@article {pmid41429282,
year = {2025},
author = {Akram, J and Jin, Y and Song, C and Li, C and Chen, C and Liu, G},
title = {Stimulating anaerobic degradation of biodegradable plastics by promoting direct interspecies electron transfer via conductive materials.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133850},
doi = {10.1016/j.biortech.2025.133850},
pmid = {41429282},
issn = {1873-2976},
abstract = {Although biodegradable plastics (BPs) are promoted as environmentally friendly, they exhibit low degradability and slow degradation rates under anaerobic conditions, creating challenges similar to conventional plastics. This study explores the effects of granular activated carbon and magnetite on the anaerobic digestion of BPs. Results showed that conductive materials improved digestion rates for readily degradable BPs but had no effect on recalcitrant ones unless pretreated. Magnetite increased the maximum methane production rates of cellulose diacetate, poly(3-hydroxybutyrate-co-3-hydroxyvalerate), and thermoplastic starch by 18 %, 37 % and 15 %, respectively, at an organic loading (OL) of 8 gVS/L. Supplementation was especially effective at high OLs, where unamended controls were inhibited by excessive acidification. Metagenomic analysis revealed enrichment of direct interspecies electron transfer-capable microorganisms such as Syntrophaceticus and Methanosarcina, along with associated functional genes, in the supplemented groups. Overall, the findings suggest that conductive materials are most beneficial for readily degradable BPs, especially under high OL conditions.},
}

@article {pmid41429225,
year = {2025},
author = {Chen, J and Cao, H and Xu, Y and Chang, Y and Qin, X and Zhang, Z and Yang, W},
title = {Is light-to-moderate alcohol drinking associated with the onset of metabolic dysfunction-associated steatotic liver disease in a Chinese cohort?.},
journal = {The American journal of clinical nutrition},
volume = {},
number = {},
pages = {101144},
doi = {10.1016/j.ajcnut.2025.101144},
pmid = {41429225},
issn = {1938-3207},
abstract = {BACKGROUND: The association between light-to-moderate alcohol drinking (≤14 g/d for females; ≤28 g/d for males) and the risk of steatotic liver disease (SLD), including its metabolic dysfunction-associated subtype (MASLD), remains unclear, as does the role of related gut microbiota.

OBJECTIVES: We investigated the association between light-to-moderate alcohol drinking and incident SLD/MASLD, identified gut microbial species associated with such drinking, and evaluated their associations with disease risk.

METHODS: Among 1297 adults from a Chinese community-based cohort, alcohol intake was assessed by validated questionnaire, and SLD was diagnosed by vibration-controlled transient elastography. In a subset with fecal samples at follow-up (n=665), gut microbiota was profiled using shotgun metagenomic sequencing. We used the average alcohol intake from baseline and follow-up to represent long-term drinking habits. Species differentially associated with alcohol intake were identified using zero-inflated Gaussian models with false discovery rate (FDR) correction. Cox and logistic regression were used to estimate hazards ratio (HR) and odds ratio (OR) with 95% confidence interval (CI), respectively.

RESULTS: During follow-up (2020-2025), 513 incident SLD cases were identified. Light-to-moderate drinkers showed higher risks of SLD (HR=1.27, 95% CI: 1.03, 1.58) and MASLD (HR=1.27, 95% CI: 1.01, 1.59) versus abstainers. For the same comparison, liquor consumption was positively associated with SLD (HR=1.29, 95% CI: 1.01, 1.65). We identified 89 microbial species associated with alcohol intake and constructed a microbial score, which was positively associated with SLD (ORT3 vs T1=1.54, 95% CI: 1.03, 2.31, Ptrend=0.05) and MASLD (ORT3 vs T1=1.50, 95% CI: 1.00, 2.26, Ptrend=0.05). Among these species, Stenotrophomonas maltophilia AQ, Olsenella E timonensis, and Firm 11 sp., which were less abundant in drinkers, showed inverse associations with both conditions after FDR correction.

CONCLUSIONS: Light-to-moderate alcohol consumption was associated with increased risks of SLD and MASLD. A gut microbial score based on alcohol-associated species also predicted higher disease risk.},
}

@article {pmid41429195,
year = {2025},
author = {Ji, J and Guo, J and Huang, Y and Chen, K and Xu, Y and Liang, W and Lin, Z and Xiong, C and Han, X and Liu, J and Hei, Z and Chen, S and Yao, W and Chen, C},
title = {Electroconvulsive therapy modulates brain plasticity in male depression: Links to gut microbial metabolites and diet-derived regulation of Wnt/BDNF signaling.},
journal = {The Journal of nutritional biochemistry},
volume = {},
number = {},
pages = {110240},
doi = {10.1016/j.jnutbio.2025.110240},
pmid = {41429195},
issn = {1873-4847},
abstract = {Electroconvulsive therapy (ECT) stands as the most effective intervention for treatment-resistant depression; however, its interaction with dietary regulation of the gut-brain axis has not been thoroughly explored. This study aimed to elucidate the mechanistic link between ECT, gut microbiota remodeling, short-chain fatty acid (SCFA) production, and neural plasticity. In this study, mice were subjected to chronic restraint stress (6 h/day for 28 consecutive days) to establish a depression-like model. Utilizing a translational approach that incorporated behavioral assessments, multimodal neuroimaging techniques such as PET-CT and laser speckle contrast imaging, along with multi-omics analyses including metagenomics, metabolomics, and transcriptomics in rodent models, we demonstrated that ECT induced significant gut microbiota remodeling, characterized by an enrichment of SCFA-producing genera like Lactobacillus and Bifidobacterium. This remodeling was associated with restored intestinal barrier integrity and elevated plasma SCFA levels. Mechanistically, these microbial metabolites activated hippocampal Wnt/β-catenin signaling pathways, enhancing synaptic plasticity restoration, while concurrent probiotic supplementation further amplified brain-derived neurotrophic factor (BDNF) expression via SCFA-dependent epigenetic mechanisms. Neuroimaging corroborated the normalization of cerebral glucose metabolism and hemodynamic function post-ECT. In conclusion, our findings unveil a novel gut-brain communication pathway by which ECT exerts its antidepressant effects, positioning SCFAs as vital mediators connecting microbial metabolic alterations to neural plasticity. This research not only redefines the role of nutritional biochemistry in neuromodulation but also suggests the potential of microbial metabolite monitoring to tailor antidepressant therapies for enhanced efficacy.},
}

@article {pmid41428801,
year = {2025},
author = {Sauša, S and Zodāne, A and Kumar, S and Plūme, J and Baranova, J and Kozlova, T and , and Saušs, H and Kloviņš, J and Pīrāgs, V and Mitravinda, KS and Kistkins, S and Brīvība, M},
title = {Rapid and Selective Gut Microbiome Modulation by Polyherbal Formulation in Type 2 Diabetes.},
journal = {Endocrine connections},
volume = {},
number = {},
pages = {},
doi = {10.1530/EC-25-0463},
pmid = {41428801},
issn = {2049-3614},
abstract = {BACKGROUND: Metformin, the first-line treatment for type 2 diabetes, often induces gastrointestinal side effects, affecting treatment adherence. Recent research suggests that the gut microbiome mediates both the efficacy and tolerability of metformin. This study evaluates the effect of a polyherbal formulation, used as an add-on to metformin, on the gut microbiota in patients with type 2 diabetes and metformin intolerance.

METHODS: We report preliminary findings from the first 7-day intervention phase of an ongoing randomized, placebo-controlled, crossover trial (NCT06846138) in 27 adults with type 2 diabetes. Participants received either polyherbal formulations or a placebo alongside metformin for 7 days. Stool samples were collected pre- and post-intervention for shotgun metagenomic sequencing. Microbial diversity, composition, and pathway functions were analyzed using Kraken2, Bracken, and HUMAnN3. Continuous glucose monitoring was used to assess glycemic metrics.

RESULTS: No significant alpha-diversity changes were observed; however, beta-diversity differed significantly between arms (PERMANOVA R2 = 0.04, p = 0.04). In the polyherbal formulation group, 17 species changed post-treatment (FDR < 0.25), with significant increases in six Bifidobacterium spp. (e.g., B. adolescentis, B. ruminantium). In contrast, the placebo group showed no major microbial shifts. Polyherbal formulation also altered 10 microbial pathways (FDR < 0.25). Continuous glucose monitoring revealed no short-term changes in glycemic levels.

CONCLUSION: Short-term polyherbal formulation co-administration significantly modulates gut microbiota, promoting beneficial taxa like Bifidobacterium in metformin-treated type 2 diabetes patients. This supports the potential role of the polyherbal formulation in microbiome-targeted strategies to improve metformin tolerability and effectiveness.},
}

@article {pmid41428733,
year = {2025},
author = {Yang, Z and Yu, M and Li, P and Li, Z and Teng, Y and Zhou, Y and Zhao, M and Liu, C and Zhao, Z and Wang, Z and Li, J and Jing, Y and Li, Y and Zhao, H and Song, W and Bian, C and Zhao, H and Chen, J and Xin, B and Lai, J},
title = {Casδ, an evolutionary transitional CRISPR system enables efficient genome editing across animals and plants.},
journal = {Nucleic acids research},
volume = {53},
number = {22},
pages = {},
doi = {10.1093/nar/gkaf1358},
pmid = {41428733},
issn = {1362-4962},
support = {//Agriculture Science and Technology/ ; 2023YFD1202900//National Key Research and Development Program of China/ ; PC2023A01004//Pinduoduo-China Agricultural University/ ; //Agriculture Science and Technology/ ; },
mesh = {*Gene Editing/methods ; *CRISPR-Cas Systems/genetics ; Humans ; Animals ; *CRISPR-Associated Proteins/genetics/metabolism/chemistry ; Genome, Plant ; RNA, Guide, CRISPR-Cas Systems/genetics ; Zea mays/genetics ; Evolution, Molecular ; Oryza/genetics ; },
abstract = {Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas (CRISPR-associated) adaptive immune systems provide sequence-specific mechanisms for targeting foreign DNA or RNA and have been widely used in genome editing and DNA detection. Type V CRISPR-Cas systems are characterized by a single RNA-guided RuvC domain-containing effector, Cas12. Here, through comprehensive mining of large-scale genomic and metagenomic data from microbial sources, we identified a new Class 2 CRISPR-Cas effector superfamily, designated Casδ, comprising three members with protein sizes ranging from 867 to 936 amino acids. Biochemical analyses revealed that Casδ-1 functions as a single RNA-guided endonuclease with specific recognition of 5'-RYR-3' protospacer-adjacent motifs, where R represents A or G, and Y represents T or C. Casδ-1 exhibits robust double-stranded DNA cleavage activity and target-dependent trans-cleavage activity. Casδ-1 mediates efficient genome editing across species, achieving up to 60% indel rates in human cells while generating homozygous knockout lines in two agriculturally important monocot species (Oryza sativa and Zea mays) through stable transformation. Structural and evolutionary analyses reveal Casδ as an evolutionary transitional nuclease bridging Cas12n and canonical type V systems, featuring a C-terminal loop that is essential for activity. Collectively, Casδ is an evolutionarily distinct, compact (<1000 aa), tracrRNA-free CRISPR system enabling versatile cross-kingdom genome editing.},
}

*Gene Editing/methods
*CRISPR-Cas Systems/genetics
Humans
Animals
*CRISPR-Associated Proteins/genetics/metabolism/chemistry
Genome, Plant
RNA, Guide, CRISPR-Cas Systems/genetics
Zea mays/genetics
Evolution, Molecular
Oryza/genetics

@article {pmid41428602,
year = {2025},
author = {Zhang, Y and Chen, W and Wang, B and Rehman, KU and van Huis, A and Henawy, AR and Cai, M and Zheng, L and Ren, Z and Huang, F and Zhang, J},
title = {Enhancing Salmonella Inhibition in Black Soldier Fly Larvae (Hermetia illucens L.) Conversion by Bioaugmentation With Gut Microbiota.},
journal = {Microbial biotechnology},
volume = {18},
number = {12},
pages = {e70242},
doi = {10.1111/1751-7915.70242},
pmid = {41428602},
issn = {1751-7915},
support = {31770136//National Natural Science Foundation of China/ ; 2662022SKYJ006//Fundamental Research Funds for the Central Universities/ ; 2662023DKPY003//Fundamental Research Funds for the Central Universities/ ; 2022hszd013//Major Project of Hubei Hongshan Laboratory/ ; 2024BCA006//Hubei Province Technological Innovation Plan Project/ ; },
mesh = {Animals ; Larva/microbiology ; *Gastrointestinal Microbiome ; *Salmonella/growth & development ; Manure/microbiology ; *Diptera/microbiology ; Chickens ; Bacillus ; Metagenomics ; *Antibiosis ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {Black soldier fly larvae (BSFL) can efficiently convert organic waste into biomass and reduce pathogenic bacteria in organic waste. The microbial composition of the substrate and the gut of BSFL is a pivotal factor in determining the efficacy of BSFL in pathogen elimination. However, there are insufficient data on the gut microbiology of BSFL in relation to pathogen inhibition. To address this gap, we investigated the dynamics of Salmonella during the conversion of chicken manure by BSFL and examined the role of intestinal bacterial communities and core bacteria in reducing Salmonella levels. The results indicate that BSFL treatment can reduce the amount of Salmonella in chicken manure, with the gut microbiome of the BSFL playing a crucial role in this reduction. Combining metagenomic analysis with culturomics methods, we isolated 158 strains from the larval gut, in which seven gut bacteria belonging to the genus Bacillus can promote BSFL to reduce Salmonella. In reinoculation and validation experiments, the combination of BSFL and Bacillus velezensis A2 enhanced the elimination of Salmonella from chicken manure and larvae. This study provides insight into how BSFL can reduce pathogenic bacteria in chicken manure and suggests that pairing BSFL with functional microorganisms can improve the biosafety of organic waste conversion by BSFL.},
}

Animals
Larva/microbiology
*Gastrointestinal Microbiome
*Salmonella/growth & development
Manure/microbiology
*Diptera/microbiology
Chickens
Bacillus
Metagenomics
*Antibiosis
Bacteria/classification/genetics/isolation & purification

@article {pmid41428487,
year = {2025},
author = {Deng, C and Hu, J and Chen, Q and Zhou, S and Ni, J},
title = {Expanded global groundwater microbial diversity reveals bioprospecting potential.},
journal = {Cell reports},
volume = {45},
number = {1},
pages = {116760},
doi = {10.1016/j.celrep.2025.116760},
pmid = {41428487},
issn = {2211-1247},
abstract = {Although the terrestrial subsurface harbors a substantial fraction of Earth's microbial biomass, the genomic diversity of groundwater microbiomes and their potential for bioprospecting remain poorly characterized. Here, we recovered 44,320 bacterial and archaeal genomes from in-house and publicly available metagenomic datasets, establishing a large-scale groundwater microbiota catalog (GWMC) spanning 167 phyla, including four candidate phyla and over 12,000 previously uncharacterized species. This unprecedented phylogenetic diversity was accompanied by a bimodal genome size distribution (0.3-12.8 Mbp), revealing divergent strategies of genomic allocation. By mining extensive genomic resources, we found that small genomes prioritized molecular defense and redox regulation, whereas large genomes frequently harbored greater biosynthetic potential. Notably, we establish the largest selenoprotein catalog to date and highlight groundwater as an overlooked hotspot of microbial selenium metabolism. Overall, this work advances our understanding of microbial diversity in aquifers and uncovers underexplored genomic resources with potential for biotechnology and biomedicine.},
}

@article {pmid41428281,
year = {2025},
author = {Yu, J and Cheng, L and Zhan, H and Huang, Y and Wang, S and Li, H and Liu, Y and Xu, Y and Guo, Y and Li, Y},
title = {Potential Mechanisms and Hypotheses for Pathogenic Microorganisms Triggering Kawasaki Disease.},
journal = {Clinical reviews in allergy & immunology},
volume = {68},
number = {1},
pages = {110},
pmid = {41428281},
issn = {1559-0267},
support = {2024YFA1307604//National Key Research and Development Program of China/ ; 8247082356//Natural Science Foundation of China/ ; },
mesh = {Humans ; *Mucocutaneous Lymph Node Syndrome/etiology/immunology/epidemiology/microbiology ; Gastrointestinal Microbiome/immunology ; Animals ; Host-Pathogen Interactions/immunology ; Dysbiosis ; Disease Susceptibility ; *Virus Diseases/immunology/complications ; Superantigens/immunology ; Immunoglobulin A/immunology/metabolism ; Cytokines/metabolism ; },
abstract = {Kawasaki disease (KD) is an acute, self-limiting systemic vasculitis of early childhood and remains the leading cause of acquired heart disease in developed nations. Despite decades of investigation, its etiology and immunopathogenesis are still not fully understood. This review integrates nearly six decades of histopathological, epidemiological, and immunological research to examine infection-driven mechanisms underlying KD. Current evidence indicates that KD may result from a convergence of microbial and host factors: viral infections can trigger mucosal IgA-mediated immune activation; superantigens may induce T-cell receptor (TCR) Vβ-skewed cytokine release; conventional antigens appear to elicit oligoclonal adaptive immune responses consistent with infection-associated vasculitis; and gut microbiota dysbiosis may amplify systemic inflammation through disruption of intestinal barrier integrity and short-chain fatty acid metabolism. Rather than a single-pathogen infection, KD likely reflects infection-triggered immune dysregulation in genetically susceptible children. By contrasting these mechanistic hypotheses, this review highlights the need for longitudinal, multi-omics studies integrating metagenomic, transcriptomic, and serologic analyses to delineate causal microbial signatures, identify diagnostic biomarkers, and guide precision immunomodulatory strategies for this complex pediatric vasculitis.},
}

