toxicity ; *Soil Microbiology ; Methylation ; Soil/chemistry ; *Plant Diseases/microbiology ; *Soil Pollutants/metabolism ; Bacteria/metabolism/genetics ; Cacodylic Acid/metabolism ; Food Contamination/analysis ; }, abstract = {Arsenic contamination in rice poses a global challenge to food safety and agricultural productivity, as toxic methylated arsenic species-dimethylarsinic acid (DMA) and its highly toxic derivative, methylated monothioarsenate (DMMTA)-accumulate in rice grains. These arsenic species endanger human health and trigger rice straighthead disease, a crop disorder that drastically reduces yields. However, the microbial ecological processes driving arsenic speciation in paddy soils, and their link to striking geographic disparities in rice arsenic speciation profiles and disease prevalence, remain poorly understood. Here, we integrate soil chronosequences spanning 1 to 2,000 y of rice cultivation, a global metagenomic survey of 801 paddy soils, controlled incubations, and field surveys to demonstrate that the balance between arsenic-methylating and arsenic-demethylating microbes is the key determinant of rice grain arsenic speciation and straighthead disease susceptibility. We show that young and moderate-age paddy soils (<700 y), common in regions such as the Americas and Europe, are enriched in arsenic-methylating bacteria, leading to elevated DMA and DMMTA in soils and rice grains. In contrast, ancient paddies in Southeast Asia harbor robust populations of DMA-demethylating methanogenic archaea that effectively mitigate the buildup of these toxic arsenic species. We identify core microbial taxa whose abundances serve as predictive biomarkers and construct a global risk map linking a high methylator-to-demethylator ratio in soils with increased straighthead disease incidence. These findings advance our understanding of arsenic biogeochemistry in agroecosystems and establish a predictive framework for identifying regions at elevated risk of arsenic-induced crop disorders and food contamination.}, }
@article {pmid40966087, year = {2025}, author = {Pu, Y and Qi, X and Huang, L and Wu, W and Zhou, X and Li, W and Yang, Z and Kong, M and Shen, J and Qi, W and Sun, Z and Mei, Z and Wang, Q and Yang, W and Gao, X and Wang, X and Liu, Z and Yuan, C and Zheng, Y}, title = {Gut metagenome and plasma metabolome profiles in older adults suggest pyruvate metabolism as a link between sleep quality and frailty.}, journal = {Cell reports}, volume = {44}, number = {10}, pages = {116297}, doi = {10.1016/j.celrep.2025.116297}, pmid = {40966087}, issn = {2211-1247}, abstract = {Poor sleep quality is associated with increased frailty in older adults, but the role of the gut microbiome in this relationship remains unclear. Here, gut metagenome and plasma metabolome were profiled in 1,225 individuals aged 62-96 years. Poor sleep quality was associated with reduced abundances of potential probiotics such as Faecalibacterium prausnitzii and elevated abundances of pathobionts. A gut microbiome sleep quality index (GMSI) was developed to quantify microbial balance related to better sleep quality; higher GMSI scores were inversely associated with frailty and related clinical traits. Pyruvate metabolism emerged as a key microbial pathway linking sleep quality to frailty, with features such as F. prausnitzii abundance and microbial pyridoxal 5'-phosphate biosynthesis implicated in this connection. These findings deepen our understanding of microbiome-metabolome pathways related to sleep quality and frailty in aging and provide a valuable resource for future longitudinal and interventional studies.}, }
@article {pmid40966011, year = {2025}, author = {Pan, Y and Lv, Y}, title = {Challenges and prospects for the application of skin microbiome to forensic individual identification: A narrative review.}, journal = {Medicine, science, and the law}, volume = {}, number = {}, pages = {258024251378811}, doi = {10.1177/00258024251378811}, pmid = {40966011}, issn = {2042-1818}, abstract = {The microbiome has been at the center of a cross-section of disciplines with a wide range of applications and research methodologies, the impact of which is also reflected in forensic science. The skin microbiome is considered a "microbial fingerprint" due to its highly personalized characteristics and can be used for forensic individual identification. This narrative review systematically combs through the literature on skin microbiome and forensic applications, focusing on the characteristics, current applications, challenges, and future prospects of the skin microbiome in the field of forensic individual identification. It first explores host specificity, temporal stability, and marker characteristics. Then, by linking individuals with objects, individuals, and the environment, it analyzes the applications in forensic scenarios. It also introduces two commonly used main analytical techniques and their respective advantages and disadvantages. With the development of technology, machine learning has gradually been applied to forensic work. However, there are still four major challenges in practical application, namely ethical, technical, database and biological challenges. In this context, we provide a standardized process through a hypothetical case and propose a multi-omics collaborative analysis framework for the first time, combining metagenomics, metabolomics, and non-omics data (such as geographical information, image records) to illustrate its enhanced effects in scenarios such as sexual assault and disaster victim identification. Overall, despite the challenges, the application of skin microbiome in forensic science is promising and is expected to play an important role in the future of forensic practice.}, }
@article {pmid40965271, year = {2025}, author = {Dell'Acqua, AN and Scicchitano, D and Simoncini, N and Mercanti, I and Leuzzi, D and Turroni, S and Corlatti, L and Rampelli, S and Colonna, M and Corinaldesi, C and Candela, M and Palladino, G}, title = {Ski Tourism Shapes the Snow Microbiome on Ski Slopes in the Italian Central Alps.}, journal = {Environmental microbiology reports}, volume = {17}, number = {5}, pages = {e70195}, doi = {10.1111/1758-2229.70195}, pmid = {40965271}, issn = {1758-2229}, mesh = {Italy ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; *Skiing ; *Snow/microbiology/virology ; RNA, Ribosomal, 16S/genetics ; *Tourism ; Humans ; Viruses/classification/genetics/isolation &amp; purification ; Metagenomics ; Seasons ; }, abstract = {Winter sports exert significant anthropogenic pressures on the snow microbiome, affecting the entire alpine ecosystem. The massive usage of artificial snow, human occupation, and the release of xenobiotics like microplastics or ski wax components on ski tracks can profoundly alter snow microbial ecology. Here, we reconstructed the temporal dynamics of the snow microbiome at three sites in the Italian Alps: inside and outside a ski track at the impacted site of Santa Caterina Valfurva and near Cancano lake as an unimpacted control. Using epifluorescence microscopy, 16S rRNA amplicon sequencing, and inferred metagenomics, we found that the snow microbiome inside the track presented a higher load of prokaryotes and viruses. Notably, N2-fixing microorganisms from cryospheric environments and host-associated taxa, like Terrisporobacter, Clostridium sensu stricto, Enterococcus, and Muribaculaceae, and the opportunistic pathogen Citrobacter characterised the impacted site. These microorganisms could originate from the river water used to produce artificial snow during winter. Our findings highlight the complexity and multifunctionality of the snow microbiome, where microorganisms with different ecological propensities can coexist, and the detectable impact of ski tourism, which enriches host-associated and xenobiotic-degrading microorganisms. This underscores the need for systematic monitoring and protection of the snow microbiome in the Alpine environment from anthropogenic threats.}, }
@article {pmid40965152, year = {2025}, author = {Singh, N and Braukmann, TWA and Neale, M and Long, GS and Stein, D and Van Caeseele, P and MacKenzie, KD and Minion, J and Van Domselaar, G and Graham, M and Tyler, A and Patel, SN and Duvvuri, VR and Tsang, RSW}, title = {Complete genome sequences of two Treponema pallidum subsp. pallidum specimens from Canadian patients.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0064125}, doi = {10.1128/mra.00641-25}, pmid = {40965152}, issn = {2576-098X}, abstract = {We report the genome sequences of two Treponema pallidum subsp. pallidum specimens in Canada, with basic details on the genetic diversity and antimicrobial resistance. This data contributes to the understanding of T. pallidum evolution and epidemiology, supporting syphilis surveillance and public health efforts.}, }
@article {pmid40965138, year = {2025}, author = {Barker, HA and Bhimani, S and Tirado, D and Canas, JJ and Lemos, LN and Roesch, LFW and Ferraro, MJ}, title = {Deficiency of cannabinoid receptors enhances host susceptibility to bacterial infection.}, journal = {mBio}, volume = {}, number = {}, pages = {e0208825}, doi = {10.1128/mbio.02088-25}, pmid = {40965138}, issn = {2150-7511}, abstract = {Host resilience to bacterial infection depends on tightly regulated immune responses, which can be shaped by metabolic cues, including the contribution from bioactive lipids. The endocannabinoid system (ECS), a lipid signaling network known for its neuromodulatory roles, also influences immunity; however, the receptor-specific contributions of cannabinoid receptor 1 (CB1R) and cannabinoid receptor 2 (CB2R) in host-pathogen interactions remain incompletely defined in this context. Using receptor-deficient mouse models, we investigated how CB1R and CB2R modify immune responses to Salmonella Typhimurium. CB1R-deficient (CB1R-KO) mice exhibited heightened systemic inflammation, impaired bacterial clearance, and reduced survival in systemic infection, associated with dysregulated macrophage polarization and diminished neutrophil recruitment. In contrast, CB2R-KO mice showed increased susceptibility in both systemic and mucosal infection models, marked by a pro-inflammatory macrophage profile, enhanced neutrophilia, and microbiota dysbiosis. Shotgun metagenomic analysis revealed a reduced abundance of specific protective commensals and altered microbial metabolic pathway profiles in CB2R-KO mice, suggesting a role for CB2R in maintaining mucosal immune-microbiota homeostasis. Collectively, these findings highlight non-redundant roles for CB1R and CB2R in regulating immune dynamics and salmonellosis disease severity, and they point to the ECS as a potential target for host-directed immunomodulatory therapies.IMPORTANCEEffective immunity against bacterial pathogens requires a delicate balance between microbial clearance and the containment of inflammatory damage encountered during many infections. The molecular pathways that regulate this equilibrium remain incompletely defined, and the involvement of bioactive lipid signaling mechanisms also needs to be better described. Here, we show that the endocannabinoid receptors CB1R and CB2R play non-redundant roles in host defense against Salmonella infection. CB1R deficiency results in exacerbated systemic inflammation, defective bacterial clearance, and dysregulated macrophage polarization. In contrast, CB2R deficiency leads post-infection to gut dysbiosis and has been found to negatively affect the outcome for the host in both systemic and mucosal infection with Salmonella. By describing cannabinoid receptor-specific contributions to immune regulation and microbiota dynamics, our findings reveal a previously underappreciated axis of host-pathogen interaction. This study broadens our understanding of lipid-mediated immune modulation and identifies CB1R and CB2R as potential targets for therapies aimed at restoring immune homeostasis and improving infectious disease outcomes.}, }
@article {pmid40964666, year = {2025}, author = {Shao, X and Zheng, M and Ye, C and Lu, J and Li, M and Su, K and Lin, H and He, L and Qi, X and Wang, J}, title = {The protective effect of Blautia coccoides in secondary injury of intracerebral hemorrhage.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1616222}, pmid = {40964666}, issn = {1664-302X}, abstract = {Intracerebral hemorrhage (ICH) is a severe stroke with high rates of disability and mortality. Emerging evidence suggests a link between neurological disorders and gut microbiota dysbiosis, though the underlying mechanisms remain unclear. To investigate the role of gut microbiota in ICH, we conducted metagenomic analysis of fecal samples from 35 healthy individuals and 36 patients with ICH, including 29 survivors and seven deceased patients. Metagenomic analysis revealed decreased gut microbiota diversity in patients with ICH, with Blautia genus identified as potential biomarkers. We also established an ICH mouse model via stereotactic autologous blood injection to assess the therapeutic potential of Blautia genus. Blautia coccoides (BC), a representative strain, improved neurofunctional outcomes in ICH mice, reduced tissue damage and neuronal apoptosis, and decreased glial cell activation markers (GFAP and Iba1). BC treatment also lowered the serum levels of pro-inflammatory cytokines (TNF-α, IL-6, and IL-1β) and partially restored gut microbial homeostasis. These findings suggest that BC plays a crucial role in ICH progression and may serve as a potential therapeutic agent by modulating gut microbiota. Further research and clinical trials are necessary to validate its efficacy and safety in humans.}, }
@article {pmid40964625, year = {2025}, author = {López Clinton, S and Iwaszkiewicz-Eggebrecht, E and Miraldo, A and Goodsell, R and Webster, MT and Ronquist, F and van der Valk, T}, title = {Small Bugs, Big Data: Metagenomics for Arthropod Biodiversity Monitoring.}, journal = {Ecology and evolution}, volume = {15}, number = {9}, pages = {e72163}, pmid = {40964625}, issn = {2045-7758}, abstract = {Obtaining genome-wide data from complex samples, such as environmental material or bulk species collections, is increasingly feasible, yet inferring species presence and population genomic insights remains challenging. We applied metagenomic sequencing to 40 arthropod bulk samples collected with Malaise traps across Sweden and compared results with metabarcoding of the same material. Using a custom genome database, we achieved genus-level classification largely consistent with metabarcoding. While metagenomics detected all genera identified by metabarcoding, conservative filtering thresholds designed to minimise false positives also excluded some true signals, particularly for low-abundance taxa. Taxonomic overlap between methods was further constrained by limited reference database representation. Beyond taxonomic assignment, metagenomic sequencing yielded genome-level information: we inferred haplotype diversity, heterozygosity and geographic population structure for several abundant species, including variable degrees of hybrid origin in red wood ants and the genetic distinctiveness of Gotland bumblebees. Finally, by-catch plant DNA present in the bulk samples revealed plausible arthropod-plant interactions, several of which align with known ecological associations. Together, these results demonstrate the potential of metagenomics for biodiversity monitoring and population genomics, while underscoring the importance of filtering criteria and comprehensive reference databases.}, }
@article {pmid40964394, year = {2025}, author = {Urban, J and Kav, AB and Kindschuh, WF and Park, H and Khan, RR and Watters, E and Pe'er, I and Uhlemann, AC and Korem, T}, title = {Identification of Sample Processing Errors in Microbiome Studies Using Host Genetic Profiles.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.09.07.674724}, pmid = {40964394}, issn = {2692-8205}, abstract = {In microbiome studies, sample processing errors are frequent and difficult to detect, especially in large studies involving multiple sites, personnel, and sample types. We present two complementary approaches to identify such errors using host DNA profiled via metagenomic sequencing of microbiome samples. The first approach compares host SNPs inferred from metagenomics to independently obtained genotypes (e.g., microarray genotypes) to match samples to their donors, while the second method compares metagenomics-inferred SNPs between samples to identify samples supplied by the same donor. Furthermore, we demonstrate that combining these methods with experimental metadata provides greater confidence in the identification of errors. Analyzing a longitudinal vaginal microbiome dataset, we demonstrate the ability of our approach to identify mislabeled samples. Using subsampling, we further show that our methods are robust to low sequencing coverage. Overall, our analysis highlights the frequency of processing errors in microbiome studies. We therefore recommend applying error-detection methods in all studies with suitable data.}, }
@article {pmid40964292, year = {2025}, author = {Yao, ML and Lin, P and Hua, K and Zhang, W}, title = {The biosynthetic gene cluster landscape of the oral microbiome across health and dental caries.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.09.04.674288}, pmid = {40964292}, issn = {2692-8205}, abstract = {Specialized metabolites encoded by biosynthetic gene clusters (BGCs) in the oral microbiome remain largely unexplored in the context of oral health and disease. Previous genome-centric surveys have cataloged hundreds of uncharacterized BGCs in the oral cavity associated with health and disease, but these studies relied on reference genomes and did not capture strain-level variation or the native distribution of BGCs. Here, we assembled three independently sourced metagenomic datasets from healthy and dental caries samples, extracted BGCs, and quantified their abundance alongside expression in a metatranscriptomic dataset. We first identified that aryl polyene, ribosomally synthesized and post-translationally modified peptide (RiPP), and nonribosomal peptide (NRP) encoding BGCs were the most abundant BGC classes across all three metagenomic datasets. We then grouped these BGCs into homology-based families and found that homologous clusters were usually consistently associated with either health or dental caries, suggesting conserved community-level roles for BGCs. An elastic-net regression model further selected 45 BGCs out of >5000 that could distinguish healthy and dental caries samples in the metatranscriptomic dataset, which demonstrated that BGCs could be predictive markers of disease. This analysis emphasizes the importance of high-quality metagenomic and metatranscriptomic datasets to resolve BGC expression patterns and to guide discovery of metabolites relevant to oral health and disease.}, }
@article {pmid40964253, year = {2025}, author = {France, M and Chaudry, I and Elsherbini, J and Ravel, J}, title = {kSanity: A k-mer based application for precision bacterial strain detection and quantification.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.09.04.674052}, pmid = {40964253}, issn = {2692-8205}, abstract = {MOTIVATION: Accurate detection and quantification of bacterial strains in clinical samples is necessary to measure their colonization and persistence. Past methods to achieve this relied either on strain-specific qPCR assays, or shotgun metagenomic read mapping approaches. The resident microbial community is a major source of interference in both assays because it can contain conspecific strains bearing similarity to the focal strain(s).<br><br>RESULTS: We present kSanity, a k-mer based application for the detection and quantification of targeted bacterial strains in shotgun metagenomic data. Because kSanity uses exact string matches between the reads and reference, it is less sensitive to interference by conspecific strains. We test the performance of kSanity using a combination of in silico spike-in experiments, and in vivo observational data. Our results demonstrate that kSanity provides precise and accurate quantification of targeted bacterial strains, even when they are present at low sequence coverage in the metagenome.<br><br>kSanity is available at: https://github.com/ravel-lab/kSanity.}, }
@article {pmid40964170, year = {2025}, author = {So, SHS and Jiang, W and Li, Y and Hold, GL and Goodrick, K and Min, A and Bourke, MJ and El-Omar, EM and Jiang, XT and Yim, HCH}, title = {Mucosal DNA and RNA virome alterations and their interactions with human RNA and microRNA transcriptomes in colorectal polyps.}, journal = {eGastroenterology}, volume = {3}, number = {3}, pages = {e100194}, pmid = {40964170}, issn = {2976-7296}, abstract = {BACKGROUND: Imbalance in the gut microbiome is known to play a role in colorectal cancer (CRC) development. Recent studies observed alterations in the faecal and mucosal DNA virome in CRC, but the role of mucosal virome including both DNA and RNA viruses in colorectal adenomas, the precursors to CRC, is unclear. Here, we investigated the human host transcriptome, mucosal virome and potential correlations between them in paired biopsy samples of colorectal polyps and their adjacent normal tissue.<br><br>METHODS: Paired colorectal polyp and adjacent normal mucosa biopsies from the same individuals were collected from 41 patients and subjected to comprehensive multiomics profiling. Total RNA and microRNA were analysed using whole transcriptome sequencing, while virus-like particles were enriched from paired samples and profiled via shotgun metagenomic sequencing. Integrated statistical and network analyses were performed to compare expression profiles and virome composition between polyp and adjacent normal mucosa from the same individuals, and to identify host-virome associations.<br><br>RESULTS: The host transcriptome was found to be highly altered in polyps, whereby numerous differentially expressed RNAs and microRNAs were identified compared with their paired adjacent normal mucosa from the same individuals. Pathway enrichment analysis revealed that these differentially expressed genes were enriched in metabolism and absorption, neurotransmission and cell signalling pathways. The mucosal virome was also altered in polyps, with reduced viral richness and evenness and distinct community composition compared with their paired adjacent normal mucosa from the same individuals. Poxviridae, Retroviridae and BeAn 58058 virus were enriched, whereas Caudoviricetes sp was depleted. Such mucosal virome signatures correlated with host transcriptomic signatures in polyps. Caudoviricetes sp was negatively correlated with genes involved in cancer pathways, thus is potentially CRC-protective. Conversely, Poxviridae, Retroviridae and BeAn 58058 virus were negatively correlated with genes involved in tumour suppression, thus are potentially CRC-inducing.<br><br>CONCLUSION: This study suggests that alterations in host transcriptomes and virome of colorectal polyps are correlated, providing a foundation for future functional studies.}, }
@article {pmid40964040, year = {2025}, author = {Knight, R and Din, MO and Salido, R and Wright, G and Brennan, C and Ambre, M and Hansen, L and Boyer, T and Cao, J and Oles, R and Patel, L and Weng, Y and McDonald, D and Bhute, S and Solini, G and Karthikeyan, S and Humphrey, G and DeHoff, P and Kralicek, S and Levy, J and Zeller, M and Hecht, G and Laurent, L and Yeo, G and Andersen, K and Bartko, A}, title = {Versatile wastewater monitoring of pathogens and antimicrobial resistance enabled by metatranscriptomics and long-read metagenomics.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-7492978/v1}, pmid = {40964040}, issn = {2693-5015}, abstract = {Widespread interest in the development of population-wide pathogen and antimicrobial resistance (AMR) monitoring has revealed wastewater's microbial footprint as a marker of public health. Near-source wastewater remains a difficult sample type for microbiome analyses but represents a closer link to human health than the downstream products of its treatment. Few studies integrate methods for non-targeted monitoring applications, and critically, current methods cannot connect AMR genes to species, nor resolve full genomes. We address these challenges by developing a pipeline that enables untargeted metagenomics, metatranscriptomics, and novel long-read metagenomics (LRG). We achieve untargeted pathogen detection, limited by highly abundant resident species, while retaining microbial information with near-source sampling. Furthermore, LRG identifies antibiotic resistance gene-containing microbes and enables assembly of culture-independent genomes with previously unreported AMR genes. We establish an integrated approach to broadly monitor pathogens in wastewater, while demonstrating the importance of LRG to illuminate microbial AMR at the species level.}, }
@article {pmid40963959, year = {2025}, author = {Sarkar, A and Groer, M and Ho, TTB and Dishaw, LJ}, title = {Distribution of microsporidia in preterm and full-term infant gut microbiomes and implications for host health.}, journal = {Frontiers in pediatrics}, volume = {13}, number = {}, pages = {1651866}, pmid = {40963959}, issn = {2296-2360}, abstract = {BACKGROUND: Microsporidia are a group of single-celled fungi which infect various chordates including humans, where they mainly pose a risk to immunocompromised individuals. This study aimed to investigate the occurrence of microsporidia in groups of very low birth weight (VLBW) and extremely low birth weight (ELBW) infants, comparing the findings with a publicly available dataset of term infant samples.<br><br>METHODS: Metagenomic sequencing was conducted on stool samples from two cohorts of preterm infants: cohort 1, which included 10 samples collected at 2, 4, and 8 weeks, and cohort 2, which consisted of 12 samples taken at 6 weeks and 2 years. These results were compared with data from a previously published cohort of term infants (cohort 3), which had 19 samples (in duplicates) collected between 1 and 14 weeks. Microsporidia identified from the data were separated and principal component analysis (PCA) was utilized to compare the microbiome of term and preterm infants. Microsporidia species that were significantly different between the two groups were identified using ALDEx2.<br><br>RESULTS: Early-stage microsporidia distribution did not show significant differences between the cohorts. However, significant differences emerged as the preterm infants grew, particularly at the age of 2 years (cohort 2). The levels of Mitosporidium daphniae (p&#x2009;=&#x2009;0.03) and Nematocida homosporus (p&#x2009;=&#x2009;0.04) were significantly higher in preterm infants compared to those born at term. Additionally, Encephalitozoon romaleae and Nosema ceranae, revealed an increase in cohort 2 from 6 weeks to 2 years.<br><br>CONCLUSIONS: This manuscript reports, to the best of our knowledge, the first occurrence of microsporidia in the early stages of human life. Some microsporidia not only persist into childhood but also become more prevalent during this time. However, we wish to emphasize that the findings from this study should be interpreted with caution, considering the low sample size and comparing cohorts examined at different time points of infants' age. Future studies with larger sample sizes and more mechanistic approaches could help clarify their role in childhood development and long-term health.}, }
@article {pmid40963667, year = {2025}, author = {Thakur, R and Dhar, H and Wozniak, TM and Mathew, S}, title = {Addressing the overlooked frontier in AMR research and surveillance.}, journal = {Frontiers in public health}, volume = {13}, number = {}, pages = {1625515}, pmid = {40963667}, issn = {2296-2565}, }
@article {pmid40963618, year = {2025}, author = {Zhang, S and Sun, L and Wang, L and Liu, Y and Tan, G and Liu, T and Yang, W and Liu, X}, title = {Human cytomegalovirus infection-induced lymphocytosis diagnosed by metagenomic next-generation sequencing: a case report and literature review.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1637085}, pmid = {40963618}, issn = {1664-3224}, mesh = {Humans ; *Cytomegalovirus Infections/diagnosis/virology/drug therapy/complications ; Male ; *High-Throughput Nucleotide Sequencing/methods ; Adult ; *Lymphocytosis/diagnosis/etiology/virology ; *Cytomegalovirus/genetics ; *Metagenomics/methods ; }, abstract = {BACKGROUND: Human cytomegalovirus (HCMV) exhibits a high prevalence and is a major threat to immunocompromised individuals. Conventional diagnostic modalities are increasingly struggling to meet evolving clinical needs. Metagenomic next-generation sequencing (mNGS) represents a valuable tool for expeditious microbial identification in diagnostically complex cases.<br><br>CASE PRESENTATION: A 35-year-old man presented with fever, pharyngitis, fatigue, and marked lymphocytosis. No significant abnormalities were detected in imaging and routine tests, and conventional pathogen detection methods failed to identify any suspected pathogens. Targeted next-generation sequencing (tNGS) identified five pathogens: Staphylococcus aureus, Streptococcus mitis group, rhinovirus C, cytomegalovirus (CMV), and human herpesvirus-7. Clinical symptoms alleviated within 7 days of ganciclovir therapy initiation; however, lymphocytosis persisted. Subsequently, mNGS was performed, confirming HCMV infection and providing a definitive diagnosis. During follow-up, the patient's symptoms had largely resolved.<br><br>CONCLUSION: Symptomatic HCMV infections primarily affect immunocompromised individuals, while persistent lymphocytosis associated with HCMV is uncommon. This case highlights the diagnostic and therapeutic utility of mNGS in HCMV infection, especially when conventional diagnostic methods are limited, pathogen abundance is low, and the patient is immunocompromised.}, }
@article {pmid40963595, year = {2025}, author = {Wang, Q and Luo, Y and Mao, C and Xiang, X and Chen, J}, title = {Combined metagenomic and metabolomic analyses reveal gut microbiota dysbiosis and metabolic dysfunction in pediatric neurodevelopmental disorders.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1645137}, pmid = {40963595}, issn = {1664-3224}, mesh = {Humans ; *Gastrointestinal Microbiome ; Female ; Male ; *Metabolomics/methods ; *Metagenomics/methods ; Child, Preschool ; *Dysbiosis/metabolism/microbiology ; *Neurodevelopmental Disorders/metabolism/microbiology/etiology ; Child ; Feces/microbiology ; Metabolome ; }, abstract = {INTRODUCTION: Neurodevelopmental disorders (NDDs) are chronic brain diseases linked to innate immune signaling abnormalities, affecting children with complex gut-brain axis etiologies and limited targeted therapies. While infant microbes/metabolites may predict childhood NDDs, their landscape and host-metabolism interactions in NDDchildren remain unclear.<br><br>METHODS: This study enrolled 40 NDDchildren (mean age: 5.18 &#xb1; 1.77, F:M = 11:29) and 60 healthy controls (HCs; mean age:5.11 &#xb1; 1.42, F:M = 25:35) from Gansu Province Hospital Rehabilitation Center. Shotgun metagenomics and untargeted metabolomics was used to analyze gut microbiota and fecal/plasma metabolites, multi-omics integration analysis was performed to explore host-microbe interactions.<br><br>RESULTS: Clinically, NDD children showed self-care, concentration, and social behavior deficits, with grandparents as primary caregivers, versus parents in HCs. Microbiome analysis revealed reduced gut diversity and dysregulation in NDDs: depleted beneficial taxa including Akkermansia muciniphila and Lactococcus lactis, but enriched GABA/lactateproducing bacteria; and disrupted pathways included polysaccharides/fatty acids/amino acid/purine ribonucleosides metabolism. Fecal metabolomics identified 100 enriched metabolites including polyamines and GABA in 45 pathways and 254 depleted metabolites including bile acids and butyrate in 57 pathways. Plasma metabolomics showed 321 enriched metabolites like free fatty acids in 143 pathways and 270 depleted metabolites including glycerophospholipids in 84 pathways. Notably, phenolic acids, arginine/proline metabolism, and HIF-1 signaling were enriched in both feces and plasma of NDDs children. Benzene derivatives, indoles, steroid hormone biosynthesis, and tryptophan/tyrosine/phenylalanine metabolism were increased in plasma but decreased in feces, while oxidized lipids, amino acids and derivatives, metabolism of glycine/serine/threonine, alanine/aspartate/glutamate, and cysteine/methionine showed the opposite pattern. Venn analysis identified 29 common metabolites, with eight in KEGG maps. 11-dehydrocorticosterone, LPC (17:0/0:0), adipic acid, and sucralose were decreased in feces but increased in plasma; 1-methylhistidine and trigonelline were decreased in both; L-asparagine anhydrous was increased in feces but decreased in plasma; and sarcosine increased in both. Microbe-metabolite correlation analyses linked these metabolites to NDDs depleted species A. muciniphila, L. lactis, A. butyriciproducens, and etc.<br><br>DISCUSSIONS: Collectively, our study presents the first integrated profile of gut microbiome, microbial metabolites, and host metabolome, reveals gut microbiota dysbiosis, functional impairment, and metabolic disturbance in pediatric NDDs. These findings provide a theoretical foundation for microbiotaand metabolite-targeted therapeutic strategies in childhood NDDs.}, }
@article {pmid40963245, year = {2025}, author = {Zeng, L and Guan, J and Wen, S and Gui, S and Wang, L and Li, S and Cheng, X and Cheng, Y and Long, B}, title = {Construction of an autotrophic nitrifying granular sludge partial nitritation system based on reaction rate.}, journal = {Environmental technology}, volume = {}, number = {}, pages = {1-16}, doi = {10.1080/09593330.2025.2558240}, pmid = {40963245}, issn = {1479-487X}, abstract = {This study presented a strategy for rapid establishing partial nitritation using autotrophic nitrifying granular sludge (ANGS), offering a green and efficient solution for treating ionic rare earth mining wastewater, which is characterised by acidic pH, low organic content, and elevated ammonia nitrogen. Experiments were conducted in a sequencing batch reactor (SBR) inoculated with stored granules. By Day 8, the ANGS demonstrated excellent recovery of activity, with the nitrite accumulation rate (NAR) exceeding 90%. Through controlled aeration intensity, the ammonia oxidation rate and nitrite oxidation rate of the ANGS were leveraged to regulate aeration time. A NO2[-]-N/NH4[+]-N ratio of approximately 1.32 was firstly achieved by Day 25 when the nitrogen loading rate (NLR) was 0.24 kg/m[3]·d, and partial nitritation was also achieved by Days 41, 54, 70 and 85 respectively when the NLRs were 0.30, 0.36, 0.42, and 0.48 kg/m[3]·d. Ammonia oxidising bacteria (AOB) remained highly active, while nitrite oxidising bacteria (NOB) were effectively suppressed. By the conclusion of the experiment on Day 90, the dominant microbial communities in the reactor were Nitrosomonas (20.32%), Thauera (12.57%), and OLB8 (10.60%). Metagenomic analysis revealed a significant enhancement in the relative abundance and activity of amoC (encoding ammonia monooxygenase) and hao (encoding hydroxylamine oxidoreductase) in AOB. The calculated conversion costs for different NLRs per cycle were 4.646, 6.845, 8.901, 9.538 and 10.222 RMB/m[3].}, }
@article {pmid40962574, year = {2025}, author = {Schlebusch, S and Graham, RMA and Moss, S and Jennison, AV and Boyle, S and Milne, N}, title = {Rat bite fever diagnosed with clinical metagenomics.}, journal = {Pathology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.pathol.2025.06.008}, pmid = {40962574}, issn = {1465-3931}, }
@article {pmid40962254, year = {2025}, author = {Park, S and You, YA and Lee, G and Hur, YM and Go, YY and Park, S and Kim, YJ}, title = {Vaginal microbiome and its implications in preterm birth.}, journal = {Obstetrics &amp; gynecology science}, volume = {}, number = {}, pages = {}, doi = {10.5468/ogs.25085}, pmid = {40962254}, issn = {2287-8572}, abstract = {Preterm birth (PTB), defined as birth occurring before 37 weeks of gestation, remains a major global public health challenge, affecting approximately 10% of pregnancies worldwide and contributing significantly to neonatal morbidity and mortality. Despite extensive research, the etiology of PTB is multifactorial and not yet fully understood, with ongoing debates regarding the contributions of inflammation, hormonal dysregulation, genetic predisposition, and environmental factors such as microbial dysbiosis. Recent studies have highlighted the role of the vaginal microbiome in pregnancy outcomes, particularly its association with PTB. This review consolidates current findings on the vaginal microbiome's influence on PTB, addressing microbial dysbiosis as a key risk factor. Despite differences in ethnicity, gestational age at sample collection, and analytical methodologies, a common observation is that a decrease in Lactobacillus species is associated with an increased risk of PTB. These differences influence study outcomes by affecting variations in microbial composition, host immune regulation, genetic predisposition, and environmental influences. However, a consistently observed trend is that a Lactobacillus-dominant vaginal microbiome is generally associated with a lower risk of PTB across diverse populations. This review also discusses the limitations of existing research and suggests directions for future microbiome studies.}, }
@article {pmid40961693, year = {2025}, author = {Pan, Z and Wang, W and Xu, W and Yin, Y and Xu, X and Zhu, L and Duan, Y and Lin, J and Ferraro, DO and de Paula, R and Torabi, E and Huang, Q}, title = {Continental-scale characterization of pesticide cocktails in paddy soils: Associations with microbial community structure, function, and extracellular vesicle occurrence.}, journal = {Journal of hazardous materials}, volume = {498}, number = {}, pages = {139879}, doi = {10.1016/j.jhazmat.2025.139879}, pmid = {40961693}, issn = {1873-3336}, abstract = {Modern agricultural practices lead to complex pesticide cocktails in paddy ecosystems, yet their extensive ecological associations with microbial communities and soil biogeochemical cycles remain largely uncharacterized under real-world conditions. Continental-scale investigation across 48 Chinese paddy regions revealed pervasive pesticide contamination, detecting 50 prevalent pesticide residues with widespread co-occurrence patterns (≥ 9 compounds at 90 % sites). Triazole fungicides correlated with suppression of nitrification, denitrification, and dissimilatory nitrate reduction to ammonium (DNRA) genes, suggesting potential disruptions in nitrogen fluxes and nutrient dynamics, possibly contributing to nitrate/nitrite accumulation. Risk quotient-based stratification revealed that high-risk sites exhibited reduced network robustness and modularity, alongside elevated metabolic potential for xenobiotic biodegradation. Notably, 41.2 % of the recovered metagenome-assembled genomes, dominated by Chitinophagales and Gemmatimonadales, encoded dual capabilities for xenobiotic biodegradation and nitrogen cycling, highlighting a potential trade-off. Ubiquitous extracellular vesicles (EVs) were detected in paddy soils at substantial concentrations and were functionally enriched in TonB-dependent transporters and stress-response proteins, suggesting their potential involvement in overcoming pesticide bioavailability barriers. In vitro co-incubation assays further confirmed EVs' capacity as nanoscale carriers for pesticides like tebuconazole. This continental-scale multi-omics integration (pesticide-microbe-EV) advances our understanding of pesticide cocktails' impacts on soil ecological resilience, with significant implications for the sustainability of global rice cultivation systems.}, }
@article {pmid40961667, year = {2025}, author = {Wu, J and Xiong, L and Yang, Y and Li, C and Mao, P and Zhou, Q and Yu, G and Huang, X and Tyagi, RD and He, X and Wong, JWC}, title = {Greenhouse gas emissions from black soldier fly composting of silver and silver sulfide nanoparticle-enriched sludge.}, journal = {Water research}, volume = {288}, number = {Pt A}, pages = {124608}, doi = {10.1016/j.watres.2025.124608}, pmid = {40961667}, issn = {1879-2448}, abstract = {Silver nanoparticles (Ag-NPs) are widely used as antibacterial materials and accumulate in sewage sludge as silver sulfide nanoparticles (Ag2S-NPs) after wastewater treatment. Composting using black soldier fly (BSF) is an effective method for treating sewage sludge. This study investigated the impact of Ag/Ag2S-NP-containing sludge on greenhouse gas emissions during BSF composting. The results indicated that BSF significantly increased N2O and CH4 emissions during composting. However, the addition of 5 mg/kg or 100 mg/kg of Ag/Ag2S-NPs significantly reduced N2O emissions by 51.7-86.1 %, and CH4 emissions by 44.3-92.9 %. Quantitative analysis of genes in the sludge revealed that the inhibition of hao and norB genes, and the enhancement of nosZ genes were critical factors reducing N2O emissions. For CH4, inhibition of methanogenic genes (mcrA) and the enhancement of methane oxidation genes (pmoA) were the primary mechanisms by which Ag2S-NPs reduced CH4 emissions. Based on X-ray absorption spectroscopy (XAS) and single-particle ICP-MS (spICP-MS), Ag was retained predominantly as Ag2S throughout, with small fractions converting to AgCl in the larval gut, and particles exhibited modest size reduction. Further metagenomic analysis revealed Ag-driven alterations in BSF gut microbiota, including decreased microbial diversity, and suppressed denitrification and methanogenesis pathways. This study offers an economical and effective method to reduce greenhouse gas emissions during sewage sludge treatment using BSF composting when Ag2S-NPs are present.}, }
@article {pmid40961652, year = {2025}, author = {Gao, X and Ning, P and Luo, S and Wang, Y and Li, W and Fan, X and Li, X}, title = {Microbiome and pathogen identification, and associated antimicrobial resistance genes and virulence factors in seafood revealed by 16S rRNA amplicon and metagenomic sequencing.}, journal = {International journal of food microbiology}, volume = {443}, number = {}, pages = {111441}, doi = {10.1016/j.ijfoodmicro.2025.111441}, pmid = {40961652}, issn = {1879-3460}, abstract = {16S rRNA amplicon sequencing and metagenomic next-generation sequencing (mNGS) were employed to comprehensively analyze the microbial communities, foodborne pathogens, antibiotic resistance genes (ARGs), and virulence factors (VFs) in four seafood categories: ready-to-eat fish (RET-fish), non-ready-to-eat fish (non-RTE-fish), shellfish, and shrimp. At the phylum level, Pseudomonadota dominated across all samples. The microbial community composition of shellfish exhibited significant distinctions compared to other seafood categories. Metagenomic profiling identified high-risk pathogens, such as pathogenic Vibrio, Salmonella enterica, and Listeria monocytogenes. ARGs and VFs displayed the highest relative abundance in RET-fish, while shellfish exhibited the lowest abundance with statistically significant differences compared to other groups. For ARGs carried hosts, Bacillus-associated tet(L) and Lactobacillus-associated Inu(A) in RTE-fish demonstrated elevated abundance. In contrast, Vibrio species in other groups carried high abundances of ARGs such as qnrS and tet(34). Additionally, Vibrio harbored high levels of VFs, such as flagella and EF-Tu. Furthermore, plasmid-derived contigs co-harboring ARGs and mobile genetic elements (MGEs) were identified, displaying broad host ranges and high homology with plasmids from previously isolated clinical pathogenic strains, which underscores the potential role of seafood as a critical reservoir for the dissemination of ARGs. High-throughput sequencing approaches, integrated with multi-tool bioinformatics pipelines, provided robust insights into microbial communities and associated safety risk factors. These findings highlight the urgent need for targeted surveillance of seafood products and stricter antibiotic regulations in aquaculture to mitigate public health risks posed by foodborne pathogens and antimicrobial resistance.}, }
@article {pmid40961576, year = {2025}, author = {Sun, H and Guo, X and Sun, J and Zhou, W and Yu, Z and Li, M and Zhang, S and Liu, X and Zhao, Y and Zhang, Y}, title = {Metagenome assembled genomes revealed the influences of mariculture and seagrass species on the microbiomes in seawater and rhizosphere biotopes.}, journal = {Marine pollution bulletin}, volume = {222}, number = {Pt 1}, pages = {118703}, doi = {10.1016/j.marpolbul.2025.118703}, pmid = {40961576}, issn = {1879-3363}, abstract = {Seagrasses provide critical ecosystem services, with their associated microbiomes playing vital roles in the health and adaptation of hosts. Metagenome sequencing has significantly advanced our understanding of seagrass-associated microbiomes; however, the application and interpretive reliability of metagenome-assembled genomes (MAGs) remain limited. This study presented a comparative analysis of high-quality MAGs from seawater and rhizosphere samples across five distinct marine habitats. A total of 93 dereplicated high-quality MAGs were obtained from seawater and rhizosphere samples and assigned to 5 and 11 phyla, respectively. Rhizosphere-derived MAGs were predominated by Desulfobacterota and exhibited enriched genes for carbon/nitrogen metabolism, dissimilatory sulfate reduction/oxidation, and glycopeptide antibiotic resistance. In contrast, MAGs from seawater primarily belonged to Pseudomonadota and Bacteroidota, with enriched genes in assimilatory sulfate reduction pathway and fluoroquinolone/tetracycline antibiotic resistance. Statistical analysis revealed that oyster culture had significantly elevated gene abundance of MAG functions linked to carbon metabolism, dissimilatory nitrate reduction, and nitrogen fixation processes in rhizosphere, while differences between seagrass species were minimal. Additionally, environmental factors, such as total organic carbon concentrations and particle sizes, exhibited closer interactions with functions of rhizosphere-associated MAGs compared to seawater samples. Our study provided novel insight into seagrass microbiome ecology, establishing a comparative genome-resolved framework to investigate functional adaptation of marine microbiome across distinct biotopes, and demonstrating the efficacy of MAG-based analysis for unrevealing environment-microbiome interactions in uncultured systems. These findings extend knowledge for developing microbial biomarkers of seagrass ecosystem health and offer methodological references for functional microbiome studies in coastal environments.}, }
@article {pmid40961238, year = {2025}, author = {Shalash, A and Ezzeldin, S and Hashish, S and Salah, Y and Dawood, NL and Moustafa, A and Salama, M}, title = {Gut microbial shifts toward inflammation in Parkinson's disease: Insights from pilot shotgun metagenomics Egyptian cohort.}, journal = {Journal of Parkinson's disease}, volume = {}, number = {}, pages = {1877718X251370156}, doi = {10.1177/1877718X251370156}, pmid = {40961238}, issn = {1877-718X}, abstract = {Gut microbiome alterations are increasingly linked to Parkinson's disease (PD), yet regional signatures remain underexplored. We performed shotgun metagenomic sequencing of stool samples from Egyptian PD patients and healthy controls. PD patients exhibited depletion of short-chain fatty acid-producing taxa, and enrichment of pathobionts. Our findings suggested a pro-inflammatory gut shift in PD and emphasized the need for geographically diverse microbiome studies. While limited in sample size (n = 7 PD patients and n = 6 controls), this pilot addressed a critical gap in African PD microbiome research.}, }
@article {pmid40960652, year = {2025}, author = {Gupta, P and Dhar, H and Bagal, YS and Jaglan, S}, title = {Smart nano-fertilizers: a path to sustainable agriculture.}, journal = {Environmental geochemistry and health}, volume = {47}, number = {10}, pages = {443}, pmid = {40960652}, issn = {1573-2983}, mesh = {*Fertilizers/analysis ; *Agriculture/methods ; *Nanostructures/chemistry ; Soil Microbiology ; Soil/chemistry ; }, abstract = {Nano-fertilizers are one of the greatest innovations for the improvement of agriculture, promoting nutrient uptake efficiency and minimizing nutrient loss and environmental pollution index as to conventional fertilizers. The important properties of nano-fertilizers that enhance their efficiency and help minimize the phenomena involving overuse and harmful runoff are characterized as a high surface-area-to-volume ratio, high solubility, and controlled-release mechanism. Numerous nanomaterials, such as carbonaceous and metal-based ones, have been explored for their potential to modulate nutrient delivery and absorption. The coupling of nanosensors and nano-fertilizers with precision farming ensures real-time nutrient monitoring with targeted fertilization, which helps to eradicate wastage while improving crop productivity. This review addresses the synthesis, mechanisms of action, delivery pathways, and effects on soil microbiota, including comparative advantages and environmental implications. In viewing the possible advantages, key challenges hindering the mass use of nano-fertilizers include potential toxicity, production costs, farmer adoption, scalability, and regulatory compliance. Long-term effects on soil health and ecology require further study. Future research should focus on developing biodegradable, sustainable nano-fertilizers with clear regulatory frameworks.}, }
@article {pmid40960358, year = {2025}, author = {Jones, JA and Moczek, AP and Newton, ILG}, title = {Metagenomes and metagenome-assembled genomes from Onthophagus taurus.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0045725}, doi = {10.1128/mra.00457-25}, pmid = {40960358}, issn = {2576-098X}, abstract = {Shotgun metagenomic sequencing was carried out on Onthophagus taurus larval gut sections, female adult midguts, and pedestals (a maternally provisioned fecal pellet provided to offspring). Here, we present the raw sequencing files for five sample types and 16 annotated metagenome-assembled genomes (MAGs).}, }
@article {pmid40960303, year = {2025}, author = {Qie, J and Cao, M and Xu, M and Zhang, Y and Luo, L and Sun, C and Ke, D and Yuan, S and Jia, W and Qiu, T and Li, T and Du, X and Xiao, C and Hong, Z and Zhang, B}, title = {Multi-cohort analysis unveils novel microbial targets for the treatment of hyperuricemia and gout.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0109125}, doi = {10.1128/msystems.01091-25}, pmid = {40960303}, issn = {2379-5077}, abstract = {The gut microbiota plays a crucial role in the development of hyperuricemia (HUA) and gout. However, the variability in study designs and analytical methods has led to inconsistent conclusions across different studies. Here, we conducted a comprehensive analysis of the gut microbiota associated with HUA and gout by examining 368 16S rRNA sequencing data from four Chinese cohorts, including 159 healthy controls (HC), 136 HUA patients, and 73 gout patients. Our findings indicate that there were significant differences in the gut microbiota composition between the three groups. Specifically, the HUA and gout groups demonstrated an increased abundance of pro-inflammatory bacteria, such as Fusobacterium and Bilophila, while beneficial bacteria known for their anti-inflammatory properties and metabolic benefits, including Christensenellaceae R-7 group, Anaerostipes, and Collinsella, are relatively reduced. Additionally, we developed a predictive model using microbial markers that achieved a high accuracy (area under the curve [AUC] > 0.8) in distinguishing between the HC, HUA, and gout groups. Notably, further metagenomic analysis identified a species-level genome bin (SGB), designated as Phil1 sp00194085, belonging to the order Christensenellales. For the first time, we discovered that this SGB carries a uric acid metabolic gene cluster and possesses enzymes associated with purine metabolism, suggesting its potential role in uric acid metabolism. Overall, our study deepens the understanding of the gut microbiota's role in HUA and gout and lays a foundation for developing innovative therapeutic strategies to effectively control uric acid levels through gut microbiota modulation.In this study, we conducted a comprehensive analysis of gut microbiota across multiple cohorts, identifying distinct microbial signatures in healthy controls, hyperuricemia (HUA), and gout patients. We observed an increase in pro-inflammatory bacteria and a decrease in beneficial bacteria for host metabolism in both the HUA and gout groups. Additionally, we developed a predictive model with high accuracy (area under the curve [AUC] > 0.8) based on microbial markers and discovered a novel species with potential for uric acid metabolism, providing new therapeutic targets for HUA and gout.}, }
@article {pmid40960301, year = {2025}, author = {Yan, Y and Zhao, X and Liang, X and Xue, Y and Niu, Q and Li, D and Zhou, X and Li, Y and Dong, S and Gai, Y}, title = {Global wastewater microbiome reveals core bacterial community and viral diversity with regional antibiotic resistance patterns.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0142824}, doi = {10.1128/msystems.01428-24}, pmid = {40960301}, issn = {2379-5077}, abstract = {Municipal wastewater treatment plants (WWTPs) serve as global repositories for diverse and dynamic microbial communities, reflecting the complex interplay of human activities, environmental conditions, and public health challenges. Despite their importance, a comprehensive understanding of the global distribution, composition, and functional roles of these microbial ecosystems has remained elusive. Here, we present a comprehensive analysis of bacterial and viral diversities in global wastewater systems by examining 575 sampling sites across 74 cities in 60 countries. Through metagenomic analysis, we reconstructed 12,758 non-redundant bacterial metagenome-assembled genomes (MAGs) spanning 70 phyla, with 4,499 MAGs representing novel species. Despite considerable regional variation, we identified a consistent core microbiome present across 70% of global samples predominantly comprising Proteobacteria. We further assembled 1.7 million viral genomes, revealing unprecedented viral diversity with over 1.5 million species-level viral operational taxonomic units (vOTUs). Network analysis demonstrated that transport proteins play crucial roles in maintaining WWTP functional resilience against disturbances. Machine learning approaches effectively predicted continental origins of wastewater samples based on microbial signatures, confirming that microbial communities reflect local environmental and socioeconomic conditions while maintaining functional conservation. We observed significant variation in the antibiotic resistance gene (ARG) distribution, with elevated prevalence in certain African and Asian regions compared to Europe and North America. Our results establish wastewater microbiomes as important indicators of human activity and provide critical insights for advancing environmental monitoring, antimicrobial resistance surveillance, and wastewater-based epidemiology.IMPORTANCEIntensifying urbanization and human activities have dramatically increased global wastewater generation, creating complex microbial ecosystems that significantly impact environmental and public health. This study presents the first large-scale, comprehensive characterization of bacterial and viral communities in wastewater treatment systems worldwide. By analyzing samples from diverse geographical, climatic, and socioeconomic contexts, we reveal how wastewater microbiomes serve as microbial fingerprints of human society, reflecting regional characteristics while maintaining functional conservation. Our findings demonstrate that these communities function as ecological extensions of human gut microbiota in the external environment, with important implications for the spread of antibiotic resistance and pathogens. The identification of viruses as key metabolic regulators in these systems provides new perspectives on microbial community dynamics. This global-scale analysis advances our understanding of wastewater microbiology and offers valuable insights for improving wastewater management, enhancing environmental monitoring systems, and strengthening public health surveillance through wastewater-based epidemiology.}, }
@article {pmid40959608, year = {2025}, author = {Zhang, Y and Guo, Q and Chen, J and Shen, H and Fang, Y and Zhang, Y and Han, P and Chen, X}, title = {Evaluation of High-Throughput Gene Chip Array for Enhanced Diagnosis of Bone and Joint Infections: A Comparative Analysis with mNGS and Conventional Culture Methods.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {4817-4826}, pmid = {40959608}, issn = {1178-6973}, abstract = {BACKGROUND: While conventional culture-based diagnosis of bone and joint infections (BJI) requires prolonged incubation periods and metagenomic next-generation sequencing (mNGS) remains cost-prohibitive for routine clinical use, there is an urgent need for diagnostic strategies that balance timeliness with economic feasibility. This study investigates the clinical utility of a high-throughput (HT) gene chip array as a novel solution, offering significantly shorter turnaround time while maintaining cost-effectiveness than mNGS expenses.<br><br>METHODS: Thirty-six patients of the BJI group (28 positives and 8 negatives diagnosed by clinician) and 20 patients of respiratory tract infection (RTI) group (14 positives and 6 negatives diagnosed by clinician) were included in this study. Synovial fluid and ultrasound fluid samples of BJI group and alveolar lavage fluid samples of RTI group were collected and subjected to microbiological analysis performed by HT gene chip array, metagenomic next-generation sequencing (mNGS) and conventional culture. Sensitivity, specificity, accuracy, positive predictive value (PPV) and negative predictive value (NPV) were calculated. Positive and negative percent agreement and Cohen`s kappa coefficient were calculated.<br><br>RESULTS: The sensitivity and accuracy of HT gene chip assay for BJI detection was 71.43% and 77.78%, respectively (p value <0.05). HT gene chip assay exhibited the 100% of specificity and PPV, which is significantly higher than those of mNGS (62.5%, 89.29%) and conventional culture (78.57% and 88.89%). Our results position HT gene chip assay as a clinically actionable solution for accurate and timely bone and joint infection management.<br><br>CONCLUSION: HT gene chip assay demonstrates superior diagnostic specificity and cost-effectiveness with rapid turnaround, significantly reducing unnecessary invasive procedures while maintaining high concordance with mNGS, and exhibited higher clinical value of BJI diagnosis compared with mNGS and conventional culture.}, }
@article {pmid40959427, year = {2025}, author = {Song, M and Guo, Y and Hao, J and Zheng, C and Zuo, H and Ye, J and Zhang, C and Chen, F and Feng, Z and Zhang, H and Zhao, Z and Gao, W and Zhang, L}, title = {Case Report: Coxiella burnetii vertebral osteomyelitis in a pigeon breeder: mNGS diagnosis of chronic Q fever.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1636778}, pmid = {40959427}, issn = {2296-858X}, abstract = {BACKGROUND: Isolated vertebral osteomyelitis represents an uncommon manifestation of chronic Q fever, posing significant diagnostic challenges. We report a case of Coxiella burnetii-induced spondylodiscitis confirmed via metagenomic next-generation sequencing (mNGS).<br><br>CASE REPORT: A 52-year-old male with occupational avian exposure (pigeon breeder) presented with chronic low back pain persisting for over 1 year, refractory to serial epidural corticosteroid injections. Lumbar MRI demonstrated multifocal osteomyelitis (L3-L5) with associated intraspinal abscess. mNGS analysis of aspirate identified C. burnetii. Targeted dual antimicrobial therapy (vancomycin/doxycycline) induced progressive clinical resolution.<br><br>CONCLUSION: Coxiella burnetii, the etiological agent of Q fever, exhibits global distribution and poses significant diagnostic challenges. Its clinical manifestations are frequently nonspecific, typically afebrile, and diagnosis is commonly delayed by months to years post-symptom onset. mNGS offers critical diagnostic utility for early identification and therapeutic intervention in rare spinal infections, thereby mitigating complication risks.}, }
@article {pmid40959143, year = {2025}, author = {Zaki, AI and Sipos, A and Kacsir, I and Kovács, NI and Kerekes, &#xc9; and Szoták, E and Freytag, C and Demény, M and Révész, I and Buglyó, P and Bényei, A and Janka, EA and Kardos, G and Somsák, L and Bai, P and Bokor, &#xc9;}, title = {Platinum-group metal half-sandwich complexes of 1-(α-d-glucopyranosyl)-4-hetaryl-1,2,3-triazoles: synthesis, solution equilibrium studies, and investigation of their anticancer and antimicrobial activities.}, journal = {Frontiers in chemistry}, volume = {13}, number = {}, pages = {1619991}, pmid = {40959143}, issn = {2296-2646}, abstract = {Although platinum-based complexes are pivotal in chemotherapy, their clinical use is limited by toxicity and resistance. Previously, we identified a set of osmium, ruthenium, and iridium half-sandwich complexes of 1-N-(β-d-glucopyranosyl)-4-hetaryl-1,2,3-triazole-type N,N-chelators with potent and selective activity against a large set of diverse neoplasia cell models and multiresistant Gram-positive bacteria (methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus (VRE)). Our aim in this study was to assess how the configuration of the C1 carbon in the glucose moiety affects the biological activity of the complexes. Thus, 1-N-(α-d-glucopyranosyl)-4-hetaryl-1,2,3-triazoles were synthesized and used as N,N-bidentate ligands to result in half-sandwich type complexes analogous to the earlier reported ones. Overall, the newly prepared complexes with the α-anomeric carbohydrate moiety had similar biological properties to the complexes with the β-anomeric carbohydrate unit in terms of their biological activity on cancer cells or primary human cells. Importantly, the bacteriostatic property of the complexes with an α-anomeric sugar moiety was inferior to that of the complexes containing the β-anomer.}, }
@article {pmid40959141, year = {2025}, author = {Pinzauti, D and Biazzo, M and Podrini, C and Alevizou, A and Safarika, A and Damoraki, G and Koufargyris, P and Tasouli, E and Skopelitis, I and Poulakou, G and Sympardi, S and Giamarellos-Bourbolis, EJ}, title = {An NGS-assisted diagnostic workflow for culture-independent detection of bloodstream pathogens and prediction of antimicrobial resistances in sepsis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1656171}, pmid = {40959141}, issn = {2235-2988}, mesh = {Humans ; Prospective Studies ; *High-Throughput Nucleotide Sequencing/methods ; RNA, Ribosomal, 16S/genetics ; *Sepsis/microbiology/diagnosis ; Male ; Aged ; *Bacteria/genetics/drug effects/isolation &amp; purification/classification ; Middle Aged ; Female ; Workflow ; Metagenomics/methods ; *Drug Resistance, Bacterial ; Blood Culture ; Greece ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Sensitivity and Specificity ; Proof of Concept Study ; Aged, 80 and over ; Adult ; Microbial Sensitivity Tests ; }, abstract = {BACKGROUND: Timely and accurate identification of bloodstream pathogens is critical for targeted antimicrobial therapy in sepsis. Conventional blood cultures remain the Standard-of-Care (SoC) for pathogen identification but are limited by low sensitivity and prolonged turnaround times, hampering timely and targeted antimicrobial stewardship. Advances in next-generation sequencing (NGS) offer potential for culture-independent, rapid, and comprehensive detection of pathogens and prediction of antimicrobial resistance. This study evaluated the diagnostic performance of PISTE™ technology, an NGS-based diagnostic workflow combining full-length 16S rRNA gene sequencing and metagenomic analysis for the diagnosis of circulating bacteria in sepsis.<br><br>METHODS: In this prospective, multicenter, phase IIa proof-of-concept study, adult patients with suspected sepsis were enrolled from four hospitals in Athens, Greece. Blood samples were collected prior to antibiotic initiation and processed using SoC cultures and PISTE platform. PISTE integrates automated DNA purification (KingFisher, Thermo Fisher Scientific), full-length 16S rRNA gene sequencing, metagenomics analysis (SQK-PRB114.24, Oxford Nanopore Technologies), and real-time sequencing using Oxford Nanopore GridION Mk1b device. A dedicated analysis pipeline was developed for accurate pathogen detection and prediction of antimicrobial resistance profiles. The primary endpoint was the diagnostic concordance between PISTE and SoC cultures.<br><br>RESULTS: A total of 100 patients (median age 79 years, median Charlson's Comorbidity Index 5) were enrolled. Of these, 71 patients met Sepsis-3 criteria. In this subgroup, PISTE showed an overall accuracy of 95.7%, with a sensitivity of 91.7%, specificity of 96.5%, positive predictive value of 84.6%, and negative predictive value of 98.2% compared to SoC. The median time to pathogen identification and Antimicrobial Susceptibility Testing (AST) with PISTE was 12.0 hours, significantly faster than in SoC cultures (30.4 hours, p < 0.0001). Resistance gene profiling showed strong agreement with SoC AST results, particularly for &#x3b2;-lactam and carbapenem resistance.<br><br>CONCLUSIONS: PISTE technology exhibited high diagnostic accuracy and significantly reduced turnaround time compared to conventional cultures, supporting its potential as a short turnaround time and reliable diagnostic tool for bloodstream infections. Further optimization and validation in larger cohorts are warranted to enhance clinical implementation and improve antimicrobial stewardship in sepsis management.}, }
@article {pmid40958777, year = {2025}, author = {Zhao, X and Wu, B and Han, P and Wang, Z and Cao, R and Chen, S and Cheng, C and Lian, H and Zha, Y and Li, M}, title = {Gut microbiota-metabolome remodeling associated with low bone mass: an integrated multi-omics study in fracture patients.}, journal = {Frontiers in molecular biosciences}, volume = {12}, number = {}, pages = {1646361}, pmid = {40958777}, issn = {2296-889X}, abstract = {BACKGROUND: The gut microbiota is increasingly implicated in the pathogenesis of osteoporosis, but its role in the specific context of fracture patients remains poorly defined. High-resolution multi-omics studies are needed to elucidate the complex interplay between microbes, their metabolites, and bone health. This study aimed to characterize the gut microbial and fecal metabolic signatures associated with low bone mass in fracture patients.<br><br>METHODS: We conducted a cross-sectional study of 51 fracture patients, stratified by bone mineral density into Normal, Osteopenia, and Osteoporosis groups. For key analyses, the latter two groups were combined into a Low Bone Mass (LBM) group. We performed shotgun metagenomic sequencing and untargeted liquid chromatography-mass spectrometry metabolomics on fecal samples. An integrated bioinformatics and statistical analysis were used to identify differential taxa and metabolites, construct correlation networks, and build diagnostic biomarker models.<br><br>RESULTS: Patients with LBM exhibited a distinct gut microbial and metabolic profile compared to controls. A notable finding was the unexpected enrichment of Lachnospira eligens in the LBM group, despite its previous association with gut health. In contrast, traditionally beneficial taxa such as Bifidobacterium species and Bacteroides stercoris were markedly depleted. Metabolomic analysis identified 127 differential metabolites, and integrated analysis revealed a strong correlation between L. eligens and inflammation-associated metabolites, including N-acetylneuraminate. A diagnostic model incorporating four key bacterial species accurately discriminated LBM patients from controls with an area under the curve (AUC) exceeding 0.9.<br><br>CONCLUSION: Our findings reveal a significant remodeling of the gut microbiota-metabolome axis in fracture patients with low bone mass, highlighting a context-dependent, potentially pathological role for the typically beneficial species L. eligens. These distinct microbial and metabolic signatures suggest potential mechanistic insights into the gut-bone axis and represent promising, non-invasive biomarkers for assessing skeletal health.}, }
@article {pmid40958540, year = {2025}, author = {Wang, X and Wang, W and Deng, L and Li, T and Lei, S and Zhang, L and Liao, L and Song, Z and Liu, G and Zhang, C}, title = {Shifts in Genome Size and Energy Utilization Strategies Sustain Microbial Functions Along an Aridity Gradient.}, journal = {Global change biology}, volume = {31}, number = {9}, pages = {e70498}, doi = {10.1111/gcb.70498}, pmid = {40958540}, issn = {1365-2486}, support = {2023YFF1305103//National Key Research and Development Program of China/ ; 42130717//National Sciences Foundation of China/ ; 42177449//National Sciences Foundation of China/ ; 2024JC-JCQN-35//Shaanxi Provincial Science Fund for Distinguished Young Scholars/ ; }, mesh = {*Soil Microbiology ; *Microbiota ; *Genome Size ; Desert Climate ; *Energy Metabolism ; *Bacteria/genetics/metabolism ; *Genome, Bacterial ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Microbes acquire energy to sustain their survival and function through the decomposition of organic carbon (C) or by oxidizing atmospheric trace gases (e.g., H2, CO, CH4). However, how these two microbial energy-acquisition strategies change along environmental gradients and the underlying mechanisms are unclear. This study investigated the energy strategies and genomic traits of soil microbiomes along a natural aridity gradient, ranging from semi-humid forests to arid deserts. By analyzing 374 metagenome-assembled genomes from 13 microbial phyla, we found that the most prevalent microbes are metabolically versatile aerobes that use atmospheric trace gases to support aerobic respiration, C fixation, and N, P, and S cycling. Soil microbes adapt genomic traits associated with reduced energy expenditure in more arid soils, including smaller genome sizes, lower GC content, and fewer 16S rRNA gene copies. Microbial communities in diverse arid habitats are capable of utilizing organic compounds and the oxidation of trace gases (e.g., H2, CO, CH4, and H2S) as energy sources. However, the utilization of organic energy decreased while reliance on trace gas oxidation increased with increasing aridity. Higher consumption rates of H2, CO, and CH4 in desert soils from ex situ culture experiments confirmed that increased aridity stimulates microbial oxidation of atmospheric trace gases. This shift in energy utilization was strongly correlated with declining soil organic C levels. As organic C decreased along the aridity gradient, the abundance of trace gas oxidizers (both specialized and multi-gas oxidizers) increased significantly, while that of non-oxidizers declined. Trace gas oxidizers exhibited smaller genomes, lower 16S rRNA operon copy numbers, and slower predicted growth rates, indicative of oligotrophic lifestyles. In contrast, copiotrophic non-oxidizers had larger genomes and faster growth rates. These findings reveal that microbial communities adapt their genomic traits and energy-acquisition strategies to sustain functionality across aridity gradients, enhancing our understanding of soil microbiome responses to climate change.}, }
@article {pmid40958166, year = {2025}, author = {Ghaly, TM and Rajabal, V and Russell, D and Colombi, E and Tetu, SG}, title = {EcoFoldDB: Protein Structure-Guided Functional Profiling of Ecologically Relevant Microbial Traits at the Metagenome Scale.}, journal = {Environmental microbiology}, volume = {27}, number = {9}, pages = {e70178}, doi = {10.1111/1462-2920.70178}, pmid = {40958166}, issn = {1462-2920}, support = {CE200100029//ARC Centre of Excellence in Synthetic Biology/ ; //Macquarie University Research Fellowship/ ; }, mesh = {*Metagenome ; *Metagenomics/methods ; *Bacteria/genetics/classification/metabolism ; Soil Microbiology ; Phylogeny ; *Microbiota/genetics ; Computational Biology/methods ; *Bacterial Proteins/genetics/chemistry ; *Databases, Protein ; Protein Conformation ; }, abstract = {Microbial communities are fundamental to planetary health and ecosystem processes. High-throughput metagenomic sequencing has provided unprecedented insights into the structure and function of these communities. However, functionally profiling metagenomes remains constrained due to the limited sensitivity of existing sequence homology-based methods to annotate evolutionarily divergent genes. Protein structure, more conserved than sequence and intrinsically tied to molecular function, offers a solution. Capitalising on recent breakthroughs in structural bioinformatics, we present EcoFoldDB, a database of protein structures curated for ecologically relevant microbial traits, and its companion pipeline, EcoFoldDB-annotate, which leverages Foldseek with the ProstT5 protein language model for rapid structural homology searching directly from sequence data. EcoFoldDB-annotate outperforms state-of-the-art sequence-based methods in annotating metagenomic proteins, in terms of sensitivity and precision. To demonstrate its utility and scalability, we performed structure-guided functional profiling of 32 million proteins encoded by 8000 high-quality metagenome-assembled genomes from the global soil microbiome. EcoFoldDB-annotate could resolve the phylogenetic partitioning of important nitrogen cycling pathways, from taxonomically restricted nitrifiers to more widespread denitrifiers, as well as identifying novel, uncultivated bacterial taxa enriched in plant growth-promoting traits. We anticipate that EcoFoldDB will enable researchers to extract ecological insights from environmental genomes and metagenomes and accelerate discoveries in microbial ecology.}, }
@article {pmid40958146, year = {2025}, author = {Yang, Q and Liu, J and Lyu, S and Li, S and Han, Q and Ma, C and Du, Z and Zhang, T}, title = {Ovalbumin Peptides Restore Intestinal Barrier Integrity via Gut-Liver Axis Modulation of Bile Salt Hydrolase and Bile Acids Crosstalk.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.5c07236}, pmid = {40958146}, issn = {1520-5118}, abstract = {Inflammatory bowel disease (IBD) is characterized by intestinal barrier dysfunction and bile acid (BA) dysmetabolism. BA metabolism was a pivotal regulator in the "gut-liver axis" to maintain intestinal homeostasis. Ovalbumin-derived peptides (OVA-Ps) exhibit potential in barrier repair; however, their systemic mechanisms within the microbiota-BA-host network remain underexplored. This study investigates the therapeutic potential of the oligomer OVA-P in a DSS-induced colitis mouse model. OVA-P administration significantly alleviated colitis symptoms, restored colon length, reduced pro-inflammatory cytokines (tumor necrosis factor-α), and enhanced antioxidant markers (SOD). Mechanistically, the OVA-P reshaped gut microbiota composition, suppressed bile salt hydrolase (BSH), and elevated conjugated BAs (e.g., taurocholic acid) levels. These changes activated the farnesoid X receptor (FXR) pathway, upregulating tight junction protein (ZO-1), and mucin (MUC-2) expression, thereby restoring intestinal barrier integrity. Metabolomic and metagenomic analyses confirmed the OVA-P-mediated modulation of the gut-liver axis through FXR-SHP/FGF15 signaling, highlighting its role in maintaining BA homeostasis. These findings provide insights into the use of OVA-P as a dietary intervention for IBD by targeting microbiota-BA-FXR interactions, offering a foundation for high-value egg protein applications in functional foods.}, }
@article {pmid40958120, year = {2025}, author = {Pérez-Martínez, C and Pontiller, B and Martínez-García, S and Hylander, S and Paerl, RW and Lundin, D and Pinhassi, J}, title = {Pronounced seasonal dynamics in transcription of vitamin B1 acquisition strategies diverge among Baltic Sea bacterioplankton.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {115}, pmid = {40958120}, issn = {2524-6372}, abstract = {BACKGROUND: Vitamin B1 (thiamin) is essential to life; yet little is known of the regulation of its availability in marine environments or how it varies seasonally. Since microbes are the key synthesizers of the vitamin in marine environments, we here used metatranscriptomics to examine the seasonal dynamics of B1 acquisition strategies (including both uptake and synthesis pathways) in Baltic Sea bacterioplankton.<br><br>RESULTS: Elevated B1-related gene expression was observed in summer, coinciding with increased temperatures and bacterial activity and decreased nutrient availability. Different bacterial taxa exhibited distinct B1 acquisition strategies. We identified filamentous Cyanobacteria of the order Nostocales as critical to sustaining B1 production during summer, potentially compensating for limited synthesis in heterotrophic bacteria, especially for 4-amino-5-hydroxymethylpyrimidine (HMP) synthesis. Also, Pelagibacterales accounted for major portions of the community transcription, primarily taking up and salvaging the B1 precursor HMP during summer. This study highlights the partitioning of B1 synthesis, salvage, and uptake among microbial taxa, underscoring that transcriptional activity was more dynamic over time than changes in the genomic potential.<br><br>CONCLUSIONS: We emphasize the influence of environmental conditions on microbial community dynamics and B1 cycling in general, and the potential implications of global change-induced increases in filamentous Cyanobacteria blooms on vitamin food web transfer in particular.}, }
@article {pmid40957978, year = {2025}, author = {Ocampo-Chih, C and Hendricks, H and Weitkamp, S and Gowda, NS and Singh, H and Banerjee, R and Rajagopala, SV and Weitkamp, JH}, title = {Impact of donor human milk pasteurization methods on the gut microbiome of preterm infants.}, journal = {Pediatric research}, volume = {}, number = {}, pages = {}, pmid = {40957978}, issn = {1530-0447}, abstract = {BACKGROUND: Preterm infants are often fed donor human milk (DHM) when the mother's own milk is insufficient or not available. Holder or Retort pasteurization is used to inactivate potential pathogens in DHM. The effects of DHM pasteurization methods on the infant gut microbiome are unknown.<br><br>METHODS: To compare the gut microbiome and clinical outcomes between preterm infants fed Holder- versus Retort-pasteurized DHM, we performed weekly collections of stool samples from infants born <34 weeks' gestation and/or <1500&#x2009;g birth weight. We analyzed stool samples from 150 patients exclusively fed DHM [Retort (n&#x2009;=&#x2009;80), Holder (n&#x2009;=&#x2009;54)] or exclusively fed mother's own milk (n&#x2009;=&#x2009;16). Whole-metagenome sequencing was performed to assess microbiome composition, diversity, and functional enrichment.<br><br>RESULTS: Compared to infants fed Retort-pasteurized DHM, infants fed Holder-pasteurized DHM showed higher alpha-diversity (Chao-1 p&#x2009;=&#x2009;0.007) and a higher abundance of beneficial anaerobes, such as Bacteroides thetaiotaomicron, Clostridium spp., and Bifidobacterium spp. Functional enrichment analysis revealed significant differences in carbohydrate metabolism, transport systems, and regulatory pathways between feeding groups. There were no statistically significant differences in short-term clinical outcomes, such as necrotizing enterocolitis, length of hospitalization or death.<br><br>CONCLUSION: Differences in pasteurization methods for DHM resulted in measurable gut microbiome changes in preterm infants.<br><br>IMPACT: It is known that the preterm infant gut microbiota is different in infants fed pasteurized donor milk compared to mother's own milk. However, the impact of different pasteurization methods for donor milk on the infant gut microbiome is unknown. We show that the type of pasteurization of donor human milk influences the gut microbiome and its function in preterm infants. In contrast to feeding Retort-pasteurized donor human milk, feeding Holder-pasteurized donor human milk generates an infant gut microbiome similar to feeding mother's own milk.}, }
@article {pmid40957694, year = {2025}, author = {Blas-Muñoz, L and Orrego, AH and Hofmeister, M and Martínez-Salvador, J and Ortega, C and Rondón Berrio, V and Díaz-Rullo, J and Finnigan, J and Charnock, S and Fessner, WD and González-Pastor, JE and Hidalgo, A}, title = {A Microfluidics-Based Ultrahigh-Throughput Screening Unveils Diverse Ketoreductases Relevant to Pharmaceutical Synthesis.}, journal = {Analytical chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.analchem.5c01029}, pmid = {40957694}, issn = {1520-6882}, abstract = {Ketoreductases (KREDs) have become increasingly valuable biocatalysts due to their ability to produce chiral alcohols with high enantioselectivity. Prior to our work, Thai et al. developed an efficient and easy assay for their discovery, but the throughput was limited. Based on their work, we developed an ultrahigh-throughput screening assay to discover KREDs. First, we optimized Thai's assay by adapting it to a droplet format and increased its throughput by combining droplet microfluidics and fluorescence-activated cell sorting (FACS). Then, we demonstrated that our new assay was reliable and sensitive by successfully screening a library of 1.5 million clones. This allowed us to discover KREDs with low identity with known enzymes or with a previously undescribed substrate scope, which could not have been predicted computationally. In conclusion, our assay was used to carry out the first metagenomic screening for KREDs in microdroplets, and it can be used to screen any large KRED library toward enzyme discovery or evolution, as well as to enable coupled ultrahigh-throughput screening assays for other enzyme activities.}, }
@article {pmid40957481, year = {2025}, author = {Ren, Y and Fang, H and Gao, Y and Yin, G and He, X and Chen, N}, title = {Effects of exercise on gut microbiota in older people with sarcopenia: Studyprotocolfor arandomisedcontrolledtrial.}, journal = {Experimental gerontology}, volume = {}, number = {}, pages = {112898}, doi = {10.1016/j.exger.2025.112898}, pmid = {40957481}, issn = {1873-6815}, abstract = {BACKGROUND: Sarcopenia is an age-related disease imposing a substantial burden on individuals and healthcare systems. Resistance training (RT) is recommended as the primary non-pharmacological treatment, and Baduanjin (BDJ) has shown positive effects for sarcopenia. However, the mechanisms through which exercise improves sarcopenia remain unclear. Research has suggested that exercise may enhance sarcopenia through the gut-muscle axis. Therefore, the present study aims to evaluate the effects of BDJ-RT on the gut microbiota in older people with sarcopenia, identify potential target microbial taxa and explore related mechanisms.<br><br>METHODS: In this 12-week randomised, single-blind controlled trial, 30 older people with sarcopenia will be randomly assigned to the BDJ-RT group (n&#x202f;=&#x202f;15) or control group (n&#x202f;=&#x202f;15). The BDJ-RT group will undergo BDJ combined with RT, and the control group will receive health education. Muscle mass, strength, physical performance, quality of life, gut microbiota and short-chain fatty acids will be assessed at baseline, post-intervention and follow-up. Potential target gut microbiota related to sarcopenia will be identified through metagenomic sequencing. The identified strains will then be gavaged to sarcopenic mice to evaluate their effects on sarcopenia. Data will be analysed using an intention-to-treat approach.<br><br>DISCUSSION: This study will be the first to systematically investigate the effects of BDJ-RT on the gut microbiota in older people with sarcopenia. The findings will provide potential microbial targets and mechanistic insights into the gut-muscle axis underlying exercise-induced improvements in sarcopenia.<br><br>TRIAL REGISTRATION: This study was registered on the International Traditional Medicine Clinical Trial Registry, with registration number ITMCTR2025000036.}, }
@article {pmid40957464, year = {2025}, author = {Shen, D and Xing, X and Ding, H and Long, Y and Hui, C}, title = {Metagenomic and metatranscriptomic insights into mechanisms of magnetite promoting 2,2',4,4'-tetrabrominated ether degradation in natural biofilms.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {133337}, doi = {10.1016/j.biortech.2025.133337}, pmid = {40957464}, issn = {1873-2976}, abstract = {The role of magnetite in shaping microbial communities in natural biofilms and the mechanisms underlying pollutant degradation remain poorly understood. This study demonstrates that magnetite enhanced the degradation of 2,2',4,4'-tetrabrominated ether (BDE-47) in biofilms, with the highest removal rate of 82%. Magnetite promoted the production of extracellular polymeric substances and cytochrome c, enhanced the activity of electron transport system and conductivity, thus inducing the formation of electroactive biofilms. In addition, magnetite increased the bacterial diversity and altered the community composition of biofilms. Metagenomic and metatranscriptomic analyses demonstrated that magnetite specifically enriches genes and microorganisms associated with both mediated and direct interspecies electron transfer (IET), thereby accelerating IET process. Moreover, dissimilatory iron-reducing bacteria and dehalogenase-expressing microorganisms were enriched with magnetite, which facilitated BDE-47 degradation in the biofilms. These findings elucidate the impacts of magnetite on biofilms and the degradation mechanisms of BDE-47, providing theoretical basis for developing biofilm-based remediation technologies.}, }
@article {pmid40957141, year = {2025}, author = {Xiao, J and Xie, WY and Wang, P}, title = {Metagenomic insights into the ecological risks of multiple heavy metals on soil bacterial communities and resistance-related genes.}, journal = {Ecotoxicology and environmental safety}, volume = {303}, number = {}, pages = {119048}, doi = {10.1016/j.ecoenv.2025.119048}, pmid = {40957141}, issn = {1090-2414}, abstract = {The simultaneous contamination of soils by various heavy metals (HMs) significantly disrupts microbial ecosystems, leading to notable shifts in bacterial community structures and the prevalence of resistance-related genes, including metal resistance genes (MRGs) and antibiotic resistance genes (ARGs). Conventional indices, such as the Nemerow Integrated Pollution Index (NIPI), primarily assess contamination from a chemical standpoint but often overlook the complex ecological responses elicited by multiple HMs. In this study, we used metagenomic analyses, network assessments, and neutral community models to investigate the agricultural soils near a nonferrous metal smelter, aiming to elucidate the collective influence of seven representative HMs (cadmium, chromium, copper, nickel, lead, zinc and arsenic) on bacterial communities and resistance-related gene dynamics. Our findings revealed that elevated levels of the seven HMs are pivotal in reshaping microbial assemblages and resistance profiles in soils. Notably, nonlinear correlations between NIPI of the seven HMs and bacterial indices suggested threshold-dependent microbial responses to HM mixtures. Among various indicators, the total relative abundance of MRGs emerged as a superior indicator for assessing the ecological risks associated with combined HM contamination, surpassing traditional bacterial diversity metrics and ARG prevalence. Furthermore, random forest modeling identified specific MRG subtypes as robust biomarkers, a discovery validated through controlled microcosm experiments. This study provides a systematic framework for evaluating the ecological risks in agricultural soils under multiple HM contamination, highlighting the intricate interplay between pollutant mixtures and microbial community dynamics.}, }
@article {pmid40956094, year = {2025}, author = {Carmichael, MM and Valls, RA and Soucy, S and Sanville, J and Madan, J and Surve, SV and Sundrud, MS and O'Toole, GA}, title = {Profiling bile acids in the stools of humans and animal models of cystic fibrosis.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0145125}, doi = {10.1128/spectrum.01451-25}, pmid = {40956094}, issn = {2165-0497}, abstract = {UNLABELLED: Cystic fibrosis (CF) is associated with aberrant bile acid (BA) metabolism. As little is known about BA in children with CF (cwCF), we performed both comprehensive (n = 89) and focused (n = 21) BA profiling in stool of children with or without CF. Our results reveal select BA species and metabolites are significantly different between cwCF and nonCF controls. Focused BA profiling revealed a significant increase in total BA levels and selected changes in a subset of BA classes for cwCF. Matched bacterial metagenomic analyses showed no change in alpha-diversity between groups in this small cohort, at odds with previous studies, whereas changes in relative abundance of Bacteroidetes (lower in cwCF) phylum are consistent with prior reports. A trend was noted toward reduced abundance of bsh gene families, a key rate-limiting enzyme required for bacterial synthesis of secondary BAs, in cwCF. Observed modest changes in both BAs and microbial BA metabolism-related gene abundances may suggest a possible combination of defects in host and microbial BA metabolic pathways in cwCF. Fecal BA profiles from both ferret and mouse CF models showed significant differences from human BA profiles, and while the ferret model reproduced significant differences between CF and nonCF animals, the nonCF animals showed higher levels of BA (opposite of what is observed in humans), indicating that neither model recapitulated BA in stool in the context of CF. Together, these results provide new insights into CF-related BA dysmetabolism in cwCF and highlight limitations of CF animal models for BA functional studies.<br><br>IMPORTANCE: Changes in the abundance and/or composition of intestinal BAs may contribute to dysbiosis and altered gastrointestinal physiology in CF. Here, we report shifts in select fecal BA classes and species for cwCF. Matched metagenomic analysis suggests possible defects in both host intestinal BA absorption and gut microbial BA metabolism. Additional analyses of mouse and ferret CF stool for BA composition suggest great care must be taken when interpreting BA functional studies using these animal models. Together, this work lays technical and conceptual foundations for interrogating BA-microbe interactions in cwCF.}, }
@article {pmid40956077, year = {2025}, author = {Morrical, SW}, title = {The bacteriophage T4 homologous recombination system: mechanism, applications, conservation, and environmental significance.}, journal = {EcoSal Plus}, volume = {}, number = {}, pages = {eesp00032025}, doi = {10.1128/ecosalplus.esp-0003-2025}, pmid = {40956077}, issn = {2324-6200}, abstract = {The homologous recombination (HR) system of bacteriophage T4 plays critical, direct roles in the replication and repair of the phage genome. This review covers the classic, UvsX-dependent HR pathway in T4, focusing on recent findings on the mechanisms of central HR proteins UvsX, UvsY, and Gp32, plus the key helicase and nuclease enzymes that affect HR and promote its coupling to T4 recombination-dependent replication and repair processes. The T4 HR pathways are paradigmatic, since they are highly conserved in all orders of viral and cellular life. Therefore, the study of T4 recombination is highly relevant to biomedicine and to environmental microbiology. At the same time, the tractability of the T4 recombination system for biochemical studies has led to the development of novel, isothermal DNA amplification technologies based on the activities of UvsX, UvsY, and Gp32, which are discussed herein. Globally, the recent revolution in metagenomics has demonstrated that T4-like phages, most encoding the genes and proteins of the T4 HR system, are abundant and widespread in the environment, where they play important roles in the dynamics of diverse microbiomes, from the earth's oceans to the animal gut. Accordingly, we discuss the conservation of T4 HR genes in representatives of T4-like jumbo phages and cyanophages. As a paradigm for HR in diverse organisms, as a source of novel technologies, and as a window on the importance of bacteriophages in the environment, the T4 HR system continues to provide new insights and reagents for a better understanding of life on earth.}, }
@article {pmid40956075, year = {2025}, author = {Yu, D and Mai, Y and Zhang, L and Xiao, Y and Zhang, M and Shao, B and Chen, B and Wang, T and Zhang, K and Zhang, L and Gao, N and Zhang, J and Yan, J}, title = {Viral community succession during cadaver decomposition and its potential for estimating postmortem intervals.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0145325}, doi = {10.1128/aem.01453-25}, pmid = {40956075}, issn = {1098-5336}, abstract = {UNLABELLED: Microbial communities play a vital role in cadaver decomposition and serve as reliable tools for postmortem interval (PMI) estimation. However, current research focuses primarily on bacterial/fungal communities, though viruses-as Earth's most abundant biological entities-play key roles in biogeochemical cycles by regulating bacterial communities via lysis-lysogeny switching. Viral succession patterns during decomposition remain insufficiently characterized, and their PMI biomarker potential is unexamined. We present metagenomic analysis of viral succession during 35-day decomposition of buried rat cadavers, revealing stage-specific dynamics: early dominance of Peduoviridae (0-3 days), mid-stage proliferation of Herelleviridae (7-21 days), and late-stage resurgence of Peduoviridae (28-35 days). Viral α-diversity exhibits a fluctuating downward trend. β-Diversity analysis (PCoA, ANOSIM, PERMANOVA; P < 0.001) confirmed PMI as a major structural driver (27% variance explained). Nine viral families exhibited significant PMI correlations (P < 0.05): Zierdtviridae, Casjensviridae, Schitoviridae, and Ackermannviridae showed strong negative correlations (r = -0.82 to -0.78), while Straboviridae correlated positively (r = 0.59). Using integrated viral abundance data, our Extremely Randomized Trees model achieved exceptional PMI prediction accuracy (test set: R[2] = 0.96, MAE = 2.54 days). Spearman correlations between dominant bacterial phyla (Bacteroidota, Bacillota, etc.) and viral families, combined with Procrustes analysis (M[2] =0.3385, P = 0.001) and Mantel tests (r = 0.8059, P = 0.001), confirmed strong virus-bacteria community consistency. This indicates viruses may regulate decomposition by targeting bacteria for lysis, releasing nutrients (e.g., organic nitrogen/phosphorus) to drive bacterial succession. Our study establishes a novel virus-based PMI prediction tool and discusses ecological drivers of decomposition.<br><br>IMPORTANCE: We present a viral succession-based framework for estimating PMI in buried remains. Our study identifies stage-specific viral biomarkers and identified nine viral families significantly correlated with PMI. By combining metagenomics and machine learning, we developed an Extremely Randomized Trees (ERT) model that achieved a low prediction error (test set: R&#xb2; = 0.96, MAE = 2.54 days). Furthermore, our findings demonstrate that viral and bacterial communities exhibit significant consistency and correlation during cadaver decomposition. This study not only provides a novel tool for the accurate estimation of forensic PMI but also advances our insight into viral regulation of bacteria and their interactions during cadaver decomposition.}, }
@article {pmid40955502, year = {2025}, author = {Wang, A and Hu, K and Hu, X and Liu, H and Dong, X and Yao, M}, title = {Spatiotemporal Distribution of Marine Viral Functions Associated with Microplastics.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c02956}, pmid = {40955502}, issn = {1520-5851}, abstract = {Microplastics (MPs) and marine viruses co-occur globally, yet the spatiotemporal distribution of MP-associated viral functional gene abundance remains poorly resolved. We synthesized 262 metagenomes to infer global MP pollution and tested associations between MPs and viral functional gene abundance against 24 physicochemical-biological variables. From 2000 to 2020, >20% of the North and southeastern Atlantic showed significant increases (p < 0.05) in viral functional gene abundance, whereas 61% of the northwestern Atlantic decreased. These shifts covaried with MP accumulation, nutrient regimes, and climate indices. In a northwestern Atlantic hotspot, neglecting MPs may lead to a ∼15% underestimation of viral functional gene abundance. In low-chlorophyll (Chl) regions (57.6% of the ocean), genes linked to carbon, nitrogen, and sulfur cycling were >30% more abundant in high- versus low-MP regions; MPs did not strongly affect the abundance of viral functional genes. Network analyses revealed cascading interactions among viral functional gene abundance, MPs, Fe, Chl, and environmental properties. Our results suggest that ignoring MPs may lead to the underestimation of viral functional potential and related biogeochemical processes, and that low-Chl regions─proposed priority protection areas─are particularly vulnerable to MPs pollution.}, }
@article {pmid40955359, year = {2025}, author = {Tombuloglu, H and Aga, O and Boudellioua, I and Anil, I and Yaman, C and Qureshi, A}, title = {Removal of hydrogen sulfide (H2S) with Thiobacillus denitrificans biofilter: study of the microbial community conducted through 16S rRNA sequencing analysis.}, journal = {3 Biotech}, volume = {15}, number = {10}, pages = {344}, pmid = {40955359}, issn = {2190-572X}, abstract = {Hydrogen sulfide (H2S) emissions from oil and gas operations, sewage treatment facilities, and landfills are challenges to the quality of life. The main objective of this work is to study the effect of different filter packing materials on Thiobacillus denitrificans-mediated lab-scale bioreactor for H2S removal using 16S rRNA metagenomic sequencing. In this study, the bioreactor column, which has three distinct layers of Ceramic Ball Filter Media (CBFM), Filter Media Ceramic Rings (FMCR), and Filter Bio Balls (FBB), was designed and operated for 60 days. The microbial community samples adhered to the surfaces of the filling materials were investigated using 16S rRNA metagenomic sequencing with paired-end 2 × 150 base reads (Illumina). The results showed that the H2S gas removal efficiency reached its maximum of 99% by the end of the seventh day, followed by a steady-state pattern. Compared with polypropylene surfaces, ceramic materials successfully hosted the T. denitrificans bacteria. Changing the filter material altered the phylum species diversity of the microcosms on the filter material, as shown by alpha diversity indices (Shannon and Simpson values). The dominant Phylum across all samples, regardless of the treatment and filter material type, was Proteobacteria, followed by Firmicutes and Bacteroidetes. Comamonas thiooxydans, Comamonas testosterone, Enterococcus faecalis, Staphylococcus aureus, Staphylococcus cohnii, and Mesorhizobium terrae are the most abundant species detected on the filter materials. In addition, changing the filter material causes a substantial alteration of the dominant species in the microcosm of the bioreactor. These findings highlight the critical role of filter material in supporting H2S-removing microorganisms.}, }
@article {pmid40955281, year = {2025}, author = {Jiang, L and Wei, L and Li, X and Zheng, D and Cao, C and Li, M}, title = {Recurrent Subcutaneous Abscess from Co-Infection with Prototheca wickerhamii and Mycobacterium haemophilum: mNGS Misdiagnosis as Leprosy.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {4827-4831}, pmid = {40955281}, issn = {1178-6973}, abstract = {Prototheca wickerhamii (P. wickerhamii) and Mycobacterium haemophilum (M. haemophilum) are both opportunistic pathogens that could cause infections in immunocompromised populations. However, these infections rarely occur in individuals with normal immunity. We reported a 39-year-old immunocompetent man presented with recurrent subcutaneous abscess on fingers who developed a co-infection of P. wickerhamii and M. haemophilum. To our knowledge, this is the first reported co-infection involving P. wickerhamii and M. haemophilum. The diagnosis was complicated by mNGS misidentifying M. haemophilum as Mycobacterium leprae (M. leprae) (98% sequence similarity) and overlooking P. wickerhamii. This case underscores the critical need to correlate mNGS results with clinical features and use complementary diagnostic methods to avoid errors. The combination of traditional and molecular methods can improve diagnostic accuracy.}, }
@article {pmid40954939, year = {2025}, author = {Chen, J and Wang, M and Liu, H and Li, Z}, title = {Novel Substitutes of Phthalate Esters (PAEs) Promote the Propagation of Antibiotic Resistance Genes via Ferroptosis: Implication for the Environmental Safety Evaluation of PAE Substitutes.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c10489}, pmid = {40954939}, issn = {1520-5851}, abstract = {The horizontal transfer of antibiotic resistance genes (ARGs) has become a major threat to global public health. Recent studies have found that ferroptosis, an iron-dependent form of regulated cell death characterized by lipid peroxidation and glutathione depletion, may play a critical role in the dissemination of ARGs among environmental microbes. Here, we demonstrated for the first time that phthalate esters (PAEs) and their substitutes significantly enhanced plasmid conjugation by triggering ferroptosis-related pathways. Classical ferroptosis-associated responses, including the hyperpolarization of the cell membrane potential, elevated production of reactive oxygen species, and heightened membrane permeability, were observed under the stress of PAEs or their substitutes. Through integrated transcriptomic and metabolomic analyses, we revealed that these compounds triggered iron dysregulation via the upregulation of iron acquisition and storage pathways while suppressing DNA replication, concurrently causing oxidative damage that stimulated the plasmid conjugation. Molecular docking simulations revealed that PAEs and their substitutes competitively disrupted the functionality of ferric uptake regulator (Fur) protein, a master controller of intracellular iron homeostasis, with superior binding affinity than its natural ligand Fe[2+]. Integrated metagenomic sequencing and homology analyses demonstrated the conservation of Fur protein across biofilm microbiota and functional implications in iron homeostasis. Structural analysis based on the characteristic molecular fingerprints of chemicals pinpointed aliphatic chains as the crucial structure responsible for enhancing ARG propagation between bacteria. Our findings uncovered a mechanism by which PAEs and their substitutes exacerbated ARG dissemination through ferroptosis-mediated conjugation, providing crucial insights for environmental risk assessment and resistance mitigation strategies.}, }
@article {pmid40954296, year = {2025}, author = {Zhang, R and Mirdita, M and Söding, J}, title = {De novo discovery of conserved gene clusters in microbial genomes with Spacedust.}, journal = {Nature methods}, volume = {}, number = {}, pages = {}, pmid = {40954296}, issn = {1548-7105}, support = {CompLifeSci project horizontal4meta//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; CompLifeSci project horizontal4meta//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; RS-2023- 00250470//National Research Foundation of Korea (NRF)/ ; }, abstract = {Metagenomics has revolutionized environmental and human-associated microbiome studies. However, the limited fraction of proteins with known biological processes and molecular functions presents a major bottleneck. In prokaryotes and viruses, evolution favors keeping genes participating in the same biological processes colocalized as conserved gene clusters. Conversely, conservation of gene neighborhood indicates functional association. Here we present Spacedust, a tool for systematic, de novo discovery of conserved gene clusters. To find homologous protein matches, Spacedust uses fast and sensitive structure comparison with Foldseek. Partially conserved clusters are detected using novel clustering and order conservation P values. We demonstrate Spacedust's sensitivity with an all-versus-all analysis of 1,308 bacterial genomes, identifying 72,843 conserved gene clusters containing 58% of the 4.2 million genes. It recovered 95% of antiviral defense system clusters annotated by the specialized tool PADLOC. Spacedust's high sensitivity and speed will facilitate the annotation of large numbers of sequenced bacterial, archaeal and viral genomes.}, }
@article {pmid40939659, year = {2025}, author = {Qiu, Y and Yang, T and Tang, J and Zhao, B and Li, H and Zhuang, WQ and Zhou, L}, title = {Dissimilatory nitrate reduction to ammonium-induced false stability masks dysfunctional Candidatus Brocadia failure during ANAMMOX start-up from municipal activated sludge.}, journal = {Bioresource technology}, volume = {439}, number = {}, pages = {133324}, doi = {10.1016/j.biortech.2025.133324}, pmid = {40939659}, issn = {1873-2976}, abstract = {Enriching anaerobic ammonium oxidation (ANAMMOX) bacteria from conventional municipal activated sludge remains difficult despite reported feasibility, particularly without highly enriched anammox cultures (HeAnAC). This study examined ANAMMOX start-up in an anaerobic-membrane-bioreactor fed ammonium (NH4[+]) and nitrite (NO2[-]) under organic carbon-free conditions. Initial nitrogen removal (NH4[+]: 78%; NO2[-]: 98%) declined sharply after day 70 (<11% and <28%, respectively), coinciding with stable hydrazine synthase gene (hzs) abundance, elevated DNRA nitrite reductase gene (nrfA) abundance, and higher enzyme activity (NrfA). Metagenomic and enzymatic analyses indicated that dissimilatory nitrate reduction to ammonium (DNRA) bacteria temporarily compensated for impaired Candidatus Brocadia, masking collapse. Prolonged DNRA dominance disrupted the NH4[+]/ NO2[-] ratio, destabilized biomass, and induced excess soluble microbial products (SMP) and extracellular polymeric substances (EPS). These changes ultimately led to late-stage NO2[-] removal decline and a shift from supportive to inhibitory effects on ANAMMOX. Monitoring nrfA and hzs may allow early detection of DNRA dominance.}, }
@article {pmid40953740, year = {2025}, author = {Wang, Q and Chen, Y and You, S and Li, Y and Li, J and Liu, C and Liang, X and Wang, X}, title = {Metagenomic insights revealing the stabilizing regulatory role of biochar in partial denitrification-anammox under carbon-limited conditions.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {133296}, doi = {10.1016/j.biortech.2025.133296}, pmid = {40953740}, issn = {1873-2976}, abstract = {Carbon utilization efficiency and microbial community stability critically constrain the nitrogen removal performance of partial denitrification/anammox (PD/A) processes. Although biochar can serve as an electron donor, its regulatory mechanisms governing microbial interactions within PD/A remain unclear. This study demonstrates that under carbon-limited conditions, biochar adaptively enhances both nitrogen removal performance and microbial community interactions in PD/A systems. Under mild carbon limitation (C/N = 2.5), the biochar-amended reactor significantly enriched denitrifiers such as Thauera (16.75 % vs. 6.72 % in the blank control reactor). It also promoted acetate metabolism to enhance electron generation and facilitated electron transfer through downstream components of the electron transport chain. Under severe carbon limitation (C/N = 2.0), the relative abundance of Candidatus Brocadia increased significantly from 2.11 % to 7.00 %, accompanied by marked upregulation of key TCA cycle enzymes and anammox-related genes, indicating a metabolic shift toward a more energy-efficient anammox pathway. The PD/A system stability was maintained, with ammonium and nitrate removal efficiencies of approximately 75.85 % and 73.11 %, respectively. Additionally, biochar stimulated extracellular polymeric substance secretion to alleviate environmental stress. These findings suggest that biochar acts as an effective niche-modulating medium, supporting the stable and efficient operation of PD/A processes under varying carbon source conditions.}, }
@article {pmid40953724, year = {2025}, author = {Lan, T and Zhang, Y and Xie, R and Wu, Q and Wang, H and Du, J and Guo, W}, title = {Aromatic hydrocarbon exposure alters soil microbial communities and redox-driven carbon metabolism.}, journal = {Environmental research}, volume = {}, number = {}, pages = {122845}, doi = {10.1016/j.envres.2025.122845}, pmid = {40953724}, issn = {1096-0953}, abstract = {The environmental behavior and toxicological impacts of benzene, toluene, ethylbenzene, and xylene (BTEX) have been widely studied. Yet their concentration-dependent effects on soil microbial structure, redox dynamics, and metabolism remain insufficiently understood, constraining predictions of ecosystem responses and the development of targeted bioremediation strategies. Here, we explored how exposure to different concentrations of BTEX reshaped microbial community structure and metabolic function by integrating phased amplicon sequencing, metagenomic analysis, and metabolite profiling. BTEX exposure did not significantly alter the overall microbial richness or diversity across treatment groups but substantially changed the taxonomic composition (Stress = 0.096, R = 0.2284, P = 0.0500). It reduced the dominance of Bacillus and enriched various Clostridium spp. closely associated with acetate and butyrate production. At higher BTEX concentrations, Sporolactobacillus was selectively enriched, directing carbon flow toward lactate production. Functionally, BTEX inhibited early reactions in the pentose phosphate pathway (PPP), while increasing the abundance of genes involved in downstream glycolysis and PPP, leading to rapid pyruvate and NADH accumulation. Meanwhile, inhibition of NADH: ubiquinone oxidoreductase indicated a reduced capacity for respiratory NADH turnover. At slight BTEX concentrations, the redox imbalance increased NADH availability, thereby enhancing alcohol synthesis by 38.03% (±29.18%) (P < 0.05). Conversely, high BTEX concentrations enhanced lactate biosynthesis, redirecting carbon and reducing equivalents away from alcohol and acid accumulation (P<0.05). These findings demonstrate that BTEX reshapes microbial redox dynamics and carbon allocation in a concentration-specific manner, providing mechanistic insights into soil microbiome responses to aromatic hydrocarbon pollution and a basis for designing and optimizing future bioremediation strategies.}, }
@article {pmid40953718, year = {2025}, author = {Liu, H and Yang, C and Qin, S and Zhang, Q}, title = {Metagenomic insights into carbon-nitrogen metabolism of heterotrophic nitrification-aerobic denitrification bacteria utilizing different biodegradable polymers.}, journal = {Environmental research}, volume = {}, number = {}, pages = {122864}, doi = {10.1016/j.envres.2025.122864}, pmid = {40953718}, issn = {1096-0953}, abstract = {Nitrogen pollution poses a critical threat to aquatic ecosystems worldwide, and biodegradable polymers have recently gained increasing attention as effective carbon sources to enhance biological nitrogen removal. This study systematically evaluated the nitrogen removal performance of heterotrophic nitrification-aerobic denitrification (HN-AD) bacteria using various biodegradable polymers. Among them, poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV, 100 kDa) showed promising performance, with a sustained carbon release rate of 2.04 mg·g[-1]·h[-1] and a total nitrogen (TN) removal rate of 1.82 mg·L[-1]·h[-1]. Metagenomic analysis indicated that Acidovorax, a key degrader of PHBV granules, played a dominant role in the denitrification process with a relative abundance of 33.89%, contributing 31.8% and 48.23% to carbon and nitrogen metabolism, respectively. In the PHBV (100 kDa) system, Stappia was identified as the predominant genus, accounting for 52.35% of the microbial community and contributing 57.87% and 64.52% to carbon and nitrogen metabolism, respectively. Functional gene profiling further suggested that PHBV significantly upregulated key nitrogen metabolism genes and enzymes, including nirK, norB, and nosZ. These results provide valuable insights into microbial mechanisms supporting polymer-based nitrogen removal and highlight the potential of PHBV as a sustainable carbon source in wastewater treatment.}, }
@article {pmid40953560, year = {2025}, author = {Zhang, F and Yang, A and Wu, Y and Li, W and Guo, J and He, F and Wang, M and Zhang, P and Li, J}, title = {Exploring sustainable fertility of live microalgal cells: Impacts on lettuce growth and soil microbial metabolic responses.}, journal = {Journal of environmental management}, volume = {394}, number = {}, pages = {127235}, doi = {10.1016/j.jenvman.2025.127235}, pmid = {40953560}, issn = {1095-8630}, abstract = {The excessive dependency on chemical fertilizers presents significant challenges to agricultural sustainability, thereby necessitating the development of eco-friendly alternatives that can enhance nutrient efficiency. This study investigates live Chlorella sp. cells (OX) as biofertilizers in lettuce cultivation, comparing their effects with freeze-thaw disrupted algal biomass (OO), bead-milled disrupted algal biomass (OZ), and a water-only control (CK). OX significantly enhanced lettuce growth-stem length (+32.6 %), leaf count (+33.3 %), chlorophyll (+233.3 %), and protein content (+47.5 %)-by continuously releasing nitrogen-rich metabolites, phytohormones, and extracellular polymers. OX also improved soil health: total nitrogen (+53.2 %), ammonium-N (+85.2 %), catalase activity (+76.6 %), and available phosphorus (+11.1 %) increased, while pH decreased due to organic acids. Metagenomic analysis revealed OX enriched nutrient-cycling bacteria (e.g., Pseudomonadota, Bacteroidota, and phosphate-solubilizing Massilia) and upregulated genes that store nitrogen (NapAB) and reduce greenhouse gases (NosZ). Crucially, live cells sustained balanced root-microbe interactions via photosynthesis, whereas disrupted biomass (OO/OZ) caused transient nutrient pulses. These findings demonstrate that live microalgae reconcile crop productivity, soil health, and environmental sustainability, reducing dependence on chemical inputs while restoring degraded soils, offering a low-carbon alternative to synthetic fertilizers.}, }
@article {pmid40953197, year = {2025}, author = {Ogarkov, O and Orlova, E and Suzdalnitsky, A and Mokrousov, I}, title = {Microbiota of the Lung Tuberculoma: Paucibacillary Bacterial Community.}, journal = {International journal of mycobacteriology}, volume = {14}, number = {3}, pages = {209-218}, pmid = {40953197}, issn = {2212-554X}, abstract = {Caseum, the central necrotic material of tuberculous lesions, is a reservoir of drug-resistant persisting Mycobacterium tuberculosis (MTB). However, tubercle bacilli are not the only bacterial inhabitants of this necrosis. We discuss the available data on metagenomic and amplicon sequencing of 16S rRNA of caseous necrosis from surgically excised tuberculosis (TB) foci. This approach facilitated the characterization of the biodiversity and the potential biochemical pathways of these bacterial communities. We postulate that in terms of MTB content relative to satellite anaerobic lipophilic bacteria, caseum may present two distinct terminal states. "True" TB necrosis, containing 99.9% tubercle bacilli, and a polymicrobial community wherein anaerobic lipophilic bacteria predominate over MTB. Isolation from caseum and genomic characterization of several Corynebacterium and Staphylococcus species support this concept.}, }
@article {pmid40953082, year = {2025}, author = {Kotaki, T and Kanai, Y and Onishi, M and Sakai, Y and Motooka, D and Chen, Z and Enoki, Y and Komatsu, S and Hirai, K and Minami, S and Kawagishi, T and Ushijima, H and Kobayashi, T}, title = {Single-round infectious rotaviruses with deletions of VP7 or VP4 genes, based on SA11 and WC3 strain backbones, and their potential use as viral vectors.}, journal = {PLoS pathogens}, volume = {21}, number = {9}, pages = {e1013484}, doi = {10.1371/journal.ppat.1013484}, pmid = {40953082}, issn = {1553-7374}, abstract = {Single-round infectious rotavirus, which lacks a gene essential for virion assembly, serves not only as a safe and effective rotavirus vaccine but also as an orally-administrable viral vector vaccine that induces mucosal immunity. Previously, we generated a single-round infectious rotavirus by partially deleting the viral VP6 gene, and demonstrated its potential as a promising vaccine platform. However, this system has several limitations; namely, low viral protein expression levels and safety concerns. Here, we addressed these challenges by introducing large deletions into the VP7 or VP4 genes, which are dispensable for viral protein expression but essential for virion assembly. These VP7- or VP4-defective viruses exhibited markedly higher protein expression in wild-type MA104 cells than the previously developed VP6-defective virus. In addition, the large deletions reduce the risk of viral reversion, thereby increasing both efficacy and safety. In a mouse model, these viruses induced neutralizing antibodies at levels comparable with those elicited by wild-type rotavirus, indicating their potential as rotavirus vaccines. Moreover, a VP4-defective rotavirus harboring a heterologous gene achieved high expression of heterologous proteins, warranting its application as a viral vector vaccine. To further increase safety, we established a reverse genetics system for the bovine rotavirus WC3 strain, a parental strain of the licensed live attenuated rotavirus vaccine, and successfully generated a single-round VP4-defective rotavirus based on the WC3 backbone. Taken together, these optimizations facilitate development of safe and effective single-round infectious rotavirus platforms suitable for human use.}, }
@article {pmid40953029, year = {2025}, author = {Park, R and Chevalier, C and Kieser, S and Marizzoni, M and Paquis, A and Armand, S and Scheffler, M and Allali, G and Assal, F and Momjian, S and Frisoni, GB}, title = {Gut microbiome signatures in iNPH: Insights from a shotgun metagenomics study.}, journal = {PloS one}, volume = {20}, number = {9}, pages = {e0330251}, doi = {10.1371/journal.pone.0330251}, pmid = {40953029}, issn = {1932-6203}, abstract = {Idiopathic normal pressure hydrocephalus (iNPH), a leading cause of reversible dementia in older adults, is marked by ventriculomegaly, gait disturbances, cognitive decline, and urinary incontinence. Emerging evidence suggests that gut dysbiosis (microbial imbalance) may influence neuroinflammation and cerebrospinal fluid dynamics, potentially contributing to glymphatic system dysfunction and ventricular enlargement. This study used shotgun metagenomics to analyze the gut microbiome in iNPH patients (n = 18) compared to healthy controls (n = 50), individuals with ventriculomegaly but no iNPH symptoms (n = 50), and Alzheimer's disease patients (n = 50). Microbiome analysis showed an enrichment of species previously linked to various disease states, such as Enterocloster bolteae and Ruminococcus gnavus, indicating general dysbiosis. In contrast, enrichment of specific taxa, including Evtepia gabavorous and Cuneatibacter sp., were specifically associated with iNPH clinical traits, pointing to possible disease-specific microbial markers. Functional analysis showed enrichment of pathways related to carbohydrate and amino acid metabolism, including the S-adenosyl-L-methionine superpathway, implicating inflammatory and immune processes. These findings suggest distinct gut microbiome signatures in iNPH, offering insights into potential gut-brain interactions that may contribute to the disorder's pathophysiology and highlighting possible targets for future therapeutic strategies.}, }
