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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

STUDY DESIGN: Prospective randomised clinical trial.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

@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.

PATIENTS AND METHODS: We studied a cohort of 6,073 pediatric ILI patients (mean age 3.1 years, range 0-18.8 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 years, range 0-17.8 years) to additional viral mNGS. PCR and mNGS were compared by agreement rates and Cohen's κ for inter-method reliability.

RESULTS: In the pilot feasibility study, the mean VIVI Disease Severity Score was above the cohort average (>67th percentile, p < 0.0001), with 'age < 2 years' as the most prevalent risk factor (n = 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 % and overall reliability was 'moderate' (κ scores of 0.1-0.85).

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.},
}

*Computer Security
Humans
Cloud Computing
*Software
Algorithms
*Genomics/methods
Databases, Genetic

@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.},
}

*Biodegradation, Environmental
*Plastics/metabolism/analysis
Waste Management/methods

@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.

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 (≤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 & 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.

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-γ 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.

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-γ 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.},
}

Humans
*Talaromyces/genetics/isolation & purification
Male
*High-Throughput Nucleotide Sequencing/methods
*Mycoses/diagnosis/drug therapy/microbiology
*Metagenomics/methods
Antifungal Agents/therapeutic use
Amphotericin B/therapeutic use
Adult
China

@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 & purification/classification/genetics ; Child, Preschool ; Rural Population ; Bacteria/classification/genetics/isolation & purification ; Metagenome ; Ascaris lumbricoides/isolation & purification ; Strongyloides stercoralis/isolation & purification ; Necator americanus/isolation & purification ; Trichuris/isolation & 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.},
}

Humans
*Gastrointestinal Microbiome/genetics
Feces/parasitology/microbiology
Animals
Gabon/epidemiology
Female
Male
Child
*Helminthiasis/parasitology/epidemiology/microbiology
Metagenomics
*Helminths/isolation & purification/classification/genetics
Child, Preschool
Rural Population
Bacteria/classification/genetics/isolation & purification
Metagenome
Ascaris lumbricoides/isolation & purification
Strongyloides stercoralis/isolation & purification
Necator americanus/isolation & purification
Trichuris/isolation & purification
Biodiversity

@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 & 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.

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.

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.

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.

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.

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.

RESULTS: No significant differences in α-diversity were observed across the groups. β-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.

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.

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.

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 = 0.80).

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 & 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.

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.

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.},
}

Humans
Retrospective Studies
Male
Female
*High-Throughput Nucleotide Sequencing/methods
Middle Aged
Aged
*Metagenomics/methods
*Aspergillus/genetics/isolation & purification/classification
Adult
Risk Factors
Aged, 80 and over
Young Adult
China
*Aspergillosis/diagnosis/microbiology
*Plasma/microbiology

@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.},
}

Fermentation
*Soy Foods/microbiology/analysis
Food Microbiology
Humans

@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 & 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.},
}

Humans
*Virome
*Skin/virology
Adult
*Viruses/classification/genetics/isolation & purification
Male
Female
Young Adult
Republic of Korea
Metagenome

@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 Innovación, Spain (grant PID2021-124174OB-I00)./ ; },
mesh = {*Polypropylenes/metabolism ; *Polyethylene/metabolism ; *Bacteria/classification/genetics/metabolism/isolation & 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.},
}

*Polypropylenes/metabolism
*Polyethylene/metabolism
*Bacteria/classification/genetics/metabolism/isolation & purification
*Soil Microbiology
RNA, Ribosomal, 16S/genetics
Agriculture
*Biodiversity
Biodegradation, Environmental
Phylogeny

@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 & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; T32AI162579//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; OPP1189217//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; INV048956//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; INV048982//Bill and Melinda Gates Foundation (Bill & 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.},
}

Biomarkers/analysis
*Metabolomics/methods
*Hot Temperature
*Wine/analysis/microbiology
*Bacteria/metabolism/classification/genetics
*Alcoholic Beverages/microbiology/analysis

@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.

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.

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.

PURPOSE: In this study, we investigated the mechanism of the targeted regulation of intestinal flora by Fangji Huangqi Tang to delay CKD.

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.

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.

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.},
}

*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

@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)/ ; },
}