Humans
*Mucocutaneous Lymph Node Syndrome/etiology/immunology/epidemiology/microbiology
Gastrointestinal Microbiome/immunology
Animals
Host-Pathogen Interactions/immunology
Dysbiosis
Disease Susceptibility
*Virus Diseases/immunology/complications
Superantigens/immunology
Immunoglobulin A/immunology/metabolism
Cytokines/metabolism

@article {pmid41427949,
year = {2025},
author = {Pan, S and Zhao, X and Shi, Q and Shen, Z and Liu, J and Li, W and Xie, Y},
title = {Significant diversity of human anelloviruses revealed by novel viral sequences identified in human metagenomic data.},
journal = {The Journal of general virology},
volume = {106},
number = {12},
pages = {},
doi = {10.1099/jgv.0.002199},
pmid = {41427949},
issn = {1465-2099},
mesh = {Humans ; Phylogeny ; Metagenomics ; *Anelloviridae/genetics/classification/isolation & purification ; *Genetic Variation ; Genome, Viral ; Open Reading Frames ; Viral Proteins/genetics ; *DNA Virus Infections/virology ; },
abstract = {Human torque teno viruses are emerging infectious agents distributed globally and have increasingly been reported to be associated with human diseases. To identify potential anelloviral sequences in available metagenomic data, an in silico screening was performed mainly employing the ORF1, ORF2 and ORF3 nucleotide/protein queries of known human anelloviruses and identified 217 complete ORF1 regions. Pairwise nucleotide-identity analysis with a 69% cut-off - consistent with ICTV species demarcation - revealed 117 novel species across the 3 major human-infecting genera: 15 in Alphatorquevirus, 51 in Betatorquevirus and 51 in Gammatorquevirus. In nearly all cases, these species assignments correspond precisely to monophyletic clusters in maximum-likelihood phylogenies of ORF1 amino acid sequences. Using AlphaFold3-guided modelling together with representative ORF1 alignments, we delineated capsid motifs - the conserved jelly-roll (JR) β-sandwich core (β-strands B-I) and the outward projection domains P1/P2 - and quantified motif lengths across genera, revealing tightly constrained JR lengths with genus-specific but overlapping variation in P1/P2. A few exceptions - where pairwise-based groupings split or merge slightly differently - highlight ongoing challenges in delineating rapidly evolving viruses. Notably, the two deeply branching isolates retain the canonical JR core while exhibiting a TTMDV-like short P2, indicating preservation of key capsid architecture in the newly proposed genus. This work nearly doubles the known species richness of human anelloviruses and introduces a novel genus, underscoring the vast, hidden diversity of the gut virome and its potential impact on human health. By coupling taxonomy with structure-informed ORF1 motif analysis, our study provides biological context for these lineages and a framework for future functional and immunological investigations.},
}

Humans
Phylogeny
Metagenomics
*Anelloviridae/genetics/classification/isolation & purification
*Genetic Variation
Genome, Viral
Open Reading Frames
Viral Proteins/genetics
*DNA Virus Infections/virology

@article {pmid41427872,
year = {2025},
author = {Gu, T and Chen, Z and Hutchins, DA and Sun, J},
title = {Urea-driven nitrification contributes to N2O production in the oligotrophic euphotic ocean.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf281},
pmid = {41427872},
issn = {1751-7370},
abstract = {Urea is an important alternative nitrogen source to ammonium for nitrification in oligotrophic oceans, yet its role in substrate-driven nitrous oxide (N2O) production remains poorly constrained. Here, we combined N2O isotopomer profiling, 15N-tracer incubations, and metagenomics to quantify and mechanistically resolve substrate-specific archaeal nitrification in the western tropical Pacific euphotic zone. Isotopomer-based mixing and fractionation model indicated that archaeal nitrification accounted for 69.6 ± 14.1% of microbial sources of N2O in oxygenated epipelagic waters. Depth-integrated urea-driven nitrification contributed 14-41% of total nitrification and 21-39% of nitrification-derived N2O, with contributions regulated by substrate proportions. Acidification experiments showed that pH decline inhibited ammonium-driven nitrification (median 21.9%) and enhanced urea oxidation (median 61.9%), whereas N2O production increased for both substrates (median 35.9% and 38.0%). In addition, experimental acidification induced opposite shifts in hybrid versus double-labelled N2O, suggesting pH-driven shifts N-intermediate chemistry and intracellular partitioning. Metagenomic results support the globally widespread urea-type AOA. Together, these results indicate that urea-driven nitrification constitutes a non-negligible, substrate-dependent source of N2O in oligotrophic euphotic zones. We recommend that Earth-system N-cycle models represent urea and ammonium oxidation as distinct pathways with pH-sensitive yields to improve projections of marine nitrification and N2O fluxes under acidification.},
}

@article {pmid41427714,
year = {2025},
author = {Bell, AG and Cable, J and Temperton, B and Tyler, CR},
title = {Assessment of the effectiveness of host depletion techniques for profiling fish skin microbiomes and metagenomic analysis.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0183825},
doi = {10.1128/spectrum.01838-25},
pmid = {41427714},
issn = {2165-0497},
abstract = {UNLABELLED: Microbiomes on fish mucosal surfaces play crucial roles in nutrient absorption, immune priming, and defense, and disruptions in these microbial communities can lead to adverse health outcomes, including disease. Studying fish microbiomes relies on sequencing microbiota within mucosal-rich samples; however, nucleic acid extraction from these samples is composed predominantly of host DNA, making subsequent bioinformatic processes difficult. Host depletion techniques address this issue by either selectively degrading host DNA before sequencing or retaining bacterial DNA post-extraction. However, their application to fish mucosal samples has been largely unexplored. Here, we assessed the efficacy of various host depletion techniques on fish skin mucosal swabs via either selectively removing CpG-methylated (predominantly eukaryotic) DNA or selectively lysing eukaryotic cells before DNA extraction. Surprisingly, none of the existing methods we assessed effectively reduced host DNA to be practically useful. Furthermore, some methods introduced a bias toward certain bacterial taxa, including the Bacilli class and the Proteobacteria phylum. Our findings illustrate that the currently available host depletion techniques are largely ineffective for reducing host DNA in fish mucosal samples. This poses a major limitation for developing an understanding of the functional composition of fish mucosal microbiomes, as enriching microbiota (and excluding host DNA) is fundamental for cost-effective metagenomic studies and facilitating more accurate analyses of the microbiota metabolome and proteome.

IMPORTANCE: Microbial communities on fish mucosal surfaces are vital for immune function and disease resistance. However, sequencing these communities is hindered by the dominance of host DNA in mucosal samples, which can exceed 99% of total nucleic acids. While host depletion techniques are routinely used in human and mammalian systems to enrich microbial DNA, their efficacy on fish samples remains uncharacterized. In this study, we assessed multiple commercial and published host depletion methods on fish skin microbiomes. None significantly reduced host DNA to levels suitable for high-quality metagenomic sequencing, and some introduced taxonomic bias. We suggest methodological reasons, including differences in fish cell structure and mucus composition compared to mammalian systems, that may explain these shortcomings. Based on our findings, we propose protocol modifications and highlight key areas for improvement. This work identifies critical limitations and offers a foundation for developing optimized host depletion strategies tailored to fish mucosal microbiome research.},
}

@article {pmid41427415,
year = {2025},
author = {Bernate, E and Shi, Y and Franck, E and Crofts, TS},
title = {A functionally selected Acinetobacter sp. phosphoethanolamine transferase gene from the goose fecal microbiome confers colistin resistance in E. coli.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2025.12.09.693354},
pmid = {41427415},
issn = {2692-8205},
abstract = {Polymyxins are last-resort antibiotics for infections caused by multidrug resistant Gram-negative bacteria such as Enterobacteriaceae, Pseudomonas aeruginosa and Acinetobacter baumannii . This makes the rise of bacteria exhibiting polymyxin E (colistin) resistance, largely through modification of lipid A moieties, concerning and suggests that it is important to document potential sources of the corresponding resistance genes. This study searched for potential emerging colistin-resistance genes from the environment by investigating a previously performed functional metagenomic selection for colistin resistance of a goose fecal microbiome. We found that the selection captured Acinetobacter sp. DNA fragments which all contained eptA genes. We confirmed their ability to confer significant colistin resistance in E. coli via modification of lipid A in the outer membrane. Furthermore, we found evidence for mobilization of closely related eptA genes in Acinetobacter strains, marking them as potential mcr genes or their precursors. This study highlights the goose fecal microbiome as a potential source for colistin resistance in the environment.},
}

@article {pmid41427287,
year = {2025},
author = {Zhang, A and Boucher, C and Noyes, N and Yu, YW},
title = {RAmpSim: A Thermodynamic Simulator for Hybridization Capture in Metagenomic Sequencing.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2025.12.05.692407},
pmid = {41427287},
issn = {2692-8205},
abstract = {UNLABELLED: Hybridization (bait) capture combined with long-read sequencing enables targeted profiling within complex metagenomes but introduces systematic biases from bait multiplicity, sequence composition, and species abundance that existing simulators ignore. We present RAmpSim , a fast simulator that models bait-target hybridization and fragment capture using a thermodynamic nearest-neighbor energy model and Boltzmann-weighted sampling of binding sites. Fragments are generated through multinomial sampling parameterized by bait concentration, binding energy, and genomic abundance before being passed to existing long-read simulators for modeling platform-specific errors. Implemented in Rust, RAmpSim reproduces empirical within-genome coverage and cross-species enrichment patterns observed in capture-based metagenomic datasets. Compared to uniform-coverage baselines, RAmpSim 's simulated coverage distributions are up to an order of magnitude closer to real data with respect to earth mover's distance. Classification analysis reveals high recall in classifying high coverage regions between simulated and experimental distributions while outperforming a uniform baseline. Supporting accurate benchmarking and bait-set evaluation, RAmpSim provides an interpretable, efficient framework for simulating capture-based metagenomic sequencing.

CODE AVAILABILITY: https://github.com/az002/RAmpSim.git.},
}

@article {pmid41427275,
year = {2025},
author = {Chen, K and Talesara, A and Thakkar, S and Shao, M},
title = {Minimum flow decomposition guided by saturating subflows.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2025.12.11.693570},
pmid = {41427275},
issn = {2692-8205},
abstract = {The minimum flow decomposition problem abstracts a set of key tasks in bioinformatics, including metagenome and transcriptome assembly. These tasks, collectively known as multi-assembly, aim to reconstruct multiple genomic sequences from reads obtained from mixed samples. The reads are first organized into a directed graph (e.g., overlap graph, splice graph), where each edge has an integer weight representing the number of supporting reads. By viewing the graph as a flow network, the underlying sequences and their abundances can be extracted through decomposition into a minimum number of weighted paths. Although this problem is NP-hard, prior work has proposed an efficient heuristic that transforms the graph by identifying nontrivial equations in the flow values. However, for graphs with complex structures, many equations cannot be fully resolved by existing mechanisms, leading to suboptimal decompositions. In this study, we revisit the theoretical framework of the flow decomposition problem and extend the equation-resolving mechanisms to jointly model all equations in the graph, enabling safe merge operations that iteratively simplify the graph. Experimental results demonstrate that our new algorithm substantially improves decomposition quality over existing heuristics, achieving near-optimal solutions for complex graphs, while running several orders of magnitude faster than the ILP formulation. Source code of our algorithm is available at https://github.com/Shao-Group/catfish-LP.git .},
}

@article {pmid41426949,
year = {2025},
author = {Allshouse, T and Amendano, M and Caruso, B and Del Campo, R and Murphy, G and Shaffer, L and Steinberg, E and Sullivan, A and Stowe, E},
title = {The Microbiota of Homemade Tepache Includes Antibiotic-Resistant Microorganisms.},
journal = {microPublication biology},
volume = {2025},
number = {},
pages = {},
pmid = {41426949},
issn = {2578-9430},
abstract = {Tepache is a traditional, homemade Mexican drink made by fermenting pineapple rinds. The natural probiotic bacteria in tepache are said to promote a healthy gut microbiome. This study assessed the microbial community in homemade tepache for diversity, survival in simulated gastric fluid, and antibiotic resistance. Simulated gastric passaging reduced total community numbers but the community density was not strongly impacted by exposure to tetracycline. Metagenomic analysis reveals a community dominated by Bacillus, Meyerozyma and Talaromyces. These results indicate that consuming home fermented beverages may provide helpful probiotic bacteria but could also expose the gut microbiome to antibiotic resistance genes.},
}

@article {pmid41426737,
year = {2025},
author = {Valente, P and Sbrenna, L and Valente, F and Sbrenna, A and Mascolo, A},
title = {Drug-Induced Gingival Overgrowth Associated With Cyclosporine Therapy: A Case Report of a 23-Year Periodontal Follow-Up in a Heart Transplant Recipient.},
journal = {Cureus},
volume = {17},
number = {11},
pages = {e97019},
pmid = {41426737},
issn = {2168-8184},
abstract = {Drug-induced gingival overgrowth (DIGO) is a common adverse effect of cyclosporine therapy, which is widely used as an immunosuppressive agent in solid organ transplant recipients. This case report describes the 23-year follow-up of a male patient with a history of orthotopic heart transplantation, performed two years prior to his first dental visit in 2002, who developed DIGO under long-term cyclosporine therapy. At the initial periodontal evaluation, a diagnosis of localized Stage I, Grade A periodontitis associated with gingivitis was made, and nonsurgical mechanical debridement, scaling and root planing, and tailored oral hygiene instruction were provided, yielding favorable early outcomes and long-term periodontal stability. After many years of stability, the patient returned following a three-year lapse in maintenance, presenting with marked gingival enlargement, bleeding on probing, discoloration, and migration of the maxillary central incisors, consistent with progression to Stage II, Grade B periodontitis. Nonsurgical retreatment was performed, and DNA-based metagenomic analysis of subgingival plaque and tongue biofilm revealed a dysbiotic microbial profile, including the persistence of key periodontopathogenic taxa associated with tissue destruction and alveolar bone loss. This case underscores the importance of sustained periodontal maintenance in transplant recipients receiving cyclosporine therapy and illustrates that even after decades of apparent stability, DIGO and periodontal deterioration may reemerge if maintenance care is interrupted. The integration of DNA-based metagenomic analysis provided valuable diagnostic and motivational support, reinforcing a personalized, multidisciplinary approach to long-term periodontal management in immunosuppressed patients.},
}

@article {pmid41426650,
year = {2025},
author = {Wang, C and Wei, H and Duan, R and Jin, S and Wen, J and Li, H and Cheng, A and Gao, C and Xue, H and Hou, Y},
title = {Habitat Diversity Sustains Ecosystem Functioning in Plateau Arid-Region Wetlands.},
journal = {Ecology and evolution},
volume = {15},
number = {12},
pages = {e72747},
pmid = {41426650},
issn = {2045-7758},
abstract = {Plateau arid-region wetlands constitute critical ecosystems for regional ecological security, yet exhibit heightened vulnerability under multiple stressors. Current understanding of the mechanisms sustaining the functions of these systems, particularly the pivotal role of habitat diversity, remains limited. Targeting the Jinzihai Wetland (Qaidam Basin, Qinghai-Tibet Plateau), we integrated metagenomic and geochemical profiling to characterize three representative habitats: sandy meadows, peat bogs, and lake sediments. Our analyses revealed that pronounced cross-habitat physicochemical gradients drive community structure differentiation predominantly through species replacement, establishing habitat diversity as a fundamental driver of wetland biodiversity. Concurrently, community differentiation drives spatial divergence in functional gene composition, manifesting distinct functional dominance: sandy meadows govern assimilation and saline-alkaline stress response; peat bogs orchestrate nutrient enrichment and transformation; lake sediments mediate element release and burial. These functionally complementary habitats collectively catalyze biogeochemical cycling. We demonstrate that within plateau arid-region wetlands, habitat diversity stabilizes ecosystem functioning by sustaining both biodiversity and functional diversity of biogeochemical processes. Consequently, prioritizing habitat diversity conservation is imperative for safeguarding the long-term stability of these vulnerable ecosystems within management frameworks.},
}

@article {pmid41426590,
year = {2025},
author = {Zhang, J and Xu, X and Chen, L and Yang, X and Matsubara, JK and Tian, Y and Liu, J and Jin, X and Chang, H and Xu, M and Zhu, C and Wang, X and Ren, L and Xie, J and Liu, J and Liu, G and Lu, M and Wang, X and Du, L and Ma, Z and Liu, X and Zhao, H and Chen, W and Huo, X and Zheng, G and Xie, C and Xu, C and Zhang, X and Qi, W and Feng, Z},
title = {Circulating microbiome profiling in transjugular intrahepatic portosystemic shunt patients: 16S rRNA vs. shotgun sequencing.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1662837},
pmid = {41426590},
issn = {2296-858X},
abstract = {BACKGROUND AND AIM: Current efforts to characterize the circulating microbiome are constrained by the lack of standardized protocols for isolating and sequencing microbial communities in blood. To address this challenge, our study compared 16S rRNA (V3-V4 region) and shotgun metagenomic sequencing for circulating microbiome detection.