@article {pmid40952163, year = {2025}, author = {Nir, I and Armoza-Zvuloni, R and Barak, H and De Los Ríos, A and McKay, CP and Kushmaro, A}, title = {The Biology, Microclimate, and Geology of a Distinctive Ecosystem Within the Sandstone of Hyper-Arid Timna Valley, Israel.}, journal = {Environmental microbiology reports}, volume = {17}, number = {5}, pages = {e70188}, doi = {10.1111/1758-2229.70188}, pmid = {40952163}, issn = {1758-2229}, support = {PID2023-147027NB-I00B//Agencia Estatal de Investigaci&#xf3;n. Write: Agencia Estatal de Investigacion (AEI), MICINN/ ; EXO-92-4//NASA AMES/ ; 3-17370//Minstry of Science and Technology (MOST), Israel/ ; }, abstract = {Microbial endolithic communities in the sandstone rocks of the southern Negev Desert, particularly in Timna Park, were initially discovered by Imre Friedmann and Roseli Ocampo-Friedmann in their pioneering study about 50 years ago. Nonetheless, this harsh microecosystem, dominated by cyanobacterial taxa, raises questions about the adaptive mechanisms that enable the survival of these microorganisms. The present study provides comprehensive data, including extensive precipitation records for the Timna Valley, and multi-year microclimatic data from a colonised site. It includes examinations of rock structure, as well as microscopic and metagenomic analysis. Our findings point to a distinct bacterial endolithic population dominated by the cyanobacterial genus Chroococcidiopsis. Although the taxa are well known, we show here how their exclusive persistence is driven by the sandstone's fine porosity and thermal properties, combined with rare, low-volume precipitation. This highly selective microenvironment highlights how specific rock and climate interactions can filter microbial diversity in hyper-arid deserts. Additionally, it demonstrates an adaptation strategy based on both short-term and decadal-scale dormancy. Thus, it offers new insights for the survival of these unique ecosystems and provides valuable perspectives for astrobiology and the search for evidence of microbial life on Mars.}, }
@article {pmid40952106, year = {2025}, author = {Xu, Q and Huang, Y}, title = {Stringent response-mediated ferroptosis-like death resistance underlies Novosphingobium persistence during ciprofloxacin stress.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0147525}, doi = {10.1128/aem.01475-25}, pmid = {40952106}, issn = {1098-5336}, abstract = {Antibiotics, as emerging hazardous materials in the environment, pose significant risks to ecosystems and contribute to the spread of antibiotic-resistant bacteria. Although extensive knowledge has been accumulated on antibiotic-resistance mechanisms in individual bacteria, less is understood about how the bacterial communities respond to antibiotic exposure under natural environmental conditions, where nutrient supplies are often limited and fluctuating. Here, we report that Novosphingobium dominated in a wetland bacterial community under 1 µg/mL ciprofloxacin (CIP) exposure and persisted during DL-serine hydroxamate-induced starvation, where the stringent response alarmer (p)ppGpp was detected. Metagenome sequencing revealed that genes associated with siderophore transport, cytochrome c, and glutathione S-transferase were significantly enriched in Novosphingobium, linking its dominance under CIP stress to iron homeostasis and oxidative stress responses. Further study on the survival mechanism of Novosphingobium pentaromativorans US6-1 under 8 µg/mL CIP stress demonstrated that stringent response regulated the growth rate and maintained cell viability by suppressing the TCA cycle and oxidative phosphorylation, deterring the entry of CIP and siderophore into cells, reducing intracellular ferrous iron and malondialdehyde, and balancing cellular redox status, thereby protecting cells from ferroptosis-like death. This study is the first to report Novosphingobium's dominance and persistence in a bacterial community during CIP stress in natural environmental conditions and to propose the stringent response-mediated ferroptosis-like death resistance as one of its key survival mechanisms.IMPORTANCEAntibiotics in the environment are increasingly recognized as a new class of pollutants that accelerate the evolutionary selection of antibiotic-resistant bacteria. However, little is known about how this selection occurs under natural conditions, including how specific bacteria taxa and mechanisms respond to particular antibiotics. This study reveals for the first time the selection effect of CIP on Novosphingobium under nutrient-limited conditions, during which stringent response and iron homeostasis play important roles. An innovative linkage between stringent response and ferroptosis-like death resistance is proposed in N. pentaromativorans US6-1, which serves as the CIP resistance mechanism for Novosphingobium. These findings may help inform strategies to combat antimicrobial resistance in the natural environment.}, }
@article {pmid40952003, year = {2025}, author = {Sun, T and Zheng, Q and Huang, R and Yang, L and Liu, Z and Zhang, Z and Liu, X and Yang, H and Li, X and Tong, J and Zhu, L}, title = {Exploring cervicovaginal microbiome differences between single and multiple endometrial polyps: implications for non-invasive classification.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0002325}, doi = {10.1128/msystems.00023-25}, pmid = {40952003}, issn = {2379-5077}, abstract = {Single and multiple endometrial polyps (EP) are common gynecological conditions with differing recurrence rates, influencing clinical treatment decisions. This study aimed to characterize the reproductive tract microbiome in both subtypes to support the development of methods for the non-invasive categorization of EPs. Using metagenomic sequencing, we analyzed vaginal and cervical samples from 27 reproductive-aged patients with single EP and 22 with multiple EP. Compared with controls and multiple EP cases, single EP vaginal and cervical samples exhibited a lower percentage of community state types (CST) I and II. Sneathia amnii was identified as a characteristic species in both the vagina (P = 0.0051) and cervix (P = 0.0398) of single EP patients compared with controls. Mesorhizobium sp. (vaginal P = 0.0110, cervical P = 0.0210), Acinetobacter baumannii (vaginal P = 8.0 × 10[-5], cervical P = 0.0314), and Pasteurella multocida (vaginal P = 0.0173, cervical P = 0.0210) were enriched in single EP compared with multiple EP. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of vaginal microbiome revealed unique pathways in single EP, including aminoacyl-tRNA biosynthesis, pantothenate and coenzyme A (CoA) synthesis, pyrimidine metabolism, glycolysis/gluconeogenesis, and biosynthesis of phenylalanine, tyrosine, and tryptophan. Using a random forest model, we further selected microbiota and clinical parameters to differentiate single and multiple EPs, thus achieving an area under curve (AUC) of 0.861. Our findings characterized the composition of the cervicovaginal microbiota of single and multiple EPs and proposed biomarkers for their non-invasive classification based on a random forest model.IMPORTANCEThe prevalence rate of endometrial polyps (EPs), a common gynecological condition, varies between 7.8% and 34.9%. Multiple EPs are associated with higher recurrence rates and chronic endometritis than single EPs and thus require more aggressive clinical interventions. However, only laparoscopic surgery can accurately identify single and multiple polyps. Non-invasive adjunctive diagnostic methods can aid in altering surgical indications preoperatively. Using metagenomic sequencing, we thoroughly analyzed the vaginal and cervical samples of 27 single EP and 22 multiple EP patients of reproductive age. We then identified distinct microbial patterns in the single and multiple samples, which were crucial for understanding EP pathogenesis and its association with gynecological health. Using a random forest model, key bacterial taxa that differentiate single and multiple EPs were identified with high accuracy. These could potentially serve as non-invasive diagnostic biomarkers. This research delineates the cervicovaginal microbiome of the reproductive tract in EP patients, offering a basis for developing non-invasive diagnostic tools and personalized treatment strategies.}, }
@article {pmid40952001, year = {2025}, author = {Raich, SS and Majzoub, ME and Haifer, C and Paramsothy, S and Shamim, MMI and Borody, TJ and Leong, RW and Kaakoush, NO}, title = {Bacterial taxonomic and functional changes following oral lyophilized donor fecal microbiota transplantation in patients with ulcerative colitis.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0099125}, doi = {10.1128/msystems.00991-25}, pmid = {40952001}, issn = {2379-5077}, abstract = {UNLABELLED: Oral lyophilized fecal microbiota transplantation (FMT) can induce remission in patients with active ulcerative colitis (UC); however, our understanding of how this form of FMT alters the patient microbiome remains limited. Here, we analyzed data from a recent randomized, double-blind, placebo-controlled clinical trial of FMT in UC to assess donor species colonization and factors responsible for efficacy using this form of therapy. The gut microbiome of donors and patients was profiled longitudinally using deep shotgun metagenomic sequencing, and microbiome diversity, species-genome bin presence, functional profiles, and the resistome were studied. The gut microbiome of patients treated with oral lyophilized FMT significantly increased in species-genome bin richness and shifted in composition toward the donor profiles; this was not observed in patients receiving placebo. While species-genome bin richness was not associated with clinical response in this trial, we identified donor- and patient-specific features associated with the induction of remission and maintenance of response. However, the presence of a Clostridium species-genome bin, as well as L-citrulline biosynthesis contributed by Alistipes spp., was seen in responders treated by either donor. Several of the above outcomes were found to be consistent when data were analyzed at the level of metagenome-assembled genomes. FMT was also found to deplete the resistome within patients treated with antibiotics to levels lower than the UC baseline. Single donor oral lyophilized FMT substantially modifies taxonomic diversity and composition as well as microbiome function and the resistome in patients with UC, with several features identified as strongly linked to response regardless of the donor used.<br><br>IMPORTANCE: There is a limited amount of work examining the effects of oral lyophilized fecal microbiota transplantation (FMT) on the microbiome of patients with ulcerative colitis (UC), and less so studies examining species-level dynamics and functional changes using this form of FMT. We performed deep shotgun metagenomic sequencing to provide an in-depth species-genome bin-level analysis of the microbiome of patients with UC receiving oral lyophilized FMT from a single donor. We identified key taxonomic and functional features that transferred into patients and were associated with clinical response. We also determined how FMT impacts the resistome of patients with UC. We believe these findings will be important in ongoing efforts to not only improve the efficacy of FMT in UC but also allow for the transition to defined microbial therapeutics, foregoing the need for FMT donors.}, }
@article {pmid40951842, year = {2025}, author = {Fenibo, EO and Nkuna, R and Matambo, T}, title = {Metagenomic Insights Into Biopile Remediation of Petroleum-Contaminated Soil Using Chicken Droppings in Rivers State, Nigeria.}, journal = {Bioinformatics and biology insights}, volume = {19}, number = {}, pages = {11779322251371117}, pmid = {40951842}, issn = {1177-9322}, abstract = {Petroleum hydrocarbon pollution is an escalating global issue, particularly in developing countries, where it has attracted significant attention from researchers focusing on bioremediation, monitoring and sustainability. This study utilised metagenomics to investigate the bacterial community's response in polluted soil undergoing field-scale biopile treatment, with chicken droppings as a nutrient source. Hydrocarbon concentrations were monitored over a 90-day remediation period using the Fourier transform infrared (FTIR) spectrometry technique. Molecular and bioinformatic analyses were conducted to track the dynamics of bacterial species, their abundance and functional roles during the bioremediation process. The initial total petroleum hydrocarbon (TPH) concentration of 446 945 ppm was first reduced to 80 332 ppm through dilution. Following a 90-day bioremediation process using poultry waste, the level further decreased to 5326 ppm, representing a 93.37% reduction. In the metagenomic analysis, a total of 26 736 reads were obtained, averaging 6684 counts per sample. In addition, the study identified diverse bacterial metagenomes, including well-established hydrocarbon-degrading bacteria from Proteobacteria, Firmicutes, Acidobacteria and Actinobacteria phyla, and species previously not reported as hydrocarbon-degrading. Biomarkers associated with hydrocarbon metabolisms, such as aromatic dioxygenases, alkane-1-monooxygenase and methanol oxidation pathways, were identified. A significant decrease in the relative abundance of bacterial genera in heavily polluted soil was observed, alongside an increased presence of Caballeronia, Paraburkholderia and Fontibacillus genera. These findings indicate that chicken droppings contribute 0.30% to the reduction of TPH in the biopiling remediation technique used for treating heavily contaminated soil. A comparative assessment of hydrocarbon attenuation in nutrient-amended vs unamended soils indicates that a 3-month remediation timeframe is insufficient to achieve optimal bioremediation outcomes. However, the TPH reduction in unamended treatment highlights the intrinsic natural attenuation capacity of the impacted soil matrix, attributable to indigenous microbial consortia and prevailing environmental conditions.}, }
@article {pmid40951757, year = {2025}, author = {Gupta, S and Angrup, A and Rana, SS and Batra, G and Rana, N and Ramola, M and Vashist, T and Bisht, K and Monga, N and Jolly, SS and Singla, M and Sareen, S and Goyal, A and Duseja, RN}, title = {Microbial overlap in dental plaque and tumor tissue of esophageal cancer patients: A pilot study.}, journal = {Journal of Indian Society of Periodontology}, volume = {29}, number = {2}, pages = {153-163}, pmid = {40951757}, issn = {0972-124X}, abstract = {INTRODUCTION: Microbial dysbiosis has been shown to be involved in various types of gastrointestinal cancers, but there is a dearth of strong studies linking the oral microbiome imbalance with esophageal cancer (EC).<br><br>OBJECTIVES: The main objective of the study was to identify the link between oral microbiome and EC.<br><br>MATERIALS AND METHODS: Twelve suspected EC and two healthy control patients were recruited. After the histological confirmation of EC, four confirmed EC patient samples and two healthy control samples were subjected to 16S metagenomics study using the Oxford Nanopore Technology sequencing platform.<br><br>RESULTS: Species richness of microbial community was higher in the healthy controls followed by diseased plaque, tumor tissue and adjacent tissue. Bacillota, Pseudomonata, Fusobacteriota, Bacteroidota, and Campylobacterota were the major phyla identified in all the groups. Majorly prevalent genera (core microbiome analysis) in all the groups were Streptococcus, Salmonella, Bacillus, Enterococcus, Veillonella, Klebsiella, Clostridioides, Prevotella, Gemella, Selenomonas, Firmicutes, and Proteobacteria followed by Bacteroidetes and Fusobacteria.<br><br>CONCLUSION: Our study suggests an association between oral microbiome and EC. The prevalence of same microbial genus in the oral cavity (dental plaque) and tumor tissue depicts a possible link. Our study opens the plausible microbe-based biomarker screening of EC.}, }
@article {pmid40951316, year = {2025}, author = {Zhang, B and Sheng, Z and Bu, C and Wang, L and Lv, W and Wang, Y and Xu, Y and Yan, G and Gong, M and Liu, L and Hu, W}, title = {Whipworm infection remodels the gut microbiome ecosystem and compromises intestinal homeostasis in elderly patients revealed by multi-omics analyses.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1663666}, pmid = {40951316}, issn = {2235-2988}, abstract = {INTRODUCTION: Whipworm (Trichuris trichiura) coexists with symbiotic microbiota in the gastrointestinal ecosystem. There is a paucity of data on the association between whipworm infection and the gut microbiota composition in elderly individuals. This study was designed to investigate changes in gut microbiota and function and its metabolite profile in patients with whipworm infection.<br><br>METHODS: We used 16S rRNA gene sequencing to identify microbial signatures associated with whipworm infection. Subsequently, shotgun metagenomic sequencing revealed functional changes that highlighted disruptions in microbial gene expression and metabolic pathways influencing host health. Ultraperformance liquid chromatography-mass spectrometry metabolomics was used to characterize whipworm infectioninduced metabolic perturbations and elucidate metabolite dynamics linked to microbial activity. Collectively, this multi-omics approach deciphered structural, functional, and metabolic remodeling of the gut ecosystem that distinguished whipworm-infected patients from healthy controls.<br><br>RESULTS: Analyses of the gut microbiome in patients with whipworm infection revealed significantly increased observed species richness and ACE indices, along with an enrichment of Prevotella 9-driven enterotypes. Additionally, metagenomic and metabolomic analyses indicated enrichment in metabolic pathways related to amino acid, energy and carbohydrate metabolism. Metabolic network analysis further suggested that the upregulated Prevotella copri and Siphoviridae sp. were positively correlated with elevated levels of myristic acid and DL-dipalmitoylphosphatidylcholine.<br><br>CONCLUSION: These findings suggest that whipworm infection significantly remodels the gut microbiome ecosystem and compromises intestinal homeostasis.}, }
@article {pmid40951304, year = {2025}, author = {Chen, J and Wang, Y and Aikebaier, R and Liu, H and Li, Y and Yang, L and Haiyilati, A and Wang, L and Fu, Q and Shi, H}, title = {RAA-CRISPR/Cas12a-based visual field detection system for rapid and sensitive diagnosis of major viral pathogens in calf diarrhea.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1616161}, pmid = {40951304}, issn = {2235-2988}, abstract = {Calf diarrhea is a complex digestive disorder in cattle that imposes significant economic losses in terms of calf mortality, growth impairment, and treatment costs. Both infectious and non-infectious agents contribute to its aetiology; however, most of the infectious cases are caused by viruses, often accompanied by severe co-infections. To identify viral culprits, we performed viral metagenomic sequencing on three pooled samples from the 150 diarrheal samples from Xinjiang, China, which helped with identification of the following four predominant agents: bovine nepovirus (BNeV), bovine coronavirus (BCoV), bovine viral diarrhea virus (BVDV) and bovine enterovirus (BEV). Currently, the process of diagnosing these pathogens involves time-consuming workflows, limited sensitivity, poor portability, and lack of field applicability. Keeping these diagnostic shortcomings in mind, an integrated platform called RAA-CRISPR/Cas12a system was developed by combining recombinase-aided amplification (RAA) at 37°C with CRISPR/Cas12a-mediated fluorescence detection, which achieved 100-100,000 times higher sensitivity than conventional polymerase chain reaction (PCR) (detection limits: 1-10 copies/μL) and demonstrated 100% specificity against non-target pathogens. Clinical validation of sensitivity and specificity of 252 samples revealed 1.6-4.9 times higher detection rates (239 positives) than PCR (81 positives), which was consistent with PCR-confirmed cases. The assay's 40-min. workflow enables rapid on-site deployment without specialized instrumentation, as it requires only a portable heat block and blue LED transilluminator. Hence, with its laboratory accuracy and field applicability, this method helps in early identification of pathogens, outbreak containment and mitigation of economic loss in the global cattle industry.}, }
@article {pmid40950993, year = {2025}, author = {Jin, L and Chen, C and Zhao, H and Chen, L and Wang, X and Wang, Q and Yuan, J and Li, J and Xu, S and Zhang, R and Chu, W and Ye, N and Zou, G and Ye, J}, title = {Fusobacterium nucleatum infection leading to rare hepatorenal abscess: a case report.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1540430}, pmid = {40950993}, issn = {2296-858X}, abstract = {Fusobacterium nucleatum is a gram-negative anaerobic bacterium commonly associated with periodontal disease. However, its role in extraoral infections, particularly in immunocompetent individuals, is increasingly recognized. We report a rare case of hepatorenal abscess caused by F. nucleatum in a previously healthy woman, initially suspected to have a malignant tumor based on PET-CT findings. Next-generation sequencing (NGS) of abscess aspirate confirmed the pathogen. The patient responded well to targeted antibiotic therapy. This case highlights the importance of considering anaerobic pathogens in deep-seated abscesses and the utility of NGS in achieving accurate microbial diagnosis.}, }
@article {pmid40950887, year = {2025}, author = {Zhu, N and Sun, J and Wu, D and Xia, H and Fei, L}, title = {Pathogen distribution and prognostic risk factors in respiratory intensive care unit (RICU) patients of a large general hospital before and after COVID-19 pandemic.}, journal = {Journal of thoracic disease}, volume = {17}, number = {8}, pages = {6176-6188}, pmid = {40950887}, issn = {2072-1439}, abstract = {BACKGROUND: The evolving pathogen spectrum and prognosis of severe pulmonary infections in the respiratory intensive care unit (RICU) during the coronavirus disease 2019 (COVID-19) pandemic remain unclear. This study aimed to investigate shifts in the pathogen landscape of pulmonary infections among intensive care unit (ICU) patients following the regular prevention and control of COVID-19.<br><br>METHODS: A total of 132 patients with pulmonary infections admitted to the RICU of the First Affiliated Hospital of Anhui Medical University between January 2022 and March 2023 were included in the study. Patients were categorized into two cohorts: pre-strategy (n=65, Jan to Nov 2022) and post-strategy (n=67, Dec 2022 to Mar 2023), based on the implementation of regular COVID-19 prevention and control measures. Metagenomic next-generation sequencing (mNGS), and conventional tests using bronchoalveolar lavage fluid (BALF) and blood samples were used to detect pathogens. Retrospective data were obtained from the patients' medical records. The spectrum of pathogens was analyzed. Additionally, univariate and multivariate logistic regression models were employed to analyze the risk factors associated with adverse outcomes.<br><br>RESULTS: After the regular prevention and control of COVID-19 in December 2022, there was a significant shift in the pathogen landscape. The proportion of patients with severe acute respiratory coronavirus 2 (SARS-CoV-2) increased dramatically from 0% to 74.6%. This was accompanied by a significant rise in the incidence of Staphylococcus aureus (S. aureus) infections. Among the COVID-19 patients, a slight decrease in Gram-negative (G-) bacterial co-infections and a corresponding increase in Gram-positive (G+) bacterial co-infections was observed. The overall mortality rate among all enrolled patients was 30.3%, with 24.6% in the pre-strategy group and 35.8% in the post-strategy group. Additionally, there was a marked increase in the detection rates of Candida and herpes simplex virus 1 (HSV-1) in COVID-19 patients following the strategy change. The analysis of risk factors revealed that a poor prognosis was strongly associated with co-infections of SARS-CoV-2 with Candida [odds ratio (OR) =2.91, 95% confidence interval (CI): 1.01-8.41] or Aspergillus (OR =3.08, 95% CI: 0.89-10.66) species. Further, bacterial and fungal co-infections (OR =3.92, 95% CI: 1.41-10.86) were identified as significant risk factors for a poor prognosis in patients without COVID-19.<br><br>CONCLUSIONS: Our findings highlight the pathogen spectrum in RICU patients changed significantly after the shift in COVID-19 policy. Co-infections with fungi and G+ bacteria require increased clinical vigilance and early intervention to improve outcomes.}, }
@article {pmid40950593, year = {2025}, author = {Silva, ACP and Migliaccio, F and Barosa, B and Gallucci, L and Yücel, M and Foustoukos, D and Le Bris, N and Bartlett, SJ and D'Alessandro, V and Vetriani, C and Giovannelli, D}, title = {Hydrodynamic flow and benthic boundary layer interactions shape the microbial community in Milos shallow water hydrothermal vents.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1649514}, pmid = {40950593}, issn = {1664-302X}, abstract = {In shallow-water hydrothermal vents, the dynamic interface between the discharged reduced hydrothermal fluids and the oxidized seawater allows the establishment of gradients capable of supporting diverse and complex microbial mats. Due to their shallow depths and proximity to land masses, shallow vents are heavily influenced by dynamic forcing, tidal fluctuations, and episodic events (e.g., storms, tides, etc.). Although several studies have investigated the microbial communities inhabiting shallow vents in the last decades, less is known about how microbial communities respond to episodic events and how the complex interplay of physical and chemical drivers shapes the establishment and structure of microbial biofilms in these systems. Here we present data combining the taxonomic and functional diversity of the white microbial mats commonly found in sulfide rich shallow-water hydrothermal vents in Paleochori Bay (Milos Island, Greece), using a combined approach of 16S rRNA transcript amplicon sequencing (from RNA) and shotgun metagenomic sequencing (from which 16S rRNA genes were retrieved). We show that the white microbial mats of Milos shallow-water hydrothermal vents are dominated by Epsilonproteobacteria, now classified as Campylobacterota, with metabolic functions associated with chemolithoautotrophic lifestyles and exposed to a diverse array of viral communities. Taxonomic names follow the classification available at the time of analysis (2012). We explore how dynamic forcing and storm events influence microbial community restructuring and turn-over, and provide evidence that dynamic interactions with the benthic boundary layer play a key role in controlling the spatial distribution of taxa. Overall, our results show diverse processes through which geodynamic events influence microbial taxonomic and functional diversity.}, }
@article {pmid40950589, year = {2025}, author = {Li, YH and Yang, M and Wei, TS and Chen, HG and Gong, L and Wang, Y and Gao, ZM}, title = {Survival strategies for the microbiome in a vent-dwelling glass sponge from the middle Okinawa Trough.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1636046}, pmid = {40950589}, issn = {1664-302X}, abstract = {The adaptive mechanisms of sponge microbiomes to harsh deep-sea environments, including hydrothermal vents and cold seeps, remain unclear. Here, we used metagenomics to investigate the microbiome of an undescribed vent-dwelling glass sponge from the middle Okinawa Trough, probably representing a novel species within the family Bolosominae. Eleven high-quality prokaryotic metagenome-assembled genomes (MAGs) were retrieved, none assignable to known species, with two representing new genera. Dominant MAGs included sulfur-oxidizing bacteria (SOB) and ammonia-oxidizing archaea, followed by methane-oxidizing bacteria (MOB) and nitrite-oxidizing bacteria. Global distribution analysis suggested that most MAGs were sponge-specific symbionts. Comparative genomics revealed functional redundancy among SOB and early-stage genome reduction in a unique MOB lineage. Additionally, a total of 410 viral contigs were identified, most exhibiting a lytic lifestyle and forming distinct clades from known viruses. Our work expands understanding of the diversity and novelty of deep-sea sponge-associated prokaryotes and viromes, and suggests their niche adaptation to hydrothermal fluid environments.}, }
@article {pmid40950585, year = {2025}, author = {Kardaras, FS and Siatravani, E and Tsilipounidaki, K and Petinaki, E and Hatzigeorgiou, AG and Miriagou, V}, title = {Identification of nasopharyngeal microbial dysbiosis in COVID-19 patients by 16S rRNA gene sequencing.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1631198}, pmid = {40950585}, issn = {1664-302X}, abstract = {BACKGROUND: The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has prompted extensive research into factors influencing the onset and severity of the disease. Among these factors, the role of the nasopharyngeal microbiome, a vital ecosystem critical for respiratory health and immune modulation, remains incompletely understood. This study aimed to elucidate the relationship between the composition of nasopharyngeal microbiota and the clinical presentation of COVID-19 during the initial phase of infection.<br><br>MATERIALS AND METHODS: A total of 81 nasopharyngeal swab samples were collected from individuals in Central Greece between January and February 2021. Following quality control, 77 samples were selected for microbiome analysis. This selection included SARS-CoV-2-negative controls (NE, n&#x202f;=&#x202f;26) and SARS-CoV-2-positive patients classified as asymptomatic (AS, n&#x202f;=&#x202f;19), mild (MI, n&#x202f;=&#x202f;16), or severe (SE, n&#x202f;=&#x202f;16) based on clinical criteria. All COVID-19-positive samples were collected within 2&#x202f;days of symptom onset, and participants with recent hospitalization or antibiotic use were excluded. Microbiome profiling was performed using 16S rRNA gene-targeted metagenomic sequencing, followed by comprehensive bioinformatics and statistical analyses.<br><br>RESULTS: Significant differences were observed in both alpha and beta diversity measures, with alpha diversity decreasing as the severity of COVID-19 increased. Three of the four individual study groups, namely NE, MI, and SE, exhibited distinct microbial profiles, while the asymptomatic group showed greater heterogeneity. Significant variations in the abundance of specific phyla, families, and genera were identified between the different study groups. When comparing the NE and SE groups, we observed a significant increase in the abundance of the Proteobacteria phylum in the SE group, while the abundance of Fusobacteria was significantly lower in the SE group. In symptomatic COVID-19 patients, we observed a significant reduction in the abundance of key family constituents of the nasopharyngeal microbiota, such as Fusobacteriaceae, Prevotellaceae, and Streptococcaceae, suggesting a disruption in microbial homeostasis during the infection. Conversely, we found an increased prevalence of families associated with pathogenic or opportunistic pathogenic bacteria, including Enterobacteriaceae and Bacillaceae, in the SE group, suggesting a potential role of these taxa in the disease progression of COVID-19.<br><br>CONCLUSION: These findings shed light on specific genera that undergo significant changes during COVID-19 infection and contribute to our understanding of the dynamic nature of the nasopharyngeal microbiome in relation to disease progression and severity.}, }
@article {pmid40950048, year = {2025}, author = {Shaw, J and Marin, MG and Li, H}, title = {High-resolution metagenome assembly for modern long reads with myloasm.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.09.05.674543}, pmid = {40950048}, issn = {2692-8205}, abstract = {Long-read metagenome assembly promises complete genomic recovery from microbiomes. However, the complexity of metagenomes poses challenges. We present myloasm, a metagenome assembler for PacBio HiFi and Oxford Nanopore Technologies (ONT) R10.4 long reads. Myloasm uses polymorphic k-mers to construct a high-resolution string graph and then leverages differential abundance for graph simplification. On real-world ONT metagenomes, myloasm assembled three times more complete circular contigs than the next-best assembler. Myloasm can make ONT and HiFi comparable for assembly: for a jointly sequenced gut metagenome, myloasm with ONT assembled more complete circular genomes than any assembler with HiFi. Myloasm recovers previously inaccessible within-species diversity; we recovered six complete Prevotella copri single-contig genomes from a gut metagenome and eight complete TM7 (Saccharibacteria) contigs with > 93% similarity from an oral metagenome. With this improved resolution, we resolved two 98% similar ermF antibiotic resistance genes spreading through distinct strain-specific mobile genetic elements in a human gut.}, }
@article {pmid40949832, year = {2025}, author = {Guo, N and Ma, G and Liu, H and Qiu, J and Yu, Y and Gao, Y and Yi, Z and Wan, Z and Zhang, L and Wu, X}, title = {Metagenomic Next-Generation Sequencing Reveals Porphyromonas gingivalis in Geriatric Severe Pneumonia Complicated by Empyema: Case Report.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {4811-4816}, pmid = {40949832}, issn = {1178-6973}, abstract = {BACKGROUND: Severe pneumonia with empyema in elderly patients presents diagnostic and therapeutic challenges. Traditional culture methods often fail to identify the causative pathogen, leading to delays in targeted treatment. Metagenomic next-generation sequencing (mNGS) has emerged as a powerful tool for detecting rare and fastidious pathogens.<br><br>CASE PRESENTATION: We report a 77-year-old male with a history of chronic smoking and alcohol consumption who presented with a two-month history of cough, sputum production, and progressive dyspnea. His condition rapidly deteriorated with high fever and respiratory failure. Initial antibiotic therapy was ineffective, and multiple cultures of blood, sputum, and pleural fluid were negative. However, mNGS of blood and pleural fluid identified Porphyromonas gingivalis, a well-known periodontal pathogen rarely associated with pulmonary infections. The patient's treatment was adjusted to include targeted anaerobic coverage (imipenem plus vancomycin) alongside chest tube drainage, leading to significant clinical improvement.<br><br>CONCLUSION: This case highlights the clinical utility of mNGS in diagnosing culture-negative pulmonary infections. Porphyromonas gingivalis should be considered a potential pathogen in patients with severe pneumonia and empyema, particularly in those with poor oral hygiene or periodontal disease.}, }
@article {pmid40949821, year = {2025}, author = {Hirose, E and Lopez, JV and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and ,  and ,  and ,  and ,  and , }, title = {The chromosomal genome sequence of the photosymbiotic ascidian, Trididemnum clinides Kott, 1977 and its associated microbial metagenome sequences.}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {357}, pmid = {40949821}, issn = {2398-502X}, abstract = {We present a genome assembly from a specimen of Trididemnum clinides (photosymbiotic ascidian; Chordata; Ascidiacea; Aplousobranchia; Didemnidae). The T. clinides genome sequence has a total length of 906.92 megabases. Most of the assembly (97.83%) is scaffolded into 23 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 14.98 kilobases in length. The host ascidian has multiple symbionts, including Prochloron, a bacterial genus that can also synthesise bioactive natural products of interest for potential therapeutic development. Biosynthesis of active compounds sometimes involves microbial associates.}, }
@article {pmid40949424, year = {2025}, author = {Hall, N and Wong, WW and Lappan, R and Ricci, F and Jeppe, KJ and Glud, RN and Kawaichi, S and Rotaru, AE and Greening, C and Cook, PLM}, title = {Coastal methane emissions driven by aerotolerant methanogens using seaweed and seagrass metabolites.}, journal = {Nature geoscience}, volume = {18}, number = {9}, pages = {854-861}, pmid = {40949424}, issn = {1752-0894}, abstract = {Methanogenesis is thought to be limited to strictly anoxic environments. While oxygenated oceans are a known methane source, it is argued that methane production is driven by methylphosphonate-degrading bacteria and potentially other sources rather than by methanogenic archaea. Here we develop in situ monitoring and ex situ manipulation experiments, combined with biogeochemical, metagenomic and culture-based experiments, to show that methane is rapidly produced by archaea in frequently oxygenated sandy sediments. We show that methane emissions from sandy sediments are not inhibited by repeated oxygen exposure and suggest the activity is driven by aerotolerant methylotrophic methanogens (primarily Methanosarcinaceae) broadly distributed in the surface layers of sandy sediments. Moreover, we show that methane emissions are driven by methylated seaweed and seagrass metabolites, revealing a feedback loop between primary production and greenhouse gas emissions.}, }
@article {pmid40949051, year = {2025}, author = {Guillemot, Q and Clemens, T and Inthasot, V and Mahadeb, B and Maillart, E and Clevenbergh, P}, title = {Community-Acquired Chlamydia psittaci Severe Pneumonia: A Case Report.}, journal = {Case reports in infectious diseases}, volume = {2025}, number = {}, pages = {6627159}, pmid = {40949051}, issn = {2090-6625}, abstract = {Chlamydia psittaci, the causative agent of psittacosis, is an intracellular bacterium typically transmitted from birds to humans, leading to atypical pneumonia. We present a case of a 60-year-old man with no reported bird exposure but a history of working as a chief cook, potentially exposed to poultry. He presented with high fever, diffuse soreness, and left-sided pulmonary consolidation. Initial treatment with β-lactams was ineffective, but a multiplex PCR on bronchoalveolar lavage identified C. psittaci DNA. Therapy was switched to moxifloxacin, resulting in rapid clinical improvement. C. psittaci causes approximately 1% of community-acquired pneumonias, often underdiagnosed due to nonspecific symptoms and the need for advanced diagnostic tools like nucleic acid amplification tests (NAATs) or metagenomic next-generation sequencing (mNGS). The bacterium is endemic in birds and poultry, with human infections linked to occupational exposure or contact with infected animals. Diagnosis relies on NAAT and mNGS, as serology and culture are less practical. Treatment with tetracyclines, quinolones, or macrolides is effective, reducing mortality from 10%-20% to < 1%. Preventive measures, including protective equipment for high-risk individuals and treatment of infected birds, are crucial. Mandatory reporting of cases could improve understanding of the disease burden. This case highlights the importance of considering psittacosis in atypical pneumonia, even without direct bird exposure, and the role of NAAT or mNGS in accurate diagnosis.}, }
@article {pmid40948444, year = {2025}, author = {Bryson, S and Sisson, Z and Nelson, B and Grove, J and Reister, E and Liachko, I and Auch, B and Graiziger, C and Khoruts, A}, title = {Use of proximity ligation shotgun metagenomics to investigate the dynamics of plasmids and bacteriophages in the gut microbiome following fecal microbiota transplantation.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2559019}, doi = {10.1080/19490976.2025.2559019}, pmid = {40948444}, issn = {1949-0984}, abstract = {Proximity ligation shotgun metagenomics facilitate the analysis of the relationships between mobile genetic elements, such as plasmids and bacteriophages, and their specific bacterial hosts. We applied this technique to investigate the changes in the fecal microbiome of patients receiving fecal microbiota transplantation (FMT) for recurrent Clostridioides difficile infections (rCDI). FMT was associated with successful engraftment of donor bacteria along with their associated bacteriophages. While fecal microbial diversity increased in all patients, the extent of specific bacterial taxa engraftment varied among individual patients. Interestingly, some donor bacteriophages remained closely linked to their original bacterial hosts, while others expanded their associations across different bacterial taxa. Notably, FMT partially reduced the content of vancomycin resistance and extended-spectrum beta-lactamase genes in the fecal microbiome of rCDI patients.}, }
@article {pmid40947719, year = {2025}, author = {Wei, CR and Basharat, Z and Osama, M and Mah, K and Waheed, Y and Hassan, SS}, title = {An Overview of the Association of the Urinary Tract Microbiome with Various Diseases and Implications for Therapeutics.}, journal = {Mini reviews in medicinal chemistry}, volume = {}, number = {}, pages = {}, doi = {10.2174/0113895575398906250825113635}, pmid = {40947719}, issn = {1875-5607}, abstract = {The urinary tract (UT) was once considered sterile, but now it is known to host a diverse community of microorganisms, known as the urinary microbiome. The collective microbiota is made up of bacteria, fungi, and viruses, necessary for maintaining UT health. This review aims to synthesize current knowledge on the urinary microbiome and clarify its emerging role as a key modulator in both health and a wide spectrum of UT disorders. Dysbiosis within this microbial community has been linked to conditions such as urinary tract infections (UTIs), interstitial cystitis/ bladder pain syndrome (IC/BPS), urinary incontinence, urolithiasis, benign prostatic hyperplasia (BPH), and even urinary tract malignancies. Advances in methodologies, such as expanded quantitative urine culture and metagenomics, have provided valuable insights into microbial variability influenced by factors like age, sex, and disease conditions. Additionally, this review explores the therapeutic potential of probiotics and bacteriophages, as well as the association of urinary microbiota with autoimmune and inflammatory conditions. Special emphasis is placed on translational relevance, including emerging microbiome-targeted therapies and personalized interventions for UTIs. Ethical considerations allied with UT microbiome research, such as data privacy, informed consent, and equitable access to emerging therapies, are also discussed. Despite substantial progress, challenges such as methodological heterogeneity, a lack of longitudinal data, and unresolved causal relationships persist. The study concludes by identifying key knowledge gaps and proposing future directions for multidisciplinary research to advance therapeutic innovation in urological health.}, }
@article {pmid40946852, year = {2025}, author = {Zheng, C and Song, J and Shan, M and Qiu, M and Cui, M and Huang, C and Chen, W and Wang, J and Zhang, L and Yu, Y and Fang, H}, title = {Nutrition cycling microbiomes drive the succession of antibiotic resistome in long-term manured soils.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2025.09.019}, pmid = {40946852}, issn = {2090-1224}, abstract = {INTRODUCTION: The spread of antibiotic resistance genes (ARGs) in the environment has received widespread attention. Nutrition cycling microbiomes specifically refer to microorganisms capable of mineralizing nitrogen and phosphorus, which dominate the microbial community in long-term manured soils. However, changes in nutrition cycling genes/microbiomes and the mechanisms by which these microbiomes mediate ARG transfer through vertical and horizontal gene transfer remain poorly understood.<br><br>OBJECTIVES: This study aimed to elucidate how nutrition cycling microbiomes mediate the dissemination and ecological risk of antibiotic resistance genes (ARGs) in long-term manure-amended soils.<br><br>METHODS: Here, we employed metagenomic assembly and binning to investigate the distribution of nutrition mineralization genes, nutrition cycling microbiomes, mobile genetic elements (MGEs), and ARGs in rapeseed cake, pig manure, duck manure and their corresponding long-term amended soils.<br><br>RESULTS: Long-term application of organic manures led to the dominance of nutrition cycling microbiomes associated with methanogenesis (pmoA and mmoX) and incomplete denitrification (norBC), thereby exacerbating soil nutrient loss. Nutrition cycling microbiomes, particularly Rhodanobacter and Pseudomonas, served as the primary host for ARGs and harbored multiple clinically relevant resistance genes, including MexF, ceoB, and mdtB. Notably, the abundance of ARGs in rapeseed cake and pig manure was 2.09-2.23-fold and 6.74-7.38-fold higher, respectively, than in duck manure, promoting the vertical transmission of ARGs via nutrition cycling microbiomes under long-term application. Furthermore, a significant positive correlation between nutrition mineralization genes and ARGs revealed a co-dispersal mechanism between nutrition cycling microbiomes and ARGs in long-term manured soils.<br><br>CONCLUSIONS: It is concluded that the nutrition cycling microbiome plays a more prominent role in shaping antibiotic resistome through vertical transfer in manured soils, compared to horizontal gene transfer mediated by MGEs.}, }
@article {pmid40946456, year = {2025}, author = {Li, C and Yuan, Z and Liu, B and Sun, Y and Wang, Y and Quan, J and Shen, X and Guo, J}, title = {Comparative recovery of carbon, nitrogen, and phosphorus from food waste via anaerobic digestion and Black Soldier Fly Larvae.}, journal = {Water research}, volume = {288}, number = {Pt A}, pages = {124587}, doi = {10.1016/j.watres.2025.124587}, pmid = {40946456}, issn = {1879-2448}, abstract = {With rising global population and energy demands, efficient recovery of carbon (C), nitrogen (N), and phosphorus (P) from food waste has become increasingly critical for sustainable resource management. Although anaerobic digestion (AD) and Black Soldier Fly Larvae (BSFL) conversion have been separately investigated for food waste treatment, direct and systematic comparisons of their nutrient recovery potential across scales remain limited. This study evaluates and compares two treatment pathways, including conventional AD and the emerging BSFL conversion for their potential to recover C-N-P across lab-scale to pilot/full-scale implementations. A full-scale anaerobic system achieved a high methane yield of 667 mL/g VS, recovering 53.2 % of the food waste C with most N and P remained in digestate. In the BSFL system, increased larval density and feeding frequency significantly enhanced larval biomass production, with a peak yield of 309.2 g/kg dry food waste. Pilot-scale trials demonstrated that 29.1 % of C, 34.4 % of N, and 32.7 % of P were effectively converted into larval biomass, which holds value as protein-rich bioresource. Metagenomic analysis revealed that acetate-producing and syntrophic acetate-oxidizing bacteria, along with hydrogenotrophic methanogens, dominated microbial metabolism in AD systems. Meanwhile, a stable gut microbiota composed of Enterococcus, Actinomyces, and Morganella facilitated organic matter assimilation in BSFL conversion. Based on these findings, we propose an integrated technological framework to optimize full-spectrum resource recovery from food waste. This is the first study to systematically compare AD and BSFL technologies for nutrient recovery from food waste, providing a scientific foundation for the development of circular and sustainable food waste management strategies.}, }
@article {pmid40946204, year = {2025}, author = {Burnett, J and Buckley, D and Grinstead, DA and Oliver, HF}, title = {Microbial Community Associations With Listeria monocytogenes in Food Processing Environments: A Systematic Review and Meta-Analysis.}, journal = {Comprehensive reviews in food science and food safety}, volume = {24}, number = {5}, pages = {e70277}, doi = {10.1111/1541-4337.70277}, pmid = {40946204}, issn = {1541-4337}, support = {//Diversey/ ; }, abstract = {Listeria monocytogenes persistence in food processing environments challenges current understanding of microbial community dynamics. This systematic review and meta-analysis examined peer-reviewed studies that screened for Listeria spp. and performed culture-independent metagenomics on FPE surface samples. Following PRISMA guidelines, we searched PubMed, Web of Science, and Food Science and Technology Abstracts databases, screening 464 studies, with 73 qualifying for full-text review. Seven studies met the inclusion criteria for final analysis, encompassing 1659 environmental samples from meat processing (n = 4 studies) and produce facilities (n = 3 studies). Meta-analysis using random effects models revealed no significant correlation between Listeria presence and overall microbial community alpha diversity (Shannon: z = -0.89, p = 0.40; inverse Simpson and Chao1 indices similarly non-significant). This finding challenges previous assumptions about the relationship between microbial diversity and pathogen persistence. Differential abundance analyses identified three genera most frequently associated with Listeria presence across multiple studies: Pseudomonas, Psychrobacter, and Acinetobacter. These Gammaproteobacteria are characterized as aerobic biofilm formers capable of growth at refrigeration temperatures. One study using rigorous mixed-effects modeling identified Veillonella as significantly associated with L. monocytogenes presence, suggesting potential anaerobic niche interactions within biofilm communities. Synthesis of metabolic capabilities reported in the literature suggests these associated genera may provide structural biofilm matrices and potentially complementary metabolic functions that could facilitate L. monocytogenes survival in FPE conditions. However, the genus-level resolution of 16S rRNA amplicon sequencing data and methodological variations across studies limit definitive conclusions about specific metabolic interactions. These findings indicate that L. monocytogenes persistence appears to be associated with specific microbial partners rather than overall community diversity metrics. Understanding these ecological relationships may inform targeted control strategies focusing on biofilm-forming genera that create favorable conditions for Listeria survival in food processing environments.}, }
@article {pmid40945449, year = {2025}, author = {Wang, X and Wang, J and Li, Z and Yang, M and Rehman, A}, title = {Alginate-driven co-metabolic degradation mechanism of sulfamethoxazole by marine consortia.}, journal = {Journal of hazardous materials}, volume = {498}, number = {}, pages = {139778}, doi = {10.1016/j.jhazmat.2025.139778}, pmid = {40945449}, issn = {1873-3336}, abstract = {Pharmaceuticals and personal care products (PPCPs), known for their severe ecological risks, are frequently detected in coastal waters worldwide. However, the environmental fate in marine systems remains poorly understood. This study investigated the co-metabolic degradation mechanism of a typical PPCP, sulfamethoxazole (SMX), by a marine consortium SAB using alginate-a natural organic matter-as a co-substrate, aiming to elucidate the biodegradation process of PPCPs in actual marine environments. An integrated approach, including metagenomic sequencing (with binning), RT-qPCR, molecular docking, metabolic modeling, and metabolomics, was employed. Results demonstrated that the SAB consortium efficiently degraded SMX at concentrations from 50 μg/L to 10 mg/L, achieving over 96 % removal within 24 h. SMX degradation was achieved through metabolic cross-feeding of alginate by key species within the SAB consortium. Specifically, alginate is initially converted by Vibrio into the central metabolite 2-keto-3-deoxy-D-gluconate (KDG). KDG is subsequently metabolized by Tritonibacter, Halopseudomonas, and Vibrio, generating key metabolites such as acetyl-CoA, serine, cysteine, and guanine. These metabolites support microbial growth and induce production of SMX-degrading enzymes, such as threonine dehydratase, cysteine S-conjugate β-lyase, and guanine deaminase, leading to SMX cleavage and mineralization. Additionally, acetyl-CoA provides acetyl groups for arylamine N-acetyltransferase-mediated SMX acetylation. These processes collectively drive the co-metabolic degradation of SMX. Overall, this study provides critical insights into PPCPs' fate in marine environments.}, }
@article {pmid40945361, year = {2025}, author = {Zhang, M and Zhang, D and Zhou, B and Wu, Q and Liu, X and Wang, M and Liang, J and Zhou, L}, title = {Metagenomic insights into fungal enzyme-mediated propionic acid production from food waste via succinic acid pathway.}, journal = {Journal of environmental management}, volume = {393}, number = {}, pages = {127243}, doi = {10.1016/j.jenvman.2025.127243}, pmid = {40945361}, issn = {1095-8630}, abstract = {Employing fungal enzyme additives as a pretreatment for propionic acid (PA) production from food waste is a promising approach to achieving sustainable waste management. This study explored the feasibility and underlying mechanisms of complex enzyme pretreatment in promoting PA-oriented metabolic via mixed cultures. PA-orienting fermentation was achieved under complex enzyme (CE) pretreatment at pH 7, with PA concentration and proportion of 12.6 ± 0.80 g·COD/L and 39.0 ± 1.10 % of total VFAs, respectively. CE addition significantly enhanced hydrolysis and acidogenesis, improving the simultaneous conversion of polysaccharides and proteins. Bacteroides, including B. ovatus, B. sp. M10, and B. xylanisolvens, P. saccharofermentans and E. coil significantly enriched as the dominant species in PA-type fermentation system. Succinic acid pathway emerged as the primary metabolic route for PA production. Functional genes associated with this pathway, including K01676, K01079, frdA, sdhAD, sucCD, MUT, and ACSS, were significantly upregulated with CE addition. The findings provide a practical strategy for designing and optimizing VFA production from food waste, advancing sustainable waste valorization.}, }
@article {pmid40945100, year = {2025}, author = {Caley, A and Marzinelli, EM and Mayer-Pinto, M}, title = {Limited microbial community responses of marine macroalgae to artificial light at night and moderate warming conditions.}, journal = {Marine environmental research}, volume = {212}, number = {}, pages = {107536}, doi = {10.1016/j.marenvres.2025.107536}, pmid = {40945100}, issn = {1879-0291}, abstract = {Multiple stressors such as Artificial Light at Night (ALAN) and warming are increasingly common in marine systems and can interact in complex ways. Microbial communities play critical roles in the functioning of coastal habitat-forming species such as seaweeds, however the effects of ALAN on seaweed-associated microbial communities remain unknown. We tested the independent and combined effects of ALAN and warming on microbial communities associated with the habitat-forming seaweeds Ecklonia radiata and Sargassum sp. In Ecklonia, ALAN increased the relative abundance of two potentially light-responsive taxa: Dokdonia sp000212355 and an unidentified ASV from Pseudomonadales, whereas warming had the opposite effect. Warming increased microbial community dispersion in Ecklonia and resulted in non-significant increases in relative abundance of putative pathogenic and agarolytic taxa (microbes capable of degrading algal polysaccharides). However, further analyses using metagenomics are needed to confirm functional roles. In contrast, neither ALAN nor warming affected dominant taxa associated with Sargassum. Contrary to expectations, cyanobacteria relative abundance was unaffected by ALAN in either seaweed host, despite their photosynthetic capacity. We found limited evidence for interactive effects of ALAN and warming, and community composition remained unchanged in both seaweed species. Our findings highlight the importance of considering species-specific microbial responses to ALAN and warming, with implications for coastal management.}, }
@article {pmid40945093, year = {2025}, author = {Niu, Y and Zhang, X and Jiao, M and Storey, KB and Shekhovtsov, SV}, title = {Metabolic plasticity and gut microbiome synergy underlie high-altitude adaptation in the plateau frog Rana kukunoris: A multi-omics perspective.}, journal = {Ecotoxicology and environmental safety}, volume = {303}, number = {}, pages = {119050}, doi = {10.1016/j.ecoenv.2025.119050}, pmid = {40945093}, issn = {1090-2414}, abstract = {Life on the Qinghai-Tibet Plateau is exposed to extreme abiotic stressors, yet endemic frog species such as Rana kukunoris thrive due to specialized adaptations. However, the metabolic and gut microbial mechanisms that enable survival at high altitude remain unclear. Here, we used metabolomic analysis and metagenomic sequencing to compare metabolic profiles of liver and skeletal muscle, as well as gut microbial composition and function, between high- (3730 m) and low-altitude (1990 m) populations. Metabolomic profiling revealed significant altitude-driven shifts, including the down-regulation of glycolysis (fructose-1,6-bisphosphate and glyceraldehyde 3-phosphate decreased by 44.2 % and 40.7 %, respectively) and tricarboxylic acid (TCA) cycle intermediates (fumaric acid and malic acid reduced by 37.7 % and 35.9 %, respectively) in the liver, and enhanced oxidative phosphorylation efficiency via elevated flavins (flavin mononucleotide and flavin adenine dinucleotide increased 1.43- and 1.28-fold, respectively) in skeletal muscle. These findings suggest a conserved strategy of metabolic rate depression and tissue-specific metabolic regulation. Significantly differential metabolites were enriched in glycerophospholipid metabolism and glycosylphosphatidylinositol (GPI)-anchor biosynthesis, highlighting membrane remodeling as a key adaptive response to cold stress at high altitudes. Moreover, gut microbiomes of high-altitude frogs exhibited increased α-diversity and functional enrichment in the biosynthesis of secondary metabolites, cofactors, amino acids, and carbohydrate-active enzymes (GHs/GTs), all likely improving tolerance to stressful environments and maintaining homeostasis. Key microbial taxa, including Candidatus Udaeobacter, Desulfovibrio, Bradyrhizobium, and Akkermansia, showed a specific dominance in high-altitude frogs, which may support host energy homeostasis and fortify gut barrier function. Multi-omics data highlighted the convergence of protective mechanisms in high-altitude frogs, including autophagy and two-component/quorum sensing systems. This study reveals significant adaptive remodeling of metabolism and gut microbiota in high-altitude R. kukunoris, providing novel insights into host-microbe synergistic interactions under extreme environments.}, }
@article {pmid40945085, year = {2025}, author = {Wang, J and Zhang, Q and Wang, M and Li, W and Zhuang, Y and Huang, T and Yang, Z and Huang, J}, title = {Integrated field-scale natural composite oxidation pond system for livestock wastewater treatment: Microbial insights and nutrient removal dynamics.}, journal = {Ecotoxicology and environmental safety}, volume = {303}, number = {}, pages = {119026}, doi = {10.1016/j.ecoenv.2025.119026}, pmid = {40945085}, issn = {1090-2414}, abstract = {Livestock wastewater rich in organic matter, nitrogen, and phosphorus can cause eutrophication and degrade aquatic ecosystems. Current water management practices in rural areas are insufficient to meet environmental protection requirements, highlighting the urgent need for low-cost, low-energy, ecologically sustainable approaches to livestock wastewater management across diverse settings. However, current hybrid systems are often limited to lab-scale or pilot studies. Therefore, we developed a natural composite oxidation pond system, integrating biological contact, oxidation ponds, and artificial aeration, to treat piggery wastewater, while simultaneously supporting aquaculture. High-resolution in-situ monitoring, metagenomic sequencing, and partial least squares modelling were employed to assess the system's pollutant removal performance and to elucidate the underlying mechanisms. The natural composite oxidation pond systems achieved average removal efficiencies of 76.6 ± 9.5 %, 60.8 ± 23.1 %, 70.8 ± 10.4 %, 74.2 ± 11.6 %, 81.9 ± 13.0 %, and 78.9 ± 39.5 % for total phosphorus, soluble reactive phosphorus, total nitrogen, NH4[+]-N, NO3[-]-N, and NO2[-]-N, respectively (n = 72), improving water quality from inferior Class V (pond 1) to Class IV or V (pond 4 or pond 5). The removal efficiencies of soluble reactive phosphorus, NO3[-]-N, and NO2[-]-N showed significant variation with temperature (p ≤ 0.01). Proteobacteria dominated nitrogen removal through dissimilatory nitrate reduction and denitrification, with sediment microbes playing a more prominent role than water-column communities. Despite seasonal variability challenges, this closed-loop system provides a sustainable, dual-purpose approach to rural wastewater treatment and resource recovery.}, }
@article {pmid40944761, year = {2025}, author = {Gundogdu, A and Nalbantoglu, OU and Ulgen, M and Sav, MA and Ekinci, G and Kelestimur, F and Türe, U}, title = {Unveiling gut microbiome divergence in sellar-parasellar masses and brain tumors: A link beyond the skull.}, journal = {Neurosurgical review}, volume = {48}, number = {1}, pages = {641}, pmid = {40944761}, issn = {1437-2320}, abstract = {The gut microbiome is increasingly linked to systemic health and central nervous system disorders, including brain tumors. This study investigated gut microbiome composition and metabolic profiles in patients with sellar-parasellar tumors (SPTs), other brain tumor types (OBTs) and healthy controls (HCs) to identify microbial and metabolic biomarkers for brain tumor phenotypes. A cross-sectional study involving 56 participants (17 SPTs, 11 OBTs, 28 HCs) was conducted. Gut microbiota composition was analyzed with 16 S rRNA sequencing, and metabolic activity was inferred via metagenome-scale metabolic models. Multivariable regression and machine learning were used to evaluate microbial and metabolic differences across groups. Taxonomic and metabolic analyses revealed distinct profiles across these groups. The result showed that HCs exhibited higher levels of Lachnospira and Comamonadaceae, while tumor patients had an over-representation of Bacilli. OBT patients showed elevated metabolic exchange scores (MES) for amino acids (D-alanine, L-glutamic acid), carbohydrates (mucin-type O-glycans, alpha-lactose), and lipids (stearic acid, choline), most likely reflecting tumor-associated metabolic demands. Conversely, SPT patients had profiles closer to HCs, with lower MES and reduced systemic disruption. Key taxa such as Akkermansia, Faecalibacterium, and Lachnospira demonstrated tumor-specific adaptive metabolic outputs, emphasizing functional microbial contributions over purely taxonomic roles. These findings highlight the role of gut microbiota in brain tumor progression through altered metabolic pathways, suggesting potential biomarkers and therapeutic targets for neuro- oncology. The study integrates genome-scale metabolic modeling with 16 S profiling to show that functional metabolic divergence can exist even when taxonomic differences are subtle, revealing overlooked biomarkers of the gut-brain axis in neuro-oncology.}, }
@article {pmid40943747, year = {2025}, author = {Pasricha, ND and Larco, P and Miller, D and Altamirano, DS and Rose-Nussbaumer, JR and Alfonso, EC and Amescua, G}, title = {Infectious Keratitis Management: 10-Year Update.}, journal = {Journal of clinical medicine}, volume = {14}, number = {17}, pages = {}, doi = {10.3390/jcm14175987}, pmid = {40943747}, issn = {2077-0383}, support = {1K08EY033859-05/NH/NIH HHS/United States ; Career Development Award//Research to Prevent Blindness/ ; Grant//All May See Foundation/ ; }, abstract = {Infectious keratitis (IK), including bacterial, fungal, parasitic, and viral etiologies, continues to represent a significant cause of ocular morbidity in the United States and around the world. Corneal scraping for smears and cultures remains the gold standard in diagnosing IK; however, molecular diagnoses, including metagenomic deep sequencing (MDS), are promising emerging diagnostic tools. Despite recent interest in procedural treatment such as riboflavin photoactivated chromophore corneal collagen cross-linking (PACK-CXL) and Rose Bengal photodynamic antimicrobial therapy (RB-PDAT), medical treatment advances have remained stagnant. Methods: This review highlights IK pathogens obtained from corneal cultures at Bascom Palmer Eye Institute (BPEI) from 2011 to 2021 and provides the current BPEI algorithms for initial management of IK or as a referred clinically worsening patient. The roles of corticosteroid therapy, PACK-CXL, and RB-PDAT for IK are also summarized. Results: A total of 9326 corneal cultures were performed at BPEI between 2011 and 2021, and only 3609 (38.7%) had a positive organism identified, of which bacteria were the most common (83.4%). Fortified vancomycin and tobramycin are recommended as first-line medical therapy for IK patients based on culture sensitivity data for the top Gram-negative (Pseudomonas aeruginosa) and Gram-positive (Staphylococcus aureus) bacteria. PACK-CXL and RB-PDAT may benefit IK patients with corneal melting and fungal IK, respectively. Conclusions: Drug holidays, minimizing contamination, and optimizing sample order are crucial to maximizing corneal culture positivity. PACK-CXL and RB-PDAT are promising procedural advancements for IK therapy.}, }
@article {pmid40943646, year = {2025}, author = {Kovenskiy, A and Katkenov, N and Ramazanova, A and Vinogradova, E and Jarmukhanov, Z and Mukhatayev, Z and Kushugulova, A}, title = {Bacteroides fragilis and Microbacterium as Microbial Signatures in Hashimoto's Thyroiditis.}, journal = {International journal of molecular sciences}, volume = {26}, number = {17}, pages = {}, doi = {10.3390/ijms26178724}, pmid = {40943646}, issn = {1422-0067}, support = {AP19675503//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; }, abstract = {Hashimoto's thyroiditis (HT) and alopecia areata (AA) are organ-specific autoimmune diseases that frequently co-occur, suggesting shared immunological and microbial pathways. The gut microbiome has emerged as a key modulator of immune function, yet disease-specific microbial signatures remain poorly defined. Fecal samples from 51 participants (HT: n = 16, AA: n = 17, healthy controls: n = 18) aged 18-65 years were analyzed using shotgun metagenomic sequencing followed by multivariate statistical analyses. While alpha and beta diversity did not differ significantly across groups, taxonomic profiling revealed disease-specific microbial patterns. Bacteroides fragilis was significantly enriched in HT, suggesting a potential role in immune modulation; although mechanisms such as polysaccharide A production and molecular mimicry have been proposed in previous studies, their involvement in HT remains to be confirmed. Microbacterium sp. T32 was elevated in both HT and AA, indicating its potential as a shared autoimmune marker. Functional analysis showed increased fermentation and amino acid biosynthesis in AA, contrasting with reduced metabolic activity and elevated carbohydrate biosynthesis in HT. HT and AA exhibit distinct gut microbial and metabolic signatures. Bacteroides fragilis and Microbacterium sp. T32 may serve as potential microbial correlates for autoimmune activity, offering new insights into disease pathogenesis and targets for microbiome-based interventions.}, }
@article {pmid40943581, year = {2025}, author = {Gałęcki, R and Nowak, A and Szulc, J}, title = {Tenebrio molitor Meal-Induced Changes in Rat Gut Microbiota: Microbiological and Metagenomic Findings.}, journal = {International journal of molecular sciences}, volume = {26}, number = {17}, pages = {}, doi = {10.3390/ijms26178663}, pmid = {40943581}, issn = {1422-0067}, support = {LIDER/5/0029/ L-12/20/NCBR/2021//National Centre for Research and Development/ ; }, abstract = {As demand for sustainable protein sources grows, edible insects like Tenebrio molitor (yellow mealworm) are gaining attention as functional feed ingredients. This study investigated how dietary inclusion of T. molitor meal affects gut microbiota composition and diversity in laboratory rats. Wistar rats were divided into three diet groups: standard feed, 35% chicken meal, and 35% T. molitor meal. Fecal samples were collected at weeks 4, 6, and 8. Microbial populations were assessed using culture-based methods, and community structure was analyzed at week 9 via Illumina MiSeq 16S rRNA sequencing. Bioinformatic analyses evaluated microbial diversity and predicted functions. Rats fed T. molitor meal showed significantly reduced counts of total aerobic/anaerobic bacteria, fungi, and coagulase-positive staphylococci. Metagenomics revealed a Firmicutes-dominated microbiota, with enrichment of protein- and cholesterol-metabolizing taxa (e.g., Eubacterium coprostanoligenes, Oscillospiraceae, Ruminococcaceae), and a decline in fiber- and mucin-degrading bacteria like Akkermansia and Muribaculaceae. Functional predictions indicated upregulated amino acid metabolism and chitin degradation. Despite compositional shifts, microbial diversity remained stable, with no signs of dysbiosis. These findings suggest that T. molitor meal supports a safe, functional adaptation of gut microbiota to high-protein, chitin-rich diets, supporting its potential use in monogastric animal nutrition.}, }
@article {pmid40943207, year = {2025}, author = {Gilyazova, I and Korytina, G and Kochetova, O and Savelieva, O and Mikhaylova, E and Vershinina, Z and Chumakova, A and Markelov, V and Abdeeva, G and Karunas, A and Khusnutdinova, E and Gusev, O}, title = {Advances in Genomics and Postgenomics in Poultry Science: Current Achievements and Future Directions.}, journal = {International journal of molecular sciences}, volume = {26}, number = {17}, pages = {}, doi = {10.3390/ijms26178285}, pmid = {40943207}, issn = {1422-0067}, support = {&#x2116; 075-15-2025-484//Government of Russian Federation/ ; }, abstract = {The poultry industry, a globally fast growing agricultural sector, provides affordable animal protein due to high efficiency. Gallus gallus domesticus are the most common domestic birds. Hybrid chicken breeds (crosses) are widely used to achieve high productivity. Maintaining industry competitiveness requires constant genetic selection of parent stock to improve performance traits. Genetic studies, which are essential in modern breeding programs, help identify genome variants linked to economically important traits and preserve population health. Next-generation sequencing (NGS) has identified millions of single nucleotide polymorphisms (SNPs) and insertions/deletions (INDELs), enabling detection of genome-wide regions associated with selection traits. Recent studies have pinpointed such regions using broiler lines, laying hen lines, or pooled genomic data. This review discusses advances in chicken genomic and transcriptomic research focused on traits enhancing meat breed performance and reproductive abilities. Special attention is given to transcriptome studies revealing regulatory mechanisms and key signaling pathways involved in artificial molting, as well as metagenome studies investigating resistance to infectious diseases and climate adaptation. Finally, a dedicated section highlights CRISPR/Cas genomic editing techniques for targeted genome modification in chicken genomics.}, }
@article {pmid40943165, year = {2025}, author = {Wang, R and Ren, W and Liu, S and Li, Z and Li, L and Ma, S and Yao, X and Meng, J and Zeng, Y and Wang, J}, title = {Metagenomic Analysis Reveals the Anti-Inflammatory Properties of Mare Milk.}, journal = {International journal of molecular sciences}, volume = {26}, number = {17}, pages = {}, doi = {10.3390/ijms26178239}, pmid = {40943165}, issn = {1422-0067}, support = {2022A02007-1 and ZYYD2025JD02.//Xinjiang Uygur Autonomous Region Major Science and Technology Special Project and the Central Guidance for Local Science and Technology Development Fund/ ; }, abstract = {This study aimed to assess the anti-inflammatory properties of mare milk by analyzing immune markers in mice following gavage of mare milk. Metagenomic sequencing was employed to examine variations in the composition and functional profiles of the intestinal microbiota across different experimental groups. Bacterial diversity, abundance, and functional annotations of gut microbiota were evaluated for each group. The results show that, compared to the control group, the mare milk group exhibited a significant decrease in the pro-inflammatory cytokine IL-6 levels and a significant increase in secretory immunoglobulin A (SIgA) levels (p < 0.05). The fermented mare milk group and the pasteurized fermented mare milk group demonstrated a significant downregulation of the pro-inflammatory cytokines TNF-α and IL-1β, along with a significant increase in the anti-inflammatory cytokine IL-10 levels (p < 0.05). Additionally, metagenomic analysis revealed that both the mare milk and fermented mare milk groups were able to regulate the imbalance of the intestinal microenvironment by improving the diversity of the gut microbiota and reshaping its structure. Specifically, the mare milk group enhanced gut barrier function by increasing the abundance of Bacteroides acidifaciens, while the fermented mare milk group increased the proportion of Bacillota and the relative abundance of beneficial bacterial genera such as Faecalibaculum and Bifidobacterium. KEGG pathway annotation highlighted prominent functions related to carbohydrate and amino acid metabolism, followed by coenzyme and vitamin metabolism activities. In conclusion, mare milk and its fermented products demonstrate anti-inflammatory effects, particularly in modulating immune responses and inhibiting inflammatory cascades. Additionally, the administration of mare milk enhances the composition and metabolic activity of intestinal microbiota in mice, supporting intestinal microecological balance and overall gut health, and offering valuable insights for the development of mare milk-based functional foods.}, }
@article {pmid40942030, year = {2025}, author = {Wang, W and Wei, J and Guo, Z and Bai, X and Song, Y}, title = {Reduction in ARGs and Mobile Genetic Elements Using 2-Bromoethane Sulfonate in an MFC-Powered Fenton System.}, journal = {Molecules (Basel, Switzerland)}, volume = {30}, number = {17}, pages = {}, doi = {10.3390/molecules30173502}, pmid = {40942030}, issn = {1420-3049}, support = {2025YSKY-20//Fundamental Research Funds for Central Public Welfare Scientific Research Institutes of China/ ; 2022-YRUC-01-050206-017//Joint Research Program for Ecological Conservation and High Quality Development of the Yellow River Basin/ ; }, abstract = {The integration of an MFC-powered Fenton (MFC-Fenton) system into the traditional anaerobic composting process can promote excess dewatered sludge (ES) decomposition. However, the antibiotic resistance gene (ARG) profiles in ES treated by MFC-Fenton systems remain poorly understood; in addition, the effect of adding 2-bromoethane sulfonate (BES, a methane inhibitor) during ES treatment using an MFC-Fenton system on ARG levels is largely unexplored. The present work focused on investigating the effects of BES and bioelectrochemical processes on ARG and MGE abundances and unraveling the ARG attenuation mechanism. According to our findings, adding BES promoted ARG reduction in ES in an MFC-Fenton system. The average ARG levels in the MFC-Fenton samples containing high BES contents (0.4 or 0.5 g BES/g VSS) markedly declined relative to those in samples containing lower BES levels. Moreover, macrolide transporter ATP-binding protein, macrolide-efflux protein, and macB levels markedly decreased as BES levels increased. BES supplementation and bioelectrochemical assistance were crucial for altering the ARG composition in the MFC-Fenton system. Changes in the microbial community composition had the greatest effect on the variation in ARG composition. Furthermore, the Actinobacteria and Firmicutes levels accounted for 52.8% of the overall ARG variation. Among MGEs, plasmids, insertion sequences, and integrons showed lower levels within the sludge metagenomes. Typically, sulI, sulII, tetG, and bla TEM levels were positively correlated with metal resistance genes (MRGs), and their levels markedly declined following the MFC-Fenton process. Thus, the collective evidence indicates that BES synergizes with bioelectrogenesis to reduce ARG abundance.}, }
@article {pmid40941824, year = {2025}, author = {Fernández-Pastrana, VM and González-Reguero, D and Robas-Mora, M and Penalba-Iglesias, D and Alonso-Torreiro, P and Probanza, A and Jiménez-Gómez, PA}, title = {Biotechnological Test of Plant Growth-Promoting Bacteria Strains for Synthesis of Valorized Wastewater as Biofertilizer for Silvicultural Production of Holm Oak (Quercus ilex L.).}, journal = {Plants (Basel, Switzerland)}, volume = {14}, number = {17}, pages = {}, doi = {10.3390/plants14172654}, pmid = {40941824}, issn = {2223-7747}, abstract = {The degradation of Mediterranean forest ecosystems, such as holm oak forests, has intensified in recent decades due to climate change, forest fires, and deforestation, compromising the natural regeneration of the soil. In this context, it is essential to apply sustainable strategies to restore soil and promote plant growth, thus helping the regeneration of the ecosystem. One of these strategies is the use of plant growth-promoting bacteria (PGPB) in combination with recovered organic waste, such as that from wastewater treatment plants (WWTPs). In this paper, the effects of a biofertilizer formulated from WWTP residue (with and without sterilization), supplemented with two PGPB strains (Bacillus pretiosus and Pseudomonas agronomica), on the growth of holm oak seedlings (Quercus ilex) were evaluated under field conditions. A study was carried out on its nutritional composition, the rhizospheric cenoantibiogram, and its functional and taxonomic microbial diversity. Nine combinations of chemical and biological treatments using irrigation with water as a control were compared. The results showed that treatments with WWTP, especially combined with PGPB strains, promoted greater plant development and a lower seedling mortality rate. The cenoantibiogram exhibited a reduction in the resistance profile in soils treated with biofertilizer, without affecting soil microbial diversity, which remained unaltered across treatments, as confirmed by metagenomic and functional diversity analyses. Overall, this research reinforces the viability of the use of biofertilizers recovered from WWTP as an ecological and effective strategy for the recovery of degraded holm oak forests.}, }
@article {pmid40941779, year = {2025}, author = {Belevich, TA and Milyutina, IA and Demidov, AB and Vorob'eva, OV and Polukhin, AA and Shchuka, SA and Troitsky, AV}, title = {Distribution and Phylogenetic Diversity of Synechococcus-like Cyanobacteria in the Late Autumn Picophytoplankton of the Kara Sea: The Role of Atlantic and Riverine Water Masses.}, journal = {Plants (Basel, Switzerland)}, volume = {14}, number = {17}, pages = {}, doi = {10.3390/plants14172614}, pmid = {40941779}, issn = {2223-7747}, support = {24-24-00022//Russian Science Foundation/ ; }, abstract = {Increased Atlantic water transport and river discharge are more pronounced effects of global warming at high latitudes. Both phenomena may lead to changes in the species composition of small-celled algae populations in marine ecosystems, as well as to the emergence of new species. This study investigated the spatial distribution of picocyanobacterial (PC) abundance and the phylogenetic diversity of PC Synechococcus in the Kara Sea. PC abundance varied from 2 to 88 cells mL[-1] and increased with warming temperatures and decreasing salinity caused by river water influence. The contribution of Synechococcus to the total picophytoplankton biomass was low (<16%). The Synechococcus community was characterized at deep taxonomic level using amplicon sequencing targeting the petB gene. Diversity was low, revealing only Synechococcus subcluster 5.1 polar lineages I and IV, and euryhaline subcluster 5.2. Synechococcus subcluster 5.1.I represented on average 97% of the total reads assigned to cyanobacteria. For the first time, the presence of estuarine Synechococcus subcluster 5.2 was documented as far north as 82° N. Modified Atlantic water was the main source of cyanobacteria in the Kara Sea, followed by river discharge. Our study contributes to the understanding of PC sources in the Kara Sea and allows for the further monitoring of PC distribution and evolution.}, }
@article {pmid40941733, year = {2025}, author = {Alatawi, AD and Hetta, HF and Ali, MAS and Ramadan, YN and Alaqyli, AB and Alansari, WK and Aldhaheri, NH and Bin Selim, TA and Merdad, SA and Alharbi, MO and Alatawi, WAH and Algammal, AM}, title = {Diagnostic Innovations to Combat Antibiotic Resistance in Critical Care: Tools for Targeted Therapy and Stewardship.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {15}, number = {17}, pages = {}, doi = {10.3390/diagnostics15172244}, pmid = {40941733}, issn = {2075-4418}, abstract = {Antibiotic resistance is a growing global health threat, with critical care settings representing one of the most vulnerable arenas due to the high burden of infection and frequent empirical antibiotic use. Rapid and precise diagnosis of infectious pathogens is crucial for initiating appropriate therapy, minimizing unnecessary antimicrobial exposure, and supporting effective stewardship programs. This review explores how innovative diagnostic technologies are reshaping infection management and antimicrobial stewardship in critical care. We examine the clinical utility of molecular assays, multiplex PCR, MALDI-TOF mass spectrometry, metagenomic sequencing, point-of-care (POC) diagnostics, and emerging tools like biosensors and AI-powered predictive models. These platforms enable earlier pathogen identification and resistance profiling, facilitating timely and targeted therapy while minimizing unnecessary broad-spectrum antibiotic use. By integrating diagnostics into stewardship frameworks, clinicians can optimize antimicrobial regimens, improve patient outcomes, and reduce resistance selection pressure. Despite their promise, adoption is challenged by cost, infrastructure, interpretation complexity, and inequitable access, particularly in low-resource settings. Future perspectives emphasize the need for scalable, AI-enhanced, and globally accessible diagnostic solutions. In bridging innovation with clinical application, diagnostic advancements can serve as pivotal tools in the global effort to curb antimicrobial resistance in critical care environments.}, }
@article {pmid40941729, year = {2025}, author = {Hu, L and Li, X and Liu, D and Yao, J and Li, X and Wang, Y}, title = {Beyond the Urogenital Tract, the Role of Ureaplasma parvum in Invasive Infection in Adults: A Case Series and Literature Review.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {15}, number = {17}, pages = {}, doi = {10.3390/diagnostics15172242}, pmid = {40941729}, issn = {2075-4418}, abstract = {Background/Objectives: Ureaplasma parvum (Up) is an opportunistic pathogen associated with urogenital tract infections, pregnancy complications, and reproductive system diseases. Advances in molecular diagnostics have expanded its pathogenic spectrum to include invasive conditions such as arthritis, meningitis, and pneumonia. However, the pathogenic significance of Up remains controversial. Methods: This study retrospectively analyzed nine adult cases of Up detected by metagenomic next-generation sequencing (mNGS) between 2023 and 2024. Results: Patients, aged 21 to 70 years, predominantly had underlying immunosuppressive conditions (66.7%). Infections involved the urinary system (44.4%), respiratory system (33.3%), and peritoneal cavity (22.2%). Symptomatic relief was achieved in five cases following treatment with tetracyclines, quinolones or tigecycline. Conclusions: These findings highlight Up as a potential causative agent of invasive infections, particularly in immunocompromised patients. Up has potential pathogenic significance, whether it is detected as a single pathogen or as a coexisting pathogen.}, }
@article {pmid40941705, year = {2025}, author = {Wang, Q and Ling, Y and Huang, Y and Zhao, L and Lou, Z and Fan, G and Xue, J}, title = {An Unveiling of the Misdiagnosis of Granulomatosis with Polyangiitis as Acute Sinusitis: A Case Report.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {15}, number = {17}, pages = {}, doi = {10.3390/diagnostics15172218}, pmid = {40941705}, issn = {2075-4418}, abstract = {Background and Clinical Significance: Granulomatosis with polyangiitis (GPA), an immune-mediated systemic small-vessel vasculitis affecting the upper/lower respiratory tracts and kidneys, frequently presents with non-specific nasal symptoms that lead to misdiagnosis. Case Presentation: We report a case of a 55-year-old female with GPA complicated by Bartter syndrome. She presented with one month of left nasal congestion, rhinorrhea, epistaxis, and headache. Initial diagnosis was acute sinusitis. Computed tomography (CT) revealed left maxillary and ethmoid sinus inflammation with bone destruction, while metagenomic next-generation sequencing (mNGS) suggested conventional bacterial infection. Postoperative pathology demonstrated chronic mucosal inflammation with lymphoid tissue hyperplasia. GPA was ultimately diagnosed based on PR3-ANCA seropositivity and chest CT findings of cavitary pulmonary nodules. Postoperatively, severe hypokalemia and hypomagnesemia secondary to Bartter syndrome emerged. Following electrolyte correction, induction therapy with glucocorticoids and cyclophosphamide was initiated. Conclusions: This case underscores that GPA's head and neck manifestations are frequently misdiagnosed as infections or malignancies. Early diagnosis requires vigilance for GPA 'red flags', such as refractory nasal symptoms to conventional therapy (e.g., bloody rhinorrhea), characteristic CT findings (e.g., sinus opacification without ostiomeatal complex obstruction), and nasal endoscopy findings (e.g., ulcers/crusting). Otolaryngologists play a pivotal role in recognizing early disease onset and initiating timely treatment.}, }
@article {pmid40941662, year = {2025}, author = {Papa Mze, N and Fernand-Laurent, C and Maxence, S and Zanzouri, O and Daugabel, S and Marque Juillet, S}, title = {Optimization of 16S RNA Sequencing and Evaluation of Metagenomic Analysis with Kraken 2 and KrakenUniq.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {15}, number = {17}, pages = {}, doi = {10.3390/diagnostics15172175}, pmid = {40941662}, issn = {2075-4418}, abstract = {Background/Objectives: 16S ribosomal RNA sequencing has, for several years, been the main means of identifying bacterial and archaeal species. Low-throughput Sanger sequencing is often used for the detection and identification of microbial species, but this technique has several limitations. The use of high-throughput sequencers may be a good alternative to improve patient identification, especially for polyclonal infections and management. Kraken 2 and KrakenUniq are free, high-throughput tools providing a very rapid and accurate classification for metagenomic analyses. However, Kraken 2 can present false-positive results relative to KrakenUniq, which can be limiting in hospital settings requiring high levels of accuracy. The aim of this study was to establish an alternative next-generation sequencing technique to replace Sanger sequencing and to confirm that KrakenUniq is an excellent analysis tool that does not present false results relative to Kraken 2. Methods: DNA was extracted from reference bacterial samples for Laboratory Quality Controls (QCMDs) and the V2-V3 and V3-V4 regions of the 16S ribosomal gene were amplified. Amplified products were sequenced with the Illumina 16S Metagenomic Sequencing protocol with minor modifications to adapt and sequence an Illumina 16S library with a small 500-cycle nano-flow cell. The raw files (Fastq) were analyzed on a commercial Smartgene platform for comparison with Kraken 2 and KrakenUniq results. KrakenUniq was used with a standard bacterial database and with the 16S-specific Silva138, RDP11.5, and Greengenes 13.5 databases. Results: Seven of the eight (87.5%) QCMDs were correctly sequenced and identified by Sanger sequencing. The remaining QCMD, QCMD6, could not be identified through Sanger sequencing. All QCMDs were correctly sequenced and identified by MiSeq with the commercial Smartgene analysis platform. QCMD6 contained two bacteria, Acinetobacter and Klebsiella. KrakenUniq identification results were identical to those of Smartgene, whereas Kraken 2 yielded 25% false-positive results. Conclusions: If Sanger identification fails, MiSeq with a small nano-flow cell is a very good alternative for the identification of bacterial species. KrakenUniq is a free, fast, and easy-to-use tool for identifying and classifying bacterial infections.}, }
@article {pmid40941485, year = {2025}, author = {Wright, SL and Slusanschi, O and Giura, AC and Părlătescu, I and Funieru, C and Gaidula, SM and Moore, NE and Weyrich, LS}, title = {SANA-Biome: A Protocol for a Cross-Sectional Study on Oral Health, Diet, and the Oral Microbiome in Romania.}, journal = {Healthcare (Basel, Switzerland)}, volume = {13}, number = {17}, pages = {}, doi = {10.3390/healthcare13172133}, pmid = {40941485}, issn = {2227-9032}, abstract = {Periodontal disease is a widespread chronic condition linked to systemic illnesses such as cardiovascular disease, diabetes, and adverse pregnancy outcomes. Despite its global burden, population-specific studies on its risk factors remain limited, particularly in Central and Eastern Europe. The SANA-biome Project is a cross-sectional, community-based study designed to investigate the biological and social determinants of periodontal disease in Romania, a country with disproportionately high oral disease rates and minimal microbiome data. This protocol will integrate metagenomic, proteomic, and metabolomic data of the oral microbiome from saliva and dental calculus samples with detailed sociodemographic and lifestyle data collected through a structured 44-question survey. This study is grounded in two complementary frameworks: the IMPEDE model, which conceptualizes inflammation as both a driver and a consequence of microbial dysbiosis, and Ecosocial Theory, which situates disease within social and structural contexts. Our aims are as follows: (1) to identify lifestyle and behavioral predictors of periodontal disease; (2) to characterize the oral microbiome in individuals with and without periodontal disease; and (3) to evaluate the predictive value of combined microbial and sociodemographic features using statistical and machine learning approaches. Power calculations based on pilot data indicate a target enrollment of 120 participants. This integrative approach will help disentangle the complex interplay between microbiological and structural determinants of periodontal disease and inform culturally relevant prevention strategies. By focusing on an underrepresented population, this work contributes to a more equitable and interdisciplinary model of oral health research and supports the development of future precision public health interventions.}, }
@article {pmid40941346, year = {2025}, author = {Ishii, PE and Teixeira, FA and Lin, CY and Naqvi, SA and Sardi, MI and Norton, SA and Jarett, JK and Khafipour, E and Frantz, N and Chakrabarti, A and Suchodolski, JS}, title = {Effects of a Saccharomyces cerevisiae Fermentation Product on Diet Palatability and Feline Intestinal Health, Immunity, and Microbiome.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {17}, pages = {}, doi = {10.3390/ani15172551}, pmid = {40941346}, issn = {2076-2615}, abstract = {This study evaluated the effects of adding a Saccharomyces cerevisiae fermentation product (SCFP) to adult cat diets on palatability, intestinal health, nutrient digestibility, immune parameters, and the fecal microbiome over 42 days. Sixty-three healthy Domestic Short-hair cats were randomized to three diets: a control diet (CD) without SCFP, or the same diet containing 1.0% or 2.0% SCFP, targeting daily intakes of 150 or 300 mg/kg body weight, respectively. Body weight and blood parameters remained within reference ranges across all groups. Stool quality was largely not affected, although compared with controls, SCFP-supplemented cats had slightly firmer stools at day 21, and increased fecal pH. Shotgun metagenomic sequencing revealed that microbiome diversity remained steady in SCFP-fed cats, whereas diversity in the control group declined over time. Fecal immunoglobulin A concentrations were lower in cats supplemented with SCFP at 150 mg/kg BW by the end of the study, and positive shifts in the circulatory leukocyte profile were observed at both inclusion levels. Apparent total tract macronutrient digestibility did not differ among groups. Palatability tests showed diets with SCFP were generally preferred, indicating a potential benefit for commercial feline feeds, particularly at the 150 mg/kg BW level, which was preferred over 300 mg/kg BW. Overall, these findings suggest that SCFP can act as a functional ingredient in feline nutrition to maintain microbial diversity and enhance diet acceptance without compromising digestibility.}, }
@article {pmid40941237, year = {2025}, author = {Xu, P and He, Y and Wang, J and Sheng, Y and Wang, J}, title = {Blueberry Anthocyanins Ameliorate Hepatic Dysfunction in High-Fat Diet-Fed Mice: Association with Altered Gut Microbiota and Bile Acid Metabolism.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {17}, pages = {}, doi = {10.3390/foods14173121}, pmid = {40941237}, issn = {2304-8158}, support = {2021DG700024-KF202407//open project titled "Identification of Anti-Damage Functional Factors in Anoectochilus roxburghii and Their Mechanisms of Action"/ ; }, abstract = {The rapid rise in obesity has evolved into a critical global public health concern. Considering the potential adverse effects of current anti-obesity medications, the development of functional foods sourced from natural materials has emerged as a viable alternative. Blueberries, a category of berry fruits, exhibit potential anti-obesity characteristics. In this research, we assessed the impacts of Blueberry extract rich in anthocyanins (BE) on lipid metabolism and liver health in a high-fat diet (HFD)-induced obese mouse model. The findings indicated that BE notably diminished lipid accumulation in both serum and the liver, and mitigated hepatic steatosis and oxidative stress. Integrated proteomic, metagenomic, and metabolomic analyses further revealed the underlying mechanisms. Consumption of BE intake reconfigured the gut microbiota composition and reduced the microbial capacity for secondary bile acid metabolism, thereby interrupting bile acid recycling and facilitating fecal excretion. This process led to a reduction in systemic cholesterol levels and ultimately alleviated hepatic lipid accumulation, resulting in enhanced liver health.}, }
@article {pmid40941211, year = {2025}, author = {Yu, Z and Zhao, H and Ma, T and Zhang, X and Yan, Y and Zhu, Y and Yu, Y}, title = {Insights into the Composition and Function of Virus Communities During Acetic Acid Fermentation of Shanxi Aged Vinegar.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {17}, pages = {}, doi = {10.3390/foods14173095}, pmid = {40941211}, issn = {2304-8158}, support = {2023M741438//China Postdoctoral Science Foundation/ ; 20220401931002//Open Project Program of Shanxi Provincial Key Laboratory for Vinegar Fermentation Science and Engineering/ ; }, abstract = {Viruses play a regulatory role in microbial ecology. Traditional fermented foods have complex fermentation environments with abundant viral participation, yet current research on viral communities in fermented foods remains insufficient. Traditional, manually produced solid-state fermented vinegar serves as an excellent model for studying the role of viral communities in fermented foods. Using metagenomic approaches, this study investigates the structure and dynamics of viral communities during the acetic acid fermentation process of Shanxi aged vinegar. All identified viruses were bacteriophages, and the dominant families were identified as Herelleviridae, Autographiviridae, and Stanwilliamsviridae. The richness and diversity of viral communities exhibited significant variations during acetic acid fermentation. Furthermore, correlation analysis revealed a strong association (p < 0.01) between core bacteria and core viruses. Functional annotation revealed the presence of viral genes associated with amino acid and carbohydrate metabolism. Notably, abundant auxiliary carbohydrate-active enzyme (CAZyme) genes were identified in viruses, with glycoside hydrolases (GHs), glycosyltransferases (GTs), and carbohydrate-binding modules (CBMs) demonstrating particularly high abundance. Additionally, several antibiotic resistance genes were detected in viruses. This study elucidates the impact of viral communities on microbial dynamics during food fermentation, advancing our understanding of viral roles in traditional fermented food ecosystems.}, }
@article {pmid40941207, year = {2025}, author = {Kyoung, M and Lee, JI and Kim, SS}, title = {Effects of UVC Treatment on Biofilms of Escherichia coli Strains Formed at Different Temperatures and Maturation Periods.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {17}, pages = {}, doi = {10.3390/foods14173091}, pmid = {40941207}, issn = {2304-8158}, abstract = {In the present study, the biofilm formation and ultraviolet-C (UVC) resistance characteristics of Escherichia coli isolated from an occluded biliary stent were compared with those of four E. coli O157:H7 strains (ATCC 35150, 43889, 43890, and 43895). To evaluate biofilm formation, the E. coli isolated from a stent and four E. coli O157:H7 strains were incubated at 37, 25, and 15 °C for 7 days, revealing that peak biofilm formation occurred at 37 °C (day 1), 25 °C (day 3), and 15 °C (day 5), with the stent-isolated strain consistently exhibiting significantly higher biofilm cell counts than the others (p < 0.05). The UVC treatment was less effective at reducing viable biofilm cells as the formation temperature decreased, with the stent-isolated E. coli biofilm formed at 15 °C showing the lowest reduction levels. Exopolysaccharide quantification revealed that all E. coli strains produced more extracellular polymeric substances (EPSs) at lower temperatures, with the stent-isolated E. coli biofilm formed at 15 °C showing significantly higher EPS levels than the other strains (p < 0.05), potentially explaining its greater UVC resistance. Based on these results, it was confirmed that the biofilm formed by the E. coli isolated from the stent at 15 °C exhibited the highest resistance to UVC, which can be attributed to its elevated exopolysaccharide production. This study demonstrates that both temperature and maturation period significantly influence E. coli biofilm characteristics and provides valuable insights into E. coli isolated from the stent, which may pose a risk of cross-contamination in food-related environments.}, }
@article {pmid40941186, year = {2025}, author = {Dissook, S and Thongkumkoon, P and Noisagul, P and Sriaporn, C and Suwannapat, S and Pramoonchakko, W and Suksawat, M and Kulthawatsiri, T and Phetcharaburanin, J and Chewonarin, T and Ruangsuriya, J}, title = {Insights into Microbial and Metabolite Profiles in Traditional Northern Thai Fermented Soybean (Tuanao) Fermentation Through Metagenomics and Metabolomics.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {17}, pages = {}, doi = {10.3390/foods14173070}, pmid = {40941186}, issn = {2304-8158}, support = {FF66/023//Fundamental Fund 2023, Chiang Mai University/ ; }, abstract = {Tuanao, a traditional Northern Thai fermented soybean product, was profiled with an integrated multi-omics workflow to clarify how microbes and metabolites co-evolve during household fermentation. Soybeans were fermented spontaneously for three days; samples from four time points were analyzed by shotgun metagenomics alongside 1H-NMR and UHPLC-ESI-QTOF-MS/MS metabolomics. Bacillus spp. (phylum Bacilliota) quickly supplanted early Enterobacterales and dominated the mature microbiome. The rise of Bacillus coincided with genes for peptide and carbohydrate utilization and with the accumulation of acetate, free amino acids (glutamine, leucine, alanine, valine) and diverse oligopeptides, whereas citrate and glucose-1-phosphate were depleted. This Bacillus-linked metabolic shift indicates that Tuanao is a promising source of probiotics and bioactive compounds. Our study provides the first system-level view of Tuanao fermentation and offers molecular markers to guide starter-culture design and quality control.}, }
@article {pmid40940618, year = {2025}, author = {Valiauga, B and Žulpaitė, D and Sharrock, AV and Ackerley, DF and Čėnas, N}, title = {Novel TdsD nitroreductase: characterization of kinetics and substrate specificity.}, journal = {Biotechnology letters}, volume = {47}, number = {5}, pages = {103}, pmid = {40940618}, issn = {1573-6776}, abstract = {The reduction of quinones and nitroaromatic compounds catalyzed by Type I nitroreductases is important due to its role in their potential cytotoxic effects and/or biodegradation. The main goal of this work was to investigate the mechanism of catalysis of a TdsD nitroreductase (NR) (TdsD1), a member from an understudied branch of the nitroreductase superfamily, derived from a soil metagenome study. Like the Type I NRs NfsA and NfsB, TdsD1 performed two-electron reduction of quinones and four-electron reduction of nitroaromatic compounds according to a "ping-pong" mechanism with a rate-limiting oxidative half-reaction. TdsD1 was also inhibited by the classical inhibitors of other NRs, dicoumarol and Cibacron blue. Despite sharing only a low degree of homology with the NfsA and NfsB subfamily enzymes, sequence comparisons and computer modelling point to the possibility of an analogous FMN isoalloxazine ring location within the intersubunit space of TdsD1. It also possesses similar specificity for nitroaromatic compounds and quinones, in particular the shared characteristic of being especially active with 2-hydroxy-1,4-naphthoquinone derivatives. It is possible that the similar character of binding of oxidants and other ligands relative to the NfsA and NfsB subfamily enzymes may be related to the conserved Arg27 and Ser53 residues in the active site of TdsD1.}, }
@article {pmid40940575, year = {2025}, author = {Abenaim, L and Mercati, D and Mandoli, A and Carpentier, J and Noël, G and Conti, B and Caparros Megido, R and Dallai, R}, title = {Exploring the plastivorous activity of Hermetia illucens (Diptera Stratiomyidae) larvae.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {40940575}, issn = {1614-7499}, abstract = {Hermetia illucens (Diptera Stratiomyidae), also known as Black Soldier Fly (BSF), is one of the insect species most investigated for biodegradation ability in its larvae. H. illucens larvae can biodegrade organic waste but also contaminants like pesticides, antibiotics, and mycotoxins. This study wants to investigate the ability of these larvae to degrade polystyrene (PS). Experiments evaluated the growth performance, survival rates, intestinal and intracellular morphological alterations, degradation by-product formation and intestinal microbiota alterations of larvae fed a PS-enriched diet. Despite the addition of PS microparticles, no significant differences in growth or survival were observed compared to the standard diet (p > 0.05). Confocal Laser Scanning Microscopy and Transmission Electron Microscopy confirmed the presence of PS microparticles in the larval gut, with potential signs of biodegradation. Metabolomic analyses identified styrene in the gut after 1 and 3 days of PS feeding, but its occurrence was likely due to thermal depolymerisation of the PS microparticles under GC-MS conditions. Metagenomic analysis revealed significant shifts in the intestinal microbiota. Notably, an enrichment of Corynebacterium, known for its role in aerobic PS degradation, and the abundance increase of other genera (Enterococcus, Enterobacteriaceae, Enterobacter, and Escherichia-Shigella) associated with synthetic polymer metabolism was observed. These results confirm the potential of BSF larvae to manage plastic waste through the interaction between their gut microbiota and synthetic materials. This study provides a foundation for future research focusing on isolating bacterial communities and enzymatic processes involved in polymer degradation, aiming to develop sustainable strategies for plastic waste management.}, }
@article {pmid40940533, year = {2025}, author = {Burian, J and Boer, RE and Hernandez, Y and Morales-Amador, A and Jiang, L and Bhattacharjee, A and Panfil, C and Ternei, MA and Brady, SF}, title = {Bioactive molecules unearthed by terabase-scale long-read sequencing of a soil metagenome.}, journal = {Nature biotechnology}, volume = {}, number = {}, pages = {}, pmid = {40940533}, issn = {1546-1696}, support = {R35GM122559//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; }, abstract = {Metagenomics provides access to the genetic diversity of uncultured bacteria through analysis of DNA extracted from whole microbial communities. Long-read sequencing is advancing metagenomic discovery by generating larger DNA assemblies than previously possible. However, harnessing the potential of long-read sequencing to access the vast diversity within soil microbiomes is hampered by the challenge of isolating high-quality DNA. Here we introduce a method that can liberate large, high-quality metagenomic DNA fragments from soil bacteria and pair them with optimized nanopore long-read sequencing to generate megabase-sized assemblies. Using this method, we uncover hundreds of complete circular metagenomic genomes from a single soil sample. Through a combination of bioinformatic prediction and chemical synthesis, we convert nonribosomal peptide biosynthetic gene clusters directly into bioactive molecules, identifying antibiotics with rare modes of action and activity against multidrug-resistant pathogens. Our approach advances metagenomic access to the vast genetic diversity of the uncultured bacterial majority and provides a means to convert it to bioactive molecules.}, }
@article {pmid40940504, year = {2025}, author = {Ruiz-Malagón, AJ and Rodríguez-Sojo, MJ and García-García, J and Ho-Plagaro, A and García, F and Vezza, T and Redondo-Cerezo, E and Griñán-Lisón, C and Marchal, JA and Rodríguez-Cabezas, ME and Rodríguez-Nogales, A and Gálvez, J}, title = {Tigecycline suppresses colon cancer stem cells and impairs tumor engraftment by targeting SNAI1-regulated epithelial-mesenchymal transition.}, journal = {Acta pharmacologica Sinica}, volume = {}, number = {}, pages = {}, pmid = {40940504}, issn = {1745-7254}, abstract = {Cancer stem cells (CSCs) play a key role in the progression of colorectal cancer (CRC). The high heterogeneity of CSCs has hindered the clinical application of CSC-targeting therapies. Tetracyclines are drugs with therapeutic potentials beyond their antibiotic activity. We previously demonstrated the efficacy of tigecycline, a third-generation tetracycline, against a model of colitis-associated colorectal cancer, primarily focusing on its immunomodulatory role with a preliminary assessment of its impact on stemness. In this study we characterize the effects of tigecycline on colon CSCs in vitro and in a CRC xenograft model, with special attention on the signaling pathways involved and the modulation of the gut microbiota. We generated secondary colonospheres from two colon tumor cell lines HCT116 and CMT93, and evaluated the effect of tigecycline on CSCs properties. We showed that tigecycline (25, 50 μM) effectively reduced colon CD133[+]CD44[+]LGR5[+]ALDH[+] subpopulations and their viability, self-renewal and migratory capacity. Moreover, tigecycline treatment hindered epithelial-mesenchymal transition (EMT) process through targeting SNAI1 and β-catenin, resulting in an upregulation of epithelial markers (E-cadherin) and a downregulation of pluripotency and mesenchymal ones (Vimentin, N-cadherin, SOX2, NANOG, MIR155, MIR146). This effect was confirmed in two independent CRC-xenograft murine models in which tigecycline administration led to a reduction in tumor volume. Finally, CRC samples were taken from HCT116 xenograft model mice for analysis of CSCs-related signaling pathways and stools were collected for gut microbiome metagenomic analysis. We found that the antibiotic modulated gut dysbiosis by increasing the abundance of beneficial bacterial species such as Parabacteroides sp., which were involved in metabolic pathways that hindered SNAI1-Wnt-β-catenin signaling. These results reinforce the new role of tigecycline in the therapy of CRC and demonstrate for the first time the effect of tigecycline on colon CSCs and their malignancies.}, }
@article {pmid40940455, year = {2025}, author = {He, P and Wang, S and Mao, R and Jiang, M and Siegel, S and Pedretti, G and Ignowski, J and Strachan, JP and Luo, R and Li, C}, title = {Real-time raw signal genomic analysis using fully integrated memristor hardware.}, journal = {Nature computational science}, volume = {}, number = {}, pages = {}, pmid = {40940455}, issn = {2662-8457}, support = {C7003-24Y, 17207925, 27210321, C1009-22GF, T45-701/22-R, GHKU707/23//Research Grants Council, University Grants Committee (RGC, UGC)/ ; 62122005//National Science Foundation of China | National Natural Science Foundation of China-Yunnan Joint Fund (NSFC-Yunnan Joint Fund)/ ; }, abstract = {Advances in third-generation sequencing have enabled portable and real-time genomic sequencing, but real-time data processing remains a bottleneck, hampering on-site genomic analysis. These technologies generate noisy analog signals that traditionally require basecalling and read mapping, both demanding costly data movement on von Neumann hardware. Here, to overcome this, we present a memristor-based hardware-software codesign that processes raw sequencer signals directly in analog memory, combining the two separated steps. By exploiting intrinsic device noise for locality-sensitive hashing and implementing parallel approximate searches in content-addressable memory, we experimentally showcase on-site applications, including infectious disease detection and metagenomic classification on a fully integrated memristor chip. Our experimentally validated analysis confirms the effectiveness of this approach on real-world tasks, achieving a 97.15% F1 score in virus raw signal mapping, with 51× speed-up and 477× energy saving over an application-specific integrated circuit. These results demonstrate that in-memory computing hardware provides a viable solution for integration with portable sequencers, enabling real-time and on-site genomic analysis.}, }
@article {pmid40940422, year = {2025}, author = {Kumar Nath, A and da Silva, RR and Gauvin, CC and Akpoto, E and Dlakić, M and Lawrence, CM and DuBois, JL}, title = {Commensal gut bacteria employ de-chelatase HmuS to harvest iron from heme.}, journal = {The EMBO journal}, volume = {}, number = {}, pages = {}, pmid = {40940422}, issn = {1460-2075}, support = {P30GM140963//HHS | National Institutes of Health (NIH)/ ; R35GM136390//HHS | National Institutes of Health (NIH)/ ; DBI-1828765//National Science Foundation (NSF)/ ; }, abstract = {Iron is essential for almost all organisms, which have evolved different strategies for ensuring a sufficient supply from their environment and using it in different forms, including heme. The hmu operon, primarily found in Bacteroidota and ubiquitous in gastrointestinal tract metagenomes of healthy humans, encodes proteins involved in heme acquisition. Here, we provide direct physiological, biochemical, and structural evidence for the anaerobic removal of iron from heme by HmuS, a membrane-bound, NADH-dependent de-chelatase that deconstructs heme to protoporphyrin IX (PPIX) and Fe(II). Heme can serve as the sole iron source for the model gastrointestinal bacterium Bacteroidetes thetaiotaomicron, when active HmuS is present. Heterologously expressed HmuS was isolated with bound heme molecules under saturating conditions. Its cryo-EM structure at 2.6 Å resolution revealed binding of heme and a pair of cations at distant sites. These sites are conserved across the HmuS family and chelatase superfamily, respectively. The proposed structure-based mechanism for iron removal by HmuS is chemically analogous to the chelatases in both unrelated heme biosynthetic pathways and homologous enzymes in the biosynthetic pathways for chlorophyll and vitamin B12, although the reaction proceeds in the opposite direction. Taken together, our study identifies a widespread mechanism via which anaerobic bacteria can extract nutritional iron from heme.}, }
@article {pmid40940010, year = {2025}, author = {Ellis, EK and Ióca, LP and Liu, J and Chen, M and Bruner, SD and Ding, Y and Paul, VJ and Donia, MS and Luesch, H}, title = {Structure Determination and Biosynthesis of Dapalides A-C, Glycosylated Kahalalide F Analogues from the Marine Cyanobacterium Dapis sp.}, journal = {Journal of natural products}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jnatprod.5c00757}, pmid = {40940010}, issn = {1520-6025}, abstract = {Kahalalides were originally isolated from the marine mollusk Elysia rufescens and its green algal diet Bryopsis sp., but the true producer was revealed as the obligate bacterial symbiont Candidatus Endobryopsis kahalalidefaciens, residing within Bryopsis sp. The most notable is kahalalide F, a broad-spectrum antitumor depsipeptide that entered the clinic but failed from lack of efficacy. We have isolated three new glycosylated analogues of kahalalide F, termed dapalides A-C (1-3), from a marine cyanobacterium, Dapis sp., collected from Guam. The planar structures were determined by extensive NMR coupled with mass spectrometry. Acid hydrolysis of 1 using amino acid analysis revealed the absolute configuration of singlet and a mixture of duplicate amino acids. Metagenomic analysis unveiled a biosynthetic gene cluster (BGC) with a nonribosomal peptide synthetase (NRPS) system and downstream glycosylation enzymes, which assisted the configurational assignment through epimerization domain analysis. The discovered BGC, termed dap, was assigned to a high-quality metagenome-assembled genome of the Dapis sp. Dapalide A (1) was subjected to phenotypic bioassays and exhibited weak anticancer cytotoxicity. This discovery expands the chemical diversity of the kahalalide F family, suggests their broad ecological role across diverse organisms, and presents an intriguing case of natural product biosynthesis evolution.}, }
@article {pmid40939728, year = {2025}, author = {de Souza, MA and Pereira, DE and da Silva, ECA and Medeiros, RG and Duarte, AM and Dutra, LMG and Araújo, DFS and de Araújo, WJ and de Oliveira, CJB and Guerra, GCB and Alves, AF and Viera, VB and Soares, JKB}, title = {Consumption of Brazilian palm fruit (Acrocomia intumescens drude) improves biochemical and gut microbiome parameters, reducing cardiovascular risk in exercised rats.}, journal = {Physiology &amp; behavior}, volume = {}, number = {}, pages = {115102}, doi = {10.1016/j.physbeh.2025.115102}, pmid = {40939728}, issn = {1873-507X}, abstract = {OBJECTIVE: This study aimed to evaluate the effects of macaiba pulp on physical, biochemical, intestinal health, and oxidative stress parameters in exercised rats.<br><br>METHODOLOGY: Forty-four male rats were divided into four groups (n&#x202f;=&#x202f;11): sedentary control (CT), exercised control (CT-EX), sedentary macaiba (MC), and exercised macaiba (MC-EX). MC and MC-EX groups received 1000 mg/kg/day of macaiba pulp, while CT and CT-EX received distilled water for eight weeks. Exercised animals underwent swimming for five days a week, beginning with 10 minutes and progressing to 60 minutes. Blood was collected to measure cholesterol (TC, HDL, LDL, VLDL), glucose, urea, liver enzymes (AST, ALT), and cardiovascular risk factors. Liver samples were analyzed for malonaldehyde (MDA), total fat, and cholesterol, while feces were collected for metagenome analysis. Body fat and adiposity index were also measured.<br><br>RESULTS: Macaiba-treated groups showed improved gut microbiome balance, reduced TC, LDL, VLDL, glucose, urea, liver enzymes, cardiovascular risks, body fat, MDA, and liver fat, with an increase in HDL.<br><br>CONCLUSION: Macaiba pulp effectively improved biochemical parameters, reduced lipid peroxidation from exercise, and lowered adipose tissue and cardiovascular risks.}, }
@article {pmid40939672, year = {2025}, author = {Ai, C and He, Y and Cheng, Z and Wu, J and Liu, C and Wang, N and Yu, Z and Liao, H and Zhou, S}, title = {Unveiling of active bacteria associated with nutrient cycling during cattle manure composting.}, journal = {Environmental research}, volume = {}, number = {}, pages = {122810}, doi = {10.1016/j.envres.2025.122810}, pmid = {40939672}, issn = {1096-0953}, abstract = {Bacteria play a pivotal role in nutrient turnover during the composting process. However, studies relying on total DNA analysis for bacterial community may be confounded by the presence of extracellular DNA from dead cells. In this study, ethidium monoazide (EMA) was employed to extract intracellular DNA from composting samples for amplicon and metagenomic sequencing, enabling the assessment of active bacterial community dynamics during cattle manure composting. The results revealed that total DNA-based 16S rRNA sequencing could only represent 36.9%-81.6% of the active bacterial communities. In contrast, EMA-based 16S rRNA sequencing identified Proteobacteria as the dominant active bacterial phylum throughout the composting process, with Actinobacteria exhibiting increased activity during the maturation phase. EMA-based metagenomic sequencing further showed that carbon and nitrogen metabolism genes showed the highest activity during the initial phase. Proteobacteria were identified as key functional bacteria in nutrient turnover, with its contribution reaching 55.4% and participating in 82.1% (23/28) of metabolic pathways. Meanwhile, Firmicutes (bin-23, g_Capillibacterium, bin-66, c_Bacilli) were the sole active nitrogen-fixing bacteria, harboring nitrogenase genes (nifH and nifD). This study offers novel understandings regarding the contribution of active bacteria in nutrient turnover and highlights the importance of distinguishing between active and total bacterial communities for a better understanding of microbial processes in composting systems.}, }
@article {pmid40939661, year = {2025}, author = {Feng, F and Zhao, C and Chen, Y and Zhang, Y and Hu, X and Mu, H and Zhang, W}, title = {Mechanistic insights into sulfidated nanoscale zero-valent iron enhanced methanogenesis: Electron redistribution and direct interspecies electron transfer-driven metabolic reconfiguration.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {133300}, doi = {10.1016/j.biortech.2025.133300}, pmid = {40939661}, issn = {1873-2976}, abstract = {Sulfidated nanoscale zero-valent iron (S-nZVI) enhances methanogenesis, yet the underlying mechanisms linking its interfacial structure to microbial metabolic responses remain unclear. This study elucidated S-nZVI's role via electron redistribution, microbial syntrophy enhancement, and metabolic pathway reconfiguration. Density functional theory revealed that sulfur-induced Fe-3d and S-3p orbital coupling, bandgap opening, and valence band shift collectively improved interfacial conductivity. At 5 g·L[-1], S-nZVI increased methane yield by 15 % and 68 % over nZVI and control, respectively. It also shortened lag phase, promoted extracellular polymeric substances secretion, and shifted electron transfer from cytochrome-based to abiotic pathways. Metagenomics confirmed enrichment of direct interspecies electron transfer (DIET)-associated genera and acetoclastic methanogenesis genes. Furthermore, the in-situ formation of conductive Fe3O4 and enhanced microbe colonization collectively reinforced DIET and methanogenesis. Overall, S-nZVI facilitated electron redistribution and drove the reconfiguration of syntrophic metabolism toward more efficient methanogenesis, offering mechanistic insights into material-microbe synergy for enhanced bioenergy recovery.}, }