MATERIALS AND METHODS: After obtaining ethics committee approval and informed consent, samples were aseptically collected from 10 patients undergoing transjugular intrahepatic portosystemic shunt (TIPS) procedures. Shotgun metagenomic reads were taxonomically classified using the Kraken2-Bracken pipeline. 16S rRNA (V3-V4) data were analyzed through an ASV-based approach, with USEARCH for denoising and VSEARCH for taxonomic annotation. The results from both sequencing methods were then systematically compared.

RESULTS: Shotgun metagenomic sequencing generated 7,024,580,376 raw reads (mean depth: 234,152,679.2 reads/sample), while 16S rRNA sequencing produced 6,612,678 raw reads (mean depth: 220,422.6 reads/sample). 16S rRNA amplicon sequencing captured a broader range of microbial signals. Although the taxonomic profiles from both sequencing methods showed limited overlap, the core microbiota common to both were still identified. These conserved core microbial communities exhibited stable α- and β-diversity indices across separate vascular compartments.

CONCLUSION: In our study, 16S rRNA amplicon sequencing captured more diverse microbial signals than shotgun metagenomics. A stable microbial community structure was observed across vascular compartments, suggesting a homogeneous microbial composition throughout the circulatory system.},
}

@article {pmid41426580,
year = {2025},
author = {Li, S and Tian, Q and Yang, X and Zhang, M and Zheng, M and Li, D and Duan, Z and Li, Y and Qiu, Z and Liu, Z},
title = {Chronic meningoencephalomyelitis caused by Nocardia nova infection: a case report and literature review.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1680771},
pmid = {41426580},
issn = {2296-858X},
abstract = {A 25-year-old female zookeeper presented with 3-month history of sore throat and headache, 2-month intermittent fever, and 1-month dizziness. Neurological examination revealed bilateral nystagmus, left-sided sensory loss, ataxia, and subtle meningeal signs. Brain and cervical spinal cord MRI showed multiple enhancing lesions with central vein signs. Cerebrospinal fluid (CSF) analysis demonstrated elevated pressure (240 mmH2O) and leukocytosis (140 × 10[6]/L). Serum MOG-IgG was positive (1:32), while CSF metagenomic next-generation sequencing (mNGS) confirmed Nocardia nova infection. Initial treatment with trimethoprim-sulfamethoxazole (TMP-SMX), amikacin, and imipenem-cilastatin was followed by regimen adjustment to TMP-SMX plus minocycline at 6 weeks. One-month post-therapy, repeat CSF showed normalized pressure, reduced leukocytes, negative mNGS, and MRI evidence of lesion regression. Complete symptom resolution occurred 2 months after treatment initiation. This case exemplifies a rare presentation of N. nova-induced meningoencephalomyelitis with craniospinal involvement in an immunocompetent individual.},
}

@article {pmid41426285,
year = {2025},
author = {Ma, X and Zhang, Q and Ji, X and Xia, Y and Cao, J and Xu, X},
title = {Metagenomic Next-Generation Sequencing of Bronchoalveolar Lavage Fluids Improves Pathogen Detection and Antimicrobial Stewardship in Lower Respiratory Tract Infections: A Retrospective Study.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {6611-6632},
pmid = {41426285},
issn = {1178-6973},
abstract = {PURPOSE: With the advancement of metagenomic next-generation sequencing (mNGS), its role in diagnosing lower respiratory tract infections (LRTIs) has expanded rapidly. LRTIs remain a major global health burden, particularly in critically ill patients where diagnosis is challenging. Routine microbiological testing (RMT), including culture, microscopy, antigen detection, and PCR-are limited by low sensitivity, long turnaround times, and restricted pathogen coverage. This study assesses the diagnostic performance of mNGS in LRTIs, with emphasis on pathogen detection and resistance gene prediction, and compares it with traditional methods to clarify its clinical benefits and limitations.

METHODS: This retrospective study included 367 hospitalized patients with suspected LRTIs. All patients underwent mNGS testing, which was compared with traditional diagnostic methods. We also used mNGS to explore the pathogen spectrum characteristics in critically ill patients with pneumonia and evaluated its applicability in predicting antimicrobial resistance genes and adjusting antibiotic treatment.

RESULTS: For patients diagnosed with LRTIs, mNGS demonstrated superior microbial detection efficacy, particularly for bacteria and fungi, relative to culture (bacteria: 56.58% vs 17.37%, P < 0.0001; fungi: 49.65% vs 16.78%, P < 0.0001) and PCR (65.14% vs 45.14%, P < 0.05). In contrast to the non-severe pneumonia group, the detection rate of Enterococcus faecium was highest in the severe pneumonia group (P < 0.001), and the severe pneumonia group had more mixed infections (P < 0.001). In addition, mNGS showed high accuracy in predicting antibiotic resistance genes, with 90.57% agreement with antibiotic susceptibility testing (AST) results. Based on the mNGS results, 97.82% of patients underwent active adjustment to their antibiotic treatment regimen.

CONCLUSION: mNGS is an effective tool for diagnosing LRTIs, with significantly higher pathogen detection rates than traditional methods. mNGS also demonstrates high accuracy in predicting antimicrobial resistance, providing crucial support for clinical treatment decisions.},
}

@article {pmid41426281,
year = {2025},
author = {Yang, L and Zhang, Y and Wu, M and Zeng, F and Chen, H and Xie, D and Shi, F},
title = {Recurrent Disseminated Talaromycosis Mimicking Liver Disease in a STAT3-Mutated HIES Patient: A Case Report.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {6605-6610},
pmid = {41426281},
issn = {1178-6973},
abstract = {BACKGROUND: Talaromycosis is increasingly recognized in immunocompromised individuals beyond those with HIV, including patients with primary immunodeficiencies such as Hyper-IgE syndrome (HIES). However, diagnosing disseminated infection remains challenging due to nonspecific clinical manifestations and limitations of conventional diagnostic methods.

CASE PRESENTATION: We report a rare case of recurrent disseminated Talaromyces marneffei (T. marneffei) infection in a 25-year-old male with STAT3-mutated HIES. Initially presenting with abnormal liver function tests, the patient had a history of T. marneffei pulmonary infection successfully treated with itraconazole. During the current admission, he developed intermittent fever, jaundice, and splenomegaly. Initial evaluations led to a misdiagnosis of chronic drug-induced liver injury (DILI). Subsequent fever recurrence and worsening liver function prompted further investigation. Metagenomic next-generation sequencing (mNGS) and histopathology of liver revealed T. marneffei, confirming disseminated infection involving the liver. Histopathological examination of the liver showed granulomatous inflammation with IgG4-positive plasma cell infiltration, further complicating the differential diagnosis. The patient responded well to intravenous voriconazole, with significant improvement in liver function and radiological findings.

CONCLUSION: Disseminated talaromycosis should be considered in immunocompromised patients presenting with unexplained fever, hepatosplenomegaly, or organ dysfunction, even in the absence of classic symptoms. Integration of mNGS into diagnostic workflows enhances pathogen detection, and long-term antifungal prophylaxis may be necessary in patients with persistent immune deficiencies.},
}

@article {pmid41424898,
year = {2025},
author = {Chattopadhyay, P and Biswas, I and Banerjee, G},
title = {Analysing the Metagenomic Dynamics of Soil Microbiota Affected by Tea Pruning and Skiffing Methods in Tea Plantations of Dibrugarh, Assam, India.},
journal = {Indian journal of microbiology},
volume = {65},
number = {4},
pages = {2015-2020},
pmid = {41424898},
issn = {0046-8991},
abstract = {Beginning with the centralization of young tea (Yt) to encourage low branch growth, subsequent light pruning (LP) and deep skiffing (DS) techniques are employed to promote branch spread, ensuring an ideal leaf area index and manageable plucking height. This study investigates the effects of LP and DS compared to Yt on soil biota, a previously unexplored topic. Soil samples from Yt, LP, and DS sites within the Rajgarh Tea Estate in Assam, India, were analyzed for standard parameters and metagenomic DNA using Illumina sequencing. While all samples exhibited a clay loam texture with minimal parameter variation, significant variations in soil phyla abundance were observed. Acidobacteria dominated across all samples, but linear discriminant analysis revealed distinct phyla compositions. At the genus level, Geobacter, Verticiella, and Glaciihabitans were most abundant in S11, S7, and S9 samples, respectively. However, the relative abundance of phyla in the soil samples from Yt, LP, and DS sites varies significantly. But the difference in bacterial community at genus level resolution was not significant at p value 0.05 level. These findings indicate that pruning and skiffing primarily impact on the relative abundance of soil phyla, not microbial diversity. Understanding the soil microbiota in relation to tea cultivation practices through metagenomics can pave the way for developing new microbial consortia for an integrated crop management system in tea cultivation.},
}

@article {pmid41423959,
year = {2025},
author = {Bao, Y and Dolfing, J and Chen, R and Qiu, C and Zhang, J and Zhou, X and Liu, L and Wang, Y and Lin, X and Feng, Y},
title = {Phages Shape the Transformation of Organic Matter During Composting.},
journal = {Microbial biotechnology},
volume = {18},
number = {12},
pages = {e70291},
doi = {10.1111/1751-7915.70291},
pmid = {41423959},
issn = {1751-7915},
support = {42207365//National Natural Science Foundation of China/ ; 42177297//National Natural Science Foundation of China/ ; 42577330//National Natural Science Foundation of China/ ; 42577352//National Natural Science Foundation of China/ ; BK20221161//Natural Science Foundation of Jiangsu Province/ ; XDA28010302//Chinese Academy of Sciences (CAS) Strategic Priority Research Program/ ; },
mesh = {*Composting/methods ; *Bacteriophages/metabolism/growth & development/genetics ; Manure/microbiology ; *Organic Chemicals/metabolism ; Soil Microbiology ; Biotransformation ; Animals ; Oryza ; Chickens ; Metagenomics ; Bacteria/metabolism/virology ; },
abstract = {Microorganisms drive the biotransformation of dissolved organic matter (DOM) during organic wastes composting, yet the role of phages with different lifestyles (i.e., temperate and virulent) in this process remains poorly understood. Here, bulk metagenomic sequencing combined with electrospray ionisation (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) was used to investigate the dynamics of temperate and virulent phage communities, microbial functional traits represented by the growth yield (Y)-resource acquisition (A)-stress tolerance (S) life-history strategies (Y-A-S) framework, and molecular changes in DOM composition, as well as their potential linkages during the composting of a rice chaff and chicken manure mixture. Our results revealed that the ratio of temperate/virulent phage, microbial Y/A strategy, and microbial-/plant-derived DOM components exhibited highly consistent dynamic patterns, all peaking during mid-composting stage when temperatures are elevated and remaining low at the initial and final stages. Random forest analysis further identified the ratio of temperate/virulent phages and the microbial Y/A strategy as key predictors of the variance in microbial Y/A trade-offs and microbial-/plant-derived DOM components, accounting for 10% and 13% of the explained variance, respectively. Together, our results demonstrate that an increased prevalence of temperate phages promoted the microbial Y-strategy and the accumulation of microbial-derived DOM components, while a greater dominance of virulent phages favoured the A-strategy and plant-derived DOM enrichment. These findings offer new insights into the ecological role of phages in mediating material transformation during organic waste composting.},
}

*Composting/methods
*Bacteriophages/metabolism/growth & development/genetics
Manure/microbiology
*Organic Chemicals/metabolism
Soil Microbiology
Biotransformation
Animals
Oryza
Chickens
Metagenomics
Bacteria/metabolism/virology

@article {pmid41423811,
year = {2025},
author = {Gordon, ES and Goc, J and Grier, A and Thomas, C and Lentine, J and Sockolow, RE and Sonnenberg, GF},
title = {Altered Gut Microbiota in Pediatric Quiescent Crohn's Disease Patients with Iron Deficiency Anemia.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izaf295},
pmid = {41423811},
issn = {1536-4844},
support = {//Weill Cornell Medicine Department of Pediatrics/ ; },
abstract = {BACKGROUND: Iron deficiency anemia (IDA) is the most common extra-intestinal complication in inflammatory bowel disease (IBD). The persistence of iron deficiency in patients living with quiescent IBD remains poorly understood. Given the extensive body of research linking IBD pathogenesis to microbiome disruptions, it is hypothesized that alterations in the microbiota or immune responses may drive the persistence of IDA in quiescent Crohn's disease. This study aimed to determine whether changes in the gut microbiota or immune phenotypes contribute to IDA, while uncovering potential mechanisms driving IDA in quiescent disease.

METHODS: This cross-sectional, descriptive, and analytical study utilized 141 samples from pediatric Crohn's disease patients with and without iron deficiency as well as healthy controls for initial 16S microbiome analysis and a smaller subset for Shotgun Metagenomics and immunologic analyses. Fecal and peripheral blood samples were obtained from the Jill Roberts Institute Live Cell Bank.

RESULTS: While no major differences were observed in the overall gut microbiome composition between pediatric patients with quiescent Crohn's disease, with or without IDA, notable shifts in specific microbial strains were identified. Specifically, levels of Anaerobutyricum soehngenii and Alistipes shahii were significantly altered. Metagenomic analysis revealed an enrichment of pathways related to short-chain fatty acid metabolism and ascorbate degradation, indicative of functional change in these microbes.

CONCLUSIONS: This is the first comprehensive microbiome analysis of quiescent pediatric Crohn's disease with concomitant IDA. The findings indicate modest but significant microbial strain-level differences and associated functional pathways, potentially implicating microbiota-mediated mechanisms in the persistence of IDA.},
}

@article {pmid41423629,
year = {2025},
author = {Cunningham-Oakes, E and Price, V and Mphasa, M and Mallewa, J and Darby, AC and Feasey, NA and Lewis, JM},
title = {Quantifying the bystander effect of antimicrobial use on the gut microbiome and resistome in Malawian adults.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-67677-6},
pmid = {41423629},
issn = {2041-1723},
support = {109105z/15/a//Wellcome Trust (Wellcome)/ ; 206545/Z/17/Z//Wellcome Trust (Wellcome)/ ; CL-2019-07-001//DH | National Institute for Health Research (NIHR)/ ; NIHR200632//DH | National Institute for Health Research (NIHR)/ ; },
abstract = {Antibiotic treatment for sepsis has an unintended yet crucial consequence: it exerts a bystander effect on the microbiome, changing its bacterial composition and resistome. Antimicrobial stewardship aims, in part, to minimise this effect to prevent development of subsequent drug-resistant infection, but data evaluating and quantifying these changes are largely lacking, especially in low-income settings which are disproportionately affected by antimicrobial resistance. Such data are critical to creating evidence-based stewardship protocols. Here, we address this data gap in Blantyre, Malawi. We use longitudinal sampling of human stool and metagenomic deep sequencing to describe microbiome composition and resistome pre-, during- and post-antimicrobial exposure. We develop Bayesian regression models to link these changes to individual antimicrobial agents. We find that ceftriaxone, in particular, exerts strong off-target effects, both increasing abundance of Enterobacterales, and the prevalence of macrolide and aminoglycoside resistance genes. Simulation from the fitted models allows exploration of different stewardship strategies and can inform practice in Malawi and elsewhere.},
}

@article {pmid41423072,
year = {2025},
author = {Song, MN and Xu, HT and Liang, SM and Fang, SY and Zhang, Y and Zhang, ZZ and Jin, RC},
title = {Ultrasound-assisted breathing revives floated anammox granules by reconnecting intra‑granular metabolic interactions.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133838},
doi = {10.1016/j.biortech.2025.133838},
pmid = {41423072},
issn = {1873-2976},
abstract = {The flotation of granular sludge is a critical bottleneck hindering the application of high-load anammox process. Here, we propose and validate an "assisted breathing" strategy, using non-destructive physical treatments to rapidly restore the functionality of floated granules. A systematic comparison of pressure transient (PT), mechanical shaking (MS), and ultrasonic radiation (UR) revealed that intermittent UR treatment was uniquely effective and it propelled the nitrogen removal rate (NRR) to a remarkable 7.19 kg-N m[-3] d[-1] within 60 days, far surpassing the PT, MS, and control reactors. Mechanistic investigations revealed that the efficacy of "assisted breathing" stems from a synergistic physio-ecological cascade. Physically, ultrasonication enhanced granule permeability and mass transfer efficiency by facilitating entrapped N2 gas release. Biologically, intermittent UR treatment stimulated the production of protein-rich extracellular polymeric substances (EPS), repurposing EPS from a pore-clogging obstacle into beneficial public goods. Most critically, metagenomic analysis demonstrated that UR treatment selectively enriched key heterotrophic partners, such as Ignavibacteriaceae sp. SMN043, which formed a tight syntrophic relationship with AnAOB by providing essential metabolites like folate in exchange for amino acids. Intriguingly, this led to a 14.1 % increase in SAA. These results demonstrate that targeted physical intervention can unlock superior performance by reviving and re‑linking the metabolic networks inside anammox granules. This process effectively transforms inert, floated biomass into highly active aggregates, opening a new avenue for active ecological engineering in bioreactors.},
}

@article {pmid41422804,
year = {2025},
author = {Tabuteau, S and Hervé, V and Irlinger, F and Monnet, C},
title = {Metagenomic Profiling and Genome-Centric Analysis Reveal Iron Acquisition Systems in Cheese-Associated Bacteria and Fungi.},
journal = {Environmental microbiology},
volume = {27},
number = {12},
pages = {e70218},
doi = {10.1111/1462-2920.70218},
pmid = {41422804},
issn = {1462-2920},
support = {//ABIES Doctoral School/ ; //MICA Department of INRAE/ ; },
mesh = {*Cheese/microbiology ; *Iron/metabolism ; Siderophores/biosynthesis/metabolism/genetics ; Metagenomics ; *Bacteria/genetics/metabolism/classification/isolation & purification ; *Fungi/genetics/metabolism/classification/isolation & purification ; *Metagenome ; Genome, Bacterial ; },
abstract = {Cheese microbial communities are composed of diverse interacting microorganisms, including both inoculated and non-inoculated strains. One limiting factor for microbial growth on cheese surfaces is iron availability. To better understand the role of iron acquisition in cheese microbial ecology, we investigated the diversity and distribution of iron uptake systems across a wide range of cheeses. We analysed 136 metagenomes and 1400 genomes and Metagenome-Assembled Genomes (MAGs) from 44 French Protected Designation of Origin (PDO) cheeses. Using an updated set of Hidden Markov Models targeting iron acquisition genes, we identified a wide diversity of iron uptake systems. Siderophore biosynthesis and import systems were more prevalent in surface-associated species than in those from the cheese core. About 20 different siderophore biosynthesis pathways were detected, with desferrioxamine and enterobactin-type being the most prevalent. Genomic analyses revealed the main bacterial and fungal producers, including Glutamicibacter, Corynebacterium, Staphylococcus, and Penicillium. While siderophore biosynthesis pathways were found in a minority of MAGs, iron/siderophore import systems were widespread, suggesting the potential for cross-feeding interactions involving siderophores. These findings enhance our understanding of microbial interactions in cheese and open perspectives for improving ripening cultures by considering iron acquisition traits.},
}

*Cheese/microbiology
*Iron/metabolism
Siderophores/biosynthesis/metabolism/genetics
Metagenomics
*Bacteria/genetics/metabolism/classification/isolation & purification
*Fungi/genetics/metabolism/classification/isolation & purification
*Metagenome
Genome, Bacterial

@article {pmid41422728,
year = {2025},
author = {Xun, J and Han, Y and Liu, B and Jiang, X and Zhang, J and Hu, Z and Yang, H and Gao, Q and Wu, Z and Wang, X and Yu, X and Zhang, Q},
title = {Baihua Dangen Tang inhibits the peritoneal metastasis of colon cancer by modulating the bacterial metabolite gentisic acid to suppress MDSCs.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {150},
number = {},
pages = {157720},
doi = {10.1016/j.phymed.2025.157720},
pmid = {41422728},
issn = {1618-095X},
abstract = {BACKGROUND: The treatment principle of Lingnan traditional compound Baihua Dangen Tang includes 'clearing heat and removing toxins, resolving stasis and dispersing stagnation, and dispelling wind and removing dampness', which is compatible with the pathogenesis of peritoneal cancer, which is characterized by 'dampness, heat, stasis and toxin'. Therefore, Baihua Dangen Tang may be an effective treatment for peritoneal metastasis of colon cancer.

OBJECTIVE: To systematically elucidate the effects and mechanisms of Baihua Dangen Tang in inhibiting the peritoneal metastasis of colon cancer.

METHODS: In this study, a peritoneal metastasis model of colon cancer was constructed by intraperitoneal injection of CT26/MC38 cells (1 × 10[6]) for 14 days. Abdominal circumference, ascites volume, tumor weight and Ki67 expression were analyzed. Mass spectrometry and flow cytometry were used to analyze changes in immune cells, such as MDSCs and T-cell subsets, in ascites and peripheral blood. Changes in the fecal flora and metabolites were analyzed by macrogenomic and untargeted metabolomics to screen for key differential flora metabolites. In vitro experiments were performed to determine the effects of Baihua Dangen Tang and differential flora metabolites on tumor cell migration and invasion and MDSC function.

RESULTS: In this study, we observed that Baihua Dangen Tang significantly inhibited peritoneal metastasis of colon cancer; reduced abdominal circumference, bloody ascites content, and metastatic tumor weight; and decreased metastatic tumor Ki67 expression. Analysis of ascites and peripheral blood by mass spectrometry and flow cytometry revealed that Baihua Dangen Tang increased the numbers of CD4[+] T cells and CD8[+] T cells and decreased the number of MDSCs in ascites and peripheral blood. Combined macrogenomic and metabolomic analyses revealed that the metabolite gentisic acid, which was positively correlated with Lactobacillus spp. and negatively correlated with Desulfovibrio spp., significantly changed. In vivo experiments confirmed that gentisic acid inhibited the progression of CT26 peritoneal metastases. In vitro experiments confirmed that Baihua Dangen Tang and its regulatory bacterial colony metabolite gentisic acid inhibited the migration and invasion ability of colon cancer cells and their recruitment of MDSCs, in addition to directly inhibiting the function of MDSCs, thus enhancing T-cell activity.

CONCLUSION: Baihua Dangen Tang and its microbiota-derived metabolite gentisic acid inhibit cancer cell metastasis and MDSCs function, demonstrating multitarget suppression of colorectal cancer peritoneal metastasis.},
}

@article {pmid41422454,
year = {2025},
author = {Kruis, T and Wassermann, M and Graf, B and Lührig, K and Menzel, P and Schwarzer, R and Ziegler, J and Isner, C},
title = {Unmasking the mimic: vertebral alveolar echinococcosis diagnosed by metagenomic next-generation sequencing.},
journal = {Infection},
volume = {},
number = {},
pages = {},
pmid = {41422454},
issn = {1439-0973},
abstract = {A Siberian woman in her forties presented to a public hospital in northeastern Germany with chronic back pain and a paravertebral mass, initially misdiagnosed as spinal tuberculosis. Repeated biopsies and metagenomic next-generation sequencing (mNGS) ultimately confirmed vertebral alveolar echinococcosis. Haplotype analysis revealed a novel Asian-cluster variant, supporting the presumed origin of infection.},
}

@article {pmid41422269,
year = {2025},
author = {Wang, Y and Xu, J and Liang, G and Liang, S and Hou, M and Sun, L and Wang, J and Chen, H and Zhao, Y and Chen, W and Wang, E and Huang, J and Jiao, X and Zhang, Y},
title = {Gut microbiome profiling of a migratory Anser serrirostris population reveals two groups with distinct pathogen and ARG contents.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-025-00888-3},
pmid = {41422269},
issn = {2055-5008},
abstract = {Migratory birds are key vectors of pathogens and antibiotic-resistance genes (ARGs), yet intrapopulation variation and its microbiome-mediated basis remain poorly understood. Here, we characterized the gut microbiome of 70 individuals from a migratory Anser serrirostris population using full-length 16S rDNA sequencing, followed by metagenomic analysis of 25 representative samples. Both approaches consistently identified two distinct groups (E1 and E2). Network analysis revealed impaired microbial interactions in E1 compared to E2. E1 exhibited higher abundances of opportunistic pathogens (e.g., Pseudomonas, Erwinia) and enriched functions related to pathogenicity and ARGs, predominantly driven by these taxa. Conversely, E2 showed function enrichment in short-chain fatty acid biosynthesis and plant metabolite degradation, mediated mainly by Bradyrhizobium and Ligilactobacillus. Genome-centric analysis identified several pathogenic genomes (e.g., Salmonella, Vibrio parahaemolyticus) harboring critical virulence factors and ARGs predominantly in E1. These results provide valuable insights into microbiome-driven variation in pathogen/ARG loads within migratory bird populations.},
}

@article {pmid41422081,
year = {2025},
author = {Arnaud-Haond, S and Trouche, B and Liautard-Haag, C and Alain, K and Aubé, J and Bonhomme, F and Brandt, MI and Caillarec-Joly, A and Cambon, MA and Cornette, F and Cueff-Gauchard, V and Durand, P and de Vargas, C and Felix, C and Fuchs, S and , and Günther, B and Henry, N and Hourdez, S and Jollivet, D and Le Port, AS and Lesongeur, F and Maignien, L and Comtet-Marre, S and Matabos, M and Omnes, E and Peyret, P and Pradillon, F and Sarrazin, J and Schauberger, C and Tran Lu Y, A and Ulloa, O and Vaz, S and Zeppili, D and Viard, F and Gavory, F and Gaz, S and Guy, J and Jacoby, E and Oliveira, PH and Samson, G and Aury, JM and Wincker, P and Pesant, S and Poulain, J and Belser, C},
title = {Omics exploration of deep-sea biodiversity: data from the "Pourquoi Pas les Abysses?" and eDNAbyss projects.},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-025-06009-1},
pmid = {41422081},
issn = {2052-4463},
support = {ANR-10-INBS-09//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-16-IDEX-0006//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0003//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-22-POCE-0007//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-10-INBS-09//Agence Nationale de la Recherche (French National Research Agency)/ ; 678760//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 669947//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; ANR-10-INBS-09//Commissariat à l'Énergie Atomique et aux Énergies Alternatives (French Alternative Energies and Atomic Energy Commission)/ ; ANR-10-INBS-09//Commissariat à l'Énergie Atomique et aux Énergies Alternatives (French Alternative Energies and Atomic Energy Commission)/ ; ANR-10-INBS-09//Commissariat à l'Énergie Atomique et aux Énergies Alternatives (French Alternative Energies and Atomic Energy Commission)/ ; ANR-10-INBS-09//Commissariat à l'Énergie Atomique et aux Énergies Alternatives (French Alternative Energies and Atomic Energy Commission)/ ; ANR-10-INBS-09//Commissariat à l'Énergie Atomique et aux Énergies Alternatives (French Alternative Energies and Atomic Energy Commission)/ ; ANR-10-INBS-09//Commissariat à l'Énergie Atomique et aux Énergies Alternatives (French Alternative Energies and Atomic Energy Commission)/ ; },
abstract = {The deep-sea floor encompasses more than half of the surface of our planet, yet the extent and distribution of deep-sea biodiversity and its contribution to large biogeochemical cycles remain poorly understood. This knowledge gap stems from several factors, including sampling issues, the magnitude of the work required for morphological inventories, and the difficulty of integrating results from disparate local studies. The application of meta-omics to environmental DNA now makes it possible to assemble interoperable datasets at different spatial scales to move towards a global assessment of deep-sea biodiversity. We present a large-scale dataset on deep-sea biodiversity, with data and metadata openly accessible at ENA and Zenodo. The resource was generated using standardized protocols developed according to FAIR principles, covering fieldwork through bioinformatic analysis, within "Pourquoi Pas les Abysses?" and eDNAbyss projects. Together with information ensuring reproducibility, this dataset -combining metagenomics, metabarcoding across the Tree of Life and capture-by-hybridization- contributes to the international concerted effort to achieve a holistic view of the biodiversity in the largest biome on Earth.},
}

@article {pmid41421910,
year = {2025},
author = {Zeng, H and Xu, H and Liu, G and Wei, Y and Zhang, J and Shi, H},
title = {Corrigendum to "Physiological and metagenomic strategies uncover the rhizosphere bacterial microbiome succession underlying three common environmental stresses in cassava" [J Hazard Mater 411 (2021) 125143].},
journal = {Journal of hazardous materials},
volume = {},
number = {},
pages = {140878},
doi = {10.1016/j.jhazmat.2025.140878},
pmid = {41421910},
issn = {1873-3336},
}

@article {pmid41421776,
year = {2025},
author = {Gao, L and Chen, Y and Li, S and Yang, Z and Guo, W and Lu, Y and Zhu, G and Gaballah, ES},
title = {Low atmospheric pressure of plateau environments shapes microbial communities, nitrogen conversion, and carbon metabolism in biological nitrogen removal systems.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123595},
doi = {10.1016/j.envres.2025.123595},
pmid = {41421776},
issn = {1096-0953},
abstract = {Wastewater treatment plants in high-altitude regions often exhibit unstable nitrogen removal under low atmospheric pressure, but the coupled impacts on oxygen transfer, microbial metabolism, and community adaptation remain poorly resolved. In this study, long-term bioreactor operation under different atmospheric pressures was performed to elucidate how low pressure reshapes biological nitrogen removal systems through changes in oxygen transfer, microbial metabolism, and community structure. Low pressure reduced oxygen solubility and gas-liquid/liquid-solid transfer, which suppressed nitrification and caused nitrite accumulation, while simultaneous nitrification-denitrification partly sustained total nitrogen removal. Multi-scale analyses integrating batch tests, enzyme activities, and metagenomics showed a consistent shift from oxidative to more electron-efficient pathways, with strengthened denitrification and expanded carbon metabolism that enhanced the use of carboxylic acids and amino acids and secured carbon and electron supply. The microbial community reorganized toward denitrifying polyphosphate-accumulating organisms (DPAOs), denitrifying glycogen-accumulating organisms (DGAOs), and conventional denitrifiers, with stronger functional associations despite a simpler network structure. These findings explain performance deterioration under plateau atmospheric conditions and indicate feasible control points to sustain nitrogen removal in high-altitude wastewater treatment systems.},
}

@article {pmid41421745,
year = {2025},
author = {Mandelbrot, L and Kennedy, S and Rousseau, J and Goffinet, F and Landraud, L and Plainvert, C and Marcou, V and Desfrère, L and Barral, T and Allal, L and Baud, A and Grall, N and Poyart, C and Ancel, PY and Tazi, A},
title = {Predicting neonatal infection in PPROM with vaginal microbiology and metagenomics: a prospective cohort study.},
journal = {American journal of obstetrics and gynecology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajog.2025.12.042},
pmid = {41421745},
issn = {1097-6868},
abstract = {OBJECTIVE: Early-onset neonatal sepsis (EONS) due to ascending infection is a potentially preventable complication of preterm premature rupture of membranes (PPROM). Our objective was to determine whether the analysis of bacteria from vaginal swab samples is predictive of the risk of EONS in PPROM.

STUDY DESIGN: In a prospective 3-center observational cohort, patients with PPROM were enrolled between 22 and 36 weeks' gestation (WG) + 6 days. Vaginal swab samples at delivery were analyzed using two different approaches, classical bacterial cultures and shotgun metagenomic sequencing analysis. A metagenomics score was constructed combining the characterization of the vaginal microbiome and the presence of pathogens and the optimal cut-off to predict EONS was tested on a receiver operating curve.

RESULTS: 563 PPROM cases were enrolled, with 646 liveborn neonates. PPROM occurred < 32 WG in 41.9% and deliveries were < 34 WG in 41.0%. The incidence of EONS was 29/646 (4.5%). When considering all central and peripheral microbiological samples available for 26 neonates, the main pathogens isolated were Escherichia coli in 14 cases (53.8 %), other gram-negatives in 5 (19.2%), strict anaerobes in 3 (11.5%); there was a single case (3.8%) each with Group B Streptococcus (GBS), Streptococcus anginosus, Staphylococcus aureus and Ureaplasma urealyticum. We studied the prediction of EONS among 272 mothers and their 310 neonates (20 EONS, 6.4%) with both culture and metagenomic data available. A culture positive for a major or intermediate pathogen in the vaginal sample at delivery had a sensitivity of 80.0 % (95% CI=56.3-94.3) and a specificity of 37.9% (95% CI=32.3-43.8), adjusted odds ratio (aOR) of 1.6 (95 % CI [0.5-5.0]) to predict EONS. The presence of E. coli was associated with an EONS risk of 10.6% vs 4.9%, in the absence of E. coli (p=0.07). The metagenomics score was highly associated with EONS, with an area under the receiver operating curve of 0.75 (95% CI, 0.61-0.90). At the optimal cutoff value, sensitivity was 70% (95% CI, 64-95%), specificity was 85% (95% CI, 81-89%). A metagenomics score greater than 40 was associated with a significantly increased risk of EONS with an aOR of 8.9 (95 % CI [3.5; 22.3]) in multivariate analysis adjusted for latency period and gestational age, p<0.001.