@article {pmid40939657, year = {2025}, author = {Tan, HT and Lei, Y and Chek, MF and He, M and Pow, KC and Gong, S and Hao, Q and Hakoshima, T and Sudesh, K and Liu, G}, title = {Engineering chimeric polyhydroxyalkanoate synthases for enhanced copolymerization of poly(3-hydroxybutyrate-co-3-hydroxyhexanoate): A promising biotechnological approach.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {133307}, doi = {10.1016/j.biortech.2025.133307}, pmid = {40939657}, issn = {1873-2976}, abstract = {The escalating health and environmental threats posed by microplastics and nanoplastics (MNPs) highlight the urgent need for sustainable alternatives like polyhydroxyalkanoates (PHAs), biodegradable polyesters synthesized by bacterial PHA synthases (PhaCs). However, natural PhaCs exhibit suboptimal substrate specificity and polymer heterogeneity, limiting industrial scalability. To address this, chimeric PhaCs were engineered by swapping N-terminal domains between PhaC from mangrove soil metagenome (PhaCBP-M-CPF4; low 3-hydroxyhexanoate [3HHx] content, fewer but larger granules) and PhaC2 of Rhodococcus aethirovorans I24 (PhaC2Ra; high 3HHx, numerous small granules). This strategy aimed to combine enhanced 3HHx incorporation with controlled granule morphology. Using structural predictions, chimeric enzymes were constructed and tested, revealing that the C-terminal domain retained compatibility with diverse N-terminal regions. The resulting chimeras exhibited improved PHA production, enhanced 3HHx incorporation, and optimized granule formation, overcoming historical challenges in chimeric enzyme design by avoiding β-strand interference. Among the chimeras, distinct strains achieved: (i) up to 200 % increase in PHA production; (ii) up to 45 mol% 3HHx incorporation; and (iii) optimized granule formation, approaching a single-granule-per-cell phenotype (mean count: 1.079) and a granule size increase of up to 7.2-fold (mean area: 1.272 µm[2]). This approach provides a robust framework for tailoring PhaCs to produce high-performance copolymers. By elucidating domain compatibility, the study advances strategies in synthetic biology for creating modular enzymes with tailored functionalities, offering transformative potential in sustainable materials, protein engineering, and innovation in biodegradable plastics.}, }
@article {pmid40939655, year = {2025}, author = {Hu, F and Qin, J and Yang, H and Al-Dhabi, NA and Dong, Y and Bai, Z and Liu, L and Chai, F and Jin, B and Tang, W and Ji, J}, title = {An effective strategy for restoring the biofilm system of anammox/endogenous partial denitrification combined with continuous-flow partial nitration from deterioration.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {133311}, doi = {10.1016/j.biortech.2025.133311}, pmid = {40939655}, issn = {1873-2976}, abstract = {Hydroxylamine supplementation has recently emerged as a potential strategy to persistent sustain partial nitration (PN), but its feasibility in the biofilm system of anammox/endogenous partial denitrification combined with continuous-flow partial nitration (SAEPD-CFPN) systems remains unexplored. Thus, this study assessed the feasibility of hydroxylamine dosing for restoring PN in continuous-flow biofilm reactor and investigated the impact of continuous-flow partial nitration (CFPN) deterioration on biofilm system of SAEPD-CFPN. Results showed that nitrogen removal efficiency (NRE) decreased from 88.86 % to 39.56 %, with the nitrite accumulation rate (NAR) dropping from 87.28 % to 34.33 % due to the deterioration of CFPN. After effective hydroxylamine dosing, the average NRE increased to 89.90 %, while the average NAR rose to 83.83 %. The SAEPD biofilm system could handle insufficient NO2[-]-N supply caused by CFPN performance insignificant deterioration; however, its effectiveness diminished when CFPN performance severely deteriorated over the long term due to lower influent COD concentrations. Metagenomic analysis revealed that CFPN recovery was attributed to the effective inhibition of Nitrobacter and NxrAB. The robustness of the SAEPD biofilm reactor against fluctuations in influent NO2[-]-N was attributable to its complex microbial community structure. Additionally, intermittent hydroxylamine dosing was proposed as a sustainable strategy to ensure stable SAEPD-CFPN biofilm process operation.}, }
@article {pmid40938427, year = {2025}, author = {Sharma, S and Gajjar, B and Desai, C and Madamwar, D}, title = {Metagenomic analysis reveals the influence of wastewater discharge on the microbial community structures and spread of antibiotic-resistant bacteria at Mohar river, Gujarat.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {10}, pages = {1112}, pmid = {40938427}, issn = {1573-2959}, support = {GSBTM/JD(R&amp;D)/616/21-22/1236//Gujarat State Biotechnology Mission, Department of Science and Technology, Government of Gujarat/ ; }, abstract = {An extensive use of antibiotics has evolved bacterial antimicrobial resistance (AMR) and its spread through horizontal gene transfer within microbial communities of the natural environment. The water bodies receiving wastewater from sewage treatment plant (STP) serve as a conducive reservoir for the spread of antibiotic-resistant bacteria (ARB). This study revealed occurrence of multidrug-resistant and extended spectrum β-lactamase (ESBL) producing bacteria present in STP inlet (SI1), outlet (SO1), riverine environment receiving the STP wastewater (MP1), and control site (C1) of the river Mohar, Gujarat. Microbial community analysis revealed Proteobacteria and Firmicutes as dominating phyla in water samples of Mohar River sites. Shotgun analysis showed presence of antibiotic-degrading enzymes and pathways. The resistance profiling of ARBs showed the higher resistance towards cefotaxime at MP1 (77.4%), followed by SO1 (70.5%), SI1 (64.14%), and the least at C1 (57.13%). The highest ESBL isolates were observed at MP1 (96.42%), followed by SI1 (84.51%), SO1 (80.55%), and C1 (78.57%). Moreover, the RT-qPCR analysis for abundance of intI1 gene (responsible for HGT) showed a descending pattern from SI1 to the C1. The abundance of intI1 was found to correlate positively with mercury, chromium, and chlorine, and a negative correlation was observed with arsenic. The results obtained in this research suggest that AMR spreads and evolves in the water environment via discharge of wastewaters from STPs into the river ecosystems.}, }
@article {pmid40938103, year = {2025}, author = {Desingu, PA and Arunkumar, S and Nagarajan, K and Saikumar, G}, title = {Metagenomic detection of the complete coding regions of Tanay virus from mosquitoes (Armigeres subalbatus) in India.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0038925}, doi = {10.1128/mra.00389-25}, pmid = {40938103}, issn = {2576-098X}, abstract = {So far, the Tanay virus has only been detected in the Philippines and China. Here, we report that a complete coding region-wide virus with 3.7-16.7% nucleotide diversity to the Tanay viruses identified in China and 25.2% nucleotide diversity to those identified in the Philippines is circulating in mosquitoes (Armigeres subalbatus) in India.}, }
@article {pmid40937156, year = {2025}, author = {Anselmi, S and Ni, Y and Tonoli, A and Wu, J and Wang, Y and Prout, L and Miodownik, M and Jeffries, JWE and Hailes, HC}, title = {The discovery of new metagenomic urethanases utilising a novel colorimetric assay for applications in the biodegradation of polyurethanes.}, journal = {Green chemistry : an international journal and green chemistry resource : GC}, volume = {}, number = {}, pages = {}, pmid = {40937156}, issn = {1463-9262}, abstract = {The enzymatic molecular recycling of plastics is of increasing interest, where polymers are converted into monomers for reuse or upcycled into value added chemicals. Polyurethanes are an important class of synthetic hydrolysable polymers found in textiles as an elastane component, also known as lycra and spandex, with most post-consumer waste currently disposed of in landfill. Here we have identified three active novel urethane hydrolytic enzymes from a drain metagenome able to breakdown methylenedianiline-based elastane model substrates. In addition, we have established a new colorimetric assay, suitable for high-throughput applications using tyrosinases. For the urethanases identified, the reaction conditions and substrate scope were explored. Finally, the urethanases and assay were used with commercial fabrics, demonstrating breakdown of the polymer.}, }
@article {pmid40936885, year = {2025}, author = {Ye, X and Li, C and Zhou, Z and Yang, J and Jiang, H and Hu, L and Pan, H and Wei, X and Huang, Y and Lin, Y and Wang, L}, title = {Metagenomic Next-Generation Sequencing-Assisted Risk Prediction and Stratification of Infections After Kidney Transplantation: A Case Study of COVID-19.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {4763-4776}, pmid = {40936885}, issn = {1178-6973}, abstract = {BACKGROUND: During the COVID-19 pandemic, COVID-19 infection has severely damaged the transplanted kidney function and health of kidney transplant patients. This study aims to investigate the clinical characteristics, risk factors and predictors of severe COVID-19 in patients after kidney transplantation.<br><br>MATERIAL AND METHODS: The clinical data of patients with COVID-19 after kidney transplantation were collected from December 2022 to January 2023 at the First Affiliated Hospital of Soochow University. Logistic regression analysis was performed to identify risk factors for severe disease and to construct a nomogram model. Concurrently, metagenomic next-generation sequencing (mNGS) was employed to detect the sputum microbiome.<br><br>RESULTS: A total of 58 patients were enrolled and were categorized into the common group (n=35) and the severe group (n=23) based on infection severity. The common group comprised 23 males with a mean age of 45.60 &#xb1; 9.11 years, while the severe group included 16 males with a mean age of 48.22 &#xb1; 9.95 years. Multivariate logistic analysis revealed that days of fever before hospitalization, C-reactive protein (CRP) and interleukin-10 (IL-10) on admission were significantly independent risk factors for severity, with an area under the ROC curve at 0.906. Comparison of the sputum microbiome revealed that there were no significant differences in &#x3b1; and &#x3b2; diversity between the two groups. Streptococcus parasanguinis was significantly more abundant in the specimens from the severe group, while Gemella sanguinis and Gemella haemolysans were significantly more abundant in the common group.<br><br>CONCLUSION: The severity of COVID-19 in kidney transplant patients is associated with days of fever before hospitalization, and the levels of CRP and IL-10 at admission, which also alter the abundance of certain species in the sputum microbiome. Therefore, it is necessary to actively monitor the clinical indicators of kidney transplant patients admitted with COVID-19 to reduce the risk of progression to severe disease.}, }
@article {pmid40936884, year = {2025}, author = {Wu, Y and Yu, X and Zhang, Y and Liu, J and Chen, Y and Wang, R and Zhang, W}, title = {Challenges in Management of Disseminated Mucormycotic Infection with Endocarditis in an Adult Patient Receiving Liver Transplantation.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {4711-4721}, pmid = {40936884}, issn = {1178-6973}, abstract = {Mucormycosis is a rare fungal infection. With the recent advancements in diagnostic technologies, including molecular diagnostic techniques, such as PCR and metagenomic next-generation sequencing, the detection rates of mucormycosis have increased. However, its mortality rates remain alarmingly high. Although post-liver transplantation mucormycosis cases are infrequently reported (less than 1%), their mortality rate ranges from 60% to 90%, while mucormycotic endocarditis is even rarer. This article summarizes the clinical manifestations of mucormycosis in a post-liver transplantation adult patient and reviews the existing literature on mucormycotic endocarditis, with the aim of outlining its clinical features, diagnostic challenges, and therapeutic strategies.}, }
@article {pmid40936227, year = {2025}, author = {Liu, C and Long, J and Li, Y and Leng, X and Zhang, J and Chen, S and Fu, J and Li, C and Zhou, Y and Feng, C and Huang, B}, title = {The Comparison of Diagnostic Performance Between Next-Generation Sequencing of Blood and Tissues for Primary Spinal Infections.}, journal = {Global spine journal}, volume = {}, number = {}, pages = {21925682251375446}, doi = {10.1177/21925682251375446}, pmid = {40936227}, issn = {2192-5682}, abstract = {Study designprospective study.ObjectivesThe hematogenous spread of pathogens from a distant infected area is the main route of primary spinal infections. It is expected that blood metagenomic next-generation sequencing (mNGS) has potential in the pathogen detection of primary spinal infections. The aim of this study is to compare the diagnostic performance of blood and tissue mNGS in primary spinal infections.MethodsA total of 21 patients with primary spinal infections were analyzed. The results of mNGS and culture of blood and spinal specimens were used to calculate the diagnostic efficiency-related parameters.ResultsThe positive rate, sensitivity and specificity of blood mNGS were significantly lower than those of tissue mNGS (42.86% vs 90.48%, 9.52% vs 95%, 12.5% vs 100%). The positive rate and sensitivity of blood mNGS were higher (42.86% vs 4.76, 9.52% vs 5%) than those of blood pathogen culture. Also, the sensitivity and specificity of blood mNGS were lower than tissue pathogen culture (9.52% vs 45%, 12.5% vs 100%). Moreover, the specificity of blood mNGS was the lowest among the 4 pathogen identification techniques.ConclusionsThe diagnostic performance of blood mNGS is worse than tissue mNGS in primary spinal infections. The application prospects of blood mNGS in pathogen identification of primary spinal infections are limited. Further studies will be required to investigate the diagnostic values of blood mNGS in other types of spinal infections or in subpopulations of spinal infections.}, }
@article {pmid40935925, year = {2025}, author = {Zhou, Y and Wang, H and Sun, J and Wicaksono, WA and Liu, C and He, Y and Qin, Y and Berg, G and Li, L and Lin, H and Chai, Y and Bai, Y and Ma, Z and Cernava, T and Chen, Y}, title = {Phenazines contribute to microbiome dynamics by targeting topoisomerase IV.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {40935925}, issn = {2058-5276}, support = {LZ23C140004//Natural Science Foundation of Zhejiang Province (Zhejiang Provincial Natural Science Foundation)/ ; U21A20219//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Phenazines are highly prevalent, natural bioactive substances secreted by microbes. However, their mode of action and potential involvement in shaping microbiomes remain elusive. Here we performed a comprehensive analysis of over 1.35 million bacterial genomes to identify phenazine-producing bacteria distributed across 193 species in 34 families. Analysis of rhizosphere microbiome and public rhizosphere metagenomic datasets revealed that phenazines could shape the microbial community by inhibiting Gram-positive bacteria, which was verified by pairwise interaction assays using Phenazine-1-carboxamide (PCN)-producing Pseudomonas chlororaphis. PCN induced DNA damage in Bacillus subtilis, a model Gram-positive target, where it directly bound to the bacterial topoisomerase IV, inhibiting its decatenation activity and leading to cell death. A two-species consortium of phenazine-producing Pseudomonas and resistant B. subtilis exhibited superior synergistic activity in preventing Fusarium crown rot in wheat plants. This work advances our understanding of a prevalent microbial interaction and its potential for biocontrol.}, }
@article {pmid40935888, year = {2025}, author = {Otani, K and Nakatsu, G and Fujimoto, K and Miyaoka, D and Sato, N and Nadatani, Y and Nishida, Y and Maruyama, H and Ominami, M and Fukunaga, S and Hosomi, S and Tanaka, F and Imoto, S and Uematsu, S and Watanabe, T and Fujiwara, Y}, title = {Development of gastric mucosa-associated microbiota in autoimmune gastritis with neuroendocrine tumors.}, journal = {Journal of gastroenterology}, volume = {}, number = {}, pages = {}, pmid = {40935888}, issn = {1435-5922}, support = {JP22K08040//Japan Society for the Promotion of Science/ ; }, abstract = {BACKGROUND: Autoimmune gastritis (AIG) is a chronic atrophic gastritis that affects the gastric corpus, leading to achlorhydria, hypergastrinemia, and a precursor of neuroendocrine tumors (NETs). This study aimed to elucidate the underlying mechanisms of gastric NET formation in AIG by analyzing gastric mucosa-associated microbiota and host tissue-derived metabolite profiles.<br><br>METHODS: A total of 19 patients diagnosed with AIG and 12 controls uninfected with Helicobacter pylori underwent gastric mucosal biopsies for microbiome analysis using next-generation sequencing with primers targeting the V3-V4 region of the 16S rRNA gene, and metabolome analysis using capillary electrophoresis time-of-flight mass spectrometry.<br><br>RESULTS: Microbiome analysis revealed significantly reduced &#x3b1;-diversity indices in patients with AIG when compared with the control group. &#x3b2;-Diversity analysis showed distinct microbial compositions among the control, NET-negative, and NET-positive groups. The NET-positive group exhibited a significantly higher abundance of Proteobacteria and Fusobacteriota, particularly Haemophilus parainfluenzae, Fusobacterium periodonticum, and Fusobacterium nucleatum, whereas Firmicutes, including Streptococcus salivarius and Veillonella atypica, were significantly decreased compared with the NET-negative group. Metabolome analysis revealed a shift away from glycolysis and tricarboxylic acid cycle activity toward alternative metabolic pathways in patients with AIG. Integrated analysis of gastric microbiota signatures (GMS) and tissue metabotypes demonstrated significant associations among GMS, tissue metabotypes, and NET diagnosis.<br><br>CONCLUSIONS: These findings highlight marked shifts in gastric mucosa-associated microbiota profiles in patients with AIG who developed gastric NETs. Tissue-specific metabolic alterations may precede mucosal dysbiosis in patients with AIG and promote the development of a microenvironment implicated in NET formation.}, }
@article {pmid40935532, year = {2025}, author = {Webster, AM and Triumph, Z and Wei, B and Martin, RM and Smith, LE and Wilhelm, SW and Cleckner, LB and Razavi, NR and Boyer, GL}, title = {First report of nodularin production by Nostochopsis sp. in a temperate eutrophic lake.}, journal = {Harmful algae}, volume = {149}, number = {}, pages = {102956}, doi = {10.1016/j.hal.2025.102956}, pmid = {40935532}, issn = {1878-1470}, abstract = {Benthic cyanobacteria are understudied in comparison to their planktonic counterparts. Consequently, our understanding of cyanotoxin production in benthic mats remains limited. We detected nodularin-R (NOD-R) in a population of Nostochopsis from Honeoye Lake (New York, United States). Identification as Nostochopsis was supported by morphological (see section 3.1 for a detailed description) and metagenomic analyses. The first metagenome assembled genome of Nostochopsis was drafted and estimated at 99.28 % complete. Cyanotoxin testing of Nostochopsis biomass showed production of NOD-R but not microcystins, anatoxins, or cylindrospermopsins. The complete nodularin synthetase cluster was confirmed in the Nostochopsis genome. To our knowledge, this is the first report of nodularin production, or any cyanotoxin production, by the benthic cyanobacteria Nostochopsis. This is the fourth genus of cyanobacteria reported to produce nodularins.}, }
@article {pmid40935105, year = {2025}, author = {Zhao, J and Guo, Z and Tang, L and Lu, X and Li, Y and Yang, K}, title = {Dynamic evolution of antibiotic resistance risk in sewage sludge-amended soil during crop growth: a field-based metagenomic perspective.}, journal = {Environmental research}, volume = {}, number = {}, pages = {122799}, doi = {10.1016/j.envres.2025.122799}, pmid = {40935105}, issn = {1096-0953}, abstract = {Sewage sludge, a ubiquitous by-product of wastewater treatment, accumulates globally. Land application, a prominent waste valorization strategy, inadvertently disseminates the sludge antibiotic resistome into ecosystems, threatening ecological security and public health. Risk assessment of antibiotic resistance (AR) during sludge land application is urgently needed. Herein, we conducted a field study by planting three crops in sludge-amended soil, and monitoring the dynamic evolution of AR risk throughout their growth cycles. Metagenomic sequencing assessed antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), virulence factors (VFs), and their co-occurrence. Sludge amendment exerted persistent, yet largely recoverable, impacts on soil microbial community and the resistome. The resulting AR risk evolution was nonlinear and fluctuating, dominated by soil microbial community reconstruction. Given the differences in crop edible parts, growth periods of crops, complex AR risk dynamics, and external factors like weather, we propose a time-sensitive control strategy targeting critical risk windows. This strategy aims to mitigate AR risk under the "One Health" paradigm for sustainable sludge land application.}, }
@article {pmid40935093, year = {2025}, author = {Marangi, M and Palladino, G and Valzano, F and Scicchitano, D and Turroni, S and Rampelli, S and Candela, M and Arena, F}, title = {Genetic characterization of enteric protozoan microorganisms in newly arrived migrants in Italy and correlation with the gut microbiome layout.}, journal = {Travel medicine and infectious disease}, volume = {}, number = {}, pages = {102901}, doi = {10.1016/j.tmaid.2025.102901}, pmid = {40935093}, issn = {1873-0442}, abstract = {The prevalence of the enteric protozoan microorganisms, its genetic characterization as well as its associated gut microbiome has been molecularly and 16S metagenomic characterized in a cohort of newly arrived migrants in Italy from African countries over the period 2022-2024. Out of 199 individuals, 92 (46.2 %) were found to be carrier of protozoan microorganisms with a higher prevalence of Blastocystis sp. (15.5 %), followed by Giardia duodenalis (12.6 %), Dientamoeba fragilis (7.5 %), Cryptosporidium parvum (6.5 %), and Entamoeba histolytica (4 %). Subtypes ST1, ST2 and ST3 were genetically characterized for Blastocystis sp., assemblages A and B for G. duodenalis, subtypes families IIa and IIc for C. parvum and genotype 1 for D. fragilis. High prevalence of Butyrivibrio, Lachnospiraceae UGC 10 and Paraprevotella, were identified in the protozoan non-carrier individual group. This work shed lights on the circulation of enteric protozoan microorganisms in apparently healthy migrants from African countries and the potential relationship with the host-microbiome composition. Moreover, these results give an overview of the importance of microbiological surveys among migrants and asylum seekers arriving to hosting countries in order to evaluate the reliable risk of several microorganisms introduction though migration. Ultimately, further investigation of interplays between the intestinal microbiota and protozoan microorganisms will provide new approaches in the diagnosis and treatment of intestinal infections.}, }
@article {pmid40934662, year = {2025}, author = {Zhang, J and Zhao, J and Gao, Z and Ding, X and Li, Y and Shi, J and Zhao, D and Shi, L and Bi, X and Miao, Y}, title = {An effective method for enhancing metabolic activity of anammox bacteria: Accelerating heme biosynthesis by glutamate.}, journal = {Journal of environmental management}, volume = {393}, number = {}, pages = {127301}, doi = {10.1016/j.jenvman.2025.127301}, pmid = {40934662}, issn = {1095-8630}, abstract = {Enhancing and maintaining anammox bacteria (AnAOB) activity is a major challenge for application of anammox process, which could be achieved by accelerating heme biosynthesis. Heme is crucial for electron transport and redox reaction and its biosynthesis may be promoted by glutamate. To explore the effect of glutamate on AnAOB activity, four parallel anammox systems (named R0, R1, R2, and R3) with different concentrations of glutamate (0, 0.125, 0.25, and 0.5 mM) were set up. The results showed that AnAOB activities and nitrogen removal efficiencies of R1 and R2 were about 58.3 % and 48.8 %, and 80.5 % and 64.1 % higher than that of R0, respectively, whereas excessive glutamate (0.5 mM) deteriorated the system performance. Moreover, heme content, activities of hydrazine synthase and hydrazine dehydrogenase, and sludge particle size in R1 and R2 were significantly higher than R0. Metagenomic sequencing analysis further revealed that the moderate amount of glutamate (0.125 mM, 0.25 mM) could effectively improve AnAOB activity by enhancing heme biosynthesis, accelerating electron transport and energy synthesis, and promoting the aggregation of microorganisms. This study provides an effective method for enhancing AnAOB metabolic activity and clarifies the underlying mechanism.}, }
@article {pmid40934587, year = {2025}, author = {Wang, F and Xiong, J and Lin, L and Xu, W and Liu, L and Yang, S and Cao, W}, title = {Antibiotic resistance genes link to nitrogen removal potential via co-hosting preference for denitrification genes in a subtropical estuary.}, journal = {Journal of hazardous materials}, volume = {498}, number = {}, pages = {139801}, doi = {10.1016/j.jhazmat.2025.139801}, pmid = {40934587}, issn = {1873-3336}, abstract = {Estuaries are important sinks for antibiotic resistance genes (ARGs) and hotspots of nitrogen cycling. However, the interactions between nitrogen cycling functional genes (NCGs) and ARGs in estuaries remain poorly understood. This study employed metagenomic sequencing to explore potential interactions between nitrogen, ARGs, and microbial-mediated nitrogen cycling processes in estuarine waters. Results showed beta-lactam was the predominant subtype of ARGs (407 species), and sul1 exhibited the highest relative abundance (4.11 %). Nitrogen was the important factor driving spatiotemporal variation of ARGs, promoting their proliferation and dispersal by enhancing microbial growth and reproduction. Network analysis revealed wide and complex correlations between ARGs and NCGs. Nitrate-reducing bacteria were the main hosts of ARGs, and the greatest number of potential hosts were those involved in assimilatory nitrate reduction to ammonium (17.44 %), dissimilatory nitrate reduction to nitrite (16.59 %), and denitrification (15.71 %). Compared with dissimilatory nitrite reduction to ammonium genes, ARGs prefer to form co-hosting relationships with denitrification genes, indicating that ARGs had a stronger effect on the nitrogen removal potential than on the nitrogen retention potential. This study highlights the complex interactions between ARGs and nitrogen cycling processes in subtropical estuaries, and will provide a scientific base for couple management strategies of nitrogen and antibiotic pollution.}, }
@article {pmid40934284, year = {2025}, author = {Lucas, A and Schäffer, DE and Wickramasinghe, J and Auslander, N}, title = {kMermaid: Ultrafast metagenomic read assignment to protein clusters by hashing of amino acid k-mer frequencies.}, journal = {PLoS computational biology}, volume = {21}, number = {9}, pages = {e1013470}, doi = {10.1371/journal.pcbi.1013470}, pmid = {40934284}, issn = {1553-7358}, abstract = {Shotgun metagenomic sequencing can determine both the taxonomic and functional content of microbiomes. However, functional classification for metagenomic reads remains highly challenging as protein mapping tools require substantial computational resources and yield ambiguous classifications when short reads map to homologous proteins originating from different bacteria. Here we introduce kMermaid for the purpose of uniquely mapping bacterial short reads to taxa-agnostic clusters of homologous proteins, which can then be used for downstream analysis tasks such as read quantification and pathway or global functional analysis. Using a nested hash map containing amino acid k-mer profiles as a model for protein assignment, kMermaid achieves the sensitivity of popular existing protein mapping tools while remaining highly resource efficient. We evaluate kMermaid on simulated data and data from human fecal samples as well as demonstrate the utility of kMermaid for classifying reads originating from new, unseen proteins. kMermaid allows for highly accurate, unambiguous and ultrafast metagenomic read assignment into protein clusters, with a fixed memory usage, and can easily be employed on a typical computer.}, }
@article {pmid40933810, year = {2025}, author = {Tigrero-Vaca, J and Villavicencio-Vásquez, M and Coronel, J and Cevallos-Cevallos, JM}, title = {Multi-platform metagenomic characterization of the microbial community during spontaneous cacao fermentation.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {13}, number = {}, pages = {1630515}, doi = {10.3389/fbioe.2025.1630515}, pmid = {40933810}, issn = {2296-4185}, abstract = {Cacao fermentation is a spontaneous process in which microorganisms play a key role in the development of distinctive chocolate flavors. The microbiota acting during cacao fermentation has been routinely characterized by culture-based techniques and next-generation sequencing using Illumina's platform. However, the potential of in situ sequencing technologies to monitor microbial dynamics during cacao fermentation has not been assessed. In this study, cacao bean samples were collected at 0, 24, 48, 72, and 96 h after the start of the fermentation. Total DNA was extracted, and sequencing libraries were prepared for further sequencing using Illumina's and Nanopore's MinION sequencing platforms. Additionally, microorganisms were isolated using traditional culture-based methods. At the order and family taxonomic levels, Illumina and MinION sequencing revealed similar microbial composition in the samples. However, discrepancies were observed at the genus and species levels. In this sense, Illumina sequencing revealed a predominance of Limosilactobacillus, Levilactobacillus, Lactiplantibacillus, Frauteria, Saccharomyces and Acetobacter, while MinION sequencing showed a prevalence of Escherichia, Salmonella, Liquorilactobacillus, Lentilactobacillus, Acetobacter and Komagataeibacter during fermentation. The three methods were consistent in detecting the major yeast (Saccharomyces cerevisiae), lactic acid bacteria (Lactiplantibacillus plantarum, Leuconostoc pseudomesenteroides, Levilactobacillus brevis, Liquorilactobacillus mali, and Lentilactobacillus hilgardii) and acetic acid bacteria (Acetobacter pasteurianus) species during fermentation. Functional analysis based on a hybrid assembly of Illumina and MinION data revealed the roles of lactic acid bacteria and acetic acid bacteria in the metabolism of carbohydrates, amino acids, and secondary metabolites such as polyphenols and theobromine. This study represents the first report assessing the applicability of MinION sequencing for the characterization of microbial populations during cacao fermentation, demonstrating its potential as a complementary tool to established sequencing platforms.}, }
@article {pmid40933579, year = {2025}, author = {Lin, B and Zhong, D and Qin, L and Liu, Q and Wu, L and Wang, B and Wang, K and Lu, X and Deng, S and Pan, L}, title = {Application of metagenomics sequencing to diagnose paralytic rabies with stroke-like onset: a case report.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1639262}, doi = {10.3389/fmed.2025.1639262}, pmid = {40933579}, issn = {2296-858X}, abstract = {BACKGROUND: Rabies is an acute zoonotic infectious disease caused by infection with a virus of the genus Lyssavirus. We report a case of paralytic rabies with a stroke-like onset, which was diagnosed using metagenomics next-generation sequencing (mNGS).<br><br>CASE PRESENTATION: A 58-year-old man was admitted to the hospital with "numbness and weakness in the right upper extremity for 2&#x202f;days, aggravated for 1&#x202f;day." Twenty-five days before his admission, the patient was bitten on the back of right hand by an unvaccinated domestic dog, resulting in a penetrating injury, classified as grade III according to the rabies exposure classification method. Following admission, the patient exhibited rapidly progressive stroke symptoms, and on the second day, he suffered a sudden respiratory arrest accompanied by a weakened heartbeat and a decreased heart rate. He was treated with emergency tracheal intubation, cardiopulmonary resuscitation, and dehydration to lower cranial pressure.<br><br>RESULTS: The patient's condition deteriorated rapidly after admission. A lumbar puncture was conducted on the morning of the second day of admission, and cerebrospinal fluid (CSF) was sent to Weiyuan Genetic Laboratories (Guangzhou, China) for rabies virus identification. The patient died on the third day of admission. Pathogen capture macro-genomics was performed on CSF using an Illumina NextSeq second-generation sequencer, and nine rabies virus sequences, which shared more than 99% nucleotide homology with the genome sequence of the rabies virus Rabies lyssavirus (NCBI accession no. MN175989.1), were detected. The Q30 ratio of this test was 98.3%.<br><br>CONCLUSION: Compared to polymerase chain reaction (PCR) and direct fluorescent antibody (DFA) test, mNGS shortens the diagnostic window and improves sensitivity to low-virus or seronegative manifestations by simultaneously capturing and sequencing the entire pathogen genome. The mNGS technology can effectively aid in the diagnosis of paralytic rabies.}, }
@article {pmid40933366, year = {2025}, author = {Gutleben, J and Podell, S and Mizell, K and Sweeney, D and Neira, C and Levin, LA and Jensen, PR}, title = {Extremophile hotspots linked to containerized industrial waste dumping in a deep-sea basin.}, journal = {PNAS nexus}, volume = {4}, number = {9}, pages = {pgaf260}, doi = {10.1093/pnasnexus/pgaf260}, pmid = {40933366}, issn = {2752-6542}, abstract = {Decaying barrels on the seafloor linked to DDT contamination have raised concerns about the public health implications of decades old industrial waste dumped off the coast of Los Angeles. To explore their contents, we collected sediment cores perpendicular to five deep-sea barrels. The concentration of DDT and its breakdown products were highly elevated relative to control sites yet did not vary with distance from the barrels, suggesting that they were not associated with the contamination. Sediment cores collected through white halos surrounding three barrels were enriched in calcite and had elevated pH. The associated microbial communities were low diversity and dominated by alkalophilic bacteria with metagenome-assembled genomes adapted to high pH. A solid concretion sampled between a white halo and barrel was composed of brucite, a magnesium hydroxide mineral that forms at high pH. Based on these findings, we postulate that leakage of containerized alkaline waste triggered the formation of mineral concretions that are slowly dissolving and raising the pH of the surrounding sediment pore water. This selects for taxa adapted to extreme alkalinity and drives the precipitation of "anthropogenic" carbonates forming white halos, which serve as a visual identifier of barrels that contained alkaline waste. Remarkably, containerized alkaline waste discarded >50 years ago represents a persistent pollutant creating localized mineral formations and microbial communities that resemble those observed at some hydrothermal systems. These formations were observed at one-third of the visually identified barrels in the San Pedro Basin and have unforeseen, long-term consequences for benthic communities in the region.}, }
@article {pmid40933132, year = {2025}, author = {Li, X and Lu, H}, title = {Enhanced metagenomic strategies for elucidating the complexities of gut microbiota: a review.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1626002}, doi = {10.3389/fmicb.2025.1626002}, pmid = {40933132}, issn = {1664-302X}, abstract = {The human gastrointestinal tract (GIT) is inhabited by a heterogeneous and dynamic microbial community that influences host health at multiple levels both metabolically, immunologically and via neurological pathways. Though the gut microbiota-overwhelmingly Bacteroidetes and Firmicutes-has essential functions in nutrient metabolism, immune regulation, and resistance to pathogens, its dysbiosis is likewise associated with pathologies, such as inflammatory bowel disease (IBD), obesity, type 2 diabetes (T2D), and neurodegenerative diseases. While conventional metagenomic techniques laid the groundwork for understanding microbial composition, next-generation enhanced metagenomic techniques permit an unprecedented resolution in exploring the functional and spatial complexity of gut communities. Advanced frameworks such as high-throughput sequencing, bioinformatic and multi-omics technologies are expanding the understanding of microbial gene regulation, metagenomic pathways, and host-microbe communication. Beyond taxonomic profiling, they map niche-specific activities of gut microbiota along a dichotomy of facultative mutualism, evidenced by relations of beneficial symbionts, represented here by Enterobacteriaceae. In this review, we critically consider the latest approaches (e.g., long-read sequencing, single-cell metagenomics and AI-guided annotation) that mitigate biases stemming from DNA extraction, sequencing depth and functional inference.}, }
@article {pmid40933127, year = {2025}, author = {Akhtar, MF and Wenqiong, C and Umar, M and Changfa, W}, title = {Biochemical properties of lactic acid bacteria for efficient silage production: an update.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1581430}, doi = {10.3389/fmicb.2025.1581430}, pmid = {40933127}, issn = {1664-302X}, abstract = {Ensiling, a microbial-driven process employed for preserving fresh forage in both bio-refineries and animal production, triggers significant biochemical transformations. These changes have spurred the exploration of novel silage additives, with a particular emphasis on the potential of microbial strains that exhibit superior biopreservation capabilities. Lactic acid bacteria (LAB) species have gained widespread recognition for their diverse applications as additives in the fermentation of crops and forage biomasses during ensiling. Nonetheless, recent variations in silage quality might be attributed to a lack of comprehensive information on the gene expression and molecular mechanisms of the microbiota involved in silage production. Contemporary research efforts have been directed toward uncovering nutrient-rich animal feed solutions through enhanced LAB inoculants. This review aims to shed light on the role of LAB inoculants in silage production and the modern biotechnological methods, including metabolomics, proteomics, metagenomics, genomics, transcriptomics, and genetic manipulation. These powerful tools are instrumental in the identification, enhancement, and development of high-performance LAB strains. Additionally, the review outlines emerging trends and prospective developments in LAB advancement for the enhancement of silage, which holds significant promise for breakthroughs in sustainable agriculture and improved animal feed production.}, }
@article {pmid40933007, year = {2025}, author = {Le, J and Hakimjavadi, H and Parsana, R and Chamala, S and Michail, S}, title = {Fecal Microbiota Transplantation Induces Sustained Gut Microbiome Changes in Pediatric Ulcerative Colitis: A Combined Randomized and Open-Label Study.}, journal = {Gastro hep advances}, volume = {4}, number = {10}, pages = {100741}, doi = {10.1016/j.gastha.2025.100741}, pmid = {40933007}, issn = {2772-5723}, abstract = {BACKGROUND AND AIMS: Fecal microbiota transplantation (FMT) is a promising tool to modulate the gut microbiome in pediatric ulcerative colitis (UC). We investigated the long-term impact of FMT on the gut microbiome and identified microbial signatures associated with disease severity and clinical outcomes.<br><br>METHODS: This study combined a randomized, double-blind trial comparing FMT to autologous placebo with an open-label extension to assess FMT's effects on the gut microbiome in pediatric UC patients over 48 weeks. Stool samples were collected at baseline and postintervention, and clinical response was evaluated using the Pediatric Ulcerative Colitis Activity Index. Shotgun metagenomic sequencing characterized the fecal microbiome's composition and functional potential. Taxon set enrichment analysis identified microbial taxon sets associated with UC and FMT.<br><br>RESULTS: FMT induced significant, sustained increases in gut microbial diversity over 48 weeks. Key changes included decreases in Klebsiella oxytoca and increases in Coprobacter fastidiosus post-FMT. Microbial signatures were associated with disease severity, including increased indole producers and decreased mucin degraders in mild UC compared to remission. Patients with clinical improvement post-FMT showed decreased Fusobacterium nucleatum and Veillonella parvula. Klebsiella pneumoniae and Klebsiella variicola decreased after open-label FMT.<br><br>CONCLUSION: FMT induces sustained changes in the pediatric UC gut microbiome, with distinct microbial signatures associated with disease severity and clinical outcomes. However, the high autologous placebo response rate underscores the need for further research to elucidate the mechanisms underlying FMT and placebo responses. Our study provides insights into the gut microbiome's role in pediatric UC, laying the foundation for developing personalized microbiome-targeted therapies. ClinicalTrials.gov number, NCT02291523.}, }
@article {pmid40932661, year = {2025}, author = {Sachdeva, S and Sarethy, IP}, title = {Antibiotic resistance profiling in an ancient Indian sulfur-rich stepwell: a case study of Gandhak-ki-Baoli.}, journal = {Molecular biology reports}, volume = {52}, number = {1}, pages = {895}, pmid = {40932661}, issn = {1573-4978}, mesh = {India ; *Sulfur/analysis ; *Bacteria/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; Metagenomics/methods ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; Water Microbiology ; Metagenome ; }, abstract = {BACKGROUND: Antimicrobial resistance (AMR) is a growing global health concern, increasingly recognized to emerge not only from clinical and agricultural sources but also from natural and historical environments. Despite their ecological and cultural significance, ancient water bodies such as stepwells remain largely unexplored in the context of environmental resistomes.<br><br>METHOD: This study investigates AMR in Gandhak-ki-Baoli, an ancient sulfur-rich stepwell located in Delhi, India. A combined methodological approach involving culture-based microbial isolation and metagenomics sequencing was used to identify bacterial taxa and associated antibiotic resistance genes (ARGs).<br><br>RESULTS: The analysis revealed a diverse microbial community harboring ARGs, including those conferring multidrug resistance. Several genes showed evidence of co-selection mechanisms with heavy metals and biocides. The stepwell's unique environmental conditions characterized by stagnant water, low light, variable moisture, and limited nutrients that likely contribute to the persistence and potential horizontal transfer of resistance traits.<br><br>CONCLUSIONS: This is the first study to profile AMR in a historical stepwell, revealing the presence of a complex environmental resistome. The findings suggest that ancient water structures like stepwells can act as hidden reservoirs of AMR. These insights highlight the need to include such environments in future AMR surveillance efforts to better understand the broader ecological landscape of resistance.}, }
@article {pmid40932534, year = {2025}, author = {Wang, F and Xia, J and Sun, J}, title = {Microbiological diagnostics and their impact on hematology nursing.}, journal = {Folia microbiologica}, volume = {}, number = {}, pages = {}, pmid = {40932534}, issn = {1874-9356}, abstract = {Microbiological diagnostics have become a foundational element in hematology nursing, where early and accurate infection detection is vital for immunocompromised patients. This review explores how both traditional techniques, such as microscopy, culture, and antigen detection, and emerging technologies, including polymerase chain reaction (PCR), metagenomic next-generation sequencing (mNGS), and MALDI-TOF mass spectrometry, contribute to clinical decision-making and infection control. These tools not only accelerate pathogen identification and resistance profiling but also support precision medicine approaches tailored to hematologic patient needs. The expanding role of hematology nurses is emphasized, particularly in diagnostic stewardship, specimen collection, result interpretation, and coordination of infection management strategies. Educational interventions have proven effective in reducing contamination rates and improving antimicrobial targeting. Furthermore, novel point-of-care platforms, such as CRISPR-based diagnostics and AI-enhanced digital PCR, are shifting diagnostic capabilities closer to the bedside, redefining nursing workflows and responsibilities. These innovations empower nurses to engage in real-time clinical decisions, monitor therapy responses, and enhance patient education regarding diagnostic procedures and infection risks. However, gaps remain in microbiology-related training and confidence among nurses, highlighting the need for integrated educational curricula and interdisciplinary collaboration. By aligning technological advancements with frontline nursing practice, microbiological diagnostics not only optimize patient outcomes but also elevate the role of nurses as key stakeholders in infection prevention, antimicrobial stewardship, and evidence-based care. This review underscores the urgent need to equip hematology nurses with the skills and tools necessary to adapt to the rapidly evolving diagnostic landscape in order to support safe, timely, and personalized healthcare delivery.}, }
@article {pmid40932289, year = {2025}, author = {Zhao, Y and Du, L and Song, J and Sun, W and Chen, Y and Yu, X and Huang, H and Huang, G and Huang, E and Wang, N and An, S and Ai, L and Chen, P}, title = {Hierarchical integration of mNGS, PCR, and other conventional methods for precision TB diagnostics.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0193125}, doi = {10.1128/spectrum.01931-25}, pmid = {40932289}, issn = {2165-0497}, abstract = {UNLABELLED: This study systematically compared the diagnostic accuracy of seven assays for detecting the Mycobacterium tuberculosis complex, including metagenomic next-generation sequencing (mNGS), droplet digital polymerase chain reaction, real-time quantitative polymerase chain reaction, EasyNAT MTC, GeneXpert MTB/RIF, interferon-gamma release assay (IGRA), and acid‒fast staining (AFS). We try to select appropriate combinations of tuberculosis (TB) detection methods for regions with varying levels of medical resources, based on sensitivity, cost-effectiveness, and operational feasibility. A retrospective analysis was conducted on 141 samples collected from patients with suspected active TB at The First Affiliated Hospital of Sun Yat-sen University between April 2022 and April 2024. Among these samples, there were 100 cases assigned to the case group and 41 cases to the control group, based on the tuberculosis diagnostic criteria. Historical data for Xpert, IGRA, and AFS were collected, and parallel experiments using mNGS, droplet digital PCR (ddPCR), real-time quantitative polymerase chain reaction (RT-qPCR), and EasyNAT were conducted on all samples. Diagnostic performance was evaluated by comparing it with the final clinical diagnoses. Sensitivity, specificity, positive predictive value, negative predictive value, and receiver operating characteristic (ROC) curve analysis were conducted, along with DeLong tests for statistical comparison. Compared with the final clinical diagnosis, mNGS demonstrated the highest sensitivity (100%), followed by IGRA (79.2%), EasyNAT (79.1%), RT-qPCR (78.0%), ddPCR (75.8%), Xpert (75.3%), and AFS (16.7%). The specificity was 100% for both Xpert and AFS, followed by ddPCR (97.6%), RT-qPCR (95.1%), EasyNAT (92.7%), IGRA (72.7%), and mNGS (75.6%). ROC analysis revealed a significantly greater area under the ROC curve for mNGS (0.878) than for ddPCR (0.817, P = 0.031). DeLong tests revealed statistically significant differences in diagnostic performance between mNGS and ddPCR (P < 0.05) and between IGRA and AFS (P < 0.01). mNGS uniquely identified the pathogens involved in co-infection and quantified pathogen-specific sequencing reads. Through a comprehensive evaluation of the diagnostic efficacy, cost-effectiveness, and timeliness of tuberculosis detection methods, we propose corresponding combinations of TB testing approaches for regions with different healthcare resources. For undeveloped regions with limited resources, a combination of AFS +EasyNAT + chest X-ray is recommended. Primary care facilities may additionally employ IGRA + RT-qPCR. Intermediate-level hospitals can incorporate Xpert MTB/RIF for drug resistance testing, while tertiary hospitals or specialized centers should, on the basis of these fundamental tests, utilize mNGS for diagnosis and ddPCR for therapeutic monitoring in patients with complex mixed infections.<br><br>IMPORTANCE: This study is the first to comprehensively evaluate the diagnostic efficacy, cost-effectiveness, and timeliness of seven TB detection methods in a single-center cohort. Our findings provide actionable solutions for optimizing TB diagnostics in diverse healthcare ecosystems, aligning with the WHO's End TB Strategy to ensure equitable access to rapid diagnostics.}, }
@article {pmid40931802, year = {2025}, author = {Gernert, JA and Klein, M and Schöberl, F and Müller, KJ and Schmidbauer, ML and Forbrig, R and Roeber, S and Herms, J and Terpolilli, N and Milakovic Obradovic, M and Graf, A and Dächert, C and Keppler, OT and Münchhoff, M and Dimitriadis, K}, title = {Severe course of tick-borne encephalitis (TBE) in a patient with relapsing multiple sclerosis (MS) treated with ocrelizumab.}, journal = {Multiple sclerosis (Houndmills, Basingstoke, England)}, volume = {}, number = {}, pages = {13524585251369425}, doi = {10.1177/13524585251369425}, pmid = {40931802}, issn = {1477-0970}, abstract = {Description of a patient with multiple sclerosis (MS) who underwent immunotherapy with ocrelizumab and suffered a severe course of tick-borne encephalitis (TBE): A 33-year-old man presented with acute cerebellitis with tonsillar herniation. The initial suspected diagnosis of TBE was confirmed after a significant diagnostic delay, likely caused by negative serological testing due to B-cell depletion from ocrelizumab treatment for underlying MS. TBE diagnosis was made using polymerase chain reaction (PCR) and oligo-hybrid capture metagenomic next-generation sequencing (mNGS) of cerebral spinal fluid and brain biopsy samples which yielded a near-full length TBE Virus (TBEV) genome.}, }
@article {pmid40931531, year = {2025}, author = {Gasparini, J}, title = {Targeted 'infectiosome' for disease ecology: A new tool to answer old questions.}, journal = {The Journal of animal ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1365-2656.70130}, pmid = {40931531}, issn = {1365-2656}, abstract = {Research Highlight: Bralet, T., Aaziz, R., Tornos, J., Gamble, A., Clessin, A., Lejeune, M., Galon, C., Michelet, L., Lesage, C., Jeanniard du Dot, T., Desoubeaux, G., Guyard, M., Delannoy, S., Moutailler, S., Laroucau, K. and Boulinier, T. (2025). High-throughput microfluidic real-time PCR as a promising tool in disease ecology. Journal of Animal Ecology, https://doi.org/10.1111/1365-2656.70088. Disease ecology aims to understand the causes and consequences of the maintenance and transmission of pathogenic infectious agents. A crucial step in studying disease ecology is identifying the 'infectiosome', which I define as all infectious agents circulating among individuals, populations and the community of a given ecosystem. In a recent study, Bralet et al. (2025) propose a new, cheap and adaptable toolkit for determining a targeted 'infectiosome', which appears very useful in disease ecology approaches: high-throughput microfluidic real-time PCR (Htrt PCR). This method is a good alternative to costly metagenomic approaches and consists of running several dozen PCRs from a single tissue sample. This technique enables screening, from a single sample, the presence of dozens of targeted infectious agents: the targeted 'infectiosome', allowing one to answer several questions. For example, Bralet et al. (2025) applied this method to 274 seabirds and 80 mammals samples collected from the Southern Ocean islands and detected pathogenic infectious agents in new locations. The results also show that some species are potential 'reservoirs' of several infectious agents in this ecosystem. This method is really promising and can be easily adapted and used to test different hypotheses in disease ecology at the scales of the population and the community in other ecosystems, such as the urban ecosystem.}, }
@article {pmid40931350, year = {2025}, author = {Ye, G and Hong, H and Li, T and Li, J and Wu, JQ and Jiang, S and Meng, ZT and Yuan, HT and Xue, W and Li, AL and Zhou, T and Li, TT and Li, T}, title = {MAGdb: a comprehensive high quality MAGs repository for exploring microbial metagenome-assemble genomes.}, journal = {Genome biology}, volume = {26}, number = {1}, pages = {276}, pmid = {40931350}, issn = {1474-760X}, support = {No. 32100421//China National Natural Science Foundation/ ; No. 82341098//China National Natural Science Foundation/ ; No. 82130052//China National Natural Science Foundation/ ; No. NSS2021CI05002//Nanhu Laboratory/ ; No. 2024ZYYDSA400333//The Central Government Guides Local Science and Technology Development Fund Projects/ ; }, mesh = {*Metagenome ; *Metagenomics/methods ; *Databases, Genetic ; *Microbiota ; }, abstract = {Metagenomic analyses of microbial communities have unveiled a substantial level of interspecies and intraspecies genetic diversity by reconstructing metagenome-assembled genomes (MAGs). The MAG database (MAGdb) boasts an impressive collection of 74 representative research papers, spanning clinical, environmental, and animal categories and comprising 13,702 paired-end run accessions of metagenomic sequencing and 99,672 high quality MAGs with manually curated metadata. MAGdb provides a user-friendly interface that users can browse, search, and download MAGs and their corresponding metadata information. It represents a valuable resource for researchers in discovering potential novel microbial lineages and understanding their ecological roles. MAGdb is publicly available at https://magdb.nanhulab.ac.cn/ .}, }
@article {pmid40931024, year = {2025}, author = {Tan, MH and Bangre, O and Rios-Teran, CA and Tiedje, KE and Deed, SL and Zhan, Q and Rasyidi, F and Pascual, M and Ansah, PO and Day, KP}, title = {Metagenomic complexity of high, seasonal transmission of Plasmodium spp. in asymptomatic carriers in Northern Sahelian Ghana.}, journal = {Communications medicine}, volume = {5}, number = {1}, pages = {386}, pmid = {40931024}, issn = {2730-664X}, support = {R01-AI149779//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R01-AI149779//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; }, abstract = {BACKGROUND: Mixed-species, mixed-strain plasmodia infections are known to occur in humans in malaria endemic areas. It may be surprising that to date, the extent of this complexity has not been systematically explored in high-burden countries of sub-Saharan Africa, especially in the reservoir of asymptomatic infections in all ages, which sustains transmission.<br><br>METHODS: Here we take a metagenomic lens to these infections by sampling variable blood volumes from 188 afebrile residents living in high, seasonal transmission in Northern Sahelian Ghana. We estimated multiplicity of infection for different Plasmodium spp. through genotyping of antigens and microsatellites. We further defined 'metagenomic complexity' as a measure of overall within-host complexity across the combination of species and strains.<br><br>RESULTS: We show that prevalence of Plasmodium spp. and inter-/intra-species complexity is significantly higher in larger blood volumes from these individuals. Overall, malaria infections display high levels of metagenomic complexity comprising single-, double-, and triple-species infections with varying levels of intra-species complexity for P. falciparum, P. malariae, P. ovale curtisi, and P. ovale wallikeri. We also report a subset of individuals with highly-complex infections that cannot be explained by age or location. The implications of these findings to malaria epidemiology and control are illustrated by a geographic scaling exercise to district and region levels in northern Ghana.<br><br>CONCLUSIONS: Our metagenomic investigation underscores the need to more sensitively measure within-host Plasmodium spp. complexity in asymptomatic carriers of infection. This will optimise strategies for malaria surveillance and control.}, }
@article {pmid40930091, year = {2025}, author = {Minich, JJ and Allsing, N and Din, MO and Tisza, MJ and Maleta, K and McDonald, D and Hartwick, N and Mamerto, A and Brennan, C and Hansen, L and Shaffer, J and Murray, ER and Duong, T and Knight, R and Stephenson, K and Manary, MJ and Michael, TP}, title = {Culture-independent meta-pangenomics enabled by long-read metagenomics reveals associations with pediatric undernutrition.}, journal = {Cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cell.2025.08.020}, pmid = {40930091}, issn = {1097-4172}, abstract = {The human gut microbiome is linked to child malnutrition, yet traditional microbiome approaches lack resolution. We hypothesized that complete metagenome-assembled genomes (cMAGs), recovered through long-read (LR) DNA sequencing, would enable pangenome and microbial genome-wide association study (GWAS) analyses to identify microbial genetic associations with child linear growth. LR methods produced 44-64× more cMAGs per gigabase pair (Gbp) than short-read methods, with PacBio (PB) yielding the most accurate and cost-effective assemblies. In a Malawian longitudinal pediatric cohort, we generated 986 cMAGs (839 circular) from 47 samples and applied this database to an expanded set of 210 samples. Machine learning identified species predictive of linear growth. Pangenome analyses revealed microbial genetic associations with linear growth, while genome instability correlated with declining length-for-age Z score (LAZ). This resource demonstrates the power of comparing cMAGs with health trajectories and establishes a new standard for microbiome association studies.}, }
@article {pmid40929977, year = {2025}, author = {Han, F and Guo, Y and Zhao, C and Zhang, W and Zhang, M and Zhou, W}, title = {Halophilic heterotrophic ammonia assimilation biosystem shows stronger resilience and decreased ARGs abundance under sulfamethoxazole gradient stress compared with halophilic nitrification biosystem.}, journal = {Journal of hazardous materials}, volume = {498}, number = {}, pages = {139749}, doi = {10.1016/j.jhazmat.2025.139749}, pmid = {40929977}, issn = {1873-3336}, abstract = {Differences of niche and nitrogen metabolism between halophilic nitrification (AN) and heterotrophic ammonia assimilation (HAA) biosystems determine microbiome resilience and antibiotic resistance genes (ARGs) transfer under antibiotic stress. However, the underlying mechanism of this difference remains unclear. This study compared the bioresponses and ARGs characteristics of the two biosystems under sulfamethoxazole (SMX) stress. Results revealed that both biosystems maintained above 90 % NH4[+] -N and 95 % SMX removal efficiencies at SMX concentrations below 1 mg/L. However, exposure to 5 mg/L SMX impaired both NH4[+]-N and SMX removal efficiencies. HAA biosystem exhibited stronger robustness and resilience than the AN biosystem under SMX stress. The microbial products synthesis, extracellular protein structure, and extracellular electron transfer in both biosystems displayed distinct responses to SMX. Metagenomic results revealed SMX shock decreased the abundance of ammonia-oxidizing bacteria and ammonia-monooxygenase gene in the AN biosystem, while the rapid turnover of heterotrophic microorganisms and the flexibility of ammonia assimilation genes maintained the HAA function in the HAA biosystem. Furthermore, SMX stress induced ARGs enrichment in the AN biosystem, whereas the abundance and diversity of ARGs in the HAA biosystem decreased under SMX stress. These findings highlighted the potential of novel HAA biosystem for antibiotics degradation and ARGs control.}, }
@article {pmid40929972, year = {2025}, author = {Liu, K and Wang, X and Li, F and Tao, J and Weng, CH and Hu, Q and Kang, D and Luo, Z and Tang, Z and Liu, N and Qiu, J}, title = {Metagenomic characterization of antibiotic resistance genes and human bacterial pathogens in groundwater from agricultural, landfill, and hazardous waste disposal sites (HWDS) sources: Drivers, risks, and source tracking.}, journal = {Journal of hazardous materials}, volume = {498}, number = {}, pages = {139803}, doi = {10.1016/j.jhazmat.2025.139803}, pmid = {40929972}, issn = {1873-3336}, abstract = {Agricultural sources, landfills, and hazardous waste disposal sites (HWDS) are major hotspots for the spread of groundwater antibiotic resistance genes (ARGs) and human bacterial pathogens (HBPs). However, there is a lack of systematic understanding regarding the environmental behavior of groundwater ARGs, the pathogenic risks of HBPs, and the relative contribution mechanisms of different sources, presenting critical scientific challenges for developing targeted groundwater pollution control strategies. To address this, this study collected 26 groundwater metagenomic samples to characterize the composition, influencing factors, and health risks of ARGs and HBPs near key ARG reservoirs, and constructed a source-tracking indicator system. The research identified 16 clinically critical high-risk ARGs (e.g., tetM, sul1) and 14 priority HBPs (e.g., Escherichia coli, Klebsiella pneumoniae) associated with severe human diseases and high transmissibility. Screening ARG source-specific indicators demonstrated high accuracy in predicting contributions from artificially mixed sources (prediction errors < 4 %). Validation with real groundwater samples showed that landfills contributed more significantly to groundwater ARGs pollution than other sources. This study deepens our understanding of antibiotic resistance risks in groundwater near key ARG reservoirs and provides a robust framework for tracing ARGs in complex groundwater environments by integrating microbe-gene-environment interactions across multiple pollution sources.}, }
@article {pmid40929881, year = {2025}, author = {Liu, Y and Li, K and Xu, J and Shen, W and Li, Y and Ma, J and Wang, T and Liu, J and Li, T and Zhang, X and Tian, W and Tian, J and Wang, H and Zhang, X}, title = {Alpha-linolenic acid ameliorates T2DM via reshaping gut-liver axis and inflammatory GPR120-NF-κB/NLRP3 pathway in mouse and rat models.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {147}, number = {}, pages = {157214}, doi = {10.1016/j.phymed.2025.157214}, pmid = {40929881}, issn = {1618-095X}, abstract = {BACKGROUND: The gut-liver axis, pivotal in managing glucose balance and insulin responsiveness, is central to the development of type 2 diabetes mellitus (T2DM). Research has highlighted the regulatory effects of dietary alpha-linolenic acid (ALA), but it remains unclear how ALA modulates gut microbiota and liver inflammation in T2DM.<br><br>PURPOSE: This study aimed to systematically investigate ALA's influence on liver inflammation, intestinal barrier integrity, gut microbial composition, and metabolic homeostasis in T2DM, with a focus on the underlying molecular mechanisms.<br><br>STUDY DESIGN: A dual-model approach was employed using both db/db mouse model and the SCZ/NA-induced T2DM rat model to ensure robust species and model validation.<br><br>METHODS: Animals received oral ALA supplementation, followed by assessments of glucose tolerance, insulin sensitivity, hepatic histology, and inflammatory markers. Intestinal barrier function, permeability, and systemic LPS levels were evaluated. Mechanistic analysis focused on the GPR120-NF-&#x3ba;B/NLRP3 signaling pathway. Multi-omics profiling including fecal metagenomics, SCFA quantification, and plasma metabolomics were conducted to assess gut microbiota and host metabolic responses.<br><br>RESULTS: Our results revealed that ALA therapy significantly mitigated insulin resistance and glucose intolerance in db/db mice. Histopathological analysis revealed a decrease in hepatic steatosis following ALA administration, alongside a reduction in inflammatory markers indicative of T2DM. Importantly, our findings demonstrated that ALA mitigates liver inflammation by inhibiting the NF-&#x3ba;B/NLRP3 pathway, possibly via its interaction with GPR120. Beyond this, augmenting ALA bolstered intestinal integrity, minimized permeability, curbed lipopolysaccharide leakage, and suppressed pro-inflammatory cytokine expression within the intestines. Significantly, an integrated multi-omics investigation, encompassing fecal metagenomic sequencing, SCFA evaluation, and plasma non-targeted metabolomics, disclosed a potent correlation between ALA's hypoglycemic efficacy and the modulation of gut microbial community structure, elevation of SCFA synthesis, and enhancement of metabolic signatures.<br><br>CONCLUSION: Our study's initial insights indicated that dietary ALA modulates inflammation and metabolism in T2DM via the gut-liver axis, specifically through the GPR120-NF-&#x3ba;B/NLRP3 pathway. This elucidates ALA's dual function in reshaping the gut microbiota and combating systemic inflammation, positioning it as a potentially efficacious dietary component for managing T2DM.}, }
@article {pmid40929831, year = {2025}, author = {Liu, F and Yang, B and Han, T and Li, F and Wang, L and Xu, H}, title = {Metagenomic and Micro-CT insights into Fe(III)-modulated extracellular polymeric substances driving anammox granulation and enhancement of nitrogen removal.}, journal = {Journal of environmental management}, volume = {393}, number = {}, pages = {127283}, doi = {10.1016/j.jenvman.2025.127283}, pmid = {40929831}, issn = {1095-8630}, abstract = {Multivalent cations are commonly employed to accelerate sludge aggregation and granulation, yet they often compromise intragranular mass transfer and diminish microbial activity. Here, the effect of Fe(III) dosing on granule formation and anammox-driven nitrogen removal over a 110-day continuous operation was investigated. Fe(III) supplementation enhanced interactions with extracellular polymeric substances (EPS), transforming flocculent biomass into highly porous granules and yielding a 67.9 % increase in specific anammox activity (SAA). During the first 30 days of Fe(III) dosing, the Zeta potential shifted from -12.0 to -9.3 mV and EPS content surged from 32.8 mg/g VSS to 49.0 mg/g VSS, accelerating primary floc aggregation. Subsequently, the protein-to-polysaccharide ratio of EPS escalated from 1.7 to 5.3, reflecting a transition from a carbohydrate-rich, hydrophilic gel to a protein-dominated, hydrophobic network that facilitated granulation. Micro-computed tomography revealed that smaller (1.5 mm) granules exhibited dense architectures, whereas larger (2.5 mm) granules developed internal cavities as a result of mass transfer limitations, approaching structural fragmentation. Metagenomic analysis showed that Fe(III) upregulated pathways for hydrophobic amino acids (e.g., isoleucine, leucine, valine) synthesis and downregulated polysaccharide biosynthesis, thereby increasing EPS hydrophobicity and promoting granulation. The observed SAA enhancement was linked to Fe(III)-dependent activation of iron-containing enzymes (e.g., hzs ABC), cytochrome c maturation, and Fe-S cluster assembly. Concurrently, the relative abundance of Ca. Kuenenia rose from 14.1 % during aggregation to 18.6 % after sludge granulation. This work elucidates the mechanism of Fe(III)-EPS-mediated granulation and offers a sustainable strategy to reconcile structural integrity with metabolic efficiency in metal-driven anammox wastewater treatment processes.}, }
@article {pmid40929513, year = {2025}, author = {Bhaya, D and Birzu, G and Rocha, EPC}, title = {Horizontal Gene Transfer and Recombination in Cyanobacteriota.}, journal = {Annual review of microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1146/annurev-micro-041522-100420}, pmid = {40929513}, issn = {1545-3251}, abstract = {Cyanobacteria played a pivotal role in shaping Earth's early history and today are key players in many ecosystems. As versatile and ubiquitous phototrophs, they are used as models for oxygenic photosynthesis, nitrogen fixation, circadian rhythms, symbiosis, and adaptations to harsh environments. Cyanobacterial genomes and metagenomes exhibit high levels of genomic diversity partly driven by gene flow within and across species. Processes such as recombination and horizontal transfer of novel genes are facilitated by the mobilome that includes plasmids, transposable elements, and bacteriophages. We review these processes in the context of molecular mechanisms of gene transfer, barriers to gene flow, selection for novel traits, and auxiliary metabolic genes. Additionally, Cyanobacteriota are unique because ancient evolutionary innovations, such as oxygenic photosynthesis, can be corroborated with fossil and biogeochemical records. At the same time, sequencing of extant natural populations allows the tracking of recombination events and gene flow over much shorter timescales. Here, we review the challenges of assessing the impact of gene flow across the whole range of evolutionary timescales. Understanding the tempo and constraints to gene flow in Cyanobacteriota can help decipher the timing of key functional innovations, analyze adaptation to local environments, and design Cyanobacteriota for robust use in biotechnology.}, }
@article {pmid40929468, year = {2025}, author = {Xiang, Y and Man, X and Zhang, H and Chen, M and Yang, R}, title = {Nitrogen removal efficiency and pathways of the simultaneous nitrification and denitrification process under ultra-low oxygen conditions.}, journal = {Environmental technology}, volume = {}, number = {}, pages = {1-12}, doi = {10.1080/09593330.2025.2556497}, pmid = {40929468}, issn = {1479-487X}, abstract = {To explore strategies for further reducing aeration energy consumption in the simultaneous nitrification and denitrification (SND) process, an SND reactor was constructed to treat low carbon-to-nitrogen (C/N) ratio domestic wastewater under ultra-low dissolved oxygen (DO) conditions (DO < 0.05 mg·L[-][1]). The effects of hydraulic retention time (HRT) and C/N ratio on nitrogen removal performance were systematically evaluated, and batch experiments were conducted to determine nitrification and denitrification rates. Under influent condition of 50.0 mg·L[-][1] ammonia and a C/N ratio of 2.2, the reactor maintained stable ultra-low DO levels, achieved effluent ammonia concentrations below 5.0 mg·L[-][1], and attained optimal SND efficiencies exceeding 80.0%. Although a shortened HRT destabilised performance, increasing the C/N ratio successfully restored nitrogen removal stability. Nitrification and denitrification rates ranged from 4.20-30.89 mg·L[-][1]·h[-][1] and 1.57-21.92 mg·L[-][1]·h[-][1], respectively, under C/N ratios from 2.2-8.0. High-throughput sequencing and metagenomic analysis revealed that heterotrophic nitrification and aerobic denitrification dominated nitrogen transformation, with microorganisms utilising low-energy nap and nirK enzymes to adapt to the ultra-low DO environment. These findings provide novel insights into energy-efficient nitrogen removal pathways under ultra-low oxygen conditions.}, }
@article {pmid40929372, year = {2025}, author = {Huereca, A and Allen, CCG and McMullin, RT and Simon, A and Belosokhov, A and Spribille, T}, title = {Evidence for extensive diversity in the pollen-parasitic genus Retiarius in western North America, including two new species associated with lichens.}, journal = {Mycologia}, volume = {}, number = {}, pages = {1-27}, doi = {10.1080/00275514.2025.2513197}, pmid = {40929372}, issn = {1557-2536}, abstract = {Understanding the diversity of microscopic hyphomycetes is an ongoing effort, and many species remain undescribed. While studying lichen organismal composition in western Canada, metagenomic data revealed the presence of an unknown species of Retiarius (Orbiliaceae, Ascomycota), a genus of pollen-parasitic fungus with no previous records in the region. We developed genus-specific primers to amplify Retiarius DNA in lichen and adjacent substrate extractions, successfully detecting multiple lineages of Retiarius across a wide geographic range within North America. We proceeded to screen accumulations of pollen on the undersurface of lichen thalli to isolate any pollen-associated fungi. Using dilution series and PCR for identification, we isolated two specifically distinct strains of Retiarius with morphology unlike any described member of the genus. Inclusion of DNA from these strains in a multilocus phylogeny using the internal transcribed spacer regions ITS1-5.8S-ITS2 (ITS), partial nuc 28S rDNA (28S), and nuc small subunit (18S) confirmed their evolutionarily distinct position in the genus. We describe these two species here as Retiarius canadensis and R. crescentus. The former possesses trinacrium-shaped conidia, similar to those of R. bovicornutus and R. revayae but morphometrically different, and the latter is distinguished by its canoe-shaped conidia, a morphological character heretofore unknown from Retiarius.}, }
@article {pmid40929115, year = {2025}, author = {Gonzalez, FL and Kettenburg, G and Ranaivoson, HC and Andrianiaina, A and Andry, S and Raharinosy, V and Randriambolamanantsoa, TH and Lacoste, V and Dussart, P and Héraud, JM and Brook, CE}, title = {Genomic characterization of novel bat kobuviruses in Madagascar: Implications for viral evolution and zoonotic risk.}, journal = {PloS one}, volume = {20}, number = {9}, pages = {e0331736}, doi = {10.1371/journal.pone.0331736}, pmid = {40929115}, issn = {1932-6203}, mesh = {*Chiroptera/virology ; Animals ; Madagascar ; Phylogeny ; *Zoonoses/virology ; *Genome, Viral ; *Evolution, Molecular ; *Viral Zoonoses/virology ; Humans ; Genomics ; High-Throughput Nucleotide Sequencing ; *Picornaviridae Infections/virology/veterinary/epidemiology ; }, abstract = {Kobuviruses (family Picornaviridae, genus Kobuvirus) are enteric viruses that infect a wide range of both human and animal hosts. Much of the evolutionary history of kobuviruses remains elusive, largely due to limited screening in wildlife. Bats have been implicated as major sources of virulent zoonoses, including coronaviruses, henipaviruses, lyssaviruses, and filoviruses, though much of the bat virome still remains uncharacterized. While most bat virus research has historically focused on immediately recognizable zoonotic clades (e.g., SARS-related coronaviruses), a handful of prior reports catalog kobuvirus carriage in bats and posit the role of bats as progenitors of downstream kobuvirus evolution. As part of a multi-year study, we carried out metagenomic Next Generation Sequencing (mNGS) on fecal samples obtained from endemic, wild-caught Madagascar fruit bats to characterize potentially zoonotic viruses circulating within these populations. The wild bats of Madagascar represent diverse Asian and African phylogeographic histories, presenting a unique opportunity for viruses from disparate origins to mix, posing a significant public health threat. Here, we report detection of kobuvirus RNA in Malagasy fruit bats (Eidolon dupreanum) and undertake phylogenetic characterization of Malagasy kobuvirus sequences, which nest within the Aichivirus A clade - a kobuvirus clade known to infect a wide range of hosts including humans, rodents, canids, felids, birds, and bats. Given the propensity of kobuviruses for recombination and cross-species transmission, further characterization of this clade is critical for accurate evaluation of future zoonotic threats.}, }
@article {pmid40928986, year = {2025}, author = {Miao, Q and Qu, L and Jiang, J and Liu, Q and Zhao, W and Tan, L and Li, J and Cao, W and Wang, B and Xia, X}, title = {Identification and Molecular Characterization of Two Novel Picorna-Like Viruses in Armigeres subalbatus Mosquitoes in Yunnan, China.}, journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)}, volume = {}, number = {}, pages = {}, doi = {10.1177/15303667251372308}, pmid = {40928986}, issn = {1557-7759}, abstract = {Background: Mosquitoes harbor diverse insect-specific viruses (ISVs) frequently overlooked in arbovirus surveillance. Comprehensive characterization of ISVs is crucial for understanding their impact on host ecology and potential roles in arbovirus transmission. Methods: Using metagenomic sequencing on Armigeres subalbatus from Yunnan, China, we identified two novel picorna-like viruses, assembled their genomes, and conducted phylogenetic analysis. Detection was confirmed via RT-PCR and Sanger sequencing. Results: Both viruses are closely related to Hubei picorna-like virus 59, previously reported in spiders but unconfirmed. This work provides the first genomic evidence of this lineage in mosquitoes. Conclusion: This study characterizes two novel ISVs, expanding known picorna-like virus diversity and offering insights into cross-species virus evolution and arbovirus ecology.}, }
@article {pmid40928296, year = {2025}, author = {Martinez, A and Ruth, N and Hatch, A and Chain, P and Shakya, M}, title = {Aerosol biome of a cafeteria and medical facility in Los Alamos, New Mexico, USA.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0076625}, doi = {10.1128/mra.00766-25}, pmid = {40928296}, issn = {2576-098X}, abstract = {Aerosol sampling with next-generation sequencing was used to characterize microbial communities in a cafeteria and medical facility waiting room in Los Alamos, New Mexico, USA. We detected sequences from human, bacteria, archaea, fungi, other eukaryotes, and viruses, providing insights into the diversity of the aerosol microbiome.}, }
@article {pmid40928292, year = {2025}, author = {Fujii, C and Vernon, S and Félix, M-A and Wang, D}, title = {Orsay virus variants isolated from wild Caenorhabditis elegans nematodes, France.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0055025}, doi = {10.1128/mra.00550-25}, pmid = {40928292}, issn = {2576-098X}, abstract = {Four new variants of Orsay virus were identified from wild isolates of Caenorhabditis elegans nematodes collected from decaying plant matter in France. Near-complete genomes of the viruses were determined by metagenomic sequencing. The four genomes share 96.1-98.9% nucleotide identity with the reference Orsay virus sequence JUv1580.}, }
@article {pmid40928236, year = {2025}, author = {Liu, D and Hu, J and Zhang, D and Ren, S and Zhao, L and Gao, H and Hu, S and Xu, S and Liang, G}, title = {Use of the CHM13-T2T genome improves metagenomic analysis by minimizing host DNA contamination.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0084025}, doi = {10.1128/msystems.00840-25}, pmid = {40928236}, issn = {2379-5077}, abstract = {Human-associated metagenomic data often contain human nucleic acid information, which can affect the accuracy of microbial classification or raise ethical concerns. These reads are typically removed through alignment to the human genome using various metagenomic mapping tools or human reference genomes, followed by filtration before metagenomic analysis. In this study, we conducted a comprehensive analysis to identify the optimal combination of alignment software and human reference genomes using benchmarking data. Our findings show that the combination of bwa-mem and the telomere-to-telomere human genome (CHM13-T2T) is the most effective in removing human reads in simulated data. We also analyzed CHM13-T2T-derived sequences in RefSeq to understand how CHM13-T2T reduces false positive results. Finally, we assessed clinical samples and found that CHM13-T2T effectively reduces host-derived contamination, particularly in low microbial biomass samples. This study provides a thorough overview of the application of CHM13-T2T in metagenomic analysis and highlights its significance in improving microbial classification accuracy.IMPORTANCEHuman gene sequences account for a large proportion of metagenomic sequences. To gain accurate and precise microbiome information, effective host-derived contamination removal methods are required. Both the alignment algorithm and the reference genome could influence the effectiveness of this process. The telomere-to-telomere human genome (CHM13-T2T) is a state-of-the-art human genome with 216 Mbp of additional new sequences compared with the commonly used GRCh38.p14. Our findings show the optimal dehosting effect of CHM13-T2T combined with the bwa-mem software in metagenomic analysis. We also investigate the reasons for the superiority of CHM13-T2T. Our study provides insights into optimal strategies for host sequence removal from metagenomic data. A standard reference is proposed for future metagenomic analysis, which can improve the accuracy of microbial identification.}, }
@article {pmid40928232, year = {2025}, author = {Allman, HM and Bernate, EP and Franck, E and Oliaro, FJ and Hartmann, EM and Crofts, TS}, title = {Preparation of functional metagenomic libraries from low biomass samples using METa assembly and their application to capture antibiotic resistance genes.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0103925}, doi = {10.1128/msystems.01039-25}, pmid = {40928232}, issn = {2379-5077}, abstract = {A significant challenge in the field of microbiology is the functional annotation of novel genes from microbiomes. The increasing pace of sequencing technology development has made solving this challenge in a high-throughput manner even more important. Functional metagenomics offers a sequence-naive and cultivation-independent solution. Unfortunately, most methods for constructing functional metagenomic libraries require large input masses of metagenomic DNA, putting many sample types out of reach. Here, we show that our functional metagenomic library preparation method, METa assembly, can be used to prepare useful libraries from much lower input DNA quantities. Standard methods of functional metagenomic library preparation generally call for 5-60 µg of input metagenomic DNA. We demonstrate that the threshold for input DNA mass can be lowered at least to 30.5 ng, a 3-log decrease from prior art. We prepared functional metagenomic libraries using between 30.5 ng and 100 ng of metagenomic DNA and found that despite their limited input mass, they were sufficient to link MFS transporters lacking substrate-specific annotations to tetracycline resistance and capture a gene encoding a novel GNAT family acetyltransferase that represents a new streptothricin acetyltransferase, satB. Our preparation of functional metagenomic libraries from aquatic samples and a human stool swab demonstrates that METa assembly can be used to prepare functional metagenomic libraries from microbiomes that were previously incompatible with this approach.IMPORTANCEBacterial genes in microbial communities, including those that give resistance to antibiotics, are often so novel that sequencing-based approaches cannot predict their functions. Functional metagenomic libraries offer a high-throughput, sequence-naive solution to this problem, but their use is often held back due to their need for large quantities of metagenomic DNA. We demonstrate that our functional metagenomic library preparation method, METa assembly, can prepare these libraries using as little as ~30 ng of DNA, approximately 1,000-fold less than other methods. We use METa assembly to prepare functional metagenomic libraries from low-biomass aquatic and fecal swab microbiomes and show that they are home to novel tetracycline efflux pumps and a new family of streptothricin resistance gene, respectively. The efficiency of the METa assembly library preparation method makes many otherwise off-limits, low-biomass microbiome samples compatible with functional metagenomics.}, }
@article {pmid40928220, year = {2025}, author = {Dong, L and Yang, J and Wu, H and Sun, Y and Liu, J and Yuan, H and Wang, M and Dai, Y and Teng, F and Jing, G and Yang, F}, title = {Metagenomic research on the structural difference of plaque microbiome from different caries stages and the construction of a caries diagnostic model.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0004425}, doi = {10.1128/msystems.00044-25}, pmid = {40928220}, issn = {2379-5077}, abstract = {Development of dental caries is a dynamic process; yet, there is limited knowledge on microbial differences at various stages of caries at higher resolution. To investigate the shifting microbiome profiles across different caries stages, 30 children were enrolled in this study, including 15 caries-active patients and 15 caries-free individuals. Plaque samples were collected from the buccal surface of caries-free subjects, defined as confident health (CH; n = 15). For caries-active individuals, plaque samples were collected from non-cavitated surfaces (defined as relative health [RH], n = 15), enamel caries (EC; n = 15), and dentin caries samples (DC; n = 15). All the above samples were sequenced through the 2bRAD sequencing platform to reveal the microbial community structures in each group. We identified significant differences in microbial community structures from different caries stages. First, the CH group showed the highest species richness (P < 0.05), and then followed by the RH and EC groups with lower richness, and the lowest richness was found in the DC group, yet no significant difference was found among the last three groups (P > 0.05). Second, the microbial structure exhibited the greatest difference between CH and DC groups, followed by the distance between RH/EC and DC groups, and the smallest difference was found between RH and EC groups. Third, specific species were found with a significant difference during the different caries stages. Therefore, we developed a diagnostic model using deep learning methods based on neural networks to diagnose different caries stages with an AUC of over 98%. This may provide methodological support for the understanding of the etiological factor in the pathological progression of dental caries.IMPORTANCEThe diagnosis and treatment of dental caries are crucial for human oral health. Previous studies have focused on the microbial differences between caries and healthy teeth, but there was not enough knowledge on the microbial differences at different stages of dental caries. Our findings could provide a high-resolution understanding of the microbial divergencies among different stages of dental caries and thus build microbial-based diagnostic models for differentiating dental caries status using deep learning methods with an accuracy of over 98%. This may provide methodological support for the understanding of the etiological factor in the pathological progression of dental caries.}, }
@article {pmid40928217, year = {2025}, author = {Russell, JN and Kos, D and Yacoub, E and Sies, AN and Warr, B and Jelinski, M and Ruzzini, A and Cameron, ADS}, title = {Enhanced metagenomic surveillance for bovine respiratory disease pathogens and antimicrobial resistance by hybridization capture sequencing.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0097725}, doi = {10.1128/aem.00977-25}, pmid = {40928217}, issn = {1098-5336}, abstract = {UNLABELLED: Bovine respiratory disease (BRD) is the primary disease of cattle and is responsible for most of the antibiotic use in the beef industry, both for metaphylaxis and treatment. Infection prevention and targeted treatments would benefit from detecting and identifying bacterial pathogens and, ideally, assessing antibiotic sensitivity. Here, we report success refining targeted metagenomics by hybridization capture sequencing (CapSeq) to detect and genotype bacterial pathogens and genes for antibiotic resistance in BRD. We developed a novel multi-locus sequence typing (MLST) strategy to both enhance assay sensitivity and provide epidemiological data compatible with traditional typing assays. Phylogenetically informed panel design by ProbeTools coupled with hybridization capture enabled the sequencing of novel genotypes and elucidated coinfection by distinct strains of Mycoplasmopsis bovis. CapSeq was orders of magnitude more sensitive than classical metagenomics at a scale compatible with low-throughput DNA sequencing capacity in diagnostic laboratories. Iterative design and testing of longer typing loci confirmed improvements in locus detection through a strategy applicable to future target selection. CapSeq detected bacterial pathogens that evaded detection by traditional metagenomics, and it demonstrated greater range and sensitivity for antibiotic resistance gene detection.<br><br>IMPORTANCE: Shotgun metagenomic sequencing for infectious disease diagnostics and surveillance benefits from simultaneous detection of multiple pathogens in a sample. Adding a hybridization probe capture step to the metagenomics workflow enriches targeted loci to improve the sensitivity of pathogen detection without compromising the ability to detect pathogen variants. Our custom probe panel enables multi-locus sequence typing of bovine respiratory disease agents as well as capture of antibiotic resistance genes, which improves the sensitivity of metagenomic testing and provides genotyping data compatible with traditional assays. This study demonstrates the utility of new design principles for probe panels; it also demonstrates how targeted metagenomics provides important new insights into co-infections and is equally useful for surveillance of environmental reservoirs of disease agents.}, }
@article {pmid40928095, year = {2025}, author = {Darwiche, L and Goff, JL}, title = {Beyond tellurite: the multifunctional roles of genes annotated as tellurium resistance determinants in bacteria.}, journal = {Critical reviews in microbiology}, volume = {}, number = {}, pages = {1-21}, doi = {10.1080/1040841X.2025.2555936}, pmid = {40928095}, issn = {1549-7828}, abstract = {The metalloid tellurium (Te) is toxic to bacteria; however, the element is also extremely rare. Thus, most bacteria will never encounter Te in their environment. Nonetheless significant research has been performed on bacterial Te resistance because of the medical applications of the element. The so-called "tellurium resistance (Te[R]) genes" were first described on plasmids isolated from clinically relevant Enterobacteriaceae. With time, it has become apparent that, given the rarity of Te on the planet, these genes may have functions beyond tellurium resistance. Nonetheless, the description of these genes as "tellurium resistance genes" has persisted. In this review, we first examine the history and discovery of the Te[R] genes. We then performed an analysis of 184,000 high-quality, prokaryotic (meta)genomes, which revealed that terZABCDF, telA, and tehAB are relatively common in genome annotations and that they are frequently described as "tellurium resistance genes". We synthesized the literature to describe the functions of these ubiquitous genes beyond tellurium resistance. These genes have functions in diverse cellular processes including phage resistance, antibiotic resistance, virulence, oxidative stress resistance, cell cycle regulation, metal resistance, and metalation of exoenzymes. Considering this analysis, we propose that it is time to appreciate the multifunctional nature of the "tellurium resistance genes".}, }
@article {pmid40927879, year = {2025}, author = {Wang, X and Wang, J and Chen, J and Bezemer, TM and Song, Z and Wanek, W and Liu, G and Zhang, C}, title = {Environmental Stresses Constrain Soil Microbial Community Functions by Regulating Deterministic Assembly and Niche Width.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {e70096}, doi = {10.1111/mec.70096}, pmid = {40927879}, issn = {1365-294X}, support = {2023YFF1305103//National Key Research and Development Program of China/ ; 42130717//National Sciences Foundation of China/ ; 42177449//National Sciences Foundation of China/ ; 2024JC-JCQN-35//Shaanxi Provincial Science Fund for Distinguished Young Scholars/ ; }, abstract = {Increasing evidence indicates that the loss of soil microbial α-diversity triggered by environmental stress negatively impacts microbial functions; however, the effects of microbial α-diversity on community functions under environmental stress are poorly understood. Here, we investigated the changes in bacterial and fungal α- diversity along gradients of five natural stressors (temperature, precipitation, plant diversity, soil organic C and pH) across 45 grasslands in China and evaluated their connection with microbial functional traits. By quantifying the five environmental stresses into an integrated stress index, we found that the bacterial and fungal α-diversity declined under high environmental stress across three soil layers (0-20 cm, 20-40 cm and 40-60 cm). Metagenomic-based analyses showed that the diversity of functional genes decreased along the stress gradients. High stress enhanced the abundance of genes associated with broad functional categories (e.g., glycolysis/gluconeogenesis, TCA cycle, DNA replication/repair and cell growth/death) but reduced the abundance of genes linked to specialised functional categories (e.g., C, N, S and methane metabolism). Phylogenetic null models and niche analyses indicated that stochastic assembly processes predominated in high-diversity communities, in which bacterial and fungal taxa had a narrow ecological niche. However, in low-diversity communities, deterministic assembly processes were dominant, and taxa had wide niches, correlating with the reduction in gene abundance observed for broad and specialised functional categories. Given the essential role of the microbiome in regulating ecosystem functions, our findings suggest that low-diversity-induced deterministic community assembly processes and a wide niche under high environmental stress may regulate microbial functions. These findings emphasise the ecological mechanisms through which microbial biodiversity regulates terrestrial ecosystem functioning.}, }
@article {pmid40927726, year = {2025}, author = {Eiman, L and Moazzam, K and Anjum, S and Kausar, H and Sharif, EAM and Ibrahim, WN}, title = {Gut dysbiosis in cancer immunotherapy: microbiota-mediated resistance and emerging treatments.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1575452}, pmid = {40927726}, issn = {1664-3224}, mesh = {Humans ; *Dysbiosis/immunology/therapy ; *Gastrointestinal Microbiome/immunology ; *Neoplasms/therapy/immunology/microbiology ; *Immunotherapy/methods ; Animals ; *Drug Resistance, Neoplasm ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; Tumor Microenvironment/immunology ; }, abstract = {Cancer is a multifaceted disease driven by a complex interplay of genetic predisposition, environmental factors and lifestyle habits. With the accelerating pace of cancer research, the gut microbiome has emerged as a critical modulator of human health and immunity. Disruption in the gut microbial populations and diversity, known as dysbiosis, has been linked with the development of chronic inflammation, oncogenesis, angiogenesis and metastasis. This review discusses the microbial species associated with various types of cancer and the pathways involved in their tumorigenic effect including mechanisms like inflammatory cytokine response, immune modulation, genotoxicity and modification of the tumor microenvironment. Diagnostic tools such as metagenomics, metabolomics, and the use of dysbiosis indexes help in the detection of gut bacterial imbalances, enabling early detection of cancer and potential intervention. Gut dysbiosis diminishes the efficacy of cancer treatments including immunotherapies, and creates immunotherapy resistance by altering drug metabolism and driving immunometabolic reprogramming, allowing tumor cells to evade immune attack. Immunometabolic reprogramming through gut microbiota modulation provides a new avenue to be explored that can restore anti-tumor immunity and reverse resistance to cancer treatments. This review also highlights the use of fecal microbiota transplantation and probiotics to mitigate chances of dysbiosis-related cancer progression. Through a comprehensive assessment of the role of gut microbiota in cancer, this review underscores the need for the use of gut microbial biomarkers for cancer detection and microbiome-targeting strategies to individualize cancer treatment.}, }
@article {pmid40927460, year = {2025}, author = {Feng, Y and Chang, Q and Zhou, H and Zhang, W and Xie, L and Deng, X and Chen, T and Liu, W}, title = {Effects of gut microbiota on cognitive impairment in Parkinson's disease: a comprehensive Mendelian randomization and case-control study.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1620449}, pmid = {40927460}, issn = {1664-302X}, abstract = {BACKGROUND: Increasing evidence suggests a potential role of the gut microbiota in Parkinson's disease (PD). However, the relationship between the gut microbiome (GM) and PD dementia (PDD) remains debated, with their causal effects and underlying mechanisms not yet fully understood.<br><br>METHODS: Utilizing data from large-scale genome-wide association studies (GWASs), this study applied bidirectional and mediating Mendelian randomization (MR) to investigate the causal relationship and underlying mechanisms between the GM and PDD. In our analysis, inverse-variance weighting (IVW) was used as the primary method. Clinical validation was performed using metagenomic sequencing and bioinformatic analysis. The relationships between the GM and PDD were visualized using receiver operating characteristic (ROC) curves, confusion matrices, and correlation analyses.<br><br>RESULTS: Our study revealed a significant causal impact of five GM genera, 10 metabolites, two metabolite ratios, and 22 immune cells on PDD. Notably, the maltose to sucrose ratio was identified as a mediator of the positive causal effect of Subdoligranulum on PDD, with a mediation value of 13.2%. The clinical samples confirmed the efficacy of Subdoligranulum sp. in distinguishing patients with PDD from normal controls (area under the curve (AUC)&#x202f;=&#x202f;0.80, 95% CI: 0.674-0.924). In addition, correlation analysis revealed a potential negative association between Subdoligranulum abundance and the Mini-Mental State Examination (MMSE) scores (r&#x202f;=&#x202f;-0.316, p&#x202f;=&#x202f;0.006). Finally, bioinformatic analysis suggested that Subdoligranulum may influence PDD risk through the regulation of starch and sucrose metabolism pathways.<br><br>CONCLUSION: Our study confirms the potential role of Subdoligranulum in PDD progression, potentially mediated through starch and sucrose metabolism. These findings highlight the importance of the gut-brain axis in PDD and may provide insights into targeted interventions for PDD.}, }
@article {pmid40927458, year = {2025}, author = {Li, Y and Duan, Y and Zhang, J and Petropoulos, E and Zhao, J and Wu, F and Wang, L and Chen, Y and Wang, X}, title = {Structure and function of the topsoil microbiome in Chinese terrestrial ecosystems.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1595810}, pmid = {40927458}, issn = {1664-302X}, abstract = {While soil microorganisms underpin terrestrial ecosystem functioning, how their functional potential adapts across environmental gradients remains poorly understood, particularly for ubiquitous taxa. Employing a comprehensive metagenomic approach across China's six major terrestrial ecosystems (41 topsoil samples, 0-20 cm depth), we reveal a counterintuitive pattern: oligotrophic environments (deserts, karst) harbor microbiomes with significantly greater metabolic pathway diversity (KEGG) compared to resource-rich ecosystems. We provide a systematic catalog of key functional genes governing biogeochemical cycles in these soils, identifying: 6 core CAZyme genes essential for soil organic carbon (SOC) decomposition and biosynthesis; 62 nitrogen (N)-cycling genes (KOs) across seven critical enzymatic clusters; 15 sulfur (S)-cycling genes (KOs) within three key enzymatic clusters. These functional gene abundances exhibit distinct, geography-driven clustering patterns, strongly correlated with eight environmental drivers (latitude, NDVI, pH, EC, SOC, TN, C:N ratio, and MAP). This work provides a predictive framework and actionable genetic targets (e.g., specific CAZyme, N/S cycling genes) for potentially manipulating soil microbiomes to enhance ecosystem resilience and biogeochemical functions under stress.}, }
@article {pmid40926888, year = {2025}, author = {Chen, WY and Lan, YC and Chen, JW and Wu, JH}, title = {Genomic personalities of Dehalococcoides subspecies and Dehalogenimonas illuminate complete trichloroethene dechlorination in high-salt conditions.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf101}, pmid = {40926888}, issn = {2730-6151}, abstract = {Global salinization increasingly threatens ecosystem integrity and the regulation of biogeochemical cycles. Our study reveals novel insights into the microbial contributions to the organohalide decomposition in saline environments, demonstrating the unprecedented ability of organohalide-respiring bacteria Dehalococcoides and Dehalogenimonas to completely dechlorinate trichloroethene to non-toxic ethene under hypersaline conditions (up to 31.3 g/L) in long-term operations. Using gradient salinity reactors and metagenomic analyses, we identified the evolved genomic features associated with high-salt tolerance. The Cornell subgroup of Dehalococcoides and Dehalogenimonas exhibit significantly lower average protein isoelectric points and retain the ribosomal protein L33p gene, unlike the Victoria and Pinellas subgroups. Dehalococcoides shows subspecies-level genomic divergence and unique codon usage biases. Intriguingly, the L33p gene is found in diverse bacterial phyla from saline environments, suggesting it may provide a growth advantage under salt stress. These genomic traits, hypothesized to enhance salt tolerance and dechlorination efficiency under salt stress, correlate with performance at elevated salinity. Our findings advance the understanding of microbial salt adaptation mechanisms and support the development of bioremediation strategies tailored for saline environments.}, }
@article {pmid40926875, year = {2025}, author = {Zhao, J and Ye, J}, title = {Diagnostic Challenges of Six-Pathogen Detected by mNGS in an Immunocompromised ICU Patient with Severe Community-Acquired Pneumonia-Induced Sepsis: A Case Report and Literature Review.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {4659-4665}, pmid = {40926875}, issn = {1178-6973}, abstract = {INTRODUCTION: Severe community-acquired pneumonia (SCAP) in immunocompromised patients is often caused by rare atypical pathogens, which are difficult to detect using conventional microbiological tests (CMTs) and can progress to sepsis in severe cases. Metagenomic next-generation sequencing (mNGS), an emerging pathogen detection technique, enables rapid identification of mixed infections and provides valuable guidance for clinical treatment decisions. SCAP-induced sepsis caused by a six-pathogen co-infection has not been previously reported, but interpretation remains a challenge.<br><br>CASE PRESENTATION: This report describes a case of SCAP-induced sepsis detected six pathogens by mNGS in a patient with IgA nephropathy who developed immunosuppression following long-term treatment with rituximab and corticosteroids. Bronchoalveolar lavage fluid (BALF) mNGS detected six pathogens, including Pneumocystis jirovecii, Klebsiella pneumoniae, Primate bocaparvovirus 1, Cytomegalovirus, Elizabethkingia anophelis, and Candida albicans. The patient was admitted to the intensive care unit (ICU) and received a combination of meropenem, trimethoprim-sulfamethoxazole, ganciclovir, piperacillin-tazobactam, and caspofungin. Following appropriate treatment, the patient recovered and was successfully discharged.<br><br>CONCLUSION: mNGS offers significant advantages for the diagnosis and identification of mixed infections in immunocompromised patients with SCAP-induced sepsis. It enables clinicians to initiate timely and targeted antimicrobial therapy, which facilitates early recovery, reduces the overuse of broad-spectrum antibiotics, and ultimately improves patient prognosis. Nevertheless, its interpretation requires caution, as distinguishing true pathogens from colonizers or contaminants still relies on clinical correlation and complementary diagnostic methods.}, }
@article {pmid40926846, year = {2025}, author = {Prihambodo, TR and Mulianda, R and Wulandari, W and Anggrahini, S and Qomariyah, N and Ella, A and Winarti, E and Yusriani, Y and Suyatno, S and Firison, J and Fitra, D and Harahap, AE and Sari, DAP and Hidayat, T and Jayanegara, A}, title = {Scopus-based bibliometric analysis of research trends in silage feed and its impact on rumen fermentation in ruminants.}, journal = {Veterinary world}, volume = {18}, number = {7}, pages = {1972-1990}, pmid = {40926846}, issn = {0972-8988}, abstract = {BACKGROUND AND AIM: Silage plays a pivotal role in ruminant nutrition, significantly influencing rumen fermentation, animal productivity, and environmental sustainability. Despite extensive research on silage and fermentation, a comprehensive synthesis of global trends and collaborations in this domain has not been systematically explored. This study aimed to conduct a bibliometric analysis of global research on silage feed and its effects on rumen fermentation in ruminants. It sought to identify publication trends, leading contributors, research themes, and international collaboration networks, thereby informing future directions in ruminant nutrition research.<br><br>MATERIALS AND METHODS: A total of 1,007 documents published between 1961 and 2024 were retrieved from the Scopus database using targeted keywords. Bibliometric and network analyses were performed using VOSviewer, Bibliometrix (R package), and Microsoft Excel. Inclusion criteria were limited to peer-reviewed English-language articles focused on silage feed and rumen fermentation in ruminants. Data cleaning and preprocessing involved harmonization of author names, keywords, and institutional affiliations.<br><br>RESULTS: Publication output has increased significantly since 2010, with China, the United States, and Canada emerging as the top contributors. Major research themes include silage quality, microbial fermentation, methane mitigation, and feed efficiency. Core journals identified include Journal of Dairy Science and Journal of Animal Science. Leading institutions such as China Agricultural University and the University of Florida demonstrated high productivity and citation impact. Keyword analysis highlighted emerging trends, including microbiome, methanogenesis, and sustainability. Collaboration network analysis revealed strong regional clusters, with North America and Europe forming central hubs, while Asia and South America showed growing but less integrated networks.<br><br>CONCLUSION: Research on silage and rumen fermentation has evolved from foundational studies to interdisciplinary approaches integrating microbiology, environmental science, and precision agriculture. The field is rapidly expanding, with increasing emphasis on reducing methane emissions and enhancing livestock performance through improved silage practices. However, global collaboration remains fragmented, particularly in underrepresented regions. Future research should focus on metagenomics, smart technologies (e.g., Artificial Intelligence and Internet of Things), and policy-driven strategies to optimize feed systems and support sustainable livestock production.}, }
@article {pmid40926709, year = {2025}, author = {Zhao, R and He, G and Zhou, D and Li, X and Kuyper, TW and Zhang, F and Zhang, J}, title = {Arbuscular mycorrhizal fungi enhance nitrate ammonification in hyphosphere soil.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.70561}, pmid = {40926709}, issn = {1469-8137}, support = {U23A2054//National Natural Science Foundation of China/ ; 42377128//National Natural Science Foundation of China/ ; 201913043//China Scholarship Council/ ; 201906350223//China Scholarship Council/ ; }, abstract = {Microbial nitrate ammonification is a crucial process to retain nitrogen (N) in soils, thereby reducing N loss. Nitrate ammonification has been studied in enrichment and axenic bacterial cultures but so far has been merely ignored in environmental studies. In particular, the capability of arbuscular mycorrhizal fungi (AMF) to regulate nitrate ammonification has not yet been explored. Here, nitrate ion ([15]NO3 [-]) was used to trace N transformations in hyphosphere and bulk soils. Metagenomic analysis was conducted, and cross-kingdom interactions between AMF and an isolated nirBD-carrying Paenibacillus sp. strain DP01 from hyphosphere soil were investigated. AMF hyphae significantly increased ammonium ion (NH4 [+]) concentration and [15]NH4 [+] derived from [15]NO3 [-] in hyphosphere soil, which were 1.42 and 5.01 times as high as those in bulk soil. Metagenomic analysis showed that the nirB gene involved in nitrite reduction to ammonium was prevalent in hyphosphere and bulk soils. Hyphal exudates enhanced ammonification efficiency and biofilm formation of the nitrite-ammonifying strain DP01. Additionally, accelerated oxygen depletion was detected on hyphal surface. This study demonstrates a novel interaction in which AMF significantly enhanced nitrate ammonification in the hyphosphere. Given the widespread presence of nitrate-ammonifying microbes in soils, this newly described interkingdom interaction offers guidance for agricultural practices aimed at increasing N efficiency and environmental sustainability.}, }
@article {pmid40926344, year = {2025}, author = {Sarango Flores, S and Cordovez, V and Oyserman, BO and Arias Giraldo, LM and Stopnisek, N and Raaijmakers, JM and van 't Hof, P}, title = {Microbiome-Mediated Resistance of Wild Tomato to the Invasive Insect Prodiplosis longifila.}, journal = {Environmental microbiology reports}, volume = {17}, number = {5}, pages = {e70190}, doi = {10.1111/1758-2229.70190}, pmid = {40926344}, issn = {1758-2229}, support = {024.004.014/NWO_/Dutch Research Council/Netherlands ; CZ07-000440-2018//SENESCYT scholarship/ ; 10093//Chancellor Research Grant/ ; }, mesh = {*Solanum lycopersicum/microbiology/parasitology/immunology ; Animals ; *Microbiota ; *Soil Microbiology ; *Diptera/physiology ; Ecuador ; Plant Roots/microbiology/parasitology ; Introduced Species ; Bacteria/classification/genetics/isolation &amp; purification ; Plant Leaves/parasitology ; }, abstract = {Plant roots are colonised by diverse communities of microorganisms that can affect plant growth and enhance plant resistance to (a) biotic stresses. We investigated the role of the indigenous soil microbiome in the resistance of tomato to the invasive sap-sucking insect Prodiplosis longifila (Diptera: Cecidomyiidae). Native and agricultural soils were sampled from the Andes in Southern Ecuador and tested, in greenhouse bioassays, for leaf tissue damage caused by P. longifila on domesticated Solanum lycopersicum cv. Moneymaker and wild tomato S. pimpinellifolium. We observed no significant differences in insect damage between domesticated and wild tomatoes grown in live native or agricultural soils. However, when grown in sterilised native and agricultural soils, wild tomato was more severely affected by the insect than the domesticated tomato. Microbiome analyses revealed that soil sterilisation impacted overall rhizobacterial diversity and abundance in wild tomato. Particularly, Actinoplanes abundance was reduced upon sterilisation, which significantly correlated with loss of insect resistance. Metagenome analyses and genome assembly of Micromonosporaceae (Actinoplanes family) suggested a putative association between motility, chemotaxis, membrane transport, chorismate, and lanthipeptide biosynthesis and insect resistance. This indicates that wild S. pimpinellifolium, in contrast to domesticated S. lycopersicum, relies on specific members of the root-associated microbiome for P. longifila protection.}, }
@article {pmid40925458, year = {2025}, author = {Zhao, Z and Gao, B and Henawy, AR and Ur Rehman, K and Ho, JWK and Xue, Y and Wu, J and Jiménez, N and Subirats, J and Zheng, L and Huang, F and Yu, C and Zhang, J and Cai, M}, title = {Effects of chicken manure-derived black soldier fly organic fertilizer on soil carbon and nitrogen cycling: insights from metagenomic and microbial network analysis.}, journal = {Environmental research}, volume = {}, number = {}, pages = {122775}, doi = {10.1016/j.envres.2025.122775}, pmid = {40925458}, issn = {1096-0953}, abstract = {Black soldier fly (BSF) organic fertilizer is known to enhance soil fertility and promote plant growth. However, its effects on soil carbon (C) and nitrogen (N) cycling remains unclear. In this study, we established a BSF chicken manure bioconversion system to produce BSF organic fertilizer and investigate its impacts on soil C and N cycling, as well as microbial ecological networks through metagenomic analysis. Compared to the control, BSF organic fertilizer significantly increased soil organic matter by 16.1% (p < 0.05) and total potassium by 11.0% (p < 0.05). Metagenomic sequencing revealed that BSF organic fertilizer significantly enhanced soil C and N cycling. For instance, the abundance of carbon fixation genes such as Calvin-Benson-Bassham (CBB) cycle genes pyc, pycA, and pycB increased by 35.7% (p < 0.01), 107.1% (p < 0.001), and 14.6% (p < 0.05), respectively. In nitrogen cycling, denitrification genes nirB, nirK, and nirS increased by 181.5 % (p < 0.001), 102.7% (p < 0.001), and 25.9% (p < 0.05), respectively. Furthermore, soils amended with BSF organic fertilizer displayed a 9.9% higher proportion of positive microbial interactions, particularly enhancing synergistic associations between bacteria and fungi, suggesting improved microbial community stability. Importantly, bacteria and fungi were interdependent in regulating C and N cycling processes, together orchestrating soil ecosystem functions. Overall, BSF organic fertilizers effectively promoted soil C and N cycling and maintained the stability of microbial communities. These findings provide valuable insights for the rational selection of fertilizers and the optimization of fertilization management practices, thereby contributing to the sustainable development of agricultural production.}, }
@article {pmid40779866, year = {2025}, author = {Lin, XQ and Li, ZL and Chen, XQ and Wang, L and Yu, L and Wang, AJ}, title = {Microbial synergistic metabolic mechanism of enhanced tetrabromobisphenol A removal by bio-electrochemical system coupled constructed wetland.}, journal = {Journal of hazardous materials}, volume = {496}, number = {}, pages = {139382}, doi = {10.1016/j.jhazmat.2025.139382}, pmid = {40779866}, issn = {1873-3336}, mesh = {Biodegradation, Environmental ; *Bioreactors/microbiology/statistics &amp; numerical data ; Desulfovibrio/metabolism ; Geobacter/metabolism ; Metagenome ; *Microbiota ; Nitrates/metabolism ; *Polybrominated Biphenyls/metabolism ; *Water Pollutants, Chemical/metabolism ; *Water Purification/methods/statistics &amp; numerical data ; Wetlands ; Electrochemical Techniques ; }, abstract = {The widespread existence of tetrabromobisphenol A (TBBPA) in the aquatic environment requires efficient treatment technology. The feasibility and related molecular mechanisms for the simultaneous deep removal of nitrate and TBBPA in a bio-electrochemical system coupled with a constructed wetland (BES-CW) are unclear. This study fabricated the BES-CW to achieve simultaneously deep removal of nitrate and TBBPA. TBBPA majorly went through reductive debromination, hydrolytic debromination, ring-cleavage, and oxidation in the open and closed circuits of BES-CW. Electricity activated key genes encoded in oxidoreductase (pflA, pflX) and oxygenase (dmpB, pobA) from electroactive bacteria (Geobacter and Desulfovibrio), accelerating TBBPA metabolites' oxidation and mineralization. Nitrate enriched the Acinetobacter and stimulated genes encoded in hydrolytic dehalogenase, inducing TBBPA hydrolytic debromination and further mineralization. Electricity and nitrate synergistically enhance TBBPA degradation and mineralization, guiding the advanced treatment of emerging pollutants in the aquatic environment.}, }
@article {pmid40925130, year = {2025}, author = {Sahu, KK and Yadav, K and Pradhan, M and Sharma, M and Dubey, A and Sucheta,  and Kirubakaran, JJ}, title = {Pharmacological insights into gut microbiota modulation in systemic lupus erythematosus: Mechanisms, treatment strategies, and clinical implications.}, journal = {The Journal of pharmacology and experimental therapeutics}, volume = {392}, number = {9}, pages = {103659}, doi = {10.1016/j.jpet.2025.103659}, pmid = {40925130}, issn = {1521-0103}, abstract = {Systemic lupus erythematosus (SLE) is a complex autoimmune disease characterized by widespread inflammation and immune system dysregulation. Recent research suggests that the gut microbiota may play a role in the development of SLE by modulating immune system responses, affecting cytokine production, and altering the activity of T and B cells lymphocytes. As a result, there is a growing interest in microbiota-targeted therapies, including probiotics, dietary changes, and fecal microbiota transplantation. These methods may help restore the balance of microbes and reduce disease activity, but there are still a number of problems to solve. For example, microbiota composition varies greatly from person to person, and it is not clear how dysbiosis causes disease onset. There are also safety concerns about fecal microbiota transplantation. Experimental and clinical studies have started to shed light on the complicated ways in which microbial communities and immune function affect each other in SLE. These studies provide useful information, but their results are often inconsistent. As research continues, integrative methods like metagenomics and metabolomics may help find microbial signatures linked to disease, helping create more accurate and personalized treatments. The gut microbiome is a promising yet still developing area of research that could help us learn more about autoimmune diseases and their treatment, such as SLE. SIGNIFICANCE STATEMENT: Grasping the complex interplay between gut microbiota and systemic lupus erythematosus (SLE) has provided an avenue for therapeutic intervention. This study emphasizes the importance of gut dysbiosis in immune dysregulation, with connections between microbial translocation, molecular mimicry, and inflammatory pathways as contributing factors to the progression of SLE. This work sets the stage for novel and targeted approaches to treating SLE and improving patient outcomes by investigating microbiota-centric treatment options, such as probiotics, dietary interventions, and fecal microbiota transplantation.}, }
@article {pmid40925069, year = {2025}, author = {Ji, Y and Gu, J and Xiao, S and Zhao, M and Xu, J and Lin, J and Cui, J and Zhao, W}, title = {Prognostic value of Nanopore sequencing-based metagenomics next-generation sequencing in clinical infectious cases: A retrospective observational study.}, journal = {Diagnostic microbiology and infectious disease}, volume = {114}, number = {1}, pages = {117092}, doi = {10.1016/j.diagmicrobio.2025.117092}, pmid = {40925069}, issn = {1879-0070}, abstract = {OBJECTIVES: This study aimed to evaluate the prognostic value of metagenomic next-generation sequencing(mNGS) using Nanopore sequencing technology (NST) versus traditional culture methods in infectious disease cases.<br><br>METHODS: We conducted a retrospective, single-center observational study comparing clinical outcomes between patients and specimen types in NST group and those in culture-based control group. Cox Proportional Hazards regression and Kaplan-Meier survival analysis were conducted to evaluate the association between diagnostic strategy and 28-day mortality. To minimize bias, Propensity Score Matching (PSM) and robust multivariate Cox regression analysis were employed to control for confounding factors. Diagnostic accuracy was quantified by calculating sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV).<br><br>RESULTS: The NST-based diagnosis was independently associated with a significantly reduced 28-day mortality rate, as indicated by the robust multivariate Cox regression analysis. (HR = 0.29, 95 %CI:0.09-0.91, p = 0.033). The sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of NST in detecting bacterium were 0.93,0.54, 0.5and 0.94, respectively. Additionally, the NST group was associated with higher Antibiotic De-escalation Rate (ADE) and reduced Duration of Therapy (DOT), with p values of 0.0238 and 0.008, respectively.<br><br>CONCLUSION: NST-based mNGS demonstrated superior performance in diagnosing bacterial infections compared to traditional culture methods. The NST group and positive pathogen detection were associated with a reduced 28-day mortality rate. Additionally, higher APACHE II scores upon admission were identified as independent predictors of worse prognosis, highlighting the importance of early severity assessment in patient outcomes.}, }