CONCLUSION: In PPROM, conventional microbial culture of maternal vaginal samples was associated with EONS, but its predictive values remain insufficient to guide perinatal care. Metagenomic microbial signatures improved predictive values. This opens the perspective for a rapid point-of-care test.},
}

@article {pmid41421679,
year = {2025},
author = {Huang, P and Zhou, Y},
title = {Metabolic responses of purple phototrophic bacteria to elevated hydrogen partial pressure: Metatranscriptomic insights into biohydrogen production and consumption.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133831},
doi = {10.1016/j.biortech.2025.133831},
pmid = {41421679},
issn = {1873-2976},
abstract = {During biohydrogen production, self-generated gas accumulation can lead to elevated hydrogen partial pressure (HPP) in the headspace. However, the effects of elevated HPP on hydrogen yield in photo fermentation systems and the metabolic responses of phototrophic bacteria (PPB) under such conditions remain poorly understood. This study investigated the effects of elevated HPP on PPB-based biohydrogen production and examined the underlying metabolic responses using metagenomic and metatranscriptomic analysis. PPB maintained efficient H2 production (0.67 ± 0.09 L H2·g COD[-1]; 0.09 ± 0.01 L H2·L[-1]·d[-1]) until HPP reached about 30 %, after which both H2 production and growth declined. Transcriptomic results showed reduced nitrogenase and increased hydrogenase expression, disturbing electron allocation and redox balance and suppressing the tricarboxylic acid (TCA) cycle, gluconeogenesis, and photosynthesis. When HPP increased to about 40 %, H2 production stopped and shifted to H2 consumption, while alternative electron sinks such as the reverse TCA cycle and branched-chain amino acid synthesis were activated to partially restore metabolism. Upon headspace flushing, H2 production rapidly resumed, demonstrating the robustness of the PPB system to short-term HPP inhibition. This study provides practical insight for PF system operation, highlighting the importance of maintaining HPP below inhibitory threshold to sustain efficient H2 production.},
}

@article {pmid41421358,
year = {2025},
author = {Wang, J and Qian, X and Li, Q and Jin, Z and Liu, N and Zhao, J and Chen, W and Wang, S and Tian, P},
title = {Bacteriocin gene-mediated ecological adaptation of Bifidobacterium breve in the adult human gut.},
journal = {Cell genomics},
volume = {},
number = {},
pages = {101106},
doi = {10.1016/j.xgen.2025.101106},
pmid = {41421358},
issn = {2666-979X},
abstract = {The ecological persistence of Bifidobacterium breve across life stages reflects adaptive strategies beyond the classical infant- versus adult-type dichotomy, historically attributed to differential nutrient utilization. Here, comparative genomics revealed no major differences in shared carbohydrate-related genes or accessory genome content between infant- and adult-derived strains. Instead, a distinct type III lanthipeptide bacteriocin cluster, lanKC, was specifically detected in adult-derived isolates. Functional assays combining gene knockout, in vitro co-cultivation, and human intervention demonstrated that lanKC enhances strain-level competitive fitness and promotes community stability. Phylogenetic and metagenomic analyses of 5,475 lanKC homologs and 6,122 infant gut metagenomes further suggested a possible early-life acquisition via intra-genus horizontal gene transfer. These findings uncover a previously unrecognized genetic basis underlying B. breve adaptation to the gut environment and support a multi-factorial model in which metabolic flexibility and interference competition jointly sustain bifidobacterial persistence and host-microbe symbiosis throughout life.},
}

@article {pmid41421350,
year = {2025},
author = {Chen, W and Wang, X and Zhu, R and Gao, W and Tao, L and Yang, R and Wei, Q and Zhang, Y and Gong, Y and Zhong, H and Huang, L and Zhu, X and Yang, Y and Zhang, L and Wan, L and Yang, G and Li, Y and Jiao, N and Wang, J and Qin, H and Zhu, L},
title = {Integrative multi-omics reveals microbial genomic variants driving altered host-microbe interactions in autism spectrum disorder.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102516},
doi = {10.1016/j.xcrm.2025.102516},
pmid = {41421350},
issn = {2666-3791},
abstract = {Emerging evidence links the gut microbiome to autism spectrum disorder (ASD), yet the role of microbial genomic variation remains underexplored. We generated a large-scale metagenomic and metabolomic dataset from over 1,100 children, integrating public datasets, to characterize ASD-associated microbial changes. We identified 35 species, 213 genes, 28 pathways, and 99 metabolites, alongside 1,369 single-nucleotide variants, 233 insertions/deletions, and 195 structural variants with differential abundance. Profiling of microbial genomic variation revealed 33 species and 196 enzymes lacking abundance differences, yet exhibiting significant sequence variation. Integrated analysis of microbial variants and metabolites uncovered 357 neurological associations, with mediation analysis showing that several metabolites link microbial variants to the ASD phenotype. Importantly, diagnostic models incorporating microbial variant and/or metabolite features achieved superior performance and generalizability. Our findings highlight microbial genomic variation as a critical, previously overlooked dimension of ASD-associated dysbiosis, offering valuable insights for diagnosis and mechanistic studies.},
}

@article {pmid41421332,
year = {2025},
author = {Wang, Q and Liang, E and Xu, J and Liu, Y and Chao, C and Wan, H and Zhao, Y},
title = {Microbial self-regulation and electron transport reconstruction under Cr(VI)-4-CP stress: From synergistic inhibition to antagonistic interaction.},
journal = {Water research},
volume = {291},
number = {},
pages = {125138},
doi = {10.1016/j.watres.2025.125138},
pmid = {41421332},
issn = {1879-2448},
abstract = {Understanding how microbial communities adapt to multi-pollutant stress is crucial for efficient denitrification. Although previous studies reported the effects of heavy metals and phenolic compounds individually or in mixtures, the deep mechanisms by which combined stressors reshape microbial electron transport and community structure remain unclear. This study explored the denitrification response to combined Cr(VI) and 4-chlorophenol (4-CP) stress, revealing a temporal shift from synergistic inhibition (acute exposure) to antagonistic interaction (long-term adaptation). Acute Cr(VI)-4-CP exposure caused complete inhibition of denitrification within 18T, accompanied by the activation of dissimilatory nitrate reduction to ammonium. Cr(VI) intracellular accumulation (71.78 %) induced oxidative imbalance and 4-CP prioritized metabolism disrupted electron donor availability, collectively causing FMN decreasing, which decreased NAR electron capture efficiency. Prolonged exposure activated microbial self-regulation (denitrification efficiency recovered to 31.42 %), including extracellular Cr(III) immobilization (84.19 %), antioxidant enzyme upregulation, reshaping oxidative-antioxidant homeostasis. Concomitantly, the electron transport was remodeled via FMN/FAD complementarity, enabling partial recovery of NAR activity and suppression of N2O accumulation. Metagenomic analysis further identified functional cooperation among Microbacterium, Thermomonas, Diaphorobacter, and Acidovorax, supporting glucose/4-CP co-metabolism (COD4CP/CODglucose=1/1.26) and stabilized denitrification performance. This study established a mechanistic framework linking microbial self-regulation and electron transport remodeling, providing new insights into the resilience of denitrifiers under multi-pollutant stress.},
}

@article {pmid41421325,
year = {2025},
author = {Yang, Z and Yang, Y and Ning, D and Fan, X and Lv, Y and Zhuang, L and Wu, L},
title = {Metagenomic insights into the global distribution and functional potentials of major polyphosphate-accumulating organisms (PAOs) in activated sludge wastewater treatment plants.},
journal = {Water research},
volume = {291},
number = {},
pages = {125191},
doi = {10.1016/j.watres.2025.125191},
pmid = {41421325},
issn = {1879-2448},
abstract = {Polyphosphate accumulating organisms (PAOs) are essential for phosphorus removal in wastewater treatment plants (WWTPs); however, their global distribution patterns and potential ecological functions across diverse activated sludge systems remain poorly understood. Here, we analyzed 226 activated sludge metagenomes from 142 WWTPs across six continents, encompassing both enhanced biological phosphorus removal (EBPR) and non-EBPR processes. We reconstructed 29 near-complete PAO metagenome-assembled genomes, identifying putative members of several previously unrecognized Candidatus Accumulibacter clades. Our results revealed that Dechloromonas and Ca. Accumulibacter dominated in most WWTPs, while the former Tetrasphaera genus was prevalent in certain European samples. Furthermore, these PAOs demonstrated high metabolic versatility in carbon, nitrogen, and phosphorus cycling, though this functional potential varied significantly across genera. The link between PAOs and plant performance was process-dependent: while pollutant removal across the entire dataset showed comparable associations with both PAO abundance and the total abundance of phosphorus-cycling genes, the relationship was stronger for PAO abundance in EBPR plants. Collectively, these results represent a major expansion of the known genomic diversity of PAOs, and provide a foundational global baseline of PAO diversity that can help inform the future development of region- and process-specific optimization strategies.},
}

@article {pmid41420927,
year = {2025},
author = {Zhou, J and Yu, F and Wang, W and Zhang, D and Xie, M and Yuan, L and Zheng, J and Wang, J and Li, B and Lou, B and Han, D},
title = {Clinical metagenomics for pathogen detection in lower respiratory infections: a diagnostic study.},
journal = {Diagnostic microbiology and infectious disease},
volume = {114},
number = {3},
pages = {117232},
doi = {10.1016/j.diagmicrobio.2025.117232},
pmid = {41420927},
issn = {1879-0070},
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) enables comprehensive detection of all potential pathogens in a sample. However, its diagnostic performance in various clinical settings requires further validation through real-world data.

METHODS: This retrospective study included 186 patients from the First Affiliated Hospital of Zhejiang University School of Medicine who underwent mNGS testing on respiratory samples. We compared mNGS with traditional culture method using the same samples and also assessed its performance against conventional microbiological testing combinations (CMTs) for the same patients. Additionally, we analyzed the diagnostic performance of mNGS in different disease states (immunosuppressive status and mechanical ventilation).

RESULTS: The positivity rate of mNGS was 81.2 % (151/186). In lower respiratory tract infections (LRTIs), mNGS successfully detected 84.6 % (137/162) of bacteria, 89.0 % (65/73) of fungi, 100.0 % (72/72) of viruses, 88.9 % (16/18) of Mycobacterium tuberculosis, and 100.0 % (9/9) of non-tuberculous mycobacteria. Mixed infections were the most common infection type in LRTIs in this study (69/145, 47.6 %). The detection rate of mixed infections by mNGS was significantly higher than that of CMTs (91.3 % vs 43.5 %, P < 0.01). In the comparison based on a composite LRTI diagnostic standard, mNGS showed significantly higher sensitivity than paired culture (89.0 % vs 32.4 %, P < 0.01) and CMTs (89.0 % vs 57.2 %, P < 0.01), but lower specificity (46.3 % vs 87.8 % and 46.3 % vs 82.9 %, P < 0.01). In non-mechanically ventilated patients, mNGS maintained high sensitivity (87.0 % vs 96.7 %, P = 0.19), while culture and CMTs showed significant sensitivity decline (P < 0.01).

CONCLUSION: mNGS demonstrates superior diagnostic performance for LRTIs compared to CMTs.},
}

@article {pmid41420859,
year = {2025},
author = {Beghini, F and Brito, IL and Gerstein, M and Christakis, NA},
title = {Characterization of gut microbiomes in rural Honduras reveals uncharacterized species and associations with human genetic variation.},
journal = {Cell reports},
volume = {45},
number = {1},
pages = {116724},
doi = {10.1016/j.celrep.2025.116724},
pmid = {41420859},
issn = {2211-1247},
abstract = {The gut microbiome is integral to human health, yet research data to date have emphasized industrialized populations. Here, we performed large-scale shotgun metagenomic sequencing on 1,893 individuals from rural Honduras, providing the most comprehensive microbiome dataset from Central America. We identify a distinct microbial composition enriched in Prevotella species. Longitudinal analysis in 301 individuals reveals microbiome instability, with shifts in taxonomic diversity and metabolic potential, including changes associated with severe acute respiratory syndrome coronavirus 2 infection. Additionally, we characterize the gut virome and eukaryotic microbiome, identifying uncharacterized viral taxa and a high prevalence of Blastocystis species in individuals with greater microbial diversity. Finally, by integrating host genomic data, we uncover significant host-microbiome associations, highlighting the influence of human genetic variation on microbial composition. These findings expand our understanding of microbiome diversity in non-industrialized populations, underscoring the need for global microbiome research.},
}

@article {pmid41420661,
year = {2025},
author = {Ngangbam, AK and Nongmaithem, BD and Haojam, RS and Khundrakpam, L and Singh, LL and Meetei, KB},
title = {First functional and taxonomic insights into the microbiome of edible snail, Cipangopaludina lecythis via shotgun metagenomics.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {1},
pages = {18},
pmid = {41420661},
issn = {1572-9699},
mesh = {*Snails/microbiology ; *Metagenomics/methods ; Animals ; *Bacteria/classification/genetics/isolation & purification ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The freshwater snail Cipangopaludina lecythis holds both ecological and medicinal importance, yet its microbiome remains unexplored. This study presents the first shotgun metagenomic profiling of edible tissues of C. lecythis. Illumina HiSeq sequencing generated over 42 million high-quality reads, revealing 38 bacterial phyla dominated by Pseudomonadota (32%), followed by Bacillota and Actinomycetota. At the genus level, Pseudomonas, Klebsiella, Acinetobacter, Bacillus, Clostridium, Staphylococcus, and Streptomyces were prevalent. Functionally important genera such as Aeromonas, Vibrio, and Pseudoalteromonas which are known for their probiotic and immunomodulatory properties were also detected. The dominant species included Pseudomonas sp. REST10, Escherichia coli, Klebsiella pneumoniae, and Streptomyces sp. T12, many of which were associated with fermentation and host microbe interactions. Interestingly, the microbial profiles differed from those in marine snails, indicating environment-specific microbiome signatures. Functional annotation revealed key enzymes including 17 beta-hydroxysteroid dehydrogenase type 3 (HSD17B3) and malonyl-CoA:ACP transacylase, involved in fatty acid metabolism and energy regulation. Enzymes such as glutathione S-transferase and arylacetamide deacetylase were also detected, along with chitinase and chitin synthases, suggesting host microbe interactions in chitin metabolism. High alpha diversity showed a rich and functional microbiome. Overall, this study highlights the metabolic potential and ecological relevance of the C. lecythis microbiome, supporting its application in biotechnology and nutraceutical industry.},
}

*Snails/microbiology
*Metagenomics/methods
Animals
*Bacteria/classification/genetics/isolation & purification
*Microbiota
Phylogeny
RNA, Ribosomal, 16S/genetics

@article {pmid41420363,
year = {2025},
author = {Babaoğlu, AS and Demirci, T and Karakaya, M and Unal, K},
title = {Assessment of bacterial and fungal profiles in fermented sucuk production using high-throughput sequencing: influence of ripening conditions and starter culture addition.},
journal = {Journal of the science of food and agriculture},
volume = {},
number = {},
pages = {},
doi = {10.1002/jsfa.70390},
pmid = {41420363},
issn = {1097-0010},
support = {//Scientific Research Projects of Selçuk University/ ; },
abstract = {BACKGROUND: This study investigated the effects of various ripening conditions and starter culture additions on the microbial composition and physicochemical properties of Turkish fermented sucuk. Ripening conditions (spontaneous, controlled, and controlled with starter culture) were evaluated using metagenomic technology. Key physicochemical properties, including moisture, pH, water activity, titratable acidity, residual nitrate, residual nitrite, and color properties, were analyzed.

RESULTS: Three groups were produced: group A (spontaneous conditions); group B (controlled conditions); and group C (controlled conditions with starter culture). Microbial and physicochemical properties were assessed at three key time points: beginning (t1 - sucuk dough), middle (t2), and end (t3) of the ripening process. Physicochemical analyses showed a decrease in moisture content (from 53-54% to 39%), an increase in acidity (from 0.59% to 1%), and a reduction in nitrate levels (especially in sucuk produced with starter cultures under controlled conditions from 65.22% to 5.97%) throughout the ripening period (P < 0.05). Microbial analyses revealed that Latilactobacillus sakei dominated the bacterial composition (57.9%) in group B, while the lowest bacterial diversity was observed in group C, and the highest diversity was in group A. The most detected fungal genus in the sucuk samples was Pichia, followed by Hanseniospora, Alternaria, Kluyveromyces, Cladosporium, and Monascus.

CONCLUSION: The ripening conditions and starter culture application significantly influenced both microbial and physicochemical characteristics of fermented sucuk. Controlled fermentation, particularly with starter cultures, resulted in reduced microbial diversity but enhanced the dominance of beneficial microorganisms. These findings contribute to optimizing sucuk production for improved safety and consistent quality. © 2025 Society of Chemical Industry.},
}

@article {pmid41419973,
year = {2025},
author = {Rojas, MA and Serrano, G and Torres, J and Ortega, J and Gálvez, G and Vilches, E and Parra, V and Reyes-Jara, A and Maracaja-Coutinho, V and Pizarro, L and Latorre, M and Di Genova, A},
title = {Genome-resolved metagenomics and evolutionary analysis reveal conserved metabolic adaptations in extremophile communities from a copper mining tailing.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {153},
pmid = {41419973},
issn = {2524-6372},
support = {ACT210004//Agencia Nacional de Investigación y Desarrollo/ ; },
abstract = {BACKGROUND: Microbial communities in mining environments exhibit unique metabolic adaptations to extreme conditions, such as high metal concentrations and low pH. Their relatively low species complexity makes them an attractive model for fine-scale evolutionary analysis; nonetheless, genome-resolved metagenomic data from these environments are still scarce. Here, we employed genome-resolved metagenomics to analyze a high-quality Illumina-sequenced sample from the Cauquenes copper tailing in central Chile, one of the world's largest and oldest copper waste deposits. We aimed to uncover the taxonomic composition, metabolic potential, and evolutionary pressures shaping this extremophile community.

RESULTS: We reconstructed 44 medium- and high-quality metagenome-assembled genomes (MAGs), predominantly from the phyla Actinomycetota, Pseudomonadota, and Acidobacteriota. Taxonomic analysis revealed limited species-level classification, with only five MAGs assigned to known species, highlighting the challenges of characterizing extreme environments. Functional profiling identified enhanced metabolic capabilities in sulfur and copper pathways, critical for survival in mining ecosystems. Using evolutionary analysis on mining MAGs using dN/dS ratios, we uncoverd strong negative selection on genes involved in sulfur, copper, and iron metabolism, indicative of a conservative evolutionary state. In contrast, genes under positive selection were linked to motility, biofilm formation, and stress resistance, suggesting adaptive mechanisms for resource acquisition and survival.

CONCLUSIONS: Our study provides a metagenome-wide evolutionary analysis of mining MAGs, demonstrating that microbial communities in copper tailings are highly specialized, with conserved metabolic pathways under strong purifying selection. At the same time, the recovery of previously unclassified species of extremophiles expands the known biodiversity of mining ecosystems. These findings emphasise the challenges of leveraging these communities for biotechnological applications, such as biomining, due to their evolutionary constraints.},
}

@article {pmid41419779,
year = {2025},
author = {Liu, Y and Chen, S and Li, H and Mahtab, N and Sun, Y and Li, Y and Song, J and Sun, D and Liang, M and Chen, J and Sun, J and Gong, B and Jing, J and Bu, R},
title = {Reconstruction of 2,965 Microbial Genomes from Mangrove Sediments across Guangxi, China.},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-025-06438-y},
pmid = {41419779},
issn = {2052-4463},
support = {2024GXNSFBA010371//Natural Science Foundation of Guangxi Province (Guangxi Natural Science Foundation)/ ; 2025GXNSFHA069226//Natural Science Foundation of Guangxi Province (Guangxi Natural Science Foundation)/ ; 2025GXNSFHA069232//Natural Science Foundation of Guangxi Province (Guangxi Natural Science Foundation)/ ; },
abstract = {Mangrove sediments, being organic-rich and anoxic, host diverse and functionally important microorganisms that play crucial roles in global biogeochemical cycling. In order to characterize this diversity at the genome-resolved level, we collected 38 sediment samples encompassing both surface (0-5 cm) and core (up to 90 cm) depths from six representative mangrove sites across Guangxi Province, China. Using a standardized pipeline for assembly, binning, and dereplication, we reconstructed 2,965 non-redundant metagenome-assembled genomes (MAGs), comprising 2,383 bacterial and 582 archaeal genomes spanning 78 microbial phyla. This dataset captures the high microbial diversity and functional potential within mangrove sediments under variable environmental conditions. It provides a valuable genomic resource for investigating the structure, metabolism, and ecological roles of sediment microbial communities in intertidal, nutrient-rich ecosystems, supporting future studies on microbial adaptation and biogeochemical cycling in global blue carbon environments.},
}

@article {pmid41419527,
year = {2025},
author = {Takeda, Y and Kato-Kogoe, N and Sakaguchi, S and Ieda, S and Tasaka, Y and Mizobata, N and Omori, M and Hamada, W and Nakamura, S and Nakano, T and Ueno, T and Matsumura, T},
title = {Characteristics of salivary IgA responses to oral microbiota in patients with oral lichen planus.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {44167},
pmid = {41419527},
issn = {2045-2322},
mesh = {Humans ; *Lichen Planus, Oral/microbiology/immunology ; *Saliva/immunology/microbiology ; Female ; Male ; Middle Aged ; *Microbiota/immunology ; RNA, Ribosomal, 16S/genetics ; Adult ; *Immunoglobulin A, Secretory/immunology ; Aged ; *Immunoglobulin A/immunology ; Bacteria/genetics/classification ; Metagenomics ; Case-Control Studies ; },
abstract = {Oral lichen planus (OLP) is a chronic inflammatory disease of the oral mucosa with a risk of malignant transformation. Oral bacteria are associated with OLP development and progression; however, the immune response, especially the salivary immunoglobulin A (IgA) response to these bacteria remains poorly understood. Therefore, this study aimed to characterize the salivary microbiota in patients with OLP and evaluate the corresponding salivary IgA response. Stimulated saliva samples were collected from 21 patients with OLP and 56 control participants, and 16S rRNA metagenomic analysis was performed to characterize the composition of the microbiota. In addition, IgA-enriched and non-enriched fractions from the saliva samples were separated via magnetic-activated cell sorting, followed by 16S rRNA metagenomic analysis. To evaluate differences in IgA responses to each bacterium between the two groups, we calculated the IgA index. The diversity and bacterial composition of the salivary microbiota differed considerably between the OLP and control groups. Several bacterial genera, including Leptotrichia, Fusobacterium, and Streptococcus, showed markedly lower IgA index in the OLP group than the control group. In conclusion, patients with OLP exhibited a distinctive salivary IgA response to salivary microbiota, suggesting a potential association between OLP and this altered response.},
}

Humans
*Lichen Planus, Oral/microbiology/immunology
*Saliva/immunology/microbiology
Female
Male
Middle Aged
*Microbiota/immunology
RNA, Ribosomal, 16S/genetics
Adult
*Immunoglobulin A, Secretory/immunology
Aged
*Immunoglobulin A/immunology
Bacteria/genetics/classification
Metagenomics
Case-Control Studies

@article {pmid41419481,
year = {2025},
author = {Gómez-Consarnau, L and Hassanzadeh, B and Villarreal, E and Cuevas-Cruz, M and Arístegui, J and Logares, R and Latorre, F and Lago-Lestón, A and Steindler, L and Sañudo-Wilhelmy, SA},
title = {Unexpected microbial rhodopsin dynamics in sync with phytoplankton blooms.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-67474-1},
pmid = {41419481},
issn = {2041-1723},
support = {OCE1924464//NSF | GEO | Division of Ocean Sciences (OCE)/ ; PID2023-152792NB-I00//Ministry of Economy and Competitiveness | Agencia Estatal de Investigación (Spanish Agencia Estatal de Investigación)/ ; 2019612//United States - Israel Binational Science Foundation (BSF)/ ; },
abstract = {The surface ocean is the largest sunlit environment on Earth where marine microalgae are known as the main drivers of global productivity. However, rhodopsin phototrophs are actually the most abundant metabolic group, suggesting a major role in the biogeochemical cycles. While previous studies have shown that rhodopsin-containing bacterioplankton thrive in the most severely nutrient-depleted environments, growing evidence suggest that this type of phototrophy may also be relevant in nutrient-rich environments. To examine its role in productive waters, we investigated the monthly rhodopsin dynamics in the upwelling system of the Southern California Bight by measuring retinal-the photoreactive chromophore essential for rhodopsin function-in seawater. Unlike oligotrophic regions, rhodopsin levels peaked during the highly productive spring phytoplankton bloom, coinciding with the highest chlorophyll concentrations. Heterotrophic bacterial abundances, particularly within the order Flavobacteriales, correlated strongly with rhodopsin concentrations, allowing us to build linear models to predict rhodopsin distributions in a productive environment. Metagenomic data further showed that Flavobacteriales also dominated the rhodopsin gene pool when the highest rhodopsin levels were recorded, underscoring their key contribution to light-driven energy capture. Overall, our findings reveal that rhodopsin phototrophy plays a substantial role in productive marine systems, broadening its recognized importance far beyond oligotrophic oceans.},
}

@article {pmid41418867,
year = {2025},
author = {Ma, X and Xu, Q and Wang, Y and Lu, J and Zhu, K and Deng, J and Wu, S and Wang, Y and Wang, B and Zhang, H},
title = {Profiling of soil bio-composite pollution and driving factors in China.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123578},
doi = {10.1016/j.envres.2025.123578},
pmid = {41418867},
issn = {1096-0953},
abstract = {Soil biological contamination driven by antibiotic resistance poses escalating global health threats, yet national-scale assessments remain scarce. To bridge this knowledge gap, metagenomic analysis of 300 samples spanning five ecosystems (agricultural, bare land, forest, grassland, wetland) was employed to study the diversity, co-occurrence patterns, and driving factors of the soil resistome and pathogens across China. Our analyses revealed that antibiotic resistance genes (ARGs) were ubiquitously detected (23 types; 0.03-2.6 copies/cell), with multidrug (mexF, mexW), vancomycin (vanR/S), and bacitracin (bacA) resistance dominating. Eleven major mobile genetic element (MGE) types were identified, and co-occurrence network analysis confirmed robust ARG-MGE associations. Notably, 272 ARG-carrying pathogens (APs) were identified as a severe consequence mediated by bio-composite contamination, with widely distributed genera including Enterobacter, Klebsiella, Nocardia, Pseudomonas, exhibiting potential for multidrug and vancomycin resistance. AP richness peaked in agricultural soils and was lowest in bare lands. Random forest modeling and correlation analysis revealed mean annual precipitation (MAP; ρ = 0.19, P < 0.05) and grain production (GP; ρ = 0.18, P < 0.05) were weakly but significantly associated with ARG abundance, while soil pH, organic carbon and meat production governed AP richness. These findings demonstrate nationwide soil bio-composite pollution and underscore the need for prioritized interventions in high-risk ecosystems, though further mechanistic studies are required to validate the observed correlations.},
}

@article {pmid41418855,
year = {2025},
author = {Laue, HE and Kook, D and Khatchikian, C and Coto, SD and Jackson, BP and Palys, TJ and Peacock, JL and Karagas, MR and O'Toole, GA and Hoen, AG and Madan, JC},
title = {Early-life arsenic exposure modulates the developing microbiome in a rural cohort.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123588},
doi = {10.1016/j.envres.2025.123588},
pmid = {41418855},
issn = {1096-0953},
abstract = {BACKGROUND: Studies reported associations between arsenic and the infant gut microbiome measured contemporaneously. We tested the hypothesis that early-life arsenic associates with longitudinal microbiome differences and examined sex-specific effects.

METHODS: Participants provided urine and fecal samples at six weeks (6W; n=219) or twelve months (12M; n=219), a subset of whom provided samples at both (n=167). Total arsenic (tAs), inorganic arsenic, monomethylarsinic acid, and dimethylarsinic acid (DMA) were quantified in 6W and 12M urine with high-performance liquid chromatography with inductively-coupled plasma mass spectrometry. We estimated gut microbiome composition at 6W and 12M with metagenomic sequencing. Using generalized linear and mixed-effect models, we evaluated cross-sectional and longitudinal associations of arsenic concentrations with bacterial diversity and species/ gene pathway relative abundance.

RESULTS: DMA and tAs at 6W were associated with bacterial species at 6W but similar associations were not observed at 12M. At 6W, associations between arsenic and metabolic pathways tended to be sex-specific. In longitudinal analyses, tAs associated with higher Shannon diversity [β=0.07 per doubling (95%CI: 0.05, 0.09)], with a diminishing trend in this association with sampling age [β=-0.04 per doubling (95%CI: -0.07, -0.004)]. We observed a similar longitudinal pattern between at least one arsenic measure and ten bacterial species, with stronger associations among males than females.

CONCLUSIONS: We observed longitudinal and cross-sectional associations of arsenic and the gut microbiome in the first year of life. Early-life arsenic concentrations were more strongly associated with disruptions in the infant gut microbiome than later infancy, highlighting the importance of early-life exposures in microbiome dysbiosis.},
}

@article {pmid41418614,
year = {2025},
author = {Ahmed, I and Zhang, D and Farooq, MU and Sheikh, Z and Dai, X},
title = {Microplastics exacerbate antibiotic resistance by regulating microbial and functional gene dynamics in sludge and food waste composting.},
journal = {Water research},
volume = {291},
number = {},
pages = {125161},
doi = {10.1016/j.watres.2025.125161},
pmid = {41418614},
issn = {1879-2448},
abstract = {The presence of antibiotic resistance genes (ARGs) and microplastics (MPs) as co-contaminants in sewage sludge possess environmental concern. Nevertheless, the effect of specific MP types on ARGs propagation and the mechanistic drivers during composting require further elucidation. This study analyzed the impact of MPs polyethylene (PE), polypropylene (PP), and their mixture (PE+PP) on the propagation of ARGs and mobile genetic elements (MGEs) during sludge composting. Results revealed that MPs significantly increased ARGs abundance, with the highest enrichment observed in PE (2.06 log-fold), followed by PP (1.74) and PE+PP (1.65), compared to control trial. MGEs also increased by up to 1.3 log-fold in MP-treated groups. MPs altered bacterial community composition, enhancing the abundance of Brevibacterium, Microbacterium, and Streptomyces. MPs exhibited a partial reduction of up to 30.2 % during composting which modified the compost's chemical properties, elevating carbon content and depleting oxygen. Metagenomic analysis revealed MPs affected microbial functional pathways, upregulating ABC transporters, two-component regulatory systems, and the conjugation gene VirD4. Functionally, MPs enhanced denitrification and dissimilatory nitrate reduction to ammonium, inhibited assimilatory nitrate reduction, and promoted inorganic nitrogen assimilation. Redundancy analysis exhibited MGEs as the primary drivers of ARGs proliferation in MP-amended compost, while temperature was dominant in the control. Network analysis identified key bacterial hosts Staphylococcus, Weissella, Lactiplantibacillus, Sphingobacterium carrying multiple ARGs and MGEs. This study highlights the potential of MPs, even at low concentrations, to promote ARG dissemination by altering microbial communities and enhancing gene transfer, offering new insights into ecological risks associated with MP-contaminated composting systems.},
}

@article {pmid41418611,
year = {2025},
author = {Du, R and Tang, M and Cao, S and Peng, Y},
title = {Overcoming temperature and substrate limitations of anammox via partial denitrification: Stable performance, microbial structure, and N2O mitigation.},
journal = {Water research},
volume = {291},
number = {},
pages = {125186},
doi = {10.1016/j.watres.2025.125186},
pmid = {41418611},
issn = {1879-2448},
abstract = {The widespread application of the anaerobic ammonium oxidation (anammox) process remains constrained by its narrow substrate range (nitrite-to-ammonia ratio of 1.32), sensitivity to low temperatures, and difficulty in controlling nitrous oxide (N2O). This study demonstrated that under different substrate types and proportions (nitrate-nitrite, NOx[-]-N), the partial denitrification coupled with anammox (PD/A) process with high nitrogen load (1.35 kg N/m[3]/d) still maintained stable nitrogen removal efficiencies (83.5 %∼98.5 %), even at long-term continuous cooling (29.4∼11.6°C) and persistent low temperature (15.1∼9.6°C). In the presence of coexisting NO3[-]-N and NO2[-]-N (NO3[-]-N: NO2[-]-N of 1:1), carbon sources were preferentially utilized for the reduction of NO3[-]-N to NO2[-]-N, effectively circumventing the strict substrate dependence inherent to anammox. The stable nitrogen removal of the PD/A process at low temperatures was attributed to the low activation energy (35.1 kJ/mol) of partial denitrification and the cold-resistant granular sludge, ensuring a highly efficient supply of the essential NO2[-]-N for anammox. Cold-resistant granule sludge provided a spatial environment for the synergistic symbiosis of partial denitrification, anammox, and other heterotrophic bacteria, facilitating anammox adaptation to persistent low-temperature conditions. Metagenomic sequencing revealed a high relative abundance of Candidatus Brocadia (14.9 %) within the granular sludge, while Thauera (18.0 %) dominated the flocculent sludge at low temperatures. It further revealed the cross-feeding relationship of the bacterial community between granular and flocculent sludge. Notably, N2O emissions from the PD/A process can be effectively regulated by controlling the COD/NO3[-]-N ratio, achieving a balance between improving nitrogen removal efficiency and mitigating N2O emissions. This research provides a theoretical foundation for the stable operation and N2O control of non-specifically dependent PD/A process under long-term low-temperature conditions.},
}

@article {pmid41418312,
year = {2026},
author = {Braga, LPP and Wang, Y and Huang, Z and Willerslev, E and Tanentzap, AJ},
title = {The Contributions of Microbial Interactions to Abrupt Ecosystem Changes during the Late Quaternary.},
journal = {The American naturalist},
volume = {207},
number = {1},
pages = {182-195},
doi = {10.1086/738433},
pmid = {41418312},
issn = {1537-5323},
mesh = {*Soil Microbiology ; *Ecosystem ; *Climate Change ; Europe ; *Microbial Interactions ; Fungi ; Mycorrhizae/physiology ; Grassland ; Forests ; },
abstract = {AbstractAbrupt ecosystem shifts during the Late Quaternary coincided with major climatic changes and intensified human activities, but the precise causes of these shifts remain debated. Here, building on previous hypotheses and work, we propose a new hypothesis that both plant beneficial and antagonistic soil microorganisms were the proximate drivers of Late Quaternary change. We synthesized evidence from paleoecological studies and contemporary ecosystems to understand how microbes and their interactions with plants shift ecosystem function. Because relevant paleoecological data are nonexistent, we reanalyzed a contemporary survey from grasslands and woodlands across Europe to test the general role of microbial diversity versus climate in controlling ecosystem function. Our models found that the richness of different microbial groups, including Proteobacteria, mycorrhizas, and plant fungal pathogens, were more strongly associated with the magnitude of direct effects on net primary productivity than temperature and precipitation. The richness of most of these groups was also influenced by climate, supporting our hypothesis that climate change may have indirectly caused past ecosystem shifts by changing microbial composition and function. We end by highlighting the potential of environmental DNA to reconstruct the biota and conditions of past ecosystems. Ultimately, improving our understanding of how microbes drove past ecosystem shifts may improve our ability to respond to future environmental changes.},
}

*Soil Microbiology
*Ecosystem
*Climate Change
Europe
*Microbial Interactions
Fungi
Mycorrhizae/physiology
Grassland
Forests

@article {pmid41417461,
year = {2025},
author = {Drew, G and Kraft, CS and Mehta, N},
title = {Fecal Microbiota Therapy: Clinical Laboratory Testing and Metabolomic Approaches for Donor Screening, Product Assessment, and Patient Monitoring.},
journal = {Clinical chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1093/clinchem/hvaf156},
pmid = {41417461},
issn = {1530-8561},
abstract = {BACKGROUND: The safety and efficacy of fecal microbiota transplantation for prevention of recurrent Clostridioides difficile infection relies on complex interactions between the donor and recipient microbiome.