@article {pmid40924942, year = {2025}, author = {Hooper, C and Tidy, AM and Jessop, R and Bateman, KS and Green, MJ and Ross, SH and Ward, GM and Hazelgrove, R and Hunt, JE and Parker, M and Bass, D}, title = {Genomic and morphological characterization of a novel iridovirus, bivalve iridovirus 1 (BiIV1), infecting the common cockle (Cerastoderma edule).}, journal = {Microbial genomics}, volume = {11}, number = {9}, pages = {}, doi = {10.1099/mgen.0.001494}, pmid = {40924942}, issn = {2057-5858}, mesh = {Animals ; *Iridovirus/genetics/classification/isolation &amp; purification/ultrastructure ; Phylogeny ; *Cardiidae/virology ; *Genome, Viral ; Base Composition ; Open Reading Frames ; Genomics ; }, abstract = {High rates of mortality of the common cockle, Cerastoderma edule, have occurred in the Wash Estuary, UK, since 2008. A previous study linked the mortalities to a novel genotype of Marteilia cocosarum, with a strong correlation between cockle moribundity and the presence of M. cocosarum. Here, we characterize a novel iridovirus, identified by chance during metagenomic sequencing of a gradient purification of Marteilia cells, with the presence also correlated to cockle moribundity. The novel 179,695 bp iridovirus, bivalve iridovirus 1 (BiIV1), encodes 193 predicted ORFs and has a G+C content of 41 mol%. BiIV1 clusters together with other aquatic invertebrate iridoviruses in phylogenetic analyses and has a similar genome size to other invertebrate iridoviruses. Comparative analysis revealed that BiIV1 has lost three genes that were previously thought to be common amongst all iridoviruses but has also gained genes, potentially from horizontal transfer from its bivalve mollusc host(s). Electron microscopy showed 158 nm icosahedral virions present in the haemocytes of cockles, typical of those observed in host tissues infected with viruses of the family Iridoviridae. Prevalence of BiIV1 in moribund cockles was higher than that in apparently healthy cockles at most sites in the Wash Estuary, with up to 100% PCR prevalence in moribund cockles. Our findings provide the first genome for a bivalve-infecting iridovirus and identify a second bivalve-associated iridovirus in publicly available genomic datasets, adding to the knowledge of invertebrate iridovirus genomics and diversity.}, }
@article {pmid40924621, year = {2025}, author = {Liu, L and Hu, L and Kuzyakov, Y and Rillig, MC and Duan, G and Wei, G and Chen, C}, title = {Microbial Physiological Adaptation to Biodegradable Microplastics Drives the Transformation and Reactivity of Dissolved Organic Matter in Soil.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c09633}, pmid = {40924621}, issn = {1520-5851}, abstract = {The turnover of dissolved organic matter (DOM) in soil regulated by biodegradable microplastics (MPs) has garnered much attention due to its profound impact on the storage and stability of soil organic matter. However, the transformation and reactivity of plant-derived and microbially derived DOM by microorganisms adapted to biodegradable MPs, and the involved microbial physiological processes, remain nearly unknown. Here, we added virgin and aged polylactic acid (PLA) and polyhydroxyalkanoate (PHA) to agricultural soils and incubated for 56 days. Using stable isotope techniques, reactomics, and metagenomics, we found that the addition of both virgin and aged PLA induced hydroxylation, demethylation, and dehydrogenation of lignin-derived DOM, resulting in a 3-fold increase in their oxidation degree. PLA activated the enzymatic pathway for lignin-derived DOM decomposition and downregulated genes involved in bacterial anabolism, such as those related to protein, amino sugar, and peptidoglycan biosynthesis. In contrast, PHA increased the content of microbially derived DOM compounds such as proteins and amino sugars by 2.1-fold relative to the control with peptide chain elongation. PHA resulted in the degradation of lignin-derived DOM into pyruvate and acetyl-CoA, accelerated bacterial ATP synthesis, the de novo biosynthesis of proteins and peptidoglycan, and cell renewal and death, thereby increasing PHA- and soil organic matter-derived microbial necromass carbon. Our study provides new insights into the impact of biodegradable MPs on soil DOM transformation and underscores the importance of the microbial physiological processes involved.}, }
@article {pmid40924014, year = {2025}, author = {Wei, Y and Chen, Y and Zhao, T and Zhang, X and Wang, N and Shen, L and Liang, Y and Ye, S and He, H}, title = {Treatment of non-sterile biogas slurry from a pig farm using microalgae isolated from the activated sludge of sewage plants.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0068825}, doi = {10.1128/spectrum.00688-25}, pmid = {40924014}, issn = {2165-0497}, abstract = {UNLABELLED: Microalgae treatment is regarded as a green and environmentally acceptable method of treating pig farm biogas slurry (BS). Numerous studies have been conducted on the use of microalgae to treat sterilized BS. Nevertheless, in large-scale application settings, this method will undoubtedly result in high costs and low efficiency. In this study, microalgae were isolated from activated sludge, and their capacity to treat non-sterile BS with high ammonium nitrogen levels was investigated, along with examining alterations in microbial composition within BS. The results showed that both Chlorella sp. HH01 and Chlorella sp. HS02 treatments effectively removed ammonia nitrogen and phosphorus from BS. They also showed some removal capabilities for chemical oxygen demand, heavy metals, and antibiotics. Algal treatment significantly reduced the number of species, richness, variety, and pathogens within the microorganisms of BS, according to the results of metagenomic research. Meanwhile, algal treatment demonstrated a significant removal effect on certain antibiotic resistance genes, while increasing the abundance of some others. This study provides a comprehensive exploration of microalgae-mediated mitigation effects on antibiotic resistance genes in BS.<br><br>IMPORTANCE: Numerous studies have been conducted on the use of microalgae to treat sterile biogas slurry (BS). However, in large-scale applications, this approach undoubtedly results in high costs and inefficiencies. Therefore, it is crucial to identify microalgae capable of growing in non-sterilized and undiluted BS while effectively treating major pollutants. The findings of this study reveal that microalgae isolated and purified from activated sludge in sewage treatment plants can withstand crude BS containing high concentrations of ammonia nitrogen and effectively remove ammonia nitrogen and total phosphorus. Additionally, they exhibit some removal capabilities for chemical oxygen demand, heavy metals, pathogens, antibiotics, and certain antibiotic resistance genes.}, }
@article {pmid40923736, year = {2025}, author = {Zhang, X and He, Q and Mao, G and Liang, M}, title = {Diagnosis of Pulmonary Actinomycosis Caused by Actinomyces graevenitzii: a Case Series of Three Patients.}, journal = {Clinical laboratory}, volume = {71}, number = {9}, pages = {}, doi = {10.7754/Clin.Lab.2025.250254}, pmid = {40923736}, issn = {1433-6510}, mesh = {Humans ; *Actinomycosis/diagnosis/microbiology/drug therapy ; *Actinomyces/isolation &amp; purification/genetics ; Male ; Middle Aged ; Female ; High-Throughput Nucleotide Sequencing ; Bronchoalveolar Lavage Fluid/microbiology ; *Lung Diseases/microbiology/diagnosis ; Aged ; Adult ; Lung/microbiology ; }, abstract = {BACKGROUND: Actinomyces graevenitzii is a relatively uncommon Actinomyces species, which is an oral species and predominantly recovered from respiratory locations [1,2]. It is a gram-positive anaerobic bacteria or microaerobic filamentation bacteria, which can induce pyogenic and granulomatous inflammation characterized by swelling and concomitant pus, sinus formation, and the formation of yellow sulfur granules. All tissues and organs can be infected; the most common type involves the neck and face (55%), followed by the abdominal and pelvic cavities (20%). Chest involvement is the third most common type (15%), affecting the lung parenchyma, central airway, pleura, mediastinum, and chest wall [3-5]. Diagnosis of actinomycosis mainly relies on sputum, pus or biopsy specimens to find actinomycetes. Metagenomics next-generation sequencing (mNGS) in recent years has been increasingly valued and recognized for its application in infectious diseases. It provides a more efficient and accurate means for the pathological diagnosis of respiratory infections, updating the diagnostic strategy for lower respiratory tract infections [6].<br><br>METHODS: This study systematically summarized the clinical characteristics of Actinomyces graevenitzii infection by analyzing three cases of this pathogen. Bronchoalveolar lavage fluid (BAL) samples were collected for bacterial culture and mNGS. The isolated strains were routinely identified by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS).<br><br>RESULTS: Microbiological analysis demonstrated Actinomyces graevenitzii growth in all three bronchoalveolar la-vage (BAL) cultures. Metagenomic next-generation sequencing (mNGS) results showed concordant detection of A. graevenitzii in two cases, while unexpectedly identifying Tropheryma whipplei as the predominant pathogen in the remaining case.<br><br>CONCLUSIONS: Actinomycosis infections often present with subtle and nonspecific clinical manifestations, making them difficult to distinguish from pulmonary tuberculosis, fungal infections, and lung malignancies through imaging studies alone, frequently resulting in misdiagnosis or delayed diagnosis. Early and accurate diagnosis can be achieved through timely analysis of BAL fluid using advanced diagnostic techniques, including MALDI-TOF/MS for bacterial identification and mNGS, facilitating prompt and appropriate treatment.}, }
@article {pmid40923351, year = {2025}, author = {Stensvold, CR}, title = {Aspects of Genetic Diversity, Host Specificity and Public Health Significance of Single-Celled Intestinal Parasites Commonly Observed in Humans and Mostly Referred to as 'Non-Pathogenic'.}, journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica}, volume = {133}, number = {9}, pages = {e70036}, doi = {10.1111/apm.70036}, pmid = {40923351}, issn = {1600-0463}, mesh = {Humans ; *Intestinal Diseases, Parasitic/parasitology ; *Genetic Variation ; *Host Specificity ; *Public Health ; Blastocystis/genetics ; Animals ; }, abstract = {Clinical microbiology involves the detection and differentiation of primarily bacteria, viruses, parasites and fungi in patients with infections. Billions of people may be colonised by one or more species of common luminal intestinal parasitic protists (CLIPPs) that are often detected in clinical microbiology laboratories; still, our knowledge on these organisms' impact on global health is very limited. The genera Blastocystis, Dientamoeba, Entamoeba, Endolimax and Iodamoeba comprise CLIPPs species, the life cycles of which, as opposed to single-celled pathogenic intestinal parasites (e.g., microsporidia and sporozoa), do probably not include gut-invasive stages that could result in pathological processes and thereby disease (except for Entamoeba histolytica). All five genera are parasites in the sense that they use a host to complete their life cycle; still, by many specialists, these are considered to be of limited clinical relevance and could possibly be referred to as 'eukaryotic endobionts' or even 'endosymbionts', in case they would have health-protective effects. The articles included in this thesis exemplify the work and the data that support the view that it might be more relevant to study these genera in a public health and gut ecology context than in a clinical microbiology context. Essential to investigating the impact of intestinal parasites on health and disease are accurate diagnostic tools, including DNA-based technology such as PCR and sequencing, plus accurate reference databases. Small subunit (SSU) ribosomal RNA (rRNA) genes consistently present in both pro- and eukaryotic organisms are today avidly used as taxonomic markers. DNA-based methods have been developed for genetic characterisation of microorganisms and provided data on species/subtypes/genotypes, etc. Metagenomics and metabarcoding (the use of low-specific PCR coupled with next-generation sequencing) can provide information on co-infection/co-colonisation with other organisms and enable screening for genetic diversity, even in complex matrices. By developing and implementing sensitive and specific DNA-based diagnostic tools and typing assays primarily based on the SSU rRNA gene, we have increased insight into the diversity, distribution and significance of CLIPPs. With these tools, we have shown that the genera Blastocystis and Dientamoeba are far more common than previously thought. Only 10-15 years ago, hypotheses on their distribution typically relied on data generated by traditional parasitological diagnostic methods, such as light microscopy. Hence, we have shown that most older children in Nigeria host Blastocystis, and that most children in day-care institutions in Denmark, if not all, get colonised by Dientamoeba at some point. Single-celled non-pathogenic intestinal parasites can be hosted by patients with diarrhoea and functional or inflammatory bowel diseases. However, emerging data appear to suggest that CLIPPs are generally more common in gut-healthy individuals than in patients with gastrointestinal symptoms. The research we have carried out on associations between CLIPPs and gut bacteria suggests that colonisation with these parasites is seen primarily in individuals with a healthy 'gut flora' (eubiosis). This observation should prompt future research projects focusing on the use of CLIPPs as biomarkers, and it should be investigated to which extent manipulation with CLIPPs could lead to changes in the gut flora and thereby be used as probiotics. In the event that it makes sense to speak of 'infection' by CLIPPs, we still lack tools to differentiate between colonisation and infection. We have known for decades that morphologically similar parasites can differ in terms of clinical impact and be genetically distinct, a feature that we refer to as 'cryptic genetic diversity'. One example is E. histolytica, which cannot be differentiated from Entamoeba dispar by cyst morphological features. However, whereas E. histolytica can be invasive and give rise to amoebic dysentery and amoebiasis, E. dispar is by most specialists considered non-invasive and generally non-pathogenic. This insight led us to investigate genetic diversity among other species of Entamoeba as well as other CLIPPs genera. If we could demonstrate similar-or higher-degrees of diversity within Blastocystis, Dientamoeba, Endolimax and Iodamoeba, these differences might be key to explaining differences in parasite phenotype and thereby differences in the ability of the parasites to cause symptoms. Despite the disclosure of striking genetic diversity among some CLIPPs, we have found little support for such theories; however, more studies are needed. As for Dientamoeba, we have observed a more or less clonal expansion of one of the two genotypes known to exist, and this genotype appears to have global predominance. In contrast, extensive genetic diversity is observed between and within subtypes of Blastocystis: to date, more than 30 species, the so-called subtypes, have been acknowledged. We, and many others, have sought to identify whether one or more of these subtypes could be linked to the development of intestinal symptoms, but there is little evidence to support this hypothesis. We know that Subtypes 1-4 reflect about 95% of Blastocystis colonisation in humans, and we have shown that individuals with zoonotic subtypes (e.g., ST6, ST7 and ST8) might typically experience symptoms. We have disclosed astonishing genetic variation among other CLIPPs, which has led to the recognition of Iodamoeba bütschlii, Endolimax nana, Entamoeba coli and Entamoeba hartmanni as species complexes, where each species should be regarded as a complex of species (referred to as 'subtypes' or 'ribosomal lineages') with overlapping morphology. And where E. histolytica and E. dispar differ by only 1%-2% diversity across the SSU rRNA gene, we have observed up to at least 10% and 30% genetic difference among ribosomal lineages within E. coli and I. bütschlii, respectively, challenging species concepts currently applied. Our research has resulted in the recognition of three ribosomal lineages within both E. coli and E. hartmanni, as well as two ribosomal lineages of E. nana and I. bütschlii. Moreover, we have discovered a new lineage of Entamoeba moshkovskii. Molecular characterisation of intestinal parasites collected from different host species (humans, non-human primates, other mammals, birds, etc.) can help identify opportunity for transmission between human and non-human hosts. We have shown that pigs can host a few species/lineages that can readily colonise humans, such as Entamoeba hartmanni and I. bütschlii. Many other species of larger mammals are common hosts of Blastocystis and Entamoeba. However, for the two latter genera, the species/genetic variants observed in non-human hosts are typically different from those observed in humans, which could indicate that many species of CLIPPs have adapted to their respective hosts over a long period, resulting in relatively high host specificity. For Blastocystis, we have shown that even though a given subtype may be found in more than one host species, it is possible to demonstrate cryptic host specificity at allele level. For instance, even though both human and non-human primates can be colonised by ST3, host species-specific strains of ST3 circulate within these two host populations. With regards to E. coli, it is possible that ST1 has adapted to human hosts, while E. coli ST2 has adapted to a broader host range, including non-human primates and rodents. It has become clear that CLIPPs are common colonisers of the human background population, and even though we cannot disprove the existence of infection by any of these, it should be reasonable to consider clinical and medical intervention redundant in most cases. Perhaps it might even be so that one should try not to eradicate these organisms from the gut when first established. However, more studies are warranted to elucidate the significance of the pronounced genetic diversity observed in some CLIPPs with regards to transmission patterns and clinical significance. Future research in CLIPPs should also include studies that can elucidate those factors that favour colonisation with CLIPPs and what role CLIPPs have in host-gut ecology, metabolism and overall health condition. Finally, as human and non-human hosts share these parasitic genera, and as some protozoa possibly contribute to overall gut function in ruminants, it would be interesting to study these in domesticated and wild animals to learn more about the role of these parasites in health and disease, including investigations into whether some CLIPPs might be endosymbionts.}, }
@article {pmid40923293, year = {2025}, author = {Lauritsen, JG and Carøe, C and Gaun, N and Martin-Bideguren, G and Leonard, A and Eisenhofer, R and Odriozola, I and Gilbert, MTP and Aizpurua, O and Alberdi, A and Pietroni, C}, title = {Robust, Open-Source and Automation-Friendly DNA Extraction Protocol for Hologenomic Research.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e70042}, doi = {10.1111/1755-0998.70042}, pmid = {40923293}, issn = {1755-0998}, support = {CF20-0460//Carlsbergfondet/ ; DNRF143//Danmarks Grundforskningsfond/ ; //The Danish Dairy Association and the Danish Agriculture and Food Sector Dairy/ ; }, abstract = {Global efforts to standardise methodologies benefit greatly from open-source procedures that enable the generation of comparable data. Here, we present a modular, high-throughput nucleic acid extraction protocol standardised within the Earth Hologenome Initiative to generate both genomic and microbial metagenomic data from faecal samples of vertebrates. The procedure enables the purification of either RNA and DNA in separate fractions (DREX1) or as total nucleic acids (DREX2). We demonstrate their effectiveness across faecal samples from amphibians, reptiles and mammals, with reduced performance observed on bird guano. Despite some variation in laboratory performance metrics, both DREX1 and DREX2 yielded highly similar microbial community profiles, as well as comparable depth and breadth of host genome coverages. Benchmarking against a commercial kit widely used in microbiome research showed comparable recovery of host genomic data and microbial community complexity. Our open-source method offers a robust, cost-effective, scalable and automation-friendly nucleic acid extraction procedure to generate high-quality hologenomic data across vertebrate taxa. The method enhances research comparability and reproducibility by providing standardised, high-throughput, open-access protocols with fully transparent reagents. It is designed to integrate automatised pipelines, and its modular structure also supports continuous development and improvement.}, }
@article {pmid40923121, year = {2025}, author = {Li, Z and Zhao, K and Liu, H and Liu, J and Chen, X and Hu, W and Wen, E and Zhang, K and Chen, L}, title = {Construction of Predictive Machine Learning Model of Glioma-Associated Gut Microbiota.}, journal = {Brain and behavior}, volume = {15}, number = {9}, pages = {e70843}, doi = {10.1002/brb3.70843}, pmid = {40923121}, issn = {2162-3279}, support = {W2024SNKT13//the Research on Neurological Diseases and Nutritional Health at the Capacity Building and Continuing Education Center of the National Health Commission of China/ ; 82172680//the National Natural Science Foundation of China/ ; 82303586//the National Natural Science Foundation of China/ ; 82373220//the National Natural Science Foundation of China/ ; 82473264//the National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Machine Learning ; *Gastrointestinal Microbiome/physiology/genetics ; *Glioma/microbiology/diagnosis ; *Brain Neoplasms/microbiology/diagnosis ; Male ; Female ; Middle Aged ; Adult ; Feces/microbiology ; }, abstract = {BACKGROUND: The gut microbiota plays a crucial role in the development of glioma. With the evolution of artificial intelligence technology, applying AI to analyze the vast amount of data from the gut microbiome indicates the potential that artificial intelligence and computational biology hold in transforming medical diagnostics and personalized medicine.<br><br>METHODS: We conducted metagenomic sequencing on stool samples from 42 patients diagnosed with glioma after operation and 30 non-intracranial tumor patients and developed a Gradient Boosting Machine (GBM) machine learning model to predict the glioma patients based on the gut microbiome data.<br><br>RESULTS: The AUC-ROC for the GBM model was 0.79, indicating a good level of discriminative ability.<br><br>CONCLUSIONS: This method's efficacy in discriminating between glioma cells and normal controls underscores the potential of machine learning models in leveraging large datasets for clinical insights.}, }
@article {pmid40922296, year = {2025}, author = {Li, J and He, J and Yin, Y and Liu, Y}, title = {Timely diagnosis of atypical Japanese spotted fever: A case report.}, journal = {Medicine}, volume = {104}, number = {36}, pages = {e44345}, doi = {10.1097/MD.0000000000044345}, pmid = {40922296}, issn = {1536-5964}, mesh = {Humans ; Female ; Middle Aged ; *Spotted Fever Group Rickettsiosis/diagnosis/drug therapy ; Anti-Bacterial Agents/therapeutic use ; Doxycycline/therapeutic use ; Rickettsia/isolation &amp; purification/genetics ; }, abstract = {RATIONALE: Japanese spotted fever (JSF) is a rare tick-borne disease caused by Rickettsia japonica. Atypical manifestations and a lack of standardized diagnostic assays often result in delayed diagnosis and treatment, potentially leading to life-threatening complications.<br><br>PATIENT CONCERNS: A 57-year-old immunocompetent female from a region with no previously reported JSF cases presented with acute-onset high-grade fever (39.5&#xb0;C), a generalized maculopapular rash, and systemic symptoms after participating in agricultural activities. The patient denied having any history of tick exposure and presented without eschar, leading to the initial misdiagnosis of respiratory infection.<br><br>DIAGNOSES: Metagenomic sequencing (MetaCAP) technology enabled a definitive diagnosis by identifying Rickettsia japonica-specific DNA sequences in the patient's blood. The genomic results completely aligned with the clinical presentation.<br><br>INTERVENTIONS: The patient was treated with doxycycline, which achieved rapid clinical resolution.<br><br>OUTCOMES: The patient achieved full recovery with only residual lower-limb hyperpigmentation at the month follow-up, without disease recurrence.<br><br>LESSONS: This case demonstrates the diagnostic value of metagenomic testing for fevers of unknown origin. JSF should be a key consideration for agricultural and forestry workers presenting with compatible symptoms, even in nonendemic areas without documented insect bites. The optimal diagnostic approach combines clinical evaluation with advanced molecular testing to ensure the accurate identification and proper management of tropical febrile illnesses.}, }
@article {pmid40922266, year = {2025}, author = {Liu, Y and Yue, Y and Dong, C and Wang, Z}, title = {Isolated spinal osteomyelitis caused by Nocardia farcinica in an immunocompetent patient: A case report and literature review.}, journal = {Medicine}, volume = {104}, number = {36}, pages = {e42797}, doi = {10.1097/MD.0000000000042797}, pmid = {40922266}, issn = {1536-5964}, mesh = {Humans ; Female ; *Osteomyelitis/microbiology/drug therapy/diagnosis/diagnostic imaging ; *Nocardia Infections/drug therapy/diagnosis/microbiology ; *Nocardia/isolation &amp; purification ; Child ; Anti-Bacterial Agents/therapeutic use ; Trimethoprim, Sulfamethoxazole Drug Combination/therapeutic use ; Magnetic Resonance Imaging/methods ; Immunocompetence ; Tomography, X-Ray Computed ; *Spinal Diseases/microbiology/drug therapy ; }, abstract = {RATIONALE: Nocardia spp. are opportunistic pathogens that invade the human body via respiratory inhalation or direct skin wounds. Spinal nocardial osteomyelitis is a rare disease with only a few cases reported to date. To the best of our knowledge, this is the second case of spinal osteomyelitis caused by Nocardia farcinica.<br><br>A 12-year-old immunocompetent girl was diagnosed with spinal osteomyelitis. The causative agent has been confirmed as N farcinica by metagenomic next-generation sequencing analysis of vertebral biopsy tissue in December 2022. It was noteworthy that the onset of the disease in this patient was insidious and the symptoms were atypical, which differed from previously reported cases.<br><br>INTERVENTIONS: Trimethoprim/sulfamethoxazole was given first, showing good clinical effects. To clarify the changes in the patient's condition, we performed magnetic resonance imaging (MRI) and computed tomography examinations on the patient in August 2023.<br><br>OUTCOMES: After 2 months of medication, the patient's clinical symptoms completely disappeared. The results of the latest computed tomography and MRI scans showed the formation of hardened bone in the area of the L2 vertebral body bone erosion, and MRI showed a significant reduction in the abnormal signal range of the L2 vertebral body, which was considered cured.<br><br>LESSONS: This study suggests that N farcinica, a rare pathogen, can present with atypical symptoms and can easily be misdiagnosed in immunocompromised patients. Its diagnosis relies on advanced testing techniques, and determining the nature of the pathogen is of great significance for a clear diagnosis. Moreover, early, sufficient, and comprehensive treatment with sulfonamide antibiotics or combination therapy usually results in a good prognosis.}, }
@article {pmid40922265, year = {2025}, author = {Zhao, C and Li, H and Guo, L and Jia, M and Liu, J}, title = {Diagnosis of Cytomegalovirus infection in a very low birth weight infant using metagenomic next-generation sequencing: A case report.}, journal = {Medicine}, volume = {104}, number = {36}, pages = {e44264}, doi = {10.1097/MD.0000000000044264}, pmid = {40922265}, issn = {1536-5964}, mesh = {Humans ; Infant, Newborn ; Antiviral Agents/therapeutic use ; *Cytomegalovirus/genetics/isolation &amp; purification ; *Cytomegalovirus Infections/diagnosis/drug therapy/virology ; Ganciclovir/therapeutic use ; *High-Throughput Nucleotide Sequencing/methods ; *Infant, Very Low Birth Weight ; *Metagenomics/methods ; }, abstract = {RATIONALE: Cytomegalovirus (CMV) is a DNA virus from the herpesvirus family that is widespread among humans. Very low birth weight infants (VLBWI) are particularly susceptible to postnatal CMV infection due to their compromised immune systems. The clinical manifestations of postnatal CMV infection are often nonspecific, which complicates early detection and may lead to multi-organ dysfunction and long-term sequelae.<br><br>PATIENT CONCERNS: A VLBWI developed unexplained persistent fever during hospitalization. Conventional diagnostic methods, including routine microbiological tests, failed to identify the causative pathogen.<br><br>DIAGNOSES: Metagenomic next-generation sequencing (mNGS) was performed and successfully identified CMV as the etiologic agent. Traditional diagnostic approaches were insufficient, but mNGS provided a comprehensive analysis of microbial nucleic acids, leading to a definitive diagnosis.<br><br>INTERVENTIONS: The patient received antiviral treatment with ganciclovir following the identification of CMV by mNGS.<br><br>OUTCOMES: After antiviral therapy, the fever resolved, and no long-term sequelae were observed during follow-up.<br><br>LESSONS: This case demonstrates the efficacy of mNGS as a powerful diagnostic tool for identifying the causes of unexplained infections in VLBWI. Compared with conventional methods, mNGS offers significant advantages, particularly in detecting a wide range of pathogens simultaneously. The successful diagnosis and treatment in this case underscore its clinical utility in managing complex neonatal infectious diseases.}, }
@article {pmid40922218, year = {2025}, author = {Di Gianvito, P and Englezos, V and Ferrocino, I and Cocolin, L and Rantsiou, K}, title = {Survey of a grapevine microbiome through functional metagenomics.}, journal = {Food research international (Ottawa, Ont.)}, volume = {219}, number = {}, pages = {117000}, doi = {10.1016/j.foodres.2025.117000}, pmid = {40922218}, issn = {1873-7145}, mesh = {*Vitis/microbiology ; *Metagenomics/methods ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation &amp; purification ; Fungi/genetics/classification/isolation &amp; purification ; Rhizosphere ; Fruit/microbiology ; Plant Leaves/microbiology ; }, abstract = {Microorganisms colonizing grapevines possess diverse functional capabilities that influence the health, growth, productivity and, consequently, wine quality. In this study, spatial and temporal dynamics of the microbiome of Vitis vinifera cv. Barbera grapevine were determined by shotgun sequencing. Bacterial and fungal populations and functions were monitored in samples of rhizosphere, leaves, and grapes, collected at different stages from fruit development to harvest in a conventionally managed vineyard. A compartmental specificity of diverse species was observed within both bacterial and fungal communities. A core microbiome was also identified. LEfSe analysis revealed significantly discriminant taxa associated with each plant compartment, but not according to the sampling time. KEGG genes associated with carbohydrate metabolism were the most abundant in all samples, followed by genes related to amino acid metabolism, respectively involved in carbon and nitrogen metabolic pathways. Interestingly, differences were observed in the functions of rhizosphere and phyllosphere communities with additional differences observed between functions of bacterial and fungal communities. Pathways involved in critical functions like nutrient acquisition, stress resistance, metabolic flexibility, and interaction with the grapevine, were detected within the microbiome. The findings of this study unravel ecological and functional characteristics of the Barbera microbiome. This fundamental understanding is a prerequisite for the development of tailored strategies to protect vineyards and promote sustainability in grapevine production.}, }
@article {pmid40922213, year = {2025}, author = {Zhang, Z and Guo, Z and Cao, L and Hou, Q and Liu, Z and Zhong, J and Liu, N and Mei, X and Wang, Y}, title = {Dissecting the microbial, physicochemical, and flavor dynamics of core and peel layers in Houhuo Daqu: Insights into quality regulation.}, journal = {Food research international (Ottawa, Ont.)}, volume = {219}, number = {}, pages = {116992}, doi = {10.1016/j.foodres.2025.116992}, pmid = {40922213}, issn = {1873-7145}, mesh = {*Taste ; *Fruit/microbiology/chemistry ; Odorants/analysis ; *Food Microbiology ; *Microbiota ; Bacteria/classification/genetics ; Humans ; Amino Acids/analysis ; Metagenomics ; }, abstract = {Houhuo Daqu (HHD) exhibits significant heterogeneity between its core and peel layers, yet their differences remain underexplored. This study integrates metagenomic sequencing and electronic sensory technologies to compare the physicochemical properties, microbial communities, and flavor profiles of HHD's core and peel. Results reveal distinct microbial communities and diversity between the layers. Both are dominated by bacteria (>90 % relative abundance). The core shows significantly higher relative abundance of Bacillus licheniformis, Bacillus haynesii, and Bacillus paralicheniformis, while the peel has elevated levels of Streptomyces sp. NHF165, Pantoea agglomerans, and Lactiplantibacillus plantarum. Bacillus licheniformis is linked to acetic acid biosynthesis. Flavor analysis indicates both layers are rich in pyrazines, contributing to HHD's distinctive aroma. Enzyme activities differed markedly between the core and peel. Structural equation modeling, regression, and ENVFIT analyses show that amino acid nitrogen directly influences enzymatic activity and indirectly affects it by shaping microbial community and diversity. Additionally, amino acid nitrogen significantly impacts HHD's taste and aroma, modulated by starch and ash content. These findings highlight amino acid nitrogen as a key factor for controlling HHD quality in future production.}, }
@article {pmid40922169, year = {2025}, author = {Li, X and Liao, B and Wang, X and Dong, W and Li, J and Hu, Y and Li, Y and Peng, N and Zhao, S}, title = {Non-Saccharomyces yeasts enhance yield and flavor in industrial xiaoqu light-flavor baijiu production.}, journal = {Food research international (Ottawa, Ont.)}, volume = {219}, number = {}, pages = {117040}, doi = {10.1016/j.foodres.2025.117040}, pmid = {40922169}, issn = {1873-7145}, mesh = {Fermentation ; *Pichia/metabolism/growth &amp; development ; *Taste ; Saccharomyces cerevisiae/metabolism/growth &amp; development ; *Flavoring Agents/metabolism ; Food Microbiology ; Rhizopus/metabolism/growth &amp; development ; *Alcoholic Beverages/microbiology/analysis ; Volatile Organic Compounds/analysis ; *Wine/microbiology/analysis ; Butylene Glycols ; }, abstract = {This study investigated the effects of adding Saccharomycopsis fibuligera (SF) and Pichia kudriavzevii (PK) on microbial communities and flavor substances in industrial xiaoqu light-flavor baijiu production. The result showed that the highest acidity was found in the control group (CK: Saccharomyces cerevisiae and Rhizopus) at the end of fermentation. SF and PK promoted the growth of Rhizopus while decreasing the abundance of S. cerevisiae during the saccharification stage. Metagenomic sequencing showed that S. cerevisiae and Lactobacillus helveticus were the dominant fungus and bacterium during the late stage of fermentation, and the fungal community tended to be stable before the bacterial community. Notably, the temperature change rate in zaopei (fermented grains) of PK was faster than that in CK and SF, whereas the synthesis of flavor substances was later than that in CK and SF. Moreover, the liquor yield of SF and PK increased by 4.08 % and 4.26 %, respectively. Flavor substance analysis of the base liquor demonstrated that both SF and PK elevated ethyl acetate content and decreased ethyl lactate. Meanwhile, β-phenethyl alcohol, 2,3-butanediol, isoamyl alcohol, and isobutanol contents were increased in SF, and 2,3-butanediol, isoamyl alcohol, and methanol contents were lowest in PK. These findings demonstrate the potential of non-Saccharomyces yeasts for flavor and yield optimization in baijiu production.}, }
@article {pmid40922105, year = {2025}, author = {Petraro, S and Tarracchini, C and Mancabelli, L and Lugli, GA and Turroni, F and Ventura, M and Milani, C}, title = {Plastic-Microbial BioRemediation DB: A Curated Database for Multi-Omics Applications.}, journal = {Environmental microbiology reports}, volume = {17}, number = {5}, pages = {e70178}, doi = {10.1111/1758-2229.70178}, pmid = {40922105}, issn = {1758-2229}, mesh = {Biodegradation, Environmental ; *Plastics/metabolism ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; Metagenomics ; Soil Microbiology ; Metagenome ; Genomics ; Multiomics ; }, abstract = {Plastic pollution is a major environmental challenge, with millions of tonnes produced annually and accumulating in ecosystems, causing long-term harm. Conventional disposal methods, such as landfilling and incineration, are often inadequate, emphasising the need for sustainable solutions like bioremediation. However, the bacterial biodiversity involved in plastic biodegradation remains poorly understood. To address this gap, we present the Plastic-Microbial BioRemediation (Plastic-MBR) database, a curated multi-omics resource that integrates publicly available genetic and enzymatic data related to putative plastic-degrading microorganisms. This database supports in silico analyses of metagenomic data from plastic-contaminated environments and comparative genomics, aiming to identify microbial taxa with potential plastic-degrading functions. We validated the functionality of the Plastic-MBR database by applying it to metagenomic datasets from plastic-contaminated soil and river water, successfully identifying numerous putative plastic-degrading genes across diverse microbial taxa. These results support the use of the Plastic-MBR database as a tool to identify candidate bacteria for future experimental validation, strain isolation, and functional studies, ultimately contributing to a deeper understanding of microbial potential in plastic bioremediation. While this study focuses on database development and computational validation, future studies will be essential to confirm and translate these genomic predictions into effective bioremediation strategies.}, }
@article {pmid40921745, year = {2025}, author = {Zhang, X and Li, Y and Qin, Y and Liao, Z and Deng, C and Chen, Y and Li, Y and Qian, H and He, Y and Chen, S and Shi, G and Liu, Y}, title = {Vientovirus capsid protein mimics autoantigens and contributes to autoimmunity in Sjögren's disease.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {40921745}, issn = {2058-5276}, support = {82471833//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82101841//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82171779//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82371802//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2023J06055//Natural Science Foundation of Fujian Province (Fujian Provincial Natural Science Foundation)/ ; 2022XMSLCYX01//Xiamen Municipal Bureau of Science and Technology (Xiamen Science and Technology Bureau)/ ; }, abstract = {Viral infections are implicated in the pathogenesis of autoimmune diseases, including Sjögren's disease (SjD), but the mechanisms linking viral antigens to disease development remain poorly understood. To address this, we conducted shotgun metagenomic sequencing of saliva samples from 35 patients with SjD and 25 healthy controls. The salivary virome of the patients with SjD, particularly those with high disease activity, had an expansion of Siphoviridae bacteriophages and increased eukaryotic viral sequences, including Vientovirus. This virus was associated with lacrimal gland dysfunction and elevated anti-SSA/Ro52 autoantibody levels. Alignment analysis and cross-blocking assay identified molecular mimicry between the Vientovirus capsid protein and the autoantigen SSA/Ro52. Mice immunized with a Vientovirus capsid peptide developed anti-SSA/Ro52 antibodies and showed immunological features resembling those of patients with SjD. These findings highlight distinct virome profiles in SjD and provide mechanistic evidence supporting the role of Vientovirus in triggering autoimmunity through molecular mimicry.}, }
@article {pmid40921287, year = {2025}, author = {Akel, R and Zaki, AI and Kerekes, &#xc9; and Kacsir, I and Kiss, GA and Freytag, C and Szoták, E and Boros-Pál, D and Janka, EA and Kardos, G and Bai, P and Somsák, L and Kun, S and Sipos, A and Bokor, &#xc9;}, title = {Platinum-group metal half-sandwich complexes with C-glucopyranosyl 1,2,3-triazoles and isoxazoles as ligands: synthesis and evaluation as antineoplastic and antimicrobial agents.}, journal = {European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences}, volume = {}, number = {}, pages = {107259}, doi = {10.1016/j.ejps.2025.107259}, pmid = {40921287}, issn = {1879-0720}, abstract = {Half-sandwich complexes of platinum-group metals are a widely studied subgroup of organometallic compounds with promising anticancer and antimicrobial properties. Recently, we have published a set of polyhapto arene/arenyl Ru(II), Os(II), Ir(III) and Rh(III) complexes with hetaryl-substituted 1-N-glucopyranosyl-1,2,3-triazole and C-glycopyranosyl-1,3,4- and -1,2,4-oxadiazole-type N,N-bidentate ligands, several of which exhibited (sub)micromolar antineoplastic and bacteriostatic potencies. The structure-activity relationships of these series indicated that the nature of the azole ring and its way of connection to the pyranoid sugar unit played crucial roles in the biological activity of such complexes. In order to further study the influence of the five-membered heteroaromatic moiety, in this work we have synthesised new complexes with O-protected 4-C-(β-D-glucopyranosyl)-1-(pyridin-2-yl)-1,2,3-triazoles and 5-C-(β-D-glucopyranosyl)-3-(pyridin-2-yl)-isoxazoles as N,N-chelating ligands of η[6]-p-cym-Ru(II)/Os(II) and η[5]-Cp*-Ir(III)/Rh(III) complexes and have studied their cytostatic and antibacterial properties. All but the Rh(III)-derived complexes exerted cytostasis on a plethora of neoplasia cell models. The Ru(II)- and Os(II)-based complexes had the best IC50 values. The isoxazole-containing compounds outperformed the triazole-containing ones in terms of their cytostatic properties with submicromolar IC50 values. A subset of the complexes with Ru(II) and Ir(III) ions had bacteriostatic properties with low micromolar MIC values.}, }
@article {pmid40920777, year = {2025}, author = {Nendl, A and Raju, SC and Braadland, PR and Nordborg, A and Bratseth, V and Broch, K and Jørgensen, SF and Aukrust, P and Kristiansen, K and Hov, JR and Trøseid, M and Awoyemi, A}, title = {Circulating metabolites in patients with chronic heart failure are not related to gut leakage or gut dysbiosis.}, journal = {PloS one}, volume = {20}, number = {9}, pages = {e0331692}, doi = {10.1371/journal.pone.0331692}, pmid = {40920777}, issn = {1932-6203}, mesh = {Humans ; *Dysbiosis/blood/microbiology/metabolism ; *Heart Failure/blood/microbiology/metabolism/physiopathology ; Male ; Female ; *Gastrointestinal Microbiome ; Middle Aged ; Aged ; Feces/microbiology ; Chronic Disease ; Case-Control Studies ; Metabolomics ; Metabolome ; }, abstract = {BACKGROUND: The gut microbiota produces numerous metabolites that can enter the circulation and exert effects outside the gut. Several studies have reported altered gut microbiota composition and circulating metabolites in patients with chronic heart failure (HF) compared to healthy controls. Limited data is available on the interplay between dysbiotic features of the gut microbiota and altered circulating metabolites in HF patients. We aimed to examine differences in circulating metabolites between people with and without chronic HF, and their association with gut microbiota dysbiosis and cardiac function.<br><br>METHODS: We collected plasma, serum, and stool samples from 123 adult patients with stable chronic HF and left ventricular ejection fraction (LVEF) &#x2264;40%, and healthy controls (plasma: n&#x2009;=&#x2009;51, stool samples: n&#x2009;=&#x2009;69). Metabolomic and lipidomic profiling of plasma was performed using liquid chromatography with tandem mass spectrometry. Principal component analysis was used to explore differences in circulating profiles. Over-representation analysis was performed to identify pathways in which relevant metabolites were involved. Stool samples were sequenced using shotgun metagenomics. We calculated a dysbiosis index based on differential abundances of microbial taxa in patients vs. controls.<br><br>RESULTS: After adjusting for age, sex, and sampling location, we identified 67 enriched metabolites and 24 enriched lipids, and 115 depleted metabolites and 6 depleted lipids in HF patients compared to healthy controls. LVEF, N-terminal pro B-type natriuretic peptide, gut leakage markers, dysbiosis index, and fiber intake were not significantly related to any of the differentially abundant metabolites or lipids. Pathways related to energy metabolism differed most between HF patients and controls, however medication adjustment abolished all differences in circulating profiles.<br><br>CONCLUSIONS: Patients with chronic HF had distinct metabolomic and lipidomic profiles and energy metabolism differed significantly compared to healthy controls before adjusting for medication use. However, the alterations were not related to gut dysbiosis, gut leakage markers, cardiac function, or fiber intake.}, }
@article {pmid40920735, year = {2025}, author = {Mumcu, H and Zaugg, J and Keles, I and Kayrav, A and Balci, N and Nelson, DR and Hugenholtz, P and Gillam, EMJ and Gul Karaguler, N}, title = {Exploring extreme environments in Türkiye for novel P450s through metagenomic analysis.}, journal = {PloS one}, volume = {20}, number = {9}, pages = {e0330523}, doi = {10.1371/journal.pone.0330523}, pmid = {40920735}, issn = {1932-6203}, mesh = {*Metagenomics/methods ; *Cytochrome P-450 Enzyme System/genetics/metabolism/classification ; Phylogeny ; *Extreme Environments ; *Metagenome ; }, abstract = {Cytochrome P450 enzymes (P450s), particularly those of microbial origin, are highly versatile biocatalysts capable of catalyzing a broad range of regio- and stere-oselective reactions. P450s derived from extremophiles are of particular interest due to their potential tolerance to high temperature, salinity, and acidity. This study aimed to identify and classify novel microbial P450 enzymes from extreme environments across Türkiye, including hydrothermal springs, hypersaline lakes, and an acid-mine drainage site. The focus of this study was on classifying the sequence diversity of P450 enzymes in these sites. To that end, shotgun metagenomic analysis of six sites, using de novo binning, phylogenetic analysis, and functional gene annotation, was used to discover 311 putative P450 sequences, assigned to 87 families and 158 subfamilies, including 8 novel families and 49 new subfamilies. Of these, 237 were in 138 metagenomic bins, including 45 high-quality metagenome-assembled genomes. The distribution of P450 families varied across sites, reflecting distinct environmental conditions and microbial community compositions. These findings highlight the untapped potential of Türkiye's extreme habitats as a source of novel biocatalysts. Beyond their industrial relevance, extremophile-derived P450s may also play key roles in enabling microbial adaptation to harsh environmental conditions, through their involvement in stress-responsive metabolic pathways and structurally resilient enzyme forms. This work provides a foundation for future studies into both their biotechnological applications and ecological functions.}, }
@article {pmid40920725, year = {2025}, author = {Deng, S and Wu, Y and Hu, P and Lin, J and Yao, J and Wang, B}, title = {Detection of pathogens and epidemiological characteristics of community-acquired pneumonia in children using metagenomic next-generation sequencing.}, journal = {Journal of infection in developing countries}, volume = {19}, number = {8}, pages = {1189-1195}, doi = {10.3855/jidc.20668}, pmid = {40920725}, issn = {1972-2680}, mesh = {Humans ; *Community-Acquired Infections/epidemiology/microbiology/virology ; Child, Preschool ; Infant ; Child ; Male ; Retrospective Studies ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Female ; Bronchoalveolar Lavage Fluid/microbiology/virology ; Infant, Newborn ; *Pneumonia/epidemiology/microbiology ; Seasons ; Adolescent ; Sputum/microbiology/virology ; *Bacteria/isolation &amp; purification/classification/genetics ; Fungi/isolation &amp; purification/genetics/classification ; Community-Acquired Pneumonia ; }, abstract = {INTRODUCTION: Community-acquired pneumonia (CAP) is a common respiratory disease in children and a significant factor in child mortality.<br><br>METHODOLOGY: We aimed to investigate metagenomic next-generation sequencing (mNGS) technology to explore pathogens and epidemiological characteristics of pediatric CAP. We retrospectively analyzed mNGS detection and microbiological culture results of bronchoalveolar lavage fluid (BALF) and sputum samples from children with CAP.<br><br>RESULTS: Mycoplasma pneumoniae was the predominant pathogen. Bacteria/fungi detection rates using mNGS in sputum and BALF were higher than those using microbiological culture (p < 0.05). Cytomegalovirus was the predominant pathogen in children aged 0-1; Mycoplasma pneumoniae was the predominant pathogen in those over 1. Haemophilus influenzae, Mycoplasma pneumoniae, human bocavirus 1, and Streptococcus pneumoniae were the predominant pathogens in spring, summer, autumn, and winter, respectively.<br><br>CONCLUSIONS: mNGS is superior to traditional microbiological culture for pediatric CAP potential pathogen detection. CAP pathogenic infection characteristics at different ages and seasons detected by mNGS will benefit clinical practitioners in the prevention and treatment of pediatric CAP in their local/regional areas.}, }
@article {pmid40920721, year = {2025}, author = {Wang, SK and Zhang, XT and Liu, YE and Wang, MT}, title = {Metagenomic next-generation sequencing for diagnosis of severe pneumonia caused by Nocardia otitidiscaviarum.}, journal = {Journal of infection in developing countries}, volume = {19}, number = {8}, pages = {1269-1275}, doi = {10.3855/jidc.20869}, pmid = {40920721}, issn = {1972-2680}, mesh = {Humans ; Female ; Aged ; *Nocardia/genetics/isolation &amp; purification/classification ; *Nocardia Infections/diagnosis/drug therapy/microbiology ; *High-Throughput Nucleotide Sequencing ; *Pneumonia, Bacterial/diagnosis/microbiology/drug therapy ; Anti-Bacterial Agents/therapeutic use ; *Metagenomics/methods ; Tomography, X-Ray Computed ; Community-Acquired Infections/diagnosis/microbiology/drug therapy ; Trimethoprim, Sulfamethoxazole Drug Combination/therapeutic use ; }, abstract = {INTRODUCTION: Nocardia spp. are Gram-positive, aerobic actinomycetes, which can cause pulmonary, primary cutaneous, and lymphocutaneous infections. However, severe pneumonia caused by Nocardia otitidiscaviarum has rare reported.<br><br>PATIENT CONCERNS: In this case report, a 73-year-old female presented with a 7-day history of fever, cough, followed by a 1-day history of dyspnea. Both lungs showed patchy shadows on a chest CT scan. Bronchoalveolar lavage and mNGS were performed for the rapid diagnosis of the Nocardia otitidiscaviarum induced infection.<br><br>DIAGNOSIS: Community-acquired pneumonia was diagnosed following clinical assessment, including characteristic physical examination findings, abnormal laboratory results, and consolidations observed on CT imaging. And the evidence of pathogen was supplied by mNGS.<br><br>INTERVENTIONS: The anti-infection therapy regimen was: trimethoprim-sulfamethoxazole (1.44 g q6h) for 3 months according to the detection of the Nocardia otitidiscaviarum.<br><br>OUTCOMES: After 3 months of follow-up, the patient has a good outcome and chest CT suggested that the inflammation in the lungs had been almost absorbed.<br><br>CONCLUSIONS: Rapid pathogen identification is pivotal for enhancing clinical outcomes and survival in severe pneumonia patients. This case report presents an exceptional case of severe pneumonia caused by Nocardia otitidiscaviarum and the uncommon potential occurrence of human-to-human transmission. mNGS could help avoid misdiagnosis and mistreatment in clinical practice.}, }
@article {pmid40920635, year = {2025}, author = {Xie, P and Shen, J and Yang, Y and Wang, X and Liu, W and Cao, H and Zheng, Y and Wu, C and Mao, G and Chen, L and He, J and Zheng, W and Yang, Z and Zhang, X and Jiang, X and Yang, X and Fang, K and Zhang, Z and Xue, X and Chen, X and Wang, C and Liu, X and Liu, L and Yao, X and Jing, N and Xie, W and Liu, J and Cao, H and Luo, Z and Fang, X and Lin, C}, title = {Digital reconstruction of full embryos during early mouse organogenesis.}, journal = {Cell}, volume = {188}, number = {17}, pages = {4754-4772.e18}, doi = {10.1016/j.cell.2025.05.035}, pmid = {40920635}, issn = {1097-4172}, mesh = {Animals ; *Organogenesis/genetics ; Mice ; *Embryo, Mammalian/metabolism ; Gene Expression Regulation, Developmental ; Mesoderm/metabolism ; Embryonic Development ; Signal Transduction ; Transcriptome ; Endoderm/metabolism ; Female ; Heart/embryology ; }, abstract = {Early organogenesis is a crucial stage in embryonic development, characterized by extensive cell fate specification to initiate organ formation but also by a high susceptibility to developmental defects. Here, we profiled 285 serial sections from six E7.5-E8.0 embryos to generate full spatiotemporal transcriptome and signal maps during early organogenesis at single-cell resolution. By developing SEU-3D, we reconstructed digital embryos, enabling investigation of regionalized gene expression in the native spatial context. We established a space-informed gene-cell co-embedding approach, systematically characterized the spatial atlas of endoderm and mesoderm derivatives, and elucidated signaling networks across germ layers and cell types. Furthermore, we characterized a primordium determination zone (PDZ) formed along the anterior embryonic-extraembryonic interface at E7.75, and it revealed that the coordinated signaling communications contribute to the formation of cardiac primordium. Collectively, the high-resolution "digital embryo" provides significant insights into early organogenesis and a unique spatial platform for studying development and diseases.}, }
@article {pmid40920605, year = {2025}, author = {Yu, L and Jia, R and Liu, S and Li, S and Shen, Y and Rensing, C and Zhou, S}, title = {Rice Root Iron Plaque as a Mediator to Stimulate Methanotrophic Nitrogen Fixation.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.4c11221}, pmid = {40920605}, issn = {1520-5851}, abstract = {Iron plaque (IP) on rice root surfaces has been extensively documented as a natural barrier that effectively reduces contaminant bioavailability and accumulation. However, its regulatory mechanisms in rhizospheric methane oxidation and biological nitrogen fixation (BNF) remain elusive. This study reveals a previously unrecognized function of IP: mediating methanotrophic nitrogen fixation through coupled aerobic methane oxidation and IP reduction (Fe-MOX). Using a hydroponic coculture system integrating methane-oxidizing bacteria and rice seedlings, we demonstrated that IP enhanced microbial methane oxidation by 46.8% and significantly stimulated BNF rate by 33.6%, with methane-derived carbon accounting for 89.1% of the BNF energy source. Notably, dissolved iron removal did not diminish the BNF enhancement, excluding mediation by soluble iron species. Intriguingly, ferrihydrite supplementation at equivalent iron concentrations failed to replicate the BNF stimulation observed with IP, suggesting the indispensability of root-associated iron redox cycling. Mechanistic analyses identified that Methylosinus/Methylocystis species mediated Fe(III) reduction, synergistically collaborating with specific rhizobial strains to execute Fe-MOX-dependent BNF. These findings uncover a previously overlooked yet pronounced contribution of IP to BNF, providing novel insights for developing dual-strategy approaches to mitigate methane emissions and reduce nitrogen fertilizer dependency in paddy ecosystems.}, }
@article {pmid40920330, year = {2025}, author = {Allos, H and John, TM and Stewart, AG}, title = {Microbial cell-free DNA for diagnosis of bacterial and fungal infection in the immunocompromised host - what do we know?.}, journal = {Current opinion in infectious diseases}, volume = {}, number = {}, pages = {}, pmid = {40920330}, issn = {1473-6527}, abstract = {PURPOSE OF REVIEW: Plasma metagenomic next-generation sequencing (mNGS) enables detection of microbial cell-free deoxyribonucleic acid (mcfDNA) in blood without the need for culture or organism-specific primers. Here, we review clinical performance, methodological variability, and real-world application of plasma mNGS for infectious disease diagnosis in immunocompromised hosts (ICHs).<br><br>RECENT FINDINGS: Plasma mNGS has rapidly gained attention as a novel diagnostic tool for infections in ICHs, offering broad-range pathogen detection from a noninvasive blood sample. A growing number of observational studies have assessed its diagnostic yield, clinical impact, and potential to reduce invasive procedures or time to diagnosis. However, results remain variable, with significant differences in study design, patient populations, and adjudication methods. While some studies report meaningful added value, others highlight challenges related to clinical interpretation, limited standardization, and uncertain cost-effectiveness. Moreover, although mNGS offers a wide organismal scope, its sensitivity is influenced by pathogen type, immune status, and technical limitations - particularly in fungal infections and low-burden diseases. Overall, mNGS has yet to find a clearly defined role in routine diagnostic workflows.<br><br>SUMMARY: Understanding the current evidence, limitations, and variability surrounding plasma mNGS is essential to guide its appropriate clinical use and to inform future integration into diagnostic pathways for ICHs.}, }
@article {pmid40919923, year = {2025}, author = {Francis, JD and Yanaç, K and Uyaguari-Diaz, MI}, title = {Seasonal patterns of viromes in urban aquatic environments of Manitoba.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0040824}, doi = {10.1128/aem.00408-24}, pmid = {40919923}, issn = {1098-5336}, abstract = {UNLABELLED: Although wastewater treatment plants harbor many pathogens, traditional methods that monitor the microbial quality of surface water and wastewater have not changed since the early 1900s and often disregard the presence of other types of significant waterborne pathogens such as viruses. We used metagenomics and quantitative PCR to assess the taxonomy, functional profiling, and seasonal patterns of DNA and RNA viruses, including the virome distribution in aquatic environments receiving wastewater discharges. Environmental water samples were collected at 11 locations in Winnipeg, Manitoba, along the Red and Assiniboine rivers during the Spring, Summer, and Fall 2021. Samples were filtered and underwent skimmed milk flocculation for viral concentration. The taxonomy of classified DNA was primarily bacteriophages such as Autographiviridae, Kyanoviridae, and Peduoviridae, which were abundant to a lesser extent. Phage-related functionalities such as portal proteins and bacteriophage T4 major head proteins accounted for approximately 20%-40% of aquatic samples across seasons, which may possibly correspond to the DNA phages that were previously identified. RNA viruses went unclassified in the study; however, similar to DNA viruses, many were found to be non-enveloped or "naked viruses" such as Partiviridae, Picobirnaviridae, Tombusviridae, and Picornaviridae, which accounted for 3%-30% of RNA viruses in the study locations across season. Interestingly, aquatic samples were revealed to maintain an abundance of RNA phage-related functionalities such as long tail fiber protein and putative tail proteins, which accounted for approximately 2%-5% of aquatic samples during the Fall of 2021.<br><br>IMPORTANCE: Municipal wastewater effluents discharged into the Red and Assiniboine rivers of Winnipeg, Manitoba, rely on traditional methods that monitor the microbial quality of effluents and receiving surface waters focus solely on the detection of coliforms, which are not necessarily good indicators of viruses or other pathogens. There is also a lack of current wastewater system effluent regulations at the federal and provincial level. Furthermore, previous literature has shown that when viral DNA and RNA sequences are blasted against current genomic databases, approximately 50% of the viral reads are classified as unknown. The significance of our research in characterizing the virome distribution in aquatic environments addresses a knowledge gap in the current effluent guidelines and a need for regulatory practices. In the long run, fecal indicator bacteria, combined with the detection of enteric viruses, may complement assessment of water quality in effluents discharged into rivers.}, }
@article {pmid40919801, year = {2025}, author = {Chamonara, K and Uddin, MS and Masum, MHU}, title = {16S rRNA metagenome analysis of gut bacteriome of Rohu (Labeo rohita) from Halda River and Kaptai Lake, Bangladesh.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0059025}, doi = {10.1128/mra.00590-25}, pmid = {40919801}, issn = {2576-098X}, abstract = {This research evaluated the gut microbiota of Rohu fish from the Halda River and Kaptai Lake in Bangladesh by 16S rRNA sequencing. Distinct microbial profiles were identified, with Halda samples concentrated in pathogens and Kaptai samples abundant in probiotics.}, }
@article {pmid40919785, year = {2025}, author = {Zou, Y-y and Yu, B-j and He, C and Ding, L and Xu, X and Wan, J-h and Lei, Y-p and Huang, X and Xiong, H-f and He, W-h and Luo, L-y and Xia, L and Lv, N-h and Zhu, Y}, title = {Rifaximin reduces gut-derived inflammation in severe acute pancreatitis: an experimental animal model and randomized controlled trial.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0129925}, doi = {10.1128/spectrum.01299-25}, pmid = {40919785}, issn = {2165-0497}, abstract = {UNLABELLED: Severe acute pancreatitis (SAP) is characterized by systemic inflammation and intestinal barrier dysfunction and is often associated with gut microbiota dysbiosis. Rifaximin, a gut-specific non-absorbable antibiotic, is known to modulate the gut microbiota. Here, we investigated rifaximin's effects and mechanisms in SAP using murine models and a single-center, open-label, randomized controlled trial (Chinese Clinical Trial Registry: ChiCTR2100049794). In mice, rifaximin attenuated pancreatic injury and systemic inflammation and altered gut microbiota composition by decreasing mucin-degrading genera such as Akkermansia (P < 0.05). These protective effects persisted in antibiotic-treated and germ-free mice, suggesting mechanisms not solely dependent on gut microbiota modulation. In patients with predicted SAP (n = 60), rifaximin significantly reduced systemic inflammation compared with controls. WBC decreased from a median of 11.50 × 10[9]/L (IQR 8.76-15.68) to 8.49 × 10[9]/L (6.93-10.20; P = 0.04) and TNF-α from 15.05 pg/mL (12.73-19.75) to 11.00 pg/mL (8.74-15.40; P = 0.009). However, the incidence of culture-confirmed infection did not differ between the rifaximin and control groups (13.3% vs. 13.3%; RR, 1.00; 95% CI, 0.28-3.63). Adverse events were comparable between groups. Metagenomic analyses revealed suppression of mucin-degrading bacteria (e.g., Akkermansia, Bacteroides fragilis, and Hungatella hathewayi) (P < 0.05) and reductions in mucin-degrading carbohydrate-active enzymes, including sialidases and fucosidases. In conclusion, among patients with predicted SAP, rifaximin did not reduce culture-confirmed infectious complications within 90 days after randomization compared with standard care, despite significant improvements in systemic inflammatory markers and selected fecal microbiome features. Larger randomized controlled trials are warranted to validate these findings.<br><br>IMPORTANCE: Although rifaximin has been used to target gut-derived inflammation in other contexts, its role in SAP remains largely unexplored. In this study, rifaximin treatment was associated with reduced pancreatic injury and systemic inflammation in both murine models and patients with predicted SAP. Treatment also led to changes in gut microbial composition, notably a decrease in mucin-degrading taxa. Importantly, similar protective effects were also observed in antibiotic-treated and germ-free mice, indicating that rifaximin may act via microbiota-dependent and host-directed pathways. These findings offer novel insights into the gut-pancreas axis and suggest that rifaximin holds therapeutic potential by modulating gut microbial composition and host inflammatory responses in SAP.}, }
@article {pmid40919775, year = {2025}, author = {Liu, J and Yu, L and Ma, X and Wang, Q and Jin, X and Peng, S and Fu, L}, title = {Clinical Characteristics, Radiological, and Outcomes of Mucormycosis: A 14-Year Retrospective Study From Southern China.}, journal = {Mycoses}, volume = {68}, number = {9}, pages = {e70110}, doi = {10.1111/myc.70110}, pmid = {40919775}, issn = {1439-0507}, support = {//National Natural Science Foundation of China/ ; //Natural Science Foundation of Hunan Province/ ; }, mesh = {Humans ; *Mucormycosis/epidemiology/diagnostic imaging/drug therapy/diagnosis/microbiology/pathology ; Retrospective Studies ; Male ; Female ; China/epidemiology ; Middle Aged ; Adult ; Aged ; Antifungal Agents/therapeutic use ; Tomography, X-Ray Computed ; Treatment Outcome ; Tertiary Care Centers ; Comorbidity ; Amphotericin B/therapeutic use ; Young Adult ; }, abstract = {BACKGROUND: Mucormycosis is a rare, rapidly progressive fungal infection with a high mortality rate. However, clinical data of mucormycosis patients, especially those related to adverse outcomes in China, remain limited.<br><br>OBJECTIVE: To enhance understanding of the clinical characteristics of different infection site mucormycosis and identify the factors associated with adverse outcomes.<br><br>METHODS: A 14-year retrospective study was conducted at a tertiary care hospital in China. Patients were categorised based on the site of infection and clinical outcomes.<br><br>RESULTS: From 2010 to 2024, 32 cases of mucormycosis were identified. Among these, pulmonary mucormycosis (PM) was the most common infection site, followed by disseminated mucormycosis. All patients had underlying comorbidities, predominantly chronic lung disease (37.5%) and diabetes mellitus (34.3%). All received pharmacological treatment, most commonly amphotericin B; 15.6% of patients additionally underwent surgical intervention. Chest CT findings in PM cases most frequently revealed bilateral involvement (68.8%) and cavitation (43.8%). Diagnosis was primarily based on metagenomic next-generation sequencing (mNGS, n&#x2009;=&#x2009;14) and histopathological examination (n&#x2009;=&#x2009;11). Adverse outcomes were observed in 46.9% of patients and were significantly associated with corticosteroid or immunosuppressant use, COVID-19 co-infection, disseminated disease, thrombocytopenia, hypoalbuminemia, elevated aspartate aminotransferase (AST), increased incidence of complications, and ICU admission (all p&#x2009;<&#x2009;0.05).<br><br>CONCLUSION: Pulmonary mucormycosis was the predominant subtype in this cohort and was frequently associated with chronic lung disease and diabetes. The high incidence of adverse outcomes highlights the necessity for early diagnosis, prompt antifungal therapy, and aggressive management of complications to improve patient survival.}, }
@article {pmid40919702, year = {2025}, author = {Zhang, L and Tian, Y and Li, L and Zhan, W and Sun, H and Ren, N and Tang, Z and Ngo, HH}, title = {Movement Mechanisms Harness Lévy Flight for Energy-Efficient Wastewater Treatment in Microalgae-Bacteria Systems.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e04676}, doi = {10.1002/advs.202504676}, pmid = {40919702}, issn = {2198-3844}, support = {52341001//National Natural Science Foundation of China/ ; 2022M710953//Postdoctoral Research Foundation of China/ ; 2022ZX02C16//Heilongjiang Key R&amp;D Programme/ ; ES202424//The Open Project of State Key Laboratory of Urban Water Resources and Environment/ ; }, abstract = {Microalgae-bacteria symbiosis system is significant for sustainable and low-carbon wastewater treatment, with self-aggregation being key to its stable operation and effective pollutant removal. Cellular motility is the main driving force behind self-aggregation, crucial for symbiosis stability, but the characteristics and patterns involved still remain largely unexplored. Here, cellular movement dynamics into the microalgae-activated sludge model (ASM3) is incorporated, enabling synchronized simulation of metabolic activities and movement behaviors through physical and biochemical interactions in bioreactor systems. These findings indicate that microalgae induce bacterial movement towards Lévy flights, thereby increasing the bacterial encounter rate by 12.20%, augmenting signaling molecule concentration and biomass by 20.0% and 27.3%, respectively, which in turn strengthens the bacteria self-aggregation effect. Through practical reactor operations with metagenomic analysis, the efficacy of this model in elucidating self-aggregation is further corroborated, improving system stability and pollutant removal efficiency. An optimized microalgae-bacteria system reduces energy costs associated with cellular aggregation processes, economizing on the cost of chemotaxis-related proteins. This study not only elucidate the unique role of Lévy flight in self-aggregation, enhancing the understanding of microalgae-bacteria symbiosis, but also establish response mechanisms between motility patterns and operation dynamics. This allows for targeted regulation across various biosystems, ensuring cost-effective wastewater treatment and proactive prediction.}, }
@article {pmid40919477, year = {2025}, author = {Xiang, S and Li, J and Chen, Z and Cheng, R and Wang, L and Yu, L and Wei, G and Guan, X and Briggs, BR and King, G and Jiang, H and Shao, Z}, title = {Ecological diversity and metabolic strategies of widespread Marinisomatota in global oceans.}, journal = {Marine life science &amp; technology}, volume = {7}, number = {3}, pages = {523-536}, pmid = {40919477}, issn = {2662-1746}, abstract = {UNLABELLED: Marinisomatota (formerly recognized as Marinimicrobia, Marine Group A, and SAR406) are ubiquitous and abundant in marine environments, traditionally characterized as heterotrophic microorganisms. However, certain members of Marinisomatota have demonstrated the capacity to harness light for carbon dioxide fixation and the synthesis of organic compounds, thriving in the translucent zone or transitioning between the translucent and aphotic layers. The metabolic strategies driving the shift in trophic behaviors, and the factors influencing these transitions, remain largely unexplored. In this study, we investigate the metabolic strategies, ecological distribution, and dietary patterns of Marinisomatota through the analysis of metagenomic and metatranscriptomic data sourced from the global open oceans. A total of 1,588 Marinisomatota genomes were retrieved, representing one class, two orders, 14 families, 31 genera, and 67 species. These organisms are predominantly found in low-latitude marine regions, with relative abundances ranging from 0.18 to 36.21%. Among the 14 families, S15-B10, TCS55, UBA1611, UBA2128, and UBA8226 exhibit potential for light-dependent processes associated with Crassulacean acid metabolism (M00169). Three distinct metabolic strategies were identified within Marinisomatota: MS0 (photoautotrophic potential), MS1 (heterotrophic with a pronounced glycolytic pathway), and MS2 (heterotrophic without glycolysis). The emergence of these metabolic strategies may be a response to nutrient limitations within the ocean. This study reveals the potential for mixotrophic strategies in Marinisomatota, underscoring the critical interplay between life history traits and metabolic strategies in the evolution of novel nutritional groups.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-025-00293-x.}, }
@article {pmid40919468, year = {2025}, author = {Liu, S and Chen, Q and Qiu, X and Li, W and Tang, K}, title = {Metagenomic analysis reveals genetic coupling between TonB-dependent transporters and extracellular enzymes in coastal bacterial communities.}, journal = {Marine life science &amp; technology}, volume = {7}, number = {3}, pages = {478-491}, pmid = {40919468}, issn = {2662-1746}, abstract = {UNLABELLED: Marine heterotrophic prokaryotes initially release extracellular enzymes to cleave large organic molecules and then take up ambient substrates via transporters. Given the direct influence of extracellular enzymes on nutrient availability, understanding their diversity and dynamics is crucial in comprehending microbial interactions and organic matter cycling in aquatic ecosystems. In this study, metagenomics was employed to investigate the functional diversity and dynamics of extracellular enzymes and transporters in coastal waters over a 22-day period. The metagenome-derived gene pool of organic matter-degrading secretory enzymes and transporters was primarily contributed by three major bacterial classes. Bacteroidota were the primary contributors to the gene pool of secretory carbohydrate-active enzymes (CAZymes), whereas Gammaproteobacteria contribute more to secretory peptidases and TonB-dependent transporters (TBDTs), and Alphaproteobacteria to ATP-binding cassette (ABC) transporters. The distinct substrate targets of the enzymes and transporters combined with the unique dynamics of these taxa across depth layers suggest that organic matter degradation and uptake machinery played a role in ecological niche partitioning. At the community level, the abundance of TBDT genes was more positively correlated with extracellular enzymes than ABC transporters. To further explore taxon-specific differences, we reconstructed 163 bacterial and archaeal metagenome-assembled genomes (MAGs). Correlation patterns at the MAG level varied across taxa: Bacteroidota MAGs exhibited significant positive correlations between TBDTs and extracellular enzymes, whereas Gammaproteobacteria and Alphaproteobacteria MAGs showed weak or no significant correlations. These results suggest the diversity of ecological strategies among marine heterotrophic bacteria and highlight a potential coregulation or functional linkage between extracellular enzymes and TBDTs in the metabolism of marine heterotrophic prokaryotes. Our study advances the understanding of the microbial adaptations driving carbon and nutrient cycling.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-025-00314-9.}, }
@article {pmid40919007, year = {2025}, author = {Wei, L and Yu, Y and Wang, S and Dong, G and Niu, Y}, title = {Comparison of the Diagnostic Performance of Culture, Histopathology, and mNGS for Periprosthetic Joint Infection Using Periprosthetic Tissue Samples: A Prospective Clinical Study.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {4647-4657}, pmid = {40919007}, issn = {1178-6973}, abstract = {BACKGROUND: This study evaluated the applicability of histopathology, culture, and Metagenomic next-generation sequencing (mNGS) in diagnosing periprosthetic joint infection (PJI).<br><br>METHODS: In this prospective trial, 215 consecutive patients with suspected knee PJI were enrolled. Tissue specimens were aseptically collected and processed for histopathological analysis, culture, and mNGS. PJI diagnosis was primarily based on the 2011 MSIS criteria, with reference to the 2018 ICM criteria for improved diagnostic accuracy. Sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), positive likelihood ratio (PLR), and negative likelihood ratio (NLR) of each diagnostic method were calculated.<br><br>RESULTS: Among 58 patients included in the final analysis, 38 were diagnosed with PJI and 20 without PJI. The mNGS assay demonstrated a sensitivity of 63.2% (95% CI: 53.6-77.7%), specificity of 80.0% (75.7-90.1%), PPV of 85.7% (76.4-95.3%), NPV of 53.3% (44.6-61.2%), PLR of 1.84 (1.22-2.77), and NLR of 0.27 (0.10-0.40). Culture showed higher specificity at 95.0% (84.6-99.8%) and PPV at 96.5% (88.7-99.7%), with sensitivity of 68.4% (58.2-78.9%). Histopathology exhibited 52.6% sensitivity and perfect specificity (100%). The most commonly detected pathogens by both culture and mNGS were Staphylococcus aureus and coagulase-negative Staphylococci, which are frequently implicated in PJI.<br><br>CONCLUSION: mNGS shows promise as a complementary tool for diagnosing PJI, especially in culture-negative or atypical cases. However, it did not outperform conventional methods in accuracy. Its limitations-including a high false-positive rate, interpretive challenges, and lack of susceptibility data-warrant cautious use. Further large-scale studies are needed to define its role in clinical decision-making.}, }
@article {pmid40919002, year = {2025}, author = {Yang, L and Zhang, Z and Liang, Q and Zhang, H and Wang, Y and Zhuo, C}, title = {Severe Acute Bacterial Skin and Skin Structure Infection Following Fish Spine Injury: A Case Report and Literature Review.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {4633-4645}, pmid = {40919002}, issn = {1178-6973}, abstract = {This study presents a rare case of severe acute bacterial skin and soft tissue infection (ABSSSI) following freshwater fish spike injury in a 73-year-old man. Within 24 hours of sustaining the wound, the patient developed septic shock and progressive necrotizing fasciitis. Despite early administration of broad-spectrum antibiotics and intensive care, his condition deteriorated, necessitating below-the-elbow amputation on hospital day four. Metagenomic next-generation sequencing (mNGS) identified Aeromonas veronii as the causative agent. Although the patient showed temporary improvement postoperatively, he later developed hospital-acquired pneumonia and succumbed to complications two months later. This case highlights the potential severity of ABSSSIs caused by aquatic pathogens, particularly in immunocompromised individuals. mNGS provides a comprehensive pathogen snapshot within hours of sample receipt, enabling timely refinement of empiric regimens prior to antimicrobial susceptibility testing availability. Early surgical intervention is essential to control infections and improve clinical outcomes.}, }
@article {pmid40918894, year = {2025}, author = {Apuy Rodríguez, F and Chacón Quirós, M and Alvarado Fernández, ML and Alvarado Mora, ML and Vanegas Navarro, P}, title = {Microbiome of the Ocular Surface: Resident or Transient Ecosystem?.}, journal = {Cureus}, volume = {17}, number = {8}, pages = {e89487}, pmid = {40918894}, issn = {2168-8184}, abstract = {The ocular surface microbiome (OSM) is a low-density, low-diversity microbial ecosystem influenced by host and environmental factors, including age, hygiene, contact lens use, and systemic disease. Unlike other mucosal sites, the eye lacks a well-defined core microbiome, and its microbial composition varies significantly between individuals. Advances in metagenomics have revealed that commensals such as Corynebacterium and Staphylococcus may contribute to immune regulation and homeostasis. Dysbiosis has been linked to ocular surface disorders, such as dry eye disease (DED), allergic conjunctivitis (AC), and contact lens-related inflammation, with shifts in microbial abundance and diversity. Continued research is needed to define resident versus transient species and to develop microbiome-based diagnostics and therapies.}, }
@article {pmid40918253, year = {2025}, author = {McMahon, S and Franklin, S and Galloway-Peña, J}, title = {Utilization of machine learning to predict antibiotic resistant event outcomes in acute myeloid leukemia patients undergoing induction chemotherapy.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1629422}, pmid = {40918253}, issn = {2235-2988}, mesh = {Humans ; *Machine Learning ; *Leukemia, Myeloid, Acute/drug therapy/microbiology/complications ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Gastrointestinal Microbiome/drug effects ; Male ; Female ; Middle Aged ; *Induction Chemotherapy/adverse effects ; Bacteria/drug effects/genetics/classification ; Aged ; Adult ; Feces/microbiology ; Metagenomics ; *Drug Resistance, Bacterial ; }, abstract = {INTRODUCTION: Acute myeloid leukemia (AML) patients are highly susceptible to infection. Moreover, prophylactic and empirical antibiotic treatment during chemotherapy disrupts the gut microbiome, raising the risk for antibiotic-resistant (AR) opportunistic pathogens. There is limited data on risk factors for AR infections or colonization events in treated cancer patients, and no predictive models exist. This study aims to combine metagenomic and antibiotic administration data to develop a model predicting AR event outcomes.<br><br>METHODS: Baseline stool microbiome, antibiotic administration, resistome, and clinical metadata from 95 patients were utilized to build a Random Forest model to predict AR infection and colonization events by serious AR threats. Additionally, sparse canonical correlation analysis assessed correlations between microbiome and resistome data, while Spearman correlation networks identified direct associations with AR event outcomes and secondary variables.<br><br>RESULTS: AR-events were identified in 14 of the 95 included patients, with 8 developing AR infections and 9 identified as AR colonized. A Random Forest model predicted AR event outcomes (AUC = 0.73), identifying bacterial taxa and antibiotic resistance gene (ARG) classes as key variables of importance. Methanobrevibacter smithii, Clostridium leptum, and Bacteroides dorei were identified as key taxa associated with reduced risk of AR events, suggesting the potential roles of commensals in maintaining gut microbial resilience during chemotherapy. ARG classes, particularly those conferring resistance to lincosamides, macrolides, and streptogramins, were negatively associated with AR events.<br><br>CONCLUSION: These results underscore the value of integrating microbiome and resistome features to reveal potential protective mechanisms and improve risk prediction for AR outcomes in vulnerable patients.}, }
@article {pmid40918207, year = {2025}, author = {He, X and Zhang, R and Dong, J and Zhen, W and Zhu, L and Ren, J and Ma, X and Wang, F and Zhang, S and Xu, K and Qiu, F and Su, Q and He, J and Zhou, W and Wu, G}, title = {A metagenomic approach for microbial risk assessment and source attribution in high-risk ports of entry environments.}, journal = {Biosafety and health}, volume = {7}, number = {4}, pages = {228-237}, pmid = {40918207}, issn = {2590-0536}, abstract = {The epidemiological characteristics of emerging infectious disease outbreaks in recent years have underscored the critical importance of controlling imported infectious diseases. In this study, we implemented dynamic tracking of microbial invasions by monitoring environmental microbes at the customs and ports. From July to September 2024, a total of 126 environmental samples were collected from three ports of entry in Shenzhen, China. Metagenomic analysis detected 55 non-viral microbial communities and 12 viral taxa. Among these, 26.8 % of the bacteria, 100 % of the fungi, 71.4 % of the protists, and none of the archaea exhibited potential pathogenic properties. Viruses were the most prevalent, including bacteriophages (100 %), unclassified viruses (96.8 %), giant viruses (27.8 %), fungal viruses (4.8 %), and vertebrate viruses (1.6 %). No statistical differences were observed in viral distribution across areas (χ[2] = 18.70, P = 0.541), sites (χ[2] = 14.02, P = 0.597), or ports of entry (χ[2] = 10.27, P = 0.247). However, viral distribution varied significantly across three sampling months (χ[2] = 21.06, P = 0.002), with a higher proportion of giant viruses detected in July. Thirty-nine and forty microorganisms were identified across the six areas and five sites, respectively, with relatively few area/site-specific microorganisms. Four distinct disinfection level zones were categorized: relatively safe zone, less safe zone, general disinfection zone and key disinfection zone. Two strains of viruses with potential pathogenicity were identified: pigeon circovirus and Influenza A virus (H4N2). This study established a metagenomics-based surveillance framework for microbial risk assessment in high-risk port environments and proposed a four-tier disinfection strategy to prioritize high-contact zones. Our findings highlighted environmental metagenomics as a critical complement to traveler screening and provided early warning signals for the prevention and control of imported infectious diseases.}, }
@article {pmid40917822, year = {2025}, author = {Li, Q and Jian, L and Zhao, Q}, title = {Improved Etiological Diagnosis of Nonresolving or Slowly Resolving Pneumonia Through Combined Endobronchial Ultrasound-Guided Biopsy and Metagenomic Sequencing.}, journal = {Canadian respiratory journal}, volume = {2025}, number = {}, pages = {7651699}, pmid = {40917822}, issn = {1916-7245}, mesh = {Humans ; Male ; Female ; Middle Aged ; Aged ; *Pneumonia/diagnosis/microbiology/etiology ; Metagenomics/methods ; Bronchoscopy/methods ; Image-Guided Biopsy/methods ; Adult ; High-Throughput Nucleotide Sequencing ; Pneumonia, Bacterial/diagnosis ; }, abstract = {Background: Nonresolving or slowly resolving pneumonia (NRP) poses a diagnostic challenge because infectious and noninfectious etiologies often mimic community-acquired pneumonia on imaging. Endobronchial ultrasound-guided transbronchial lung biopsy (EBUS-TBLB) improves tissue acquisition for peripheral lesions, whereas metagenomic next-generation sequencing (mNGS) offers culture-independent pathogen detection. Whether their combination enhances etiological clarification of NRP remains uncertain. Methods: A total of 109 consecutive adults with NRP unresponsive to standard antimicrobial therapy were randomized to EBUS-TBLB alone (n = 66) or EBUS-TBLB + mNGS (n = 43). Baseline characteristics, diagnostic yield, and procedure-related complications were recorded. Diagnostic positivity, sensitivity for infectious agents, and safety profiles were compared using χ [2] or Fisher's exact tests, with p < 0.05 considered significant. Results: Overall diagnostic yield increased from 50.0% with EBUS-TBLB to 72.1% with the combined approach (χ [2] = 4.37, p < 0.05). mNGS significantly improved detection of bacterial/fungal pneumonia (0% vs. 13.9%; p < 0.05) and pulmonary tuberculosis (0% vs. 20.9%; p < 0.05). Malignancy remained the predominant diagnosis (57.8% of all cases); yields for most tumor subtypes were comparable between groups. Complication rates did not differ between the two groups: minor bleeding (19.7% vs. 23.3%), hypoxia (50.0% vs. 48.8%), pneumothorax (4.5% vs. 0%), and delayed recovery (4.5% vs. 7.0%) (p > 0.05). No severe adverse events occurred. Conclusions: EBUS-TBLB + mNGS represents a paradigm shift in the diagnosis of complex respiratory cases, integrating imaging with advanced genomics to enhance precision medicine. In practice, early implementation of the EBUS-TBLB + mNGS diagnostic protocol in patients with NRP can help exclude malignancy or confirm an infectious etiology.}, }
@article {pmid40916941, year = {2025}, author = {Blecksmith, SE and Kalanetra, KM and Weng, CY and Suarez, C and Sitepu, IR and Tang, Y and Ehlers Cheang, S and Jiang, S and Cernioglo, K and Damian-Medina, K and Smilowitz, JT and Lebrilla, CB and Mills, DA and Lemay, DG}, title = {Fecal microbiomes from healthy adult consumers of fruits and vegetables exhibit fiber- and donor-specific fermentation: "5 a day" is not enough.}, journal = {Food &amp; function}, volume = {}, number = {}, pages = {}, doi = {10.1039/d5fo00947b}, pmid = {40916941}, issn = {2042-650X}, abstract = {To determine the fermentation capacity of gut microbiomes with diverse plant carbohydrate active enzyme (CAZyme) repertoires, we collected fecal samples from 18 healthy adults who reported consuming at least 5 different fruits and vegetables daily and conducted shotgun metagenome analysis. Five fecal samples with the most diverse CAZymes were then fermented in vitro with 7 different fibers selected for their unique monosaccharide profiles-banana, kale,13-bean soup, flax, coconut flour, MS Prebiotic (resistant starch) and Sunfiber (guar gum)-for 72 hours. Samples were collected at 4 timepoints for 16S sequencing, and pH, SCFAs, and monosaccharide measurements. The largest changes in pH, microbial diversity, monosaccharides, and short chain fatty acids (SCFAs) occurred in the first 24 hours of fermentation. SCFA production was highest with flax and lowest with coconut flour. Fermentation patterns ranged from little change to primary degradation (liberated monosaccharides) to robust production of SCFAs. Abundance of Bifidobacteriaceae, Butyricicoccaceae, and Ruminococcaceae correlated with the highest fermentation, Clostridiaceae, Enterococcaceae, and Eggerthellaceae with the lowest. Samples from three of the participants were more responsive than the other two. The donor-specific and fiber-specific responses seen in our study indicate that dietary guidance to consume 5 servings of fruits and vegetables per day may not be enough to ensure that our gut microbiota is capable of unlocking all of fiber's benefits.}, }
@article {pmid40916294, year = {2025}, author = {Wang, W and Wu, H and Sun, J and Zhai, C and Song, J and Chen, D and Yang, G and Dai, Y and Wang, S and Kong, F}, title = {Enhanced removal of Cr (VI) in constructed wetland with Fe-Ni-LDH-modified crayfish shell biochar: Performance, removal pathways and synergy mechanisms of substrate-microorganism.}, journal = {Journal of hazardous materials}, volume = {497}, number = {}, pages = {139724}, doi = {10.1016/j.jhazmat.2025.139724}, pmid = {40916294}, issn = {1873-3336}, abstract = {In this study, Fe-Ni-layered double hydroxide modified crayfish shell biochar substrate (Fe-Ni-LDH@CSBC) was successfully prepared and introduced into constructed wetland (CW) to research the Cr(VI) removal mechanism through substrate adsorption and microbial action. Adsorption experiments demonstrated the equilibrium adsorption capacities of Fe-Ni-LDH@CSBC for Cr(VI) could reach 1058.48 (C0=10 mg/L) and 1394.59 mg/kg (C0=20 mg/L), respectively. The CW with Fe-Ni-LDH@CSBC showed higher removal efficiencies of COD, TN, TP, and Cr(VI), which respectively reached 72.9 %, 66.8 %, 79.6 %, and 99.3 % with influent Cr(VI) concentration of 50 mg/L. The Fe-Ni-LDH@CSBC stimulated the secretion of extracellular polymeric substances (EPS) (570.6 mg/g VSS), conducive to absorbing Cr(VI) and also delaying or preventing Cr(VI) from entering microorganisms. The increased reduction of Cr(VI) by Fe-Ni-LDH@CSBC was due to its role in enhancing extracellular electron transfer (EET) through boosting cytochrome c, ETSA and NADH levels. Metagenomic sequencing showed that Fe-Ni-LDH@CSBC increased the abundances of resistant microorganisms (Mycobacterium, Mycolicibacterium, and Hyphomicrobium) in CW, and the relative abundance of key functional genes from Cr(VI) reductase (chrR, GST, czcD, zitB, and merR), electron transfer genes (mtrC, fbpC, insB, and afuC) and transport proteins genes (rhtC, pcoB, bpeT, pecM, chrA, and exbB). This research presented an effective method to enhance the removal of Cr(VI) from electroplating wastewater using CW with Fe-Ni-LDH@CSBC.}, }
@article {pmid40915974, year = {2025}, author = {Ribeiro, MC and Colombo, APV and de Oliveira, AM and Lourenço, TGB and Honório, HM and de Freitas, EC and Messora, MR and Furlaneto, FAC}, title = {The Interplay Between Lifestyle and Oral/Faecal Microbial Profiles Among Periodontal Disease Patients: A Cross-Sectional Study.}, journal = {Journal of clinical periodontology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jcpe.70029}, pmid = {40915974}, issn = {1600-051X}, abstract = {AIM: To characterise periodontal and faecal microbiomes of individuals with periodontal health (PH) and diseases, and evaluate associations with periodontal, sociodemographic, anthropometric, nutritional and lifestyle factors.<br><br>MATERIALS AND METHODS: Dental biofilm and faecal samples from individuals (n&#x2009;=&#x2009;24/group) with PH, gingivitis (GG) and periodontitis (PE) were sequenced (16S rRNA). Anthropometric data and questionnaires on demographics, lifestyle, diet and intestinal habits were collected. Data were statistically analysed (p&#x2009;<&#x2009;0.05).<br><br>RESULTS: GG and PE groups showed higher age, BMI, waist/abdominal circumferences and trans-fat intake and lower selenium and vitamin E intake compared to PH. Individuals with PE had higher hip circumference and lower income, education and intake of iron as well as vitamins A and B9. PE microbiomes (oral and faecal) showed distinct compositions, with the highest number of unique oral species. Faecal richness was lower in PE and GG compared to PH. Specific microbial taxa correlated with periodontal status and host factors.<br><br>CONCLUSION: Periodontal and faecal microbiomes vary across periodontal conditions. Discriminant analysis classified 77% of individuals by periodontal status, with key markers for PE including older age, poor dietary quality and distinct microbial oral and faecal signatures. These findings highlight the role of clinical, dietary and microbial factors in periodontal disease profiling.}, }
@article {pmid40671648, year = {2025}, author = {Maiello, G and Lippert, MR and Neave, EF and Hanson, EA and Palumbi, SR and Mariani, S}, title = {Multi-Tool Marine Metabarcoding Bioassessment for Baselining and Monitoring Species and Communities in Kelp Habitats.}, journal = {Molecular ecology resources}, volume = {25}, number = {7}, pages = {e70010}, doi = {10.1111/1755-0998.70010}, pmid = {40671648}, issn = {1755-0998}, support = {//The Pew Charitable Trusts under the Lenfest Ocean Program/ ; //The Gordon and Betty Moore Foundation/ ; //Oceankind Labs/ ; }, mesh = {*DNA Barcoding, Taxonomic/methods ; *Kelp ; Ecosystem ; California ; Animals ; *Biodiversity ; *Aquatic Organisms/classification/genetics ; *DNA, Environmental/genetics ; *Metagenomics/methods ; *Biota ; }, abstract = {The astonishing biological diversity found in Californian kelp forests requires efficient and robust monitoring tools to better understand ecological trends and mitigate against loss or disruption of ecosystem services due to human pressure and climate changes. With environmental DNA (eDNA) metabarcoding becoming a popular biodiversity assessment approach, we set out to evaluate a combination of powerful, rapid and sustainable eDNA solutions for characterising marine community composition in kelp-dominated habitats along the central California coast, in the newly proposed Chumash Heritage National Marine Sanctuary. We employed and compared the efficiency of several eDNA collection approaches, including 'traditional' surface water filtration, the collection of organisms encrusting cobble rocks and various deployments of an artificial passive sampler, the metaprobe (i.e., attached to divers, dangled from a boat and cast from the shore using a fishing rod). By combining the information from fish specific (Tele02 12S) and universal metazoan (COI) markers, we 'captured' 501 unique marine taxa, belonging to at least 36 phyla, over 400 of which were identified to genus/species level, and including 52 vertebrate species typical of Californian kelp forest ecosystems. Despite differences in the type of biodiversity returned by the tested sampling methods, the overall community structure of the surveyed area was highly spatially structured and strongly influenced by the biogeographic break around Point Conception (Humqaq). We discuss the benefits of integrating eDNA metabarcoding in existing monitoring programs and devising a reproducible approach to monitor faunal changes in kelp forest habitats and beyond.}, }
@article {pmid40464364, year = {2025}, author = {Rousseau, C and Henry, N and Rousvoal, S and Tanguy, G and Legeay, E and Leblanc, C and Dittami, SM}, title = {A Practical Comparison of Short- and Long-Read Metabarcoding Sequencing: Challenges and Solutions for Plastid Read Removal and Microbial Community Exploration of Seaweed Samples.}, journal = {Molecular ecology resources}, volume = {25}, number = {7}, pages = {e14129}, doi = {10.1111/1755-0998.14129}, pmid = {40464364}, issn = {1755-0998}, support = {AAPG2020//Agence Nationale de la Recherche/ ; ANR-20-CE43-0013//Agence Nationale de la Recherche/ ; }, mesh = {*Seaweed/microbiology/genetics ; *DNA Barcoding, Taxonomic/methods ; High-Throughput Nucleotide Sequencing/methods ; *Plastids/genetics ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics ; *Metagenomics/methods ; Sequence Analysis, DNA/methods ; DNA Primers/genetics ; Fungi/genetics/classification ; }, abstract = {Short-read metabarcoding analysis is the gold standard for accessing partial 16S and ITS genes with high read quality. With the advent of long-read sequencing, the amplification of full-length target genes is possible, but with low read accuracy. Moreover, 16S rRNA gene amplification in seaweed results in a large proportion of plastid reads, which are directly or indirectly derived from cyanobacteria. Primers designed not to amplify plastid sequences are available for short-read sequencing, while Oxford Nanopore Technology (ONT) offers adaptive sampling, a unique way to remove reads in real time. In this study, we compare three options to address the issue of plastid reads: deleting plastid reads with adaptive sampling, using optimised primers with Illumina MiSeq technology, and sequencing large numbers of reads with Illumina NovaSeq technology with universal primers. We show that adaptive sampling using the default settings of the MinKNOW software was ineffective for plastid depletion. NovaSeq sequencing with universal primers stood out with its deep coverage, low error rate, and ability to include both eukaryotes and bacteria in the same sequencing run, but it had limitations regarding the identification of fungi. The ONT sequencing helped us explore the fungal diversity and allowed for the retrieval of taxonomic information for genera poorly represented in the sequence databases. We also demonstrated with a mock community that the SAMBA workflow provided more accurate taxonomic assignment at the bacterial genus level than the IDTAXA and KRAKEN2 pipelines, but many false positives were generated at the species level.}, }
@article {pmid40459094, year = {2025}, author = {Dahl, MB and Brachmann, S and Söllinger, A and Schnell, M and Ahlers, L and Wutkowska, M and Hoff, KJ and Nath, N and Groß, V and Wang, H and Weil, M and Piecha, M and Schaffer, M and Jensen, C and Kuss, AW and Gall, C and Wimmer, E and Pribasnig, T and Tveit, AT and Sigurdsson, BD and Schleper, C and Richter, A and Urich, T}, title = {Quantifying Soil Microbiome Abundance by Metatranscriptomics and Complementary Molecular Techniques-Cross-Validation and Perspectives.}, journal = {Molecular ecology resources}, volume = {25}, number = {7}, pages = {e14130}, doi = {10.1111/1755-0998.14130}, pmid = {40459094}, issn = {1755-0998}, support = {21-17322M//The Czech Science Foundation/ ; BO 5559/1-1//Deutsche Forschungsgemeinschaft/ ; INST 292/146-1 FUGB//Deutsche Forschungsgemeinschaft/ ; UR198/7-1//Deutsche Forschungsgemeinschaft/ ; 813114//HORIZON EUROPE European Innovation Council/ ; //Research Council of Norway/ ; }, mesh = {*Soil Microbiology ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; *Gene Expression Profiling/methods ; *Bacteria/genetics/classification ; Transcriptome ; Soil/chemistry ; }, abstract = {Linking meta-omics and biogeochemistry approaches in soils has remained challenging. This study evaluates the use of an internal RNA extraction standard and its potential for making quantitative estimates of a given microbial community size (biomass) in soil metatranscriptomics. We evaluate commonly used laboratory protocols for RNA processing, metatranscriptomic sequencing and quantitative reverse transcription polymerase chain reaction (qRT-PCR). Metatranscriptomic profiles from soil samples were generated using two library preparation protocols and prepared in triplicates. RNA extracted from pure cultures of Saccharolobus solfataricus was added to the samples as an internal nucleic acid extraction standard (NAEstd). RNA reads originating from NAEstd were identified with a 99.9% accuracy. A remarkable replication consistency between triplicates was seen (average Bray-Curtis dissimilarity 0.03 ± 0.02), in addition to a clear library preparation bias. Nevertheless, the between-sample pattern was not affected by library type. Estimates of 16S rRNA transcript abundance derived from qRT-PCR experiments, NAEstd and a previously published quantification method of metatranscriptomics (hereafter qMeTra) were compared with microbial biomass carbon (MBC) and nitrogen (MBN) extracts. The derived biomass estimates differed by orders of magnitude. While most estimates were significantly correlated with each other, no correlation was observed between NAEstd and MBC extracts. We discuss how simultaneous changes in community size and the soils nucleic acid retention strength might hamper accurate biomass estimation. Adding NAEstd has the potential to shed important light on nucleic acid retention in the substance matrix (e.g., soil) during extraction.}, }
@article {pmid40375355, year = {2025}, author = {Shaffer, MR and Andruszkiewicz Allan, E and Van Cise, AM and Parsons, KM and Shelton, AO and Kelly, RP}, title = {Observation Bias in Metabarcoding.}, journal = {Molecular ecology resources}, volume = {25}, number = {7}, pages = {e14119}, doi = {10.1111/1755-0998.14119}, pmid = {40375355}, issn = {1755-0998}, support = {N00014-22-1-2719//Office of Naval Research/ ; }, mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; Polymerase Chain Reaction/methods ; *Fishes/genetics/classification ; *Metagenomics/methods ; DNA Primers/genetics ; Cetacea/genetics/classification ; }, abstract = {DNA metabarcoding is subject to observation bias associated with PCR and sequencing, which can result in observed read proportions differing from actual species proportions in the DNA extract. Here, we amplify and sequence a mock community of known composition containing marine fishes and cetaceans using four different primer sets and a variety of PCR conditions. We first compare metabarcoding observations to two different sets of expected species proportions based on total genomic DNA and on target mitochondrial template DNA. We find that calibrating observed read proportions based on template DNA concentration is most appropriate as it isolates PCR amplification bias; calibration with total genomic DNA results in bias that can be attributed to both PCR amplification bias and differing ratios of template to total genomic DNA. We then model the remaining amplification bias and find that approximately 60% can be explained by inherent species-specific DNA characteristics. These include primer-template mismatches, amplicon fragment length, and GC content, which vary somewhat across Taq polymerases. Finally, we investigate how different PCR protocols influence community composition regardless of expected proportions and find that changing protocols most strongly influence the amplification of templates with primer mismatches. Our findings suggest that using primer-template pairs without mismatches and targeting a narrow taxonomic group can yield more repeatable and accurate estimates of species' true, underlying DNA template proportions. These findings identify key factors that should be considered when designing studies that aim to apply metabarcoding data quantitatively.}, }
@article {pmid40243260, year = {2025}, author = {Bayer, PE and Bennett, A and Nester, G and Corrigan, S and Raes, EJ and Cooper, M and Ayad, ME and McVey, P and Kardailsky, A and Pearce, J and Fraser, MW and Goncalves, P and Burnell, S and Rauschert, S}, title = {A Comprehensive Evaluation of Taxonomic Classifiers in Marine Vertebrate eDNA Studies.}, journal = {Molecular ecology resources}, volume = {25}, number = {7}, pages = {e14107}, doi = {10.1111/1755-0998.14107}, pmid = {40243260}, issn = {1755-0998}, support = {//Minderoo Foundation/ ; }, mesh = {Animals ; *Vertebrates/classification/genetics ; *Aquatic Organisms/classification/genetics ; *DNA Barcoding, Taxonomic/methods ; RNA, Ribosomal, 16S/genetics ; *DNA, Environmental/genetics ; Computational Biology/methods ; Australia ; *Metagenomics/methods ; Biodiversity ; RNA, Ribosomal/genetics ; }, abstract = {Environmental DNA (eDNA) metabarcoding is a widely used tool for surveying marine vertebrate biodiversity. To this end, many computational tools have been released and a plethora of bioinformatic approaches are used for eDNA-based community composition analysis. Simulation studies and careful evaluation of taxonomic classifiers are essential to establish reliable benchmarks to improve the accuracy and reproducibility of eDNA-based findings. Here we present a comprehensive evaluation of nine taxonomic classifiers exploring three widely used mitochondrial markers (12S rDNA, 16S rDNA and COI) in Australian marine vertebrates. Curated reference databases and exclusion database tests were used to simulate diverse species compositions, including three positive control and two negative control datasets. Using these simulated datasets ranging from 36 to 302 marker genes, we were able to identify between 19% and 89% of marine vertebrate species using mitochondrial markers. We show that MMSeqs2 and Metabuli generally outperform BLAST with 10% and 11% higher F1 scores for 12S and 16S rDNA markers, respectively, and that Naive Bayes Classifiers such as Mothur outperform sequence-based classifiers except MMSeqs2 for COI markers by 11%. Database exclusion tests reveal that MMSeqs2 and BLAST are less susceptible to false positives compared to Kraken2 with default parameters. Based on these findings, we recommend that MMSeqs2 is used for taxonomic classification of marine vertebrates given its ability to improve species-level assignments while reducing the number of false positives. Our work contributes to the establishment of best practices in eDNA-based biodiversity analysis to ultimately increase the reliability of this monitoring tool in the context of marine vertebrate conservation.}, }
@article {pmid40915677, year = {2025}, author = {Costa, FF and Lustosa, BPR and Perico, CP and Belmonte-Lopes, R and Carvalho, JLVR and Razzolini, EL and Santos, GDD and Lima, BJFS and Souza-Motta, CM and Raittz, RT and Song, Y and Selbmann, L and de Hoog, GS and Meis, J and Vicente, VA}, title = {In silico search reveals the association of lichens with black yeast-like fungi in the order Chaetothyriales.}, journal = {Fungal biology}, volume = {129}, number = {6}, pages = {101618}, doi = {10.1016/j.funbio.2025.101618}, pmid = {40915677}, issn = {1878-6146}, mesh = {*Lichens/microbiology/classification ; *Ascomycota/genetics/classification/isolation &amp; purification/physiology ; Metagenomics ; Symbiosis ; Phylogeny ; Computer Simulation ; Metagenome ; }, abstract = {Lichens exemplify a unique symbiotic relationship between fungi and algae or cyanobacteria, where fungi (mycobionts) provide structural support, while algae or cyanobacteria (photobionts) provide nutrients. Recent discoveries in the order Chaetothyriales have led to the description of several lichenicolous species, underscoring an intricate relationship of some black yeast-like fungi with lichens. The present study aims to investigate public metagenomic data of lichens available in the SRA database, covering a total of 2888 samples. The analysis incorporated 122 molecular marker sequences (barcodes and padlock probes) previously documented in the literature for species classified within Chaetothyriales. Additionally, 11 novel barcodes for species recently identified in lichens of the genera Cladophialophora and Paracladophialophora are described. The selected metagenomes were then compared with molecular marker sequences using local BLASTn (v2.6.0+), considering only alignments with a coverage cut-off and 100 % identity (perfect match). Reads from each sample were retrieved from the SRA as a multifasta file and analyzed with the SWeeP method for vector-based, alignment-free sequence analysis. The analysis identified fungi that are known as environmental inhabitants and, occasionally, opportunistic pathogens of vertebrates, including species in the genera Cladophialophora, Cyphellophora, and Exophiala. These species were distributed across 11 BioProjects from various locations around the world. The findings of this study corroborate extant knowledge concerning fungal colonization in diverse extremophilic environments, including deserts, tundra, and rocky surfaces.}, }
@article {pmid40915583, year = {2025}, author = {Zhang, Y and Wang, B and Hassan, M and Zhang, X}, title = {Biochar-calcium alginate composite immobilizing Pseudomonas sp. H6 for phosphate and ammonium recovery: Multi-omics insights and practical application evaluation.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {133274}, doi = {10.1016/j.biortech.2025.133274}, pmid = {40915583}, issn = {1873-2976}, abstract = {Water eutrophication has emerged as a pervasive ecological challenge worldwide. To realize the resource utilization of waste and nutrients, a novel rape straw-derived biochar-calcium alginate composite (M-CA-RBC) immobilized Pseudomonas sp. H6 was synthesized to simultaneously remove phosphate (PO4[3-]) and ammonium (NH4[+]) from distillery wastewater. The removal performance of PO4[3-] and NH4[+] by M-CA-RBC were investigated. The removal mechanisms were explored by using different adsorption models combined with microbial degradation kinetics, analysis of dissolved organic matter components, electrochemical analysis, metagenomics, and metabolomics. The resource application potential of M-CA-RBC was evaluated. The results showed that M-CA-RBC had good removal performance for PO4[3-] (17.81 mg/g) and NH4[+] (25.78 mg/g). Surface precipitation, electrostatic attraction, Poly-P accumulation, microbial-induced calcium precipitation, and microbial assimilation were the main removal mechanisms of PO4[3-] by M-CA-RBC. The removal mechanisms of NH4[+] were micropore filling, ion exchange, electrostatic attraction, and heterotrophic nitrification-aerobic denitrification (HN-AD). M-CA-RBC had a good application potential in the practical distillery wastewater, with removal rates of PO4[3-] and NH4[+] reaching 88% and 65%, respectively. After adsorption saturation, M-CA-RBC exhibited good stability, which could be used as a slow-release fertilizer to promote the growth of mung beans. This study provides practical significance for the efficient removal and recovery of nitrogen and phosphorus in wastewater.}, }
@article {pmid40915551, year = {2025}, author = {Akel, R and Kacsir, I and Kerekes, &#xc9; and Freytag, C and Szoták, E and Boros-Pál, D and Janka, EA and Bényei, A and Kardos, G and Bokor, &#xc9; and Somsák, L and Bai, P and Sipos, A and Kun, S}, title = {Platinum-group metal half-sandwich complexes of sugar-isoxazol(in)e conjugates - synthesis and evaluation of their antineoplastic and antimicrobial activities.}, journal = {European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences}, volume = {}, number = {}, pages = {107260}, doi = {10.1016/j.ejps.2025.107260}, pmid = {40915551}, issn = {1879-0720}, abstract = {Platinum-group metal half-sandwich complexes are considered to be potential replacements of the clinically widely used platins which have several side effects and tend to cause resistance to develop. In our previous works, we used a range of 2-pyridyl-substituted N- and C-glycosyl heterocycles as N,N-chelating ligands to prepare ruthenium(II), osmium(II), iridium(III) and rhodium(III) polyhapto arene/arenyl half-sandwich complexes. Some of these complexes, particularly with the C-glucopyranosyl isoxazole derived ligand in its O-perbenzoylated form, exhibited greater anticancer efficiency than cisplatin and had minimal or negligible effects on non-transformed fibroblasts. Additionally, these cytostatic compounds exhibited micromolar antibacterial activity against multiresistant Gram-positive bacteria. In the present work, novel modes of conjugation between the sugar and the isoxazole moieties have been studied. Specifically, glycosylidene-spiro-isoxazoline and polyhydroxyalkylisoxazole scaffolds were synthesised and utilised in complex formation reactions. The spiro-isoxazolines were obtained in 1,3-dipolar cycloadditions of exo-glycals and nitrile oxides generated from pyridine-2-carbaldoximes. Ring opening of the spiro-isoxazolines under basic or transition-metal-mediated conditions produced polyhydroxyalkylisoxazoles. These compounds were then transformed into their O-peracetylated, O-perbenzoylated and O-unprotected variants, which were used for complex formation with the above-mentioned platinum-group metal ions. The complexes induced cytostasis in cellular models of ovarian cancer and pancreatic adenocarcinoma; the best compounds had submicromolar IC50 values (0.4-0.5 µM). A subset of the cytostatic complexes retained their activity on cisplatin resistant ovarian cancer cells. Furthermore, a reasonable therapeutic index was detected when complexes were assessed on primary human fibroblasts pointing towards a potential applicability of the complexes. Unexpectedly, none of the complexes induced bacteriostasis in Gram-positive bacteria as Staphylococcus aureus or Enterococcus species.}, }
@article {pmid40915262, year = {2025}, author = {Liu, S and Feng, K and Zhang, D and Liu, Y and Wang, J and Lu, B and Xing, D}, title = {Self-regulating adaptability of biofilm microbiomes enhances manganese and ammonia removal in microbial electrochemical filters under dioxane exposure.}, journal = {Journal of hazardous materials}, volume = {497}, number = {}, pages = {139776}, doi = {10.1016/j.jhazmat.2025.139776}, pmid = {40915262}, issn = {1873-3336}, abstract = {Understanding the stability and assemblage of biofilm microbiomes under oligotrophic conditions is critical for improving groundwater bioremediation. In this study, a novel microbial electrochemical filter (MEF) was developed to explore the impact of weak electrical stimulation on functional adaptability of biofilms under oligotrophic and 1,4-dioxane exposure conditions. Under 20 mg/L 1,4-dioxane stress, the MEF achieved 94.72 % manganese removal and 27.27 % ammonia nitrogen removal, while the conventional biofilter exhibited 88.76 % manganese removal with negligible ammonia nitrogen removal. Metagenomics analyses revealed that dominant populations in the MEF included Nitrospira, Bradyrhizobium, and Nitrosomonas, with relative abundance of 6.23 -10.78 %, 5.81 -6.15 %, and 1.62 -5.58 %, respectively. Weak electrical stimulation enriched the manganese oxidation-associated genes cotA, mnxG, and mcoA, whose total relative abundances being 6.3 times that of the conventional biofilter before dioxane exposure and 2.0 times after exposure. Genes encoding ammonia monooxygenase (amoABC), hydroxylamine dehydrogenase (hao) increased by 2.4- and 1.9-fold, respectively, compared to the conventional biofilter. Additionally, genes involved in the reductive tricarboxylic acid cycle and nitrogen fixation were twice as abundant in the MEF than in the conventional biofilter, suggesting enhanced nutrients availability for heterotrophic bacteria during start-up. These findings demonstrated that weak electrical stimulation effectively regulated biofilm microbiomes and enhance pollutant removal in MEF under oligotrophic conditions.}, }
@article {pmid40915207, year = {2025}, author = {Zhang, M and Xu, Y and Wang, S and Su, W and Zhang, Y and Xu, H and Li, L and Wang, M and Zhang, J and Yang, Z}, title = {Resistomic features and novel genetic element identified in hospital wastewater with short- and long-read metagenomics.}, journal = {Ecotoxicology and environmental safety}, volume = {303}, number = {}, pages = {118991}, doi = {10.1016/j.ecoenv.2025.118991}, pmid = {40915207}, issn = {1090-2414}, abstract = {The global spread of antimicrobial resistance (AMR) poses a serious threat to public health, with hospital wastewater treatment plants (WWTPs) recognized as a key hotspot for resistant pathogens and antibiotic resistance genes (ARGs). This study employed advanced hybrid sequencing platforms to provide a comprehensive resistomic analysis of a Qingdao WWTP in China, revealing previously uncovered AMR transmission risks. We identified 175 ARG subtypes conferring resistance to 38 antimicrobials, including the last-resort antibiotics, highlighting the extensive and concerning resistance reservoir within this environment. Multidrug resistance genes predominated, followed by ARGs targeting aminoglycoside, β-lactam, tetracycline, glycopeptide, and macrolide classes, reflecting clinically relevant resistance patterns. Co-occurrence analysis revealed ARGs were strongly associated with mobile genetic elements, especially for ARGs targeting sulfonamide, glycopeptide, macrolide, tetracycline, aminoglycoside, and β-lactam classes, providing concrete evidence of their high dissemination potential. A striking 85 % of 131 metagenome-assembled genomes (MAGs) carried ARGs, demonstrating prevalent resistance in the wastewater microbiome. Furthermore, the identification of several rarely studied genomic islands (GIs), including those conferring resistance to antibiotics and heavy metals, and notably, the novel variant GIAS409 carrying transposases and heavy metal resistance operons, reveals a significant and previously neglected mechanism for co-selection and dissemination. This study significantly advances our understanding of AMR dynamics in hospital WWTPs, demonstrating that current treatment approaches (42 % ARG removal) have limited efficacy and that WWTP may serve as potential hotspots for multidrug resistance development. Collectively, these findings emphasize the urgent need for improved wastewater management to safeguard public health.}, }
@article {pmid40915146, year = {2025}, author = {Leonard, SR and Mammel, MK and Brassill, N and Champ, C and Lacher, DW and Saber, B and Kase, JA and Kataoka, A and Bell, RL and Brown, EW and Rock, CM and Musser, SM}, title = {Air microbiomes reveal presence of Shiga toxin-producing Escherichia coli in airborne cattle pen soil adjacent to large feedlot.}, journal = {The Science of the total environment}, volume = {1000}, number = {}, pages = {180375}, doi = {10.1016/j.scitotenv.2025.180375}, pmid = {40915146}, issn = {1879-1026}, abstract = {Cattle are a reservoir for the zoonotic human foodborne pathogen Shiga toxin-producing Escherichia coli (STEC), the causative agent of many disease outbreaks associated with contaminated fresh leafy greens. Concentrated animal feeding operations (CAFOs) housing cattle generate fugitive dust, however the potential risk of STEC movement by means of the aerosolized dust is not well known. In this investigation, we used metagenome sequencing of air samples collected in an agricultural setting to investigate airborne transfer of STEC from a large CAFO to the surrounding area. Shiga toxin genes and other E. coli virulence genes were observed in air metagenomes, and their presence was positively correlated with abundance of cattle mitochondrial DNA (mtDNA). Air bacterial community composition differed based on STEC presence, and source tracking utilizing the air metagenomes indicated that cattle feedlot soil contributed to the air bacterial communities. Moreover, a novel biomarker for cattle pen soil, Corynebacterium maris, was identified that correlated with both E. coli virulence gene presence and cattle mtDNA abundance. Overall, our results demonstrate a definitive link between aerosolized cattle feedlot dust and airborne STEC transfer to adjacent and nearby agricultural fields. This work highlights the importance of including the potential for airborne transmission of pathogens in risk assessments for contamination by human foodborne pathogens of fresh produce grown in proximity to CAFOs.}, }