CONTENT: Screening of donor stool has largely aimed to ensure safety; however, metagenomic and metabolic features of the stool, which may affect efficacy of the fecal microbiota transplantation (FMT), have been largely overlooked.

SUMMARY: In this review, we discuss the nascent field of metagenomic and metabolic donor and recipient characteristics that may affect efficacy of FMT and future directions for this field to allow for more precise and personalized therapies.},
}

@article {pmid41416507,
year = {2025},
author = {Wang, Y and Wan, Y and Wang, H and Yan, J and Sun, J and Yang, J and Zhang, F and Cao, H and Li, D},
title = {Oral Supplementation of Indole-3-acetic Acid Alleviates High-Fat-Induced Obesity by Activating the Gpha2-Mediated Thyroid-Stimulating Hormone Pathway.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c14556},
pmid = {41416507},
issn = {1520-5118},
abstract = {Obesity is a major global public health challenge. Indole-3-acetic acid (IAA), a gut microbiota-derived tryptophan metabolite, exhibits antiobesogenic potential. In this study, we found that in high-fat-diet-induced obese mice, oral IAA supplementation dose dependently attenuated body weight gain, adiposity, hepatic steatosis, and dyslipidemia while improving insulin sensitivity. Notably, intraperitoneal administration of IAA (50 mg/kg/day) paradoxically exacerbated weight gain. Metagenomic sequencing showed that oral IAA selectively enriched beneficial genera (Ileibacterium, Anaerotignum, and Clostridium) and significantly increased short-chain fatty acid (SCFA) production, particularly acetate and butyrate. In vitro experiments in Saccharomyces cerevisiae further confirmed that IAA directly suppresses de novo fatty acid biosynthesis and triacylglycerol assembly. Mechanistically, IAA upregulated hepatic Gpha2 expression, thereby activating the TSH-THR-PGC-1α-PPARγ signaling cascade and concomitantly repressing key lipogenic genes (Fasn, Acaca, and Srebp-1c). Collectively, these findings position IAA as a promising microbiota-derived metabolite with substantial preventive and therapeutic potential for obesity and related metabolic disorders.},
}

@article {pmid41416110,
year = {2025},
author = {Jun, L and Wan, X and Zhang, D and Zheng, Y and Chen, X and Mi, L and Xiao, B},
title = {Mixed vaginal infection status in women infected with Trichomonas vaginalis: comparison of microscopy method and metagenomic sequencing analysis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1638464},
pmid = {41416110},
issn = {2235-2988},
mesh = {Female ; Humans ; *Trichomonas vaginalis/genetics/isolation & purification ; *Metagenomics/methods ; Adult ; *Vagina/microbiology/parasitology/pathology ; *Trichomonas Vaginitis/diagnosis/microbiology ; *Microscopy/methods ; Microbiota/genetics ; *Coinfection/microbiology/diagnosis/parasitology ; Young Adult ; Middle Aged ; Lactobacillus/isolation & purification/genetics ; },
abstract = {Trichomonas vaginalis (TV) infection is a common non-viral sexually transmitted infection, often combined with mixed vaginal infections. These mixed infections worsen inflammation, disrupt vaginal microbiota, and affect treatment. Currently, TV and its mixed infections are mainly diagnosed by wet mount microscopy, which has low sensitivity and cannot identify complex microbes well. This study compared microscopy with metagenomic sequencing to explore vaginal microbiota changes and improve diagnosis of TV-related mixed infections. We enrolled 30 participants: 20 TV-infected patients (diagnosed by wet mount microscopy) and 10 healthy controls (with Lactobacillus as dominant vaginal microbiota). Then tested by Gram staining, microscopy, and metagenomic sequencing. We analyzed microbial composition and identified different abundant taxa. We also measured clinical indices (Lactobacillus grade, vaginal pH, Nugent score for BV, Donders score for AV) to assess vaginal microecology. Among 20 TV patients, microscopy and clinical criteria found a 65% mixed infection rate (13/20), including TV+AV (5 cases), TV+BV+AV (7 cases), and TV+VVC (1 case). Metagenomic sequencing showed TV patients had higher alpha diversity (Shannon index: p=0.0276) and different beta diversity (ANOSIM, r=0.21, p=0.000167) than controls. At the genus level, TV patients had more anaerobic taxa (Fannyhessea, Atopobium, Peptostreptococcus, FDR<0.05) and less Lactobacillus (FDR<0.05) than controls. All TV patients were CST IV (low Lactobacillus, high mixed bacteria), including 12 cases of CST IV-C and 7 cases of CST IV-B. Microscopy and sequencing had low diagnostic consistency in diagnosing mixed infections, especially for mixed vaginitis. TV infection causes significant vaginal microecological imbalance (less Lactobacillus, more anaerobes, high mixed infection rate). Metagenomic sequencing is better than microscopy at identifying complex microbes and low-abundance pathogens, making it more accurate for diagnosing TV-related mixed infections. These results suggest molecular diagnostic methods should be used as complementary tools for precise analysis improve TV and its mixed infection diagnosis and treatment.},
}

Female
Humans
*Trichomonas vaginalis/genetics/isolation & purification
*Metagenomics/methods
Adult
*Vagina/microbiology/parasitology/pathology
*Trichomonas Vaginitis/diagnosis/microbiology
*Microscopy/methods
Microbiota/genetics
*Coinfection/microbiology/diagnosis/parasitology
Young Adult
Middle Aged
Lactobacillus/isolation & purification/genetics

@article {pmid41416071,
year = {2025},
author = {Zheng, Y and Hou, J and Yang, L and Jiang, Y and Wang, S and Yu, J and Ye, X},
title = {Cavitary pulmonary tuberculosis with Orientia tsutsugamushi coinfection in a non-endemic region: a case report.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1692918},
pmid = {41416071},
issn = {2296-858X},
abstract = {INTRODUCTION: Coinfection of pulmonary tuberculosis and scrub typhus caused by Orientia tsutsugamushi is exceptionally rare. Overlapping clinical and radiologic features, together with the frequent absence of clear epidemiologic clues, complicate timely diagnosis.

CASE PRESENTATION: A 57-year-old man residing in a non-endemic region presented with a left-sided cavitary lung lesion on imaging. Computed tomography (CT)-guided percutaneous lung biopsy, acid-fast bacillus staining, and Mycobacterium tuberculosis DNA PCR established the diagnosis of active cavitary pulmonary tuberculosis. Despite initiation of a standard first-line anti-tuberculosis regimen, high-grade fever persisted. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) detected O. tsutsugamushi, which was subsequently confirmed by a positive IgM indirect immunofluorescence assay (IFA). Doxycycline was added, leading to defervescence within 48 h and marked symptomatic improvement. On follow-up, chest CT demonstrated lesion absorption and cavity shrinkage, while new fibrotic changes emerged. The patient was started on maintenance pirfenidone and prescribed home oxygen therapy.

CONCLUSION: In patients with pulmonary tuberculosis who exhibit persistent fever or suboptimal response despite appropriate therapy-and after excluding drug resistance-scrub typhus should be included in the differential diagnosis, even in non-endemic settings without a typical exposure history. Longitudinal imaging in this case also shows that irreversible structural remodeling may occur despite microbiologic control, underscoring the need to pair prompt pathogen-directed therapy with ongoing monitoring and early strategies to preserve lung function.},
}

@article {pmid41415824,
year = {2025},
author = {Lai, W and Guo, J and Zhou, X and Luo, Y and Zheng, M and Mai, Q and Xiong, J and Luo, M},
title = {Co-infection in pediatric pertussis during 2023 and 2024 in southern China: pathogen distribution characteristic and influence on manifestation of pertussis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1722003},
pmid = {41415824},
issn = {1664-302X},
abstract = {OBJECTIVE: We sought to examine the pathogen composition of co-infections in pertussis during 2023 and 2024 and assess the impacts of co-infection on pertussis.

METHODS: Clinical data of pediatric pertussis patients were retrospectively analyzed. The impact of co-infections on pertussis, the detection rate and composition of co-pathogens were analyzed. Culture, polymerase chain reaction, or metagenomic sequencing were used in pertussis or co-pathogens detection.

RESULTS: Among 620 pertussis patients, 110 patients co-infected with bacteria, 106 co-infected with virus, and 98 co-infected with both bacteria and virus. M. pneumoniae (114, 18.39%), M. catarrhalis (44, 7.1%), and H. influenzae (26, 4.19%) were the most common bacterial co-pathogens, and Rhinovirus (100, 16.12%), Cytomegalovirus (31, 5%), and Influenza virus A&B (28, 4.52%) were the most common viral co-pathogens. Patients with co-infections exhibited more severe manifestations than those with pertussis alone, and the severity was associated with the type and number of pathogens. The composition of co-pathogens linked to the age and hospitalization status of the patients. M. pneumoniae (91, 21.06%), M. catarrhalis (32, 7.41%), and Influenza virus A&B (22, 5.09%) primarily caused co-infections in older, non-hospitalized patients, whereas Cytomegalovirus [(19, 14.39%) non-ICU, (12, 21.43%) ICU] and Respiratory syncytial virus [(8, 6.06%) non-ICU, (8, 14.28%) ICU] were more common in younger, hospitalized patients.

CONCLUSION: Co-infections are common among pertussis and can intensify clinical symptoms. Distribution of co-infecting pathogens is associated with age and hospitalization status, and the impacts of co-infection on the manifestations of pertussis varied according to the types and number of co-pathogens.},
}

@article {pmid41415820,
year = {2025},
author = {Bao, Y and Wang, T and Adina, W and Yao, R and Chu, H and Yao, X and Meng, J and Wang, J and Ren, W and Zeng, Y},
title = {Gut microbial signatures and cardiac-microbiota axis in Yili horses with divergent exercise-induced cardiac remodeling.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1689293},
pmid = {41415820},
issn = {1664-302X},
abstract = {This study aimed to investigate how different training outcomes affect the gut microbiota composition in racehorses. Twenty-six Yili horses underwent a 9-month conditioning training regimen under uniform husbandry and management conditions. Post-training, the horses were divided into an excellence group (D. Y group) and a general group (D. P group) based on their athletic performance, with the top 10 performers constituting the D. Y group and the bottom 10 the D. P group. Cardiac morphology and function were quantitatively assessed via echocardiography, and metagenomic sequencing was performed on fresh fecal samples. Results indicated that there were no significant differences in gut microbiota and echocardiographic parameters between the two groups prior to training. However, significant differences were observed post-training (p < 0.05). At the genus level, Parabacteroides, Bacteroides, and Prevotella exhibited significantly greater abundance n the D. Y group. LEfSe analysis showed that Prevotella was markedly enriched in the D. Y group (LDA > 4). Functional profiling indicated that multiple metabolic pathways were significantly enriched in global and overview maps, with map00534 and map00190 being particularly enriched in the D. Y group (LDA > 2). Within CAZymes genes, eight were significantly enriched in the D. Y group, including four glycoside hydrolase genes, two carbohydrate esterase genes, and two carbohydrate-binding module genes. Echocardiography revealed significant differences in seven parameters between the groups, with the D. Y group exhibiting notably higher LV_MASS_I and LVM values (p < 0.01). dbRDA analysis demonstrated a significant association between LV_MASS_I and LVM and the gut microbiota profile (p < 0.01). These findings suggest that training-induced cardiac remodeling, particularly the increase in LV_MASS_I and LVM, is closely related to alterations in gut microbiota, with Prevotella enrichment potentially serving as a marker of favorable adaptation to the training regimen. The study provides robust evidence for understanding the interaction between aerobic training, gut microbiota, and cardiac characteristics in racehorses, and highlights potential directions for optimizing athletic performance and probiotic strategies in equine athletes.},
}

@article {pmid41415819,
year = {2025},
author = {Miao, M and Ma, C and Yang, J and Yang, X and Liu, Z and Liu, A and Qian, Z and Ge, Y and Chen, Y and Yin, G and Hu, Z},
title = {BALF metagenomic next-generation sequencing for the diagnosis of pulmonary mycobacterial infection in persons with HIV: a retrospective, diagnostic accuracy study.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1689997},
pmid = {41415819},
issn = {1664-302X},
abstract = {Severely immunocompromised persons with HIV (PWH) are vulnerable to pulmonary mycobacterial infections (MBI), including Mycobacterium tuberculosis (MTB) and non-tuberculous mycobacteria (NTM). This study aimed to assess the effectiveness of metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) in aiding the diagnosis of pulmonary mycobacterial infections in PWH. This study encompassed 146 hospitalized PWH who had a CD4+ T cell count of less than 200 cells/μL. We employed BALF mNGS to pinpoint the causative pathogens of pulmonary infections, with particular focus on pulmonary mycobacterial infections. We evaluated the diagnostic performance of BALF mNGS, and interpreted its clinical significance in detecting mixed infections as appropriate. The median CD4+ T cell count of the participants was 22.5 (IQR: 7.0-63.0) cells/uL. BALF mNGS analysis of 146 severely immunocompromised PWH identified Mycobacterium tuberculosis (13.0%) and M. avium complex (7.5%) as the predominant mycobacterial species, with 9.3% (4/43) of mycobacterial infections showing mixed speciation including TB-NTM co-infections or interspecies NTM coinfections. Furthermore, mNGS demonstrated 78.8% sensitivity (95% CI: 62.2%-89.3%) for proven mycobacterial infections, outperforming conventional culture (68.4% vs. 42.1%, P < 0.01), though missing 7 proven MBI cases. Finally, among 158 co-detected pathogens, Pneumocystis jirovecii (67.1%) and cytomegalovirus (63.0%) were most prevalent, demonstrating co-occurrence rates of 53.5% and 55.8%, respectively in mycobacterial-infected patients. These rates were elevated to 81.2% (P. jirovecii) and 65.3% (CMV) in the subset of 101 patients with CD4+ counts <50 cells/μL. The presence of atypical clinical presentations, along with the coexistence of multiple opportunistic pathogens in BALF, complicates the management of pulmonary MBI in PWH. In this context, mNGS has emerged as a highly promising microbiological test that could revolutionize the management of pulmonary MBI in PWH.},
}

@article {pmid41415818,
year = {2025},
author = {Wu, H and Du, X and Zheng, J and Li, X and Song, Q and Yan, Y and Ma, A and Xu, A and Li, J},
title = {Top-down enrichment of oil-degrading microbial consortia reveals functional streamlining and novel degraders.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1656448},
pmid = {41415818},
issn = {1664-302X},
abstract = {INTRODUCTION: Top-down microbial enrichment is a reliable approach for understanding and designing microbiomes for crude oil remediation. Environmental variables serve as valuable determinants for selecting desired microbiomes with superior performance. However, the linkages between selection methods and the structure and function of desired microbiomes remain unclear.

METHODS: This study integrated substrate concentration gradients and cultivation patterns to investigate how selection pressures shape top-down enriched crude oil-degrading consortia. The resulting communities were analyzed using 16S rRNA gene sequencing, metagenomics, and co-occurrence network analysis. Key bacterial strains were isolated to validate their individual degradation capabilities.