@article {pmid40915131, year = {2025}, author = {Zhu, X and Lin, L and Ju, F}, title = {Tracking mitigation and expression patterns of the antibiotic resistome during full-scale livestock wastewater treatment: Comparison between summer and winter conditions.}, journal = {Water research}, volume = {287}, number = {Pt B}, pages = {124515}, doi = {10.1016/j.watres.2025.124515}, pmid = {40915131}, issn = {1879-2448}, abstract = {Livestock wastewater is a critical reservoir of antibiotic resistance genes (ARGs) that poses significant public health risks. This study comprehensively evaluated the seasonal dynamics and associated risks of ARGs in a full-scale livestock wastewater treatment plant using an integrated metagenomic and metatranscriptomic approach. The results showed that untreated livestock wastewater harbored high abundance (4.69 ± 1.93 copies/cell, GPC) and high diversity (838 subtypes) ARGs comparable to and sometimes higher than those found in human and pig guts. These ARGs primarily encode resistance to common veterinary antibiotics including Tetracycline (7.4 %), Macrolide-Lincosamide-Streptogramin (10.4 %), and Aminoglycoside (13.2 %). Notably, 39 % of livestock wastewater ARGs (based on relative abundance) were further identified as high-risk (i.e., mobilizable, pathogen-carriable and clinically relevant) ARGs. Moreover, these livestock-associated ARGs showed marked seasonal variation in removal efficacy: summer and autumn treatments reduced ARG abundance by 48-55 % in biological units (anaerobic digestion and activated sludge), while winter witnessed a 40 % increase in ARGs, driven by certain plasmid-associated ARGs notably enriched during anaerobic digestion but inefficiently removed in the subsequent activated sludge process due to slow microbial community turnover. Transcriptional profiling revealed 66 % to 93 % of ARGs were actively expressed, with disproportionately high activity of high-risk ARGs (e.g., erm(B) and cfr) in winter. The findings emphasize spreading potential of antibiotic resistome through land application of winter livestock wastewater treatment and suggest that temperature control of treatment facilities or membrane filtration might be a promising strategy to remove high-risk ARGs and their hosts. This study provides actionable insights for optimizing livestock wastewater treatment to mitigate spread risks of antimicrobial resistance.}, }
@article {pmid40915037, year = {2025}, author = {Baud, D and Peric, A and Vidal, A and Weiss, JM and Engel, P and Das, S and Stojanov, M}, title = {Genital microbiota in infertile couples.}, journal = {Reproductive biomedicine online}, volume = {51}, number = {5}, pages = {105056}, doi = {10.1016/j.rbmo.2025.105056}, pmid = {40915037}, issn = {1472-6491}, abstract = {RESEARCH QUESTION: What is the composition of bacterial communities at various genital sites and are there potential interactions between partners' microbiota?<br><br>DESIGN: This observational study involved metagenomic analyses of samples collected from male and female partners of couples undergoing fertility treatment. Samples included vaginal and penile swabs, as well as follicular fluid and semen, which were analysed using next-generation sequencing.<br><br>RESULTS: The bacterial community profiles of different genital tract niches were distinct, niche-specific compositions, with female samples predominantly featuring Lactobacillus species and male samples displaying greater microbial diversity, including genital-specific and skin-associated taxa. Significant differences were observed between the sample types and intra-couple comparisons, which suggested potential microbiota interactions between partners. Differential abundance analyses further identified genera specifically enriched in female versus male samples, and correlations between partner samples point towards possible microbial transmission or shared influences on genital microbiota composition.<br><br>CONCLUSIONS: Despite advances in reproductive medicine, many infertility cases remain idiopathic, prompting exploration into how the genital microbiota (both in female and male reproductive tracts) might influence reproductive success. Our findings reveal that, although female samples were predominantly colonized by Lactobacillus species, particularly in the lower genital tract, male samples had greater microbial diversity (including bacteria linked to bacterial vaginosis), with only limited evidence of inter-partner microbiota transmission, underscoring the need for further longitudinal studies on the effect of sexual activity on microbial dynamics.}, }
@article {pmid40914968, year = {2025}, author = {Cho, Y and Kim, E and Kim, M and Rho, M}, title = {DeepMobilome: predicting mobile genetic elements using sequencing reads of microbiomes.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {5}, pages = {}, doi = {10.1093/bib/bbaf450}, pmid = {40914968}, issn = {1477-4054}, support = {RS-2023-00217123//MSIT/ ; RS-2023-KH135226//Ministry of Health/ ; 2023ER210902/GF/NIH HHS/United States ; }, mesh = {*Microbiota/genetics ; *Interspersed Repetitive Sequences ; Metagenome ; Metagenomics/methods ; Humans ; Neural Networks, Computer ; Sequence Analysis, DNA ; Drug Resistance, Microbial/genetics ; Computational Biology/methods ; High-Throughput Nucleotide Sequencing ; }, abstract = {MOTIVATION: Mobile genetic elements (MGEs) play an important role in facilitating the acquisition of antibiotic resistance genes (ARGs) within microbial communities, significantly impacting the evolution of antibiotic resistance. Understanding the mechanism and trajectory of ARG acquisition requires a comprehensive analysis of the ARG-carrying mobilome-a collective set of MGEs carrying ARGs. However, identifying the mobilome within complex microbiomes poses considerable challenges. Existing MGE prediction methods, designed primarily for single genomes, exhibit substantial limitations when applied to metagenomic data, often producing high false positive rates in identifying target MGEs from metagenome sequencing data.<br><br>RESULTS: To address these challenges, we developed DeepMobilome, a novel approach for accurately identifying target MGEs within the microbiome. DeepMobilome leverages a convolutional neural network trained on read alignment data derived from sequence alignment map (SAM) files, providing superior accuracy in detecting MGEs. Trained on 364 647 cases, DeepMobilome achieved a high validation accuracy of 0.99. DeepMobilome consistently outperformed existing methods in discerning the presence of target MGE sequences across diverse test sets. In single-genome test scenarios, DeepMobilome showed an F1-score of 0.935, compared to 0.755 and 0.670 for MGEfinder and ISMapper, respectively, demonstrating its substantial improvements in prediction accuracy. Extensive evaluations across simulated microbiomes further validated the robustness and reliability of DeepMobilome in practical applications. In real microbiome data, DeepMobilome successfully identified six ARG-carrying MGEs across diverse populations. By addressing the limitations of current methods, DeepMobilome offers a powerful tool for advancing our understanding of ARG dissemination and supports targeted interventions in combating antibiotic resistance.}, }
@article {pmid40914379, year = {2025}, author = {El-Gendi, H and El-Maradny, YA and El-Sayed, MH and Saleh, AK and El-Fakharany, EM}, title = {Exploring biocontrol strategies for Phytopathogens using plant growth-promoting rhizobacteria-derived enzymes: A review of current advances and future directions.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {147434}, doi = {10.1016/j.ijbiomac.2025.147434}, pmid = {40914379}, issn = {1879-0003}, abstract = {The growing demand for sustainable agriculture imposes innovative biocontrol strategies to mitigate phytopathogen threats while reducing dependence on chemical pesticides. This review explores the current knowledge on enzyme-based biocontrol, focusing on hydrolytic enzymes (e.g., chitinases, pectinases, cellulases, proteases, and β-glucanases) produced by plant-growth-promoting-rhizobacteria (PGPRs) and their dual roles in direct pathogen suppression and plant immunity elicitation. We systematically evaluate their mechanisms, from cell wall degradation to induced systemic resistance (ISR), and highlight synergistic interactions that enhance efficacy under field conditions. Despite promising laboratory and greenhouse results, commercial implementation faces challenges: high production costs, environmental instability, and formulation limitations. We critically analyze advances in immobilization techniques (e.g., nanoencapsulation, biochar carriers) and low-cost production using agro-industrial wastes to improve scalability. Furthermore, we discuss the market potential of enzyme-based biocontrol agents, which is projected to grow at a Compound Annual Growth Rate (CAGR) of 16.4 %, and identify gaps in rhizosphere compatibility and regulatory frameworks. By integrating metagenomic insights and molecular engineering, this review proposes a roadmap for optimizing enzyme cocktails tailored to specific crops and pathogens. Our findings highlight the transformative potential of enzyme-driven biocontrol in achieving sustainable crop protection, influencing interdisciplinary collaboration to bridge lab-to-field disparities and meet global food security challenges.}, }
@article {pmid40914221, year = {2025}, author = {Geng, J and Zhang, W and Christie-Oleza, JA and Abdolahpur Monikh, F and Yang, Q and Yang, Y}, title = {Succession-driven potential functional shifts in microbial communities in the Tire-plastisphere:Comparison of pristine and scrap tire.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {127074}, doi = {10.1016/j.envpol.2025.127074}, pmid = {40914221}, issn = {1873-6424}, abstract = {Tire microplastics (TMPs) represent a major contributor to microplastic pollution, posing threats to aquatic ecosystems. As carbon-rich substrates, TMPs influence microbial colonization and ecological functions. This study investigates the impacts of pristine (P-TMPs) and scrap (S-TMPs) TMPs from the same brand on microbial communities within the tire-plastisphere. We incubated wood particles, P-TMPs, and S-TMPs in situ in a lake environment for 60 days. Utilizing amplicon and metagenome sequencing, we analyzed structural and potential functional changes in microbial communities across five colonization time points. Our findings reveal that TMPs establish distinct ecological niches, functioning as hotspots of microbial activity in aquatic environments. Both niche specificity and colonization time significantly shape microbial community structure. During the early adaptation stage, we observed clustering patterns in both microbial composition and functional genes associated with the particles. Over time, divergent succession in community composition and potential function emerged, primarily driven by differences in substrate availability between niches. Notably, the substrate availability of S-TMPs promoted microbial community shifts, whereas the P-TMPs posed challenges to microbial adaptation. This study elucidates the long-term adaptive processes exhibited by microbial communities when colonizing the contrasting ecological niches represented by these two TMP states (pristine vs. scrap), documenting the progression from community structural change to functional adaptation. The results underscore the complexity of TMP impacts on microbial ecology and highlight the critical need for long-term monitoring to fully understand their environmental implications.}, }
@article {pmid40914165, year = {2025}, author = {Anani, H and Destras, G and Bulteau, S and Castain, L and Semanas, Q and Burfin, G and Petrier, M and Martin, FP and Poulain, C and Dickson, RP and Bressollette-Bodin, C and Roquilly, A and Josset, L}, title = {Lung virome convergence precedes hospital-acquired pneumonia in intubated critically ill patients.}, journal = {Cell reports. Medicine}, volume = {}, number = {}, pages = {102289}, doi = {10.1016/j.xcrm.2025.102289}, pmid = {40914165}, issn = {2666-3791}, abstract = {Hospital-acquired pneumonia (HAP) is one of the most common nosocomial infections, leading to significant morbidity and mortality in critically ill patients. HAP is previously associated with dysbiosis of the microbiota. However, the composition of the lung virome and its role in HAP pathogenesis remain unclear. Here, we longitudinally analyze the endotracheal virome in 87 critically ill patients, including 48 with HAP. Within the virome dominated by Caudoviricetes, a decrease in viral beta-diversity toward a bacteriophage-dominated signature and a distinct viral-bacterial interactome is observed 5-4 days before HAP onset. Lung virome composition, viral convergence before HAP onset, and conservation of 18% of the bacteriophage signature are validated in an external cohort of 40 patients. In silico causal inference further identifies bacteriophages associated with Streptococcus and Prevotella as a key regulator of HAP onset. These findings suggest an uncovered pathophysiological mechanism of HAP with virome involvement in lung microbiota dysbiosis. The discovery and validation studies are registered at ClinicalTrials.gov (NCT02003196 and NCT04793568).}, }
@article {pmid40914155, year = {2025}, author = {Muñoz, VR and Moreau, F and Soto, M and Watanabe, Y and Pham, LD and Zhong, J and Zimmerman, S and Brandao, BB and Girdhar, K and Avila, J and Pan, H and Dreyfuss, JM and Mi, MY and Gerszten, RE and Altindis, E and Kostic, A and Clish, CB and Kahn, CR}, title = {Portal vein-enriched metabolites as intermediate regulators of the gut microbiome in insulin resistance.}, journal = {Cell metabolism}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cmet.2025.08.005}, pmid = {40914155}, issn = {1932-7420}, abstract = {Diet and obesity contribute to insulin resistance and type 2 diabetes, in part via the gut microbiome. To explore the role of gut-derived metabolites in this process, we assessed portal/peripheral blood metabolites in mice with different risks of obesity/diabetes, challenged with a high-fat diet (HFD) + antibiotics. In diabetes/obesity-prone C57BL/6J mice, 111 metabolites were portally enriched and 74 were peripherally enriched, many of which differed in metabolic-syndrome-resistant 129S1/129S6 mice. Vancomycin treatment of HFD-fed C57BL/6J mice modified the microbiome and the portal/peripheral ratio of many metabolites, including upregulating tricarboxylic acid (TCA) cycle-related metabolites, like mesaconate, in portal blood. Treatment of isolated hepatocytes with mesaconate, itaconate, or citraconate improved insulin signaling and transcriptionally regulated genes involved in gluconeogenesis, fatty acid oxidation, and lipogenesis in vitro and in vivo. In humans, citraconate levels are inversely correlated with plasma glucose. Thus, portal versus peripheral metabolites play important roles in mediating effects of the microbiome on hepatic metabolism and the pathogenesis of HFD-related insulin resistance.}, }
@article {pmid40914041, year = {2025}, author = {Zhang, J and Li, W and Zhang, X and Wang, X and Guo, X and Bai, C and Lv, L}, title = {Higher chlorine dosage does not consistently enhance antibiotic resistance mitigation in the Cl2-UV process.}, journal = {Water research}, volume = {287}, number = {Pt B}, pages = {124534}, doi = {10.1016/j.watres.2025.124534}, pmid = {40914041}, issn = {1879-2448}, abstract = {Health problems arising from antibiotic resistance are a global concern. The Cl2-UV disinfection process has shown potential for controlling antibiotic resistance in water; however, the influence of disinfectant dosage on its effectiveness remains insufficiently understood. Can antibiotic resistance be controlled by simply increasing the disinfectant dosage? This study demonstrated that higher disinfectant levels improved antibiotic resistance gene (ARG) removal, with certain ARGs reaching 1.82 log removal under conventional conditions. Nevertheless, higher disinfectant dosages also led to an increase in the relative abundance of multidrug resistance genes (MRGs), aminoglycoside resistance genes (AmRGs), and fosmidomycin resistance genes (FRGs). Correlation analysis of ARGs with mobile genetic elements (MGEs) and ARG-host bacteria indicated that this enrichment was primarily driven by enhanced horizontal gene transfer (HGT). Notably, increases in UV fluence and chlorine dose had distinct impacts on the total relative abundance of ARGs: higher UV fluence reduced total relative abundance, whereas higher chlorine dose increased it. These contrasting trends are likely linked to differences in the dominant HGT pathways under each condition. Greater UV fluence tended to promote conjugative transfer among surviving bacteria, while higher chlorine dosages more effectively facilitated natural transformation. Considering both the absolute and relative abundances of ARGs, along with calculated health-risk indices for each treatment condition, the findings indicated that increasing UV fluence is more effective for controlling ARGs in water. These results provide valuable insights for optimizing the Cl2-UV disinfection process to better manage antibiotic resistance in aquatic environments.}, }
@article {pmid40914040, year = {2025}, author = {Li, J and Wang, X and Zheng, J and Liu, Y and Zhang, D and Pan, X}, title = {Virulence-mediated colonization mechanism for TEP as a promising watershed-scale recorder and source-tracking indicator of human pathogens.}, journal = {Water research}, volume = {287}, number = {Pt B}, pages = {124537}, doi = {10.1016/j.watres.2025.124537}, pmid = {40914040}, issn = {1879-2448}, abstract = {Waterborne pathogens related diseases have been a global health concern. Precise source tracking of pathogens in rivers is crucial for understanding and reducing waterborne pathogens transmission risks. Current microbial source tracking techniques are still limited by identifying pathogen indicators at low concentrations, particularly in highly dynamic confluence zones of rivers where the coalescence of microbiomes exacerbates community disturbances. This study explored the potential of transparent exopolymeric particles (TEP) as effective carriers for pathogen source tracking, owing to their capacity to concentrate surrounding pathogenic bacteria as hitchhikers. The relative abundance of TEP-associated pathogenic bacteria (TAPs) was 1.61 times higher than that of overall pathogenic bacteria (OPs), which enhanced the detectability of pathogenic bacteria. Deterministic processes, particularly homogeneous selection, which accounts for 36 % of the variance, were found to govern the assembly of TAPs communities in contrast to OPs communities. In addition to nutrient and shelter functions of TEP, the selective enrichment of TAPs is mediated by virulence factors including adherence, motility, and biofilm-forming capacity, which are predominantly encoded within pathogenic bacteria. Furthermore, the relative stability of TAPs communities across watershed enabled them to record footprint of the hitchhiking pathogenic bacteria. Watershed-scale FEAST analysis confirmed superior capabilities of TAPs for source tracing than OPs, with fluctuations reduced by 0.11-32.02 %. This new MST technique based on TAPs can overcome some limitations with the traditional OPs-based methods and enables us to more precisely track pathogen sources and take evidence-based countermeasures to reduce pathogen transmission risk via rivers.}, }
@article {pmid40914035, year = {2025}, author = {Ballén, V and Mondéjar, L and Gabasa, Y and Castellsagués, L and Alcalde-Rico, M and Pinar-Méndez, A and Vilaró, C and Galofré, B and Soto, SM}, title = {Integrated metagenomic, culture-based, and whole genome sequencing analyses of antimicrobial resistance in wastewater and drinking water treatment plants in Barcelona, Spain.}, journal = {International journal of hygiene and environmental health}, volume = {270}, number = {}, pages = {114664}, doi = {10.1016/j.ijheh.2025.114664}, pmid = {40914035}, issn = {1618-131X}, abstract = {The misuse and overuse of antimicrobials drive the emergence of antimicrobial resistance (AMR), a critical global health concern. While wastewater treatment plants (WWTPs) are essential for removing microorganisms and contaminants, they also serve as hotspots for antibiotic-resistant bacteria (ARB) and antimicrobial resistance genes (ARGs), facilitating their persistence and dissemination. This study investigated AMR in two WWTPs and one drinking water treatment plant (DWTP) in the Baix Llobregat area of Barcelona, Spain. Four sampling campaigns were conducted during winter and summer 2023 across different treatment stages. Due to drought conditions, reclaimed water from the Baix Llobregat WWTP was discharged upstream of the DWTP intake to supplement water resources for indirect potable reuse. A total of 991 cultivable ARB were obtained, enabling phenotypic and genotypic characterisation. The most prevalent included Aeromonas spp. (44.3 %), Enterobacterales (27.9 %), Pseudomonas spp. (19.1 %), Acinetobacter spp. (4.8 %), Shewanella spp. (2.2 %), Stenotrophomonas spp. (1 %), and others (0.7 %). Among these, 57.3 % were multidrug-resistant and 2.7 % were extensively drug-resistant. Furthermore, 34.6 % produced extended-spectrum beta-lactamases, 14.1 % harboured carbapenemase genes, and 2.9 % exhibited colistin resistance. Shotgun metagenomic analysis revealed high taxonomic diversity, without dominant genera across treatment stages. The resistome was dominated by ARGs conferring resistance to beta-lactams, aminoglycosides, and macrolides, alongside genes linked to biocide resistance and heavy metal tolerance. Spearman correlation analysis of selected sequenced strains suggested a weak to moderate co-occurrence between ARGs and biocide or heavy metal tolerance genes. These findings underline WWTPs as AMR hotspots and reinforce the need to monitor DWTP source water within the One Health framework.}, }
@article {pmid40913922, year = {2025}, author = {Uprety, T and Durazo, J and Paul, L and Metiner, K and Ruby, R and Loynachan, A and Janes, J and Kenndy, L and Cassone, L and Molly, E and Quick, M and Morgan, J and Beyhan, S and Erol, E}, title = {Detection of Neorickettsia risticii in antemortem fecal and postmortem fetal samples, with genomic insights from complete genome sequencing of a strain recovered from an aborted equine fetus.}, journal = {Veterinary microbiology}, volume = {310}, number = {}, pages = {110705}, doi = {10.1016/j.vetmic.2025.110705}, pmid = {40913922}, issn = {1873-2542}, abstract = {Neorickettsia risticii (N. risticii) is an obligatory intracellular bacterium that causes Potomac horse fever (PHF), a disease clinically characterized by diarrhea, pyrexia, and laminitis in horses. Although sporadic reports of N. risticii infection have been linked to abortion in mares, a detailed retrospective study, including genomic analysis of the pathogen from an aborted fetus, has not been published. This study examined 546 fecal samples from clinically ill horses (January 1, 2017-December 31, 2024) and 833 colon samples from aborted equine fetuses (September 20, 2018-December 31, 2024). Using real-time PCR, N. risticii was detected in 11.5 % of fecal samples and 1.08 % of fetal colon samples. Positive antemortem cases were detected between May and September, while fetal cases occurred from September to December. The fetuses were 5-8 months of gestational age, all showing microscopic evidence of colitis. A shotgun metagenomic approach was applied directly to an archived fetal colon sample using the MiSeq platform, yielding a complete genome of N. risticii (strain KY18-EqFetus) with 99.72 % nucleotide identity to the N. risticii strain Illinois reference genome. The genome was 879,923 bp with a GC content of 41.3 %, and 2024 variants (including indels and nucleotide polymorphisms) were identified. Notably, three genes coding for small hypothetical proteins present in the reference strain were absent in KY18-EqFetus. This study provides a comprehensive investigation of N. risticii in both antemortem and postmortem equine samples and reports the first complete genome assembly of the pathogen directly from an aborted equine.}, }
@article {pmid40913558, year = {2025}, author = {Cai, TG and Lin, D and Ni, B and Zhang, TL and Wang, YF and Zhu, D}, title = {Microplastic Diversity as a Potential Driver of Soil Denitrification Shifts.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c04981}, pmid = {40913558}, issn = {1520-5851}, abstract = {Microplastics (MPs) are raising significant global concerns due to their environmental impacts. While most studies have focused on the effects of individual MP types, MPs in natural environments typically coexist as multiple types, and their combined effects remain poorly understood. In this study, we conducted a microcosm experiment with four levels of MP diversity (0, 1, 3, and 5 types) to investigate the effects of MP diversity on soil ecosystem functions using metagenomic sequencing. Our results revealed that increasing MP diversity significantly raised soil pH and organic carbon content while reducing available nitrogen. Notably, bacterial alpha diversity (Shannon and Invsimpson indices) increased significantly with higher MP diversity. Moreover, increasing MP diversity markedly shifted bacterial life-history strategies to adapt to the altered environment. Importantly, the abundance of nitrogen-related functional genes also increased with MP diversity. In particular, the abundance of denitrifying genes, predominantly driven by Rhodocyclaceae, was notably enhanced, resulting in a reduction of soil available nitrogen. Collectively, these findings offer valuable insights into the impact of MP diversity on soil function─especially within the nitrogen cycle─and have important implications for soil management strategies under MP stress.}, }
@article {pmid40912563, year = {2025}, author = {Lu, Q and Qin, JX and Xie, SL and Chen, R and Xu, YQ and Ban, YM and Gao, CC and Li, PY and Wang, X and Tian, XZ}, title = {Effects of a commercial buckwheat rhizome flavonoid extract on milk production, plasma pro-oxidant and antioxidant, and the ruminal metagenome and metabolites in lactating dairy goats.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2024-26208}, pmid = {40912563}, issn = {1525-3198}, abstract = {Buckwheat is a common straw crop that contains an abundance of flavonoids and could be used as an antioxidant additive in animal diets. In this study, the effects of a commercial buckwheat rhizome flavonoid extract (BRFE) on milk production, plasma pro-oxidant and antioxidant, the ruminal metagenome, and ruminal metabolites in dairy goats were evaluated. Forty healthy, multiparous, nonpregnant Guanzhong dairy goats were blocked by DIM (122 ± 5.1 d), milk yield (1,461 ± 91 g/d), parity (3.80 ± 0.76 lactations), and BW (44.18 ± 2.47 kg), and were assigned to 1 of 4 diets. The control (CON) goats were fed the basal total mixed ratio, whereas the goats in treatment groups 1, 2, and 3 were fed the CON diet supplemented with 70, 140 (MB), and 210 mg/kg of a commercial BRFE (Shaanxi Haiyisi Biotechnology Co. Ltd., Xian, China) on a DM basis of the diet, respectively. The goats were fed these diets for a total of 63 d, with a 21-d adaptation period and a 42-d experimental period. Individual DMI and milk yield were recorded daily. Milk component samples were collected on d 6, 7, 13, 14, 20, 21, 27, 28, 34, 35, 41, and 42 of the experimental period; blood and ruminal fluid samples were collected on d 1, 21, and 42 of the experimental period. The results indicated that all milk production variables (milk yield, 3.5% FCM, fat, protein, lactose, and SNF yields) linearly and quadratically increased with increasing BRFE supplementation, and these variables were the highest in the MB group. The plasma total antioxidant capacity and superoxide dismutase increased linearly and quadratically with increasing BRFE supplementation. The plasma malondialdehyde and superoxide anion contents linearly and quadratically decreased with increasing dietary BRFE content. The ruminal fluid propionate content linearly and quadratically increased with BRFE supplementation. The ruminal acetate:propionate ratio linearly and quadratically decreased with increasing BRFE content. Compared with CON, feeding 140 mg/kg BRFE reduced the ruminal fluid abundances of Synergistetes at the phylum level and Quinella at the genus level. Dietary supplementation with BRFE increased the abundance of carbohydrate-digesting enzymes in ruminal fluid, among which glycoside hydrolase family 2 was the most dominant. Metabolomic analysis indicated that supplementation with BRFE enriched tryptophan metabolism in the rumen. Overall, this study revealed that dietary supplementation with BRFE increased plasma antioxidant capabilities and milk production and improved ruminal fermentation, the ruminal metagenome, and ruminal tryptophan metabolism in lactating dairy goats.}, }
@article {pmid40912476, year = {2025}, author = {Lu, Z and Petersen, C and Dai, R and Reyna, ME and Ahmadiankalati, M and Sifuentes, E and Dai, DLY and Hoskinson, C and Del Bel, KL and Miliku, K and Moraes, TJ and Mandhane, PJ and Becker, AB and Azad, MB and Simons, E and Lou, W and Ambalavanan, A and Duan, Q and Turvey, SE and Subbarao, P}, title = {Early preschool wheeze trajectories are predominantly non-allergic with distinct biologic and microbiome traits.}, journal = {The Journal of allergy and clinical immunology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jaci.2025.07.034}, pmid = {40912476}, issn = {1097-6825}, abstract = {BACKGROUND: Disentangling preschool wheezing heterogeneity in terms of clinical traits, temporal patterns, and collective healthcare burden is critical for precise and effective interventions.<br><br>OBJECTIVE: We aimed to collectively define contributions and distinct characteristics of respiratory phenotypes based on longitudinal wheeze and atopic sensitization patterns in the first 5 years of life.<br><br>METHODS: Group-based trajectory analysis was performed in the CHILD Cohort study to identify distinct wheeze and allergic sensitization trajectories. Trajectories were evaluated for associated risk factors, healthcare utilization, biological determinants, and clinical outcomes. Stool samples for shotgun metagenomic sequencing profiles from infant microbiomes collected at 3-months and 1-year were assessed for phenotype-specific biomarkers.<br><br>RESULTS: Six distinct respiratory phenotypes were identified from 2902 children that differed by temporal wheeze and allergic sensitization patterns. While allergic wheeze phenotypes (11&#xb7;6% of participants) carried the highest asthma diagnosis risk, the more common non-allergic phenotypes (88&#xb7;3% of participants) contributed to the majority of 5-year asthma diagnoses (61&#xb7;4% of diagnoses). Most importantly, non-allergic phenotypes accounted for over 2/3 of healthcare utilization in this age group. Phenotypes differed by lung function, blood eosinophils, allergic comorbidities and weight-for-age z-score. Moreover, microbiome profiles from 1439 infants revealed largely non-overlapping microbial signatures at 1 year were associated with each phenotype.<br><br>CONCLUSION: We identified novel early childhood respiratory phenotypes to disentangle non-overlapping paths to preschool wheezing. Our findings highlight the continued clinical relevance of non-atopic wheeze phenotypes, which remain undertreated despite accounting for a substantial proportion of healthcare utilization and asthma diagnoses.}, }
@article {pmid40911772, year = {2025}, author = {Li, Q and Yang, F and Zhou, CZ}, title = {Cyanophages: Billions of Years of Coevolution with Cyanobacteria.}, journal = {Annual review of microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1146/annurev-micro-042924-095145}, pmid = {40911772}, issn = {1545-3251}, abstract = {Prevalent in marine and freshwater ecosystems, cyanophages compose a class of double-stranded DNA viruses that specifically infect cyanobacteria. During billions of years of coevolution, cyanophages and cyanobacteria have significantly contributed to the biogeochemical cycling and genetic diversity of aquatic ecosystems. As natural predators of cyanobacteria, cyanophages hold promise as eco-friendly agents against harmful cyanobacterial blooms. Recent technical advances in omics and cryo-electron microscopy have revealed the remarkable diversity of cyanophages in genome sequence and tail morphology. In this review, we summarize the genomic and metagenomic data, phylogenetic analyses, and diverse three-dimensional structures of cyanophages, in addition to their interplays with hosts. We also discuss the in vivo assembly processes of cyanophages, the exploration of uncultured cyanophages and host pairing, and the synthetic engineering and potential applications of cyanophages.}, }
@article {pmid40911291, year = {2025}, author = {Zhang, G and Yue, Y and Tu, L and Liu, Q and Zhang, Q and Shang, K}, title = {Responses of microbial communities during oilseed plant-based phytoremediation of heavy metal contaminated soils.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxaf226}, pmid = {40911291}, issn = {1365-2672}, abstract = {AIMS: Phytoremediation is an effective method of remediating soils contaminated with heavy metals. However, it has some limitations in practical applications with regard to rare plant species, poor environmental adaptability, and long growth cycles. The dynamic response mechanisms of soil microbial communities during phytoremediation are still unclear, which restricts the optimization and promotion of this approach.<br><br>METHODS AND RESULTS: No ethical approval was required for this study. In this study, soil bacterial, fungal, and archaeal communities during the remediation of Cu-, Pb-, and Zn-contaminated soils with five industrial oilseed plants (Xanthium strumarium (XS), Bidens pilosa (BP), Kosteletzkya virginica (KV), Sesbania cannabina (SC), and Commelina communis (CC)) were analyzed using metagenome sequencing. Compared with soil contaminated with heavy metals, remediation through five industrial oilseed plants significantly reduced the content of heavy metals in the soil, with soil Cu, Pb, and Zn decreasing by 44.01%, 46.32%, and 27.62%, respectively, and WSCu, WSPb, and WSZn content decreasing by 28.23%, 50.68%, and 75.26%, respectively. Microbial diversity analysis showed that phytoremediation significantly affected the soil microbial communities, with a significant decrease in archaeal diversity. Variation partitioning analysis and Mantel tests revealed that heavy metals and soil physicochemical properties significantly affected microbial communities, and heavy metals exerted stronger effects on archaeal communities. Meanwhile, soil contaminated with heavy metals was mainly dominated by fungal-fungal interactions, whereas phytoremediation increased the complexity of microbial symbiotic networks.<br><br>CONCLUSION: Collectively, these results provide fundamental insights into the microbial community structure during phytoremediation of heavy metal contaminated soil, which may aid in the bioregulation of phytoremediation.}, }
@article {pmid40910796, year = {2025}, author = {Gaun, N and Pietroni, C and Martin-Bideguren, G and Lauritsen, J and Aizpurua, O and Fernandes, JM and Ferreira, E and Aubret, F and Sarraude, T and Perry, C and Wauters, L and Romeo, C and Spada, M and Tranquillo, C and Sutton, AO and Griesser, M and Warrington, MH and Pérez I de Lanuza, G and Abalos, J and Aguilar, P and de la Cruz, F and Juste, J and Alonso-Alonso, P and Groombridge, J and Louch, R and Ruhomaun, K and Henshaw, S and Cabido, C and Barrio, IG and Šunje, E and Hosner, P and Prates, I and While, GM and García-Roa, R and Uller, T and Feiner, N and Bonaccorso, E and Klein-Ipsen, P and Rotovnik, RM and Alberdi, A and Eisenhofer, R}, title = {The Earth Hologenome Initiative: Data Release 1.}, journal = {GigaScience}, volume = {14}, number = {}, pages = {}, doi = {10.1093/gigascience/giaf102}, pmid = {40910796}, issn = {2047-217X}, support = {DNRF143//Danmarks Grundforskningsfond/ ; CF20-0460//Carlsbergfondet/ ; 101066225//HORIZON EUROPE Framework Programme/ ; PD/BD/150645/2020//Ag&#xea;ncia Regional para o Desenvolvimento da Investiga&#xe7;&#xe3;o, Tecnologia e Inova&#xe7;&#xe3;o/ ; 25925//Villum Fonden/ ; }, mesh = {Animals ; *Metagenomics/methods ; *Metagenome ; *Microbiota/genetics ; Earth, Planet ; *Vertebrates/genetics/microbiology ; Databases, Genetic ; }, abstract = {BACKGROUND: The Earth Hologenome Initiative (EHI) is a global endeavor dedicated to revisit fundamental ecological and evolutionary questions from the systemic host-microbiota perspective, through the standardized generation and analysis of joint animal genomic and associated microbial metagenomic data.<br><br>RESULTS: The first data release of the EHI contains 968 shotgun DNA sequencing read files containing 5.2 TB of raw genomic and metagenomic data derived from 21 vertebrate species sampled across 12 countries, as well as 17,666 metagenome-assembled genomes reconstructed from these data.<br><br>CONCLUSIONS: The dataset can be used to address fundamental questions about host-microbiota interactions and will be available to the research community under the EHI data usage conditions.}, }
@article {pmid40910779, year = {2025}, author = {Hanawa, S and Son, A and Kato, T and Matsuo, Y and Omae, T and Omori, Y and Yoshikawa, K and Yamanegi, K and Hirota, K and Ohno, H and Ogura, H and Ishido, S and Noguchi, K and Kishimoto, H}, title = {Identification of beneficial symbiont candidates in commensalism as potential oral gatekeepers.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0158825}, doi = {10.1128/spectrum.01588-25}, pmid = {40910779}, issn = {2165-0497}, abstract = {The basis of the development of oral cancer has been reported to be inflammation (e.g., periodontitis) caused by dysbiosis of the oral microbiota (i.e., a decrease in beneficial oral symbionts). Since a decrease in beneficial symbionts is connected to oral cancer, restoring these bacteria may help prevent it. Based on this, oral probiotics using beneficial oral symbionts are under development. Therefore, it is necessary to understand how beneficial oral symbionts are maintained in a healthy oral cavity. We evaluated a cohort consisting of 42 healthy volunteers and 39 oral cancer patients via 16S metagenomic analysis. Beneficial symbiont candidates were mined by comparing the oral microbiota of healthy volunteers with that of oral cancer patients, and the interaction mode among the beneficial symbiont candidates was further examined. Cancer patients exhibited decreased relative abundance of the genera Rothia and Streptococcus. In addition, both bacterial genera further decreased in advanced cancer, highlighting them as beneficial candidates. Furthermore, these two bacterial genera demonstrated a positive correlation in terms of relative abundance. Rothia dentocariosa isolated from a representative healthy volunteer was suggested to support the survival of Streptococcus salivarius through possible syntrophic interaction. Thus, we report a potential syntrophic interaction between Streptococcus spp. and Rothia spp. as a possible mechanism underlying oral health maintenance. Given that S. salivarius is currently employed as an oral probiotic, our findings provide insights into the development of probiotics for oral cancer.IMPORTANCEPathobiont candidates associated with oral cancer are currently being thoroughly investigated. However, it is not clear which bacteria and how their interactions contribute to preventing the development of oral cancer. In this report, we demonstrate for the first time the presence of a potential syntrophic interaction between Rothia spp. and Streptococcus spp., both of which were identified as beneficial symbiont candidates in the oral cavity.}, }
@article {pmid40910778, year = {2025}, author = {Aasmets, O and Taba, N and Krigul, KL and Andreson, R and ,  and Org, E}, title = {A hidden confounder for microbiome studies: medications used years before sample collection.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0054125}, doi = {10.1128/msystems.00541-25}, pmid = {40910778}, issn = {2379-5077}, abstract = {Medication usage is a known contributor to the inter-individual variability of the gut microbiome. However, medications are often used repeatedly and for long periods, a notion yet unaccounted for in microbiome studies. Recently, we and others showed that not only the usage of antibiotics and antidepressants at sampling, but also past consumption, is associated with the gut microbiome. This effect can be "additive"-the more a medication is used, the stronger the impact on the microbiome. Here, by utilizing retrospective medication usage data from the electronic health records and the observational Estonian microbiome cohort shotgun metagenomics data set (n = 2,509), we systematically evaluate the long-term effects of antibiotics and human-targeted medications on the gut microbiome. We show that past usage of medications is associated with the gut microbiome. For example, the effects of antibiotics, psycholeptics, antidepressants, proton pump inhibitors, and beta-blockers are detectable several years after use. Furthermore, by analyzing a subcohort (n = 328) with a second microbiome characterization, we show that similar changes in the gut microbiome occur after treatment initiation or discontinuation, possibly indicating causal effects.IMPORTANCEThis is the first study using detailed retrospective medication usage data from electronic health records to systematically assess the long-term effects of medication usage on the gut microbiome. We identified carryover and additive effects on the gut microbiome for a range of antibiotics and non-antibiotic medications, such as benzodiazepine derivatives, antidepressants and glucocorticoids, among others. These findings highlight a collateral effect of diverse drug classes on the gut microbiome, which warrants accounting for long-term medication usage history when assessing disease-microbiome associations.}, }
@article {pmid40910361, year = {2025}, author = {Mayr, MJ and Parra, SA and Connon, SA and Narayanan, AK and Murali, R and Crémière, A and Orphan, VJ}, title = {Distinct Microbial Communities Within and On Seep Carbonates Support Long-term Anaerobic Oxidation of Methane and Divergent pMMO Diversity.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf153}, pmid = {40910361}, issn = {1751-7370}, abstract = {At methane seeps worldwide, syntrophic anaerobic methane-oxidizing archaea and sulfate-reducing bacteria promote carbonate precipitation and rock formation, acting as methane and carbon sinks. Although maintenance of anaerobic oxidation of methane (AOM) within seep carbonates has been documented, its reactivation upon methane exposure remains uncertain. Surface-associated microbes may metabolize sulfide from AOM, maintain carbonate anoxia, contribute to carbonate dissolution, and support higher trophic levels; however, these communities are poorly described. We provide insights into microbial diversity, metabolism, activity, and resiliency within and on seep carbonates through amplicon and metagenomic sequencing, incubations, and non-canonical amino acid tagging combined with fluorescence in situ hybridization (BONCAT-FISH). Ca. Methanophaga (ANME-1) dominated the carbonate interiors in active and low activity seeps, co-occurring with Ca. Desulfaltia as main sulfate reducer, potentially a new syntrophic partner in AOM. Single-cell BONCAT-FISH revealed variability in ANME-1 activity, suggesting potential dormancy in carbonates from low activity seep sites. However, incubations with carbonates from low activity seeps (≥24 months) showed exponential AOM reactivation (~44-day doubling), suggesting these carbonates retain the potential as long-term methane sinks under dynamic seepage conditions. Surface-associated microbial communities were heterogeneous and distinct from the carbonate interior and other seep habitats. Anaerobic methane-oxidizing biofilms and sulfide-oxidizing mats were associated with carbonates with high and intermediate AOM rates potentially influencing carbonate precipitation/dissolution. Shared aerobic methanotrophs between carbonate surfaces and invertebrates indicated carbonate surfaces may represent animal epibiont reservoirs. Recovered particulate methane monooxygenases included both aerobic methanotrophs and divergent forms associated with the Methylophagaceae, suggesting a new function in this group.}, }
@article {pmid40910191, year = {2025}, author = {Yehezkel-Cortes, AM and Ruiz-Ordaz, N and Galíndez-Mayer, J and González-Juárez, S and Gómez-Murcia, V}, title = {Modeling and simulation of a modified Ludzack-Ettinger wastewater treatment bioprocess based on the concept of multifunctional microbiota.}, journal = {Environmental technology}, volume = {}, number = {}, pages = {1-15}, doi = {10.1080/09593330.2025.2551907}, pmid = {40910191}, issn = {1479-487X}, abstract = {This research investigates the behavior of key components within aerobic and anoxic bioreactors in Biological Nitrogen Removal (BNR) bioprocesses. A mathematical model based on the Modified Ludzack-Ettinger (MLE) configuration is proposed. The model comprises an ensemble of ten differential equations derived from mass balances in the MLE system, complemented with a set of biokinetic models. To reduce complexity and enhance applicability, the model treats all nitrogen and phosphorus compounds as atomic N and P, and aggregates carbon sources as Chemical Oxygen Demand (COD), eliminating the need for tuning complex compound-specific parameters. The model was calibrated and validated using analytical determinations of nitrogen, phosphorus, COD, dissolved oxygen, and biomass concentrations from experiments conducted with synthetic wastewater in aerobic and anoxic reactors. Complementing this, a metagenomic study characterized the diversity and relative abundance of taxonomic groups involved in nitrogen and phosphorus metabolism within the microbial communities. Utilizing biokinetic and stoichiometric parameters for the entire microbiota, the model can be solved for both transient and steady-state conditions across a range of operational variables. It enables the estimation of bioprocess resilience following disturbances and the subsequent recovery time to a new steady state. A one-at-a-time (OAT) sensitivity analysis identified the parameters most significantly affecting state variables. The experimental results confirm the model's validity and reliability in simulating BNR processes.}, }
@article {pmid40909844, year = {2025}, author = {Hussain, FA and Bergerat, A and Kelly, J and Demidkina, BC and Worrall, D and Xu, J and Kannan, A and Brunner, T and Culler, N and Goldenberg, M and Arar, WE and Katukota, AV and Murthy, M and Elsherbini, J and Hussain, S and Dong, M and Kwon, DS and Mitchell, CM}, title = {Donation strain engraftment demonstrates feasibility of vaginal microbiota transplantation to prevent recurrent bacterial vaginosis.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.08.27.25334544}, pmid = {40909844}, abstract = {Although bacterial vaginosis (BV) affects 30% of women worldwide and is associated with adverse health outcomes, current standard-of-care antibiotics fail in over half of cases and treatments have not improved in over 40 years. Probiotics have been proposed as alternative treatments, but fail to restore an optimal lactobacilli-dominated microbiome in the vast majority of patients. Here, we present findings from a pilot clinical trial demonstrating the successful engraftment of vaginal microbiota transplantations (VMTs) after antibiotic treatment in individuals with recurrent BV. Following an investigational donation protocol under an FDA IND, we treated eight recipients with material from a single donor. Using 16S rRNA gene amplicon sequencing we show that VMT results in a shift toward an optimal, Lactobacillus crispatus -dominated microbial community in three out of four VMT recipients at one month post-transplant. In two successful transplantations, this shift lasted at least six months post-VMT. In contrast, no placebo recipients exhibited L. crispatus dominance. Bacterial culturing and whole genome sequencing combined with metagenomic sequencing from donations and recipient longitudinal samples revealed colonization by donor-derived strains of L. crispatus in VMT recipients. Additionally, we observed no increase in genital inflammatory markers or changes in endocervical immune cell proportions when comparing treatment to placebo, indicating transplant safety. Together, these findings support the hypothesis that transferring the entire vaginal microbiota can lead to a more complete restoration of the vaginal ecosystem compared to single strain probiotics and lay the foundation for designing novel microbial therapies for BV. Vaginal microbiota transplantations lead to stable L. crispatus engraftment in the microbiomes of certain patients with recurrent bacterial vaginosis.}, }
@article {pmid40909705, year = {2025}, author = {Cumbo, F and Blankenberg, D}, title = {Characterization of microbial dark matter at scale with MetaSBT and taxonomy-aware Sequence Bloom Trees.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.08.25.672238}, pmid = {40909705}, issn = {2692-8205}, abstract = {UNLABELLED: Metagenomics has become a powerful tool for studying microbial communities, allowing researchers to investigate microbial diversity within complex environmental samples. Recent advances in sequencing technology have enabled the recovery of near-complete microbial genomes directly from metagenomic samples, also known as metagenome-assembled genomes (MAGs). However, accurately characterizing these genomes remains a significant challenge due to the presence of sequencing errors, incomplete assembly, and contamination. Here we present MetaSBT, a new tool for organizing, indexing, and characterizing microbial reference genomes and MAGs. It is able to identify clusters of genomes at all seven taxonomic levels, from the kingdom all the way down to the species level, using the Sequence Bloom Tree (SBT) data structure that relies on Bloom Filters (BFs) to index massive amounts of genomes based on their k-mers composition. We have built an initial set of databases composed of over 190 thousand viral genomes from NCBI GenBank and public sources grouped into sequence consistent clusters at different taxonomic levels, making it the first software solution for the classification of viruses at different ranks, including still unknown ones. This results in the definition of over 40 thousand species clusters where ∼80% do not match with any known viral species in reference databases to date. Furthermore, we show how our databases can be used as a new basis for existing quantitative metagenomic profilers to unlock the detection of unknown microbes and the estimation of their abundance in metagenomic samples. Finally, the framework is released open-source and, along with its public databases, is fully integrated into the Galaxy Platform enabling broad accessibility.<br><br>IMPORTANCE: The MetaSBT framework and its databases, together with its integration in the Galaxy Platform, provide a powerful resource for microbial research. MetaSBT provides a powerful and scalable approach for classifying microbial genomes, including previously unknown ones. This facilitates the discovery and characterization of novel taxa, a crucial feature for expanding our knowledge of microbial diversity and its implications within host health and environmental factors. Furthermore, MetaSBT databases can serve as a reference base for other state-of-the-art tools, enhancing their capabilities to identify, analyze, and classify unknown microbes in metagenomic samples.}, }
@article {pmid40909542, year = {2025}, author = {Mahlich, Y and Sohi, H and Piehowski, P and McDermott, JE and Gosline, SJ}, title = {spammR: an R package designed for analysis and integration of spatial multi-omic measurements.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.08.26.672472}, pmid = {40909542}, issn = {2692-8205}, abstract = {SUMMARY: Spatial omics is a young and evolving field and as such shows rapid development of novel technologies and analysis methods to measure transcripts, proteins, metabolites, and post-translational modifications at high spatial resolution. These advances in technology have enabled the simultaneous generation of abundance profiles for multiple different omics types and associated microscopy imaging data, as well as their analysis in a spatial context. However, most analytical tools are designed for spatial transcriptomics platforms and are challenging to use in other contexts such as mass spectrometry-based measurements or metagenomics. To this end we present spammR (sp atial a nalysis of m ulti-omics m easurements in R), an R package that enables end-to-end analysis with a specific focus on mass-spectrometry derived spatial omics datasets with (1) smaller sample sizes and spatial sparsity of samples, (2) considerable missingness, and (3) no a-priori knowledge about proteins or genes of interest, relying on a fully data-driven approach.<br><br>spammR is implemented in R. The package is currently installable from GitHub (https://github.com/PNNL-CompBio/spammR).}, }
@article {pmid40909440, year = {2025}, author = {Feng, M and Chai, Y and Li, J and Wang, Q and Zhang, D}, title = {A metagenome-wide association study of gut microbiota in hepatitis B virus-related cirrhosis in northwest China.}, journal = {Frontiers in genetics}, volume = {16}, number = {}, pages = {1619911}, pmid = {40909440}, issn = {1664-8021}, abstract = {BACKGROUND AND PURPOSE: In recent years, research on the relationship between hepatitis B virus-related cirrhosis (HBV-LC) and gut microbiota has grown, but studies focusing on the Northwest Chinese population are scarce. This study characterized the gut microbiota composition and function in HBV-LC patients vs. healthy individuals in Northwest China, aiming to provide a scientific basis for region-specific precision therapies.<br><br>MATERIALS AND METHODS: A cross-sectional study enrolled 43 HBV-LC patients and 43 age-/sex-matched healthy controls (HC) from Gansu Province. Clinical parameters including liver function, blood routine, coagulation function, blood biochemistry were measured. Shotgun metagenomic sequencing was conducted to analyze gut microbiota taxonomic composition and function.<br><br>RESULTS: HBV-LC patients showed significantly elevated alanine aminotransferase (ALT), aspartate aminotransferase (AST), alkaline phosphatase (ALP), &#x3b3;-glutamyl transferase (&#x3b3;-GGT), prothrombin time, international normalized ratio (INR), and thrombin time, but reduced triglycerides (TG), total cholesterol (TC), erythrocytes, thrombocytes, total protein, albumin, and prothrombin time activity (PT-ratio). Alpha-diversity based on Shannon and Simpson indices was lower in HBV-LC. At the genus level, Bacteroides, Prevotella, Escherichia, Parabacteroides, Veillonella, and Klebsiella were enriched in HBV-LC, while Bifidobacterium, Faecalibacterium, Roseburia, Ruminococcus, Anaerostipes, Blautia, Eubacterium, and Fusicatenibacter were reduced. Species-level analysis identified distinct enrichment of Prevotella copri, Bacteroides vulgatus, Escherichia coli, Fusobacterium nucleatum, and Veillonella spp. in HBV-LC. Functional analysis revealed 482 metabolic pathways. HBV-LC showed enhanced lipid, amino acid, and nucleotide metabolism, menaquinol biosynthesis, and anaerobic energy metabolism, but reduced acetate/lactate production, lactose/galactose degradation, and peptidoglycan biosynthesis. Metagenome-wide association study revealed HBV-LC-enriched opportunistic species (e.g., E. coli, Veillonella spp.) correlated positively with hepatic enzymes and coagulation parameters, and negatively with TC, TG, and erythrocyte counts.<br><br>CONCLUSION: HBV-LC patients in Northwest China exhibit altered clinical indicators, gut microbial composition (reduced diversity, increased opportunistic pathogens, decreased beneficial species), and metabolic function. These findings highlight the potential of gut microbiome-targeted interventions for regional precision medicine of HBV-LC.}, }
@article {pmid40909338, year = {2025}, author = {Borgognone, A and Prats, A and Sharma, AA and Martinez-Zalacaín, I and Soriano-Mas, C and Brander, C and Clotet, B and Moltó, J and Mothe, B and Sekaly, RP and Paredes, R and Muñoz-Moreno, JA}, title = {Interactions between gut microbiota, plasma metabolome and brain function in the setting of a HIV cure trial.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1629901}, pmid = {40909338}, issn = {2235-2988}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Metabolome ; *HIV Infections/drug therapy/complications/microbiology ; Male ; Female ; *Brain/physiopathology/physiology ; Adult ; Biomarkers/blood ; Middle Aged ; Feces/microbiology ; Metagenomics ; Bacteria/classification/genetics/isolation &amp; purification ; HIV-1/drug effects ; }, abstract = {BACKGROUND: The intestinal microbiota composition has been linked to neurocognitive impairment in people with HIV (PWH). However, the potential interplay of microbial species and related metabolites, particularly in the context of an HIV cure strategy remains underexplored. The BCN02 trial evaluated the impact of romidepsin (RMD), used as a HIV-1 latency reversing agent and with reported beneficial neurological effects, combined with the MVA.HIVconsv vaccine on virus control during 32-weeks of monitored antiretroviral treatment interruption (MAP) in early-treated HIV-infected individuals. Here, we analyzed longitudinal gut microbiome, plasma metabolome and brain functioning data to identify potential associations and novel putative biomarkers of HIV-associated neurocognitive disorders (HAND).<br><br>METHODS: Data from fecal shotgun metagenomics, plasma metabolome, cognitive (standardized neuropsychological test score covering 6 cognitive domains, NPZ-6), functional (neuropsychiatric symptoms) and neuroimaging assessments were obtained and evaluated in 18 participants before and after RMD administration, and at the study end (post-MAP follow-up) in the BCN02 trial.<br><br>RESULTS: Participants with neurocognitive impairment (Lower vs. Higher NPZ-6 score group) were enriched in bacterial species, including Desulfovibrio desulfuricans, Sutterella wadsworthensis and Streptococcus thermophilus, and showed higher 1,2-propanediol degradation microbial pathway levels, before RMD administration. A multi-omics profiling showed significant and positive correlations between these microbial features and lipid-related metabolic pathways, previously linked to neurological disorders (i.e., sphingolipid, ether lipid, and glycerophospholipid metabolism), in participants with neurocognitive impairment, before RMD administration. Three indices (microbial-, metabolite-based and combined) obtained from the discriminant features were assessed longitudinally, showing progressive similarities between NPZ-6 score groups over time. Furthermore, the three indices and related discriminant features correlated negatively with functional outcomes, such as quality of life and daily functioning, and positively with depression, stress and CNS-related symptoms before RMD administration, while these associations became less discernible at the subsequent timepoints.<br><br>CONCLUSIONS: While the direct effect of the intervention on the observed shifts cannot be conclusively determined in this study settings, these findings strengthen the link between gut bacteria, related metabolites, and neurocognitive function in PWH, and provide an analytical framework for future validation studies aimed at discovering predictive biomarkers for neurocognitive impairment in PWH.}, }
@article {pmid40909218, year = {2025}, author = {Tigrero-Vaca, J and Díaz, B and Gu, G and Cevallos-Cevallos, JM}, title = {Next-generation sequencing applications in food science: fundamentals and recent advances.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {13}, number = {}, pages = {1638957}, pmid = {40909218}, issn = {2296-4185}, abstract = {Next-generation sequencing (NGS) has revolutionized food science, offering unprecedented insights into microbial communities, food safety, fermentation, and product authenticity. NGS techniques, including metagenetics, metagenomics, and metatranscriptomics, enable culture-independent pathogen detection, antimicrobial resistance surveillance, and detailed microbial profiling, significantly improving food safety monitoring and outbreak prevention. In food fermentation, NGS has enhanced our understanding of microbial interactions, flavor formation, and metabolic pathways, contributing to optimized starter cultures and improved product quality. Furthermore, NGS has become a valuable tool in food authentication and traceability, ensuring product integrity and detecting fraud. Despite its advantages, challenges such as high sequencing costs, data interpretation complexity, and the need for standardized workflows remain. Future research focusing on optimizing real-time sequencing technologies, expanding multi-omics approaches, and addressing regulatory frameworks is suggested to fully harness NGS's potential in ensuring food safety, quality, and innovation.}, }
@article {pmid40909207, year = {2025}, author = {Li, D and Pan, J and Yang, M and Zhong, J and Ding, H and Chen, W and Zhang, J and Liao, G}, title = {Positive Metagenomic Next-Generation Sequencing of Renal Lavage Fluid Associates with Delayed Graft Function in Kidney Transplants from Donors After Circulatory Death: A Retrospective Study.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {4579-4592}, pmid = {40909207}, issn = {1178-6973}, abstract = {BACKGROUND: Delayed graft function (DGF) is a major complication in kidney transplants from donation after circulatory death (DCD). This study assessed the association between metagenomic next-generation sequencing (mNGS) results and the occurrence of DGF during the perioperative period in DCD kidney transplant recipients.<br><br>METHODS: We analyzed 191 DCD kidney transplant recipients in this single-center retrospective cohort study. All recipients underwent routine mNGS testing of renal lavage fluid between July 2021 and July 2024. Demographic, clinical, and microbial data were collected. Associations between mNGS results and DGF were evaluated using logistic regression models adjusted for covariates.<br><br>RESULTS: The study revealed a strong association between mNGS positivity and DGF development. mNGS-positive recipients (n=97/191) showed significantly higher DGF incidence than mNGS-negative cases (30.9% vs 6.4%, p<0.001), highlighting the potential clinical utility of mNGS in predicting DGF. Multivariate analysis confirmed this association after adjusting for confounders (aOR=7.90, 95% CI 1.63-38.24). Bacterial pathogens constituted the majority of detected microorganisms (62.7%), with prevalent isolates including Enterococcus (37 cases) and Staphylococcus (29 cases) that harbored clinically relevant resistance genes.<br><br>CONCLUSION: Our findings demonstrate a significant association between mNGS positivity in renal lavage fluid and DGF development in DCD kidney recipients (aOR 7.90, 95% CI 1.63-38.24), These findings support further investigation into mNGS as a tool for early risk stratification and targeted antimicrobial therapy in DCD kidney recipients.}, }
@article {pmid40909168, year = {2025}, author = {Siegwald, L and Cherta-Murillo, A and Christen, S and Boulangé, CL and Chou, CJ and Foata, F and Lahiry, A and Frézal, A and Giner, MP and Godin, JP and Sakwinska, O}, title = {The Impact of Low-Lactose, High Galacto-Oligosaccharides Milk on Gut Microbiome and Plasma Metabolome in Healthy Adults: A Randomized, Double-Blind, Controlled Clinical Trial Complemented by Ex Vivo Experiments.}, journal = {Current developments in nutrition}, volume = {9}, number = {9}, pages = {107506}, pmid = {40909168}, issn = {2475-2991}, abstract = {BACKGROUND: Galacto-oligosaccharides (GOS) intake has been linked to health benefits via modulation of the gut microbiome. Milk, where the majority of lactose is enzymatically converted to GOS (called here Novel or "N milk"), retains milk's nutritional value with reduced lactose and a high amount of prebiotic GOS.<br><br>OBJECTIVES: The aim of this study was to investigate the effect of N milk on the gut microbiome and related changes in health-related biomarkers, complemented by ex vivo fermentation experiments.<br><br>METHODS: In a 2-arm crossover, double-blind, randomized controlled clinical trial, 26 healthy adults consumed either N milk (containing 9 g GOS and 1.7 g of lactose per serving) or lactose-free milk (control), for 2 wk with a 2-wk washout period. Stool and fasting blood samples were collected at the start and the end of the intervention periods. Gut microbiome was analyzed using shotgun metagenomics, and metabolites using both targeted and untargeted methods. In addition, we tested lactose-free milk, N milk, and GOS in ex vivo colonic fermentation to obtain insights into the bacterial processing of substrates.<br><br>RESULTS: N milk intake led to a 3-fold increase in median gut bifidobacteria (P < 0.0001) and significant increases in plasma acetate, octanoic acid, &#x3b2;-alanine, and nicotinamide (all P < 0.05). Untargeted plasma metabolomics revealed a shift in amino acid metabolism, with an increase in 3-indole propionate, accompanied by a decrease in 2 uremic toxins, p-cresol sulfate, and indoxyl-sulfate (P < 0.05 without false discovery rate adjustment). Ex vivo fermentation experiments supported the results of the clinical study, whereby N milk increased bifidobacteria accompanied by higher production of short-chain fatty acids and a shift in microbial tryptophan metabolism, and indicated unique effects of N milk compared with GOS.<br><br>CONCLUSIONS: N milk resulted in a significant increase in gut bifidobacteria, along with changes in plasma metabolites previously associated with immune and metabolic health benefits.This study was registered at clinicaltrials.gov as NCT05207839.}, }
@article {pmid40908554, year = {2025}, author = {Susilowati, A and Christita, M and Larekeng, SH and Lateef, AA and Ren, W and Azeez, AA and Simarmata, R and Khairina, Y and Khumairah, FH and Elfiati, D and Asiegbu, FO}, title = {Forest Type, Bark Wounding, and Tapping: Their Combined Influence on Bacteria Biota of Styrax Paralleloneurus in Natural and Community Forest.}, journal = {Environmental microbiology reports}, volume = {17}, number = {5}, pages = {e70184}, doi = {10.1111/1758-2229.70184}, pmid = {40908554}, issn = {1758-2229}, support = {353365//Research Council of Finland/ ; 13/UN5.2.3.1/PPM/KP-WCU/2022//Universitas Sumatera Utara/ ; }, mesh = {*Forests ; *Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; *Plant Bark/microbiology ; Biodiversity ; Indonesia ; Phylogeny ; *Trees/microbiology ; DNA, Bacterial/genetics ; *Biota ; }, abstract = {Styrax paralleloneurus is a resin-producing tree native to Sumatra, Indonesia. This study investigated the effects of tapping, bark wounding and forest type on bacterial biota in the stem of styrax in natural and community forests. Amplicon metagenomic sequencing of the 16S rRNA region was deployed to identify the bacterial communities associated with tapped and untapped trees across various environmental and experimental conditions. The results of the study showed that tapped trees had lower abundance and diversity of Pseudomonas compared to untapped trees, largely due to their increased exposure to external microbe communities and environmental elements. Serratia and Pantoea were more abundant in natural forest than community forest, while Bradyrhizobium lablabi was found abundantly in untapped trees. Additionally, the taxonomic analysis revealed distinct responses of bacterial genera to tapping and forest type, indicating that community forests could play a significant role in promoting biodiversity in forest ecosystems. This finding underscores the importance of community forests in biodiversity conservation. These insights can inform future conservation and management strategies to enhance biodiversity and underscore the need for sustainable forest management practices to maintain forest health and productivity.}, }
@article {pmid40908532, year = {2025}, author = {Wei, M and Mehravar, S and Leite, G and Naji, P and Barlow, GM and Hosseini, A and Rashid, M and Sanchez, M and Fajardo, CM and Pimentel, M and Mathur, R}, title = {Relationship between hypothyroidism, risk of small intestinal bacterial overgrowth, and duodenal microbiome alterations.}, journal = {The Journal of clinical endocrinology and metabolism}, volume = {}, number = {}, pages = {}, doi = {10.1210/clinem/dgaf495}, pmid = {40908532}, issn = {1945-7197}, abstract = {CONTEXT: There is an association between hypothyroidism and small intestinal bacterial overgrowth (SIBO), but the exact mechanistic link between these two conditions is not fully elucidated.<br><br>OBJECTIVE: We evaluate the incidence and risks of subsequently developing SIBO, and changes in small bowel microbial populations, in subjects with hypothyroidism or autoimmune thyroiditis.<br><br>DESIGN AND OUTCOME MEASURES: Duodenal aspirates from REIMAGINE study subjects with a history of hypothyroidism (hypothyroid group, N=49) and controls (N=323) underwent 16S rRNA sequencing (MiSeq, Illumina); a subset also underwent metagenomic sequencing (NovaSeq6000, Illumina). Separately, the TriNetX Analytics platform was used to evaluate ten-year cumulative incidences and relative risk [RR] of developing SIBO in subjects with hypothyroidism (unspecified etiology, HUE), and a subset with autoimmune thyroiditis, vs. propensity score matched (PSM) control groups.<br><br>RESULTS: Among REIMAGINE subjects, SIBO prevalence was higher in the hypothyroid group (32.65%) vs. controls (15.17%). In the TriNetX analysis, ten-year cumulative incidences of SIBO were higher in HUE (RR=2.20) and autoimmune thyroiditis (RR=2.40) subjects vs. matched controls. However, these risks appeared to be mitigated both in HUE (RR=0.33) and autoimmune thyroiditis (RR=0.78) subjects taking levothyroxine. Analyzing the duodenal microbiome, genus Neisseria was part of the core microbiome in the hypothyroid group (Hypo+/SIBO-, Hypo+/SIBO+) but not in non-hypothyroid subjects (Hypo-/SIBO-, Hypo-/SIBO+). Increased prevalence of Gram-negative coliforms occurred in both SIBO+ groups, but Escherichia/Shigella formed part of the core in non-hypothyroid subjects (Hypo-/SIBO+), whereas Klebsiella species were prevalent in hypothyroid group subjects with SIBO (Hypo+/SIBO+).<br><br>CONCLUSION: These findings suggest there is an increased risk for development of SIBO in individuals with a history of hypothyroidism which may be ameliorated by treatment, and may involve specific Gram-negative coliforms.}, }
@article {pmid40908508, year = {2025}, author = {Boden, L and Bludau, D and Sieber, G and Deep, A and Baikova, D and David, GM and Hadžiomerović, U and Stach, TL and Buchner, D and Boenigk, J}, title = {Varying Responses to Heat Stress and Salinization Between Benthic and Pelagic Riverine Microbial Communities.}, journal = {Environmental microbiology}, volume = {27}, number = {9}, pages = {e70173}, doi = {10.1111/1462-2920.70173}, pmid = {40908508}, issn = {1462-2920}, support = {CRC 1439/1//Deutsche Forschungsgemeinschaft/ ; //Open Access Publication Fund of the University of Duisburg-Essen/ ; }, mesh = {*Salinity ; *Microbiota ; Geologic Sediments/microbiology ; Hot Temperature ; Ecosystem ; *Rivers/microbiology/chemistry ; Bacteria/genetics/classification/isolation &amp; purification ; *Heat-Shock Response ; Climate Change ; Archaea/genetics ; Fresh Water/microbiology ; }, abstract = {Microbial communities play a crucial role in the functioning of freshwater ecosystems but are continuously threatened by climate change and anthropogenic activities. Elevated temperatures and salinisation are particularly challenging for freshwater habitats, but little is known about how microbial communities respond to the simultaneous exposure to these stressors. Here, we use mesocosm experiments and amplicon sequencing data to investigate the responses of pelagic and benthic microbial communities to temperature and salinity increases, both individually and in combination. Our results highlight the varying responses of freshwater microbial communities, with sediment communities exhibiting greater stability in response to environmental changes compared to water column communities, and salinisation having a more pronounced impact on microeukaryotes compared to prokaryotes. Simultaneous exposure to elevated temperature and salinity reduced the impact of salinisation on prokaryotes, while microeukaryotes were similarly affected by the combined treatments and salinisation alone. These findings emphasise the complexity of microbial responses to single and multiple stressors, underscoring the need to consider both individual and interactive effects when predicting ecosystem responses to environmental changes.}, }
@article {pmid40816430, year = {2025}, author = {Kong, Z and Wang, H and Man, S and Yan, Q}, title = {Magnetite modulates bacterial cooperation during cathodic nitrogen removal in bioelectrochemical systems under trace dissolved oxygen.}, journal = {Bioresource technology}, volume = {437}, number = {}, pages = {133147}, doi = {10.1016/j.biortech.2025.133147}, pmid = {40816430}, issn = {1873-2976}, mesh = {*Bioelectric Energy Sources/microbiology ; *Denitrification/drug effects ; Electrodes ; *Ferrosoferric Oxide/pharmacology ; Oxygen ; *Water Purification/methods ; Metagenome ; Ammonium Compounds/metabolism ; *Microbiota ; }, abstract = {Nitrate and ammonium co-contamination poses a major challenge for sustainable nitrogen removal, especially under microoxic conditions. This study investigated the effect of magnetite on microbial nitrogen metabolism and nitrite accumulation in biocathodes of bioelectrochemical systems under 0.25 mg/L dissolved oxygen. Magnetite improved total nitrogen removal by 22.8 %, reduced peak nitrite levels by 22.6 %, and lowered residual ammonium by 49.2 %. Magnetite promoted interspecies cooperation, driving modular specialization in nitrite reduction while suppressing dissimilatory nitrate reduction to ammonium. Concurrently, it stimulated ammonia-oxidizing bacteria activity, accelerating ammonium conversion and mitigating nitrite accumulation through enhanced denitrification. A cooperative microbial pattern emerged, with dominant species such as Hanamia sp. and Moheibacter sp. carrying out nitrite reduction, while less abundant species performed single nitrogen metabolic processes. This study highlights the role of magnetite in integrating aerobic and anaerobic nitrogen pathways, offering a sustainable strategy for controlling complex nitrogen pollution.}, }
@article {pmid40907413, year = {2025}, author = {Nono, JKN and Ayemele, AG and Fotsidie, HG and Tang, H and Li, Y and Huang, X and Hu, N and Li, X and Xu, J}, title = {Manganese accumulation characteristics and rhizosphere decontamination mechanisms of Phytolacca icosandra L.}, journal = {Ecotoxicology and environmental safety}, volume = {303}, number = {}, pages = {118970}, doi = {10.1016/j.ecoenv.2025.118970}, pmid = {40907413}, issn = {1090-2414}, abstract = {The role of microbial metagenomics in understanding ecological changes associated with rhizosphere heavy metal decontamination by plants has often been overlooked. The aim of this study was to scrutinize the structural, enzymological and metagenomic mechanisms leading to manganese (Mn) decontamination in the rhizosphere by Phytolacca icosandra. Seedlings of P. icosandra were planted for three months under six sets of Mn treatment (addition of 0, 250, 500, 100, 2500, and 5000 µg/g Mn in original soils) using a complete randomized block design. When Mn addition increased to 2500 and 5000 µg/g, the shoot biomass of P. icosandra was reduced by 3.14% and 51.85% respectively, while root biomass was reduced by 5.91% and 47.29% respectively. When Mn uptake increased in the roots/shoots and leaves after the addition of 5000 µg/g Mn, plant chlorophyll a, and malondialdehyde (MDA) concentrations decreased by 4% and 17% respectively. As a result, lipids in the cell membranes of the leaves were no longer destroyed and cell membrane degradation was inhibited by Mn gradients. With addition of 2500-5000 µg/g Mn, the overall weight and height biomasses of P. icosandra was reduced in size to absorb excess Mn. Soil N bioavailability decreased the most at the highest Mn concentration. Above 2500 µg/g Mn, rhizosphere acidification increased (pH < 7). The abundances of rhizosphere bacteria Ramlibacter sp. and Planctomycetaceae bacterium LX124 decreased when soil Mn concentration increased, while those of Tumebacillus avium, Devosia riboflavina, and Flavobacterium fevense increased, paving the way towards microbial biomarkers of soil Mn decontamination. These findings provide valuable knowledge on remediating heavy metal-contaminated agricultural soils.}, }
@article {pmid40907321, year = {2025}, author = {Lv, H and Chi, Q and Wang, J and Xu, Y and Li, M and Jiang, X and Shen, J}, title = {Electron transfer mediates position-dependent hydrolytic dichlorination during dichlorophenols biodegradation under nitrate-reducing conditions.}, journal = {Journal of hazardous materials}, volume = {497}, number = {}, pages = {139753}, doi = {10.1016/j.jhazmat.2025.139753}, pmid = {40907321}, issn = {1873-3336}, abstract = {Polychlorinated phenols (PCPs) are persistent pollutants due to strong C-Cl bonds and toxicity, posing challenges for bioremediation. Although electron acceptor activation can facilitate degradation, the effect of chlorine-substituent positions on isomer-specific biodegradability remains unclear. To address this gap, dichlorophenols (DCPs) were selected as chlorine substitution patterns shape degradation kinetics and microbial responses. Six UASB bioreactors were operated under nitrate-reducing conditions for 130 days to investigate isomer-specific degradation behaviors. The results revealed complete removal (100 %) of ortho-substituted DCPs (2,6-/2,4-DCP) versus limited removal (27.86 ± 2.26 %) of 3,4-DCP (meta-para), establishing a reactivity hierarchy among DCP isomers: dual ortho (2,6) > ortho-para (2,4) > ortho-meta (2,3/2,5) > meta substituted (3,4/3,5). Metagenomic analysis indicated that dehalogenators (Gordonia, Chryseobacterium) were enriched in 2,4-/2,3-DCP systems, nitrate-reducing Pseudomonas dominated the 3,5-DCP system, and Desulfovibrio contributed to electron transfer in the 2,3-DCP system. Molecular docking confirmed that badk (PDB ID: 7P98) and paaF (PDB ID: 6IJK) hydratases regulated degradation kinetics through substrate-specific binding, with computed affinities strongly correlating with observed removal efficiencies. Collectively, these findings demonstrate that chlorine substituent positions fundamentally govern the biodegradability of halogenated aromatics, underscoring the importance of structure-specific bioremediation strategies for effective wastewater treatment.}, }
@article {pmid40907234, year = {2025}, author = {Shi, X and Zhang, J and Chen, X and Li, Q and Hui, Y and Han, J and Jin, X and Jin, P}, title = {Impact of bacteriophage MS2 adsorption on biofilm microbial communities, metabolic pathways, and protein expression in sewer systems.}, journal = {Journal of environmental management}, volume = {393}, number = {}, pages = {126998}, doi = {10.1016/j.jenvman.2025.126998}, pmid = {40907234}, issn = {1095-8630}, abstract = {The stability of microbial communities within sewer systems is essential for maintaining effluent quality and infrastructure longevity. However, the functional consequences of viral interactions with biofilms remain poorly characterised. This study examines the effects of bacteriophage MS2 adsorption on biofilm structure, metabolism, and pathogenic potential in a simulated 1 km sewer pipeline. Quartz crystal microbalance with dissipation monitoring (QCM-D) revealed irreversible phage adsorption onto extracellular polymeric substances (EPS), inducing a biphasic viscoelastic response. During the first 24 h, the ΔD/Δf slope increased from 0.204 to 0.420, indicating initial loosening of the EPS matrix. This was followed by a compaction phase, with the slope decreasing to 0.102 by 96 h. Metagenomic profiling indicated a shift in community functionality, with sulphur-metabolising Chlorobium decreasing by 27.8 % and the pathogenic genus Novosphingobium increasing by 4.87 %. Corresponding trends were observed in enzymatic activity: sulphate reduction genes (e.g., EC 2.7.7.4) declined to 10 % of baseline levels at 24 h, before recovering to 14542 annotations at 96 h. Metaproteomic analysis revealed divergent regulatory responses, with acetyl-CoA synthetase (EC 6.2.1.1) transcriptionally upregulated, while phosphate acetyltransferase (EC 2.3.1.8) increased independently of gene expression, indicating potential post-translational control. These findings demonstrate that phage adsorption perturbs biofilm integrity and reprogrammes microbial metabolism, underscoring the need for virus-informed strategies in sewer monitoring and pathogen management.}, }
@article {pmid40906991, year = {2025}, author = {Norman, RS and Granger, CO and Cochran, KH and Isanovic, M and Self, S and Klein, E and Richardson, SD}, title = {Aerosolization of Azithromycin, Ofloxacin, and Co-occurring Antibiotic Resistance Genes during Municipal Wastewater Treatment.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c08502}, pmid = {40906991}, issn = {1520-5851}, abstract = {To effectively combat antibiotic resistance, it is critical to understand antibiotic usage patterns and their environmental dissemination. Wastewater treatment plants (WWTPs) are well-documented sources of antibiotics discharged into aquatic environments, but their role in releasing antibiotics via bioaerosols has not previously been investigated. In this study, seasonal air and liquid samples were collected throughout 2019 from a midsize WWTP employing both mechanical surface agitation and fine bubble aeration of activated sludge. Azithromycin and ofloxacin were detected in bioaerosols collected near aeration tanks at concentrations ranging from below detection limits up to 29 pg L[-1] air, suggesting that bioaerosols may represent a previously underappreciated route of environmental and occupational antibiotic exposure. Metagenomic analysis confirmed the co-occurrence of antibiotic resistance genes (ARGs) conferring resistance to macrolides and fluoroquinolones in both air and liquid samples. These findings highlight bioaerosols as an important yet overlooked pathway for the dissemination of antibiotics and ARGs, emphasizing the necessity of integrating airborne pathways into environmental antibiotic resistance surveillance programs, especially given the global scale of WWTP operations.}, }
@article {pmid40906773, year = {2025}, author = {Liu, Z and Ji, S and Chang, Q and Wang, J and Galon, EM and Xu, Y and Yin, G and Li, J and Gao, X and Tian, W and Han, Z and Li, C and Xu, Z and Du, R and Xue, S}, title = {Surveillance of tick-borne viruses in the border regions of the Tumen River Basin: Co-circulation in ticks and livestock.}, journal = {PLoS neglected tropical diseases}, volume = {19}, number = {9}, pages = {e0013500}, doi = {10.1371/journal.pntd.0013500}, pmid = {40906773}, issn = {1935-2735}, abstract = {BACKGROUND: The unique eco-geographical patterns and climatic conditions of the China-Tumen River border region, combined with frequent cross-border tourism and trade activities, collectively establish this area as a recognized hotspot for tick-borne disease outbreaks. However, critical knowledge gaps persist regarding the eco-epidemiology of emerging tick-borne viruses and the distribution of their potential reservoir hosts within this trinational ecosystem spanning China, North Korea, and Russia.<br><br>METHODS: We collected a total of 2,004 ticks from the study area, along with blood samples obtained from 42 sheep and 45 cattle. Following viral metagenomic analysis of the ticks, dual verification of target pathogens in all samples was performed using qRT-PCR and RT-PCR assays. Phylogenetic trees were constructed and nucleotide sequences were analyzed to delineate relationships between the obtained virus strains and reference sequences.<br><br>RESULTS: Viral metagenomics identified three viruses in ticks: Dabieshan tick virus (DBTV), Songling virus (SGLV), and Yanggou tick virus (YGTV). PCR analysis detected DBTV exclusively in Hunchun ticks (minimum infection rates, MIR:4.73%) and YGTV in Antu specimens (MIR:0.97%). Conversely, SGLV was detected in ticks from all four regions, with MIR of 1.68% (Helong), 0.74% (Hunchun), 1.61% (Antu), and 4.79% (Longjing). Concurrently, SGLV was detected in 19 sheep blood samples from Longjing, yielding a positivity rate of 45.24%, while YGTV was identified in 13 cattle blood samples from Antu, with a positivity rate of 28.89%. Phylogenetically, the DBTV strain clustered with previously reported DBTV and Yongjia tick virus 1 isolates. Sheep-derived SGLV strains shared close evolutionary ties with tick-borne SGLV, whereas YGTV from cattle and ticks formed a distinct cluster with Russian strains but diverged into two branches from Chinese variants, suggesting evolutionary instability.<br><br>CONCLUSION: These findings address critical knowledge gaps in the transmission dynamics and genetic diversity of emerging arboviruses while providing vital insights for developing cross-border surveillance strategies with significant public health implications.}, }
@article {pmid40906457, year = {2025}, author = {Rahube, TO and Selvarajan, R and Nduna, B and Nthaba, B and Molwalefhe, L and Shemang, E}, title = {Evaluation of Bacterial Population Changes and Ecological Dynamics in Oil-Impacted Soils Using 16S rRNA Amplicon Sequencing.}, journal = {Biology}, volume = {14}, number = {8}, pages = {}, doi = {10.3390/biology14081074}, pmid = {40906457}, issn = {2079-7737}, support = {BIUST//Botswana International University of Science and Technology/ ; }, abstract = {Soils are vibrant and diverse natural entities situated at the juncture between Earth, air, water, and life [...].}, }
@article {pmid40906400, year = {2025}, author = {Zeng, Q and Wang, Z and Shen, Z and Li, W and Luo, K and Qin, Q and Li, S and Gu, Q}, title = {Microbiome Diversity and Dynamics in Lotus-Fish Co-Culture Versus Intensive Pond Systems: Implications for Sustainable Aquaculture.}, journal = {Biology}, volume = {14}, number = {8}, pages = {}, doi = {10.3390/biology14081092}, pmid = {40906400}, issn = {2079-7737}, support = {2023YFD2400902//National Key Research and Development Program of China/ ; 2023YFD2401605//National Key Research and Development Plan Program/ ; 23B0073//Scientific Research Foundation of Hunan Provincial Education Department/ ; }, abstract = {The lotus-fish co-culture (LFC) system leverages plant-fish symbiosis to optimize aqua-culture environments, enhancing both economic and ecological yields. However, the eco-logical mechanisms of microbial communities in LFC systems remain poorly understood, particularly regarding the functional roles of fungi, archaea, and viruses. This study compared microbiota (viruses, archaea, fungi) in water, sediment, and fish (crucian carp) gut of LFC and intensive pond culture (IPC) systems using integrated metagenomic and environmental analyses. Results demonstrated that LFC significantly reduced concentrations of total nitrogen, total phosphorus, and nitrite nitrogen and chemical oxygen demand in water, and organic matter and total nitrogen in sediment compared to IPC. Community diversity analysis, LefSe, and KEGG annotation revealed suppressed viral diversity in LFC, yet increased complexity and stability of intestinal virus communities compared to IPC. Archaeal and functional analyses revealed significantly enhanced ammonia oxidation and OM decomposition in LFC versus IPC, promoting methane metabolism equilibrium and sediment organic matter decomposition. Moreover, crucian carp intestines in LFC harbored abundant Methanobacteria, which contributed to maintaining a low hydrogen partial pressure, suppressing facultative anaerobes and reducing intestinal infection risk. The abundance of fungi in sediment and crucian carp intestine in LFC was significantly higher than that in IPC, showing higher ecological self-purification ability and sustainability potential in LFC. Collectively, LFC's optimized archaeal-fungal networks strengthened host immunity and environmental resilience, while viral community suppression reduced pathogen risks. These findings elucidate microbiome-driven mechanisms underlying LFC's ecological advantages, providing a framework for designing sustainable aquaculture systems through microbial community modulation.}, }
@article {pmid40906131, year = {2025}, author = {Yuan, J and Sun, Z and Sun, R and Wang, J and Wu, C and Liu, B and Zhao, X and Li, Q and Zhao, J and Cai, K}, title = {A Spatiotemporal Atlas of the Gut Microbiota in Macaca mulatta brevicaudus: Implications for Health and Environment.}, journal = {Biology}, volume = {14}, number = {8}, pages = {}, doi = {10.3390/biology14080980}, pmid = {40906131}, issn = {2079-7737}, abstract = {The gut microbiota of macaques, highly homologous to humans in biological characteristics and metabolic functions, serves as an ideal model for studying the mechanisms of human intestinal diseases and therapeutic approaches. A comprehensive characterization of the macaque gut microbiota provides unique insights into human health and disease. This study employs metagenomic sequencing to assess the gut microbiota of wild M. mulatta brevicaudus across various ages, sexes, and physiological states. The results revealed that the dominant bacterial species in various age groups included Segatella copri and Bifidobacterium adolescentis. The predominant bacterial species in various sexes included Alistipes senegalensis and Parabacteroides (specifically Parabacteroides merdae, Parabacteroides johnsonii, and Parabacteroides sp. CT06). The dominant species during lactation and non-lactation periods were identified as Alistipes indistinctus and Capnocytophaga haemolytica. Functional analysis revealed significant enrichment in pathways such as global and overview maps, carbohydrate metabolism and amino acid metabolism. This study enhances our understanding of how age, sex, and physiological states shape the gut microbiota in M. mulatta brevicaudus, offering a foundation for future research on (1) host-microbiome interactions in primate evolution, and (2) translational applications in human health, such as microbiome-based therapies for metabolic or immune-related disorders.}, }
@article {pmid40906071, year = {2025}, author = {Zeng, X and Chen, J and Liu, G and Zhou, Y and Wang, L and Zhang, Y and Liu, S and Shao, Z}, title = {Host Shaping Associated Microbiota in Hydrothermal Vent Snails from the Indian Ocean Ridge.}, journal = {Biology}, volume = {14}, number = {8}, pages = {}, doi = {10.3390/biology14080954}, pmid = {40906071}, issn = {2079-7737}, support = {2023YFC2812903, 2021YFF0501304, and 2018YFC0310702.//National Key R&amp;D Program of China/ ; }, abstract = {Snails at hydrothermal vents rely on symbiotic bacteria for nutrition; however, the specifics of these associations in adapting to such extreme environments remain underexplored. This study investigated the community structure and metabolic potential of bacteria associated with two Indian Ocean vent snails, Chrysomallon squamiferum and Gigantopelta aegis. Using microscopic, phylogenetic, and metagenomic analyses, this study examines bacterial communities inhabiting the foot and gland tissues of these snails. G. aegis exhibited exceptionally low bacterial diversity (Shannon index 0.14-0.18), primarily Gammaproteobacteria (99.9%), including chemosynthetic sulfur-oxidizing Chromatiales using Calvin-Benson-Bassham cycle and methane-oxidizing Methylococcales in the glands. C. squamiferum hosted significantly more diverse symbionts (Shannon indices 1.32-4.60). Its black variety scales were dominated by Campylobacterota (67.01-80.98%), such as Sulfurovum, which perform sulfur/hydrogen oxidation via the reductive tricarboxylic acid cycle, with both Campylobacterota and Gammaproteobacteria prevalent in the glands. The white-scaled variety of C. squamiferum had less Campylobacterota but a higher diversity of heterotrophic bacteria, including Delta-/Alpha-Proteobacteria, Bacteroidetes, and Firmicutes (classified as Desulfobacterota, Pseudomomonadota, Bacteroidota, and Bacillota in GTDB taxonomy). In C. squamiferum, Gammaproteobacteria, including Chromatiales, Thiotrichales, and a novel order "Endothiobacterales," were chemosynthetic, capable of oxidizing sulfur, hydrogen, or iron, and utilizing the Calvin-Benson-Bassham cycle for carbon fixation. Heterotrophic Delta- and Alpha-Proteobacteria, Bacteroidetes, and Firmicutes potentially utilize organic matter from protein, starch, collagen, amino acids, thereby contributing to the holobiont community and host nutrition accessibility. The results indicate that host species and intra-species variation, rather than the immediate habitat, might shape the symbiotic microbial communities, crucial for the snails' adaptation to vent ecosystems.}, }
@article {pmid40905761, year = {2025}, author = {Abbasi, E}, title = {Forensic Entomology in Criminal Investigations: Advances in Insect-Mediated Postmortem Interval Estimation, Species Identification, and Environmental Influences.}, journal = {The American journal of forensic medicine and pathology}, volume = {}, number = {}, pages = {}, doi = {10.1097/PAF.0000000000001067}, pmid = {40905761}, issn = {1533-404X}, abstract = {Forensic entomology is a crucial discipline in forensic investigations, primarily used for postmortem interval (PMI) estimation, species identification, and crime scene reconstruction. Recent advancements in molecular techniques, computational models, and climate-adaptive forensic entomology have enhanced the field's forensic applications. However, challenges related to methodological standardization, environmental variability, and legal admissibility persist. This comprehensive review examines recent developments in forensic entomology, focusing on molecular methodologies, AI-assisted species identification, and environmental influences on forensic insect succession. Literature was sourced from Scopus, Web of Science, and PubMed, emphasizing peer-reviewed studies published in the last 2 decades. Key themes include PMI estimation advancements, forensic insect ecology, and legal challenges in forensic entomology. Findings highlight improved accuracy in PMI estimation through genetic and computational approaches, the expansion of forensic molecular entomology applications, and the impact of climate change on forensic insect activity. While AI and molecular forensics have revolutionized species identification, standardization and legal frameworks remain insufficient. The study underscores the need for globally harmonized forensic entomology protocols, forensic training programs, and ethical guidelines. Future research should integrate metagenomics, forensic AI, and climate-adaptive forensic models to enhance forensic accuracy and reliability.}, }
@article {pmid40905099, year = {2025}, author = {Gem, H and Ebadi, M and Sebastian, G and Abasaeed, R and Lloid, M and Minot, SS and Dean, DR and Rashidi, A}, title = {Dental plaque microbiota following allogeneic hematopoietic cell transplantation and risk of chronic graft-versus-host disease.}, journal = {Haematologica}, volume = {}, number = {}, pages = {}, doi = {10.3324/haematol.2025.288279}, pmid = {40905099}, issn = {1592-8721}, abstract = {Microbiota disruptions have been associated with short-term complications after allogeneic hematopoietic cell transplantation (alloHCT). However, only a few studies have examined the relationship between dysbiosis and chronic graft-versus-host disease (cGVHD), the main long-term immunologic toxicity of alloHCT. Considering the role of oral microbiota in systemic inflammatory diseases, we evaluated whether oral microbiota at day 28 post-HCT corresponding to clinical recovery from the acute events after transplantation is associated with subsequent cGVHD. Shotgun metagenomic sequencing of 207 saliva and supragingival plaque samples collected longitudinally at baseline (pre-conditioning), day +28, and day +84 from 37 patients (11 with subsequent moderate/severe cGVHD) revealed a significant association between day +28 plaque microbiota composition and cGVHD. Two orthogonal statistical approaches demonstrated Streptococcus sanguinis and Prevotella loescheii in day +28 plaque to be associated with cGVHD. Metagenome-based functional analysis identified 4 microbial metabolic pathways associated with future cGVHD, two of which were highly attributed to S. sanguinis. These pathways - ethanolamine utilization and glycerol metabolism - increase bacterial fitness by providing an alternative carbon/nitrogen source and improving survival in inflamed tissues. Our findings propose a novel mechanism by which the early post-transplant dental biofilm may contribute to cGVHD months later, offering a potential target for early prophylactic intervention.}, }
@article {pmid40904740, year = {2025}, author = {Sapthanakorn, T and Choopong, P and Sermsripong, W and Boriboonhirunsarn, C and Khamwachirapitak, C and Krasaesin, A and Sutthiboonyaphan, P and Siripaiboonpong, N and Mahanonda, R and Wiriyakijja, P and Pelekos, G and Porntaveetus, T and Srithanyarat, SS}, title = {Functional and taxonomic dysbiosis of the supragingival plaque metagenome in Behçet's disease.}, journal = {Journal of oral microbiology}, volume = {17}, number = {1}, pages = {2552165}, pmid = {40904740}, issn = {2000-2297}, abstract = {BACKGROUND: Behçet's Disease (BD), a complex autoinflammatory disorder, is increasingly linked to microbial dysbiosis, yet the specific microbial signatures and their functional consequences remain incompletely characterized. Elucidating these alterations is crucial for understanding BD pathogenesis.<br><br>OBJECTIVE: To identify distinct microbial community structures and functional potentials in supragingival plaque microbiomes of BD patients versus healthy controls (HC) using high-resolution shotgun metagenomic sequencing.<br><br>METHODS: Supragingival plaque from 18 BD patients and 22 HCs was subjected to shotgun metagenomics. Analyses included alpha/beta diversity, taxonomic composition, and MetaCyc pathway abundance, with statistical comparisons.<br><br>RESULTS: Despite similar age and clinical attachment levels, BD patients exhibited significantly increased alpha diversity and distinct beta diversity compared to HCs. Differential abundance analysis revealed an enrichment of anaerobic and opportunistic taxa in BD (implicating 4 phyla and 28 genera), alongside 19 significantly altered MetaCyc pathways, indicating substantial functional reprogramming within the BD oral microbiome.<br><br>CONCLUSION: This high-resolution metagenomic analysis reveals profound oral microbiome dysbiosis in Beh&#xe7;et's Disease, characterized by altered diversity, a distinct taxonomic signature enriched with pathobionts, and significant functional shifts. These comprehensive microbial alterations are implicated in contributing to the local and systemic inflammatory processes driving BD pathogenesis, offering potential avenues for diagnostic biomarkers and targeted therapies.}, }
@article {pmid40904363, year = {2025}, author = {Zeng, W and Feng, X and Liang, B and Ou, X}, title = {Good syndrome presenting with multiple pulmonary infections: a case report involving metagenomic sequencing diagnosis.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1649584}, pmid = {40904363}, issn = {2296-858X}, abstract = {Good syndrome (GS), alternatively termed thymoma with immunodeficiency, is a rare adult-onset immunodeficiency disorder characterized by concurrent thymoma and hypogammaglobulinemia, accompanied by defects in both B-cell-mediated immunity and T-cell-mediated immunity. Owing to the non-specific clinical presentation, diagnosis is frequently delayed, resulting in poor prognosis and elevated mortality. In this study, we report the case of a 69-year-old man with GS who presented with symptoms of recurrent cough and productive sputum. Metagenomic next-generation sequencing (mNGS) of oropharyngeal swabs detected multiple microorganisms, including SARS-CoV-2 (35,047 reads), Epstein-Barr virus (7,236 reads), Micromonas pusilla (3,674 reads), Bacillus spp. (3,284 reads), cytomegalovirus (1,203 reads), and herpes simplex virus type 1 (575 reads). Following a comprehensive clinical evaluation-including recurrent pulmonary infections, history of thymoma, and lymphopenia with immunodeficiency-the diagnosis of GS was confirmed. This patient received an intensified anti-infective regimen, with broad-spectrum carbapenem, meropenem, as the backbone therapy, combined with antifungal agents and antiviral treatment (IV ganciclovir and oral molnupiravir). After aggressive anti-infection therapy, the patient experienced clinical improvement, and chest CT demonstrated significant radiographic improvement. Although intravenous immunoglobulin (IVIG) is foundational in GS, intensive antimicrobial therapy is also critical for clinical outcomes.}, }
@article {pmid40904108, year = {2025}, author = {Meaden, S and Westra, ER and Fineran, PC}, title = {Phage defence-system abundances vary across environments and increase with viral density.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {380}, number = {1934}, pages = {20240069}, pmid = {40904108}, issn = {1471-2970}, support = {/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; //James Cook Research Fellowship (RSNZ, Te Ap&#x101;rangi)/ ; //Philip Leverhulme/ ; //Bioprotection Aotearoa (Tertiary Education Commission, NZ)/ ; //UK Horizon Funding Guarantee/ ; }, mesh = {*Bacteriophages/physiology ; *Bacteria/virology/immunology ; *Microbiota ; *Metagenome ; *Virome ; }, abstract = {The defence systems bacteria use to protect themselves from their viruses are mechanistically and genetically diverse. Yet the ecological conditions that predict when defences are selected for remain unclear, as substantial variation in defence prevalence has been reported. Experimental work in simple communities suggests ecological factors can determine when specific defence systems are most beneficial, but applying these findings to complex communities has been challenging. Here, we use a comprehensive and environmentally balanced collection of metagenomes to survey the defence landscape across complex microbial communities. We also assess the association between the viral community and the prevalence of defence systems. We identify strong environmental effects in predicting overall defence abundance, with animal-host-associated environments and hot environments harbouring more defences overall. We also find a positive correlation between the density and diversity of viruses in the community and the abundance of defence systems. This study provides insights into the ecological factors that influence the composition and distribution of bacterial defence systems in complex microbial environments and outlines future directions for the study of defence-system ecology.This article is part of the discussion meeting issue 'The ecology and evolution of bacterial immune systems'.}, }
@article {pmid40903950, year = {2025}, author = {Liu, Y and Tang, T and Cai, H and Liu, Z}, title = {Bidirectional communication between the gut microbiota and the central nervous system.}, journal = {Neural regeneration research}, volume = {}, number = {}, pages = {}, doi = {10.4103/NRR.NRR-D-25-00434}, pmid = {40903950}, issn = {1673-5374}, abstract = {In recent years, an increasing number of researchers have become interested in the bidirectional communication between the gut microbiota and the central nervous system. This communication occurs through the microbiota-gut-brain axis. As people age, the composition of the gut microbiota undergoes considerable changes, which are now known to play an important role in the development of many neurodegenerative diseases. This review aims to investigate the complex bidirectional signaling pathways between the gut and the brain. It summarizes the latest research findings on how the gut microbiota and its metabolites play critical roles in regulating inflammation, maintaining gut health, and influencing the development of neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. The review also analyzes the current clinical applications of gut microbiota-based treatments for neurological disorders, including fecal microbiota transplantation, probiotics, and prebiotics. Many studies show that the gut microbiota affects the brain in several ways. For example, it can produce substances such as short-chain fatty acids and activate inflammatory pathways. Studies involving animals and laboratory models have demonstrated that adjusting the gut microbiota can help improve behavior and reduce neurological problems. Recent metagenomic and metabolomics studies have shown that the microbiota plays a crucial role in maintaining the organism's health. Microorganisms primarily colonize the gut and are involved in host nutrient metabolism, maintaining the structural integrity of the intestine, preserving the intestinal mucosal barrier, and modulating the immune system. The gut microbiota communicates with the brain through a bidirectional microbiota-gut-brain axis. The composition of the gut flora changes considerably with age, and ecological dysregulation has been recognized as one of the twelve most recent hallmarks of aging. Recent studies have linked these changes to a variety of age-related neurological disorders, including Alzheimer's disease, amyotrophic lateral sclerosis, Parkinson's disease, multiple sclerosis, and Huntington's disease. Specifically, the gut microbiota influences the brain through the production of key metabolites such as short-chain fatty acids and the activation of inflammatory and other relevant signaling pathways. In preclinical studies, targeted modulation of the gut microbiota, through methods such as fecal microbiota transplantation, probiotics, and prebiotics, has demonstrated potential in improving host behavioral outcomes. Therefore, gut microbiotabased treatments offer new hope for the treatment of nervous system diseases. However, due to the complexity of the gut microbiota and the potential adverse reactions associated with these therapies, researchers need to carefully assess their safety and efficacy before widespread clinical application.}, }
@article {pmid40903035, year = {2025}, author = {Hou, Y and Wu, H and Zhang, Z and Wang, J and Chen, Q and Lian, C and He, D and Li, Z and Wei, W and Lin, X and Sun, D and Cao, B and Xu, T and Cai, M and Wang, G and Zhang, X and Duan, L and Hao, H and Zheng, X}, title = {Bacteroides intestinalis mediates the sensitivity to irinotecan toxicity via tryptophan catabolites.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2024-334699}, pmid = {40903035}, issn = {1468-3288}, abstract = {BACKGROUND: Late-onset diarrhoea remains a poorly managed concern for clinical irinotecan therapy. Although bacterial β-glucuronidases (β-GUS) mediated SN-38 production is prevailingly thought to mediate intestinal toxicity, β-GUS inhibitors confer limited benefits in the clinic.<br><br>OBJECTIVE: This study aimed to explore the role and mechanism of endogenous bacterial metabolites in susceptibility to irinotecan toxicity.<br><br>DESIGN: Gut microbiota profiles and metabolites in patients with colorectal cancer (CRC) with or without diarrhoea were investigated via 16S rRNA sequencing, shotgun metagenomics and metabolomics. The role of microbial metabolites was investigated in mice by metabolic bioengineering and intestinal organoid culture. The mechanism of microbial metabolites on intestinal stem cells was investigated by transcriptional profiling and chemical intervention.<br><br>RESULTS: Gut microbial configuration was differentially remodelled in diarrhoea and non-diarrhoea patients with irinotecan therapy, and the susceptibility was transmissible to recipient mice via transplantation of baseline faecal microbiome. Bacteroides intestinalis (B. intestinalis) was notably expanded in the diarrhoea-prone cohorts as well as in irinotecan-treated mice. B. intestinalis colonisation sensitised intestinal epithelia to irinotecan-induced chemical injury, partially via tryptophan metabolite indole-3-acetate (IAA). Both B. intestinalis and bioengineered bacteria that produce IAA exacerbated irinotecan-induced intestinal epithelial injury in mice. Mechanistically, IAA suppressed PI3K-Akt signalling, thereby impairing the renewal of intestinal epithelia under the insult of irinotecan. In clinical patients receiving irinotecan therapy, faecal IAA level was closely associated with the diarrhoea severity.<br><br>CONCLUSION: Our study uncovers the mechanism of endogenous bacterial metabolite in shaping the individual susceptibility to irinotecan toxicity and suggests IAA as a potential predictive biomarker.}, }
@article {pmid40902732, year = {2025}, author = {Blecksmith, SE and Oliver, A and Alkan, Z and Lemay, DG}, title = {Gut microbiome genes involved in plant and mucin breakdown correlate with diet and gastrointestinal inflammation in healthy US adults.}, journal = {The Journal of nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tjnut.2025.08.027}, pmid = {40902732}, issn = {1541-6100}, abstract = {BACKGROUND: Dietary carbohydrates shape the composition and function of gut microbes which may potentially influence human health. It is not known if these diet-microbiome relationships are relevant to healthy American adults.<br><br>OBJECTIVE: We hypothesized that intake of dietary fiber by healthy adults would be associated with the carbohydrate active enzyme (CAZyme) capacity of their gut microbiome and that this capacity would be negatively correlated with gastrointestinal (GI) inflammation.<br><br>METHODS: We analyzed dietary data, GI inflammation and CAZyme profiles from shotgun metagenomes of fecal samples in the USDA Nutritional Phenotyping Study cohort of healthy US adults (n=330).<br><br>RESULTS: CAZyme diversity varied across participants. Plant CAZyme diversity and abundance correlated significantly with fecal pH (Shannon: adjusted R[2] = 0.053, p < 0.001; Chao1: adjusted R[2] = 0.056, p < 0.001; abundance: adjusted R[2] = 0.036, p < 0.001) and habitual energy-adjusted total fiber (Shannon: adjusted R[2] = 0.015, p = 0.029; abundance: adjusted R[2] = 0.015, p = 0.010) and soluble fiber intake (Shannon: adjusted R[2] = 0.017, p = 0.019; abundance: adjusted R[2] = 0.015, p = 0.0010). The ratio of mucin-degrading CAZymes to plant-degrading enzymes, coined here as the metric Muc2Plant, varied across participants and differed by sex (Wilcoxon, p = 0.035) and BMI (adjusted R[2] = 0.028, p = 0.017). Muc2Plant positively correlated with GI inflammation (calprotectin: adjusted R[2] = 0.038, p = 0.001; neopterin: adjusted R[2] = 0.071, p < 0.001). ML classification models were used to identify specific foods (e.g. potatoes) and microbes (e.g. Lachnospiraceae) as predictors of low Muc2Plant.<br><br>CONCLUSION: These results support the relevance of diet-microbiome relationships even in healthy adults, and that reduction of Muc2Plant, via dietary and/or microbial interventions, would be a beneficial health target to potentially prevent dysbiosis and reduce GI inflammation.<br><br>CLINICAL TRIALS REGISTRY: NCT02367287, ClinicalTrials.gov.}, }
@article {pmid40902606, year = {2025}, author = {Zhang, D and Zou, Y and Shi, Y and Zhang, J and Liu, J and Wu, G and Zhang, J and Gao, Y and Chen, M and Li, YX}, title = {Systematically investigating and identifying bacteriocins in the human gut microbiome.}, journal = {Cell genomics}, volume = {}, number = {}, pages = {100983}, doi = {10.1016/j.xgen.2025.100983}, pmid = {40902606}, issn = {2666-979X}, abstract = {Human gut microbiota produces unmodified bacteriocins, natural antimicrobial peptides that protect against pathogens and regulate host physiology. However, current bioinformatic tools limit the comprehensive investigation of bacteriocins' biosynthesis, obstructing research into their biological functions. Here, we introduce IIBacFinder, a superior analysis pipeline for identifying unmodified class II bacteriocins. Through large-scale bioinformatic analysis and experimental validation, we demonstrate their widespread distribution across the bacterial kingdom, with most being habitat specific. Analyzing over 280,000 bacterial genomes, we reveal the diverse potential of human gut bacteria to produce these bacteriocins. Guided by meta-omics analysis, we synthesized 26 hypothetical bacteriocins from gut commensal species, with 16 showing antibacterial activities. Further ex vivo tests show minimal impact of narrow-spectrum bacteriocins on human fecal microbiota. Our study highlights the huge biosynthetic potential of unmodified bacteriocins in the human gut, paving the way for understanding their biological functions and health implications.}, }
@article {pmid40902595, year = {2025}, author = {Guinet, B and Oskolkov, N and Moreland, K and Dehasque, M and Chacón-Duque, JC and Angerbjörn, A and Arsuaga, JL and Danilov, G and Kanellidou, F and Kitchener, AC and Muller, H and Plotnikov, V and Protopopov, A and Tikhonov, A and Termes, L and Zazula, G and Mortensen, P and Grigorieva, L and Richards, M and Shapiro, B and Lister, AM and Vartanyan, S and Díez-Del-Molino, D and Götherström, A and Pečnerová, P and Nikolskiy, P and Dalén, L and van der Valk, T}, title = {Ancient host-associated microbes obtained from mammoth remains.}, journal = {Cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cell.2025.08.003}, pmid = {40902595}, issn = {1097-4172}, abstract = {Ancient genomic studies have extensively explored human-microbial interactions, yet research on non-human animals remains limited. In this study, we analyzed ancient microbial DNA from 483 mammoth remains spanning over 1 million years, including 440 newly sequenced and unpublished samples from a 1.1-million-year-old steppe mammoth. Using metagenomic screening, contaminant filtering, damage pattern analysis, and phylogenetic inference, we identified 310 microbes associated with different mammoth tissues. While most microbes were environmental or post-mortem colonizers, we recovered genomic evidence of six host-associated microbial clades spanning Actinobacillus, Pasteurella, Streptococcus, and Erysipelothrix. Some of these clades contained putative virulence factors, including a Pasteurella-related bacterium that had previously been linked to the deaths of African elephants. Notably, we reconstructed partial genomes of Erysipelothrix from the oldest mammoth sample, representing the oldest authenticated host-associated microbial DNA to date. This work demonstrates the potential of obtaining ancient animal microbiomes, which can inform further paleoecological and evolutionary research.}, }
@article {pmid40902558, year = {2025}, author = {Chen, A and Li, J and Yao, A and Du, G and Li, J and Chen, J}, title = {Advancing kombucha fermentation: Microbial interactions, functional metabolites, and innovative optimization strategies.}, journal = {Food chemistry}, volume = {494}, number = {}, pages = {146121}, doi = {10.1016/j.foodchem.2025.146121}, pmid = {40902558}, issn = {1873-7072}, abstract = {Kombucha is a fermented tea beverage that has attracted increasing attention due to its diverse microbial ecosystem and potential health benefits. This review presents a comprehensive and innovative perspective on kombucha fermentation by integrating recent advances in microbial interactions, functional metabolite production, and emerging biotechnological approaches. The synergistic roles of bacteria and yeasts in shaping its physicochemical and bioactive properties are explored, with a focus on how multi-omics techniques, including metagenomics and metabolomics, are redefining microbial dynamics. Additionally, advancements in precision fermentation, engineered microbial consortia, and AI-assisted fermentation optimization offer novel insights into improving product consistency, metabolic efficiency, and functional enhancement. By bridging traditional fermentation knowledge with modern biotechnological innovations, this review establishes a foundation for future research and industrial applications, positioning kombucha as a highly customizable functional beverage.}, }
@article {pmid40902385, year = {2025}, author = {Zhang, C and Zhang, Z and Zhang, S and Chen, Y and Li, D and Li, Y}, title = {Methionine-based insights into C-S-Fe-P transformations in anaerobic co-digestion of sludge containing iron-phosphorus compounds.}, journal = {Water research}, volume = {287}, number = {Pt B}, pages = {124458}, doi = {10.1016/j.watres.2025.124458}, pmid = {40902385}, issn = {1879-2448}, abstract = {Anaerobic co-digestion of sulfur-containing organic wastes with waste-activated sludge containing iron-phosphorus compounds (FePs) was recently suggested as an environment-friendly strategy to promote phosphate release, energy recovery, and hydrogen sulfide (H2S) control. Nevertheless, the mechanistic coupling between FePs speciation and the concurrent transformation of carbon, sulfur, iron, and phosphorus within this system remains to be fully elucidated. To address this knowledge gap, methionine, a typical hydrolysis product of sulfur-containing organics, and five FePs prevalent in sludge (ferric-phosphate tetrahydrate (FePO4⋅4H2O), ferric-phosphate dihydrate (FePO4⋅2H2O), vivianite (Fe3(PO4)2·8H2O), phosphate coprecipitated with Fe(III) (COP-P), and phosphate adsorption on hydrous ferric oxide (HFO-P)) were selected to elucidate C-S-Fe-P transformations in this study. The results showed that the H2S and methyl mercaptan productions decreased by >96 % and >99 %, respectively, while the methane production rate increased by 51.60-103.9 % in the presence of FePs. The reaction between FePs and sulfide promoted the transformation of gaseous H2S and aqueous S[2-] to solid sulfur species (elemental sulfur and iron sulfide precipitates), while simultaneously promoting the release of PO4[3-] from FePs. The formation of Fe(II) species derived from both abiotic sulfide-driven reduction and microbial-mediated iron reduction processes. The reduction rates of FePO4⋅2H2O and FePO4⋅4H2O were higher than those of COP-P and HFO-P, owing to their higher thermodynamic favorability. A negative correlation was observed between the Fe/P molar ratio and PO4[3-] release efficiency. FePO4 (FePO4⋅2H2O and FePO4⋅4H2O) with the lowest Fe/P molar ratio achieved the highest P release efficiency (89.83-91.01 %). Metagenomics analysis revealed that the SELENBP1 gene related to the degradation of methanethiol to sulfide was upregulated by 21.12-51.72 % in the presence of FePs, and the genes involved in propionate metabolism, methylotrophic, and hydrogenotrophic methanogenesis were up-regulated concurrently. This study provides an in-depth understanding of C-S-Fe-P interactions and transformations during the anaerobic co-digestion of sulfur-containing organic wastes with FePs-containing sludge, helping to enhance methane production and the recovery of phosphorus and sulfur.}, }
@article {pmid40902348, year = {2025}, author = {Zhou, N and Gu, T and Duan, M and Tian, Y and Chen, L and Zeng, T and Hou, X and Wang, X and Xu, Q and Zhang, Y and Lu, L}, title = {Gut microbiota dysbiosis exacerbates polystyrene microplastics-induced liver inflammation via activating LPS/TLR4 signaling pathway in ducks.}, journal = {Poultry science}, volume = {104}, number = {11}, pages = {105757}, doi = {10.1016/j.psj.2025.105757}, pmid = {40902348}, issn = {1525-3171}, abstract = {Ubiquitous microplastics can bioaccumulate in organisms, resulting in detrimental health impacts, such as liver inflammation. Nonetheless, the exact mechanism by which polystyrene microplastics (PS-MPs) trigger liver inflammation via the gut-liver axis in ducks remains unclear. The purpose of this study was to clarify the impact of PS-MPs exposure to liver inflammation through the gut-liver axis in ducks. Our investigation indicated that exposure to PS-MPs markedly upregulated the levels of MDA and ROS in the liver tissue and enhanced the release of pro-inflammatory cytokines (TNF-α, IL-6, and IL-1β). Additionally, PS-MPs exposure increased the LPS level, which ultimately triggered the TLR4/NF-κB signaling pathway. Notably, exposure to PS-MPs resulted in a marked change in the gut microbiota composition, primarily indicated by an increase in the relative abundance of Brachyspiraceae and a reduction in that of CAG-74 and Oscillospiraceae. Metabolome analysis further revealed that different expressed metabolites (DEMs) in the positive and negative mode were identified between the control and HMPs groups, including 1-methylhistamine, DL-Methionine sulfoxide, Guanidinoethyl sulfonate, l-Cysteic acid, Deoxyinosine, Camp. Both metagenomic and metabolome analyses showed enrichment in the lysosomal pathway. Correlation analysis suggested association among representative gut microbiota, serum LPS, oxidative stress factors, liver DEMs and key liver inflammatory indicators. Our study sheds light on the mechanism by which PS-MPs exposure induced liver inflammation in ducks via the modulation of the gut-liver axis. These findings improved our understanding of the underlying mechanisms that contribute to PS-MPs-induced hepatotoxicity in avian species.}, }
@article {pmid40901999, year = {2025}, author = {Prabakaran, R and Bromberg, Y}, title = {Deciphering enzymatic potential in metagenomic reads through DNA language models.}, journal = {Nucleic acids research}, volume = {53}, number = {16}, pages = {}, doi = {10.1093/nar/gkaf836}, pmid = {40901999}, issn = {1362-4962}, support = {80NSSC18M0093//NASA Astrobiology Institute/ ; 2310114//National Science Foundation/ ; }, mesh = {*Metagenomics/methods ; Metagenome ; Molecular Sequence Annotation ; *Enzymes/genetics/metabolism ; Microbiota/genetics ; Software ; Sequence Analysis, DNA/methods ; }, abstract = {Microbial communities drive essential global processes, yet much of their functional potential remains unexplored. Metagenomics stands to elucidate this microbial "dark matter" by directly sequencing the microbial community DNA from environmental samples. However, the exploration of metagenomic sequences is mostly limited to establishing their similarity to curated reference sequences. A paradigm shift-language model (LM)-based methods-offers promising avenues for reference-free analysis of metagenomic reads. Here, we introduce two LMs, a pretrained foundation model REMME (Read EMbedder for Metagenomic Exploration), aimed at understanding the DNA context of metagenomic reads, and the fine-tuned REBEAN (Read Embedding-Based Enzyme ANnotator) for predicting the enzymatic potential encoded within the read-corresponding genes. By emphasizing function recognition over gene identification, REBEAN labels gene-encoded molecular functions of previously explored and new (orphan) sequences. Even though it was not trained to do so, REBEAN identifies the gene's function-relevant parts. It thus expands enzymatic annotation of unassembled metagenomic reads. Here, we present novel enzymes discovered using our models, highlighting model impact on our understanding of microbial communities.}, }
@article {pmid40901934, year = {2025}, author = {Witsø, IL and Baral, A and Llarena, AK and Aspholm, M and Myrmel, M and Wasteson, Y}, title = {Plastispheres as reservoirs of antimicrobial resistance: Insights from metagenomic analyses across aquatic environments.}, journal = {PloS one}, volume = {20}, number = {9}, pages = {e0330754}, doi = {10.1371/journal.pone.0330754}, pmid = {40901934}, issn = {1932-6203}, mesh = {*Metagenomics/methods ; *Bacteria/genetics/drug effects ; Wastewater/microbiology ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Humans ; Metagenome ; Water Microbiology ; Fresh Water/microbiology ; Drug Resistance, Microbial/genetics ; }, abstract = {Evidence suggests that plastic particles from various environments can accumulate harmful microorganisms and carry bacteria with antimicrobial resistance genes (ARGs). The so-called "plastisphere" might facilitate the spread of pathogens and antimicrobial resistance across environments, posing risks to human and animal health. This study aimed to analyze the diversity and abundance of ARGs found in plastispheres from various aquatic environments, identify clinically relevant pathogenic species, and ascertain bacterial hosts carrying ARGs. We present data from 36 metagenomes collected from plastispheres in different environments (freshwater, raw wastewater, and treated wastewater). The diversity and abundance of ARGs in the resistome of the plastispheres were analyzed through metagenomic methods. A total of 537 high-quality metagenomic-assembled genomes (MAGs) were constructed to identify clinically relevant pathogens and to link the detected ARGs to their bacterial hosts. The results show that the environment has the greatest influence on the abundance and diversity of ARGs in the plastispheres resistome, with the wastewater plastisphere containing a resistome with the highest diversity of ARGs. Resistance to beta-lactams, aminoglycosides, and tetracyclines were the most abundant resistance mechanisms detected in the different plastispheres. The construction of MAGs identified potential pathogens and environmental bacteria that confer resistance to one or several drug classes, with beta-lactams being the most pervasive form of AMR detected. This work enhances our understanding of the plastisphere's role in antimicrobial resistance dissemination and its ecological and public health risks.}, }
@article {pmid40901884, year = {2025}, author = {Robes, JMD and Liebergesell, TCE and Beals, DG and Yu, X and Brazelton, WJ and Puri, AW}, title = {Inverse stable isotope probing-metabolomics (InverSIP) identifies an iron acquisition system in a methane-oxidizing bacterial community.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {36}, pages = {e2507323122}, doi = {10.1073/pnas.2507323122}, pmid = {40901884}, issn = {1091-6490}, support = {R35 GM147018/GM/NIGMS NIH HHS/United States ; 2339190//National Science Foundation (NSF)/ ; LS-ECIAMEE-00006628//Simons Foundation (SF)/ ; T32 AI055434/AI/NIAID NIH HHS/United States ; }, mesh = {*Methane/metabolism ; *Iron/metabolism ; *Metabolomics/methods ; Oxidation-Reduction ; Isotope Labeling/methods ; *Microbiota ; *Bacteria/metabolism/genetics ; Siderophores/metabolism ; Multigene Family ; }, abstract = {Methane is a potent greenhouse gas and a target for near-term climate change mitigation. In many natural ecosystems, methane is sequestered by microbial communities, yet little is known about how constituents of methane-oxidizing communities interact with each other and their environment. This lack of mechanistic understanding is a common issue for many important microbial communities, but it is difficult to draw links between available sequencing information and the metabolites that govern community interactions. Here, we develop and apply a technique called inverse stable isotope probing-metabolomics (InverSIP) to bridge the gap between metagenomic and metabolomic information and functionally characterize interactions in a complex methane-oxidizing community. Using InverSIP, we link a highly transcribed biosynthetic gene cluster in the community with its secondary metabolite product: methylocystabactin, a triscatecholate siderophore not previously observed in nature. We find that production of methylocystabactin is widespread among methanotrophic alphaproteobacteria and that it can be used by another methanotroph in the community that does not produce this siderophore itself. Functional assays reveal that methylocystabactin supports methanotroph growth and the activity of the methane-oxidizing enzyme soluble methane monooxygenase under conditions where bioavailable iron is limited, establishing an important molecular link between methane-oxidation and the insoluble iron found in many natural environments. These findings contribute to a molecular-level understanding of these environmentally important bacterial communities and establish InverSIP as a broadly applicable genomics-guided strategy for characterizing metabolites in microbial ecosystems.}, }
@article {pmid40901853, year = {2025}, author = {Gómez-Palacio, A and Junca, H and Vivero-Gomez, RJ and Suaza, J and Moreno-Herrera, CX and Cadavid-Restrepo, G and Pieper, DH and Uribe, S}, title = {Metagenomic profiling of the insect-specific virome in non-urban mosquitoes (Culicidae: Culicinae) from Colombia's Northern inter-Andean valleys.}, journal = {PloS one}, volume = {20}, number = {9}, pages = {e0331552}, doi = {10.1371/journal.pone.0331552}, pmid = {40901853}, issn = {1932-6203}, mesh = {Animals ; Colombia ; *Virome/genetics ; *Culicidae/virology ; *Metagenomics/methods ; *Metagenome ; Phylogeny ; *Insect Viruses/genetics/classification ; }, abstract = {Hematophagous mosquitoes are major vectors of diverse pathogens and serve as bioindicators in tropical ecosystems, yet their virome in non-urban Neotropical regions remains poorly characterized. We analyzed the virome of 147 mosquitoes from two natural ecosystems in Colombia using a hybrid viral identification approach, combining high-confidence and less stringent methods. Most high-confidence viral contigs remained unclassified or unknown, as expected for metagenomic surveys in novel ecosystems. However, members for the Magrovirales and Ortervirales, and other six orders were detected at lower abundance. Using a complementary, less stringent approach, we identified 168 viral species from 68 genera and 22 families across four mosquito tribes (Aedini, Culicini, Orthopodomyiini, Sabethini), with dominance of Metaviridae, Retroviridae, Iridoviridae, and Poxviridae, though many sequences could not be taxonomically assigned. Insect-specific viruses predominated, while no medically relevant arboviruses were detected. Both methods consistently identified Trichoplusia ni TED virus, Cladosporium fulvum T-1 virus, Lymphocystis disease viruses, and Oryctes rhinoceros nudivirus among the most abundant and frequently detected taxa across samples. Alpha diversity indices revealed the highest virome diversity in Sabethini, followed by Orthopodmyiini, and substantially lower richness and diversity in Aedini and Culicini. These results provide a baseline for virome characterization in sylvatic mosquitoes from Colombia and highlight the need for further research on the ecological roles of the mosquito virome in pathogen transmission and microbiome evolution.}, }
@article {pmid40901820, year = {2025}, author = {Ergunay, K and Golubiani, G and Kirkitadze, G and Reinbold-Wasson, DD and Bourke, BP and Phelps, CA and Kotorashvili, A and Kotaria, N and Hulseberg, CE and Chunashvili, T and Sydenstricker, A and Shubashishvili, A and Musich, TA and Linton, YM}, title = {Ongoing circulation of emerging tick-borne viruses in Poland, Eastern Europe.}, journal = {PloS one}, volume = {20}, number = {9}, pages = {e0330544}, doi = {10.1371/journal.pone.0330544}, pmid = {40901820}, issn = {1932-6203}, mesh = {Poland/epidemiology ; Animals ; Phylogeny ; Genome, Viral ; *Tick-Borne Diseases/virology/epidemiology ; *Ixodes/virology ; *Dermacentor/virology ; Humans ; Europe, Eastern/epidemiology ; }, abstract = {In order to investigate previously reported expansion of tick-borne pathogenic viruses in Eastern Europe, we conducted this study using pooled ticks collected from various locations in Poland, utilizing Sequence Independent Single Primer Amplification (SISPA) and metagenomic sequencing. We processed 575 Dermacentor reticulatus and Ixodes ricinus ticks and generated 280 virus assemblies in 20 pools. Viruses representing 28 species or strains classified in 12 families or higher taxonomic ranks were observed. We identified four tick-borne human pathogens including Alongshan virus (ALSV), Tacheng tick virus 1 (TcTV-1), Tacheng tick virus 2 (TcTV-2) and Nuomin virus (NUMV), in 55% of the pools, comprising 19.2% of the assemblies. We detected ALSV in I. ricinus ticks, with virus genome segments in complete or near-complete forms, comprising the initial reporting of ALSV from Poland. Further analyses revealed phylogenomic clustering with ALSV strains from Europe and lack of recombination signals among virus genomes. TcTV-1 was detected in 35% of the pools comprising D. reticulatus and I. ricinus ticks, implicating I. ricinus in TcTV-1 transmission for the first time. Maximum likelihood analyses on TcTV-1 and TcTV-2 genome segments indicated separate clustering patterns suggesting geographically-segregated clades. Evidence for NUMV or a closely-related chuvirus in I. ricinus ticks was further noted. In conclusion, we identified persistence of previously-documented tick-borne pathogens in Poland as well as additional viruses such as ALSV. Assessment of temporal and spatial patterns for virus circulation and diagnostic assays for these agents is needed. The distribution and public health impact of these pathogens throughout Europe require further investigation.}, }
@article {pmid40901081, year = {2025}, author = {Dong, W and Peng, Y and Ma, J and Hu, Y and Chen, S and Zhao, S}, title = {Yeasts in traditional Baijiu fermentation: diversity, functions, microbial interactions and applications.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1652173}, doi = {10.3389/fmicb.2025.1652173}, pmid = {40901081}, issn = {1664-302X}, abstract = {Baijiu is a traditional distilled liquor unique to China. Its distinctive flavor is shaped by the synergistic activity of complex microbial communities, among which yeasts play a central role in sugar metabolism, ethanol fermentation, and aroma synthesis. In recent years, the advancement of isolation and cultivation techniques, high-throughput sequencing, metagenomics, and multi-omics technologies has deepened our understanding of yeast community compositions, succession patterns, and functional characteristics during Baijiu brewing. Among these, Saccharomyces cerevisiae was recognized as the core ethanol-producing species and has been extensively studied for its metabolic traits and stress tolerance in Baijiu fermentation. Studies have shown that, in addition to S. cerevisiae, non-Saccharomyces yeasts such as Pichia, Wickerhamomyces, Saccharomycopsis, Kazachstania, and Candida et al. are widely distributed across strong-, sauce-, and light-flavor Baijiu and their respective starters (Daqu), exhibiting robust ester-producing capacities and stress resistance. These yeasts occupy distinct ecological niches throughout fermentation stages and engage in dynamic and environment-dependent interactions with lactic acid bacteria, molds, and other microbes. This review systematically summarizes yeast diversity, community structure, metabolic traits, key functional genes, microecological interactions, recent discoveries of novel yeast species, and advances in genetic engineering in Baijiu brewing. It further highlights future research priorities, including multi-omics integration, functional exploration of non-Saccharomyces yeasts, and synthetic biology-guided strain development, with the goal of supporting high-quality and intelligent Baijiu production.}, }
@article {pmid40901069, year = {2025}, author = {Xu, C and Lin, R and Bai, Y and Han, Y and Hu, J and Hu, J and Hu, Y and Huang, F and Huang, X and Ji, C and Li, X and Liang, A and Lu, P and Ma, J and Mei, H and Niu, T and Ouyang, J and Qian, W and Shi, J and Song, Y and Sun, A and Tan, Y and Wang, H and Wang, J and Wang, Y and Wu, D and Xiao, Z and Yang, T and Zhang, C and Zhang, X and Zhang, X and Zhao, W and Zheng, Z and Zhu, Z and Feng, S and Liu, Q}, title = {China Expert consensus on the application of metagenomic next-generation sequencing for the etiological diagnosis of infections in hematological disorders (2024).}, journal = {Blood science (Baltimore, Md.)}, volume = {7}, number = {3}, pages = {e00241}, doi = {10.1097/BS9.0000000000000241}, pmid = {40901069}, issn = {2543-6368}, abstract = {Infections are frequent complications in patients with hematological disorders, and pathogen diagnosis remains challenging. Metagenomic next-generation sequencing (mNGS) is an unbiased high-throughput technology that has been widely applied in the diagnosis of infectious diseases. However, to date, there are no established international guidelines or expert consensuses regarding the use of mNGS to diagnose infections in patients with hematologic disorders. The Anti-Infection Study Group of the Chinese Society of Hematology invited experts in the fields of hematology, microbiology, and mNGS technology to draft an expert consensus focused on clinical indications, sample collection, quality control, and interpretation of results. This consensus will likely contribute to clarifying the medical indications for mNGS testing, optimizing the interpretation of reports, and becoming an inspiration for global practice.}, }
@article {pmid40901009, year = {2025}, author = {Shao, M and Ni, L and Jiang, L and Hou, J and Xu, S and Lin, Y and Xie, X}, title = {A Case Report of Refractory Mycobacterium wolinskyi Knee Infection in a Metabolic Syndrome Patient: mNGS Diagnosis and Pharmacist-Guided Therapy.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {4427-4434}, doi = {10.2147/IDR.S542439}, pmid = {40901009}, issn = {1178-6973}, abstract = {Mycobacterium wolinskyi (M. wolinskyi), which is a rare rapidly growing mycobacterium (RGM), and the infections it causes are predominantly linked to surgery or invasive procedures. We detailed a case of refractory surgical site infection (SSI) caused by M. wolinskyi. The causative pathogen was identified by metagenomic next-generation sequencing (mNGS) analysis, 16S rRNA and rpoB gene sequencing. What renders this case particularly remarkable is the complexity introduced by a series of antibiotic-induced adverse effects, which seem to be deeply intertwined with the patient's underlying metabolic syndrome. With the meticulous pharmaceutical guidance provided by the clinical pharmacist, the patient experienced a substantial improvement in his knee joint infection.}, }
@article {pmid40901000, year = {2025}, author = {Huang, F and Li, J and Liu, D and Li, Y and Tang, J}, title = {Neonatal microbiome dysbiosis decoded by mNGS: from mechanistic insights to precision interventions.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1642072}, doi = {10.3389/fcimb.2025.1642072}, pmid = {40901000}, issn = {2235-2988}, mesh = {Humans ; Infant, Newborn ; *Dysbiosis/microbiology/diagnosis/therapy ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Infant, Newborn, Diseases/microbiology/diagnosis/therapy ; Precision Medicine/methods ; *Microbiota/genetics ; }, abstract = {The neonatal period is a critical stage for microbial colonization and immune system development, with dynamic changes in the microbiome closely linked to the pathogenesis of various diseases. Traditional microbiological testing methods have low sensitivity and time-consuming limitations compared to metagenomic next-generation sequencing (mNGS), which makes it difficult to meet the diagnostic and therapeutic needs of critically ill neonates. mNGS analyzes the total DNA in a sample without bias, allowing comprehensive identification of bacteria, viruses, fungi, and parasites, and resolution of functional genes, providing new avenues for precision diagnosis and treatment of diseases such as neonatal sepsis, necrotizing enterocolitis, neonatal pneumonia, neonatal meningitis, neonatal jaundice, and other diseases. However, challenges remain, including the need to optimize sample processing workflows and develop portable devices to enhance clinical conversion potential. In this review, we summarize the application, efficacy, and limitations of mNGS in neonatal diseases. This approach paves the way for novel avenues in mechanistic research, early diagnosis, and personalized therapy for these conditions.}, }
@article {pmid40900671, year = {2025}, author = {Day, AS and Slater, R and Young, RB and Wheeler, RZ and Marcelino, VR and Maddigan, NK and Forster, SC and Costello, SP and Uylaki, W and Probert, CSJ and Andrews, JM and Yao, CK and Gibson, PR and Bryant, RV}, title = {Functional Profiling Demonstrates That a Sulfide-Reducing Diet Achieves Microenvironmental Targets in Ulcerative Colitis.}, journal = {Inflammatory bowel diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/ibd/izaf177}, pmid = {40900671}, issn = {1536-4844}, support = {//Hospital Research Foundation/ ; //University of Adelaide/ ; }, abstract = {BACKGROUND: As a dietary approach to reducing inflammation in ulcerative colitis, the 4-SURE (4 Strategies to Sulfide Reduction) diet was designed to correct pathogenic alterations of excessive protein fermentation and hydrogen sulfide (H2S) production in the distal colon. We aimed to perform a deep functional analysis (microbial and metabolomic) of the feces of 28 adults with mild-moderately active ulcerative colitis who adhered to the 4-SURE diet over 8 weeks to explore whether the 4-SURE diet could modulate the intraluminal environment as intended.<br><br>METHODS: Fecal samples were collected at week 0 and 8 of dietary intervention, processed and aliquoted. Metagenomic sequencing was undertaken to identify changes in H2S-metabolizing genes, while gas chromatography-mass spectrometry was used to analyze fecal volatile organic compounds and H2S production.<br><br>RESULTS: The 4-SURE diet significantly increased alpha diversity between weeks 0 and 8. By random forest plot classifier, the abundance of taxonomic groups comprising known H2S-producing genera were markedly lower at week 8, specifically Odoribacter and Peptostreptococcaceae, and were of highest importance in discriminating between before- and after-diet samples. The capacity for bacterial H2S metabolism was altered with diet, with differences in 12 of 67 analyzed sulfur-metabolizing genes identified. H2S production and indole, a specific marker of protein fermentation, were significantly decreased due to the diet.<br><br>CONCLUSIONS: Here, we demonstrate that the objectives of the 4-SURE diet were fulfilled. This application of deep functional analysis to a dietary intervention study is novel and highlights an exemplar framework for including microbial and metabolomic biomarkers of pathogenic relevance in the analysis of therapeutic diet strategies. (Australian New Zealand Clinical Trials Registry, Number: ACTRN12619000063112).}, }
@article {pmid40900113, year = {2025}, author = {Wendling, CC and Vasse, M and Wielgoss, S}, title = {Phage quest: a beginner's guide to explore viral diversity in the prokaryotic world.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {5}, pages = {}, pmid = {40900113}, issn = {1477-4054}, support = {PZ00P3_179743/SNSF_/Swiss National Science Foundation/Switzerland ; }, mesh = {*Bacteriophages/genetics/classification ; *Computational Biology/methods ; Metagenomics/methods ; *Prokaryotic Cells/virology ; Machine Learning ; *Bacteria/virology ; Genome, Viral ; }, abstract = {The increasing interest in finding new viruses within (meta)genomic datasets has fueled the development of computational tools for virus detection and characterization from environmental samples. One key driver is phage therapy, the treatment of drug-resistant bacteria with tailored bacteriophage cocktails. Yet, keeping up with the growing number of automated virus detection and analysis tools has become increasingly difficult. Both phage biologists with limited bioinformatics expertise and bioinformaticians with little background in virus biology will benefit from this guide. It focuses on navigating routine tasks and tools related to (pro)phage detection, gene annotation, taxonomic classification, and other downstream analyses. We give a brief historical overview of how detection methods evolved, starting with early sequence-composition assessments to today's powerful machine-learning and deep learning techniques, including emerging language models capable of mining large, fragmented, and compositionally diverse metagenomic datasets. We also discuss tools specifically aimed at detecting filamentous phages (Inoviridae), a challenge for most phage predictors. Rather than providing an exhaustive list, we emphasize actively maintained and state-of-the-art tools that are accessible via web or command-line interfaces. This guide provides basic concepts and useful details about automated phage analysis for researchers in different biological and medical disciplines, helping them choose and apply appropriate tools for their quest to explore the genetic diversity and biology of the smallest and most abundant replicators on Earth.}, }
@article {pmid40899487, year = {2025}, author = {Gu, T and Zerry, Y and Zhang, B and Tan, J and Taft, DH}, title = {Influence of Resistant Starch-Added Meat Analogs on the Resistome of Fecal Fermentations Using Human Gut Microbiota.}, journal = {Journal of food science}, volume = {90}, number = {9}, pages = {e70430}, doi = {10.1111/1750-3841.70430}, pmid = {40899487}, issn = {1750-3841}, support = {//University of Florida/ ; //U.S. Department of Agriculture/ ; }, mesh = {Humans ; *Feces/microbiology ; *Gastrointestinal Microbiome ; Fermentation ; *Starch/metabolism ; Bacteria/genetics/classification/isolation &amp; purification/drug effects/metabolism ; *Meat/analysis ; Adult ; Male ; Female ; *Resistant Starch ; Drug Resistance, Bacterial/genetics ; Middle Aged ; Drug Resistance, Microbial ; Meat Substitutes ; }, abstract = {Meat analogs are emerging as a sustainable alternative to meat products, and novel meat analog products could potentially offer additional health benefits. Antimicrobial resistance (AMR) poses a serious threat to global human health. Dietary choices affect the composition of bacteria in the human gut microbiome and can influence the carriage of antimicrobial resistance genes (ARGs). Individuals with lower ARG carriage tend to consume more fiber, suggesting that novel fiber-rich meat analogs may help tackle the growing AMR crisis. We therefore hypothesized that adding resistant starch to meat analogs would reduce the number and abundance of ARGs in human gut microbial communities and tested this using in vitro fecal fermentation. Fecal samples were collected from three human donors. Meat analogs formulated from raw ingredients (pea, soy, and resistant starch)-including 100% pea, 90% pea and 10% resistant starch, 100% soy, and 90% soy and 10% resistant starch-served as the carbohydrate source for fecal fermentations. Whole metagenomic sequencing was performed on DNA from the fermentations. ANOVA showed significant differences in normalized ARG abundance by carbohydrate source (p = 0.021), though not in total ARG counts. Meat analogs with resistant starch resulted in a lower median normalized abundance of drug-resistant ARGs than meat analogs without resistant starch, but post-hoc testing could not determine which groups differed from each other due to limited sample size. Adding resistant starch to meat analogs is associated with reduced ARGs in human gut microbial communities, but more research is needed. PRACTICAL APPLICATIONS: Lowering the prevalence of antimicrobial resistance genes (ARGs) is an important public health goal, and emerging work suggests that diet may contribute to controlling the spread of ARGs. One association with diet and the resistome is a lower carriage of ARGs in individuals who consume more dietary fiber. This research therefore sought to pilot if adding resistant starch to meat analogs has the potential to reduce resistance gene carriage. The results found that adding resistant starch to plant-based meat products may help lower the abundance of antimicrobial resistance genes in the human gut microbiome. This provides the justification for larger scale studies and suggests that food manufacturers may be able to develop foods, including healthier meat alternatives, to assist in preserving the function of antibiotics for future generations.}, }
@article {pmid40899150, year = {2025}, author = {Ürel, H and Benassou, S and Marti, H and Reska, T and Sauerborn, E and Pinheiro Alves De Souza, Y and Perlas, A and Rayo, E and Biggel, M and Kesselheim, S and Borel, N and Martin, EJ and Venegas, CB and Schloter, M and Schröder, K and Mittelstrass, J and Prospero, S and Ferguson, JM and Urban, L}, title = {Nanopore- and AI-empowered microbial viability inference.}, journal = {GigaScience}, volume = {14}, number = {}, pages = {}, doi = {10.1093/gigascience/giaf100}, pmid = {40899150}, issn = {2047-217X}, support = {//Helmholtz Principal Investigator Grant/ ; HIDSS-006//Munich School for Data Science/ ; BB/M010996/1//BBSRC/ ; //STFC Food Network+ Scoping Grant/ ; //Helmholtz Association Initiative and Networking Fund/ ; 1336/2004//Vontobel-Stiftung/ ; //University of Zurich/ ; }, mesh = {*Microbial Viability ; *Nanopores ; *Artificial Intelligence ; *Nanopore Sequencing/methods ; Metagenomics/methods ; Escherichia coli/genetics ; Computational Biology/methods ; }, abstract = {BACKGROUND: The ability to differentiate between viable and dead microorganisms in metagenomic data is crucial for various microbial inferences, ranging from assessing ecosystem functions of environmental microbiomes to inferring the virulence of potential pathogens from metagenomic analysis. Established viability-resolved genomic approaches are labor-intensive as well as biased and lacking in sensitivity.<br><br>RESULTS: We here introduce a new fully computational framework that leverages nanopore sequencing technology to assess microbial viability directly from freely available nanopore signal data. Our approach utilizes deep neural networks to learn features from such raw nanopore signal data that can distinguish DNA from viable and dead microorganisms in a controlled experimental setting of UV-induced Escherichia cell death. The application of explainable artificial intelligence (AI) tools then allows us to pinpoint the signal patterns in the nanopore raw data that allow the model to make viability predictions at high accuracy. Using the model predictions as well as explainable AI, we show that our framework can be leveraged in a real-world application to estimate the viability of obligate intracellular Chlamydia, where traditional culture-based methods suffer from inherently high false-negative rates. This application shows that our viability model captures predictive patterns in the nanopore signal that can be utilized to predict viability across taxonomic boundaries. We finally show the limits of our model's generalizability through antibiotic exposure of a simple mock microbial community, where a new model specific to the killing method had to be trained to obtain accurate viability predictions.<br><br>CONCLUSIONS: While the potential of our computational framework's generalizability and applicability to metagenomic studies needs to be assessed in more detail, we here demonstrate for the first time the analysis of freely available nanopore signal data to infer the viability of microorganisms, with many potential applications in environmental, veterinary, and clinical settings.}, }
@article {pmid40898498, year = {2025}, author = {Liu, Y and Yue, X and Zhou, Y and Wang, J and Yang, F and Jin, Y and Zhang, G}, title = {Recurrent breast abscess caused by Lawsonella clevelandensis: A case report and literature review.}, journal = {Medicine}, volume = {104}, number = {35}, pages = {e44218}, doi = {10.1097/MD.0000000000044218}, pmid = {40898498}, issn = {1536-5964}, support = {202501AY070001-203//Joint Special Fund for Basic Research of Yunnan Provincial Department of Science and Technology and Kunming Medical University/ ; }, mesh = {Humans ; Female ; Middle Aged ; *Abscess/microbiology/diagnosis/drug therapy/therapy ; Recurrence ; Anti-Bacterial Agents/therapeutic use/administration &amp; dosage ; *Breast Diseases/microbiology ; *Gram-Positive Bacterial Infections/microbiology/diagnosis/drug therapy ; }, abstract = {RATIONALE: Lawsonella clevelandensis is a gram-positive bacterium, partially acid-fast, strictly anaerobic, nonspore-forming, and catalase-positive. This microorganism was once overlooked in clinical microbiology due to its stringent growth requirements in laboratory cultures, but it has recently attracted recognition as a potential pathogen. Available reports implicate Lawsonella clevelandensis infection with abscess formation, including breast, spinal, abdominal, and deep soft tissue abscesses. Here, we present a case of recurrent breast abscess caused by Lawsonella clevelandensis infection.<br><br>PATIENT CONCERNS: A 46-year-old female patient had a history of left breast abscess for 6 years, with recurrent episodes and persistent symptoms.<br><br>DIAGNOSES: Three milliliters of pus obtained from abscess puncture were examined. The results were negative for tuberculosis, interferon-&#x3b3;, the rifampicin resistance gene rpoB, and Mycobacterium tuberculosis complex. The Kingfield metagenomics capture (MetaCAP) test identified Lawsonella clevelandensis (sequence number 17,296) with a 99% confidence level and no detected resistance genes.<br><br>INTERVENTIONS: Following abscess puncture and irrigation under ultrasound guidance, intravenous infusion of "piperacillin-tazobactam (4.5&#x2009;g q8h)" was administered for 16 days, resulting in an improvement in the patient's condition. Oral treatment with "amoxicillin-clavulanate 2.0&#x2009;g bid and metronidazole 1.2&#x2009;g tid" was continued after discharge.<br><br>OUTCOMES: One month after discharge, color Doppler ultrasound showed a significant reduction in the abscess size. At the 3-month telephone follow-up, the patient reported that she had not taken the medication for over a month and had experienced no symptoms of redness, swelling, or pain in the left breast.<br><br>LESSONS: The clinical manifestations of Lawsonella clevelandensis infection are similar to those of other acid-fast bacilli (e.g., Nocardia and Mycobacterium tuberculosis), potentially leading to misdiagnosis and mistreatment, thereby delaying resolution of the condition. The methods used for treating infections by bacterial pathogens differ significantly, as do the prognoses, indicating the importance of precise diagnosis. Lawsonella clevelandensis should be included in the differential diagnosis of infections caused by acid-fast bacteria. Due to the extreme difficulty in culturing this bacterium in vitro, gene sequencing is used primarily for diagnosis. Overall, the prognosis of patients with Lawsonella clevelandensis infection is good. Timely debridement and drainage, combined with antibiotic treatment, can usually lead to a cure.}, }
@article {pmid40897609, year = {2025}, author = {Visioli, F and Urbistondo, DM and Gkipalis, S and Vidal-Ostos De Lara, F and Ruiz-Saavedra, A and Leon, M and Beddar Chaib, F and Hernández, AH and Landecho Acha, MF and Laparra, M and Vizmanos, B and Ramos-Lopez, O and Yannakoulia, M and Martínez, JA}, title = {Translational biomarkers for integrated cardiovascular disease risk assessment: A multidisciplinary review with applications in precision medicine.}, journal = {Nutrition, metabolism, and cardiovascular diseases : NMCD}, volume = {}, number = {}, pages = {104215}, doi = {10.1016/j.numecd.2025.104215}, pmid = {40897609}, issn = {1590-3729}, abstract = {AIMS: Cardiovascular disease (CVD) continues to be a leading cause of morbidity and mortality, significantly impacting healthcare systems and individual lives. This pragmatic review focuses on the assessment of CVD utilizing traditional and emerging risk factors that provide a basis for personalized medicine and precision nutrition, highlighting the knowledge and application of these insights for accurate risk diagnosis, individualized interventions, and precise outcome/evaluation prognosis.<br><br>DATA SYNTHESIS: Critical biochemical markers such as lipid metabolism signatures, inflammatory molecules, endocrine mediators, homeostatic signals (including omics data), and lifestyle factors such as unhealthy dietary habits, physical inactivity, smoking, alcohol abuse, along with anthropometric variables and body composition measurements, play a pivotal role in assessing and managing CVD. This progression starts with early vascular and cardiac dysfunctions, advancing to atherosclerosis, and ultimately leading to cardiovascular events. Major adverse cardiovascular events, including myocardial infarction, stroke, and heart failure, highlight the need for effective and accurate risk stratification and objective assessment. Various CVD risk scores, such as the Framingham Risk Score, SCORE, and the Atherosclerotic Cardiovascular Disease Risk Calculator, provide valuable global frameworks for predicting individual risk based on recognized conventional factors. Additionally, omics markers-which encompass genomic, transcriptomic, epigenomic, proteomic, metabolomic, and metagenomic data-offer deeper insights into the molecular mechanisms underlying CVD, alongside novel lipidomic and immunomic determinants.<br><br>CONCLUSIONS: Integrating these various determinants and risk factors through a comprehensive approach is essential for advancing and implementing precision medicine and nutrition in the management of CVD.}, }
@article {pmid40897178, year = {2025}, author = {Xu, T and Jiao, X and Liu, G and Chen, X and Luo, Q and Zhang, G and Li, B and Zhang, Y and Li, X and Cheung, Y and Chai, X and Huang, Y and Wu, H and Deng, F and Chen, F and Liang, G}, title = {Oral virome metagenomic catalog links Porphyromonas gingivalis phages to obesity and type 2 diabetes.}, journal = {Cell reports. Medicine}, volume = {}, number = {}, pages = {102325}, doi = {10.1016/j.xcrm.2025.102325}, pmid = {40897178}, issn = {2666-3791}, abstract = {The human microbiota has a critical role in maintaining human microbiome homeostasis and health, yet the viral component of the oral microbiome remains largely unidentified. We establish the Human Oral Virome Database (HOVD) catalog, a freely accessible online resource cataloging 24,440 bacteriophage viral operational taxonomic units and 83 eukaryotic viral genomes. Utilizing HOVD, we investigate oral virome variation and its correlation with oral bacteria and gut virome in 220 obese individuals with or without type 2 diabetes mellitus (T2D). Obese individuals with T2D exhibit reduced oral viral diversity, lower correlations with clinical features, disrupted viral-bacterial correlations, and enhanced oral-gut virome transmission. Furthermore, we computationally identify bacteriophages that infect Porphyromonas gingivalis and screen six putative endolysins. Experimental validation reveals that a mixture of three endolysins significantly inhibits Porphyromonas gingivalis growth. These findings highlight the potential of phage-derived endolysins for periodontitis with T2D, offering a path toward oral and systemic disease intervention.}, }
@article {pmid40897099, year = {2025}, author = {Ma, X and Zhai, T and Bao, X and Wu, Z and Yang, Y and Yin, R and Cai, C and Liu, G}, title = {Salinity-driven trade-offs between nitrogen removal and microbiome dynamics in Fe-C-CWs toward saline aquaculture tailwater management.}, journal = {Water research}, volume = {287}, number = {Pt B}, pages = {124519}, doi = {10.1016/j.watres.2025.124519}, pmid = {40897099}, issn = {1879-2448}, abstract = {Salinity-driven nitrogen removal mechanisms in iron-carbon CWs (Fe-C-CWs) remain poorly understood for aquaculture tailwater management. Through a 155-day trial under four salinities (designated as S0, S10, S20, and S30), result showed that S20 achieved optimal removals of total nitrogen (84.9 ± 3.1 %), nitrate (81.8 ± 2.5 %), and ammonium (79.3 ± 3.0 %), significantly outperforming other groups (P < 0.05). Metagenomics revealed that S20 significantly enriched denitrifying taxa (Halothiobacillus, Prolixibacter) and upregulated nitrogen cycling genes (nirB, nrfA, nrfH, hao) and iron cycling genes (feoA, feoB), highlighting the functional synergy between microbial composition and biogeochemical cycling processes. Dual isotope signatures (δ[15]NNO2/ δ[18]ONO2) first applied in Fe-C-CWs confirmed salinity-mediated pathway shifts: nitrite oxidation dominated in saline groups, especially in S20 versus reduction in S0. Enzymatic profiling substantiated the concurrent operation of nitrification, denitrification, and anammox pathways across all groups, with activities exhibiting significant salinity-dependent modulation. S20 demonstrated remarkable enzymatic potentiation, where core nitrogen-cycling enzymes including nitrite oxidoreductase (NXR: 8.79 ± 0.67 U/g), nitrate reductase (NAR: 18.13 ± 1.19 U/g), and nitrite reductase (NIR: 6.74 ± 0.47 U/g) showed 16.00∼32.18 % higher than S0 (P < 0.01). This enzymatic synergy suggests salinity-optimized coupling between dissimilatory iron reduction and nitrogen transformation processes. Ecological network analysis revealed significant interactions among microbial phyla, particularly between Proteobacteria and Planctomycetota. This study demonstrates that S20 can enhance interaction between Fe-C matrix and microorganisms, thereby improving the efficiency of Fe-C-CWs in removing nitrogen pollutants from aquaculture tailwater. These findings offer theoretical insights for further understanding the internal operational mechanisms of the Fe-C-CWs.}, }
@article {pmid40897066, year = {2025}, author = {Slobodkina, GB and Merkel, AY and Kondrasheva, KV and Stroeva, AR and Bonch-Osmolovskaya, EA and Davranov, KD and Slobodkin, AI}, title = {Taxonomic and metabolic diversity of microbial communities in a thermal water stream in Uzbekistan and proposal of two new classes of uncultivated bacteria, Desulfocorpusculia class. nov. and Tepidihabitantia class. nov., named following the rules of SeqCode.}, journal = {Systematic and applied microbiology}, volume = {48}, number = {5}, pages = {126650}, doi = {10.1016/j.syapm.2025.126650}, pmid = {40897066}, issn = {1618-0984}, abstract = {Thermal ecosystems in Uzbekistan remain poorly characterized, particularly through culture-independent approaches. In this study, we performed 16S rRNA gene metabarcoding and metagenomic sequencing of microbial communities from a hot stream formed by the discharge of thermal artesian groundwater in the Navoiy region. The taxonomic composition of microbial communities varied with temperature and sample type, with the phylum Chloroflexota abundant in most samples. Members of Aquificota, Deinococcota, and Thermotogota dominated in sediments with temperatures around 60 °C, while Desulfobacterota and Cyanobacteriota were more abundant at lower temperatures. Metagenomic sequencing of the microbial community in sediment under orange-brown mat (54 °C) revealed a dominance of the phyla Chloroflexota, Armatimonadota, Aquificota, Ignavibacteriota, Desulfobacterota and Bacteroidota. Metagenomic data indicated that fermentation, aerobic degradation of organic matter, hydrogen oxidation, and sulfur cycling are the main metabolic processes. Two high-quality metagenome-assembled genomes (MAGs) were described as novel taxa named following the rules of SeqCode. Genome analysis suggests that both organisms are heterotrophic anaerobes capable of sulfate reduction or fermentation. We provide the description of Desulfocorpusculum asiaticum[Ts] gen. nov., sp. nov. affiliated with the novel family Desulfocorpusculaceae fam. nov., order Desulfocorpusculales ord. nov. and class Desulfocorpusculia class. nov.; and the description of the new species and genus Tepidihabitans asiaticus[Ts] gen. nov., sp. nov. affiliated with the novel family Tepidihabitantaceae fam. nov., order Tepidihabitantales ord. nov. and class Tepidihabitantia class. nov.}, }
@article {pmid40896938, year = {2025}, author = {Qiao, K and Wang, WX}, title = {Subtle biogeochemical consequences of biodegradable and conventional microplastics in estuarine blue carbon systems.}, journal = {Journal of hazardous materials}, volume = {497}, number = {}, pages = {139705}, doi = {10.1016/j.jhazmat.2025.139705}, pmid = {40896938}, issn = {1873-3336}, abstract = {Blue carbon ecosystems act as critical sinks for microplastics (MPs), yet field-based evidence of their biogeochemical consequences remains scarce. In this study, we conducted in situ exposures of estuarine mangroves to environmentally relevant concentrations of polypropylene (PP) and polylactic acid (PLA) MPs for 30 and 100 days. Metagenomic analyses revealed stable microbial community composition across treatments. However, PLA exposure transiently induced significant functional disturbances in carbon, nitrogen, and phosphorus cycling processes. These responses also increased the sediment total organic carbon by 52.8 % and available phosphorus by 86.5 % under PLA exposure. Simultaneously, enhanced carbon decomposition and inhibited methane oxidation potentially exacerbate greenhouse gas emissions. PP amendments triggered no comparable functional shifts. Intriguingly, long-term exposure indicated microbial functional resilience and restored metabolic pathways, while PLA exposure remained associated with a 54.9 % increase in sediment available phosphorus. Two-dimensional diffusive gradients in thin films further suggested that PP may have restructured redox gradients, while PLA-driven acidification likely mobilized phosphorus, increasing labile phosphorus concentrations by 98.6 % and 64.4 %, respectively. These findings demonstrate that ostensibly low-impact MPs can subtly disrupt biogeochemical networks. Notably, biodegradable MPs pose unexpected long-term risks of phosphorus leakage, underscoring the need to consider conventional and biodegradable plastics in sustainable coastal ecosystem management.}, }
@article {pmid40896934, year = {2025}, author = {Zhang, S and Chen, X and Gu, W and Fang, Y and Qu, Y and Bai, J and Xu, Y}, title = {Metagenomic and molecular simulation insights into plastic degradation: Microenvironmental matching and the key role of residue Phe392.}, journal = {Journal of hazardous materials}, volume = {497}, number = {}, pages = {139706}, doi = {10.1016/j.jhazmat.2025.139706}, pmid = {40896934}, issn = {1873-3336}, abstract = {Due to their chemical inertness, polyethylene (PE) and polystyrene (PS) persistently accumulate in the environment. This study integrates metagenomics, degradation profiling, and molecular simulations to elucidate their divergent microbial degradation pathways. PE degradation was dominated by Burkholderia (97 %), with selective C-C bond cleavage causing a 29.8 % reduction in weight-average molecular weight (Mw) and a 35.46 % degradation rate. PS degradation relied on multispecies cooperation, primarily involving Acinetobacter (52 %), Bacillus (21 %), and Achromobacter (17 %), resulting in random main-chain cleavage, a 9.0 % reduction in number-average molecular weight (Mn), and an 18.63 % degradation rate. Molecular docking and dynamics simulations showed that PS-degrading enzymes exhibit higher binding affinity (-8.0 kcal/mol) via π-π stacking and cation-π interactions, outperforming the hydrophobic interaction-dominated PE-degrading enzymes (-5.4 kcal/mol). Residue Phe392 exhibited dual functionality in PS degradation for the first time. These findings reveal a divergence in microbial strategies: single-species dominance in PE degradation versus functional consortia for PS. The underlying mechanism is the structural compatibility between polymer substrates and enzyme active sites. This work provides a mechanistic framework for understanding microbial plastic degradation and offers insights for engineering microbial consortia and enzymes for efficient bioremediation of mixed plastic pollution.}, }
@article {pmid40896895, year = {2025}, author = {Jiang, Z and Yang, S and Pang, Q and Abdalla, M and Karbin, S and Qi, S and Hu, J and Qiu, H and Song, X and Smith, P}, title = {Metagenomic insights into the influence of soil microbiome on greenhouse gas emissions from paddy fields under varying irrigation and fertilisation regimes.}, journal = {Journal of environmental management}, volume = {393}, number = {}, pages = {127129}, doi = {10.1016/j.jenvman.2025.127129}, pmid = {40896895}, issn = {1095-8630}, abstract = {Integration of diverse fertilisation strategies with water-saving irrigation techniques presents a promising sustainable agricultural practice, offering the potential to reduce greenhouse gases (GHGs) emissions, enhance carbon sequestration and boost crop yields. However, existing research on the influence of soil microorganisms on biogeochemical processes of GHGs is limited. Herein, we explored the microbial mechanisms influencing GHGs emissions through a 3-year field experiment and metagenomic sequencing conducted in southeastern China. We investigated two irrigation patterns (controlled irrigation [CI] and flooded irrigation [FI]) and three fertilisation strategies (chemical fertiliser [F], straw returning [S] and manure substitution [M]). Results indicated that irrigation patterns significantly affected the microbial community structure in paddy soil. The key environmental factors affecting microorganisms at the phylum level included soil pH, moisture content, total nitrogen content and CH4 emissions. Random forest analysis further identified Cyanobacteria, Nitrospirae, Kiritimatiellaeota, Proteobacteria, and Balneolaeota as dominant phyla driving the differences in microbial communities across treatments. Under CI, an increase in N2O emissions was observed, which was driven by key genes, such as nirS, nirK, nosZ and norB. Compared with CF (CI with F), S increased the abundance of nirS and nirK, leading to higher N2O emissions, whereas M increased the abundance of nosZ, thereby reducing N2O emissions. The genes mcrA, pmoA and pmoC were responsible for elevated CH4 emissions through straw incorporation and manure application. Structural equation model analysis revealed that the irrigation pattern significantly affected CH4 emissions and rice yield, while the fertilisation type mainly influenced soil pH and rice yield. Organic input, particularly manure, resulted in higher C emissions owing to the presence of more CH4-producing gene mcrA in the soil. Overall, the combination of CI and manure is recommended for reducing GHGs emissions, enhancing C sequestration and boosting rice yields.}, }
@article {pmid40896389, year = {2025}, author = {Li, D and Liu, H and Wang, Y and Guo, W and Wen, H and Yang, J and Dai, Q and Jia, S and Zhang, J}, title = {A patient with severe fever with thrombocytopenia syndrome complicated with intracranial and pulmonary aspergillosis.}, journal = {IDCases}, volume = {41}, number = {}, pages = {e02347}, doi = {10.1016/j.idcr.2025.e02347}, pmid = {40896389}, issn = {2214-2509}, abstract = {Some patients with severe fever with thrombocytopenia syndrome (SFTS) develop complications including viral encephalitis and fungal infections, with a mortality rate reaching 44.7 %. In this case, the patient was admitted on Day 5 of illness, with symptoms of apathy and a delayed response. Computed tomography (CT) scans of the head and lungs revealed no abnormalities. After admission, the patient was diagnosed with SFTS. Following treatment, the patient's body temperature returned to normal, and laboratory tests revealed increased white blood cell and platelet counts and decreased myocardial enzymes. However, on Day 10 of illness, the patient experienced convulsions and somnolence. Enhanced brain magnetic resonance imaging (MRI) revealed multiple nodular abnormal signal shadows in the skull. Cerebrospinal fluid metagenomic sequencing revealed Aspergillus fumigatus infection. The patient also developed respiratory symptoms, and a chest CT revealed inflammatory changes. As the patient was suspected to have both intracranial and pulmonary Aspergillus infections, antifungal treatment was initiated. The patient's condition gradually improved with antifungal therapy, and the patient is currently receiving oral treatment with isavuconazole.}, }
@article {pmid40895792, year = {2025}, author = {Yu, HL and Hou, XW and Zhao, JX and Liu, GH and Meng, JX and Wei, YJ and Cai, Y and Liu, J and Shang, KM and Ni, HB and Liu, R and Ma, H and Nan, FL and Zhang, XX and Chen, BN and Yang, X}, title = {Insights from metagenomics on microbial biosynthesis of vitamins B and K2 in chicken gut microbiota.}, journal = {Frontiers in veterinary science}, volume = {12}, number = {}, pages = {1646825}, doi = {10.3389/fvets.2025.1646825}, pmid = {40895792}, issn = {2297-1769}, abstract = {INTRODUCTION: The chicken gut microbiome plays a pivotal role in nutrient absorption and overall health, contributing to the biosynthesis of essential vitamins. However, the biosynthesis of vitamins B and K2 by the whole gut microbiome, as well as their abundances across different gut regions, remains largely unknown.<br><br>METHODS: We employed both metagenomic sequencing and culture-based techniques, collecting a total of 25,825 genomes (25,764 metagenome-assembled genomes and 61 isolated genomes). After quality assessment and average nucleotide identity (ANI), 13,734 genomes were retained for downstream analysis.<br><br>RESULTS: Whole-genome clustering analysis identified 2,675 species-level genome bins (SGBs), predominantly from the phyla Bacillota, Bacteroidota, Pseudomonadota, and Actinomycetota. A gene catalog comprising 9.69 million genes revealed that 195,517 genes are involved in the biosynthesis of vitamins B and K2, exhibiting significant regional variation. The large intestine exhibited greater species richness and evenness compared to the small intestine. From the 13,734 genomes, we discovered 3,063 high-quality ones capable of synthesizing at least one vitamin. Genomic analysis revealed that a mere 8.2% of genomes were capable of producing five or more vitamins, while almost half were limited to synthesizing just one. Comparative genomics of cobalamin (B12) biosynthesis highlighted the predominance of the anaerobic pathway. Additionally, changes in microbial abundance were observed, such as increased abundance of the genera Phocaeicola and Faecalibacterium during bacterial infections, and Limisoma during parasitic infections.<br><br>DISCUSSION: This study provides detailed metagenomic insights into the capacity of chicken gut microbiome for vitamins B and K2 biosynthesis, revealing significant regional and taxonomic variations. These results suggest a collaborative microbial effort in vitamin biosynthesis, with potential implications for optimizing poultry health and nutrition through targeted microbial interventions.}, }
@article {pmid40895484, year = {2025}, author = {Liu, S and Chen, Y and Zhang, K and Tang, D and Zhang, J and Wang, Y and Zhao, J and Li, D and Wang, T}, title = {Exploring vaginal microbiome: from traditional methods to metagenomic next-generation sequencing-a systematic review.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1578681}, doi = {10.3389/fmicb.2025.1578681}, pmid = {40895484}, issn = {1664-302X}, abstract = {Recent research has highlighted the vaginal microbiome as a crucial factor in women's health and fertility. The growing recognition of its significance has intensified the focus on studying the female reproductive tract's microbial ecosystem. While various analytical methods exist for examining the vaginal microbiome, metagenomic next-generation sequencing (mNGS) has emerged as an auspicious approach. This study examines how mNGS technology can be applied to analyze vaginal microbiota. We begin by exploring the relationship between vaginal bacterial communities and women's health, followed by a comparative analysis of metagenomics against other detection methods, highlighting their respective strengths and limitations. The paper systematically reviews different detection techniques, examining their fundamental principles, constraints, and advantages. Several factors can affect data quality, including sampling procedures, contamination issues, and PCR amplification errors. We suggest implementing third-generation sequencing (TGS) to address these challenges to enhance reproducibility and read length, utilizing single-molecule sequencing (SMS) to eliminate PCR amplification-related errors, and integrating multiple analytical approaches to provide comprehensive insights. In summary, mNGS technology allows us to collect valuable information at a lower cost, and it remains a leading method for detecting female reproductive tract microbes. The goal of this review is to describe the principle, benefits and drawbacks, and application areas of mNGS, as well as to serve as a reference for research into female reproductive tract microbial detection methods, promote the improvement of mNGS in the detection of female reproductive tract microbial technology, and ensure the health of the female reproductive tract.}, }
@article {pmid40895312, year = {2025}, author = {Wang, G and Chen, W and Chen, X and Hou, H and Zhang, J and Han, Z}, title = {Detection of Ureaplasma parvum in amniotic fluids via reanalysis of prenatal copy number variation sequencing data: an exploratory study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1579049}, doi = {10.3389/fcimb.2025.1579049}, pmid = {40895312}, issn = {2235-2988}, abstract = {BACKGROUND: Detecting microbes in amniotic fluids via amniocentesis represents the standard method for diagnosing intrauterine infections. Given its similarity to metagenomic next-generation sequencing, copy number variation sequencing (CNV-seq) data may also contain microbial sequences. This exploratory study aimed to investigate the feasibility of prenatal CNV-seq for detecting Ureaplasma parvum (U. parvum) in amniotic fluids and to evaluate the pregnancy outcomes in U. parvum-positive cases.<br><br>METHODS: This retrospective study enrolled 2419 singleton pregnant women who underwent genetic amniocentesis for fetal CNV-seq testing and completed the follow-up with documented pregnancy outcomes. The CNV-seq data were reanalyzed to extract the read counts of U. parvum from each sample's raw data, and reads per million (RPM) was used to quantify its relative abundance.<br><br>RESULTS: The prevalence of asymptomatic intrauterine U. parvum positivity in this cohort was 1.4% (33/2419), with read counts ranging 1 to 30423 and RPM from 0.09 to 3580.65 by reanalysis of CNV-seq data. There was a statistically significantly higher risk for early spontaneous preterm labor (<32 gestational weeks; P<0.001) and preterm premature rupture of the membranes (P<0.001) in women with positive U. parvum compared to negative cases. Among U. parvum positive cases, six cases (6/33, 18.2%) had relatively higher read counts ranging from 2483 to 30423, with corresponding RPM of 406.45 to 3580.65. Adverse pregnancy outcomes were exclusively observed among women with high reads of U. parvum as opposed to those with low reads. Four cases with high U. parvum reads in amniotic fluids, not treated with antibiotics, showed a latency period of 6 to 10 weeks from positive detection to the onset of clinical manifestations.<br><br>CONCLUSIONS: CNV-seq may be a feasible method for detecting intraamniotic U. parvum infection. High abundance of asymptomatic U. parvum in amniotic fluids are statistically associated with adverse pregnancy outcomes, highlighting its importance in preliminary screening.}, }
@article {pmid40895097, year = {2025}, author = {Jin, Y and Wang, H and Song, J}, title = {Gut-brain axis modulation in remote rehabilitation of Parkinson's disease: reconstructing the fecal metabolome and nigral network connectivity.}, journal = {Frontiers in neurology}, volume = {16}, number = {}, pages = {1644490}, doi = {10.3389/fneur.2025.1644490}, pmid = {40895097}, issn = {1664-2295}, abstract = {The pathogenesis of Parkinson's disease (PD) is gradually evolving from a central neurodegeneration-centered concept to a multi-pathway pathological model at the gut-brain system level. Studies have shown that PD patients commonly exhibit dysbiosis, reduced short-chain fatty acids (SCFAs; microbial fermentation products of dietary fiber that play key roles in host metabolism and immune regulation), abnormal tryptophan metabolism, and impaired gut barrier function. These alterations may contribute to dopaminergic neuronal damage through mechanisms including neuroinflammation, oxidative stress, and α-synuclein (α-syn) aggregation. The vagus nerve plays a critical role in bidirectional gut-brain signaling, and its dysfunction may represent a key route for pathological protein transmission from the periphery to the brain. In response, remote rehabilitation and gut-targeted interventions-including probiotics, prebiotics, dietary modulation, fecal microbiota transplantation (FMT), and transcutaneous vagus nerve stimulation (tVNS)-have shown potential in improving neurological function and inflammation in both animal and clinical studies. Multimodal data analyses have revealed significant associations between SCFA levels in fecal metabolomics and brain imaging features. Despite ongoing challenges in mechanistic extrapolation, biomarker sensitivity, and translational implementation, the integration of metagenomics, metabolomics, neuroimaging, and digital therapeutics-collectively referred to as multi-omics and digital profiling techniques-represents an emerging research direction with the potential to inform future clinical paradigms for precision remote management of PD.}, }
@article {pmid40895054, year = {2025}, author = {Cárdenas-Hernández, V and Lemos-Lucumi, C and Toro-Perea, N}, title = {Uncovering tissue-specific endophytic microbiota composition and activity in Rhizophora mangle L.: a metagenomic and metatranscriptomic approach.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e19728}, doi = {10.7717/peerj.19728}, pmid = {40895054}, issn = {2167-8359}, abstract = {The interaction of mangrove trees with endophytic microorganisms contributes to the successful establishment of these plants in the challenging intertidal environment. The red mangrove, Rhizophora mangle L. (Rhizophoraceae), is one of the dominant species in mangrove ecosystems and is characterized by the provision of several ecologically relevant services. In this work, we integrated metagenomics and metatranscriptomics to perform a robust characterization of the community of endophytic microorganisms associated with R. mangle leaf and root tissues. The microbiota were characterized at taxonomic and functional levels, and abundance and gene expression profiles were compared between these two plant tissues. We found that the endophyte community consisted mainly of bacteria and eukaryotes, which were the most active groups at the transcriptional level, while archaea and viral groups were identified in lower abundance and expression. In addition, the results show that the community of endophytic microorganisms changes depending on the tissue type, with root-associated microorganisms being the most abundant at the metagenome level and active at the metatranscriptome level. It was also found that R. mangle endophytes actively contribute to key functions for adaptation to an intertidal ecosystem with high human intervention, such as salinity tolerance and degradation of heavy metals and xenobiotic compounds. Thus, according to the functions found and contributed by the endophyte community of red mangrove leaf and root tissues, it can be concluded that these microbial communities are crucial for the survival of R. mangle in the extreme environment of mangrove forests. This study provides a solid basis for future research aimed at understanding the role of plant-endophyte interactions.}, }
@article {pmid40894769, year = {2025}, author = {Shih, J and Bloom, SM and Xu, J and Mitchell, CM and Elsherbini, J and Kwon, DS}, title = {StrainFacts accurately quantifies both endogenous and live biotherapeutic product strain abundances in simulated and clinical vaginal microbiota samples.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.08.15.670563}, pmid = {40894769}, issn = {2692-8205}, abstract = {Live biotherapeutic products (LBPs) deliver microbial strains to modulate the host microbiota in order to promote health or treat and prevent disease. Since endogenous strains are already present, accurately evaluating LBP efficacy and mechanism of action requires distinguishing administered from endogenous strains. Although computational tools exist for inferring strains from short-read metagenomic data, few have been rigorously tested in the context of LBP treatment. Here, we assess the ability of StrainFacts, a computational tool for inferring strains from short-read metagenomic data, to estimate strain abundances and genotypes of endogenous and administered strains. We performed a simulation study of a single-strain LBP trial, modeling serial samples across a range of administered strain abundance, co-occurring endogenous strains, and sequencing depths. We found that StrainFacts accurately estimated both LBP and endogenous strain abundances and genotypes within simulated samples. We further validated methods using human vaginal microbiota samples spiked with CTV-05, the Lactobacillus crispatus strain contained in the LBP LACTIN-V, which has been shown to reduce recurrent bacterial vaginosis. Our findings demonstrate that StrainFacts can robustly assess LBP and endogenous strain colonization, abundance, and dynamics in simulated and experimental microbiota samples, supporting its utility as an analysis tool for vaginal LBP therapeutic trial data.}, }
@article {pmid40894694, year = {2025}, author = {Regan, MD and Chiang, E and Grahn, M and Tonelli, M and Assadi-Porter, FM and Suen, G and Carey, HV}, title = {Host-microbiome mutualism drives urea carbon salvage and acetogenesis during hibernation.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.02.13.638127}, pmid = {40894694}, issn = {2692-8205}, abstract = {UNLABELLED: Hibernation is a seasonal survival strategy employed by certain mammals that, through torpor use, reduces overall energy expenditure and permits long-term fasting. Although fasting solves the challenge of winter food scarcity, it also removes dietary carbon, a critical biomolecular building block. Here, we demonstrate a process of urea carbon salvage (UCS) in hibernating 13-lined ground squirrels, whereby urea carbon is reclaimed through gut microbial ureolysis and used in reductive acetogenesis to produce acetate, a short-chain fatty acid (SCFA) of major value to the host and its gut microbiota. We find that urea carbon incorporation into acetate is more efficient during hibernation than the summer active season, and that while both host and gut microbes oxidize acetate for energy supply throughout the year, the host's ability to absorb and oxidize acetate is highest during hibernation. Metagenomic analysis of the gut microbiome indicates that genes involved in the degradation of gut mucins, an abundant endogenous nutrient, are retained during hibernation. The hydrogen disposal associated with reductive acetogenesis from urea carbon helps facilitate this mucin degradation by providing a luminal environment that sustains fermentation, thereby generating SCFAs and other metabolites usable by both the host and its gut microbes. Our findings introduce UCS as a mechanism that enables hibernating squirrels and their gut microbes to exploit two key endogenous nutrient sources - urea and mucins - in the resource-limited hibernation season.<br><br>SIGNIFICANCE STATEMENT: 3. When food becomes scarce during winter, hibernating mammals induce torpor to minimize energy demands and enable monthslong fasting. However, fasting eliminates the intake of essential nutrients such as carbon. We identified a two-step microbial-host interaction in ground squirrels - urea carbon salvage (UCS) - which counters carbon limitation by salvaging carbon from waste urea. Through activities of ureolytic and acetogenic bacteria, urea-derived CO 2 is reduced by free hydrogen to form acetate, whose oxidation provides energy for gut microbes and the host. This process also helps maintain a permissive environment for fermentation of other host-derived, energy-dense compounds such as mucins. UCS broadens our understanding of host-microbe mutualism under extreme nutritional constraints and may represent a widespread adaptation among fasting mammals.}, }
@article {pmid40894501, year = {2025}, author = {Monteiro, E and Baptista, P and Silva, S and Carvalho, M and Bragança, R and Guinan, KJ and Sujeeth, N and Cortez, I and Gonçalves, B and Castro, I}, title = {Metagenomic analysis of the effects of plant- and yeast-based formulations on the grapevine leaf microbiome of cv. 'Touriga Franca'.}, journal = {Frontiers in plant science}, volume = {16}, number = {}, pages = {1637143}, doi = {10.3389/fpls.2025.1637143}, pmid = {40894501}, issn = {1664-462X}, abstract = {INTRODUCTION: Grapevine is highly susceptible to fungal diseases such as downy mildew and powdery mildew, which are traditionally managed through the intensive use of chemical fungicides. However, in the context of increasingly sustainable viticulture, biofungicides derived from plant and yeast extracts are gaining attention. Despite this, their impact on the grapevine leaf microbiome, crucial for plant health and disease resilience, remains underexplored.<br><br>MATERIAL AND METHODS: This study evaluated the effects of foliar applications of biofungicides (nettle extract, Japanese knotweed extract, and a yeast-based formulation - T66 and T90) in comparison with conventional chemical treatments and control (no treatment). Over two consecutive growing seasons, high-throughput sequencing was used to assess the diversity and composition of fungal and bacterial communities on grapevine leaves.<br><br>RESULTS: Bacterial communities were more sensitive to treatments and interannual variability than fungal communities, which remained relatively stable. Conventional treatment (CT) showed the highest influence on fungal and bacterial composition, reducing the diversity of both. Some important fungal (Aureobasidium and Sporobolomyces) and bacterial (Pseudomonas and Sphingomonas) genera associated with the promotion of plant growth, health, and biocontrol were detected.<br><br>DISCUSSION: These findings reinforce the potential of new treatments with putative fungicide effects to modulate the leaf microbiome, particularly bacterial communities, without disrupting the natural fungal balance. Thus highlight their relevance for developing sustainable viticultural practices aimed at improving plant protection.}, }
@article {pmid40894332, year = {2025}, author = {Zhai, J and Choi, Y and Yang, X and Chen, Y and Knox, K and Twigg, HL and Won, JH and Zhou, H and Zhou, JJ}, title = {DeepBiome: A Phylogenetic Tree Informed Deep Neural Network for Microbiome Data Analysis.}, journal = {Statistics in biosciences}, volume = {17}, number = {1}, pages = {191-215}, doi = {10.1007/s12561-024-09434-9}, pmid = {40894332}, issn = {1867-1764}, abstract = {Evidence linking the microbiome to human health is rapidly growing. The microbiome profile has the potential as a novel predictive biomarker for many diseases. However, tables of bacterial counts are typically sparse, and bacteria are classified within a hierarchy of taxonomic levels, ranging from species to phylum. Existing tools focus on identifying microbiome associations at either the community level or a specific, pre-defined taxonomic level. Incorporating the evolutionary relationship between bacteria can enhance data interpretation. This approach allows for aggregating microbiome contributions, leading to more accurate and interpretable results. We present DeepBiome, a phylogeny-informed neural network architecture, to predict phenotypes from microbiome counts and uncover the microbiome-phenotype association network. It utilizes microbiome abundance as input and employs phylogenetic taxonomy to guide the neural network's architecture. Leveraging phylogenetic information, DeepBiome is applicable to both regression and reduces the need for extensive tuning of the deep learning architecture, minimizes overfitting, and, crucially, enables the visualization of the path from microbiome counts to disease. It classification problems. Simulation studies and real-life data analysis have shown that DeepBiome is both highly accurate and efficient. It offers deep insights into complex microbiome-phenotype associations, even with small to moderate training sample sizes. In practice, the specific taxonomic level at which microbiome clusters tag the association remains unknown. Therefore, the main advantage of the presented method over other analytical methods is that it offers an ecological and evolutionary understanding of host-microbe interactions, which is important for microbiome-based medicine. DeepBiome is implemented using Python packages Keras and TensorFlow. It is an open-source tool available at https://github.com/Young-won/DeepBiome.}, }
@article {pmid40894237, year = {2025}, author = {Fissel, JA and Bergman, Y and Campodónico, VL and Walsh, DM and Fanelli, B and Arogyaswamy, K and Kwon, JH and Milstone, AM and Tamma, PD and Simner, PJ}, title = {Microbiome and resistome characterization of patients colonized with carbapenem-resistant Enterobacterales by long-read metagenomic next-generation sequencing of rectal swabs.}, journal = {JAC-antimicrobial resistance}, volume = {7}, number = {4}, pages = {dlaf152}, doi = {10.1093/jacamr/dlaf152}, pmid = {40894237}, issn = {2632-1823}, abstract = {OBJECTIVES: Evaluation of differences in the intestinal microbiome and resistome among high-risk patients (i.e. intensive care, oncology, transplant recipients) who are and are not colonized with carbapenem-resistant Enterobacterales (CRE).<br><br>METHODS: One hundred and twelve rectal swabs were obtained from 85 patients with known CRE colonization status and cohorted. Long-read metagenomic next-generation sequencing (mNGS) was performed on rectal swabs. Microbiome and resistome analysis were performed by assessing &#x3b1;-diversity, &#x3b2;-diversity, relative abundance assessment and linear discriminant analysis effect size (LEfSe), comparing patients colonized (CRE positive) and not colonized (CRE negative) with CRE. Longitudinal analysis of sequential swabs collected over multiple hospital encounters on a subset of patients was performed at the patient level.<br><br>RESULTS: The microbiomes of cohorts were similar when comparing &#x3b1;- and &#x3b2;-diversity measures and relative abundance. LEfSe analysis identified Gram-negative pathobionts enriched among CRE-positive samples and Gram-positive taxa enriched among CRE-negative samples. &#x3b1;-Diversity of the resistome differed at class, gene and allele levels. Relative abundance and LEfSe analysis demonstrated enrichment of genes conferring &#x3b2;-lactam resistance among CRE-positive patients; LEfSe also demonstrated enrichment of antimicrobial resistance genes to multiple antimicrobial classes. At the patient level, fluctuations in the microbiome and resistome among longitudinally collected swabs were associated with antibiotic exposure.<br><br>CONCLUSIONS: Differences between the microbiomes of CRE-positive- and CRE-negative-colonized patients at the cohort level were relatively muted, whereas statistically significant differences were observed among their resistomes. In patients followed longitudinally, shifts in microbiome and resistome composition were dramatic in between encounters and antibiotic exposures.}, }
@article {pmid40894205, year = {2025}, author = {Narsing Rao, MP and Quadri, SR and Sathish, M and Quach, NT and Li, WJ and Thamchaipenet, A}, title = {Exploring omics strategies for drug discovery from Actinomycetota isolated from the marine ecosystem.}, journal = {Frontiers in pharmacology}, volume = {16}, number = {}, pages = {1634207}, doi = {10.3389/fphar.2025.1634207}, pmid = {40894205}, issn = {1663-9812}, abstract = {Marine Actinomycetota are prolific producers of diverse bioactive secondary metabolites, making them vital for drug discovery. Traditional cultivation and bioassay-guided isolation techniques often lead to the rediscovery of the same compounds, revealing the limitations of these traditional approaches and emphasizing the need for more advanced methods. The emergence of omics technologies such as genomics, metagenomics, transcriptomics, and metabolomics has dramatically enhanced the ability to investigate microorganisms by providing detailed insights into their biosynthetic gene clusters, metabolic pathways, and regulatory mechanisms. These comprehensive tools facilitate the discovery and functional analysis of new bioactive compounds by revealing the genetic blueprints underlying their biosynthesis. Omics and function-driven techniques like heterologous expression, analytical techniques (including high-resolution mass spectrometry and nuclear magnetic resonance spectroscopy), and culture condition optimization have enabled access to previously silent or cryptic gene clusters, expanding the chemical diversity available for exploration. This review emphasizes the integration of omics-based insights with function-driven methodologies and innovative culture techniques, forming a holistic approach to unlock the extensive biosynthetic capabilities of marine Actinomycetota. Combining these strategies holds great promise for discovering new marine-derived compounds with potential therapeutic applications.}, }
@article {pmid40894109, year = {2025}, author = {Lopez, JV and Pomponi, SA and Hentschel, U and Erpenbeck, D and Pruzinsky, N and Fiore, C and Mulheron, R and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and ,  and ,  and ,  and ,  and , }, title = {The chromosomal genome sequence of the giant barrel sponge, Xestospongia muta Schmidt 1870 and its associated microbial metagenome sequences.}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {336}, doi = {10.12688/wellcomeopenres.24173.1}, pmid = {40894109}, issn = {2398-502X}, abstract = {We present a genome assembly from a specimen of Xestospongia muta (Caribbean barrel sponge; Porifera; Demospongiae; Haplosclerida; Petrosiidae). The genome sequence has a total length of 158.52 megabases. Most of the assembly (99.56%) is scaffolded into 15 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 18.99 kilobases in length. Several symbiotic bacterial genomes were assembled as MAGs, including Candidatus Poribacteria species, Candidatus Latescibacteria, Acidobacteriota, Actinomycetota Gemmatimonadota, multiple Chloroflexota and the archaeon Nitrosopumilus. Gene annotation of this assembly on Ensembl identified 20,220 protein-coding genes.}, }
@article {pmid40894108, year = {2025}, author = {de Goeij, JM and Mueller, B and Achlatis, M and Campana, S and Hudspith, M and Kornder, NA and Hentschel, U and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and ,  and ,  and ,  and ,  and , }, title = {The scaffold-level genome sequence of an encrusting sponge, Halisarca caerulea Vacelet &amp; Donadey, 1987, and its associated microbial metagenome sequences.}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {344}, doi = {10.12688/wellcomeopenres.24281.1}, pmid = {40894108}, issn = {2398-502X}, abstract = {We present a scaffold-level genome assembly from a Halisarca caerulea specimen (encrusting sponge; Porifera; Demospongiae; Chondrillida; Halisarcidae). The genome sequence is 195.70 megabases in span. The mitochondrial genome has also been assembled and is 19.15 kilobases in length. Gene annotation of this assembly on Ensembl identified 26,722 protein-coding genes. The metagenome of the specimen was also assembled and four binned bacterial genomes related to the relevant sponge symbiont clades Alphaproteobacteria bacterium GM7ARS4 and Gammaproteobacteria bacterium AqS2 ((Tethybacterales) were identified.}, }
@article {pmid40894065, year = {2025}, author = {Chen, LX and Camargo, AP and Qin, Y and Wang, H and Zou, Y and Duan, Y and Li, H and Koonin, E}, title = {A prevalent huge phage clade in human and animal gut microbiomes.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-7356405/v1}, pmid = {40894065}, issn = {2693-5015}, abstract = {Huge phages are widespread in the biosphere, yet their prevalence and ecology in the human gut remain poorly characterized. Here, we report Jug (Jumbo gut) phages with genomes of 360-402 kilobase pairs that comprise ~1.1% of the reads in human gut metagenomes, and are predicted to infect Bacteroides and/or Phocaeicola. Although three of the four major groups of Jug phages shared >90% genome-wide sequence identity, their large terminase subunits exhibited only 38-57% identity, suggesting horizontal acquisition from other phages. Over 1,500 genomes of Jug phages were recovered from human and animal gut metagenomes, revealing their broad distribution, with largely shared gene content suggestive of frequent cross-animal-host transmission. Jug phages displayed high gene transcription activities, including the gene for a calcium-translocating P-type ATPase not detected previously in phages. These findings broaden our understanding of huge phages and highlight Jug phages as potential major players in gut microbiome ecology.}, }
@article {pmid40893472, year = {2025}, author = {Xu, T and Huang, D and Huang, T and Wang, Y and Chen, W and Chen, S and Qian, Y and Yue, H}, title = {Gene Surfing: An efficient and versatile tool for targeted enzyme mining in metagenomics.}, journal = {Synthetic and systems biotechnology}, volume = {10}, number = {4}, pages = {1377-1387}, doi = {10.1016/j.synbio.2025.07.006}, pmid = {40893472}, issn = {2405-805X}, abstract = {Microbial community studies have established enzymes' pivotal catalytic roles in ecosystem metabolism, yet cultivation-dependent methods fail to exploit uncultured microbial enzyme resources. Metagenomics overcomes this by directly accessing microbial genetic information, but its massive data generation challenges precise enzyme identification: (1) Restricted applicability across varied sample types. (2) Narrow functional scope in target enzyme discovery. To address this, we developed Gene Surfing, a bioinformatics workflow platform based on Snakemake. It integrates modules for data quality control (Fastp), genome assembly (MEGAHIT), assembly evaluation (QUAST and MetaQUAST), functional annotation (Prokka), and homologous sequence retrieval (MMseqs2). Gene Surfing offers scalability, reproducibility, and efficiency, addressing key challenges in enzyme identification. Validation results include: Cellulose-degrading enzymes (GH5 family): 1,311,316 potential lignocellulolytic enzyme sequences were identified, with 127 sequences functionally validated (84.25 % activity rate); Polyethylene-degrading enzymes: 705 candidate sequences were found, 38 of which were heterologously expressed, showing an 81.5 % activity rate (31/38); Endonucleases (HNH superfamily): 585 potential sequences were retrieved, with 4 out of 7 tested showing activity (57.1 % success rate).}, }
@article {pmid40893417, year = {2025}, author = {Liu, T and Zhang, C and Ming, M and Chen, L and Chen, W and Xu, Y and Shen, M and Liu, J and Ou, Q and Bao, H and Chen, X and Lu, G and Yan, G}, title = {A Case of Measles Virus-caused Subacute Sclerosing Panencephalitis Diagnosed by Molecular and Clinical Analysis.}, journal = {Open forum infectious diseases}, volume = {12}, number = {8}, pages = {ofaf453}, doi = {10.1093/ofid/ofaf453}, pmid = {40893417}, issn = {2328-8957}, abstract = {Subacute sclerosing panencephalitis (SSPE) is a rare and lethal neurodegenerative encephalitis caused by persistent measles virus infection. We report an SSPE case in a patient infected at 6 months old, diagnosed using clinical methods and metagenomic sequencing, highlighting the benefits of combining clinical and molecular techniques for improved diagnosis.}, }
@article {pmid40892879, year = {2025}, author = {Liu, W and Xie, S and Zhu, G and Qin, S and Li, M and Yin, S and Lai, W and Lu, C and Chen, Q and Feng, P}, title = {Concurrent chromoblastomycosis and eumycetoma: a unique case of dual neglected tropical fungal diseases in Asia.}, journal = {PLoS neglected tropical diseases}, volume = {19}, number = {9}, pages = {e0013484}, doi = {10.1371/journal.pntd.0013484}, pmid = {40892879}, issn = {1935-2735}, abstract = {Chromoblastomycosis (CBM) and mycetoma, as implantation mycoses, have been listed as neglected tropical diseases (NTDs) by the World Health Organization. The concurrent occurrence of these two NTDs in a single patient is extremely rare. A 69-year-old female patient presented with papules on the dorsum of her left hand for over 5 months and nodules on the left lower limb accompanied by ulceration and pain for 20 days. Histopathological examination of the papule on the dorsum of the left hand revealed muriform cells and fungal culture of the tissue identified Fonsecaea monophora. Microscopic examination of the purulent secretion from the ulcer on the left lower calf revealed the presence of grains, and the tissue culture result was Scedosporium apiosperma complex, with metagenomic next-generation sequencing further identifying S. dehoogii as the predominant pathogen. The clinical diagnosis was CBM caused by F. monophora combined with eumycetoma due to S. dehoogii. The patient was treated with voriconazole at a dosage of 200 mg twice daily for 4 weeks, after which the papules on the dorsum of the left hand and the ulcer on the left lower calf showed gradual improvement. This case represents the first reported instance of concurrent CBM caused by F. monophora and eumycetoma due to S. dehoogii, providing a novel perspective on the clinical manifestations and early identification of neglected implantation mycoses.}, }
@article {pmid40892803, year = {2025}, author = {Haugum, K and Ravi, A and Afset, JE and Ås, CG}, title = {Evaluation of shotgun metagenomics as a diagnostic tool for infectious gastroenteritis.}, journal = {PloS one}, volume = {20}, number = {9}, pages = {e0331288}, pmid = {40892803}, issn = {1932-6203}, mesh = {*Metagenomics/methods ; Humans ; *Gastroenteritis/diagnosis/microbiology ; Feces/microbiology ; Polymerase Chain Reaction ; Bacteria/genetics/isolation &amp; purification ; }, abstract = {Infectious gastroenteritis is a significant health issue globally. Identifying the causative pathogen is crucial for treatment, infection control and epidemiological surveillance. While PCR-based analyses are fast and sensitive, they only detect known pathogens. Clinical metagenomics can potentially identify novel or unexpected pathogens. This study aimed to evaluate shotgun metagenomics for detecting diarrhoeal pathogens in faecal samples from patients with infectious gastroenteritis and spiked samples from healthy donors, compared to PCR. DNA from clinical faecal samples (n = 12), spiked samples (n = 36), and control samples (n = 7) were analysed by PCR and shotgun metagenomics sequencing. Reads were taxonomically assigned, assembled, and binned into MAGs. MAGs were taxonomically assigned, and virulence genes were detected in bacterial assemblies and MAGs. Pathogens detected by PCR were also identified by taxonomic assignment of reads, though with lower sensitivity. Taxonomic assignment of MAGs identified 50% of bacterial pathogens and HAdV-F. Additional potential pathogens were observed in most samples. More bacterial virulence genes were detected in assemblies than in MAGs. In spiked samples, C. jejuni and HAdV-F were detected by both PCR and metagenomics, with significant correlation between Cq values and reads. Parasites were detected by few reads. Metagenomics has lower sensitivity compared to PCR but can provide supplementary information relevant for treatment. Challenges include additional potential pathogens, background microbiome, and introduced kitome, necessitating optimized extraction methods and strict quality controls.}, }
@article {pmid40892742, year = {2025}, author = {Zhu, J and Chen, Y and Han, Y and Li, J}, title = {Mechanism of Huanglian Wendan Decoction in ameliorating non-alcoholic fatty liver disease via modulating gut microbiota-mediated metabolic reprogramming and activating the LKB1/AMPK pathway.}, journal = {PloS one}, volume = {20}, number = {9}, pages = {e0331303}, pmid = {40892742}, issn = {1932-6203}, mesh = {Animals ; *Non-alcoholic Fatty Liver Disease/drug therapy/metabolism/microbiology/pathology ; *Gastrointestinal Microbiome/drug effects ; *Drugs, Chinese Herbal/pharmacology/therapeutic use/chemistry ; Rats ; Male ; *AMP-Activated Protein Kinases/metabolism ; Rats, Sprague-Dawley ; Signal Transduction/drug effects ; *Protein Serine-Threonine Kinases/metabolism ; Lipid Metabolism/drug effects ; Liver/metabolism/drug effects/pathology ; AMP-Activated Protein Kinase Kinases ; Disease Models, Animal ; Carnitine O-Palmitoyltransferase/metabolism ; Metabolic Reprogramming ; }, abstract = {BACKGROUND: Huanglian Wendan Decoction (HLWDD), a classical traditional Chinese medicine (TCM) formula, has shown therapeutic promise in treating metabolic disorders. However, its underlying mechanisms against non-alcoholic fatty liver disease (NAFLD) remain unclear.<br><br>OBJECTIVE: This study aimed to elucidate the pharmacological mechanisms by which HLWDD ameliorates NAFLD, focusing on its impact on lipid metabolism, gut microbiota, and amino acid regulation.<br><br>METHODS: A NAFLD rat model was established by administering a high-sugar, high-fat, high-salt diet for 20 weeks. The core components of HLWDD were identified and quantified using UPLC-Q-TOF-MS/MS and HPLC, and further validated via network pharmacology and molecular docking. Therapeutic efficacy was assessed through analysis of body weight, serum lipid profiles, inflammatory cytokines, hepatic histology, and protein expression. Gut microbiota composition and liver-intestine metabolite profiles were evaluated using metagenomic sequencing and LC-MS/MS.<br><br>RESULTS: Seven key constituents, including quercetin and berberine, were quantified (15.11-164.37 &#x3bc;g/mL) and shown to interact with lipid metabolism targets such as liver kinase B1 (LKB1), AMP-activated protein kinase (AMPK), peroxisome proliferator-activated receptor alpha (PPAR&#x3b1;), and carnitine palmitoyltransferase 1A (CPT1A). HLWDD treatment significantly reduced body weight, hepatic lipid accumulation, and serum levels of triglycerides, total cholesterol, and low-density lipoprotein cholesterol, while increasing high-density lipoprotein cholesterol. Proinflammatory cytokines (IL-6, IL-1&#x3b2;, TNF-&#x3b1;) were notably suppressed. Mechanistically, HLWDD activated the LKB1/AMPK signaling pathway and modulated aspartic acid metabolism in association with increased abundance of Akkermansia in the gut. Metabolomic analysis identified 13 differential metabolites, with aspartic acid showing strong correlations with Akkermansia and LKB1/AMPK activity.<br><br>CONCLUSION: HLWDD exerts its anti-NAFLD effects by enhancing Akkermansia-mediated aspartate metabolism, thereby activating the LKB1/AMPK axis and promoting lipid oxidation via CPT1A and PPAR&#x3b1;. This study provides new mechanistic insight into the gut-liver axis in NAFLD and highlights HLWDD as a multi-targeted therapeutic approach for restoring metabolic balance.}, }
@article {pmid40890888, year = {2025}, author = {Wang, S and Zhao, Z and Cheng, R and Cui, L and Wang, J and Rubin-Blum, M and Zhang, Y and Liu, B and Chen, X and Baltar, F and Cao, X and Wen, X and Alain, K and Chen, Z and Liao, J and Jiang, L and Shao, Z}, title = {Phylogenetically and metabolically diverse active carbon-fixing microbes reside in mangrove sediments.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {194}, pmid = {40890888}, issn = {2049-2618}, support = {42306127//National Natural Science Foundation of China/ ; 42306127//National Natural Science Foundation of China/ ; 42176134//National Natural Science Foundation of China/ ; 42030412//National Natural Science Foundation of China/ ; 2024002//Scientific Research Foundation of Third Institute of Oceanography/ ; 2019021//Scientific Research Foundation of Third Institute of Oceanography/ ; }, mesh = {*Geologic Sediments/microbiology ; *Carbon Cycle ; Wetlands ; Phylogeny ; China ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Carbon/metabolism ; Metagenomics/methods ; Gammaproteobacteria/metabolism/genetics/classification/isolation &amp; purification ; Microbiota ; }, abstract = {BACKGROUND: Mangroves are hotspots of carbon sequestration in transitional zones between marine and terrestrial ecosystems. Microbially driven dark carbon fixation (DCF) is prominent in sediments, yet our understanding of the DCF process across this continuum remains limited. In this study, we explored DCF activities and associated chemoautotrophs along the sediment depth of different mangrove sites in Fujian Province, China, using radiocarbon labeling and molecular techniques.<br><br>RESULTS: Our results showed that the DCF rates ranged from 0.02 to 3.27&#xa0;mmol C m[-2]&#xa0;day[-1] in all samples, showing a depth-dependent spatial variation. These rates of DCF were closely related to the environmental factors such as DIC, TS, AVS, NH4[+], NO3[-], and NO2[-]. Metagenomic analysis revealed six carbon-fixing pathways, with the Calvin-Benson-Bassham (CBB) cycle and Wood-Ljungdahl (WL) pathway being predominant. Further analysis of MAGs revealed that Gammaproteobacteria, Desulfobacteria, and Campylobacteria were the most abundant carbon-fixing groups. Intriguingly, some new lineages were found to have carbon-fixing potential, including two candidatus taxa JAJVIF01 and BMS3Abin14. Metatranscriptomic analyses confirmed that these carbon-fixing microbes were active in situ and occupied different niches. In the surface layers, Gammaproteobacteria with the CBB cycle played an important role in DCF, mainly driven by sulfur and hydrogen oxidation with oxygen reduction; in the deeper layers, Campylobacteria with the reductive tricarboxylic acid (rTCA) cycle and Desulfobacteria with the WL pathway were active members for DCF, mainly through sulfur, hydrogen, and CO oxidation. While in the deepest layers of 18-20&#xa0;cm, methane-producing archaea Methanosarcinia was the essential member driving DCF. In addition, most taxa containing the WL pathway displayed a mixotrophic lifestyle corresponding to flexible carbon acquisition strategies.<br><br>CONCLUSIONS: Overall, this study provides new insights into the understanding of biological carbon fixation and its ecological functions in mangrove sediments. Video Abstract.}, }
@article {pmid40890809, year = {2025}, author = {Xue, S and Shi, T and Xie, J and Liu, W and Yao, S and Li, N and Liu, H and Kong, W and Gao, F}, title = {Integrated fecal macrogenomic and metabolomic analyses reveal celiac disease flora and metabolic profiles associated with Chinese populations.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {972}, pmid = {40890809}, issn = {1479-5876}, support = {2022D01C831//Natural Science Foundation of Xinjiang/ ; 82260116//National Natural Science Foundation of China/ ; 82460117//National Natural Science Foundation of China/ ; }, mesh = {Adolescent ; Adult ; Female ; Humans ; Male ; Middle Aged ; Young Adult ; Case-Control Studies ; *Celiac Disease/ethnology/genetics/metabolism/microbiology ; China/ethnology ; *Feces/microbiology ; Gastrointestinal Microbiome ; *Metabolome ; *Metabolomics ; East Asian People ; }, abstract = {BACKGROUND AND AIMS: Genes and gluten intake are necessary but not sufficient to cause celiac disease (CeD), and altered intestinal flora is an additional risk factor for the development of CeD. The present study was conducted to investigate the intestinal flora and metabolic characteristics of CeD among the Chinese population, with the use of CeD patients from Xinjiang, China.<br><br>METHODS: Macrogenomic sequencing was performed to analyze the composition and differences of the intestinal flora of 40 CeD patients and 40 healthy subjects. Non-targeted metabolomics analysis was carried out using LC-MS metabolomics technology in 30 CeD patients and 30 control subjects. A model for CeD diagnosis was constructed based on differential flora and metabolites. Blood was collected from all subjects for HLA typing assay.<br><br>RESULTS: CeD-associated alterations were identified in the gut microbiome and metabolome. 15 differential bacterial strains (AUC&#x2009;=&#x2009;0.85) and 8 differential metabolites (AUC&#x2009;=&#x2009;0.9799) constructed a diagnostic panel that was effective in differentiating CeD patients from healthy subjects. Compared with non-CeD patients carrying HLA-DQ[&#xb1;], the abundances of Agathobacter_rectalis, Bifidobacterium_pseudocatenulatum, Clostridia_bacterium, Coprococcus_comes, and Fusicatenibacter_saccharivorans in CeD patients were significantly lower (P&#x2009;<&#x2009;0.05). Metabolomics analysis showed that Leoheteronin D, Pc (34:2), and GPEtn (18:1/16:0) were the major metabolites involved in multiple metabolic pathways in CeD patients.<br><br>CONCLUSION: Our study revealed specific alterations in the gut microbiome and metabolome of Chinese CeD patients through a multi-omics integration strategy. We found that CeD individuals carrying CeD risk genes may possess a unique intestinal flora composition, and this intestinal flora may, to some extent, explain the pathogenesis of CeD beyond the contributions of genes and gluten intake.}, }
@article {pmid40890622, year = {2025}, author = {Demiralay, B and Can, T}, title = {Effective primer design for genotype and subtype detection of highly divergent viruses in large scale genome datasets.}, journal = {BMC bioinformatics}, volume = {26}, number = {1}, pages = {223}, pmid = {40890622}, issn = {1471-2105}, abstract = {Identification of microorganisms in a biological sample is a crucial step in diagnostics, pathogen screening, biomedical research, evolutionary studies, agriculture, and biological threat assessment. While progress has been made in studying larger organisms, there is a need for an efficient and scalable method that can handle thousands of whole genomes for organisms with high mutation rates and genetic diversity such as single stranded viruses. In this study, we developed a novel method to identify subsequences for detection of a given species/subspecies in a (meta)genomic sample using the Polymerase Chain Reaction (PCR) method. Species detection in any analysis depends highly on the measurement method and since thermodynamic interactions are critical in PCR, thermodynamics is the main driving force in the proposed methodology. Our method is parallelized in multiple steps and involves extracting all oligonucleotides from target genomes. We then locate the target sites for each oligonucleotide using the constructed suffix array and local alignment followed by thermodynamic interaction assessment. An important requirement for subspecies identification is to avoid amplifying a non-target set of genomes and our method addresses this. We applied our method to three highly divergent viruses; (1) Hepatitis C virus (HCV), where the subtypes differ in 31-33% of nucleotide sites on average, (2) Human immunodeficiency virus (HIV), for which, 25-35% between-subtype and 15-20% within-subtype variation is observed, and (3) the Dengue virus, whose respective genomes (only DENV 1-4) share 60% sequence identity to each other. Using our method, we were able to select oligonucleotides that can identify in silico 99.9% of 1657 HCV genomes, 99.7% of 11,838 HIV genomes, and 95.4% of 4016 Dengue genomes. We also show subspecies identification on genotypes 1-6 of HCV and genotypes 1-4 of the Dengue virus with more than 99.5% true positive and less than 0.05% false positive rate, on average. None of the state-of-the-art methods can produce oligonucleotides with this specificity and sensitivity on highly divergent viral genomes like the ones studied in this article.}, }
@article {pmid40890565, year = {2025}, author = {Ivanich, K and Yackzan, A and Flemister, A and Chang, YH and Xing, X and Chen, A and Yanckello, LM and Sun, M and Aware, C and Govindarajan, M and Kramer, S and Ericsson, A and Lin, AL}, title = {Ketogenic Diet Modulates Gut Microbiota-Brain Metabolite Axis in a Sex- and Genotype-Specific Manner in APOE4 Mice.}, journal = {Journal of neurochemistry}, volume = {169}, number = {9}, pages = {e70216}, doi = {10.1111/jnc.70216}, pmid = {40890565}, issn = {1471-4159}, support = {RF1AG062480/AG/NIA NIH HHS/United States ; }, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *Diet, Ketogenic/methods ; Female ; *Apolipoprotein E4/genetics ; Mice ; Male ; *Brain/metabolism ; *Sex Characteristics ; Genotype ; Mice, Inbred C57BL ; Apolipoprotein E3/genetics ; Mice, Transgenic ; }, abstract = {The apolipoprotein E4 (APOE4) allele is the strongest genetic risk factor for late-onset Alzheimer's disease (AD), associated with early brain metabolic dysfunction and gut microbiome alterations. Targeting these early changes through dietary interventions may reduce AD risk in asymptomatic carriers. This study evaluated whether a ketogenic diet (KD) could reshape the gut microbiome and enhance key brain metabolite levels in young APOE4 mice, using APOE3 mice as a neutral-risk comparison. Male and female APOE3 and APOE4 mice were fed either a control diet or KD for 16 weeks, starting at 12 weeks of age. We used shotgun metagenomics and targeted brain metabolomics to identify microbe-metabolite signatures linked to neuroprotection. KD increased beneficial species such as Lactobacillus johnsonii and Lactobacillus reuteri while reducing pathogenic Bacteroides intestinalis. These microbial shifts correlated with improved brain metabolites related to mitochondrial function, neurotransmitter balance, redox homeostasis, and lipid metabolism. Notably, Lactobacillus species and B. intestinalis exhibited inverse correlations with key brain metabolite levels, suggesting their roles as both modulators and biomarkers of brain health. APOE4 females showed the greatest benefits, including restored microbiome diversity and normalization of brain metabolite levels. In contrast, APOE3 mice showed microbiome changes but limited brain metabolic responses. These findings highlight KD's potential to reprogram the gut-brain axis in a genotype- and sex-dependent manner, supporting its use as a precision nutrition strategy to reduce AD risk, particularly in asymptomatic female APOE4 carriers.}, }
@article {pmid40890119, year = {2025}, author = {Yuan, B and Wang, S}, title = {Microbiome data integration via shared dictionary learning.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {8147}, pmid = {40890119}, issn = {2041-1723}, support = {DBI-2243257//National Science Foundation (NSF)/ ; DMS-2515171//National Science Foundation (NSF)/ ; DBI-2243257//National Science Foundation (NSF)/ ; DMS-2515171//National Science Foundation (NSF)/ ; }, mesh = {Humans ; *Microbiota/genetics ; Metagenomics/methods ; Colorectal Neoplasms/microbiology/therapy ; Machine Learning ; Immunotherapy ; Gastrointestinal Microbiome ; Computational Biology/methods ; }, abstract = {Data integration is a powerful tool for facilitating a comprehensive and generalizable understanding of microbial communities and their association with outcomes of interest. However, integrating data sets from different studies remains a challenging problem because of severe batch effects, unobserved confounding variables, and high heterogeneity across data sets. We propose a new data integration method called MetaDICT, which initially estimates the batch effects by weighting methods in causal inference literature and then refines the estimation via novel shared dictionary learning. Compared with existing methods, MetaDICT can better avoid the overcorrection of batch effects and preserve biological variation when there exist unobserved confounding variables, data sets are highly heterogeneous across studies, or the batch is completely confounded with some covariates. Furthermore, MetaDICT can generate comparable embedding at both taxa and sample levels that can be used to unravel the hidden structure of the integrated data and improve the integrative analysis. Applications to synthetic and real microbiome data sets demonstrate the robustness and effectiveness of MetaDICT in integrative analysis. Using MetaDICT, we characterize microbial interaction, identify generalizable microbial signatures, and enhance the accuracy of outcome prediction in two real integrative studies, including an integrative analysis of colorectal cancer metagenomics studies and a meta-analysis of immunotherapy microbiome studies.}, }
@article {pmid40889931, year = {2025}, author = {Sun, XY and Qi, RT and Li, HX and Zheng, LX}, title = {Soil ammonia oxidation process and its driving factors in the riparian zone of drainage ditch in saline-alkali area of Ningxia, Northwest China.}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {36}, number = {7}, pages = {2201-2212}, doi = {10.13287/j.1001-9332.202507.033}, pmid = {40889931}, issn = {1001-9332}, mesh = {China ; *Ammonia/metabolism/chemistry ; Soil/chemistry ; Nitrification ; Oxidation-Reduction ; *Soil Microbiology ; Bacteria/metabolism ; Alkalies ; Archaea/metabolism ; *Ecosystem ; Rivers ; }, abstract = {Ammonia oxidation plays a critical role in nitrogen cycling within riparian zones. To investigate this process in saline-alkali soils of the Yinbei region, northern Yinchuan, Ningxia, we selected five distinct riparian types along the Third Drainage Ditch: gravel-reed mixed zone, reed zone, high-salt Bassia scoparia zone, Iris lactea embankment zone and bare soil zone. We quantified soil potential nitrification rates (PNR), environmental factors, and analyzed ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) communities via me-tagenomics and qPCR targeting amoA genes. The results showed that the total potential nitrification rate (PNRtotal) in the riparian zones ranged from 0.47 to 1.37 μmol N·g[-1]·d[-1], with PNRAOA (potential nitrification rate of AOA) being higher than PNRAOB (potential nitrification rate of AOB). The copy number of AOA amoA genes (2.63×10[6]-2.06×10[7] copies·g[-1]) was significantly higher than AOB amoA genes (7.14×10[5]-9.55×10[6] copies·g[-1]). The PNR and amoA gene copy number in the reed zone, gravel-reed mixed zone, and I. lactea embankment zone were higher than those in the high-salt B. scoparia zone and bare soil zone, indicating that nitrification in the riparian zones was dominated by AOA. AOA were affiliated with the phylum Nitrososphaerota, with the dominant genera being unclassified_f__Nitrososphaeraceae and Candidatus Nitrosocosmicus. The physicochemical factors, including ammonium, nitrite, nitrate, electrical conductivity, total organic carbon, and total nitrogen exhibited significant differences among different riparian zones. PNRAOA and PNRtotal were significantly influenced by ammonium, total nitrogen, total organic carbon and pH, and PNRtotal showed a highly significant positive correlation with amoA gene copy number. Structural equation modeling (SEM) results indicated that pH and total organic carbon were the primary factors affecting nitrification in the riparian zones and that AOA amoA gene copy number showed significant positive correlation with nitrification rate.}, }
@article {pmid40889848, year = {2026}, author = {Lin, X and Deng, C and Shu, Y and Li, S and Song, Y and Kong, H and Liang, Z and Liu, L and Rao, Y}, title = {Ecological presence and functional role of bacteriophages in fermented vegetables.}, journal = {Food microbiology}, volume = {133}, number = {}, pages = {104884}, doi = {10.1016/j.fm.2025.104884}, pmid = {40889848}, issn = {1095-9998}, mesh = {*Vegetables/microbiology/virology ; *Bacteriophages/genetics/isolation &amp; purification/physiology/metabolism/classification ; Fermentation ; *Fermented Foods/virology/microbiology ; Microbiota ; *Bacteria/genetics/metabolism/virology/classification/isolation &amp; purification ; Food Microbiology ; }, abstract = {Fermented vegetables are widely favored by consumers for their distinctive flavors and nutritional value, with their quality attributes being closely associated with microbiome dynamics. Recent advances in high-throughput sequencing technologies have revealed abundant bacteriophage resources within the fermented vegetable microbiome. These viral components significantly influence fermentation processes and product characteristics by modulating microbial community structure and function. However, research on optimizing vegetable fermentation processes through bacteriophage-mediated regulation remains in its nascent stage. This study systematically summarizes the compositional characteristics and dynamic patterns of microbial communities in fermented vegetables. We review the latest research progress on bacteriophage diversity and functional properties in fermented vegetables. Furthermore, by integrating multi-omics data, we provide insights into the complex interaction network among bacteriophages, host microbiota, and metabolic products. The results demonstrate that bacteriophages precisely regulate the fermentation process by mediating microbial community succession via lytic-lysogenic cycles and participating in the biosynthesis of key flavor compounds through encoded auxiliary metabolic genes. Finally, we sort out an integrated technical framework combining metagenomics and culturomics. This research provides novel insights into understanding the functional mechanisms of bacteriophages in fermented vegetables, offers a theoretical foundation for developing precision fermentation technologies based on bacteriophage regulation.}, }
@article {pmid40889843, year = {2026}, author = {Ren, F and Liu, M and Tan, B}, title = {Mycobiota of highly-preserved and easily-spoiled soybean pastes-what are their roles?.}, journal = {Food microbiology}, volume = {133}, number = {}, pages = {104876}, doi = {10.1016/j.fm.2025.104876}, pmid = {40889843}, issn = {1095-9998}, mesh = {*Glycine max/microbiology ; *Fungi/classification/genetics/isolation &amp; purification/metabolism ; *Mycobiome ; Food Preservation ; Biodiversity ; }, abstract = {Effective preservation of fermented soybean pastes is critically dependent on their microbial communities. In this study, the fungal assemblages of highly-preserved (HP) and easily-spoiled (ES) soybean paste samples were analyzed and compared mainly with Illumina sequencing of both mycobiota ITS amplicon and metagenomic functional annotation. The results showed that fungal communities of two types soybean pastes were distinct and had different α-diversity and β-diversity characteristics. The phylum Ascomycota was predominant in all samples, with Candida, Aspergillus, and Penicillium being the most abundant genera. The HP group exhibited greater richness and diversity compared to ES samples, and the relative abundance of specific fungal taxa varied significantly between the two groups. Additionally, functional annotation revealed differences in metabolic categories, with HP samples having higher levels of functions related to amino acid transport and metabolism, cell cycle control, and signal transduction mechanisms. These results enhance the understanding of the fungal diversity and functional differences of soybean pastes, providing insights that could improve preservation methods, optimize production and storage processes, and ensure the quality of the products.}, }
@article {pmid40889721, year = {2025}, author = {Gao, R and Liu, Z and Li, W and Lou, L and Xu, T and Shi, L and Cao, J and Fang, J and Liu, G}, title = {Novel compound bacterial agent effects on pig farm wastewater denitrification and nitrogen transformation.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {133232}, doi = {10.1016/j.biortech.2025.133232}, pmid = {40889721}, issn = {1873-2976}, abstract = {This research involved the screening and combination of Escherichia coli, Acinetobacter radioresistens, and Klebsiella michiganensis to create a novel compound bacterial agent known as SSF-1. The efficacy of SSF-1 in treating real pig farm wastewater was assessed, focusing on its impact on nitrogen transformation, the structure of bacterial communities, and functional genes. SSF-1 demonstrated stable ammonia nitrogen conversion under both weakly acidic and weakly alkaline conditions, exhibiting superior environmental adaptability compared to individual strains. Under optimal conditions, the ammonia nitrogen conversion rate in simulated wastewater reached 98.4 ± 0.2 %. Furthermore, SSF-1 was found to synergistically treat wastewater with functional bacteria in the sludge. Metagenomic analysis revealed that SSF-1 enhanced nitrogen transformation and the reduction of nitrate/nitrite by upregulating key nitrogen metabolism genes. This discovery expands the application potential of compound bacterial agent in actual environments and contributes to the sustainable utilization of water resources.}, }
@article {pmid40889349, year = {2025}, author = {Moraitou, M and Richards, JL and Bolyos, C and Saliari, K and Gilissen, E and Timmons, Z and Kitchener, AC and Pauwels, OSG and Sabin, R and Kokkini, P and Portela Miguez, R and Guschanski, K}, title = {Host Traits Impact the Outcome of Metagenomic Library Preparation From Dental Calculus Samples Across Diverse Mammals.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e70039}, doi = {10.1111/1755-0998.70039}, pmid = {40889349}, issn = {1755-0998}, support = {2019-00275//Svenska Forskningsr&#xe5;det Formas/ ; }, abstract = {Dental calculus metagenomics has emerged as a valuable tool for studying the oral microbiomes of humans and a few select mammals. With increasing interest in wild animal microbiomes, it is important to understand how widely this material can be used across the mammalian tree of life, refine the related protocols and understand the expected outcomes and potential challenges of dental calculus sample processing. In this study, we significantly expand the breadth of studied host species, analysing laboratory and bioinformatics metadata of dental calculus samples from 32 ecologically and phylogenetically diverse mammals. Although we confirm the presence of an oral microbiome signature in the metagenomes of all studied mammals, the fraction recognised as oral varies between host species, possibly because of both biological differences and methodological biases. The overall success rate of dental calculus processing, from extractions to sequencing, was ~74%. Although input sample weight was positively associated with the number of produced library molecules, we identify a negative impact of enzymatic inhibition on the library preparation protocol. The inhibition was most prevalent in herbivores and frugivores and is likely diet-derived. In contrast, hosts with an animalivore diet posed fewer challenges during laboratory processing and yielded more DNA relative to sample weight. Our results translate into recommendations for future studies of dental calculus metagenomics from a variety of host species, identifying required sample amounts, and emphasising the utility of dental calculus in exploring the oral microbiome in relation to broader ecological and evolutionary questions.}, }
@article {pmid40889140, year = {2025}, author = {Elton, L and Mateos, AD and Frosini, SM and Jepson, R and Rofael, S and McHugh, TD and Wey, EQ}, title = {A metagenomic approach to One Health surveillance of antimicrobial resistance in a UK veterinary centre.}, journal = {Microbial genomics}, volume = {11}, number = {9}, pages = {}, pmid = {40889140}, issn = {2057-5858}, mesh = {Animals ; *Metagenomics/methods ; One Health ; *Drug Resistance, Bacterial/genetics ; Dogs ; Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects/isolation &amp; purification/classification ; Plasmids/genetics ; Hospitals, Animal ; Microbial Sensitivity Tests ; United Kingdom ; Humans ; London ; }, abstract = {There are currently no standardized guidelines for genomic surveillance of One Health antimicrobial resistance (AMR). This project aimed to utilize metagenomics to identify AMR genes present in a companion animal hospital and compare these with phenotypic results from bacterial isolates from clinical specimens from the same veterinary hospital. Samples were collected from sites within a primary care companion animal veterinary hospital in London, UK. Metagenomic DNA was sequenced using Oxford Nanopore Technologies MinION. The sequencing data were analysed for AMR genes, plasmids and clinically relevant pathogen species. These data were compared to phenotypic speciation and antibiotic susceptibility tests of bacterial isolates from patients. The most common resistance genes identified were aph (n=101 times genes were detected across 48 metagenomic samples), sul (84), bla CARB (63), tet (58) and bla TEM (46). In clinical isolates, a high proportion of isolates were phenotypically resistant to β-lactams. Rooms with the greatest mean number of resistance genes identified per swab site were the medical preparation room, dog ward and surgical preparation room. Twenty-four and four plasmids typically associated with Gram-positive and Enterobacteriaceae, respectively, were identified. Sequencing reads matched with 14 out of 22 (64%) of the phenotypically isolated bacterial species. Metagenomics identified AMR genes, plasmids and species of relevance to human and animal medicine. Communal animal-handling areas harboured more AMR genes than areas animals did not frequent. When considering infection prevention and control measures, adherence to, and frequency of, cleaning schedules, alongside potentially more comprehensive disinfection of animal-handling areas, may reduce the number of potentially harmful bacteria present.}, }
@article {pmid40888959, year = {2025}, author = {Rajan, RJ and Sathyanathan, R and Rajnish, KN}, title = {Metabarcoding-Based Seasonal Assessment of Airborne Microbial Communities in PM10 Samples from a Semi-Urban Region in Tamil Nadu, India.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {9}, pages = {1069}, pmid = {40888959}, issn = {1573-2959}, mesh = {India ; *Air Microbiology ; Seasons ; *Environmental Monitoring/methods ; *Microbiota ; *Air Pollutants/analysis ; *Particulate Matter/analysis ; Bacteria/classification/genetics ; DNA Barcoding, Taxonomic ; Air Pollution/statistics &amp; numerical data ; }, abstract = {Airborne microbial communities show marked seasonal variability, with implications for both environmental processes and public health. In this study, metagenomic sequencing was applied to characterize airborne microbiota across four distinct seasons in India-winter (Sw), summer (Ss), southwest monsoon (Ssw), and northeast monsoon (Sne). Distinct shifts in dominant bacterial taxa were observed. Sne was dominated by Pseudomonas (42.3%) alongside sulfur-oxidizing Thiobacillus and Stenotrophomonas, likely influenced by lower temperatures and anthropogenic inputs. In Ss, Thiobacillus (72.9%) prevailed, followed by Pseudomonas (8.06%) and Sphingosinicella (6.68%), reflecting adaptation to arid, UV-intense conditions. Ssw featured Thiobacillus (58%) and Pseudomonas (18.5%) with additional plant-associated Lactobacillus and Clostridium, suggesting enhanced biogenic emissions. Sw was distinct for Enterococcus (21.9%) dominance and reduced Thiobacillus (16.2%), associated with high humidity and precipitation. Species richness followed the order Ssw > Sw > Ss > Sne, with the highest diversity during Ssw and Sw as indicated by Chao1, Fisher, Shannon, and Simpson indices. Kruskal-Wallis tests revealed no statistically significant differences in alpha diversity across seasons. Canonical Correspondence Analysis (CCA) highlighted strong seasonal structuring linked to environmental parameters such as temperature, humidity, and UV exposure. Dendrogram clustering showed greatest dissimilarity between Sne and Sw, while Ss and Ssw formed a closely related group. Ordination analyses (PCA, PCoA, NMDS) further confirmed seasonal distinctions. Seasonal variations in dominant bacterial taxa indicate potential public health risks in semi-urban tropical environments. Thiobacillus, prevalent in summer and the southwest monsoon, is generally non-pathogenic. In contrast, Pseudomonas species, abundant during the northeast monsoon and winter, are metabolically versatile, encompassing environmental strains and opportunistic pathogens known to cause respiratory and wound infections, especially in immunocompromised individuals. Winter also saw the presence of Enterococcus faecalis, a gut commensal and opportunistic pathogen linked to hospital-acquired infections and notable for multi-drug resistance. These seasonal shifts highlight varying exposure risks, emphasizing the need for public health attention to airborne microbial dynamics across different seasons.}, }
@article {pmid40888850, year = {2025}, author = {Chasapi, MN and Chasapi, IN and Aplakidou, E and Baltoumas, FA and Karatzas, E and Iliopoulos, I and Stravopodis, DJ and Emiris, IZ and Buluç, A and Georgakopoulos-Soares, I and Kyrpides, NC and Pavlopoulos, GA}, title = {metagRoot: a comprehensive database of protein families associated with plant root microbiomes.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkaf862}, pmid = {40888850}, issn = {1362-4962}, support = {23592//Hellenic Foundation for Research and Innovation/ ; //European Union's Horizon 2020/ ; 945405//Marie Sk&#x142;odowska-Curie/ ; //Penn State College of Medicine/ ; //Huck Innovative and Transformational Seed/ ; //Huck Institutes of the Life Sciences/ ; 16718-PRPFOR//Hellenic Foundation for Research and Innovation/ ; TAEDR-0539180//Hellenic Foundation for Research and Innovation/ ; DE-AC02-05CH11231//U.S. Department of Energy Office of Science/ ; //Nikos Kyrpides JGI-LBNL/ ; }, abstract = {The plant root microbiome is vital in plant health, nutrient uptake, and environmental resilience. To explore and harness this diversity, we present metagRoot, a specialized and enriched database focused on the protein families of the plant root microbiome. MetagRoot integrates metagenomic, metatranscriptomic, and reference genome-derived protein data to characterize 71 091 enriched protein families, each containing at least 100 sequences. These families are annotated with multiple sequence alignments, CRISPR elements, hidden Markov models, taxonomic and functional classifications, ecosystem and geolocation metadata, and predicted 3D structures using AlphaFold2. MetagRoot is a powerful tool for decoding the molecular landscape of root-associated microbial communities and advancing microbiome-informed agricultural practices by enriching protein family information with ecological and structural context. The database is available at https://pavlopoulos-lab.org/metagroot/ or https://www.metagroot.org.}, }
@article {pmid40888678, year = {2025}, author = {Zhou, R and Ng, SK and Sung, JJY and Wong, SH and Goh, WWB}, title = {Detecting and mitigating doppelgänger bias in microbiome data: impacts on machine learning and disease classification.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2554196}, doi = {10.1080/19490976.2025.2554196}, pmid = {40888678}, issn = {1949-0984}, mesh = {Humans ; *Machine Learning ; Clostridium Infections/microbiology ; Colorectal Neoplasms/microbiology ; Inflammatory Bowel Diseases/microbiology ; *Microbiota ; *Gastrointestinal Microbiome ; Metagenomics/methods ; Obesity/microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {Highly similar microbiome samples - so-called "doppelgänger pairs" - can distort analysis outcomes, yet are rarely addressed in microbiome studies. Here, we demonstrate that even a small proportion of such pairs (1-10% of samples) can substantially inflate machine learning performance across diverse disease cohorts including colorectal cancer (CRC), inflammatory bowel diseases (IBD), Clostridioides difficile infection (CDI), and obesity. Doppelgänger pairs also bias statistical tests and distort microbial network topology. In predictive models, classification accuracy was artificially boosted by 15-30% points across KNN, SVM, and Random Forest classifiers. In association testing, doppelgängers increased false-positive rates and decreased effect size stability; their removal reduced bootstrap variance by up to 28.3%. Moreover, the removal of doppelgängers yielded more stable networks. These effects were consistently observed across 16S, shotgun metagenomic, and simulated datasets. By accounting for highly similar samples, we reduce analytical noise and false discoveries, ultimately enabling more accurate and biologically meaningful microbiome insights.}, }
@article {pmid40888465, year = {2025}, author = {Li, Q and Wang, R and Zhou, X and Li, S and Zhang, S and Zhang, X and Wang, W and Jiao, J and Janssen, PH and Ungerfeld, EM and Müller, V and Conrad, R and Greening, C and Tan, Z and Fu, B and Wang, M}, title = {Metabolic versatility enables acetogens to colonize ruminants with diet-driven niche partitioning.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf183}, pmid = {40888465}, issn = {1751-7370}, abstract = {Enteric methane emissions are energy losses from farmed ruminants and contribute to global warming. Diverting electrons and H2 flow toward beneficial fermentation products would mitigate ruminal methane emissions while improving feed efficiency. Acetogens can direct H2 and electrons to acetate production via the Wood-Ljungdahl pathway, but methanogens have more competitive H2 affinities. Thus, it is unclear how acetogenesis subsists in the rumen. An analysis of 2102 globally derived rumen metagenomes from multiple ruminant species revealed that putative acetogens were phylogenetically diverse and capable of using carbohydrates or H2 as electron donors. The metabolic versatility of these acetogens may enable them to outcompete methanogens with lower versatility. Through animal trials, in vitro experiments, and DNA stable isotope probing, we verified the presence of diverse acetogens in beef cattle rumens and revealed that their niche partitioning is driven by contrasting fiber-rich and starch-rich diets. A fiber-rich diet enriched heterotrophic acetogens, which increased acetate formation while decreasing methane production. Overall, this study highlights the overlooked heterotrophy of acetogens in the rumen and their potential for mitigating enteric methane emissions.}, }
@article {pmid40886575, year = {2025}, author = {Agga, GE and Looft, T and Sistani, KR}, title = {Enrichment of soil microbiome and antimicrobial resistance genes following poultry litter application.}, journal = {The Science of the total environment}, volume = {999}, number = {}, pages = {180306}, doi = {10.1016/j.scitotenv.2025.180306}, pmid = {40886575}, issn = {1879-1026}, abstract = {Poultry litter (PL) is often used for soil amendment as an alternative to chemical fertilizers. However, it may enrich microbial and antimicrobial resistance genes in applied soil. The objective of this study was to investigate changes in the soil microbiome and resistome profiles following PL application. Three treatments untreated control (UC), chemical fertilizer (CF), and PL were applied to corn plots in a completely randomized block design. Total soil (metagenomic) DNA (n = 72) obtained on d0, d7, and d28 were shotgun sequenced. A composite DNA sample pooled from PL samples (n = 8) was sequenced for comparison. While Actinomycetota and Pseudomonadota were the most prevalent phyla among the soil samples, their abundance was significantly higher in the PL amended soils. PL soil amendment shifted microbial composition (Gammaproteobacteria and fungal Saccharomycetes were enriched in PL amended soils), diversity, and abundance by differentially enriching several microbial species, functional pathway genes, virulence factor genes, and antimicrobial resistance genes. Macrolides-lincosamides-streptogramin (MLS) resistance genes were the most abundant genes enriched in PL amended soils. The PL microbiome was primarily composed of the phylum Bacillota with Virgibacillus alimentarius being the most abundant species, followed by Staphylococcus nepalensis and S. simulans. The PL resistome was dominated by MLS resistance genes. Virulence factor genes associated with the genera Bacteriodes, Enterococcus and Staphylococcus were the most prevalent. The study clearly showed that PL application enriches soil microbiome and resistome, the mechanism of which is more likely through nutrient enrichment rather than their direct transfer since PL and PL-amended soils had different microbiome profiles.}, }
@article {pmid40886530, year = {2025}, author = {Miao, L and Ma, T and Qi, J and Deng, Y and Hong, Y and Gong, X and Zang, H and Cheng, Y and Li, C}, title = {Deciphering intrakingdom synergism in 17β-estradiol degradation through DNA-SIP coupled metagenomics: Metabolic cooperation and niche partitioning in bioaugmented soil microbiomes.}, journal = {Journal of hazardous materials}, volume = {497}, number = {}, pages = {139709}, doi = {10.1016/j.jhazmat.2025.139709}, pmid = {40886530}, issn = {1873-3336}, abstract = {17β-Estradiol (17β-E2), a persistent endocrine-disrupting compound, threatens ecosystem health through bioaccumulation. While bioaugmentation offers promise for environmental remediation, mechanistic insights into interspecies interactions between exogenous and indigenous degraders remain underexplored. Here, a synthetic microbial consortium (EL) was constructed by combining Rhodococcus erythropolis D310-1 and Microbacterium oxydans ML-6, which reduced the 17β-E2 degradation half-life by 53.65 % compared with that of the noninoculated control while suppressing the accumulation of the toxic intermediate estrone (E1). Temporal 16S rRNA gene amplicon sequencing profiling with co-occurrence network analysis revealed that the consortium EL dynamically reinforced ecological synergies with indigenous functional microbiota, accelerating contaminant mineralization. DNA-stable isotope probing (DNA-SIP) coupled with metagenomics identified Rhodanobacter, Mycobacterium, Rhodococcus, Sphingomonas, and Microbacterium spp. as active 17β-E2 assimilators. Furthermore, high-performance liquid chromatography coupled with quadrupole timeflight mass spectrometry (HPLCQTOFMS) was used to predict three complementary degradation pathways in the assembled genomes, revealing related functional enzymes and addressing functional partitioning between exogenous inoculants and indigenous degraders. Two novel gene clusters responsible for 17β-E2 biodegradation were evaluated. This study pioneers DNA-SIP and metagenomics to track [13]C-labelled 17β-E2 fate within bioaugmented soil microbiota, resolving intrakingdom bacteria collaborations that drive 17β-E2 biodegradation in soil. The identification of cross-consortium metabolic handoffs provides a blueprint for engineering syntrophic partnerships targeting steroidal estrogens (SEs) pollutants.}, }
@article {pmid40886152, year = {2025}, author = {Zemmel, ZM and Fan, X and Yu, Y and Markiewicz, E and Tsai, HM and Lu, L and Little, JC and Ramaswamy, R and Andrews, B and Claud, EC and Lu, J}, title = {Early-life gut microbiome maturity regulates blood-brain barrier and cognitive development.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2551879}, doi = {10.1080/19490976.2025.2551879}, pmid = {40886152}, issn = {1949-0984}, mesh = {*Gastrointestinal Microbiome/physiology ; Animals ; *Blood-Brain Barrier/metabolism/physiology/growth &amp; development ; Mice ; Female ; Humans ; *Cognition/physiology ; Pregnancy ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Mice, Inbred C57BL ; Brain/growth &amp; development/metabolism ; Male ; Germ-Free Life ; }, abstract = {The gut microbiome is an emerging factor in the neurobiology of disease. Blood-brain barrier (BBB) integrity is essential for proper brain function. However, the role the initial microbiome plays in BBB and brain development is unclear. In this study, we colonized germ-free pregnant mice with human full-term- or preterm-infant-derived gut microbiota, thereby establishing these communities in the resulting offspring. We discovered that mice harboring a full-term-associated microbiome exhibited stronger memory and learning capabilities and dramatically decreased early-life BBB permeability when compared to those with a prematurity-associated microbiome. Whole-brain single-cell RNA sequencing revealed downregulation of synaptic signaling genes in BBB cell types of mice with the prematurity-associated microbiome, indicating that microbiome maturity influences BBB transcriptional programs that support cognitive development. Comprehensive metagenomics and metabolomics uncovered bacterial populations and genomic pathways corresponding with decreased levels of circulating long-chain acylcarnitines and lysophosphatidylcholines in mice with the full-term-associated microbiome. Our findings highlight the microbiome as a therapeutic target for improving long-term neurodevelopmental outcomes due to its effect on the early-life BBB.}, }
@article {pmid40885910, year = {2025}, author = {Huang, W and Chai, Y and Li, X and Zhang, Q and Yan, Z and Wang, Y and Tao, X and Zhang, J and Qiu, F}, title = {Metagenomics and metabolomics to evaluate the potential role of gut microbiota and blood metabolites in patients with cerebral infarction.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {567}, pmid = {40885910}, issn = {1471-2180}, support = {2018YFA0108601//Clinical research on intracerebral precision transplantation of neural stem cells for stroke treatment/ ; L255012//The Huairou Innovation Joint Fund Project of Beijing Natural Science Foundation/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Cerebral Infarction/microbiology/blood/metabolism ; *Metabolomics/methods ; *Metagenomics/methods ; Male ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Middle Aged ; Female ; Aged ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Tandem Mass Spectrometry ; Adult ; Chromatography, High Pressure Liquid ; }, abstract = {Cerebral infarction, a cerebrovascular disorder, is characterized by the sudden onset of neurological deficits and clinical symptoms. It ranks among the leading causes of death and severe disability worldwide. The etiology of cerebral infarction is multifaceted, with common risk factors including dietary patterns, smoking, hypertension, and diabetes mellitus. In recent years, the role of the gut microbiota in systemic immunity and tumorigenesis has been intensively explored, thrusting the research on the gut-brain axis into the spotlight. However, there is a lack of literature investigating the relationship between the gut microbiota and blood metabolites in cerebral infarction. In this study, we employed 16S rRNA analysis and ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) for a comprehensive metagenomic and metabolomic analysis of fecal samples from cerebral infarction patients and the general population. Our results revealed a significant correlation between the gut microbiome and serum metabolites, highlighting the impact of the microbiome on metabolic pathways. Specifically, we found that 35 gut microbiome taxa, such as Actinobacteriota and Peptostreptococcales-Tissierellales, were significantly enriched in the control group (N group). Through Linear Discriminant Analysis Effect Size (LEfSe) analysis, 72 taxa showed significant differences between cerebral infarction patients and healthy individuals. Among them, 22 key taxa were identified as microbial biomarkers for differentiating patients from healthy controls. These findings suggest that variations in the microbiome and metabolites could potentially serve as biomarkers for future diagnostic and therapeutic strategies in cerebral infarction.}, }
@article {pmid40885737, year = {2025}, author = {Chatzigiannidou, I and Johansen, PL and Dehli, RK and Moll, JM and Eriksen, C and Myers, PN and Roager, HM and Yang, L and Stokholm, J and Sørensen, SJ and Krogfelt, KA and Laursen, MF and Trivedi, U and Scheynius, A and Kristiansen, K and Mie, A and Alm, J and Brix, S}, title = {Temporal dynamics and microbial interactions shaping the gut resistome in early infancy.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {8139}, pmid = {40885737}, issn = {2041-1723}, support = {2012-3011//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; 0171-00006B//Det Frie Forskningsr&#xe5;d (Danish Council for Independent Research)/ ; 4203-00005B//Innovationsfonden (Innovation Fund Denmark)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics/drug effects ; Infant ; Escherichia coli/genetics/drug effects/growth &amp; development ; Female ; Infant, Newborn ; Bifidobacterium/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; *Microbial Interactions/genetics ; *Drug Resistance, Bacterial/genetics ; Feces/microbiology ; Metagenomics ; Male ; }, abstract = {Despite the critical role of the gut resistome in spreading of antimicrobial resistance (AMR), strategies to reduce the abundance of antibiotic resistance genes (ARGs) during microbiota development in infancy remain underexplored. Using longitudinal quantitative metagenomic data, we here show that ARGs are present in the gut microbiota from the first week of life, with a peak in absolute ARG abundance and richness at 6 months. Delivery mode significantly affects early ARG dynamics, and vaginally delivered infants exhibit higher ARG abundance due to maternal transmission of Escherichia coli strains harbouring extensive resistance repertoires. The abundance of E. coli and other ARG-rich taxa inversely correlates with aromatic lactic acid-producing bifidobacteria, and aromatic lactic acids strongly inhibit the in vitro growth of E. coli and other opportunistic ARG-rich taxa. Our results highlight temporal and critical microbial interactions shaping the gut resistome in early infancy, pointing to potential interventions to curb AMR during this vulnerable developmental window by promoting colonization of aromatic lactic acid-producing bifidobacteria.}, }
@article {pmid40885534, year = {2025}, author = {Gagnon, DJ and Burkholder, KM and Weissman, AJ and Riker, RR and Ryzhov, S and May, TL and DiPalazzo, J and deKay, JT and Knudsen, L and Moore, MW and Pozzessere, NA and Weatherbee, M and Kelly, M and Nigatu, AS and Sevigny, JL and Simpson, S and Thomas, WK and Callaway, CW and Geller, BJ and Sawyer, DB and Seder, DB}, title = {Ceftriaxone to prevent early-onset pneumonia in comatose patients after out-of-hospital cardiac arrest: a pilot randomized controlled trial and resistome assessment (PROTECT).}, journal = {Chest}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chest.2025.08.007}, pmid = {40885534}, issn = {1931-3543}, abstract = {BACKGROUND: Antibiotic prophylaxis after out-of-hospital cardiac arrest (OHCA) reduces early-onset pneumonia, but has uncertain impact on mortality and non-infectious outcomes, with ongoing concerns about the subsequent development of antibiotic resistance.<br><br>RESEARCH QUESTION: Does prophylactic ceftriaxone reduce the incidence of early-onset pneumonia without increasing the acquisition of antibiotic resistance genes after OHCA?<br><br>STUDY DESIGN: and Methods: Comatose survivors of OHCA treated with targeted temperature management without a clinical diagnosis of pneumonia at admission were randomized to ceftriaxone 2 gm or matching placebo every 12 hours for three days. The primary outcome was early-onset pneumonia occurring &#x2264;4 days after intubation confirmed by blinded adjudicators. Abundance of antibiotic resistance genes recovered from rectal swabs before-and-after study drug administration were analyzed with metagenomic sequencing.<br><br>RESULTS: 411 subjects were screened, 53 (13%) were randomized, and one subject withdrew, leaving 26 in each group in the final analysis. Early-onset pneumonia was diagnosed in 10 (38%) subjects receiving ceftriaxone and 18 (69%) subjects receiving placebo (RR 0.57, 95% CI 0.21-1.001; p=0.05). Open-label antibiotics were administered to 14 (54%) subjects receiving ceftriaxone and 22 (85%) receiving placebo (RR 0.64, 95%CI 0.43-0.94), most of which were broad-spectrum (93% and 100%, respectively). After adjusting for differences in abundance of antibiotic resistance genes prior to study drug administration, subjects randomized to ceftriaxone acquired significantly fewer antibiotic resistance genes to frequently used antibiotics in the ICU compared to those randomized to placebo (IRR 0.30, 95% CI 0.13-0.70). Serious adverse drug effects were not reported in either treatment group.<br><br>INTERPRETATION: This trial was inconclusive regarding the impact of ceftriaxone prophylaxis to reduce the incidence of EOP after OHCA but ceftriaxone was associated with less frequent administration of open-label antibiotics, and reduced acquisition of ARGs to frequently used antibiotics in the ICU.<br><br>CLINICAL TRIAL REGISTRATION: National Library of Medicine at www.<br><br>CLINICALTRIALS: gov (NCT04999592).}, }
@article {pmid40885432, year = {2025}, author = {Kwon, M and Kwon, SH and Jang, H and Oh, H and Sun, S and Jung, C and Kil, EJ}, title = {Landscape-scale virome analysis uncovers endemic and emerging honey bee viruses in the Silk-Road hub of Uzbekistan.}, journal = {Journal of invertebrate pathology}, volume = {}, number = {}, pages = {108436}, doi = {10.1016/j.jip.2025.108436}, pmid = {40885432}, issn = {1096-0805}, abstract = {Honey bee health is increasingly threatened worldwide by a complex and evolving viral landscape; however, this aspect in Central Asia remains understudied despite the region being strategically positioned along historic and modern trade routes. In 2024, we conducted a nationwide virome survey of Apis mellifera across 32 cities in 11 regions of Uzbekistan, combining the metagenomic data of 14 pooled RNA-seq libraries with RT-PCR validation and phylogenetic analyses. High-quality sequencing yielded an average of approximately 60 million reads per pool. We recovered 30 viral species from 162 genomic sequences (131 complete sequences), including 11 honey bee-associated and 19 plant-infecting viruses. All samples harbored deformed wing virus type A (DWV-A), and co-infection with DWV-B predominated. Our findings provided the first full-length DWV-B genomes from Central Asia, revealing that it had > 97 % identity to European strains. New variants of the Sacbrood virus (partial sequence, approximately 4.7 kb) and Lake Sinai Virus UZB were also detected. The chronic bee paralysis virus was sequenced in full for the first time in Uzbekistan, and Varroa orthomyxovirus-1 exhibited segment-specific divergence. Additionally, we identified two novel plant viruses: Gulistan nepovirus 1 and Arpa carmo-like virus 1. Phylogenetic patterns of the identified viruses indicate that Uzbekistan serves as a genetic corridor connecting European and Asian virus populations. These findings fill critical geographical gaps, underscore the need for transboundary surveillance, and provide a genomic baseline for future diagnostics, epidemiology, and control strategies aimed at safeguarding pollinator and ecosystem health.}, }
@article {pmid40885278, year = {2025}, author = {Bastón-Paz, N and Moreno-Blanco, A and Palacios, E and Olavarrieta, L and Galeano, J and Garriga, M and Máiz, L and Vicente-Santamaría, S and Oteo-Iglesias, J and López-Causapé, C and Fuentes, I and Oliver, A and Cantón, R and Del Campo, R and de Dios-Caballero, J}, title = {Exploring the Complexities of Intestinal and Pulmonary Microbiota in Cystic Fibrosis: A Multi-Omics Approach.}, journal = {Respiratory medicine}, volume = {}, number = {}, pages = {108331}, doi = {10.1016/j.rmed.2025.108331}, pmid = {40885278}, issn = {1532-3064}, abstract = {BACKGROUND: We aimed to elucidate the cystic fibrosis (CF) microbiota composition (shotgun metagenomics) and functionality (short-chain fatty acids, SCFAs).<br><br>METHODS: Fecal and sputum samples were recruited from 39 clinically stable CF subjects.<br><br>RESULTS: Bacillota and Pseudomonadota were dominant in both gut and lung compartments, whereas Ascomycota were the most abundant fungi in feces, and Basidiomycota, especially Malassezia globosa, in sputum. Viruses accounted for 0.4% of the relative abundance in the gut and 0.6% in lungs. Mycobacteroides abscessus was genetically identified in 10 individuals, although only 2 had positive cultures. Patients with higher levels of Pseudomonas filamentous phages had negative cultures for P. aeruginosa. The protozoan Toxoplasma gondii was detected in all sputum samples, accounting for 0.25% of the metagenomic reads, with further PCR-confirmation in 50% of subjects, including children. No correlation was found between SCFA and lung function or microbial composition. The resistome of the fecal compartment was higher than that of the lungs, and a greater abundance of SCFAs in the intestine was associated with poorer lung function.<br><br>CONCLUSIONS: Patients with normal-mild lung function had higher alpha diversity in the respiratory microbiota; however, beta diversity in the stool was statistically different compared with the group with poorer lung function. Although there were no differences in SCFA concentrations, butyrate-producing bacteria were more abundant in the sputum of the group with better lung function. In fecal samples, resistome to tetracyclines, glycopeptides, and aminoglycosides predominated, whereas in sputum an enrichment of ARGs related to tetracyclines, beta-lactams, and macrolides was observed.}, }
@article {pmid40885069, year = {2025}, author = {Li, B and Feng, L and Zhang, J and Giannakis, S}, title = {PFOA and a dash of aluminum: The perfect recipe for growing drug-resistant biofilms in urban water supply.}, journal = {Journal of hazardous materials}, volume = {497}, number = {}, pages = {139660}, doi = {10.1016/j.jhazmat.2025.139660}, pmid = {40885069}, issn = {1873-3336}, abstract = {This study investigated the impact of perfluorooctanoic acid (PFOA) and aluminum (Al(III)) on the proliferation of drug-resistant pathogenic bacteria in drinking water distribution system (DWDS) biofilms, and their combined effect. Experimental simulations of stagnant residential water conditions, analyzed via comprehensive metagenomics, revealed a significant increase in bacterial biomass, extracellular polymeric substances (EPS), and the abundance of pathogenic bacteria and antibiotic resistance genes (ARGs). Biofilm formation was markedly enhanced in the presence of PFOA and Al(III), creating protective niches that facilitated the proliferation of pathogenic bacteria and ARGs. Key observations included increases in Legionella pneumophila and Pseudomonas aeruginosa, along with a shift in ARG profiles towards antibiotic efflux and target protection mechanisms. Critically, this study identified the presence and dynamics of priority drug-resistant pathogens within these biofilms, providing essential insights into pollutant-influenced risks and transmission pathways. These findings highlight the significant public health implications of PFOA and Al(III) co-contamination in drinking water systems.}, }
@article {pmid40885659, year = {2025}, author = {Klier, KM and Anantharaman, K}, title = {An updated view of metabolic handoffs in microbiomes.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2025.07.009}, pmid = {40885659}, issn = {1878-4380}, abstract = {From the human gut to the deep ocean, diverse microbial communities underpin essential ecosystem processes. Limited understanding of the dynamics and interactions that shape these communities, however, constrains efforts to culture, investigate, and harness their potential. Further, these knowledge gaps restrict the ability to predict microbial responses to broader biodiversity declines and global change. Among the numerous types of microbial interactions, metabolite exchanges, or 'metabolic handoffs', are a well-documented phenomenon. Recent methodological advances have uncovered a broader spectrum of metabolic handoffs than previously appreciated. Varying in both mechanism and ecological role, metabolic handoffs influence diverse natural environments. In this review, we define two major types of metabolic handoffs, examine their potential drivers and benefits, and highlight emerging research that underscores their widespread occurrence and importance in complex microbial ecosystems.}, }
@article {pmid40885195, year = {2025}, author = {Grujcic, V and Mehrshad, M and Vigil-Stenman, T and Lundin, D and Foster, RA}, title = {Stepwise genome evolution from a facultative symbiont to an endosymbiont in the N2-fixing diatom-Richelia symbioses.}, journal = {Current biology : CB}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cub.2025.08.003}, pmid = {40885195}, issn = {1879-0445}, abstract = {A few genera of diatoms that form stable partnerships with N2-fixing filamentous cyanobacteria Richelia spp. are widespread in the open ocean. A unique feature of the diatom-Richelia symbioses is the symbiont cellular location spans a continuum of integration (epibiont, periplasmic, and endobiont) that is reflected in the symbiont genome size and content. In this study, we analyzed genomes derived from cultures and environmental metagenome-assembled genomes of Richelia symbionts, focusing on characters indicative of genome evolution. Our results show an enrichment of short-length transposases and pseudogenes in the periplasmic symbiont genomes, suggesting an active and transitionary period in genome evolution. By contrast, genomes of endobionts exhibited fewer transposases and pseudogenes, reflecting advanced stages of genome reduction. Pangenome analyses identified that endobionts streamline their genomes and retain most genes in the core genome, whereas periplasmic symbionts and epibionts maintain larger flexible genomes, indicating higher genomic plasticity compared with the genomes of endobionts. Functional gene comparisons with other N2-fixing cyanobacteria revealed that Richelia endobionts have similar patterns of metabolic loss but are distinguished by the absence of specific pathways (e.g., cytochrome bd ubiquinol oxidase and lipid A) that increase both dependency and direct interactions with their respective hosts. In conclusion, our findings underscore the dynamic nature of genome reduction in N2-fixing cyanobacterial symbionts and demonstrate the diatom-Richelia symbioses as a valuable and rare model to study genome evolution in the transitional stages from a free-living facultative symbiont to a host-dependent endobiont.}, }
@article {pmid40884577, year = {2025}, author = {Kumar, V and Sandil, S and Verma, P and Ameen, F}, title = {Decoding microbial ecology and functions: metagenomic profiling of activated sludge contaminated with chlorolignin compounds in a pulp-paper mill treatment system.}, journal = {Archives of microbiology}, volume = {207}, number = {10}, pages = {247}, pmid = {40884577}, issn = {1432-072X}, support = {ORF-2025-364//The authors extend their appreciation to the ongoing research funding program, (ORF-2025-364), King Saud University, Riyadh, Saudi Arabia./ ; }, mesh = {*Sewage/microbiology/chemistry ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism ; Metagenomics ; *Water Pollutants, Chemical/analysis ; Microbiota ; Metals, Heavy/analysis ; Industrial Waste/analysis ; }, abstract = {This study aimed to profile the dynamics of indigenous bacterial communities in activated sludge, assess the pollutant load, and unlock the functional genes involved during the activated sludge treatment process. The physicochemical analyses of activated sludge revealed high amounts of phosphate, sulfate, chloride, and lignin, along with heavy metals like Fe, Zn, Cu, Ni, and Pb. Simultaneously, the GC-MS/MS technique identified decane, 1 bromo-2-methyl, pentadecanoic acid, methyl ester, benzene dicarboxylic acid, stigmasterol, borinic acid, diethyl, 2-hydroxymethyl cyclopropane, 2-methoxy-4-ethyl-phenol, 3,4,5-trichlorophenol, octadecanoic acid, and tetracosanic acid as major compounds. Furthermore, taxonomic classification of operational taxonomic unit (OTU) data revealed that Proteobacteria was the most abundant phylum, comprising 44.54% of the microbial community. In addition, other phyla, such as Bacteriodetes, Acidobacteria, Planctomycetes, Chlorolfexi, Actinobacteria, and Verrucomicrobia were also recorded within a range between 13.27 and 4.1% in the sludge. At the genus and species levels, the dominant organisms were unclassified (3.62%) and belonged to the family Rhodospirillacea. Further, PICRUSt2-based KEGG Orthology (KO) analysis showed enriched energy metabolism as the most abundant category, driven by oxidative phosphorylation and the TCA cycle. Furthermore, the MetaCyc analysis revealed a robust and adaptable microbial community with the dominant pathways of aerobic respiration I (cytochrome c) and fatty acid biosynthesis pathways, such as cis-vaccenate biosynthesis. The EC assignments highlighted a broad range of enzymatic functions, with a strong emphasis on oxidoreductases and transferases involved in energy production and biosynthesis. This research offers valuable insights into microbial community dynamics in wastewater treatment processes and identifies their functional role in a chlorolignin waste-polluted environment.}, }
@article {pmid40883892, year = {2025}, author = {Kanaan, G and Deming, JW}, title = {Multiple roles of DNA methylation in sea-ice bacterial communities and associated viruses.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf198}, pmid = {40883892}, issn = {1751-7370}, abstract = {Despite growing evidence for the role of DNA methylation in bacterial acclimation to environmental stress, this epigenetic mechanism remains unexplored in sea-ice microbial communities known to tolerate multiple stressors. This study presents a first analysis of DNA methylation patterns in bacterial communities and associated viruses across the vertical thickness of sea ice. Using a novel stepped-sackhole method, we collected sea-ice brines from distinct horizons of an Arctic ice floe, capturing microbial communities that had been exposed to different environmental conditions. Through Oxford Nanopore sequencing, we characterized methylation patterns in bacterial and associated viral DNA, analysing for methylation motifs and differences between ice horizons. We identified 22 unique bacterial methylation motifs and 27 viral motifs across three nucleotide methylation types (5mC, 6mA, and 4mC), with evidence of differential methylation between upper and lower ice. Analysis of metagenome-assembled genomes revealed the regulatory potential of methylation in both ice-adapted (Psychromonas and Polaribacter) and non-adapted bacteria (Pelagibacter); e.g., in Pelagibacter, differential methylation of the GANTC motif between upper and lower ice affected genes involved in core cellular processes. Viral methylation patterns showed evidence of recent infection. We also identified orphan methyltransferases in sea-ice phages, suggesting a mechanism for bypassing host restriction-modification systems and regulating host genes. Our findings reveal that DNA methylation serves functions in sea ice beyond traditional restriction-modification systems that protect against foreign DNA, opening new avenues for research on the role of epigenetic mechanisms not only in acclimation to the cryosphere but also more generally in microbial ecology and evolution.}, }
@article {pmid40883783, year = {2025}, author = {Lei, H and Du, S and Tong, X and Chan, WL and Leung, MHY and Bøifot, KO and Bezdan, D and Butler, DJ and Danko, DC and Green, DC and Hernandez, MT and Kelly, FJ and Lucaci, AG and Meydan, C and Nieto-Caballero, M and Ryon, K and Tierney, B and Udekwu, KI and Young, BG and Mason, CE and Dybwad, M and Lee, PKH}, title = {Global biogeography of airborne viruses in public transit systems and their host interactions.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {193}, pmid = {40883783}, issn = {2049-2618}, support = {SLL 20160933//Stockholm Health Authority/ ; R01AI151059 and U01DA053941//Igor Tulchinsky and the WorldQuant Foundation, US National Institutes of Health/ ; OPP1151054//Bill and Melinda Gates Foundation/ ; R1016-20F//Research Impact Fund, Hong Kong Research Grants Council/ ; 11214721 and 11206224//General Research Fund, Hong Kong Research Grants Council/ ; }, mesh = {*Viruses/genetics/classification/isolation &amp; purification ; *Air Microbiology ; Metagenomics/methods ; Genome, Viral ; Metagenome ; CRISPR-Cas Systems ; *Host Microbial Interactions/genetics ; Humans ; Phylogeography ; Cities ; }, abstract = {BACKGROUND: There is a diverse assemblage of microbes in air in built environments (BEs), but our understanding of viruses and their interactions with hosts in BEs remains incomplete. To address this knowledge gap, this study analyzed 503 metagenomes isolated from air samples from public transit systems in six global cities, namely Denver, Hong Kong, London, New York City, Oslo, and Stockholm. Viral genomes were recovered from samples via metagenomic binning, and viruses' taxonomy, functional potential, and microbial hosts were determined. The study also investigated correlations between virus and host abundances, the coevolution of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems and anti-CRISPR (Acr) proteins, and the potential impacts of auxiliary metabolic genes (AMGs) on hosts.<br><br>RESULTS: Airborne viruses in global BEs exhibited biogeographical variations in diversity, composition, function, and virus-host interactions. Nearly half of the vOTUs analyzed were from the Caulimoviridae family, while 31.8% of them could not be taxonomically classified. Diverse functions were identified within the vOTUs, together with antimicrobial resistance genes with the potential to confer resistance to various antibiotics and antimicrobial agents. Strong correlations were observed between vOTU and host abundances, with clear distinctions between virulent and temperate viruses. However, there was limited co-evolution of CRISPR-Cas systems and Acr proteins, which was likely due to the oligotrophic and physical conditions in the BEs and the dominance of vOTUs with a virulent lifestyle. Phage-encoded AMGs appeared to have the potential to enhance host fitness. These findings highlight biogeographical variations in airborne viruses in BEs and that physical and oligotrophic conditions in BEs drive virus survival strategies and virus-host coevolution.<br><br>CONCLUSION: There are biogeographical variations in airborne viruses in BEs in global cities, as physical and oligotrophic conditions in BEs drive virus survival strategies and virus-host coevolution. Moreover, the characteristics of airborne viruses in BEs are distinct from those of viruses found in other, more nutrient-rich ecosystems. Video Abstract.}, }
@article {pmid40883605, year = {2025}, author = {Yi, H and Lu, X and Chang, Q}, title = {MetaKSSD: boosting the scalability of the reference taxonomic marker database and the performance of metagenomic profiling using sketch operations.}, journal = {Nature computational science}, volume = {}, number = {}, pages = {}, doi = {10.1038/s43588-025-00855-0}, pmid = {40883605}, issn = {2662-8457}, abstract = {The performance of metagenomic profiling is constrained by the diversity of taxa present in the reference taxonomic marker database (MarkerDB) used. However, continually updating MarkerDB to include newly determined taxa using existing approaches faces increasing difficulties and will soon become impractical. Here we introduce MetaKSSD, which redefines MarkerDB construction and metagenomic profiling using sketch operations, enhancing MarkerDB scalability and profiling performance. MetaKSSD encompasses 85,202 species in its MarkerDB using just 0.17 GB of storage and profiles 10 GB of data within seconds. Leveraging its comprehensive MarkerDB, MetaKSSD substantially improves profiling results. In a microbiome-phenotype association study, MetaKSSD identified more effective associations than MetaPhlAn4. We profiled 382,016 metagenomic runs using MetaKSSD, conducted extensive sample clustering analyses and suggested potential yet-to-be-discovered niches. MetaKSSD offers functionality for instantaneous searching of similar profiles. It enables the swift transmission of metagenome sketches over the network and real-time online metagenomic analysis, facilitating use by non-expert users.}, }
@article {pmid40883585, year = {2025}, author = {Banerjee, A and Samanta, MK and Kanwar, M and Maiti, S and Mondal, KC and Thatoi, H and Das Mohapatra, PK}, title = {Characterization and Evolutionary Study of Fungal Nitrate Reductase Through Bioinformatics and Partial Gene Amplification from Aspergillus niger PKA16 employing Degenerate Primers.}, journal = {The protein journal}, volume = {}, number = {}, pages = {}, pmid = {40883585}, issn = {1875-8355}, support = {F.11-114/2008(BSR)//University Grants Commission/ ; }, abstract = {Nitrate contamination in water sources creates major health risks that primarily affect infants by causing methemoglobinemia ("blue baby syndrome") while also leading to congenital defects and cancer development. The human body absorbs nitrates mainly through drinking contaminated water. Enzyme nitrate reductase (NR) produced by microorganisms, functions as a key factor in nitrate detoxification. A partial NR gene (GenBank accession: MN833805) from Aspergillus niger PKA16 (KY907172.1) was amplified by employing degenerate primers in this research. The primer sequences were designed based on conserved protein motifs and orthologous diversity analysis of 399 NR protein sequences spanning 127 fungal genera. The NR proteins exhibited an extensive range which demonstrated extensive intra- and interspecies diversity. The multiple conserved domains included nine motifs which remained consistent despite the observed sequence variability. Two highly conserved sequences RLTGKHPFN and PDHGYPLRLV were validated through degenerate-PCR which demonstrated their effectiveness for partial NR gene detection and amplification. In the present study, the developed degenerate primers enable researchers to detect and amplify NR genes from majority of known and unknown fungal strains including those identified through metagenomic studies also. This research establishes fundamental principles for using biotechnology to amplify bioremediatory enzyme nitrate reductase from fungal origin to clean up water and food that contains nitrates, to reduce the risk of 'blue baby' disease and cancer.}, }
@article {pmid40883484, year = {2025}, author = {Havenga, B and Jacobs, K}, title = {South African Myxococcota: an untapped resource for microbial ecolo gy and biotechnology.}, journal = {Applied microbiology and biotechnology}, volume = {109}, number = {1}, pages = {192}, pmid = {40883484}, issn = {1432-0614}, support = {PSTD23032387009//National Research Foundation/ ; }, mesh = {South Africa ; *Biotechnology/methods ; *Myxococcales/genetics/classification/metabolism/isolation &amp; purification ; Secondary Metabolism ; Metagenomics ; Metagenome ; Genome, Bacterial ; }, abstract = {An extraordinary multicellular life cycle, ecological versatility, and prolific production of bioactive secondary metabolites characterise the phylum Myxococcota. While research has predominantly focused on Myxococcota in Asia, Europe, and North America, their potential occurrence in Sub-Saharan Africa remains largely unexplored. To date, only one study has isolated Myxococcota in South Africa, with additional findings limited to incidental detection through metagenomic studies. Considering South Africa's ecological diversity, its biomes may represent promising but under-examined environments for systematic bioprospecting aimed at discovering novel Myxococcota with ecological or biotechnological potential. The recent reclassification of Myxococcota from the former Deltaproteobacteria has provided a more coherent taxonomic framework to guide future ecological and systematic studies. This review presents an overview of the taxonomic revision and explores the potential occurrence of Myxococcota in South African biomes. It covers the challenges associated with conventional culture-based isolation methods and highlights potential genome- and metagenome-based approaches, including the use of metagenome-assembled genomes (MAGs) to identify cryptic biosynthetic gene clusters (BGCs), while acknowledging current limitations. Considering the increasing resistance to chemical fungicides in South African agriculture, this review further explores the potential of Myxococcota-derived secondary metabolites as candidate bioprotective alternatives. By identifying current research gaps, it aims to support future efforts towards systematic bioprospecting to investigate the ecological and biotechnological potential of Myxococcota in South Africa. KEY POINTS: • South African biomes may harbour novel Myxococcota with biosynthetic potential. • Genome mining could reveal cryptic biosynthetic gene clusters (BGCs). • Myxococcota metabolites may help control resistant fungal phytopathogens.}, }
@article {pmid40883419, year = {2025}, author = {Oh, J and Voigt, AY}, title = {Author Correction: The human skin microbiome: from metagenomes to therapeutics.}, journal = {Nature reviews. Microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41579-025-01238-y}, pmid = {40883419}, issn = {1740-1534}, }
@article {pmid40883413, year = {2025}, author = {Manzoor, M and Pussinen, PJ and Saarela, RKT and Hiltunen, K and Mäntylä, P}, title = {Metagenomic analysis of the denture-associated oral microbiome in patients with denture stomatitis.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {31913}, pmid = {40883413}, issn = {2045-2322}, support = {1340750//Research Council of Finland/ ; }, mesh = {Humans ; Female ; Male ; *Stomatitis, Denture/microbiology ; *Metagenomics/methods ; *Microbiota/genetics ; Aged, 80 and over ; Aged ; *Mouth/microbiology ; Dysbiosis/microbiology ; *Dentures/microbiology ; Metagenome ; Bacteria/genetics/classification ; }, abstract = {Denture stomatitis (DS) is an inflammatory condition that affect denture wearers and is characterized by erythema of the mucosa opposing the denture. DS is often associated with oral microbiome dysbiosis. We used shotgun metagenomics to investigate the association between the denture-associated oral microbiome (DAOM) and DS in older adults living in long-term care facilities. We included participants with DS (n = 28) and age-and sex-matched removable denture wearers without signs of DS (n = 28). Clinical oral examinations were performed, and demographic and medical data were obtained from medical records. Median (interquartile range) age of participants was 88 (9) years; 75% were females. Beta diversity differed between the DS and non-DS groups (Bray-Curtis dissimilarity, p = 0.01; Jaccard index, p = 0.004). Two phyla, nine genera, and 15 species differed significantly between groups, with the genera Candida and Scardovia, and species Candida albicans, Aggregatibacter actinomycetemcomitans, and Scardovia inopinata being enriched in DS. Network analysis revealed strongly interconnected microbial communities and more prominent bacterial-fungal co-occurrence in DS than in non-DS. These findings indicate that DS is associated with significant alterations in the DAOM, which may contribute to inflammation. Microbiome-targeted strategies are needed for the management of DS.}, }
@article {pmid40883363, year = {2025}, author = {Xiong, X and Liu, S and Huang, J and Feng, L and Liu, W}, title = {236 metagenome-assembled microbial genomes from rivers along a latitudinal gradient.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1516}, pmid = {40883363}, issn = {2052-4463}, support = {U24A20641//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32401363//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2023M733714//China Postdoctoral Science Foundation/ ; 2025AFB983//Natural Science Foundation of Hubei Province (Hubei Provincial Natural Science Foundation)/ ; }, mesh = {*Metagenome ; *Rivers/microbiology ; China ; Bacteria/genetics/classification ; Archaea/genetics ; Soil Microbiology ; Wetlands ; *Genome, Microbial ; }, abstract = {Rivers are dynamic ecosystems that play a crucial role in supporting microbial diversity and sustaining a wide range of ecological functions. Here, we used metagenomic sequencing datasets of channel sediments, riparian bulk soils, and riparian rhizosphere soils to construct metagenome-assembled genomes (MAGs) from 30 river wetlands along a latitudinal gradient in China. We identified 236 MAGs with completeness ≥ 50% and contamination ≤ 10%, including 225 bacteria and 11 archaea. Among these, 24.2% showed a completeness of 80% or higher. The dominant taxa were assigned to Pseudomonadota (78 MAGs), Actinomycetota (47 MAGs), and Bacteroidota (29 MAGs), which were particularly prevalent in riparian soils. These draft genomes provide valuable insights into microbial diversity and biogeochemical potential in river wetlands, enhancing our understanding of how microorganisms have evolved to adapt to the complex environments of rivers and latitudinal variation.}, }
@article {pmid40883308, year = {2025}, author = {Chen, T and Xiong, Y and Zhang, J and Zhang, Q and Wu, J and Xu, N and Liu, T}, title = {Temporal dynamics, microdiversity, and ecological functions of viral communities during cyanobacterial blooms in Lake Taihu.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {178}, pmid = {40883308}, issn = {2055-5008}, support = {20220808011114001//Shenzhen Natural Science Fund/ ; }, mesh = {*Lakes/microbiology/virology ; *Cyanobacteria/virology/growth &amp; development ; *Viruses/classification/genetics/isolation &amp; purification ; Metagenomics ; China ; Biodiversity ; Eutrophication ; *Harmful Algal Bloom ; *Virome ; }, abstract = {Harmful cyanobacterial blooms pose severe threats to aquatic ecosystems. Bloom-forming cyanobacteria form cyanobacterial aggregates (CAs) that create a phycosphere supporting diverse microbial interactions. Here, longitudinal metagenomics and metatranscriptomics were employed to explore the temporal variation of CA-attached viral communities throughout cyanobacterial blooms in Lake Taihu. Viral communities, represented by 5613 viral operational taxonomic units, showed increased relative abundance (RPKM) with the expansion of bloom areas. Among 1791 virus‒host linkages, host shifts followed the succession of two dominant cyanobacterial genera, Microcystis and Dolichospermum. Viruses demonstrated high virus‒host abundance ratios within all host genera and showed elevated transcriptional activities infecting Dolichospermum during the late bloom stage. Viruses featured high microdiversity and positively selected replication-associated genes in response to abundant host genera and variable trophic status. This study uncovered diverse active viral auxiliary metabolism associated with photosynthesis, biochemical cycling, and DNA biosynthesis, and highlighted the significant role of phycosphere-associated viruses during cyanobacterial blooms.}, }
@article {pmid40883297, year = {2025}, author = {Chen, XP and Zhu, D and Liu, SY and Sun, MM and Ye, M and Wang, L and Lin, D and Zhang, TL and Rillig, MC and Zhu, YG}, title = {Unique plastisphere viromes with habitat-dependent potential for modulating global methane cycle.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {8098}, pmid = {40883297}, issn = {2041-1723}, support = {42021005//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Methane/metabolism ; *Microbiota/genetics ; *Ecosystem ; *Virome/genetics ; Metagenomics/methods ; Soil Microbiology ; Bacteria/metabolism/genetics/virology ; }, abstract = {Plastispheres, novel niches in the Anthropocene, harbor microbial communities with unique functional signatures. As the most abundant biological entity on Earth, viruses are key regulators of microbial community composition and metabolism. However, little is known about viral communities and their functions in the plastisphere. Here, we investigate the composition and functional profile of plastisphere viral communities through microcosm experiments combined with global plastisphere metagenomics data. We find that the plastisphere recruits a distinct viral community with 86.9% novel viral operational taxonomic units compared to control substrates. The plastisphere viral community modulates host methane metabolism through auxiliary metabolic genes and distinctive interactions with hosts. These auxiliary metabolic genes for methane cycling are prevalent in global plastisphere viral communities. Notably, the plastisphere microbiome adopts the life history strategy of copiotrophs in the nutrient-poor water environment, making the water plastisphere a potential hot spot for methane emission compared to the soil plastisphere. Our phage transplantation experiments reveal that lysogenic viruses significantly contribute to enhancing the methanogenic capacity of microorganisms and promoting methane emission of the water plastisphere. Overall, we decipher the role of viruses in the plastisphere and reinforce the necessity of incorporating viral contributions when assessing the effects of plastisphere communities on global biogeochemical cycles.}, }
@article {pmid40882798, year = {2025}, author = {Fu, Q and Yuan, B and Wang, XY and Luo, S and Zhang, XH and Zhang, MY}, title = {Behavioural response and physiological adaptation of captive sub-adult giant pandas in response to a short-term social environment.}, journal = {Physiology &amp; behavior}, volume = {}, number = {}, pages = {115077}, doi = {10.1016/j.physbeh.2025.115077}, pmid = {40882798}, issn = {1873-507X}, abstract = {During ex-situ conservation, giant pandas inevitably transition from their natural wild habitats to captive environments. The living conditions of captive giant pandas differ significantly from those in the wild. For instance, during the sub-adult stage, solitary giant pandas are human-reared in groups. What impact does the captive social environment have on solitary giant pandas? Does it lead to changes in behavioral expression patterns? Is this pattern associated with physiological responses for environmental adaptation? To address these questions, we allocated six giant pandas into a group-housed group and a solitary-housed group, with each group consisting of three pandas. By observing their behaviors and performing analyses of urinary and fecal metabolomics, as well as metagenomics, we intended to explore the welfare status of the two groups under different management approaches. The results showed that group-housed sub-adult giant pandas exhibited significantly more playing behavior compared to those in solitary conditions. Further analysis revealed that the majority of the playing behavior involved playful interactions with companions. Additionally, we did not observe stereotyped behaviors in group-housed giant pandas. Through an exploration of the omics data, it was found that urinary metabolites associated with positive emotions, such as dopamine, along with related metabolic pathways like the dopamine synthesis system, were significantly upregulated and activated in group-housed giant pandas. Meanwhile, fecal metabolites associated with neurotransmitter synthesis and mood regulations, as well as the abundance of beneficial intestinal flora, were significantly higher in the feces of the group-housed pandas than those of the solitary-housed group. These findings indicated that short-term group housing does have an impact on the behavioral expression patterns of captive sub-adult giant pandas. Moreover, compared with those housed individually, short-term sub-adult giant pandas kept in groups seem to experience less stress. This reveals the behavioral response and physiological adaption of captive sub-adult giant pandas to group living environments.}, }
@article {pmid40882788, year = {2025}, author = {Wu, J and Li, X and Huang, X and Zhu, Y and Yu, H and Xia, Y and Guo, S and Wang, X and Dong, T and Keung Tsim, KW and Zhu, Y}, title = {Kai-Xin-San, an ancient herbal mixture for anti-depression, mitigates the fluoxetine-induced gut dysbiosis and intestinal damage in chronic unpredictable mild stressed mice.}, journal = {Journal of ethnopharmacology}, volume = {}, number = {}, pages = {120484}, doi = {10.1016/j.jep.2025.120484}, pmid = {40882788}, issn = {1872-7573}, abstract = {The gut microbiome plays a crucial role in the pathology of depression. The intestinal dysbiosis associated with prolonged use of antidepressants, such as fluoxetine, can adversely affect the efficacy of these medications. Kai-Xin-San (KXS), a traditional Chinese herbal decoction, has been utilized to treat mental disorders with a long history in China. The modulation of the gut microbiome by KXS could underlie its antidepressant effect. In the context of combining with fluoxetine, KXS could potentially mitigate fluoxetine-associated intestinal side effects during depression treatment.<br><br>AIM OF THE STUDY: This study investigates the impact of KXS on the gut of depressive mice, with a particular emphasis on its potential to mitigate fluoxetine-induced intestinal side effects.<br><br>MATERIALS AND METHODS: A high dose of fluoxetine was applied to the chronic unpredictable mild stress (CUMS)-induced mice, alone or in combination with KXS. Behavior tests were conducted to confirm the anti-depressant efficiencies. The feces of mice were collected and subjected to 16S rDNA and metagenomic sequencing. The gastrointestinal morphology and functions were assessed. The potential mechanistic action of KXS on alleviating the intestinal dysbiosis was probed.<br><br>RESULTS: Notable imbalance of microbiome and disruption of intestinal barrier were observed in CUMS mice. The intake of fluoxetine exacerbated the dysbiosis, as evidenced by the increased ratio of Firmicutes/Bacteroidetes and the elevated abundance of antibiotic-resistant genes in the gut microbiome. In addition, fluoxetine treatment further compromised the intestinal integrity and functions. Significantly, KXS treatment effectively mitigated the impairment of intestinal barrier induced by fluoxetine. These protective effects appeared to be mediated through multiple mechanisms, including the restoration of microbial homeostasis and the direct cytoprotective action on intestinal epithelial cells.<br><br>CONCLUSIONS: These findings particularly provide support for the combined usage of KXS and fluoxetine in depression treatment.}, }
@article {pmid40882565, year = {2025}, author = {Cheng, S and Hu, Y and Gu, X and Xu, X and Duan, X and Li, X and Liu, Z and Jian, Q and Oleskowicz-Popiel, P and Shen, P and Zhou, A and Xue, G and Makinia, J}, title = {Magnetite-enhanced chain elongation via endogenous electron donors through a novel fungi-bacteria microbiome.}, journal = {Water research}, volume = {287}, number = {Pt B}, pages = {124478}, doi = {10.1016/j.watres.2025.124478}, pmid = {40882565}, issn = {1879-2448}, abstract = {Anaerobic fermentation of organic waste stream into medium-chain fatty acids (MCFA) through chain elongation (CE) has emerged as a sustainable and eco-friendly approach for resource recovery. Co-culture of yeast with chain elongator achieved a promising endogenous electron donor (ED)-driven CE but was limited by the weak yeast-bacteria synergy. This study presents a novel approach to optimizing the CE process through the regulation of magnetite (0-15 g/L). Results indicated that the 5 g/L of magnetite (Mag-5) achieved MCFA production at 8.42±0.67 g COD/L, which was 2.01 times greater than the blank. In-situ ethanol and lactate served as the ED to drive the CE. Under the optimal condition (Mag-5), Streptococcus (55.83%) and Candida (57.52%) were the dominant ED-producing microorganisms, and Clostridium_sensu_stricto_12 (22.70%) was the dominant chain elongator. In addition, metagenome analysis demonstrated the enhancement in reverse β-oxidization for MCFA production. Furthermore, the truncated tricarboxylic acid cycle was enhanced by magnetite amendment to provide more reduced energy, potentially accelerating the electron transfer within the mixed fungi-bacteria consortia. Finally, the constructed network of fungi and bacteria discerned the substrate competition between yeast and bacteria, and the cooperation among chain elongators, yeast, and mold. This study first proposed to regulate the mixed fungi-bacteria microbiome with magnetite to enhance the in-situ ED-driven CE process, providing a viable approach to the bioconversion of organic streams into high-value products.}, }
@article {pmid40882554, year = {2025}, author = {Balamurugan, J and Jagadeesan, H and Vijayakumar, M}, title = {A metagenomic approach to predict the role of microbiome in a plant-microbe system for degrading the model azo dye methyl red.}, journal = {Journal of contaminant hydrology}, volume = {275}, number = {}, pages = {104703}, doi = {10.1016/j.jconhyd.2025.104703}, pmid = {40882554}, issn = {1873-6009}, abstract = {Azo dye contamination poses significant environmental challenges due to its persistence and toxicity. Plant-microbe integrated systems offer a sustainable solution for dye bioremediation, yet the functional roles of microbial communities and their interactions within community and with host plants during bioremediation remain underexplored. This study presents an integrated, multi omics approach to dissect the microbial diversity, functional potential, and plant-microbe interactions within a plant-microbe integrated bioremediation system for model azo dye, methyl red degradation. The microbial diversity of various organisms enriched under different treatment conditions for effective azo dye treatment was explored. A read-based approach using HUMAnN 3 pipeline was adopted to extract metabolic information from the shotgun metagenomic reads. Diversity analysis showed the enrichment of microorganisms capable of growing in the presence of the pollutant methyl red in an oligotrophic condition. The metabolic potential of the enriched organisms in dye removal was studied. Based on the enzymatic abundance, a pathway for the degradation of methyl red is proposed. Endophytic bacteria such as Klebsiella pneumoniae and Klebsiella varicola were responsible for encoding major dye-degrading enzymes in plant-integrated systems. In the plant-microbe integrated system both endophytic and intestinal microorganisms such as Kluyvera intestini and Escherichia coli are among the top 5 contributors of genes encoding downstream aromatic compound degradation enzymes. Notably Enterococcus casseliflavus showed highest enzyme abundance for azobenzene reductase in plant -microbe integrated strategy with 11.5-fold greater abundance than the treatment system containing only microbial inoculum. Metabolomics data from root exudates experiment revealed the role of root exudates in selective recruitment of microbial community. The role of biofilm and quorum sensing pathways in enhancing the bioremediation potential of the microbiome and the potential microbe-microbe and plant-microbe interaction was analysed. Deciphering the metabolic contribution of each microorganism and the microbiome as a whole is crucial to design engineered bioremediation systems. ENVIRONMENTAL IMPLICATIONS: Understanding the potential of microorganisms, their enrichments, and survival will help in designing specific consortia for effective degradation of pollutants. Metagenomic analysis reveal that the functional complementation in the microbiome is responsible for the pollutant degradation and the presence of plants through the root exudates, provide the nutrients lacking in the oligotrophic conditions observed in many waste streams, thereby enriching suitable microorganisms. This metagenomic study along with the metabolomics component, provides the justification for the efficiency of the plant microbe treatment of model dye methyl red and this could be exploited in real time situations.}, }
@article {pmid40882431, year = {2025}, author = {Xu, Y and He, J and Jin, P and Fei, M and Cheng, S}, title = {Beyond the lungs: a case report of disseminated cutaneous aspergillosis highlighting clinical dilemmas in invasive fungal infections of critically ill patients.}, journal = {Journal de mycologie medicale}, volume = {35}, number = {4}, pages = {101573}, doi = {10.1016/j.mycmed.2025.101573}, pmid = {40882431}, issn = {1773-0449}, abstract = {With opportunistic fungal pathogens increasingly recognized as a global public health threat, the population at high risk for invasive fungal infections (IFIs) has expanded beyond traditionally immunocompromised individuals-such as those with malignancies, organ transplantation, diabetes mellitus, or acquired immunodeficiency syndrome (AIDS)-to include critically ill patients in intensive care units (ICUs) receiving invasive support and immunomodulatory therapies. Invasive aspergillosis (IA) is one of the most lethal opportunistic infections in this population, characterized by insidious onset, clinical heterogeneity, and a lack of specific signs, often resulting in delayed diagnosis. Disseminated or breakthrough aspergillosis carries an exceedingly high mortality rate. We report the case of a female patient admitted to the ICU with fulminant myocarditis who required extracorporeal membrane oxygenation (ECMO), continuous renal replacement therapy (CRRT), and immunomodulation. Her hospitalization was complicated by a progressive pulmonary infection, and metagenomic next-generation sequencing (mNGS) of respiratory specimens identified Candida albicans, Aspergillus spp. and Staphylococcus hominis, prompting an adjustment in antimicrobial therapy. Subsequently, the patient developed multiple cutaneous nodules, which tissue biopsy and mNGS confirmed as invasive cutaneous aspergillosis. Despite aggressive antifungal treatment with isavuconazole and amphotericin B, her condition deteriorated rapidly, leading to disseminated cutaneous necrosis, irreversible septic shock and multiorgan failure. This case highlights the clinical importance of recognizing atypical IFI presentations. Heightened clinical suspicion for disseminated fungal disease is warranted in critically ill patients with extrapulmonary lesions. Prompt microbiological diagnosis and antifungal resistance surveillance are essential for effective antifungal therapy.}, }
@article {pmid40882424, year = {2025}, author = {Zheng, Z and Li, X and Huang, S and Wang, X and Jia, X and Wang, H and Zhou, J and Ma, L}, title = {Novel insights into microbial strategies for antimony (Sb) transformation coupled with carbon utilization in groundwater ecosystem.}, journal = {Environment international}, volume = {203}, number = {}, pages = {109752}, doi = {10.1016/j.envint.2025.109752}, pmid = {40882424}, issn = {1873-6750}, abstract = {Microbial-mediated antimony (Sb) metabolism and its coupling with bio-essential elements cycles are not only crucial to the biogeochemistry of Sb-contaminated groundwater but also have potential implications for human health. However, the ways in which Sb contamination affects microbial carbon, nitrogen, and sulfur metabolism, particularly carbon-utilization strategies, remain poorly understood and lack direct experimental confirmation. Herein, well and spring water samples were collected from the Xikuangshan (XKS) mine to investigate microbial responses and functional adaptations. The results showed that microbial communities in well and spring became similar during the wet season, with total Sb identified as a major shaping force in this complex environment. Communities in low-Sb samples harbored a higher potential functional diversity, whereas those in high-Sb samples exhibited convergent metabolic potential, with enrichment in genes for pyruvate metabolism. Metagenome-assembled genomes (MAGs) in low-Sb samples harbored more pathways for inorganic carbon utilization, including cynT, pycA, PRK, rbcL, and rbcS genes, primarily derived from the phyla Bdellovibrionota and Eremiobacterota. Microcosm cultivation confirmed a preference for inorganic carbon (NaHCO3) in low-Sb samples and organic carbon sources (pyruvate) in high-Sb samples. These findings provide new genomic insights and experimental evidence for the coupling between Sb transformation and carbon utilization in contaminated aquifers.}, }
@article {pmid40882374, year = {2025}, author = {Chen, Y and Zhang, Y and Li, J and Li, Y and Chen, Z and Qin, J and Deng, Z and Wang, X}, title = {Fe(Ⅱ)-mediated detoxification mitigates low-dose rare earth elements-induced stress on anammox consortia for mining tailwater treatment.}, journal = {Journal of hazardous materials}, volume = {497}, number = {}, pages = {139681}, doi = {10.1016/j.jhazmat.2025.139681}, pmid = {40882374}, issn = {1873-3336}, abstract = {Rare earth mining activities cause severe nitrogen pollution in watersheds, yet the residual hazardous rare earth elements (REEs) toxicity in tailings wastewater challenges biological nitrogen removal technology. This work demonstrated that introducing low-dose Fe(II) into partial denitrification/anammox (PD/A) system significantly alleviated REEs-induced stress on anammox consortia via detoxification and physical barrier reinforcement. The PD/A bioreactor with 15 mg/L Fe(II) (R1) was compared against a control without Fe(II) for real rare earth tailings wastewater treatment. Metagenomic analysis identified 1.14-fold upregulation of hydrazine (N2H4) dehydrogenase alongside substantial 5.82-fold downregulation of N2H4 synthase in R1, indicating a critical metabolic reconfiguration that expedited the degradation of toxic intermediates and alleviated REEs-mediated cytotoxicity. Electrons with lower redox potential released from N2H4 oxidation were more effectively utilized for carbon fixation, as evidenced by the upregulated electron transport complexes and Wood-Ljungdahl pathway. Concurrent biosynthetic modulation stimulated lipopolysaccharide production (module M00063) and carbohydrate storage (module M00064), collectively reinforcing microbial stress resilience through both defensive metabolites (lipopolysaccharides and trehalose) and hydrophobicity-driven aggregation. Moreover, modified 2-P logistic modeling confirmed elevated REEs inhibition thresholds under Fe(II) mediation. This study reveals the defense mechanism of Fe(II)-enhanced anammox consortia against REEs stress, providing new insights for sustainable bioremediation in rare earth mining areas.}, }
@article {pmid40882289, year = {2025}, author = {Bature, I and Liang, Z and Xiaohu, W and Yang, F and Yang, Y and Dong, P and Ding, X}, title = {Isolation, cloning, and characterization of a novel GH5 cellulase from yak rumen metagenome for enhanced lignocellulose hydrolysis in biofuel production and ruminant feed utilization.}, journal = {Enzyme and microbial technology}, volume = {191}, number = {}, pages = {110737}, doi = {10.1016/j.enzmictec.2025.110737}, pmid = {40882289}, issn = {1879-0909}, abstract = {Lignocellulosic biomass is a promising feedstock for biofuel production, but its complex structure, including cellulose and hemicellulose, challenges efficient enzymatic hydrolysis. CelyA, a novel cellulase from the yak rumen, has potential for improving biomass degradation and biofuel production. The CelyA gene was cloned, expressed, and purified. Biochemical characterization included assessments of pH, temperature, and salt tolerance. The enzyme's substrate specificity was tested on crystalline cellulose, CMC, and other polysaccharides. In vitro rumen fermentation was performed to evaluate its effect on fiber digestibility and microbial community composition. Biofuel production was tested by hydrolyzing maize, rice, and wheat straw. CelyA demonstrated optimal activity at pH 6.0 and 40.0 °C and maintained moderate stability across a wide pH range (3.0-12.0), retaining measurable activity even under strongly acidic and alkaline conditions. The enzyme demonstrated excellent salt tolerance, retaining 91.0 % activity in 1.0 M NaCl. CelyA efficiently degraded maize straw in hydrolysis assays, producing 7.2 µmol/L of reducing sugars. In vitro rumen fermentation with CelyA increased fiber digestibility by 8.3 % for maize straw, 14.5 % for rice straw, and 2.7 % for wheat straw. Gas production also increased significantly, with maize straw showing a 91.3 % increase. 16S rRNA sequencing revealed selective enrichment of Ruminococcus and Prevotella, key cellulolytic microbes. CelyA demonstrates strong potential for biofuel production, efficiently hydrolyzing lignocellulosic biomass and enhancing ruminal fiber digestibility. Its stability, salt tolerance, and substrate specificity make it a valuable enzyme for biofuel production and livestock feed optimization.}, }
@article {pmid40882272, year = {2025}, author = {Wang, K and Xu, J and Luo, X and Yu, Z and Tang, A and Peng, K and Song, J and Chen, X and Ren, M}, title = {Insights into microalgal-bacterial consortia in sustaining denitrification via algal-derived organic matter in harsh low-C/N wastewater.}, journal = {Journal of environmental management}, volume = {393}, number = {}, pages = {127108}, doi = {10.1016/j.jenvman.2025.127108}, pmid = {40882272}, issn = {1095-8630}, abstract = {Conventional nitrate removal processes are often hampered by insufficient carbon sources for remediating low-C/N wastewater. Herein, a microalgal-bacterial (MB) consortia system was constructed to leverage algal-derived organic matter for sustaining denitrification. The system demonstrated superior nitrate removal performance when assisted by algal-derived organic matter, achieving a 168.62 ± 4.17 % enhancement in nitrate removal capacity compared to the sole bacterial system. Furthermore, Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR-MS) analysis of algal-derived organic matter revealed that specific components facilitating nitrate elimination included unsaturated aliphatic compounds, aliphatic/peptide-like/amino sugars, lignin-like, and tannin-like substances. Notably, the consortia showed preferential utilization of unsaturated aliphatic (35.21 %) and aliphatic/amino sugars over aliphatic/peptide-like/amino acids (31.05 %) and aliphatic/peptide-like compounds (31.31 %) within the CHO, CHON, CHON2, and CHON3 classes, respectively. Metagenomic analysis identified notable disparities in microbial community composition between the bacterial and MB consortia systems. Moreover, the MB consortia exhibited higher abundances of genes encoding nitrate removal enzymes, including those involved in denitrification, assimilatory/dissimilatory reduction, and L-glutamate synthesis pathways. Genes associated with lignin degradation were also detected, suggesting potential indirect contributions to nitrate elimination. Besides, the MB symbiotic microspheres were successfully fabricated and achieved efficient nitrate removal. These findings provide novel insights into the development of innovative MB symbiotic systems for nitrate removal under harsh carbon-limited conditions.}, }
@article {pmid40882267, year = {2025}, author = {Davis, BC and Linz, D and McMinn, BR and Korajkic, A}, title = {Limited ARG removal but stable resistome dynamics in a surface flow constructed wetland.}, journal = {Journal of environmental management}, volume = {393}, number = {}, pages = {126986}, doi = {10.1016/j.jenvman.2025.126986}, pmid = {40882267}, issn = {1095-8630}, abstract = {Improperly treated wastewater and surface runoff can degrade water quality by introducing microbial contaminants, including antibiotic-resistant bacteria (ARB) and their genes (ARGs). Constructed treatment wetlands (CTWs) offer a low-resource solution for managing impaired watersheds. However, their ability to mitigate microbial contaminants, particularly ARGs, requires further study. In this study, 62 water samples from Banklick Creek CTW (BCTW) were shotgun sequenced to assess ARG dynamics and removal characteristics. Results showed minimal resistome attenuation, likely due to the wetland's horizontal surface flow design with short, variable hydraulic residence times (0.48-3.1 days). Despite this, 198 low-abundance ARGs were removed, accounting for a median of 0.52 % (0-3.1 %) of total ARG abundance upstream. The core resistome, comprising 95.6 ± 1.9 % of total ARG abundance, was stable and mainly consisted of multidrug efflux systems carried by bacterioplankton and macrophyte symbionts, indicating a native resistome reflective of regional pollution history. Resistome and microbiome structures were highly correlated (R[2] = 0.808), with ARGs rarely co-occurring with mobile genetic elements, indicating limited intercellular transfer potential. No significant correlations were found between resistome dynamics and human fecal (HF183, crAssphage) or avian (GFD) biomarkers. Although several class-one integron-integrase (intI1) contigs were enriched in treatment channels, gene cassette cargo was void of ARGs. As detection of intI1 via qPCR is generally considered indicative of resistome mobility potential, this finding carries important implication for intI1 qPCR assay selection (i.e., targeting clinical intI1 mosaics) and over-interpretation of ARG spread in the environment.}, }
@article {pmid40881965, year = {2024}, author = {Fox, JD and Sims, A and Ross, M and Bettag, J and Wilder, A and Natrop, D and Borsotti, A and Kolli, S and Mehta, S and Verma, H and Kurashima, K and Manithody, C and Verma, A and Jain, A}, title = {Bioinformatic Methodologies in Assessing Gut Microbiota.}, journal = {Microbiology research}, volume = {15}, number = {4}, pages = {2554-2574}, doi = {10.3390/microbiolres15040170}, pmid = {40881965}, issn = {2036-7473}, abstract = {Bioinformatic methodologies play a crucial role in the assessment of gut microbiota, offering advanced tools for analyzing complex microbial communities. These methodologies involve high-throughput sequencing technologies, such as 16S rRNA gene sequencing and metagenomics, which generate vast amounts of data on microbial diversity and functional potential, as well as whole-genome sequencing, which, while being more costly, has a more expansive potential. Bioinformatics tools and algorithms process these data to identify microbial taxa and quantify and elucidate their roles within the microbiome. Advanced statistical and computational models further enable the identification of microbiota patterns associated with various diseases and health conditions. Overall, bioinformatic approaches are essential for deciphering the complexities of gut microbiota so that, in the future, we may be able to discover treatments and technologies aimed at restoring or optimizing the microbiome. The goal of this review is to describe the differences in methodology and utilization of 16S versus whole-genome sequencing to address the increased understanding of the role that the gut microbiome plays in human physiology and pathology.}, }
@article {pmid40881292, year = {2025}, author = {Daddy Gaoh, S and Alusta, P and Lee, YJ and Hussong, D and Marasa, B and Ahn, Y}, title = {A metagenomic analysis coupled with oligotrophic enrichment approach for detecting specified microorganisms in potable groundwater samples.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1645324}, doi = {10.3389/fmicb.2025.1645324}, pmid = {40881292}, issn = {1664-302X}, abstract = {In pharmaceutical manufacturing, there is a significant need for the detection and identification of specified microorganisms (i.e., Burkholderia cepacia complex (BCC), E. coli, Pseudomonas aeruginosa, Salmonella enterica, Staphylococcus aureus, Clostridium sporogenes, Candida albicans, and Mycoplasma), which are often missed or not identified by traditional culture-dependent methods. We employed a metagenomic analysis coupled with oligotrophic enrichment to identify specified microorganisms and evaluate tryptic soy broth (TSB) and 1/10 strength TSB for the recovery of specific microorganisms in potable groundwater samples. A total of 589-996 genera were identified in 12 water samples taken from a cold water fountain, with Bacillus spp. (97%) in TSB and Stenotrophomonas spp. (97%) in 1/10 strength TSB, representing the primary recovered genera after a 72-h pre-enrichment at 23°C. Likewise, we also detected lower abundance of specific organisms, Clostridium spp., Burkholderia spp., and Staphylococcus spp. (0.04-0.07%) in TSB and Burkholderia spp., Pseudomonas spp., Salmonella spp., Staphylococcus spp. and Escherichia spp. (0.01-1.73%) in 1/10 strength TSB. Co-inoculation with Burkholderia cepacia complex (BCC) yielded a higher recovery rate of Pseudomonas spp. compared to uninoculated controls in 1/10 strength TSB. Further functional analyses indicated that, toluene degradation (PWY-5180 and PWY-5182) was chiefly contributed by BCC in co-cultures of TSB + BCC-24 h and TSB + BCC-48 h. Our results demonstrate the potential value of the metagenomic approach during enrichment in detecting specified microorganisms, including oligotrophs such as BCC in non-sterile pharmaceutical products.}, }
@article {pmid40880127, year = {2025}, author = {Milnitsky, BP and Junior, HLP and Chaúque, BJM and Corção, G}, title = {Successful establishment of a model of the piglet gastrointestinal microbiota and its' modulation by prebiotics.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxaf216}, pmid = {40880127}, issn = {1365-2672}, abstract = {AIMS: This study proposed an in-house in vitro model to investigate the effects of two prebiotic treatments on the gastrointestinal microbiota of piglets.<br><br>METHODS AND RESULTS: The model involved suspending piglet feces in a culture medium to simulate the ileum and proximal colon regions of the swine gastrointestinal tract. The prebiotics tested were mannanoligosaccharides (MOS) and sodium butyrate. Metabarcoding and culturomics were used to assess the impact of prebiotics on bacterial species composition. Minimum inhibitory concentration tests were conducted to examine bacterial susceptibility patterns. Key bacterial phyla identified included Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria. Culturomics detected families and several species not identified by metabarcoding. In the simulated proximal colon, MOS increased the abundance of certain species and reduced bacteria with type I fimbriae. Butyric acid promoted beneficial host-associated bacteria and decreased pathogenic species. However, the prebiotics did not significantly affect bacterial susceptibility to antibiotics.<br><br>CONCLUSION: The in-house model successfully mimicked piglet intestinal microbiota, allowing for detailed analysis. Both prebiotics positively influenced the piglets microbiota, providing insights into how these treatments potentially influenced the microbiota.}, }
@article {pmid40880079, year = {2025}, author = {Tang, Y and Oliver, A and Alkan, Z and Korf, I and Huang, L and Kable, ME and Lemay, DG}, title = {Association of lactose intake and lactase persistence genotype with microbial taxa and function in healthy multi-ethnic U.S. adults.}, journal = {Food &amp; function}, volume = {}, number = {}, pages = {}, doi = {10.1039/d5fo01640a}, pmid = {40880079}, issn = {2042-650X}, abstract = {Lactase persistence is a genetically inherited trait that enables continued lactose digestion into adulthood. Lactase non-persistence (LNP) individuals often experience incomplete lactose digestion, allowing undigested lactose to reach the colon, where it may shape microbial composition and function. We investigated the relationship between the lactase persistence (LP) genotype, lactose consumption, and the taxonomic and functional profiles of the fecal microbiome. Participants from the USDA Nutritional Phenotyping Study, a cross-sectional observational study designed to assess how dietary factors impact human health, whose fecal microbiome profile was measured using shotgun metagenomic sequencing (n = 330) were included in this analysis. Fecal SCFA levels were measured using GC-MS. Fecal microbiome taxonomy and gene abundance were quantified using shotgun metagenomic sequencing. Lactose consumption and yogurt intake were estimated based on Automated Self-Administered 24h Dietary Assessment Tool (ASA24®) dietary recalls or Food Frequency Questionnaire. The LP/LNP genotype was determined by a single nucleotide polymorphism (SNP ID: rs4988235). Several genera of lactic acid bacteria (Veillonella, Lactobacillus, Lacticaseibacillus, and Lactococcus) were differentially abundant between recent high-lactose consuming (>10.0 g lactose per day) and low-lactose consuming (<3.3 g lactose per day) individuals. Among the LNP participants who self-identified as Caucasian or Hispanic, high-lactose consumers (>10.0 g per day via 24-h recall) had significantly higher relative abundances of lactic acid bacteria and lactate-utilizing bacteria (Lacticaseibacillus, Lactobacillus, Megamonas, and Veillonella) than low-lactose consumers (<3.3 g per day). Independent of lactose intake, LNP participants had a higher abundance of fecal microbial β-galactosidase genes than LP participants. Among the LNP participants, those with high recent lactose consumption also showed a significant shift towards more fecal propionate. The abundance of the yogurt-associated microbe, Streptococcus thermophilus, was positively associated with yogurt intake independent of the genotype. Alternative milk consumption was significantly negatively associated with fecal SCFAs both in the full cohort and the Caucasian/Hispanic subset, regardless of the genotype. Our results suggest that functional and persistent host lactase enzymes may work to competitively exclude lactic acid bacteria, contributing to a smaller realized niche for lactic acid bacteria in LP individuals compared to LNP individuals. However, regardless of the host genotype, consumption of alternative milk may be associated with reduced production of health-promoting intestinal metabolites, such as SCFAs.}, }
@article {pmid40879860, year = {2025}, author = {Liu, Y and Wang, Q and Zhang, Y and Duo, R and Bian, X and Tian, J and Hao, J and Zheng, J and Shen, H}, title = {Multi-omics characterization of gut microbiota and fecal and plasma metabolites in patients with primary Sjögren's syndrome.}, journal = {Clinical rheumatology}, volume = {}, number = {}, pages = {}, pmid = {40879860}, issn = {1434-9949}, support = {CY2021-QN-A10//the Cuiying Scientific and Technological Innovation Program of Lanzhou University Second Hospital/ ; 2022-ZD-101//Science and Technology Program of Lanzhou city/ ; GSWSKY2023-08//Health Industry Scientific Research Project of Gansu Province/ ; }, abstract = {INTRODUCTION: Accumulating evidence has implicated gut microbiota and their metabolites in primary Sjögren's syndrome (pSS) pathogenesis. However, no study simultaneously explores the gut microbiome, microbial, and plasma metabolome in pSS patients.<br><br>METHOD: Thirty pSS patients and 60 healthy controls (HCs) were recruited. Shotgun metagenomic sequencing and untargeted metabolomics were performed on stool and plasma samples.<br><br>RESULTS: pSS patients exhibited significant reduction in microbial richness and diversity. Bacteroidetes and Firmicutes accounted for over 80% of all phyla. Four phyla, 48 genera, and 106 species with significant differences were identified (P&#x2009;<&#x2009;0.05). Proteobacteria, Ascomycota, Fusobacteria, and 31 genera (e.g., Escherichia, Veillonella, Prevotella, Klebsiella) were enriched in pSS, while Actinobacteria, Bifidobacterium, Dorea, and Blautia were depleted. Opportunistic pathogens (e.g., Escherichia coli, Prevotella copri, Streptococcus oralis, Klebsiella pneumoniae, Enterococcus faecalis) and pathogenic Clostridium bolteae and Fusobacterium nucleatum were more abundant in pSS, whereas beneficial Bifidobacterium longum and butyrate-producing Eubacterium hallii and Anaerostipes hadrus were in HCs. Notably, Lactobacillus spp. were enriched in pSS. Of 298 differential functional pathways, 239 pSS-enriched pathways were focused on nutrient and energy metabolism, while amino acid biosynthesis in HCs. During 881 differential fecal metabolites (pSS: HCs&#x2009;=&#x2009;631:250), fatty acyls were enriched in pSS, and glycerophospholipids in HCs. Among the 712 differential plasma metabolites (pSS: HCs&#x2009;=&#x2009;438:274), heterocyclic compounds and benzene derivatives were more abundant in pSS, while fatty acyls and glycerophospholipids prevailed in HCs. Amino acids and organic acids were predominant in both samples.<br><br>CONCLUSIONS: This study characterized gut microbiome and fecal/plasma metabolome in pSS patients, providing theoretical support for regional pSS prevention and treatment. Key Points &#x2022; This is the first study to systematically characterize the gut microbiome and fecal and plasma metabolomes of primary Sj&#xf6;gren's syndrome (pSS) patients in Northwest China via multi-omics integration analysis. &#x2022; Significant reduction in gut microbial diversity and probiotic bacteria, enrichment of opportunistic and infectious pathogens, and microbial dysfunction were observed in pSS patients. &#x2022; Much more differential fecal and plasma metabolites were observed in pSS patients, with amino acids, organic acids and derivatives, nucleotides, and metabolites being the main altered metabolites in both samples.}, }
@article {pmid40879375, year = {2025}, author = {Munguti, F and Nyaboga, EN and Holton, T and Kreuze, J and Maina, S}, title = {Genomics insight on passion fruit viral disease complexity.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0034425}, doi = {10.1128/spectrum.00344-25}, pmid = {40879375}, issn = {2165-0497}, abstract = {Passion fruit viral diseases pose a significant threat to Kenya's passion fruit industry. To unravel the complexity of these diseases, comprehensive virus surveys were conducted across major passion fruit-growing counties. Passion fruit woodiness disease symptoms, like fruit hardening, chlorotic mottling, and leaf distortion, were prevalent. The study unveiled the first 23 complete genomes of Ugandan passiflora virus (UPV) and two East Asian passiflora distortion virus (EAPDV) in Kenya. UPV showed 99% nucleotide (nt) match to a UPV genome from Uganda and 66% nt identity match to EAPDV. In addition, UPV variants and two partial passion fruit green spot virus sequences and partial (passiflora emaravirus) segment RNA1-5 (novel allexivirus and an emaravirus, respectively) were detected. Phylogenetic analysis revealed distinct lineages (I-III), indicating potential multiple introductions into Kenya. Recombination analysis detected no significant breakpoints. However, the study proposed the renaming of EAPDV to passiflora distortion virus (PDV) and UPV to passiflora virus (PV) for neutral nomenclature, without geographical association. Additionally, the study highlighted the role of coinfections in symptom expression, suggesting a potential synergistic relationship between PV, PDV, and other viruses. The results recommend stringent management strategies and enhanced surveillance to mitigate the economic impact of these viruses on the Kenyan passion fruit industry. The findings from this study underscore the need to strengthen nursery certification programs and pest diagnostic protocols in Kenya. Additionally, enhanced pest surveillance and import regulations are critical to preventing the introduction and spread of emerging plant viral diseases, thereby safeguarding the country's horticultural productivity and biosecurity. To our knowledge, this is the first comprehensive study of viral diseases of passion fruit in Kenya.IMPORTANCEThis study presents the first comprehensive survey of viral pathogens affecting passion fruit in Kenya, identifying Ugandan passiflora virus (UPV) and East Asian passiflora distortion virus (EAPDV) as major contributors. Through genomic sequencing, 23 complete genomes of UPV and two of EAPDV were characterized, revealing a 99% nucleotide (nt) similarity between UPV strains from Uganda and Kenya, and 66% nt match with EAPDV. Phylogenetic analysis identified distinct lineages, suggesting possible multiple viral introductions in Kenya. The study also highlights potential synergistic coinfections between UPV, EAPDV, and other viruses, leading to more severe disease symptoms. In light of these findings, the study proposes renaming EAPDV as passiflora distortion virus and UPV as passiflora virus for a more neutral name classification. The research underscores the urgent need for enhanced surveillance, stringent phytosanitary measures, and improved management strategies to mitigate the threat of viral diseases, to safeguard the Kenyan passion fruit industry, and elsewhere.}, }
@article {pmid40879288, year = {2025}, author = {Hao, Y}, title = {Gut Microbiota-Immune Axis in the Regulation of Rheumatoid Arthritis: From Mechanism to Precision Probiotic Strategies.}, journal = {Modern rheumatology}, volume = {}, number = {}, pages = {}, doi = {10.1093/mr/roaf081}, pmid = {40879288}, issn = {1439-7609}, abstract = {Rheumatoid Arthritis (RA) is a progressive autoimmune disorder with substantial global health and economic impacts. Despite advancements in conventional therapies, biologics, and targeted drugs, challenges such as adverse effects, cost, and interindividual heterogeneity underscore the need for safer, precision-based treatments. Notably, emerging evidence highlights the pivotal role of the gut microbiota-immune axis in RA pathogenesis. Affected individuals typically exhibit gut dysbiosis, marked by increased pro-inflammatory taxa and reduced anti-inflammatory species, which disrupts immune homeostasis through Th17/Treg imbalance, molecular mimicry, and compromised gut barrier integrity. These processes drive systemic inflammation, exacerbating both articular destruction and extra-articular manifestations. Probiotics demonstrate therapeutic potential by modulating this axis via microbiota restoration, barrier reinforcement, and immune regulation. Strain-specific effects have been documented in both preclinical and clinical studies, although efficacy varies depending on host genetics, baseline microbiota composition, and intervention protocols-a variability underscoring the need for personalized probiotic selection. This review consolidates current knowledge on gut microbiota-immune crosstalk in RA and explores probiotics as precision therapeutics. Integrating multi-omics (metagenomics, metabolomics) with targeted probiotic strategies could enable the development of personalized interventions. While translational obstacles persist, including mechanistic complexity and limited clinical validation, the gut microbiota-immune axis offers a novel paradigm for RA management. Future priorities include large-scale trials, biomarker discovery, and combinatorial approaches to advancing microbiome-guided precision medicine in autoimmune diseases.}, }
@article {pmid40879200, year = {2025}, author = {Cai, J and Mar, JS and Kapili, B and Storek, KM and Uzunovic, J and Skippington, E and Keilberg, D and Sangaraju, D and Auster, A and Khojasteh, C and Rhee, H and Triadafilopoulos, G and Shalon, D and Keir, M}, title = {Spatiotemporal Characterization of Sulfasalazine and 5-ASA Pharmacokinetics Using a Noninvasive Intestinal Sampling Device.}, journal = {Clinical pharmacology and therapeutics}, volume = {}, number = {}, pages = {}, doi = {10.1002/cpt.70035}, pmid = {40879200}, issn = {1532-6535}, support = {//Genentech, Inc./ ; 2126329//National Science Foundation/ ; }, abstract = {Sulfasalazine, a cornerstone therapy for inflammatory bowel disease, relies on bacterial azo-reduction to release its active component, 5-aminosalicylic acid (5-ASA), which is further metabolized into inactive N-acetyl-5-aminosalicylic acid (N-acetyl-5-ASA) by bacterial N-acetyltransferase. Due to complex pharmacokinetics, patient-specific microbial metabolism, and the lack of accurate, convenient direct sampling method for gastrointestinal drug concentrations, sulfasalazine clinical efficacy remains variable. The CapScan® luminal sampling device enables region-specific, minimally invasive collection of intestinal contents. To better understand sulfasalazine pharmacokinetics in relation to intestinal and systemic drug concentrations and bacterial metabolic capacity, 10 healthy volunteers ingested CapScan devices following sulfasalazine administration. Upon retrieval from the stool, CapScan samples were assigned intestinal locations based on metabolomic and metagenomic profiling. Systemic sulfasalazine peaked at 4 hours post-ingestion, while 5-ASA and N-acetyl-5-ASA peaked at 8 hours. In the gastrointestinal tract, maximal sulfasalazine concentration was observed in the proximal small intestine (SI), decreasing distally as 5-ASA and N-acetyl-5-ASA concentrations increased, peaking in the stool. 5-ASA plasma concentrations positively correlated with distal SI concentrations 4 hours after sulfasalazine ingestion. Putative bacterial azoreductase genes were detected in all gastrointestinal regions, while putative bacterial acetyltransferase genes were detected in all regions except the proximal SI. This study revealed spatially distinct luminal concentrations of sulfasalazine and its metabolites, with a strong correlation between distal SI 5-ASA levels and early plasma exposure, highlighting GI region-specific absorption and microbial metabolism. These findings support the potential utility of luminal sampling to enhance understanding of drug pharmacokinetics and inform future strategies for optimizing oral drug delivery.}, }
@article {pmid40878918, year = {2025}, author = {Liu, X and Xie, Y and Yang, S and Jiang, C and Shang, K and Luo, J and Zhang, L and Hu, G and Liu, Q and Yue, B and Fan, Z and He, Z and Li, J}, title = {Multi-omics investigation of spontaneous T2DM macaque emphasizes gut microbiota could up-regulate the absorption of excess palmitic acid in the T2DM progression.}, journal = {eLife}, volume = {14}, number = {}, pages = {}, pmid = {40878918}, issn = {2050-084X}, support = {2021YJ0136//Science and Technology Foundation of Sichuan Province/ ; 32171607//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Diabetes Mellitus, Type 2/microbiology/pathology/metabolism ; *Palmitic Acid/metabolism ; Macaca mulatta ; Mice ; Disease Models, Animal ; Male ; Gene Expression Profiling ; Metabolome ; RNA, Ribosomal, 16S/genetics ; Disease Progression ; Multiomics ; }, abstract = {Although gut microbiota and lipid metabolites have been suggested to be closely associated with type 2 diabetes mellitus (T2DM), the interactions between gut microbiota, lipid metabolites, and the host in T2DM development remains unclear. Rhesus macaques may be the best animal model to investigate these relationships given their spontaneous development of T2DM. We identified eight spontaneous T2DM macaques and conducted a comprehensive study investigating the relationships using multi-omics sequencing technology. Our results from 16 S rRNA, metagenome, metabolome, and transcriptome analyses identified that gut microbiota imbalance, tryptophan metabolism and fatty acid β oxidation disorders, long-chain fatty acid (LCFA) accumulation, and inflammation occurred in T2DM macaques. We verified the accumulation of palmitic acid (PA) and activation of inflammation in T2DM macaques. Importantly, mice transplanted with spontaneous T2DM macaque fecal microbiota and fed a high PA diet developed prediabetes within 120 days. We determined that gut microbiota mediated the absorption of excess PA in the ileum, resulting in the accumulation of PA in the serum, consequently leading to T2DM in mice. In particular, we demonstrated that the specific microbiota composition was probably involved in the process. This study provides new insight into interactions between microbiota and metabolites and confirms causative effect of gut microbiota on T2DM development.}, }
@article {pmid40877975, year = {2025}, author = {Xu, L and Jiao, JY and Ling, C and Du, RB and Wu, Q and Xu, Y and Li, WJ}, title = {Mobilome-mediated transcriptional activation of biosynthetic gene clusters and its impact on strain competitiveness in food fermentation microbiomes.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {191}, pmid = {40877975}, issn = {2049-2618}, support = {32172175//National Natural Science Foundation of China/ ; No. 111-2-06//Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; }, mesh = {Fermentation ; *Microbiota/genetics ; *Multigene Family ; Metagenome ; *Bacteria/genetics/classification/metabolism ; *Transcriptional Activation ; Gene Transfer, Horizontal ; Metagenomics/methods ; *Interspersed Repetitive Sequences ; *Food Microbiology ; Firmicutes/genetics ; *Fermented Foods/microbiology ; Microbial Interactions/genetics ; }, abstract = {BACKGROUND: Microbial interactions are critical for maintaining the stability of food fermentation microbiomes, and mobile genetic elements (MGEs) significantly influence these interactions by horizontal gene transfer events. Although MGEs are known to facilitate horizontal gene transfer, their distribution among microorganisms and specific effects on microbial interactions remain poorly understood.<br><br>RESULTS: We analyzed 590 metagenomic and 42 metatranscriptomic samples from food fermentations, recovering 1133 metagenome-assembled genomes (MAGs). Our analysis revealed that MGEs were widely distributed in food fermentation microbiomes, with higher occurrence rates in Firmicutes (Bacillota: 0.71&#x2009;~&#x2009;11.85%) and Proteobacteria (Pseudomonadota: 0.47&#x2009;~&#x2009;11.05%). MGEs tended to be located adjacent to functional genes, particularly biosynthetic gene clusters (BGCs), with co-occurrence rates ranging from 9.41 to 23.99%. Furthermore, the transcriptional activity of BGCs was significantly correlated with the number of MGEs that were co-located with BGCs, which might enhance the competitiveness of strains. Variability in the diversity of MGEs that were co-located with BGCs was also evident at the strain level. Using Lactiplantibacillus plantarum as a case, we revealed that the strain-level differences in MGEs that were co-located with BGCs are positively correlated with the transcription of BGCs and competitiveness of strains within the species.<br><br>CONCLUSIONS: This study highlighted the role of MGEs in enhancing transcription of BGCs and facilitating strain competitiveness, providing new insights into how MGEs enhance the adaptability of microbial communities. Video Abstract.}, }
@article {pmid40877570, year = {2025}, author = {Chia, M and Ng, AHQ and Ravikrishnan, A and Mohamed Naim, AN and Wearne, S and Common, J and Nagarajan, N}, title = {Skin metatranscriptomics reveals a landscape of variation in microbial activity and gene expression across the human body.}, journal = {Nature biotechnology}, volume = {}, number = {}, pages = {}, pmid = {40877570}, issn = {1546-1696}, abstract = {Metatranscriptomics methods for the skin are hampered by low microbial biomass, contamination with host cells and low RNA stability. In this study, we developed a robust, clinically tractable skin metatranscriptomics workflow that provides high technical reproducibility of profiles, uniform coverage across gene bodies and strong enrichment of microbial mRNAs. Paired application of this protocol with metagenomics to five skin sites in a cohort of 27 healthy adults identifies a notable divergence between transcriptomic and genomic abundances. Specifically, Staphylococcus species and the fungi Malassezia had an outsized contribution to metatranscriptomes at most sites, despite their modest representation in metagenomes. Species-level analysis shows signatures of microbial adaptation to their niches. Gene-level analysis identifies diverse antimicrobial genes transcribed by skin commensals in situ, including several uncharacterized bacteriocins. Correlation of microbial gene expression with organismal abundances uncovers more than 20 genes that putatively mediate interactions between microbes. This work highlights how skin metatranscriptomics identifies active species and microbial functions in situ.}, }
@article {pmid40877311, year = {2025}, author = {Wilson, BC and Zuppi, M and Derraik, JGB and Albert, BB and Tweedie-Cullen, RY and Leong, KSW and Beck, KL and Vatanen, T and O'Sullivan, JM and Cutfield, WS and , }, title = {Long-term health outcomes in adolescents with obesity treated with faecal microbiota transplantation: 4-year follow-up.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {7786}, pmid = {40877311}, issn = {2041-1723}, mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; Adolescent ; Male ; Female ; Follow-Up Studies ; Double-Blind Method ; *Pediatric Obesity/therapy ; Treatment Outcome ; Body Composition ; Body Mass Index ; Gastrointestinal Microbiome ; *Obesity/therapy ; Metabolic Syndrome/therapy ; Feces/microbiology ; }, abstract = {Faecal microbiota transplantation (FMT) has been explored as a potential treatment for obesity, but its long-term effects on metabolic health remain unclear. Here, we report 4-year follow-up findings from a double-blind, randomised, placebo-controlled trial assessing FMT in adolescents with obesity (ACTRN12615001351505, Australian New Zealand Clinical Trials Registry). This unblinded follow-up study evaluated 63% (55/87) of the original participants (27 FMT, 28 placebo). There was no difference in BMI between the two groups, after adjusting for sex, age, diet, and physical activity (-3.6 kg/m[2], p = 0.095). However, FMT recipients showed clinical improvements in body composition and metabolic health compared to the placebo group. Specifically, FMT recipients had smaller waist circumference (-10.0 cm, p = 0.026), total body fat (-4.8%, p = 0.024), metabolic syndrome severity score (-0.58, p = 0.003), and systemic inflammation (-68% hs-CRP, p = 0.002) and higher levels of HDL cholesterol (0.16 mmol/L, p = 0.037). No group differences were observed in glucose markers, or other lipid parameters. Shotgun metagenomic sequencing revealed sustained long-term alterations in gut microbiome richness, composition and functional capacity, with persistence of donor-derived bacterial and bacteriophage strains. These findings highlight the potential relevance of FMT as a microbiome-augmenting intervention for obesity management and metabolic health, warranting further investigation.}, }
@article {pmid40876701, year = {2025}, author = {Jamal, Z and Humayun, F and Haider, SA and Hakim, R and Hill, V and Saeed, SY and Baele, G and Ishaq, M and Ayub, M and Ullah, A and Hussain, N and Salman, M and Umair, M}, title = {Genomic characterization and serotype distribution of dengue virus circulating in Pakistan during 2024.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {}, number = {}, pages = {105815}, doi = {10.1016/j.meegid.2025.105815}, pmid = {40876701}, issn = {1567-7257}, abstract = {Dengue virus (DENV) remains a significant public health concern in Pakistan, with recurrent outbreaks necessitating continuous genomic surveillance. The 2024 dengue outbreak prompted an investigation into circulating serotypes and genomic diversity. The National Institute of Health (NIH), Pakistan, received 524 NS-1 confirmed dengue samples across multiple districts in 2024. Serotyping via real-time PCR confirmed DENV-2 in 93 % (n = 361) and DENV-1 in 7 % (n = 27) of 388 positive samples, with no co-infections detected. Males accounted for 65 % of cases, with a mean age of 30.78 ± 15.03 years. Metagenomic sequencing using Illumina MiSeq yielded 33 successful DENV genomes (DENV-2: 23; DENV-1: 10), including the first reports from Chilas and Kech. Phylogenetic analysis showed 2024 DENV-1 (genotype III) and DENV-2 (Cosmopolitan genotype, clade IV-A/2II_F.1.1) closely resembling 2022-2023 Pakistani strains (~99 % homology). Time-scaled analysis estimated 22 of 23 DENV-2 sequences shared a most recent common ancestor (MRCA) in 2018, while a divergent strain (NIHPAK-246) traced back to 2005. DENV-2 strains from Kech exhibited >99.8 % similarity with Rawalpindi strains, suggesting transmission links. DENV-1 sequences shared an MRCA in 2016, indicating sustained circulation. Mutation analysis identified NS4B: G240S in DENV-1 from Chilas, suggesting localized adaptation. These findings highlight the need for sustained genomic surveillance, monitoring transmission dynamics, and targeted public health interventions in Pakistan.}, }
@article {pmid40875928, year = {2025}, author = {Taga, A and Kolchinski, A and Reed, C and Probasco, JC and Simner, PJ and Green, KE and Pardo, CA}, title = {Bridging the Gap: Opsoclonus-Myoclonus Syndrome: Human Pegivirus Encephalomyelitis Diagnosed Through Metagenomic Next-Generation Sequencing.}, journal = {Neurology}, volume = {105}, number = {6}, pages = {e214091}, doi = {10.1212/WNL.0000000000214091}, pmid = {40875928}, issn = {1526-632X}, mesh = {Humans ; Male ; *Opsoclonus-Myoclonus Syndrome/diagnosis/virology/drug therapy ; Young Adult ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Encephalomyelitis/diagnosis/virology ; *Flaviviridae/genetics ; Immunoglobulins, Intravenous/therapeutic use ; }, abstract = {This case of encephalomyelitis in a previously healthy 21-year-old man who developed opsoclonus-myoclonus demonstrates the diagnostic utility of clinically validated metagenomic next-generation sequencing (mNGS), followed by appropriate confirmation, in complex cases of encephalitis. In this patient, an extensive diagnostic workup was negative for infectious, inflammatory, demyelinating, autoimmune, and paraneoplastic etiologies. However, clinically validated mNGS of the CSF identified human pegivirus (HPgV) as a potential causative agent. A 5-day course of IV immunoglobulins (IVIg) led to the resolution of the opsoclonus-myoclonus. HPgV identification provided clinical and pathophysiologic insights: (1) a possible link between HPgV and CNS pathology, including brainstem neurotropism similar to other flaviviruses; (2) expansion of the opsoclonus-myoclonus differential to include HPgV; and (3) potential immune-mediated CNS involvement, suggested by the favorable response to IVIg. Although promising, broader mNGS use remains limited by biologic, technical, and logistic challenges.}, }
@article {pmid40874749, year = {2025}, author = {Gao, J and Han, W and Jiang, X and Xi, Y and Chen, Y and Huang, S and Huang, X and Zhang, Y and Zhang, T and Zhang, M and Zhang, W and Ni, B}, title = {Unexplored viral diversity in Siberian cranes and wild geese: metagenomic insights from a global wintering haven.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0075625}, doi = {10.1128/msystems.00756-25}, pmid = {40874749}, issn = {2379-5077}, abstract = {Migratory birds are critical global carriers and vectors of various viruses, potentially driving the mutation and transmission of novel pathogens, especially zoonotic viruses. Despite advancements in sequencing technologies, the viral diversity in wintering Siberian cranes (Leucogeranus leucogeranus) and wild geese (Anser spp.) remains poorly understood. In this study, we conducted a viral metagenomic survey of fecal samples from 320 Siberian cranes and wild geese wintering in Poyang Lake, China. Through this approach, we identified 183 novel viruses associated with known and putative vertebrate-infecting viruses, including a novel coronavirus, parvoviruses, picornaviruses, picobirnaviruses, anelloviruses, and CRESS-DNA viruses. Furthermore, we detected evidence of cross-species transmission and identified viruses with zoonotic potential, such as picobirnaviruses and picornaviruses. These findings highlight the significant public health risks posed by migratory birds and provide new insights into the viral diversity within these populations, contributing to a better understanding of their role in viral evolution and transmission.IMPORTANCEUnderstanding the diversity of enteroviruses in Siberian cranes and geese is essential for biodiversity conservation and ecosystem stability. As migratory birds, these species play key roles in ecological networks while carrying intestinal viruses that may spread along migration routes, which could pose potential risks to wildlife, poultry, and human health. This study systematically analyzed enterovirus diversity and the genetic characteristics of novel viruses in wintering Siberian cranes and geese at Poyang Lake using metagenomic sequencing. We identified viral sequences distantly related to known viruses and those with potential cross-species transmission risks. These findings highlight the diversity of migratory bird viruses and their public health implications, providing data to evaluate transmission risks and monitor emerging threats, supporting strategies for wildlife conservation and disease prevention.}, }
@article {pmid40874630, year = {2025}, author = {Flancman, R and Doster, E and Gomez, DE and Ricker, N and Morley, PS and Weese, JS}, title = {Enriched Shotgun Sequencing to Assess the Effects of Interventions to Reduce Antimicrobial Use in Neonatal Dairy Calves.}, journal = {Journal of veterinary internal medicine}, volume = {39}, number = {5}, pages = {e70234}, doi = {10.1111/jvim.70234}, pmid = {40874630}, issn = {1939-1676}, mesh = {Animals ; Cattle ; Feces/microbiology ; *Cattle Diseases/drug therapy/microbiology ; Animals, Newborn ; *Diarrhea/veterinary/drug therapy/microbiology ; *Anti-Bacterial Agents/therapeutic use ; Dairying ; Drug Resistance, Bacterial/genetics ; Shotgun Sequencing ; }, abstract = {BACKGROUND: Neonatal diarrhea accounts for 20%-25% of morbidity among calves, and antimicrobial drugs (AMDs) are often administered for treatment. Systematic approaches that mitigate antimicrobial use (AMU) can be effective in decreasing antimicrobial resistance (AMR).<br><br>HYPOTHESIS/OBJECTIVES: To determine the effects of an algorithmic farm-based intervention that reduced AMU for diarrhea on the community structure of antimicrobial resistance genes (ARGs) identified in the feces of healthy dairy calves.<br><br>ANIMALS: Thirty-one fecal dairy calf samples collected at two timepoints and farms (N&#x2009;=&#x2009;7-8 per sampling point) were used. Samples were obtained before AMU reductions and 12&#x2009;months afterward.<br><br>METHODS: Target-enriched shotgun sequencing was performed to characterize all ARGs in samples. Bioinformatics processing and statistical analysis were performed using the AMR++ pipeline, MEGARes AMR database, and R.<br><br>RESULTS: Pre-intervention comparisons showed increased relative abundances (RA) consistent with the AMU on each farm. Intra-farm results showed that on Farm 1, there were significant increases in the RA of ARGs for tetracyclines (22.1%-27.4%, q&#x2009;=&#x2009;0.02) and fluoroquinolones (0%-0.1%, q&#x2009;<&#x2009;0.0001) in the Post period. On Farm 2, significant decreases were seen over time in the RA of ARGs for sulfonamides (9.6%-5.1%, q&#x2009;=&#x2009;0.006) and fluoroquinolones (0.77%-0.12%, q&#x2009;=&#x2009;0.004).<br><br>Despite similar reductions in AMU on both farms, implementing an antimicrobial stewardship algorithm was associated with differing effects on and changes to the fecal resistome.}, }
@article {pmid40874431, year = {2025}, author = {Chen, J and Fang, J and Sun, L and Zhang, Z and Ma, Q and Wu, J and Chen, Y and Liao, K and Long, T and Xu, H}, title = {Multiple concurrent opportunistic infections in patient with myasthenia gravis: A case report.}, journal = {Virulence}, volume = {16}, number = {1}, pages = {2545570}, doi = {10.1080/21505594.2025.2545570}, pmid = {40874431}, issn = {2150-5608}, mesh = {Humans ; *Myasthenia Gravis/complications/drug therapy ; Male ; *Opportunistic Infections/drug therapy/microbiology/diagnosis ; Middle Aged ; Bronchoalveolar Lavage Fluid/microbiology ; Immunosuppressive Agents/adverse effects/therapeutic use ; Stenotrophomonas maltophilia/isolation &amp; purification ; Aspergillus fumigatus/isolation &amp; purification ; *Coinfection/microbiology ; }, abstract = {Myasthenia gravis (MG), a rare autoimmune disorder with poor prognosis, especially when complicated by opportunistic infections, which pose significant risks in clinical practice. We aimed to analyse a clinical case of a middle-aged male patient with MG, who developed severe lower gastrointestinal bleeding and multiple opportunistic infections post-immunosuppressive therapy. This case report is based on comprehensive clinical evaluations, including colonoscopy, histopathological examination, bronchoscopy, bronchoalveolar lavage (BAL), and metagenomic next-generation sequencing (mNGS). The patient exhibited persistent ptosis and pulmonary infection, and was treated with Meropenem 12 mg once daily (qd), Tacrolimus 2 mg qd, and Bromhexine 60 mg three times daily (tid). Due to ongoing lower gastrointestinal bleeding, surgery was performed. Colonoscopy revealed multiple ulcers, with histopathology confirming Cytomegalovirus (CMV) and Histoplasmosis infections. Bronchoalveolar lavage fluid (BALF) identified infections with Aspergillus fumigatus, Talaromyces, and Stenotrophomonas maltophilia. mNGS further detected Pneumocystis jirovecii. Based on these findings, the treatment plan was adjusted to include Amphotericin B complex 25 mg via intravenous (IV) qd, Tigecycline 100 mg q12h, and Sulfamethoxazole (SMZ) 0.96 g q6h for anti-infection, along with Ganciclovir 250 mg IV q12h. The patient continues to receive infusions of immunoglobulins and albumin. This case underscores the importance of monitoring MG patients on immunosuppressive therapy for opportunistic infections, emphasizing the complexity of managing multiple pathogens simultaneously.}, }
@article {pmid40873785, year = {2025}, author = {Bei, Q and Williams, NLR and Furtado, LE and Blasi, DD and Williams, J and Brotas, V and Tarran, G and Rees, AP and Bowler, C and Fuhrman, JA}, title = {Quantitative metagenomics for marine prokaryotes and photosynthetic eukaryotes.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf131}, pmid = {40873785}, issn = {2730-6151}, abstract = {High-throughput sequencing has provided unprecedented insights into microbial biodiversity in marine and other ecosystems. However, most sequencing-based studies report only relative (compositional) rather than absolute abundance, limiting their application in ecological modeling and biogeochemical analyses. Here, we present a metagenomic protocol incorporating genomic internal standards to quantify the absolute abundances of prokaryotes and eukaryotic phytoplankton, which together form the base of the marine food web, in unfractionated seawater. We applied this method to surface waters collected across 50°N to 40°S during the 29[th] Atlantic Meridional Transect. Using the single-copy recA gene, we estimated an average bacterial abundance of 1.0 × 10[9] haploid genome equivalents per liter. Leveraging a recent report that the psbO gene is typically single-copy in phytoplankton, we also quantified eukaryotic phytoplankton. Metagenomic estimates closely aligned with flow cytometry data for cyanobacteria (slope = 1.03, Pearson's r = 0.89) and eukaryotic phytoplankton (slope = 0.72, Pearson's r = 0.84). Compared to flow cytometry, taxonomic resolution for nano- and picoeukaryotes was greatly improved. Estimates for diatoms, dinoflagellates, and Trichodesmium were considerably higher than microscopy counts, likely reflecting microscopy undercounts and potential ploidy variation. These findings highlight the value of absolute quantification by metagenomics and offer a robust framework for quantitative assessments in microbial oceanography.}, }
@article {pmid40873745, year = {2025}, author = {Zhang, W and Wang, M and Xu, L and Wang, S}, title = {The First Reported Case of Infant Soft Tissues Infection Caused by Legionella Maceachernii: A Case Report and Literature Review.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {4241-4248}, pmid = {40873745}, issn = {1178-6973}, abstract = {Legionella spp. predominantly Legionella pneumophila, are recognized respiratory pathogens, while soft tissue infections caused by non-pneumophila species remain exceptionally rare. We present the first documented case of L. maceachernii soft tissue infection in an infant worldwide. The patient presented with fever accompanied by occipital, anterior thoracic, and wrist masses. Diagnosis was confirmed through metagenomic next-generation sequencing (mNGS) of tissue samples with histopathological correlation. Initial empiric therapy with vancomycin and cefotaxime yielded no clinical improvement. Subsequent mNGS analysis of cerebrospinal fluid and lesional tissue identified L. maceachernii infection, prompting targeted antimicrobial therapy with levofloxacin and rifampicin that resulted in clinical resolution. A review of historical cases reveals that Legionella soft tissue infections typically occur in immunocompromised hosts or those receiving immunosuppressive therapies, and this association prompted an investigation into possible congenital immunodeficiency in our patient. Whole exome sequencing coupled with Sanger sequencing validation identified a pathogenic mutation in the IL2RG gene, confirming X-linked severe combined immunodeficiency (X-SCID) in the infant and carrier status in the mother. This case highlights three paradigm-shifting concepts in pediatric infectious disease management, including 1) L. maceachernii should be included in the differential diagnosis of pediatric soft tissue infections refractory to standard therapy, 2) underlying immunodeficiency must be systematically evaluated in pediatric patients with atypical Legionella infections, and 3) the diagnostic utility of mNGS in identifying fastidious pathogens and underscore the importance of genomic investigations in elucidating immunological comorbidities.}, }
@article {pmid40873744, year = {2025}, author = {Zhu, Y and Jia, Y and Zhang, C and Li, H and Ding, P and Huang, L and Wang, G and Cai, H and Yu, W}, title = {Clinical Characteristics and Prognosis of Patients with Severe Pneumonia with Neurological Dysfunction: A Regional Multicenter Retrospective Study in Mainland China.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {4215-4226}, pmid = {40873744}, issn = {1178-6973}, abstract = {PURPOSE: Pneumonia is common in ICU patients with neurological dysfunction, but differences in pulmonary pathogen distribution in this population remain unclear. This study aimed to compare pathogen profiles, clinical features, and outcomes between ICU patients with and without neurological dysfunction.<br><br>METHODS: This regional multicenter retrospective study included adult patients with severe pneumonia admitted to intensive care units (ICUs) in 11&#xa0;hospitals across Zhejiang and Henan Provinces in mainland China between December 2018 and November 2023. All patients required invasive mechanical ventilation and underwent bronchoalveolar lavage fluid metagenomic next-generation sequencing (mNGS). Patients were classified into neurological dysfunction (ND) and without neurological dysfunction (WND) groups. Clinical characteristics, microbiological findings, and outcomes were compared. Propensity score matching (PSM) and Cox regression were used to assess prognosis.<br><br>RESULTS: Among 1737 patients, 636 (41.8%) were in the ND group. After PSM, the ND group showed a higher 28-day ICU mortality rate and shorter time to death compared to the WND group. However, ND was not identified as an independent risk factor for 28-day mortality in Cox analysis. The prevalence of Acinetobacter baumannii, Klebsiella pneumoniae, Burkholderia, Serratia marcescens, Elizabethkingia, Clostridium spp. and Ureaplasma was higher in ND patients. Significant differences in the prevalence of Haemophilus influenzae, Fusarium oxysporum, Fusobacterium nucleatum, Porphyromonas gingivalis, Mycobacterium abscessus, Escherichia coli, varicella-zoster virus (VZV), Epstein-Barr virus (EBV), and cytomegalovirus (CMV) were also observed.<br><br>CONCLUSION: ICU patients with neurological dysfunction exhibited distinct pulmonary pathogen profiles and worse outcomes. These findings may inform empirical antimicrobial strategies. Further prospective studies are warranted to validate these results.}, }
@article {pmid40873712, year = {2025}, author = {Gao, Q and Yang, J and Wu, J and Zhu, Y and Fan, D and Han, J}, title = {New perspectives under heterogeneity: mechanism of nutrient heterogeneity on Cd-induced hormesis of soil respiration.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1647658}, pmid = {40873712}, issn = {1664-302X}, abstract = {Hormesis is a phenomenon in which low doses of toxins stimulate organisms, while high doses have inhibitory effects. Soil heterogeneity nutrient spatial profoundly influences community structure and stress responses by altering the microenvironment around microorganisms. Studies on hormesis in soil ecosystems have made significant progress, but most of them have overlooked the impact of soil nutrient spatial heterogeneity on hormesis. To examine the effects of nutrient spatial heterogeneity on the hormesis of soil ecosystem under cadmium (Cd) stress, we constructed three patches with different spatial nutrient distribution but the same total nutrient content through different spatial discharge patterns. Different levels of Cd stress were applied to the patches, and after incubation, soil respiration rate, content of dissolved organic matter (DOM) and metagenomic characteristics were measured. The results indicated that higher nutrient spatial heterogeneity enhanced the tolerance of soil respiration to Cd stress (the maximum stimulating dose increased from 0.03 to 3.0 mg·kg[-1]), and simultaneously improved the compensation capacity (Hor zone increased from 0.04 to 21.59). The results also revealed that Cd stress had the least impact on soil microbial diversity of the high heterogeneity samples. The content of DOM initially displayed a hormesis-like phenomenon with increasing Cd stress, followed by a linear increase. Notably, the biphasic change trend became more pronounced as the degree of spatial heterogeneity increased (The maximum stimulation rate of DOM content increases from 10.8 to 22.9%). The hormetic response of soil respiration to nutrient spatial heterogeneity offers novel insights for the identification and mitigation of Cd pollution in ecosystems.}, }
@article {pmid40873709, year = {2025}, author = {Wong, GC and Jung, Y and Lee, K and Fourie, C and Handley, KM and Montgomery, JM and Taylor, MW}, title = {Effect of dietary zinc supplementation on the gastrointestinal microbiome and host gene expression in the Shank3B[-/-] mouse model of autism spectrum disorder.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1607045}, pmid = {40873709}, issn = {1664-302X}, abstract = {Shank gene variants are implicated in ~1% of people with autism, and mice lacking Shank3 exhibit autism-like behaviours. Zinc deficiency and gastrointestinal problems can be common among people with autism, and zinc is a key element required for SHANK protein function and gut development. In Shank3B[-/-] mice, a supplementary zinc diet reverses autism-like behaviours. We hypothesise that dietary zinc may alter the gut microbiome, potentially affecting the gut-microbiome-brain axis, which may contribute to changes in autism-like behaviours. To test this, four types of gastrointestinal samples (ileum, caecum, colon, faecal) were collected from Shank3B[-/-] wild-type and knock-out mice on either control or supplemented-zinc diets, enabling us to examine the influence of-and interactions between-dietary zinc, the gut microbiome, and ASD-linked host genotype. Cage, genotype, and zinc diet each contributed significantly to bacterial community variation (accounting for 12.8, 3.9, and 2.3% of the variation, respectively). Fungal diversity was significantly lower in Shank3B[-/-] compared with wild-type mice on the control zinc diet, with specific fungal biota signatures detected among gut locations. Host metabolic genes, which may be regulated by the gut microbiota, and host genes involved in antimicrobial interactions were more highly expressed in Shank3B[-/-] mice. Metagenomic analyses revealed differential abundance of bacterial fatty acid biosynthesis and transporters (including zinc transport and neurotransmitter receptors) among our experimental groups. Overall these suggested increased activity of, or a switch towards, metabolic and microbial-host interactions that may benefit both host and microbe, in the presence of zinc. This raises the potential of manipulating both dietary zinc and the gut microbiota itself to ameliorate ASD-related behaviours and associated gastrointestinal issues. These data broaden understanding of the gut microbiome in autism and pave the way towards potential microbial therapeutics for gastrointestinal problems in people with autism.}, }
@article {pmid40873708, year = {2025}, author = {Catarecha, P and King, E and Díaz-González, S and Caro, E and Sacristán, S and Del Pozo, JC}, title = {Heat stress and soil thermal gradients shape root-associated fungal community recruitment.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1334648}, pmid = {40873708}, issn = {1664-302X}, abstract = {Climate change is increasing the overall temperature of the planet and increasing the number of extreme heat waves events. These phenomena are negatively affecting crop production and food security. Thus, under this scenario, understanding the adaptations that encompass the plant response to high temperature will be essential to enhance crop tolerance and yield. Plant responses to elevated temperature rely on both genetic factors and the dynamic interplay with the surrounding microbiota. Recently, the role of root microbiota as a key player in the plant's response to heat, is gaining significant relevance. This work presents the analysis of fungal microbiota from the rhizosphere and the root-associated fractions of tomato roots in response to high temperature. Although the analyses were done in an enclosed environment, we used the TGRooZ (Temperature Gradient Root Zone) system to mimic field conditions. The TGRooZ generates a temperature gradient like the natural soil during a heat wave event. We found that distinct soil/root compartments assemble a different fungal community, with the rhizosphere fraction exhibiting greater diversity and abundance, while the root-associated fraction was enriched in fewer but more specialized taxa. Notably, the experimental conditions used to analyze heat responses significantly influenced the final microbiome composition. Our data suggest that the TGRooZ system will enable more accurate analysis of plant-microbiome responses to heat stress and help evaluate the potential of beneficial microbes to enhance crop productivity under near-natural conditions.}, }
@article {pmid40873645, year = {2025}, author = {Zhou, Y and Ni, Z and Liu, J and Sun, D and Shen, P and Chen, X and Li, G and Bai, Z and Hu, Y and Wang, N and Wang, R and Guan, L and Wang, Y and Tang, X and Lu, Y and He, B and Lu, H and Zhou, W and Gao, Y}, title = {Gut Microbiota-Associated Metabolites Affected the Susceptibility to Heart Health Abnormality in Young Migrants at High-Altitude: Gut Microbiota and Associated Metabolites Impart Heart Health in Plateau.}, journal = {Exploration (Beijing, China)}, volume = {5}, number = {4}, pages = {20240332}, pmid = {40873645}, issn = {2766-2098}, abstract = {Young migrants, particularly those at high altitudes, are predisposed to heart health abnormalities, including high-altitude heart disease. Despite the profound impact of hypobaric hypoxia on the gut microbial community, the understanding of the roles played by gut microbiota and gut microbiota-associated serum metabolites in high-altitude heart diseases remains limited. Therefore, we conducted a comprehensive multi-omics analysis involving 230 graduates from the same university, with 163 Tibetan Plateau migrants and 67 Chengdu Plain residents, and identified 206 differential metabolites (82 in serum and 124 in feces) and 369 species that differed between migrants and residents. Among these, 27 microbial species and four metabolites (Ketoglutaric acid, L-Aspartic acid, 3-Guanidinopropionic acid, betaine) detected in both serum and feces were found to be associated with migrants exhibiting compromised heart health, as diagnosed through clinical examinations. Notably, the abundances of Veillonella rogosae and Streptococcus rubneri were correlated with serum levels of L-Aspartic acid, betaine, and Ketoglutaric acid in heart health-abnormal individuals. Validation of these microbiome biomarkers and gut microbiota-associated serum metabolites in an independent cohort demonstrated their excellent predictive ability for indicating heart health abnormalities in migrants (AUC = 0.7857). Furthermore, supplementation with these identified species or gut microbiota-associated serum metabolites effectively mitigated hypobaric hypoxia-induced increases in serum lactate, glycolysis, myocardial damage, and cardiac hypertrophy. Integrated analysis revealed that the alterations in the gut microbiome negatively regulated key metabolic pathways such as the malate-aspartate shuttle, tricarboxylic acid cycle, and oxidative phosphorylation in heart health-abnormal individuals. The migration to high-altitude plateaus significantly reshaped the gut microbiome and metabolome signatures. Lower abundances of Veillonella rogosae, Streptococcus rubneri, and gut microbiota-associated serum metabolites promoted the remodeling of metabolic processes, thereby increasing susceptibility to high-altitude heart health abnormalities. Overall, our findings elucidate the microbial mechanisms underlying high-altitude heart disease and provide valuable insights for potential early intervention strategies in this context.}, }
@article {pmid40873449, year = {2025}, author = {Wang, Z and Chen, G and Sun, X and Xiao, J and Kong, L and Jiang, S and Xu, T and Wang, M and Zhao, H}, title = {Multi-omics integration reveals the impact of mediterranean diet on hepatic metabolism and gut microbiota in mice with metabolic dysfunction-associated steatotic liver disease.}, journal = {Frontiers in nutrition}, volume = {12}, number = {}, pages = {1644014}, pmid = {40873449}, issn = {2296-861X}, abstract = {OBJECTIVE: To investigate the effects of the Mediterranean diet (MD) on hepatic metabolism and gut microbiota in mice with metabolic dysfunction-associated steatotic liver disease (MASLD).<br><br>METHODS: C57BL/6 mice were fed a high-fat diet for 12 weeks to induce MASLD, with normal chow (NC)-fed mice as controls. Post-modeling, MASLD mice were randomized into three groups: HF (continued high-fat diet), HF-NC (switched to normal chow), and HF-MD (switched to MD). After 18-week interventions, body/liver weights, serum liver enzymes (ALT, AST), hepatic glycolipid markers (glucose, TC, TG, IBIL, DBIL), inflammatory cytokines (IL-6, TNF-&#x3b1;; ELISA), and histopathology (H&amp;E and Oil Red O staining) were analyzed. Gut microbiota (metagenomic sequencing) and short-chain fatty acids (SCFAs; targeted metabolomics) were profiled.<br><br>RESULTS: High-fat diet induced MASLD features including obesity, increased abdominal fat mass, hepatic steatosis with lipid droplets, and inflammation. Both HF-NC and HF-MD groups exhibited reduced body weight, liver index, hepatic cytokines, serum enzymes, and improved glucolipid profiles vs. HF group (p < 0.05), with histopathology confirming attenuated steatosis. HF-MD outperformed HF-NC in lowering ALT, AST, IL-6, and TNF-&#x3b1; (p < 0.05). MASLD mice showed gut dysbiosis characterized by decreased diversity, elevated Alistipes, Helicobacter, Mucispirillum, and Chlamydia, reduced SCFAs, and increased branched-chain fatty acids (BCFAs) (p < 0.05). Both dietary interventions partially ameliorated gut dysbiosis in MASLD mice, with the HF-MD group uniquely enriching beneficial taxa including Prevotella, Muribaculum, Duncaniella, and Barnesiella.<br><br>CONCLUSION: MD alleviates MASLD progression by synergistically improving hepatic metabolic homeostasis and gut microbiota composition, demonstrating superior efficacy over NC in mitigating inflammation, enriching beneficial microbes, and regulating microbial metabolism. These findings highlight MD's potential as a targeted dietary intervention for MASLD.}, }
@article {pmid40873311, year = {2025}, author = {Xia, D and Niu, Y and Tian, J and Wang, H and Jia, D and Huang, D and Wang, Z and Zhao, W}, title = {[Differential analysis of biogas production in simulated experiments of aquitard layers in coal seam fire zones].}, journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology}, volume = {41}, number = {8}, pages = {3064-3080}, doi = {10.13345/j.cjb.240657}, pmid = {40873311}, issn = {1872-2075}, mesh = {*Biofuels ; *Coal ; *Methane/metabolism/biosynthesis ; *Fires ; *Groundwater ; *Coal Mining ; Fermentation ; China ; Anaerobiosis ; }, abstract = {To explore the differences in biological gas production in the waterlogged zone of a coal seam fire-affected area, in this study the in-situ gas production experiment was conducted with the mine water from aquitard layers in coal seam fire zones in Xinjiang. The results showed that the biogas production first increased and then decreased with the increase in distance, and the highest gas production reached 216.55 mL. The changes in key metabolic pathways during the anaerobic fermentation of coal were analyzed, which showed that as the distance from the aquitard layer in the coal seam fire zone increased, the methanogenesis pathways gradually shifted from acetic acid decarboxylation and carbon dioxide reduction to acetic acid decarboxylation and methylamine methanogenesis. The significant variability in the in-situ mine water reservoir conditions contributed to the differences. In addition, the reservoir pressure and temperature increased as the distance from the fire zone became longer, and the salinity of the farthest mine water in the reverse fault was the highest due to the lack of groundwater supply. Pearson correlation analysis revealed significant correlations of microbial communities with key functional genes and the types and concentrations of ions. The ions significantly influencing microbial enzymatic metabolic activities included Al[3+], Fe[2+], Co[2+], Ni[2+], Cu[2+], Zn[2+], Mg[2+], PO4[3-], and Mo[6+]. The differences in metabolic pathways were attributed to the integrated effects of a co-occurring environment with multiple ions. The gas production simulation experiments and metagenomic analyses provide data support for the practical application of in-situ biogas experiments, laying a foundation for engineering applications.}, }
@article {pmid40872845, year = {2025}, author = {Nassuna, CA and Yiga, F and Nakaseegu, J and Amwine, E and Nakamoga, B and Ayuro, N and Owor, N and Odongo, D and Kiconco, J and Nsibambi, T and Wasike, S and Andagalu, B and Harrington, C and Crawley, AW and Ssempiira, J and Ransom, R and Boore, AL and Bakamutumaho, B and Kayiwa, JT and Lutwama, JJ}, title = {Detection of Influenza and Other Respiratory Pathogens by RT-qPCR and Characterization by Genomic Sequencing Using ILI/SARI Hospital-Based Sentinel Surveillance System.}, journal = {Viruses}, volume = {17}, number = {8}, pages = {}, doi = {10.3390/v17081131}, pmid = {40872845}, issn = {1999-4915}, mesh = {Humans ; Sentinel Surveillance ; Child, Preschool ; Child ; Infant ; *Influenza, Human/virology/epidemiology/diagnosis ; *Respiratory Tract Infections/virology/epidemiology/diagnosis ; Adolescent ; Female ; Adult ; Uganda/epidemiology ; Young Adult ; Male ; Real-Time Polymerase Chain Reaction ; SARS-CoV-2/genetics/isolation &amp; purification ; *Viruses/genetics/isolation &amp; purification/classification ; Genome, Viral ; COVID-19/virology ; }, abstract = {Limited surveillance and laboratory testing for non-influenza viruses remains a challenge in Uganda. The World Health Organization (WHO) designated National Influenza Center (NIC) tested samples from patients with influenza-like illness (ILI) and severe acute respiratory infections (SARIs) during August 2022-February 2023. We leveraged the influenza sentinel surveillance system to detect other respiratory viruses (ORVs). Samples were tested using the US Centers for Disease Control and Prevention (CDC) influenza and SARS-CoV-2 multiplex and the FTD[TM] Respiratory Pathogens 21 assays using real-time reverse transcription polymerase chain reaction (RT-qPCR). A total of 687 (ILI = 471 (68.6%) and SARI = 216 (31.4%) samples were tested. The median age was 2 years (IQR: 1-25) for ILI and 6 years (IQR: 1-18) for SARI case definitions (p-value = 0.045). One or more respiratory pathogens were detected in 38.7% (n = 266) of all samples; 33 (12.4%) were selected for metagenomics sequencing and 8 (3%) for SARS-CoV-2 targeted sequencing. Respiratory pathogens were detected by sequencing in 23 of 33 (69.7%) samples. Our study provides insight into the usefulness of this surveillance system in conducting virological testing for other viruses and provides tools and evidence to monitor patterns and characteristics of viruses causing ILI/SARI, which will guide public health decisions and interventions in Uganda.}, }
@article {pmid40872707, year = {2025}, author = {Elbehiry, A and Marzouk, E}, title = {Staphylococci in Livestock: Molecular Epidemiology, Antimicrobial Resistance, and Translational Strategies for One Health Protection.}, journal = {Veterinary sciences}, volume = {12}, number = {8}, pages = {}, doi = {10.3390/vetsci12080757}, pmid = {40872707}, issn = {2306-7381}, abstract = {Livestock-associated Staphylococcus species-particularly Staphylococcus aureus (S. aureus), Staphylococcus pseudintermedius (S. pseudintermedius), and coagulase-negative staphylococci (CoNS)-pose escalating threats to animal health, food safety, and public health due to their evolving antimicrobial resistance (AMR) profiles. This review synthesizes recent insights into the molecular epidemiology, resistance determinants, and host adaptation strategies of these pathogens across food-producing animals. We highlight the role of mobile genetic elements (MGEs), clonal dissemination, and biofilm formation in shaping multidrug resistance (MDR) patterns. Diagnostic advancements, including MALDI-TOF MS, whole-genome sequencing (WGS), and PCR-based assays, are discussed alongside treatment challenges arising from therapeutic failures and limited vaccine efficacy. The review critically examines current AMR surveillance gaps and the need for integrative One Health frameworks that encompass animals, humans, and the environment. Novel tools such as metagenomics, real-time genomic surveillance, and artificial intelligence (AI)-driven analytics are proposed to enhance predictive monitoring and resistance management. Together, these insights underscore the urgency of coordinated, evidence-based interventions to curb the spread of MDR staphylococci and safeguard One Health.}, }
@article {pmid40872676, year = {2025}, author = {Porter, MM and Davis, DJ and McAdams, ZL and Townsend, KS and Martin, LM and Wilhite, C and Johnson, PJ and Ericsson, AC}, title = {Alterations in the Microbiome of Horses Affected with Fecal Water Syndrome.}, journal = {Veterinary sciences}, volume = {12}, number = {8}, pages = {}, doi = {10.3390/vetsci12080724}, pmid = {40872676}, issn = {2306-7381}, abstract = {Fecal water syndrome (FWS) in horses is characterized by two-phase defecation, including both solid and liquid phases. While satisfactory explanations for FWS are unavailable, bacterial dysbiosis has been suggested as a contributing or causative factor. The objectives of this study were to determine whether fecal bacterial dysbiosis is associated with FWS in horses in the midwestern USA. Fecal samples were collected from horses with FWS and from unaffected horses at the same location. In total, 16S rRNA amplicon libraries produced from fecal bacterial DNA were sequenced using the Illumina sequencing platform. Significant differences in beta diversity were detected between affected and control horses (p = 7 × 10[-4], F = 1.51), and differential abundance testing identified several features enriched in affected and control horses. These results agree with prior work regarding specific features in the bacterial microbiome associated with FWS, including Alloprevotella spp., and suggest fecal dysbiosis is associated with FWS.}, }
@article {pmid40872549, year = {2025}, author = {Nunes, CB and Ranjan, K and Rodrigues, FP and Queiroz, MCV and Marina, CLF and Muehlmann, LA and Bocca, AL and Poças-Fonseca, MJ}, title = {Antifungal and Immunomodulatory Activities of Brazilian Savannah Solanum lypocarpum Tree-Associated Streptomyces Isolates.}, journal = {Pharmaceuticals (Basel, Switzerland)}, volume = {18}, number = {8}, pages = {}, doi = {10.3390/ph18081158}, pmid = {40872549}, issn = {1424-8247}, abstract = {Background/Objectives: Actinobacteria are one of the largest bacterial phyla. These microbes produce bioactive compounds, such as antifungals, antibiotics, immunological modulators, and anti-tumor agents. Studies on actinobacteria isolated from the Brazilian Savannah biome (Cerrado) are scarce and mostly address metagenomics or the search for hydrolytic enzyme-producing microbes. Solanum lycocarpum (lobeira) is a tree widely employed in regional gastronomy and pharmacopeia in Central Brazil. Methods: In this work, 60 actinobacteria isolates were purified from the rhizosphere of S. lycocarpum. Eight Streptomyces spp. isolates were selected for in vitro antifungal activity against Cryptococcus neoformans H99, the C. neoformans 89-610 fluconazole-tolerant strain, C. gattii NIH198, Candida albicans, C. glabrata, and C. parapsilosis. The ability of the aqueous extracts of the isolates to induce the in vitro secretion of tumor necrosis factor (TNF-α), nitric oxide (NO), interleukin-6 (IL-6), and IL-10 by murine macrophages was also evaluated. Results: All extracts showed antifungal activity against at least two yeast species. Streptomyces spp. LAP11, LDB2, and LDB17 inhibited C. neoformans growth by 40-93%. Most extracts (except LAP2) also inhibited C. gattii. None inhibited C. albicans, but all inhibited C. glabrata (40-90%). Streptomyces sp. LAP8 extract increased nitric oxide production by approximately 347-fold in murine macrophages, while LDB11 extract suppressed LPS-induced TNF-α production by 70% and simultaneously increased IL-10 secretion, suggesting immunosuppressive potential. Conclusions: The results revealed that Cerrado actinobacteria-derived aqueous extracts are potential sources of antifungal and immunomodulatory biocompounds.}, }
@article {pmid40872283, year = {2025}, author = {Aung, TT and How, CKQ and Chavatte, JM and Nazir, NB and Pena, EM and Ogden, B and Lim, GR and Paramastri, YA and Zitzow, LA and Chen, H and Nagarajan, N and Tan, KSW and Malleret, B}, title = {Assessing Zoonotic Risks of Blastocystis Infection in Singapore.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {8}, pages = {}, doi = {10.3390/pathogens14080773}, pmid = {40872283}, issn = {2076-0817}, support = {NUHSRO/2019/046/PDF/19//National University of Singapore/ ; NUHSRO/2018/006/SU/01//National University of Singapore/ ; A-8000685-00-00//National University of Singapore/ ; A-8000629-00-00//National University of Singapore/ ; OC-2021-1-25116//European Cooperation in Science &amp; Technology/ ; }, mesh = {*Blastocystis Infections/epidemiology/transmission/parasitology/veterinary ; Singapore/epidemiology ; *Blastocystis/genetics/classification/isolation &amp; purification ; Humans ; Animals ; *Zoonoses/epidemiology/parasitology/transmission ; Prevalence ; Macaca fascicularis/parasitology ; Risk Assessment ; }, abstract = {Blastocystis spp. is an enteric protist that is present worldwide. Despite being discovered a century ago, there is still much to be learned about its pathogenicity and transmission. Different subtypes (ST) of Blastocystis spp. have been identified in various hosts, including humans, birds, and insects, and there is potential for zoonotic transmission through contact between humans and animals. The prevalence of Blastocystis spp. in humans and macaques in Singapore was understudied, and the findings revealed a significant prevalence of the parasite, with rates of 90% and 100% observed in each respective Macaca fascicularis population 1 and 2, with main subtypes (ST1, ST2, ST3, and ST5). Using metagenomics, the different subtypes of Blastocystis spp. (comprising ST2, ST3, and ST17) were identified in a healthy Singaporean cohort. Additionally, seven incidental findings of Blastocystis spp. were discovered in human patients with other gut parasites, including two ST1, two ST2, two ST3, and one ST8. Several factors such as diet or reverse zoonotic transmission are suggested to play a role in Blastocystis sp. subtype distribution.}, }
@article {pmid40872269, year = {2025}, author = {Britto Martins de Oliveira, J and Barbieri, M and Corrêa-Junior, D and Schmitt, M and Santos, LLR and Bahia, AC and Parente, CET and Frases, S}, title = {Urban Mangroves Under Threat: Metagenomic Analysis Reveals a Surge in Human and Plant Pathogenic Fungi.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {8}, pages = {}, doi = {10.3390/pathogens14080759}, pmid = {40872269}, issn = {2076-0817}, support = {CNE//FAPERJ/ ; 001//CAPES/ ; BP//CNPQ/ ; }, mesh = {*Metagenomics/methods ; *Fungi/genetics/classification/isolation &amp; purification ; Humans ; *Wetlands ; Ecosystem ; Biodiversity ; Mycobiome ; Geologic Sediments/microbiology ; }, abstract = {Coastal ecosystems are increasingly threatened by climate change and anthropogenic pressures, which can disrupt microbial communities and favor the emergence of pathogenic organisms. In this study, we applied metagenomic analysis to characterize fungal communities in sediment samples from an urban mangrove subjected to environmental stress. The results revealed a fungal community with reduced richness-28% lower than expected for similar ecosystems-likely linked to physicochemical changes such as heavy metal accumulation, acidic pH, and eutrophication, all typical of urbanized coastal areas. Notably, we detected an increase in potentially pathogenic genera, including Candida, Aspergillus, and Pseudoascochyta, alongside a decrease in key saprotrophic genera such as Fusarium and Thelebolus, indicating a shift in ecological function. The fungal assemblage was dominated by the phyla Ascomycota and Basidiomycota, and despite adverse conditions, symbiotic mycorrhizal fungi remained present, suggesting partial resilience. A considerable fraction of unclassified fungal taxa also points to underexplored microbial diversity with potential ecological or health significance. Importantly, this study does not aim to compare pristine and contaminated environments, but rather to provide a sanitary alert by identifying the presence and potential proliferation of pathogenic fungi in a degraded mangrove system. These findings highlight the sensitivity of mangrove fungal communities to environmental disturbance and reinforce the value of metagenomic approaches for monitoring ecosystem health. Incorporating fungal metagenomic surveillance into environmental management strategies is essential to better understand biodiversity loss, ecological resilience, and potential public health risks in degraded coastal environments.}, }
@article {pmid40872213, year = {2025}, author = {Raza, A and Ling, SJ and Wei, YL and Bahadur, S and Ren, MX}, title = {Facilitation in the Dry Season: Species Interactions Between a Limestone-Endemic Plant and Moss Altered by Precipitation Dynamics.}, journal = {Plants (Basel, Switzerland)}, volume = {14}, number = {16}, pages = {}, doi = {10.3390/plants14162588}, pmid = {40872213}, issn = {2223-7747}, support = {ZDYF2023RDYL01//Hainan Tropical Rainforest Conservation/ ; 42371054//National Natural Science Foundation of China/ ; }, abstract = {Plant-to-plant interactions are essential for structuring plant communities and supporting adaptation in nutrient-poor, seasonally dry environments. This study examined the interactions between moss Leucobryum aduncum Dozy &amp; Molk and Oreocharis hainanensis by analyzing microbial communities and physicochemical parameters across various sample types. These included soil [bare (B), O. hainanensis (O), moss (M), and moss + O. hainanensis (MO)], rhizosphere soil [O. hainanensis (ORS), moss (MRS), and moss + O. hainanensis (MORS)], and root [O. hainanensis (OHR), moss (MR), and moss + O. hainanensis (MOR)] using metagenomics sequencing across dry and wet seasons in limestone habitats on Hainan Island. During the dry season, combined plant samples MOR, MO, and MORS showed higher nutrients, supported by microbes that enhance nutrient turnover, which may indicate facilitation. Conversely, during the wet season, increased moisture leads to decreased nutrient levels and microbial communities shift, associated with slower nutrient turnover in combined plant samples, which may reflect competition. According to KEGG analysis, an increase in oxidative phosphorylation and ABC transporters in the dry season supported the facilitative interaction, while quorum sensing and two-component systems supported the competitive interaction in the wet season. These findings show how shifts between facilitation and competition arise from seasonal conditions and microbes in the limestone ecosystem.}, }
@article {pmid40872157, year = {2025}, author = {Nityagovsky, NN and Ananev, AA and Suprun, AR and Dneprovskaya, AA and Kiselev, KV and Aleynova, OA}, title = {Endophytic Bacterial and Fungal Communities of Spruce Picea jezoensis in the Russian Far East.}, journal = {Plants (Basel, Switzerland)}, volume = {14}, number = {16}, pages = {}, doi = {10.3390/plants14162534}, pmid = {40872157}, issn = {2223-7747}, support = {22-74-10001//Russian Science Foundation/ ; 124012200181-4//Ministry of Science and Higher Education of the Russian Federation/ ; }, abstract = {A wide range of microorganisms, including endophytes, frequently interact with forest trees. The role of endophytes in industrial conifers has not been fully investigated. The Yezo spruce Picea jezoensis is widely used for logging in Russia and Japan. In this work, the endophytic communities of bacteria and fungi in healthy needles, branches, and fresh wood of P. jezoensis from Primorsky Territory were analyzed using metagenomic analysis. The results indicate that the diversity of endophytic communities in P. jezoensis is predominantly influenced by the specific tree parts (for both bacteria and fungi) and by different tree specimens (for fungi). The most abundant bacterial classes were Alphaproteobacteria, Gammaproteobacteria and Actinobacteria. Functional analysis of KEGG orthologs (KOs) in endophytic bacterial community using PICRUSt2 and the PLaBAse PGPT ontology revealed that 59.5% of the 8653 KOs were associated with plant growth-promoting traits (PGPTs), mainly, colonization, stress protection, bio-fertilization, bio-remediation, vitamin production, and competition. Metagenomic analysis identified a high abundance of the genera Pseudomonas and Methylobacterium-Methylorubrum in P. jezoensis, which are known for their potential growth-promoting activity in other coniferous species. The dominant fungal classes in P. jezoensis were Dothideomycetes, Sordariomycetes, and Eurotiomycetes. Notably, the genus Penicillium showed a pronounced increase in relative abundance within the fresh wood and needles of Yezo spruce, while Aspergillus displayed elevated abundance specifically in the fresh wood. It is known that some of these fungi exhibit antagonistic activity against phytopathogenic fungi. Thus, our study describes endophytic communities of the Yezo spruce and provides a basis for the production of biologicals with potential applications in forestry and agriculture.}, }
@article {pmid40872129, year = {2025}, author = {Mametja, NM and Ramadwa, TE and Managa, M and Masebe, TM}, title = {Recent Advances and Developments in Bacterial Endophyte Identification and Application: A 20-Year Landscape Review.}, journal = {Plants (Basel, Switzerland)}, volume = {14}, number = {16}, pages = {}, doi = {10.3390/plants14162506}, pmid = {40872129}, issn = {2223-7747}, abstract = {Bacterial endophytes have emerged as critical components of plant microbiomes, offering multifaceted benefits ranging from growth promotion to stress resilience. This review synthesizes two decades of research, from 2004 to 2024, on bacterial endophyte identification and applications, highlighting advances in both traditional culture-based techniques and modern omics approaches. The review also focuses on interactions between these microorganisms and their host plants, emphasizing their roles in biocontrol, phytoremediation, and nanoparticle biosynthesis. While significant progress has been made in characterizing cultivable bacterial endophytes, challenges persist in accessing unculturable species and understanding strain-specific functional mechanisms. The integration of metagenomics, metatranscriptomics, and metabolomics has begun unraveling this hidden diversity, revealing novel metabolic pathways and plant-microbe communication systems. There have been limitations in endophyte isolation protocols and field applications, and therefore a need exists for standardized frameworks to bridge lab-based discoveries with agricultural practices. Cutting-edge multi-omics techniques, such as genomics, transcriptomics, metabolomics, proteomics, and phenomics, should be used more in future research to clarify the mechanistic underpinnings of plant-endophyte interactions to thoroughly profile the microbial communities and unlock their functional potential under diverse environmental conditions. Overall, bacterial endophytes present viable paths toward sustainable farming methods, supporting food security and crop resilience in the face of environmental difficulties by providing a transformative opportunity for next-generation agriculture, mitigating climate-related agricultural stressors, reducing dependence on synthetic agrochemicals, and enhancing crop productivity.}, }
@article {pmid40872081, year = {2025}, author = {Goche, T and Mavindidze, P and Zenda, T}, title = {Advances in Functional Genomics for Exploring Abiotic Stress Tolerance Mechanisms in Cereals.}, journal = {Plants (Basel, Switzerland)}, volume = {14}, number = {16}, pages = {}, doi = {10.3390/plants14162459}, pmid = {40872081}, issn = {2223-7747}, abstract = {Climate change, population growth and the increasing demand for food and nutritional security necessitate the development of climate-resilient cereal crops. This requires first gaining mechanistic insights into the molecular mechanisms underpinning plant abiotic and biotic stress tolerance. Although this is challenging, recent conceptual and technological advances in functional genomics, coupled with computational biology, high-throughput plant phenotyping and artificial intelligence, are now aiding our uncovering of the molecular mechanisms underlying plant stress tolerance. Integrating other innovative approaches such as genome editing, modern plant breeding and synthetic biology facilitates the development of climate-smart cereal crops. Here, we discuss major recent advances in plant functional genomic approaches and techniques such as third-generation sequencing, transcriptomics, pangenomes, genome-wide association studies and epigenomics, which have advanced our understanding of the molecular basis of stress tolerance and development of stress-resilient cereals. Further, we highlight how these genomics approaches are successfully integrated into new plant breeding methods for effective development of stress-tolerant crops. Overall, harnessing these advances and improved knowledge of crop stress tolerance could accelerate development of climate-resilient cereals for global food and nutrition security.}, }
@article {pmid40871697, year = {2025}, author = {Wang, B and Peters-Samuelson, BA and Luo, K and Cordero, C and Perreira, KM and Pirzada, A and Daviglus, ML and Li, Y and Kaplan, RC and Burk, RD and Qi, Q}, title = {Interplays of ADH1B Genotype, Alcohol Consumption, and Gut Microbiota in Relation to Insulin Resistance.}, journal = {Nutrients}, volume = {17}, number = {16}, pages = {}, doi = {10.3390/nu17162669}, pmid = {40871697}, issn = {2072-6643}, support = {R01-DK119268/DK/NIDDK NIH HHS/United States ; R01-DK126698/DK/NIDDK NIH HHS/United States ; R01-DK120870/DK/NIDDK NIH HHS/United States ; P30DK111022/DK/NIDDK NIH HHS/United States ; R01-MD011389/MD/NIMHD NIH HHS/United States ; UM1-HG008898/HG/NHGRI NIH HHS/United States ; R01-HL060712//National Heart Lung and Blood Institute/ ; R01-HL140976//National Heart Lung and Blood Institute/ ; R01-HL136266//National Heart Lung and Blood Institute/ ; }, mesh = {Humans ; *Alcohol Dehydrogenase/genetics ; *Insulin Resistance/genetics ; *Gastrointestinal Microbiome/genetics ; *Alcohol Drinking/genetics ; Male ; Female ; Cross-Sectional Studies ; Middle Aged ; *Genotype ; Adult ; Feces/microbiology ; Longitudinal Studies ; }, abstract = {BACKGROUND/OBJECTIVE: Alcohol consumption has been linked to alterations in gut microbiota and insulin resistance. The alcohol dehydrogenase 1B (ADH1B) gene plays a crucial role in alcohol catabolism, where rs1229984 variant carriers (CT/TT) catabolize ethanol at an 80-fold faster rate than non-carriers (CC). This study investigates the relationships between ADH1B gene rs1229984 mutation, alcohol consumption, gut microbiota, and insulin resistance.<br><br>METHODS: We performed cross-sectional analysis on fecal metagenomic sequencing data from diabetes-free participants in a longitudinal cohort of the Hispanic Community Health Study/Study of Latinos. We used Analysis of Composition of Microbiomes to identify gut microbial species associated with alcohol consumption in non-carriers (n = 1399) and carriers (n = 193). We constructed genotype-specific gut microbiome scores (GMSs) based on the identified species associated with alcohol consumption to examine how gut microbiota may influence the relationship between alcohol consumption and insulin resistance across ADH1B genotypes. Insulin resistance was defined as Homeostatic Model Assessment for Insulin Resistance (HOMA-IR) > 2.5.<br><br>RESULTS: Distinct microbial species associated with alcohol consumption were identified in non-carriers (54 species) and carriers (16 species). In non-carriers, the genotype-specific GMS modified the relationship between alcohol consumption and insulin resistance (Pinteraction = 0.011). The odds ratios (OR) for insulin resistance with increasing alcohol consumption levels across low, moderate, and high tertiles of GMS were 0.75 (95%CI 0.58-0.96), 0.82 (0.67-1), and 1.13 (0.93-1.39), respectively. We identified that individual alcohol-related species, such as Prevotella copri, Ruminococcus callidus, and Erysipelatoclostridium ramosum, modified the relationship between alcohol consumption and insulin resistance in non-carriers.<br><br>CONCLUSIONS: This study suggests that the ADH1B gene rs1229984 mutation is associated with gut microbiota profiles altered by alcohol consumption. Our findings also suggest a potential role of gut microbiota in the protective association between alcohol consumption and insulin resistance in the ADH1B variant non-carriers.}, }
@article {pmid40871467, year = {2025}, author = {Alanagreh, L and Mustafa, MA and Al-Zghoul, MB and Massadeh, MI and Batiha, O and Sughayer, M and Almashakbeh, RT and Abu Suilike, HB and Tout, FS and Alzoughool, F}, title = {Metagenomic Signatures of Colorectal Cancer in the Jordanian Population: A Regional Case-Control Analysis Using 16S rRNA Profiling.}, journal = {Microorganisms}, volume = {13}, number = {8}, pages = {}, doi = {10.3390/microorganisms13081963}, pmid = {40871467}, issn = {2076-2607}, support = {7/2024//The Hashemite University/ ; }, abstract = {The gut microbiota plays a pivotal role in developing colorectal cancer (CRC) through interactions with host immunity, metabolism, and inflammation. However, microbiome-based studies remain scarce in Middle Eastern populations, limiting regional insights into microbial signatures associated with CRC. This study aimed to characterize the gut microbiota profiles of Jordanian CRC patients using 16S rRNA gene sequencing and compare them to those of healthy controls from the GutFeeling KnowledgeBase (GutFeelingKB). Stool samples from 50 CRC patients were analyzed using Illumina iSeq targeting the V3-V4 region. Taxonomic profiling was conducted with a standardized 16S metagenomics pipeline and compared with GutFeelingKB reference data. CRC samples were enriched in Streptococcus, Enterococcus, Klebsiella, Escherichia, Citrobacter, Veillonella, Megamonas, and Eggerthella, while beneficial butyrate-producing genera such as Roseburia, Ruminococcus, Akkermansia, Faecalibacterium, and Bacteroides were significantly depleted. The absence of Fusobacterium nucleatum and Bacteroides fragilis-commonly seen in global studies-suggests region-specific microbial patterns. This study is the first metagenomic study profiling CRC-associated microbiota in Jordan. The findings reveal a dysbiotic microbial signature that reflects both global changes associated with CRC and local ecological influences. This research emphasizes the importance of population-specific microbiome studies and highlights the need to include appropriately matched controls in future investigations.}, }
@article {pmid40871445, year = {2025}, author = {Ghavami, SB and Moshiri, A and Bonaretti, C and Farmani, M and Squillario, M and Di Marco, E and Shahrokh, S and Balaii, H and Corrias, MV and Ponzoni, M and Sadeghi, A and Biassoni, R}, title = {Predictive Microbial Markers Distinguish Responders and Non-Responders to Adalimumab: A Step Toward Precision Medicine in Ulcerative Colitis.}, journal = {Microorganisms}, volume = {13}, number = {8}, pages = {}, doi = {10.3390/microorganisms13081941}, pmid = {40871445}, issn = {2076-2607}, support = {Ricerca Corrente to RB//Ministry of Health/ ; Ricerca Corrente to MP//Italian Ministry oh Health/ ; 2019.0880-ID ROL 32612 (RB)//Compagnia di San Paolo/ ; }, abstract = {Ulcerative colitis (UC) is a chronic, relapsing inflammatory disease of the colon, often associated with gut microbial dysbiosis. Although anti-TNF-α agents, such as Adalimumab (Cinnora[®]), are used to treat moderate-to-severe UC, the treatment response is highly variable. Identifying early microbial biomarkers of response could help support personalized therapeutic strategies and prevent unnecessary exposure to ineffective treatments. However, the long-term effects of anti-TNF therapy on both stool and mucosal microbiota remain poorly understood. This prospective longitudinal study included 23 corticosteroid-refractory or -dependent UC patients who started Adalimumab after endoscopy-confirmed flare-ups. Stool samples and inflamed colonic biopsies were collected at baseline, and 3 and 6 months. Microbiota profiling was performed using 16S rRNA sequencing. Microbial changes were analyzed over time and compared between responders (Mayo score 0-1) and non-responders (Mayo score ≥ 2). Sixty percent of patients achieved clinical remission. In responders, stool microbiota showed increased Bacteroidetes and decreased Proteobacteria abundances, along with an enrichment of beneficial taxa including Faecalibacterium prausnitzii, Bifidobacterium, and Akkermansia muciniphila. Mucosal microbiota exhibited persistent dysbiosis, characterized by an increase in Proteobacteria and a reduced Firmicutes/Proteobacteria ratio. Notably, responders showed distinct compartment-specific microbial changes, with a decrease in Gammaproteobacteria in stool and an increase in Corynebacterium in tissue. Adalimumab induces divergent microbial changes in stool and mucosa. While stool microbiota trends toward eubiosis in responders, persistent mucosal dysbiosis may reflect asymptomatic inflammation. These findings underscore the importance of niche-specific microbiome profiling in UC and support its integration into personalized treatment monitoring.}, }
@article {pmid40871434, year = {2025}, author = {Rincón-Rosales, R and Díaz-Hernández, M and Manzano-Gómez, LA and Rincón-Molina, FA and Ruíz-Valdiviezo, VM and Gen-Jiménez, A and Villalobos-Maldonado, JJ and Maldonado-Gómez, JC and Rincón-Molina, CI}, title = {Analysis of the Bacterial Community and Fatty Acid Composition in the Bacteriome of the Lac Insect Llaveia axin axin.}, journal = {Microorganisms}, volume = {13}, number = {8}, pages = {}, doi = {10.3390/microorganisms13081930}, pmid = {40871434}, issn = {2076-2607}, support = {22004.25-P//Tecnol&#xf3;gico Nacional de M&#xe9;xico/ ; 21914.25-P//Tecnol&#xf3;gico Nacional de M&#xe9;xico/ ; }, abstract = {Microbial symbioses play crucial roles in insect physiology, contributing to nutrition, detoxification, and metabolic adaptations. However, the microbial communities associated with the lac insect Llaveia axin axin, an economically significant species used in traditional lacquer production, remain poorly characterized. In this study, the bacterial diversity and community structure of L. axin axin were investigated using both culture-dependent and culture-independent (metagenomic) approaches, combined with fatty acid profile analysis. The insects were bred at the laboratory level, in controlled conditions, encompassing stages from eggs to adult females. Bacterial strains were isolated from bacteriomes and identified through 16S rRNA gene amplification and genomic fingerprinting through ARDRA analysis. Metagenomic DNA was sequenced using the Illumina MiSeq platform, and fatty acid profiles were determined by gas chromatography-mass spectrometry (GC-MS). A total of 20 bacterial strains were isolated, with Acinetobacter, Moraxella, Pseudomonas, and Staphylococcus detected in first-instar nymphs; Methylobacterium, Microbacterium, and Bacillus in pre-adult females; and Bacillus and Microbacterium in adults. Metagenomic analysis revealed key genera including Sodalis, Blattabacterium, and Candidatus Walczuchella, with Sodalis being predominant in early stages and Blattabacteriaceae in adults. Fatty acid analysis identified palmitic, oleic, linoleic, arachidic, and stearic acids, with stearic acid being the most abundant. These results suggest that dominant bacteria contribute to lipid biosynthesis and metabolic development in L. axin axin.}, }
@article {pmid40871408, year = {2025}, author = {Manzano-Gómez, LA and Rincón-Molina, CI and Martínez-Romero, E and Stopol-Martínez, SS and Santos-Santiago, A and Villalobos-Maldonado, JJ and Ruíz-Valdiviezo, VM and Rincón-Rosales, R}, title = {Native Rhizobial Inoculation Improves Tomato Yield and Nutrient Uptake While Mitigating Heavy Metal Accumulation in a Conventional Farming System.}, journal = {Microorganisms}, volume = {13}, number = {8}, pages = {}, doi = {10.3390/microorganisms13081904}, pmid = {40871408}, issn = {2076-2607}, abstract = {Enhancing crop productivity through biological strategies is critical for agriculture, particularly under conventional farming systems heavily reliant on chemical inputs. Plant probiotic bacteria offer promising alternatives by promoting plant growth and yield. This is the first field study to assess the effects of biofertilization with native rhizobial strains Rhizobium sp. ACO-34A, Sinorhizobium mexicanum ITTG-R7[T], and S. chiapasense ITTG-S70[T] on Solanum lycopersicum (tomato) cultivated under conventional farming conditions. Key parameters assessed include plant performance (plant height, plant stem width, plant dry weight, and chlorophyll content), fruit yield (fruits per plant, fruit height, fruit width, fruit weight, and estimated fruit volume), and macronutrient and micronutrient contents in plant tissue. Additionally, rhizospere bacterial communities were characterized through 16S rRNA amplicon sequencing to evaluate alpha and beta diversity. Inoculation with ITTG-R7[T] significantly improved plant height, stem width, and plant dry weight, while ITTG-S70[T] enhanced stem width and chlorophyll content. ACO-34A inoculation notably increased fruit number, size, and yield parameters. Moreover, inoculated plants exhibited reduced Fe and Cu accumulation compared to non-inoculated controls. Metagenomic analyses indicated that rhizobial inoculation did not significantly disrupt the native rhizosphere bacterial community. These findings highlight the potential of rhizobial strains as effective plant probiotics that enhance tomato productivity while preserving microbial community structure, supporting the integration of microbial biofertilizers into conventional farming systems.}, }
@article {pmid40871366, year = {2025}, author = {González, A and Fullaondo, A and Odriozola, A}, title = {Why Are Long-Read Sequencing Methods Revolutionizing Microbiome Analysis?.}, journal = {Microorganisms}, volume = {13}, number = {8}, pages = {}, doi = {10.3390/microorganisms13081861}, pmid = {40871366}, issn = {2076-2607}, support = {IT1547-22//Basque Government, Department of Education/ ; }, abstract = {Most of the knowledge available on the composition and functionality of microbial communities in different ecosystems comes from short-read sequencing methods. It implies limitations regarding taxonomic resolution, variant detection, and genome assembly contiguity. Long-read sequencing technologies can overcome these limitations, transforming the analysis of microbial community composition and functionality. It is essential to understand the characteristics of each sequencing technology to select the most suitable one for each microbiome study. This review aims to show how long-read sequencing methods have revolutionized microbiome analysis in ecosystems and to provide a practical tool for selecting sequencing methods. To this end, the evolution of sequencing technologies, their advantages and disadvantages for microbiome studies, and the new dimensions enabled by long-read sequencing technologies, such as virome and epigenetic analysis, are described. Moreover, desirable characteristics for microbiome sequencing technologies are proposed, including a visual comparison of available sequencing platforms. Finally, amplicon and metagenomics approaches and the sequencing depth are discussed when using long-read sequencing technologies in microbiome studies. In conclusion, although no single sequencing method currently possesses all the ideal features for microbiome analysis in ecosystems, long-read sequencing technologies represent an advancement in key aspects, including longer read lengths, higher accuracy, shorter runtimes, higher output, more affordable costs, and greater portability. Therefore, more research using long-read sequencing is recommended to strengthen its application in microbiome analysis.}, }
@article {pmid40871358, year = {2025}, author = {Wang, TKF and Tsang, HF and Wong, SCC and Leung, SWM}, title = {Cervical Actinomycosis Diagnosed via Metagenomic Next-Generation Sequencing of Formalin-Fixed Paraffin-Embedded Tissue: A Case Report and Literature Review.}, journal = {Microorganisms}, volume = {13}, number = {8}, pages = {}, doi = {10.3390/microorganisms13081855}, pmid = {40871358}, issn = {2076-2607}, support = {R-ZH5G//Lim Peng Suan Charitable Trust Research Grant/ ; }, abstract = {Actinomycosis is an uncommon but significant chronic bacterial infection affecting various parts of the body caused by Actinomyces species. Because of the nonspecific symptoms and rarity of the condition, the diagnosis of head-and-neck or cervicofacial actinomycosis is usually challenging and delayed. A 39-year-old woman presented with an enlarging right neck mass and dysphagia after steroid exposure for treatment of De Quervain thyroiditis. MRI showed a large irregular infiltration mass over the right side of her neck, with a multi-loculated rim-enhancing area over the right retropharyngeal space. Excisional biopsy of the lesion only showed evidence of acute on chronic inflammation, and the results of all microbiological testing (including bacterial culture, Gram-staining, and molecular detection) were negative. Metagenomic next-generation sequencing (mNGS) of the formalin-fixed paraffin-embedded (FFPE) tissue from the patient was performed. DNA of Actinomyces israelii and Methylobacterium was detected. The patient was confirmed to have cervical actinomycosis and completely recovered after 6 months of oral amoxicillin. Our patient is the first case utilizing mNGS on FFPE tissue to diagnose cervical actinomycosis. This case shows that mNGS is a promising, unbiased tool for detecting Actinomyces species in FFPE tissues and diagnosing cervical actinomycosis. It also highlights the diagnostic difficulties of cervical actinomycosis.}, }
@article {pmid40871329, year = {2025}, author = {McKay, S and Churchill, H and Hayward, MR and Klein, BA and Van Meulebroek, L and Ghyselinck, J and Marzorati, M}, title = {Effects of cRG-I Prebiotic Treatment on Gut Microbiota Composition and Metabolic Activity in Dogs In Vitro.}, journal = {Microorganisms}, volume = {13}, number = {8}, pages = {}, doi = {10.3390/microorganisms13081825}, pmid = {40871329}, issn = {2076-2607}, abstract = {Low-dose carrot rhamnogalacturonan-I (cRG-I) has shown consistent modulatory effects on the gut microbiota and immune function in humans. In this study we investigated its effects on the microbial composition and metabolite production of the gut microbiota of small (5-10 kg), medium-sized (10-27 kg), and large (27-45 kg) dogs, using inulin and xanthan as comparators. Fecal samples from six dogs of each size group were evaluated. Overall microbiome composition, assessed using metagenomic sequencing, was shown to be driven mostly by dog size and not treatment. There was a clear segregation in the metabolic profile of the gut microbiota of small dogs versus medium-sized and large dogs. The fermentation of cRG-I specifically increased the levels of acetate/propionate-producing Phocaeicola vulgatus. cRG-I and inulin were fermented by all donors, while xanthan fermentation was donor-dependent. cRG-I and inulin increased acetate and propionate levels. The responses of the gut microbiota of different sized dogs to cRG-I were generally consistent across donors, and interindividual differences were reduced. This, together with the significant increase in P. vulgatus during fermentation in both this study and an earlier human ex vivo study, suggests that this abundant and prevalent commensal species has a core capacity to selectively utilize cRG-I.}, }
@article {pmid40871308, year = {2025}, author = {Bonfanti, A and Silvestri, R and Novellino, E and Tenore, GC and Schiano, E and Iannuzzo, F and Reverberi, M and Faino, L and Beccaccioli, M and Sivori, F and Rizzello, CG and Mazzoni, C}, title = {Microbial Profiling of Buffalo Mozzarella Whey and Ricotta Exhausted Whey: Insights into Potential Probiotic Subdominant Strains.}, journal = {Microorganisms}, volume = {13}, number = {8}, pages = {}, doi = {10.3390/microorganisms13081804}, pmid = {40871308}, issn = {2076-2607}, support = {RD12318A998C70B8//Sapienza/ ; RG12218166E3EE68//Sapienza/ ; }, abstract = {Buffalo mozzarella cheese whey (CW) and ricotta cheese exhausted whey (RCEW) are valuable by-products of the Mozzarella di Bufala Campana PDO production chain. This study characterized their microbial communities using an integrated culture-dependent and -independent approach. Metabarcoding analysis revealed that the dominance of lactic acid bacteria (LAB), including Streptococcus thermophilus, Lactobacillus delbrueckii, and Lactobacillus helveticus, alongside diverse heat-resistant yeasts such as Cyberlindnera jadinii. Culture-based isolation identified subdominant lactic acid bacteria strains, not detected by sequencing, belonging to Leuconostoc mesenteroides, Enterococcus faecalis, and Enterococcus durans. These strains were further assessed for their probiotic potential. E. faecalis CW1 and E. durans RCEW2 showed tolerance to acidic pH, bile salts, and lysozyme, as well as a strong biofilm-forming capacity and antimicrobial activity against Bacillus cereus and Staphylococcus aureus. Moreover, bile salt resistance suggests potential functionality in cholesterol metabolism. These findings support the potential use of CW and RCEW as reservoirs of novel, autochthonous probiotic strains and underscore the value of regional dairy by-products in food biotechnology and gut health applications.}, }
@article {pmid40871304, year = {2025}, author = {Janković, V and Pantelic, B and Ponjavic, M and Marković, D and Radetić, M and Nikodinovic-Runic, J and Ilic-Tomic, T}, title = {Degradation of Synthetic and Natural Textile Materials Using Streptomyces Strains: Model Compost and Genome Exploration for Potential Plastic-Degrading Enzymes.}, journal = {Microorganisms}, volume = {13}, number = {8}, pages = {}, doi = {10.3390/microorganisms13081800}, pmid = {40871304}, issn = {2076-2607}, support = {451-03-136/2025-03/200042, 2025//Ministry of Science, Technological Development and Innovation of the Republic of Serbia/ ; 101046758 (EcoPlastiC)//European Union's Horizon Europe EIC Pathfinder program/ ; }, abstract = {Given the environmental significance of the textile industry, especially the accumulation of nondegradable materials, there is extensive development of greener approaches to fabric waste management. Here, we investigated the biodegradation potential of three Streptomyces strains in model compost on polyamide (PA) and polyamide-elastane (PA-EA) as synthetic, and on cotton (CO) as natural textile materials. Weight change of the materials was followed, while Fourier-Transform Infrared Spectroscopy (FTIR) and Scanning Electron Microscopy (SEM) were used to analyze surface changes of the materials upon biodegradation. The bioluminescence-based toxicity test employing Aliivibrio fischeri confirmed the ecological safety of the tested textiles. After 12 months, the increase of 10 and 16% weight loss, of PA-EA and PA, respectively, was observed in compost augmented with Streptomyces sp. BPS43. Additionally, a 14% increase in cotton degradation was recorded after 2 months in compost augmented with Streptomyces sp. NP10. Genome exploration of the strains was carried out for potential plastic-degrading enzymes. It highlighted BPS43 as the most versatile strain with specific amidases that show sequence identity to UMG-SP-1, UMG-SP-2, and UMG-SP-3 (polyurethane degrading enzymes identified from compost metagenome). Our results showcase the behavior of Streptomyces sp. BPS43 in the degradation of PA and PA-EA textiles in composting conditions, with enzymatic potential that could be further characterized and optimized for increased synthetic textile degradation.}, }
@article {pmid40871298, year = {2025}, author = {Yu, C and Li, Y and Zhou, Q and Liu, W and Liao, Y and Pan, J and Chen, Q and He, H and Wang, Z}, title = {Effects of Paramisgurnus dabryanus Density on the Growth Performance of Pelophylax nigromaculatus and the Soil Microbial Communities Within a Rice-Frog-Loach Integrated Aquaculture System.}, journal = {Microorganisms}, volume = {13}, number = {8}, pages = {}, doi = {10.3390/microorganisms13081794}, pmid = {40871298}, issn = {2076-2607}, support = {CARS-46//China Agriculture Research System of MOF and MARA/ ; JXARS-15//Jiangxi Province Famous, Special, and High-quality Aquatic Products Research System/ ; }, abstract = {This investigation examines the influence of P. dabryanus density on the growth performance of P. nigromaculatus and the structural and functional dynamics of paddy soil microbial communities within a rice-frog-loach integrated aquaculture system. Field experiments were conducted with five density gradients of P. dabryanus (0.5, 1.0, 1.5, 2.0, and 2.5 × 10[4] individuals/667 m[2]), designated as RFLS0.5, RFLS1.0, RFLS1.5, RFLS2.0, and RFLS2.5, respectively. Control treatments included rice monoculture (RM) and rice-frog co-culture (RFS). These findings demonstrated that as the density of loach increased, the weight gain ratio of P. nigromaculatus showed a unimodal pattern, reaching its peak in RFLS1. Metagenomic analysis on paddy soil revealed that the RFLS1 facilitated the enrichment of nitrogen-fixing bacteria (Proteobacteria), while concurrently suppressing proliferation of the potential pathogen Pseudomonas aeruginosa and microbial markers in metal-contaminated environments of Usitatibacter rugosus. Further, functional profiling indicated that RFLS1 group reached a peak activity in amino acid metabolism (14.52 ± 0.09%) and carbohydrate metabolism (14.44 ± 0.06%) and showed a higher proportion of glycosyltransferase (GT) abundance (41.93 ± 0.02%) than other groups. In summary, the optimal stocking density of P. dabryanus in rice-frog-loach integrated systems was determined to be 1.0 × 10[4] individuals/667 m[2]. This density not only promotes the growth of P. nigromaculatus but also improves the structure of paddy soil microbial communities.}, }
@article {pmid40871296, year = {2025}, author = {Montalvo-Fernández, G and Ortiz-Alcantara, JM and Durruty-Lagunes, C and Espinosa-Asuar, L and Reyes-Sosa, MB and Arena-Ortiz, ML}, title = {Composition and Structure of Gut Microbiota of Wild and Captive Epinephelus morio via 16S rRNA Analysis and Functional Prediction.}, journal = {Microorganisms}, volume = {13}, number = {8}, pages = {}, doi = {10.3390/microorganisms13081792}, pmid = {40871296}, issn = {2076-2607}, support = {PAPIIT IT200522//Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; }, abstract = {The gut microbiota plays an essential role in the host's metabolism. Its composition and structure depend on biological and environmental factors. This work was designed to identify the composition and structure of the wild and captive red grouper (Epinephelus morio) microbiota and make predictions regarding its metabolic functions. Our hypothesis stated that wild and captive individuals would share the most abundant taxonomic groups, forming a core microbiota, and individuals in captivity might have exclusive taxonomic groups. Metagenomic DNA was extracted from the intestinal contents of wild and captive individuals. The 16S rRNA gene was amplified and sequenced using Illumina pair-end technology. QIIME2 pipeline was used for sequence analysis and alpha and beta diversity assessment. PICRUSt was used to infer metabolic functions. Twenty-nine phyla were identified; the most abundant were Pseudomonadota, Bacillota, Fusobacteriota, and Actinomycetota. The dominant genera were Photobacterium, Vibrio, Cetobacterium, and Escherichia-Shigella. The metabolic prediction analysis suggested that the Epinephelus morio gut microbiota is related to food digestion, the immune system, antioxidant enzymes, antibiotic resistance, and vitamin B12 transport. We concluded that the microbiota of E. morio established in captivity is sensitive to environmental changes such as water pollution, which can cause a decrease in diversity.}, }
@article {pmid40871274, year = {2025}, author = {Fernández-Carro, E and Letsiou, S and Tsironi, S and Chaniotis, D and Ciriza, J and Beloukas, A}, title = {Alternatives Integrating Omics Approaches for the Advancement of Human Skin Models: A Focus on Metagenomics, Metatranscriptomics, and Metaproteomics.}, journal = {Microorganisms}, volume = {13}, number = {8}, pages = {}, doi = {10.3390/microorganisms13081771}, pmid = {40871274}, issn = {2076-2607}, abstract = {The human skin microbiota, a complex community of bacterial, fungal, and viral organisms, plays a crucial role in maintaining skin homeostasis and regulating host-pathogen interactions. Dysbiosis within this microbial ecosystem has been implicated in various dermatological conditions, including acne vulgaris, psoriasis, seborrheic dermatitis, and atopic dermatitis. This review, for the first time, provides recent advancements in all four layers of omic technologies-metagenomics, metatranscriptomics, metaproteomics, and metabolomics-offering comprehensive insights into microbial diversity, in the context of functional skin modeling. Thus, this review explores the application of these omic tools to in vitro skin models, providing an integrated framework for understanding the molecular mechanisms underlying skin-microbiota interactions in both healthy and pathological contexts. We highlight the importance of developing advanced in vitro skin models, including the integration of immune components and endothelial cells, to accurately replicate the cutaneous microenvironment. Moreover, we discuss the potential of these models to identify novel therapeutic targets, enabling the design of personalized treatments aimed at restoring microbial balance, reinforcing the skin barrier, and modulating inflammation. As the field progresses, the incorporation of multi-omic approaches into skin-microbiome research will be pivotal in unraveling the complex interactions between host and microbiota, ultimately advancing therapeutic strategies for skin-related diseases.}, }
@article {pmid40871269, year = {2025}, author = {Haynes, E and Macarthur, R and Kennedy, M and Conyers, C and Pufal, H and McGreig, S and Walshaw, J}, title = {Metagenomic Analysis of Ready-to-Eat Foods on Retail Sale in the UK Identifies Diverse Genes Related to Antimicrobial Resistance.}, journal = {Microorganisms}, volume = {13}, number = {8}, pages = {}, doi = {10.3390/microorganisms13081766}, pmid = {40871269}, issn = {2076-2607}, support = {FS301050//Food Standards Agency/ ; }, abstract = {Antimicrobial Resistance (AMR), i.e., the evolution of microbes to become resistant to chemicals used to control them, is a global public health concern that can make bacterial diseases untreatable. Inputs including antibiotics, metals, and biocides can create an environment in the agrifood chain that selects for AMR. Consumption of food represents a potential exposure route to AMR microbes and AMR genes (ARGs), which may be present in viable bacteria or on free DNA. Ready-to-eat (RTE) foods are of particular interest because they are eaten without further cooking, so AMR bacteria or ARGs that are present may be consumed intact. They also represent varied production systems (fresh produce, cooked meat, dairy, etc.). An evidence gap exists regarding the diversity and consumption of ARGs in RTE food, which this study begins to address. We sampled 1001 RTE products at retail sale in the UK, in proportion to their consumption by the UK population, using National Diet and Nutrition Survey data. Bacterial DNA content of sample extracts was assessed by 16S metabarcoding, and 256 samples were selected for metagenomic sequencing for identification of ARGs based on consumption and likely bacterial DNA content. A total of 477 unique ARGs were identified in the samples, including ARGs that may be involved in resistance to important antibiotics, such as colistin, fluoroquinolones, and carbapenems, although phenotypic AMR was not measured. Based on the incidence of ARGs in food types, ARGs are estimated to be present in a high proportion of average diets. ARGs were detected on almost all RTE food types tested (48 of 52), and some efflux pump genes are consumed in 97% of UK diets.}, }
@article {pmid40871254, year = {2025}, author = {Babenkova, P and Gureev, A and Sadovnikova, I and Burakova, I and Smirnova, Y and Pogorelova, S and Morozova, P and Gribovskaya, V and Adzhemian, D and Syromyatnikov, M}, title = {Changes in L-Carnitine Metabolism Affect the Gut Microbiome and Influence Sexual Behavior Through the Gut-Testis Axis.}, journal = {Microorganisms}, volume = {13}, number = {8}, pages = {}, doi = {10.3390/microorganisms13081751}, pmid = {40871254}, issn = {2076-2607}, support = {FZGW-2024-0003//Ministry of Science and Higher Education of the Russian Federation/ ; }, abstract = {L-carnitine and Mildronate are substances that can significantly rearrange the energy metabolism of cells. This can potentially cause changes in the bacterial composition of the gut microbiome and affect testis functionality and male sexual health. Mice of the C57Bl/6 line were used. Sexual behavior was assessed using physiological tests, and gene expression patterns were assessed by qPCR. High-throughput sequencing of mouse fecal microbiota was performed. We showed that long-term administration of Mildronate has no significant effect on the intestinal microbiome, and there was a compensatory increase in the expression of genes involved in fatty acid and leptin metabolism. No impairment of sexual motivation in male mice was observed. Prolonged L-carnitine supplementation caused a decrease in alpha diversity of bacteria and a decrease in some groups of microorganisms that are components of a healthy gut microflora. A correlation was observed between the level of bacteria from Firmicutes phylum, indicators of sexual motivation of mice, and the dynamics of body weight gain. Our results may indicate that metabolic modulators can have a significant impact on the structure of the bacterial community of the gut microbiome, which may influence male sexual health through the gut-semen axis.}, }
@article {pmid40871228, year = {2025}, author = {Nicod, O and Tré-Hardy, M and Baillon, B and Beukinga, I and Ngatchou, W and Riahi, N and Blairon, L}, title = {Polymicrobial Arthritis Following a Domestic Cat Bite Involving Rahnella aquatilis in an Immunocompetent Patient.}, journal = {Microorganisms}, volume = {13}, number = {8}, pages = {}, doi = {10.3390/microorganisms13081725}, pmid = {40871228}, issn = {2076-2607}, abstract = {Cat bites frequently lead to polymicrobial infections due to deep puncture wounds that inoculate oral flora into poorly oxygenated tissues. While Pasteurella multocida is the most commonly implicated organism, environmental and atypical pathogens may also play a role, yet often go unrecognized. This article reports a rare case of polymicrobial septic arthritis caused by a domestic cat bite in an immunocompetent adult, with isolation of Rahnella aquatilis, a freshwater-associated Enterobacterales species not previously reported in this context. A 33-year-old immunocompetent male presented with acute hand swelling, pain, and functional impairment within 24 h of the bite. Emergency surgery revealed purulent tenosynovitis and arthritis. Intraoperative cultures identified R. aquatilis, P. multocida, and Pantoea agglomerans. Identification was performed using MALDI-TOF MS. The R. aquatilis isolate was susceptible to beta-lactams (excluding ampicillin), quinolones, and co-trimoxazole. The patient received amoxicillin-clavulanic acid and fully recovered within two weeks. This is the first reported case of joint infection involving R. aquatilis following a cat bite. It highlights the importance of considering environmental Enterobacterales in animal bite wounds, and the utility of advanced microbiological tools for detecting uncommon pathogens. Broader awareness may improve diagnosis and guide targeted therapy in polymicrobial infections.}, }
@article {pmid40871218, year = {2025}, author = {Sorongpong, S and Debnath, S and Rahi, P and Bera, B and Pandey, P}, title = {Sustainable Tea Cultivation with a Rhizobacterial Consortium: A Microbiome-Driven Alternative to Chemical Fertilizers.}, journal = {Microorganisms}, volume = {13}, number = {8}, pages = {}, doi = {10.3390/microorganisms13081715}, pmid = {40871218}, issn = {2076-2607}, support = {GBPNI/NMHS-2018-19/MG 1//This research was funded by the G.B. Pant National Institute of Hima-layan Environment and Sustainable Development, Ministry of Envi-ronment, Forest &amp; Climate Change, Govt. of India/ ; }, abstract = {The excessive use of chemical fertilizers in tea cultivation threatens soil health, environmental sustainability, and long-term crop productivity. This study explores the application of plant growth-promoting bacteria (PGPB) as an eco-friendly alternative to conventional fertilizers. A bacterial consortium was developed using selected rhizobacterial isolates-Lysinibacillus fusiformis, five strains of Serratia marcescens, and two Bacillus spp.-based on their phosphate and zinc solubilization abilities and production of ACC deaminase, indole-3-acetic acid, and siderophores. The consortium was tested in both pot and field conditions using two tea clones, S3A3 and TS491, and compared with a chemical fertilizer treatment. Plants treated with the consortium showed enhanced growth, biomass, and antioxidant activity. The total phenolic contents increased to 1643.6 mg GAE/mL (S3A3) and 1646.93 mg GAE/mL (TS491), with higher catalase (458.17-458.74 U/g/min), glutathione (34.67-42.67 µmol/gfw), and superoxide dismutase (679.85-552.28 units/gfw/s) activities. A soil metagenomic analysis revealed increased microbial diversity and the enrichment of phyla, including Acidobacteria, Proteobacteria, Actinobacteria, Chloroflexi, and Firmicutes. Functional gene analysis showed the increased abundance of genes for siderophore biosynthesis, glutathione and nitrogen metabolism, and indole alkaloid biosynthesis. This study recommends the potential of a PGPB consortium as a sustainable alternative to chemical fertilizers, enhancing both the tea plant performance and soil microbial health.}, }
@article {pmid40870843, year = {2025}, author = {Elbehiry, A and Abalkhail, A}, title = {Metagenomic Next-Generation Sequencing in Infectious Diseases: Clinical Applications, Translational Challenges, and Future Directions.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {15}, number = {16}, pages = {}, doi = {10.3390/diagnostics15161991}, pmid = {40870843}, issn = {2075-4418}, abstract = {Metagenomic next-generation sequencing (mNGS) is transforming infectious disease diagnostics by enabling simultaneous, hypothesis-free detection of a broad array of pathogens-including bacteria, viruses, fungi, and parasites-directly from clinical specimens such as cerebrospinal fluid, blood, and bronchoalveolar lavage fluid. Unlike traditional culture and targeted molecular assays, mNGS serves as a powerful complementary approach, capable of identifying novel, fastidious, and polymicrobial infections while also characterizing antimicrobial resistance (AMR) genes. These advantages are particularly relevant in diagnostically challenging scenarios, such as infections in immunocompromised patients, sepsis, and culture-negative cases. Despite its potential, mNGS remains underutilized in clinical microbiology due to persistent gaps between its technical capabilities and routine diagnostic adoption. This review addresses key translational challenges that limit the broader implementation of mNGS, especially in resource-constrained and critical care settings. We provide a comprehensive overview of the entire workflow-from sample processing and host DNA depletion to sequencing platforms and downstream bioinformatics-and highlight sources of variability, including contamination, human DNA interference, and inconsistencies in resistance gene annotation. Additionally, we explore the ethical, legal, and privacy implications of host genomic data, as well as economic and regulatory obstacles hindering mNGS integration into standard clinical practice. To illustrate clinical relevance, we examine real-world evidence from large-scale trials such as MATESHIP, GRAIDS, DISQVER, and NGS-CAP. Finally, we outline future directions involving artificial intelligence, multi-omics integration, cloud-based analytics, and portable sequencing technologies for point-of-care diagnostics. By addressing both current limitations and emerging innovations, this review offers a translational framework for integrating mNGS into precision diagnostics and infection management across diverse healthcare environments.}, }
@article {pmid40870775, year = {2025}, author = {Li, J and Yang, D and Zhao, Y and Wang, D and Huang, H and Li, C}, title = {Novel Insight into Metabolism Mechanism of Biogenic Amines During Fermentation of Chinese Traditional Fermented Mandarin Fish (Chouguiyu) Based on Metabolism Pathway and Correlation Network.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {16}, pages = {}, doi = {10.3390/foods14162863}, pmid = {40870775}, issn = {2304-8158}, support = {CARS-46//the Earmarked fund for CARS/ ; NYJG202405//the Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs, China/ ; 2024CXTD26//the Guangdong Provincial Special Fund for Modern Agriculture Industry Technology Innovation Teams/ ; 2023TD78//the Central Public-interest Scientific Institution Basal Research Fund, CAFS/ ; }, abstract = {A complex microbial community gives the possibility to produce biogenic amines in traditional fermented foods. In this study, the metabolism mechanisms of biogenic amines during fermentation of fermented mandarin fish Chouguiyu were revealed based on the metabolic pathways and correlation analysis. Functional genes based on KEGG orthology related to biogenic amine metabolism were selected from the metagenome and were used to construct the biogenic amine metabolic pathways in Chouguiyu. A total of 91 and 75 genera were related to the synthesis and degradation of biogenic amines, respectively. High concentrations of cadaverine and putrescine were observed, while the other biogenic amines were detected in relatively low concentrations. The metabolic mechanisms of various biogenic amines were illuminated by correlation network maps between biogenic amines and microbial synthesis/degradation enzymes. Lactococcus, Flavobacterium, Tessaracoccus, and Yoonia could only degrade and not produce biogenic amines. Acinetobacter and Enterococcus possessed more abundant enzymes for degradation than synthesis. Amine oxidase (K00276), diamine N-acetyltransferase (K00657), and gamma-glutamylputrescine synthase (K09470) were the main biogenic amine degradation enzymes in the microbial community. Lactococcus garvieae, Flavobacterium gelidilacus, Tessaracoccus antarcticus, Yoonia vestfoldensis, Acinetobacter haemolyticus, and Enterococcus ureasiticus were the main microbial species for biogenic amine degradation and could be isolated as the potential strains for biogenic amine degradation in fermented foods.}, }
@article {pmid40870601, year = {2025}, author = {Min, JG and Min, N and Nguyen, BT and Flores, RA and Yim, D}, title = {Characterization of DNA Viruses in Hindgut Contents of Protaetia brevitarsis Larvae.}, journal = {Insects}, volume = {16}, number = {8}, pages = {}, doi = {10.3390/insects16080800}, pmid = {40870601}, issn = {2075-4450}, support = {RS-2024-00399808//the Korea IPET in Food, Agriculture and Forestry through the High-Risk Animal Infectious Disease Control Technology Development Project, funded by MAFRA/ ; 2025-01//Hoxbio/ ; }, abstract = {The scarab species Protaetia brevitarsis, an edible insect, has been used in traditional medicine, as animal feed, and for converting agricultural organic wastes into biofertilizer. The intestinal tract, which contains a diverse array of microbiota, including viruses, plays a critical role in animal health and homeostasis. We previously conducted a comparative analysis of the gut microbiota of third-instar larvae of P. brevitarsis obtained from five different farms and found significant differences in the composition of the gut bacterial microbiota between farms. To better understand the gut microbiota, the composition of DNA viruses in the hindgut contents of P. brevitarsis larvae obtained from five farms was investigated using metagenomic sequencing in this study. The β-diversity was significantly different between metagenomic data obtained from the five farms (PERMANOVA, pseudo-F = 46.95, p = 0.002). Family-based taxonomic analysis indicated that the relative abundance of viruses in the gut overall metagenome varied significantly between farms, with viral reads comprising approximately 41.2%, 15.0%, 4.3%, 4.0%, and 1.6% of metagenomic sequences from the farms Tohamsan gumbengi farm (TO), Secomnalagum gumbengi (IS), Gumbengi brothers (BR), Kyungpook farm (KB), and Jhbio (JH), respectively. More than 98% of the DNA viruses in the hindgut were bacteriophages, mainly belonging to the Siphoviridae family. At the species level, Phage Min1, infecting the genus Microbacterium, was detected in all farms, and it was the most abundant bacteriophage in intestinal microbiota, with a prevalence of 0.9% to 29.09%. The detected eukaryotic DNA viruses accounted for 0.01% to 0.06% of the intestinal microbiota and showed little or no relationship with insect viruses. Therefore, they most likely originated from contaminated feed or soil. These results suggest that the condition of substrates used as feed is more important than genetic factors in shaping the intestinal viral microbiota of P. brevitarsis larvae. These results can be used as reference data for understanding the hindgut microbiota of P. brevitarsis larvae and, more generally, the gut virome of insects.}, }
@article {pmid40869994, year = {2025}, author = {Peña, N and Lafuente, I and Sevillano, E and Feito, J and Allendez, G and Muñoz-Atienza, E and Crispie, F and Cintas, LM and Cotter, PD and Hernández, PE and Borrero, J}, title = {Exploring the Functional Potential of the Broiler Gut Microbiome Using Shotgun Metagenomics.}, journal = {Genes}, volume = {16}, number = {8}, pages = {}, doi = {10.3390/genes16080946}, pmid = {40869994}, issn = {2073-4425}, support = {2018-T1/BIO-10158//Comunidad de Madrid/ ; 2022-5A/BIO-24232//Comunidad de Madrid/ ; PEJ-2020-AI/BIO-17758//Comunidad de Madrid/ ; PID2019-104808RAI00//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; }, mesh = {Animals ; *Chickens/microbiology/genetics ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Antimicrobial Peptides/genetics ; Bacteria/genetics ; High-Throughput Nucleotide Sequencing ; Cecum/microbiology ; }, abstract = {Background/Objectives: Antimicrobial peptides (AMPs) have emerged as promising alternatives to conventional antibiotics in livestock, offering a sustainable strategy for controlling bacterial pathogens in food production systems. In addition to their direct antimicrobial effects, AMPs play a key role in modulating host-associated microbiomes, influencing both microbial composition and function. Advances in metagenomic sequencing and bioinformatic tools now enable comprehensive exploration of AMP diversity and activity within complex microbial ecosystems. Methods: In this study, we employed Illumina-based next-generation sequencing (NGS) to analyze intestinal contents from six gut sections of broiler chickens obtained from a Spanish slaughterhouse. Results: Through de novo assembly and bioinformatic annotation, we identified biosynthetic gene clusters (BGCs) encoding ribosomally synthesized and post-translationally modified peptides (RiPPs), other specialized bioactive secondary metabolites, antimicrobial resistance genes (ARGs), virulence factor genes (VFGs), and a diverse microbial community. Among all gut sections, the cecum exhibited the highest genetic richness, characterized by a high diversity of RiPP-like clusters and antimicrobial resistance determinants. Conclusions: These findings highlight the poultry gut, particularly the cecum, as a significant reservoir of antimicrobial peptides (AMPs) with potential implications in antibiotic-free poultry production and enhanced food safety.}, }
@article {pmid40869080, year = {2025}, author = {Moiseenko, F and Kechin, A and Koryukov, M and Boyarskikh, U and Gabina, A and Oganesian, A and Belukhin, S and Makarkina, M and Elsakova, E and Artemeva, E and Myslik, A and Volkov, N and Bogdanov, A and Kuligina, E and Aleksakhina, S and Iyevleva, A and Ivantsov, A and Bogdanov, A and Sidorenko, S and Gostev, V and Komissarov, A and Dudurich, V and Danilov, L and Imyanitov, E and Moiseyenko, V}, title = {Interconnection of Gut Microbiome and Efficacy of Immune Checkpoint Inhibitors in Inoperable Non-Small-Cell Lung Cancer.}, journal = {International journal of molecular sciences}, volume = {26}, number = {16}, pages = {}, doi = {10.3390/ijms26167758}, pmid = {40869080}, issn = {1422-0067}, support = {125041005115-5//Russian state-funded project for ICBFM SB RAS/ ; }, mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/drug therapy/microbiology/pathology ; *Gastrointestinal Microbiome/drug effects ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; *Lung Neoplasms/drug therapy/microbiology/pathology ; Male ; Female ; Aged ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Treatment Outcome ; Tumor Microenvironment/drug effects ; }, abstract = {The efficacy of immune checkpoint inhibitors (ICIs) in non-small-cell lung cancer (NSCLC) varies widely across patients. Growing evidence indicates that the gut microbiome, through its interaction with the tumor microenvironment, may influence the response to immunotherapy. To investigate this, we analyzed fecal and tumor samples from 63 patients with inoperable NSCLC undergoing ICI therapy. Based on microbiome profiling using 16S rRNA sequencing, patients were grouped according to treatment benefit, defined as progression-free survival (PFS) of six months or longer. Associations between α-diversity indices, microbial composition at the genus and phylum levels, and a composite Sum Index of Binary Abundance (SIBA) were examined in relation to clinical outcomes. Higher microbial α-diversity was linked to improved response to ICIs (p-value = 0.0078 for the Chao1 index). Multiple specific taxa, such as Ruminococcus gauvreauii (p-value = 2 × 10[-4]), Ruminiclostridium 9 (p-value = 8 × 10[-4]), and [Eubacterium] ventriosum (p-value = 9 × 10[-4]), were enriched in patients with favorable outcomes, whereas Oscillibacter and the Eubacterium hallii group were associated with disease progression (p-value = 2 × 10[-3] and 9 × 10[-3], respectively). The SIBA index, which reflects the absence of multiple beneficial bacterial taxa, proved to be a stronger predictor of treatment response than individual taxa alone. Median SIBA values were 18 vs. 24 in patients benefiting from IO therapy compared to non-responders (p-value = 9 × 10[-7]). These findings suggest that gut microbiome diversity and composition are closely tied to immunotherapy outcomes in NSCLC. Composite microbial metrics like SIBA may enhance predictive accuracy and inform personalized treatment approaches.}, }
@article {pmid40868053, year = {2025}, author = {Maruyama, T and Ishikawa, D and Kurokawa, R and Masuoka, H and Nomura, K and Haraikawa, M and Orikasa, M and Odakura, R and Koma, M and Omori, M and Ishino, H and Ito, K and Shibuya, T and Suda, W and Nagahara, A}, title = {Hydrogen Gas Inhalation Improved Intestinal Microbiota in Ulcerative Colitis: A Randomised Double-Blind Placebo-Controlled Trial.}, journal = {Biomedicines}, volume = {13}, number = {8}, pages = {}, doi = {10.3390/biomedicines13081799}, pmid = {40868053}, issn = {2227-9059}, support = {None//MiZ Co., Ltd/ ; }, abstract = {Background/Objective: Dysbiosis is implicated in the pathogenesis of ulcerative colitis. Hydrogen has been reported to promote intestinal microbiota diversity and suppress ulcerative colitis progression in mice models. In this study, we investigated changes in the intestinal microbiota, therapeutic effects, and safety of hydrogen inhalation in patients with ulcerative colitis. Methods: In this randomised, double-blind, placebo-controlled trial, 10 active patients with ulcerative colitis (aged ≥20 years; Lichtiger's clinical activity index, 3-10; and Mayo endoscopic subscores ≥1) participated, and they were assigned to either a hydrogen or air inhalation group (hydrogen and placebo groups, respectively). All patients inhaled gas for 4 h every day for 8 weeks. Subsequently, we performed clinical indices and microbiota analyses using the metagenomic sequencing of stool samples before and after inhalation. Results: There was significant difference in the sum of the Mayo endoscopic subscores before and after inhalation in the clinical assessment indices. The hydrogen group showed higher α-diversity (p = 0.19), and the variation in β-diversity was markedly different, compared to the placebo group, in intestinal microbiota analysis (p = 0.02). Functional gene analysis revealed 115 significant genetic changes in the hydrogen group following treatment. No inhalation-related adverse events were observed. Conclusions: Hydrogen inhalation appeared to improve intestinal microbiota diversity; however, no clear therapeutic effect on ulcerative colitis was observed. Further studies are needed, and hydrogen inhalation may possibly lead to a logical solution combined with microbiome therapy, such as faecal microbiota transplantation, with fewer adverse events.}, }
@article {pmid40868001, year = {2025}, author = {Azuma, T and Katagiri, M and Yamamoto, T and Kuroda, M and Watanabe, M}, title = {Effectiveness of Implementing Hospital Wastewater Treatment Systems as a Measure to Mitigate the Microbial and Antimicrobial Burden on the Environment.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {14}, number = {8}, pages = {}, doi = {10.3390/antibiotics14080807}, pmid = {40868001}, issn = {2079-6382}, support = {JP22fk0108131//Japan Agency for Medical Research and Development/ ; JP25fk0108666//Japan Agency for Medical Research and Development/ ; }, abstract = {Background: The emergence and spread of antimicrobial-resistant bacteria (ARB) has become an urgent global concern as a silent pandemic. When taking measures to reduce the impact of antimicrobial resistance (AMR) on the environment, it is important to consider appropriate treatment of wastewater from medical facilities. Methods: In this study, a continuous-flow wastewater treatment system using ozone and ultraviolet light, which has excellent inactivation effects, was implemented in a hospital in an urban area of Japan. Results: The results showed that 99% (2 log10) of Gram-negative rods and more than 99.99% (>99.99%) of ARB comprising ESBL-producing Enterobacterales were reduced by ozone treatment from the first day after treatment, and ultraviolet light-emitting diode (UV-LED) irradiation after ozone treatment; UV-LED irradiation after ozonation further inactivated the bacteria to below the detection limit. Inactivation effects were maintained throughout the treatment period in this study. Metagenomic analysis showed that the removal of these microorganisms at the DNA level tended to be gradual in ozone treatment; however, the treated water after ozone/UV-LED treatment showed a 2 log10 (>99%) removal rate at the end of the treatment. The residual antimicrobials in the effluent were benzylpenicillin, cefpodoxime, ciprofloxacin, levofloxacin, azithromycin, clarithromycin, doxycycline, minocycline, and vancomycin, which were removed by ozone treatment on day 1. In contrast, the removal of ampicillin and cefdinir ranged from 19% to 64% even when combined with UV-LED treatment. Conclusions: Our findings will help to reduce the discharge of ARB and antimicrobials into rivers and maintain the safety of aquatic environments.}, }
@article {pmid40867992, year = {2025}, author = {Barrantes-Jiménez, K and Mendoza-Guido, B and Morales-Mora, E and Rivera-Montero, L and Montiel-Mora, J and Chacón-Jiménez, L and Rojas-Jiménez, K and Arias-Andrés, M}, title = {Influence of Seasonality and Pollution on the Presence of Antibiotic Resistance Genes and Potentially Pathogenic Bacteria in a Tropical Urban River.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {14}, number = {8}, pages = {}, doi = {10.3390/antibiotics14080798}, pmid = {40867992}, issn = {2079-6382}, support = {C2650//Consejo Nacional de Rectores (CONARE), Costa Rica/ ; C1455//Vicerrector&#xed;a de Investigaci&#xf3;n, UCR/ ; project 0522-21//Universidad Nacional/ ; D43TW011403//National Institutes of Health Fogarty International Center ,for the project entitled 'International Training Program in Environmental Health over the Lifespan' to the Icahn School of Medicine at Mount Sinai and Universidad Nacional,/ ; }, abstract = {BACKGROUND/OBJECTIVES: This study examines how seasonality, pollution, and sample type (water and sediment) influence the presence and distribution of antibiotic resistance genes (ARGs), with a focus on antibiotic resistance genes (ARGs) located on plasmids (the complete set of plasmid-derived sequences, including ARGs) in a tropical urban river.<br><br>METHODS: Samples were collected from three sites along a pollution gradient in the Virilla River, Costa Rica, during three seasonal campaigns (wet 2021, dry 2022, and wet 2022). ARGs in water and sediment were quantified by qPCR, and metagenomic sequencing was applied to analyze chromosomal and plasmid-associated resistance profiles in sediments. Tobit and linear regression models, along with multivariate ordination, were used to assess spatial and seasonal trends.<br><br>RESULTS: During the wet season of 2021, the abundance of antibiotic resistance genes (ARGs) such as sul-1, intI-1, and tetA in water samples decreased significantly, likely due to dilution, while intI-1 and tetQ increased in sediments, suggesting particle-bound accumulation. In the wet season 2022, intI-1 remained low in water, qnrS increased, and sediments showed significant increases in tetQ, tetA, and qnrS, along with decreases in sul-1 and sul-2. Metagenomic analysis revealed spatial differences in plasmid-associated ARGs, with the highest abundance at the most polluted site (Site 3). Bacterial taxa also showed spatial differences, with greater plasmidome diversity and a higher representation of potential pathogens in the most contaminated site.<br><br>CONCLUSIONS: Seasonality and pollution gradients jointly shape ARG dynamics in this tropical river. Plasmid-mediated resistance responds rapidly to environmental change and is enriched at polluted sites, while sediments serve as long-term reservoirs. These findings support the use of plasmid-based monitoring for antimicrobial resistance surveillance in aquatic systems.}, }
@article {pmid40867980, year = {2025}, author = {Morcillo Serrano, MM and Reche-Sainz, P and González-Reguero, D and Robas-Mora, M and de la Iglesia, R and Úbeda, N and Alonso-Aperte, E and Arranz-Herrero, J and Jiménez-Gómez, PA}, title = {Effect of a Gluten-Free Diet on the Intestinal Microbiota of Women with Celiac Disease.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {14}, number = {8}, pages = {}, doi = {10.3390/antibiotics14080785}, pmid = {40867980}, issn = {2079-6382}, support = {MGI21EAA//This study was supported by a Grant for Registered Research Groups from Universidad CEU San Pablo, Madrid (Spain)/ ; }, abstract = {Background/Objectives: Celiac disease (CD) is an autoimmune disorder characterized by small intestinal enteropathy triggered by gluten ingestion, often associated with gut dysbiosis. The most effective treatment is strict adherence to a gluten-free diet (GFD), which alleviates symptoms. This study uniquely integrates taxonomic, functional, and resistance profiling to evaluate the gut microbiota of women with CD on a GFD. Methods: To evaluate the long-term impact of a GFD, this study analyzed the gut microbiota of 10 women with CD on a GFD for over a year compared to 10 healthy controls with unrestricted diets. Taxonomic diversity (16S rRNA gene sequencing and the analysis of α and β-diversity), metabolic functionality (Biolog EcoPlates[®]), and antibiotic resistance profiles (Cenoantibiogram) were assessed. Results: Metagenomic analysis revealed no significant differences in taxonomic diversity but highlighted variations in the abundance of specific bacterial genera. Women with CD showed increased proportions of Bacteroides, Streptococcus, and Clostridium, associated with inflammation, but also elevated levels of beneficial genera such as Roseburia, Oxalobacter, and Paraprevotella. Despite no significant differences in metabolic diversity, higher minimum inhibitory concentrations (MICs) in women in the healthy control group suggest that dietary substrates in unrestricted diets may promote the proliferation of fast-growing bacteria capable of rapidly developing and disseminating antibiotic resistance mechanisms. Conclusions: These findings indicate that prolonged adherence to a GFD in CD supports remission of gut dysbiosis, enhances microbiota functionality, and may reduce the risk of antibiotic resistance, emphasizing the importance of dietary management in CD.}, }
@article {pmid40867959, year = {2025}, author = {Sassi, A and Basher, NS and Kirat, H and Meradji, S and Ibrahim, NA and Idres, T and Touati, A}, title = {The Role of the Environment (Water, Air, Soil) in the Emergence and Dissemination of Antimicrobial Resistance: A One Health Perspective.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {14}, number = {8}, pages = {}, doi = {10.3390/antibiotics14080764}, pmid = {40867959}, issn = {2079-6382}, support = {IMSIU-DDRSP2502//Deanship of Scientific Research at Imam Mohammad Ibn Saud Islamic University (IMSIU)/ ; }, abstract = {Antimicrobial resistance (AMR) has emerged as a planetary health emergency, driven not only by the clinical misuse of antibiotics but also by diverse environmental dissemination pathways. This review critically examines the role of environmental compartments-water, soil, and air-as dynamic reservoirs and transmission routes for antibiotic-resistant bacteria (ARB) and resistance genes (ARGs). Recent metagenomic, epidemiological, and mechanistic evidence demonstrates that anthropogenic pressures-including pharmaceutical effluents, agricultural runoff, untreated sewage, and airborne emissions-amplify resistance evolution and interspecies gene transfer via horizontal gene transfer mechanisms, biofilms, and mobile genetic elements. Importantly, it is not only highly polluted rivers such as the Ganges that contribute to the spread of AMR; even low concentrations of antibiotics and their metabolites, formed during or after treatment, can significantly promote the selection and dissemination of resistance. Environmental hotspots such as European agricultural soils and airborne particulate zones near wastewater treatment plants further illustrate the complexity and global scope of pollution-driven AMR. The synergistic roles of co-selective agents, including heavy metals, disinfectants, and microplastics, are highlighted for their impact in exacerbating resistance gene propagation across ecological and geographical boundaries. The efficacy and limitations of current mitigation strategies, including advanced wastewater treatments, thermophilic composting, biosensor-based surveillance, and emerging regulatory frameworks, are evaluated. By integrating a One Health perspective, this review underscores the imperative of including environmental considerations in global AMR containment policies and proposes a multidisciplinary roadmap to mitigate resistance spread across interconnected human, animal, and environmental domains.}, }
@article {pmid40867666, year = {2025}, author = {Hu, Y and Cui, P and Han, S and Xiong, X and Huang, Q and Song, X and He, G and Ren, P}, title = {Gut Microbial Signatures of Broiler Lines Divergently Selected for Inosine Monophosphate and Intramuscular Fat Content.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {16}, pages = {}, doi = {10.3390/ani15162337}, pmid = {40867666}, issn = {2076-2615}, support = {32460829; 2024ZHCG0111; 24ZDYF0006//The Fund for Less Developed Regions of the National Natural Science Foundation of China; The Sichuan Science and Technology Program; The Science and Technology Program of Guangyuan City/ ; }, abstract = {Consumers are increasingly concerned about the flavor quality of poultry meat, yet the relationship between inosine monophosphate (IMP), intramuscular fat (IMF), and the gut microbiota remains largely unclear. This study aimed to characterize the cecal microbiota associated with IMP/IMF deposition in Daheng broilers selectively bred for high-IMP/IMF levels (High group) and low levels (Control group). A two-stage microbiome analysis strategy was applied. Initially, 16S rRNA gene sequencing was conducted to assess microbial diversity and composition. Significant differences were observed between groups in alpha diversity indices (Chao1 and Faith_PD) and beta diversity (p < 0.05). LEfSe analysis identified 55 differentially abundant taxa (LDA > 3, p < 0.05), primarily within the Phylum bacteroidota. To achieve species-level and functional insights, whole-metagenome shotgun sequencing was performed. Taxonomic profiling of 62,443 microbial species revealed significant beta diversity differences (p < 0.05), with 120 dominant species differentially enriched (LDA > 3, p < 0.05), including 77 species in the High group such as Merdivivens faecigallinarum. Enriched functional genes were mainly involved in methane metabolism, starch and sucrose metabolism, and the nucleoside phosphate metabolic process. A total of 882 metagenome-assembled genomes (MAGs) were reconstructed and integrated with 19,628 publicly available chicken MAGs, resulting in 2609 non-redundant genomes, including 52 novel ones. These findings suggest that cecal microbial composition and function are associated with IMP/IMF levels in broilers, providing candidate bacterial species and functional pathways for further validation through gavage-based intervention and multi-omics analysis.}, }
@article {pmid40867583, year = {2025}, author = {Ezra, R and Vanti, G and Masaphy, S}, title = {Sustainable, Targeted, and Cost-Effective Laccase-Based Bioremediation Technologies for Antibiotic Residues in the Ecosystem: A Comprehensive Review.}, journal = {Biomolecules}, volume = {15}, number = {8}, pages = {}, doi = {10.3390/biom15081138}, pmid = {40867583}, issn = {2218-273X}, mesh = {*Laccase/metabolism/chemistry ; *Biodegradation, Environmental ; *Anti-Bacterial Agents/metabolism/chemistry ; Ecosystem ; Cost-Benefit Analysis ; Fungi/enzymology ; Humans ; }, abstract = {Widespread antibiotic residues are accumulating in the environment, potentially causing adverse effects for humans, animals, and the ecosystem, including an increase in antibiotic-resistant bacteria, resulting in worldwide concern. There are various commonly used physical, chemical, and biological treatments for the degradation of antibiotics. However, the elimination of toxic end products generated by physicochemical methods and the need for industrial applications pose significant challenges. Hence, environmentally sustainable, green, and readily available approaches for the transformation and degradation of these antibiotic compounds are being sought. Herein, we review the impact of sustainable fungal laccase-based bioremediation strategies. Fungal laccase enzyme is considered one of the most active enzymes for biotransformation and biodegradation of antibiotic residue in vitro. For industrial applications, the low laccase yields in natural and genetically modified hosts may constitute a bottleneck. Methods to screen for high-laccase-producing sources, optimizing cultivation conditions, and identifying key genes and metabolites involved in extracellular laccase activity are reviewed. These include advanced transcriptomics, proteomics, and metagenomics technologies, as well as diverse laccase-immobilization technologies with different inert carrier/support materials improving enzyme performance whilst shifting from experimental assays to in situ monitoring of residual toxicity. Still, more basic and applied research on laccase-mediated bioremediation of pharmaceuticals, especially antibiotics that are recalcitrant and prevalent, is needed.}, }
@article {pmid40867077, year = {2025}, author = {Ebadi, M and Reddi, S and Senyshyn, L and Minot, SS and Gooley, T and Kabage, AJ and Lee, SJ and Hill, GR and Khoruts, A and Rashidi, A}, title = {Effect of fecal microbiota transplantation on gut microbiota functional profile in recipients of allogeneic hematopoietic cell transplantation.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2551882}, doi = {10.1080/19490976.2025.2551882}, pmid = {40867077}, issn = {1949-0984}, mesh = {Humans ; *Fecal Microbiota Transplantation ; *Hematopoietic Stem Cell Transplantation/adverse effects ; *Gastrointestinal Microbiome ; Male ; Middle Aged ; Female ; Adult ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Dysbiosis/therapy/microbiology ; Transplantation, Homologous ; Feces/microbiology ; Aged ; }, abstract = {Intestinal dysbiosis has been associated with both the effectiveness and toxicity of immunotherapy in cancer patients, inspiring multiple trials investigating fecal microbiota transplantation (FMT) in these patients. FMT restores microbial community structures damaged by antibiotics and enriches the microbiota with beneficial bacteria. However, the precise mechanism through which FMT exerts its effects and provides clinical benefits remains incompletely understood. Efforts to date have primarily focused on characterizing taxonomic changes following FMT. We hypothesized that FMT may also modify the functional pathways and metabolic capabilities of the gut microbiota, with possible clinical impact. To investigate this, we conducted a study involving 17 patients with blood disorders who received prophylactic FMT from one of the three healthy donors shortly after hematopoietic cell transplantation (HCT). By analyzing shotgun metagenomic profiles of the baseline, pre-FMT, and post-FMT gut microbiota, we demonstrate that FMT effectively restored pathways that had been depleted following HCT. However, it did not significantly reduce pathways that had expanded, indicating that FMT operates primarily through a restorative mechanism, reestablishing lost functional capabilities in the microbiota rather than suppressing overactive pathways. These findings highlight the potential for optimizing FMT protocols and identifying patient populations where FMT may be particularly beneficial.}, }
@article {pmid40866996, year = {2025}, author = {Ji'e, K and Yang, F and Su, Y and Abi, KM}, title = {Identification of a new goat torovirus strain: first detection and genomic analysis in China.}, journal = {Irish veterinary journal}, volume = {78}, number = {1}, pages = {20}, pmid = {40866996}, issn = {2046-0481}, support = {SCCXTD-2024-14//Innovation Team Development Funds for Sichuan Mutton Goat &amp; Sheep/ ; 2024CXTD08//Scientific and Technological Innovation Team for Qinghai-Tibetan Plateau Research in Southwest Minzu University/ ; 2024NSFSC1272//The Natural Science Foundation of Sichuan Province/ ; ZYN2025031//the Fundamental Research Funds for the Central Universities&#xff0c;Southwest Minzu University/ ; }, abstract = {Using viral metagenomics, we identified a novel torovirus, GToV/SWUN/SC, in diarrheal goat fecal samples with a genome length of 28,457 nt. This strain shares 96.73-96.79% nucleotide identity with Antelope torovirus (AToV) but only 88.43% with the GToV/SZ strain. Phylogenetic analysis revealed a close evolutionary relationship between GToV/SWUN/SC and AToV. Structural analysis showed three distinct structural variations in the HE protein and multiple amino acid mutations in the S gene, which may influence host adaptation. RT-PCR detected a 35.9% (240/669) positivity rate, indicating widespread circulation of GToV in Sichuan, Chongqing, and Yunnan. This study enhances the understanding of torovirus epidemiology and evolution, providing a theoretical basis for further research on viral diversity.}, }
@article {pmid40859350, year = {2025}, author = {Klaes, S and White, C and Alvarez-Cohen, L and Adrian, L and Ding, C}, title = {De novo peptide databases enable protein-based stable isotope probing of microbial communities with up to species-level resolution.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {111}, pmid = {40859350}, issn = {2524-6372}, abstract = {BACKGROUND: Protein-based stable isotope probing (Protein-SIP) is a powerful approach that can directly link individual taxa to activity and substrate assimilation, elucidating metabolic pathways and trophic relationships within microbial communities. In Protein-SIP, peptides and corresponding taxa are identified by database matching, making database quality crucial for accurate analyses. For samples with unknown community composition, Protein-SIP typically employs either unrestricted reference databases or metagenome-derived databases. While (meta)genome-derived databases represent the gold standard, they may be incomplete and are typically resource-intensive to generate. In contrast, unrestricted reference databases can inflate the search space and require complex post-processing.<br><br>RESULTS: Here, we explore the feasibility of using de novo peptide sequencing to construct peptide databases directly from mass spectrometry raw data. We then use the mass spectrometric data from labeled cultures to quantify isotope incorporation into specific peptides. We benchmark our approach against the canonical approach in which a sample-matching (meta)genome-derived protein sequence database is used on three different datasets: (1) a proteome analysis from a defined microbial community containing [13]C-labeled Escherichia coli cells, (2) time-course data of an anammox-dominated continuous reactor after feeding with [13]C-labeled bicarbonate, and (3) a model of the human distal gut simulating a high-protein and high-fiber diet cultivated in either [2]H2O or H2[18]O. Our results show that de novo peptide databases are applicable to different isotopes, detecting similar amounts of labeled peptides compared to sample-matching (meta)genome-derived databases, and also identify labeled peptides missed by this canonical approach. Furthermore, we show that peptide-centric Protein-SIP allows up to species-level resolution and enables the assessment of activity related to individual biological processes. Finally, we provide access to our modular Python pipeline to assist the construction of de novo peptide databases and subsequent peptide-centric Protein-SIP data analysis (https://git.ufz.de/meb/denovo-sip).<br><br>CONCLUSIONS: De novo peptide databases enable Protein-SIP of microbial communities without prior knowledge of the composition and can be used complementarily to (meta)genome-derived databases or as a standalone alternative in exploratory or resource-limited settings.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s40793-025-00767-6.}, }
@article {pmid40866974, year = {2025}, author = {Zhang, J and Tang, F and Ni, B and Zhang, Q and Gong, X and Mao, F and Cao, J and Liu, Y}, title = {PGIP: a web server for the rapid taxonomic identification of parasite genomes.}, journal = {Parasites &amp; vectors}, volume = {18}, number = {1}, pages = {365}, pmid = {40866974}, issn = {1756-3305}, support = {2020YFC1200100//National Key R&amp;D Program of China/ ; ZDXYS202207//Jiangsu Province Capability Improvement Project through Science, Technology, and Education/ ; 82372275//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Parasitic diseases remain a global health challenge, and traditional methods in their diagnosis face limitations in sensitivity and scalability. Genome-based sequencing technologies have improved and are increasingly employed for the identification of parasites; however, their clinical adoption remains hindered by the complexity of bioinformatics analysis, reliance on incomplete reference databases, and accessibility barriers for nonspecialists. Overcoming these challenges necessitates the development of standardized analytical workflows and high-quality genomic resources specifically tailored for parasite identification.<br><br>METHODS: We developed a user-friendly web server named the Parasite Genome Identification Platform (PGIP). The reference database was sourced from the National Center for Biotechnology Information (NCBI), WormBase, European Nucleotide Archive (ENA), and VEuPathDB, rigorously filtered for quality, and deduplicated using Cluster Database at High Identity with Tolerance (CD-HIT) to ensure accuracy and nonredundancy. To streamline analysis, we integrated a standardized identification pipeline built on Nextflow, which encompasses host DNA depletion, quality control, parasite species identification via both reads mapping and assembly-based approaches, and automated report generation for comprehensive diagnostic insights.<br><br>RESULTS: PGIP integrates a curated database of 280 parasite genomes; which is rigorously filtered for quality and taxonomic accuracy. Validation across diverse datasets demonstrated the precise species-level resolution of PGIP, and its compatibility with clinical samples. The platform features an intuitive graphic interface; and one-click analysis significantly reduces reliance on bioinformatics expertise, thus enabling rapid diagnosis.<br><br>CONCLUSIONS: PGIP offers an accurate, efficient, and a user-friendly web server designed to simplify and accelerate the taxonomic identification of parasite genomes using data from metagenomic next-generation sequencing. Its automated framework reduces the need for specialized expertise, enabling rapid application in clinical and public health settings.}, }
@article {pmid40866789, year = {2025}, author = {Kusakabe, S and Kurashige, R and Fukushima, K and Shimizu, K and Yoshihara, T and Motooka, D and Nakamura, S and Kurashige, M and Nakata, K and Hino, A and Kasahara, H and Ueda, T and Fujita, J and Hosen, N and Takehara, T and Oda, J}, title = {Fecal microbiota transplantation for Crohn's disease-like intestinal lesions arising after allogeneic stem cell transplantation.}, journal = {International journal of hematology}, volume = {}, number = {}, pages = {}, pmid = {40866789}, issn = {1865-3774}, abstract = {Several cases of inflammatory bowel disease (or similar gastrointestinal lesions) arising after allogeneic hematopoietic stem cell transplantation have been reported, but the effect of intestinal dysbiosis on development of these lesions remains unclear. We performed fecal microbiota transplantation (FMT) and 16S rRNA microbiome analysis in a patient who developed Crohn's disease-like lesions after allogeneic transplantation. A 62-year-old woman underwent haploidentical stem cell transplantation from her daughter to treat double-hit lymphoma relapsed after chimeric antigen receptor T-cell therapy, and achieved remission without developing acute graft-versus-host disease. Eight months later, she developed Crohn's disease-like intestinal lesions after cytomegalovirus enteritis. Her condition did not improve with the conventional treatment, so she underwent FMT from her daughter as part of a clinical trial. Diarrhea gradually improved, and follow-up endoscopy 4 months after the FMT showed ulcer healing and scarring. The 16S rRNA analysis revealed a reduction in the relative abundance of the Enterococcus genus after FMT, suggesting that dysbiosis may have contributed to lesion development. The patient is currently on a regular diet, with no symptom recurrence, and the primary disease remains in remission. Although this outcome suggests that FMT is effective, careful patient selection is required to reduce the risk of FMT-associated sepsis.}, }
@article {pmid40866482, year = {2025}, author = {Martin, C and Emerson, JB and Roux, S and Anantharaman, K}, title = {A call for caution in the biological interpretation of viral auxiliary metabolic genes.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {40866482}, issn = {2058-5276}, support = {R35GM143024//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; DE-SC0021198//DOE | SC | Biological and Environmental Research (BER)/ ; DE-AC02-05CH11231//DOE | SC | Biological and Environmental Research (BER)/ ; }, abstract = {Virus-encoded auxiliary metabolic genes (AMGs) are non-essential genes that increase viral fitness by maintaining or manipulating host metabolism during infection. AMGs are intriguing from an evolutionary perspective, as most viral genomes are highly compact and have limited coding capacity for accessory genes. Advances in viral (meta)genomics have expanded the detection of putative AMGs from viruses in diverse environments. However, this has also led to many instances of misannotation due to the limitations of annotation tools, resulting in misinterpretations about the roles of some viral genes. Here, we highlight studies that support claims about AMGs with more than just function predictions for guidance on best practices. We then propose the adoption of an expanded, inclusive view of all genes auxiliary to core viral functions with the term 'auxiliary viral genes' (AVGs), alongside an associated eco-evolutionary framework for considering the types of analyses that can better support claims made about AVGs.}, }
@article {pmid40865847, year = {2025}, author = {Dong, BX and Liu, YJ and Liu, SH and Lu, W and Zhu, C and Tian, YJ and Li, G}, title = {Per822: A pH-stable metagenome-derived perhydrolase for dye decolorization, oil stain removal, and benzo[a]pyrene degradation.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {147131}, doi = {10.1016/j.ijbiomac.2025.147131}, pmid = {40865847}, issn = {1879-0003}, abstract = {Per822, a newly discovered metagenomic perhydrolase, merges promiscuous catalysis with exceptional robustness, unlocking versatile solutions for sustainable chemistry. The results revealed that Per822 possesses both esterase and peroxidase activities. Its esterase activity was optimal at pH 8.5 and 40 °C, while its peroxidase activity reached optimal levels at pH 4.5 and 45 °C. Additionally, Per822 demonstrated stability across a broad pH and temperature range. It also retained high activity in various surfactants and organic solvents, highlighting its potential for industrial applications. Application studies showed that Per822 effectively removed chili oil stains from cotton fabric when used as a laundry additive. In dye decolorization experiments, Per822 achieved efficient decolorization of multiple dyes after the addition of Br[-] and Fe[2+]. Notably, in the degradation of benzo(a)pyrene (BaP), the peracetic acid generated by Per822 (at a concentration of 64 mM) achieved a degradation rate of 99.06 % within 72 h. Subsequent plant and microbial toxicity tests indicated a significant reduction in the toxicity of the BaP degradation products. In conclusion, Per822, with its multifunctionality, stability, and outstanding performance in laundry, dye decolorization, and environmental remediation, shows great potential as a candidate enzyme for various applications in industries such as detergents, environmental repair, and organic synthesis.}, }
@article {pmid40865528, year = {2025}, author = {Shi, Y and Li, Y and Li, H and Haerheng, A and Marcelino, VR and Lu, M and Lemey, P and Tang, J and Bi, Y and Pettersson, JH and Bohlin, J and Klaps, J and Wu, Z and Wan, W and Sun, B and Kang, M and Holmes, EC and He, N and Su, S}, title = {Extensive cross-species transmission of pathogens and antibiotic resistance genes in mammals neglected by public health surveillance.}, journal = {Cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cell.2025.08.016}, pmid = {40865528}, issn = {1097-4172}, abstract = {Non-traditional farmed and wild mammals are often neglected in pathogen surveillance. Through metagenomic and metatranscriptomic sequencing of fecal and tissue samples from 973 asymptomatic mammals, we identified 128 viruses (30 novel), including a new coronavirus genus, 10,255 bacterial species (over 7,000 undescribed), 201 fungi, and 7 parasites. Farmed and wild mammals shared 13.3% of virus species, including canine coronavirus in Asiatic black bears and Getah virus in rabbits, while the 2.3.4.4b clade of H5N1 avian influenza virus was found in a wild leopard cat. We identified potential bacterial pathogen transmission between farmed and wild mammals and bacterial strains with high genetic similarity to those found in humans. We observed 157 clinically prioritized antibiotic resistance genes (ARGs) in mammalian microbiomes with greater than 99% identity to ARGs from human microbiomes, often co-occurring with mobile genetic elements. Overall, this work highlights cross-species risks at the human-animal interface.}, }
@article {pmid40865345, year = {2025}, author = {Tao, X and Gao, Y and Jin, Z and Lu, S and Li, Z and Guo, S and Fan, Q and Li, J and Qiao, C and Lei, H and Zhang, Z and Zhao, C and Wu, J}, title = {Co-administration of berberine and evodiamine: Mitigating evodiamine-induced hepatotoxicity and potentiating colitis treatment.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {147}, number = {}, pages = {157185}, doi = {10.1016/j.phymed.2025.157185}, pmid = {40865345}, issn = {1618-095X}, abstract = {BACKGROUND: The combined therapeutic mechanisms of evodiamine (EVO) and berberine (BBR), which are the primary bioactive components contributing to the pharmacological effects of Euodiae Fructus and Rhizoma Coptidis, a classic herb pair used for colitis, have not yet been fully elucidated PURPOSE: This study aimed to investigate the critical mechanisms by which co-administration EVO and BBR mitigated EVO-induced hepatotoxicity while exerting therapeutic effects against colitis.<br><br>METHODS: Safety and therapeutic outcomes of EVO alone and combined BBR were validated in normal and colitis models. RNA-seq sequencing was performed on liver and colon tissues from different groups, while metagenomic sequencing was utilized to analysis fecal samples. An integrated bioinformatics analysis of transcriptomic and metagenomic data was conducted to reveal the mechanisms underlying EVO-induced hepatotoxicity and the protective and synergistic effects of BBR against colitis. Molecular biology experiments were employed to validate the regulatory mechanism, with a particular emphasis on the interactions within the