RESULTS: The top-down process led to a significant reduction in phylogenetic diversity but a notable increase in the potential for xenobiotic degradation and metabolic. The final consortia, GT4, achieved a 55.72% degradation rate of crude oil at an initial concentration of 5 g/L within 7 days. Metagenomic analysis identified Microbacterium as dominant genus harboring key enzymes for the degradation of alkanes and aromatic compounds. Co-occurrence network analysis revealed Mesorhizobium as a keystone genus, showing positive associations with multiple diazotrophic bacteria and hydrocarbon degrading bacteria. Nine bacterial strains were isolated from the consortium. Among them, Microbacterium sp. WS3 and Cellulosimicrobium sp. WS9 exhibited high degradation efficiencies (57.85 and 58.60%, respectively). To the best of our knowledge, this study provides the first experimental evidence for crude oil degradation by Paracandidimonas and Caulobacter, with degradation rates of 51.19 and 40.90%, respectively.

DISCUSSION: These findings highlight the effectiveness of top-down enrichment strategy in generating functionally streamlined consortia and uncover novel oil-degrading microbes with potential for bioremediation applications.},
}

@article {pmid41415809,
year = {2025},
author = {Li, E and Wang, S and Li, Y and Liuli, A and Liang, M and Huang, J and Li, Y and Li, H and Feng, Z},
title = {Characterization of the gut microbiota in people with different levels of obesity.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1679119},
pmid = {41415809},
issn = {1664-302X},
abstract = {PURPOSE: With the evolution of dietary habits, obesity has emerged as a significant global health issue. Numerous studies have demonstrated a close association between obesity and gut microbiota; however, the specific contribution of gut microbiota to varying degrees of obesity remains inadequately understood. Consequently, this study aims to characterize the gut microbiota of individuals across different obesity severity levels.

METHODS: We conducted a comprehensive characterization of the gut microbiome in Chinese obese patients and a healthy control group through the application of 16S rRNA gene sequencing, supplemented by metagenomic sequencing. The study cohort was stratified into five distinct categories based on body mass index (BMI): healthy, overweight, and obesity grades I, II, and III.

RESULTS: In obese populations, the gut microbiome structure shifted significantly, with beneficial genera like Faecalibacterium, Roseburia, and Ruminococcus decreasing, and potentially harmful genera such as Blautia, Collinsella, and Streptococcus increasing. These changes impacted host metabolic pathways, including ribosome synthesis, RNA polymerase activity, and DNA repair. Clinical analyses also revealed strong links between specific genera and metabolic markers like lipid metabolism and insulin resistance.

CONCLUSION: Populations with different obesity traits show unique changes in gut flora. The level of dysbiosis, or imbalance in intestinal microbiota, rises with obesity. These microbial changes are linked to host metabolism, indicating that targeting harmful bacteria and supplementing with beneficial ones from normal-weight populations could effectively reduce obesity.},
}

@article {pmid41415804,
year = {2025},
author = {Zhang, M and Zhu, Y and Sun, Z and Wang, B and Chen, J and Zhou, F and Zeng, J and Li, M and Zou, D and Jiang, Z},
title = {Chemoautotrophic Thermodesulfobacteriota as a key genomic potential group in the hypoxic diazotrophic community of the Changjiang (Yangtze River) estuary.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1671267},
pmid = {41415804},
issn = {1664-302X},
abstract = {Coastal hypoxia, intensified by global warming and eutrophication, profoundly affects marine nitrogen cycling. However, its impact on diazotrophic communities in large river estuaries remains poorly understood. During an unprecedented hypoxia event (minimum dissolved oxygen at 2.70 μmol L[-1]) in August 2016 in the Changjiang Estuary, we sampled across a dissolved oxygen (DO) gradient spanning hypoxic and non-hypoxic waters. Using nifH gene amplicon sequencing, metagenomic binning, and multivariate statistical analyses, we found that higher diazotrophic biodiversity was observed in hypoxia zone, with non-cyanobacterial diazotrophs dominating the communities. The phylum Thermodesulfobacteriota (with relative abundance of 58.93% totally) exhibited significant hypoxia-specific enrichment. LEfSe analysis identified Thermodesulfobacteriota as potential hypoxia biomarkers, while network analysis revealed their keystone role, representing 68.6% of highly connected nodes. Environmental drivers, including low DO concentrations (7.50-61.88 μmol L[-1] in hypoxic vs. 66.56-255.63 μmol L[-1] in non-hypoxic zones), elevated salinity (30.67-34.50), increased dissolved reactive phosphorus (0.39-1.26 μmol L[-1]), and nitrate depletion (0.30-22.50 μmol L[-1]), collectively created favorable conditions for the development of the observed diazotrophic community under hypoxia. Metagenomic analysis revealed a hypoxia-driven increase in nifH gene abundance, with nifH-carrying metagenome-assembled genomes affiliated with Thermodesulfobacteriota showing approximately a 4.7-fold higher relative abundance in hypoxic zone compared to non-hypoxic zone. Reconstruction of metabolic pathways from metagenome-assembled genomes (MAGs) further suggested their potential involvement in both nitrogen fixation and carbon-sulfur cycling. Amplicon and metagenomic datasets consistently demonstrated Thermodesulfobacteriota's predominant in hypoxia. These findings redefine estuarine nitrogen flux models by highlighting hypoxia-driven taxonomic and functional shifts in diazotrophic communities, and provide a foundation for assessing the potential microbial resilience and ecosystem risks in expanding coastal hypoxic zones. Our study underscores the genomic potential of Thermodesulfobacteriota as key players in the nitrogen cycle under hypoxia, a hypothesis that warrants future validation through direct activity measurements.},
}

@article {pmid41415514,
year = {2025},
author = {Chen, X and Wang, L and Li, J and Zhang, Y and Liu, C and Yang, J and Shi, J and Liang, S},
title = {Efficacy of Liposomal Amphotericin B in Treating Pulmonary Aspergillus flavus Infection in Nonneutropenic Adults: Cases Report and Literature Review.},
journal = {Clinical case reports},
volume = {13},
number = {12},
pages = {e71688},
pmid = {41415514},
issn = {2050-0904},
abstract = {Liposomal amphotericin B (L-AmB), as a modified formulation of traditional amphotericin B, have better targeting and lower toxicity. However, clinicians have limited experience with the use of L-AmB for the treatment of Aspergillus flavus (A. flavus) at present. We described two cases of immunocompetent adults; despite undergoing various antibacterial treatments, the symptoms were persistent. Based on the clinical characteristics and results of metagenomic next-generation sequencing and (or) pathology, pulmonary A. flavus infection was confirmed. Subsequently, L-AmB was added to the treatment. Following the initiation of antifungal therapy, the patients' symptoms and images were significantly improved. In conclusion, even in immunocompetent individuals, pathogen detection and pathological examination are crucial when treatment is not effective. In pulmonary A. flavus infection, L-AmB may deserve greater attention and confidence in clinic.},
}

@article {pmid41415494,
year = {2025},
author = {Petrov, TP and Rizzetto, M and Clagnan, E and Dell'Orto, M and De Nisi, P and D'Imporzano, G and Ovani, M and Pina, MP and Kron-Morelli, R and Adani, F},
title = {Trichoderma-Activated Granulated Digestate as an Alternative to Chemical Fertilization: Effects on Tomato Yield and Quality, and Soil Rhizospheric Communities.},
journal = {ACS agricultural science & technology},
volume = {5},
number = {12},
pages = {2383-2392},
pmid = {41415494},
issn = {2692-1952},
abstract = {The use of synthetic fertilizers is always more economically and environmentally unsustainable. It is necessary to improve current agricultural practices. Bioactivated fertilizers are a promising solution to enhance digestate solid fraction's fertilizing properties with an ad hoc microbial consortium and reach yields comparable to chemical fertilization (CF), thus combining circular economy with an upgraded organic agriculture. This study designed a new granulated formulation, obtained using a vacuum drying process at the industrial level, for an improved Trichoderma-activated digestate's solid fraction. This granulation aimed to improve both management operations and Trichoderma activity. After a greenhouse experimentation, yields obtained from the activated digestate (56 ± 7 g FW plant[-1]) were similar to the one obtained with CF (62 ± 9 g FW plant[-1]). Additionally, the bioactivated digestate gave yield production that were 21-30% higher yield than that of digestate alone. Microbial activation further led to higher nutritional values with an increment in the lycopene content between 8.8% and 15.8%. A metagenomic analysis further highlighted the persistence of Trichoderma in the tomato rhizosphere and its ability to establish positive interactions with other beneficial rhizospheric microorganisms. Activated digestate showed its potential to substitute CF, while granulation resulted in a functional formulation to convey this product.},
}

@article {pmid41415413,
year = {2025},
author = {Macias Calix, K and Borges, C and do Nascimento Oliveira, AL and Albuquerque de Luna, SC and Souza Cunha, CM and de Siqueira, AM and Campelo Dos Santos, AL and DeGiorgio, M and Lindo, J and Assis, R},
title = {Genomic insights into ancestry and infectious disease in 17th-century colonial Brazil.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2025.12.10.693243},
pmid = {41415413},
issn = {2692-8205},
abstract = {During urban redevelopment in the historic district of a Brazilian metropolis, archaeologists uncovered a previously undocumented 17th-century cemetery, containing the closely spaced remains of over two dozen young adult males of military age. Historical records suggest the site once housed a makeshift hospital, raising questions about the origins and causes of death of those interred, particularly given the absence of skeletal evidence for violent or fatal trauma. The current study integrates bioarchaeological, historical, and genomic data to investigate the ancestry and putative disease-related mortality of nine individuals whose remains were recovered and subsequently sequenced. Population-genetic analyses revealed strong affinities with Northern European populations, particularly from Norway, Iceland, Estonia, and Czechoslovia, consistent with their likely roles as soldiers or laborers employed by the Dutch West India Company. To explore potential causes of death, we conducted a metagenomic screening with a novel pipeline optimized for degraded DNA, which revealed widespread presence of Klebsiella pneumoniae and Mycobacterium tuberculosis pathogens across all samples. Authenticity was confirmed through post-mortem damage patterns characteristic of historical samples. These findings, together with the absence of combat trauma and the collective burial context at the site, support the hypothesis of an epidemic-related mortality event. This study contributes to the growing field of historical pathogen genomics and offers a rare genomic perspective on life, mobility, and health during a period of colonial upheaval in South America.},
}

@article {pmid41415012,
year = {2025},
author = {Zhang, W and Zhang, L and Liu, H},
title = {Necrotizing enterocolitis in a neonate with severe congenital pulmonary valve stenosis complicated by a postoperative right atrial thrombus: a case report.},
journal = {Frontiers in pediatrics},
volume = {13},
number = {},
pages = {1594899},
pmid = {41415012},
issn = {2296-2360},
abstract = {Congenital heart disease may increase the incidence of necrotizing enterocolitis, especially in low-birth-weight infants. We report a case of a newborn with pulmonary valve stenosis who developed neonatal necrotizing enterocolitis IIIB. The infant underwent initial cardiac surgery followed by a laparotomy. After cardiac surgery, a right atrial thrombus was found by cardiac ultrasound. Enterococcus faecium was identified using metagenomic next-generation sequencing of ascitic fluid. The infant received targeted antibiotic therapy and anticoagulant treatment and was then discharged.},
}

@article {pmid41414025,
year = {2025},
author = {Bian, J and Cao, YN and Han, YP and Liu, JG and Chen, Q and Liu, ZP and Li, MY},
title = {[Screening, Identification, and Performance of Microplastic-degrading Functional Bacteria in Saline-alkali Soil Environment].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {46},
number = {12},
pages = {8082-8092},
doi = {10.13227/j.hjkx.202411208},
pmid = {41414025},
issn = {0250-3301},
mesh = {*Soil Microbiology ; Biodegradation, Environmental ; *Soil Pollutants/metabolism/isolation & purification ; *Microplastics/metabolism/isolation & purification ; Soil/chemistry ; *Bacteria/metabolism/isolation & purification/classification ; Alkalies ; Polyethylene Terephthalates/metabolism ; Salinity ; },
abstract = {The combined effects of salinization and microplastic pollution will have a detrimental impact on soil fertility and the ecological integrity of soil ecosystems. Three strains of salt-resistant microplastic-degrading functional bacteria were obtained from the soil of the Hetao irrigation area, which served as a source of inoculum. The strains were identified using metagenomics and were found to belong to the genera Agrobacterium, Aspergillus fumigatus, and Streptomyces. The strains were designated Agrobacterium_salinitolerans strain （A）, Aspergillus fumigatus strain （F）, and Streptomyces sudanensis strain （S）, respectively. The degradation of polyethylene （PE） and polyethylene terephthalate （PET） by single and mixed bacteria was compared using the weight loss rate of microplastics as a constraint. The findings revealed that the weight loss rates of PE and PET under the combined conditions of the three strains of functional bacteria were 21.900% and 23.800% at 60 d, which was significantly better than that of single bacteria and the mixture of two strains. Based on the growth process of functional bacteria, the characteristics of key enzyme genes, and the changes of surface morphology and functional groups during the degradation of PE and PET, the mechanism of PE and PET being degraded after long-chain depolymerization, β oxidation cycle, and tricarboxylic acid cycle under the action of mixed functional bacteria was revealed. These findings provide a theoretical basis and technical support for the control of microplastic pollution in salinized soil.},
}

*Soil Microbiology
Biodegradation, Environmental
*Soil Pollutants/metabolism/isolation & purification
*Microplastics/metabolism/isolation & purification
Soil/chemistry
*Bacteria/metabolism/isolation & purification/classification
Alkalies
Polyethylene Terephthalates/metabolism
Salinity

@article {pmid41413769,
year = {2025},
author = {Medina-Méndez, JM and Iruzubieta, P and Fernández-López, R and Crespo, J and de la Cruz, F},
title = {Bacterial metabolic signatures in MASLD predicted through gene-centric studies in stool metagenomes.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04549-5},
pmid = {41413769},
issn = {1471-2180},
support = {PI22/01853//Spanish Carlos III Health Institute (ISCIII)/ ; PID2020-1179236B-100//Spanish MINECO/ ; },
}

@article {pmid41413663,
year = {2025},
author = {McAdams, Z and Gustafson, K and Ericsson, A},
title = {Biological and technical variability in mouse microbiota analysis and implications for sample size determination.},
journal = {Lab animal},
volume = {},
number = {},
pages = {},
pmid = {41413663},
issn = {1548-4475},
support = {U42 OD010918/CD/ODCDC CDC HHS/United States ; U42 OD010918/CD/ODCDC CDC HHS/United States ; U42 OD010918/CD/ODCDC CDC HHS/United States ; },
abstract = {The gut microbiota (GM) affects host development, behavior and disease susceptibility. Biomedical research investigating GM-mediated influences on host phenotypes often involves collecting fecal samples from laboratory mice. Many environmental factors can affect the composition of the GM in mice. While efforts are made to minimize this variation, biological and technical variability exists and may influence outcomes. Here we employed a hierarchical fecal sampling strategy (that is, sequenced multiple libraries generated from multiple pellets collected from multiple mice) to quantify the effect size of biological and technical variation and to provide practical guidance for the development of microbiome studies involving laboratory mice. We found that while biological and technical sources of variation contribute significant variability to alpha- and beta-diversity outcomes, their effect size is 3-30-times lower than that of the experimental variable in the context of an experimental group with high intergroup variability. After quantifying the variability of alpha-diversity metrics at the technical and biological levels, we simulated whether sequencing multiple fecal samples from mice improves effect size in a two-group experimental design. Our simulation determined that collecting five fecal samples per mouse increased effect size, reducing the minimum number of animals per group required by 5% while dramatically increasing sequencing costs. Our data suggest that the effect size of biological and technical factors may contribute appreciable variability to an experimental paradigm with relatively low mean differences. In addition, repeated sampling improves statistical power; however, its application is probably impractical given the increased sequencing costs.},
}

@article {pmid41413233,
year = {2025},
author = {Ikagawa, Y and Okamoto, S and Taniguchi, K and Mizoguchi, R and Hashimoto, A and Imamura, R and Arakawa, H and Ogura, K and Yanagihara, M and Tsujiguchi, H and Hara, A and Nakamura, H and Hosomichi, K and Karashima, S},
title = {Gut microbiota-derived polyamine pathways associated with mean blood pressure.},
journal = {Hypertension research : official journal of the Japanese Society of Hypertension},
volume = {},
number = {},
pages = {},
pmid = {41413233},
issn = {1348-4214},
abstract = {Hypertension is a common lifestyle-related disease and is influenced by various factors, including excessive salt intake. Recently, the gut microbiota (GM) has gained attention for its potential involvement in blood pressure regulation; however, polyamine metabolism involvement remains poorly understood. Sixty participants aged ≥40 years from Shika Town, Japan, were stratified into four groups (n = 15 each) based on mean blood pressure and urinary sodium chloride (u-NaCl) excretion. The clinical parameters were evaluated, and fecal samples were analyzed using shotgun metagenomic sequencing to assess the microbial composition and abundance of genes related to arginine-polyamine metabolism. Three major findings were observed: (1) Significant differences in the α-diversity of GM were observed between salt-sensitive and non-salt-sensitive hypertensive groups; (2) The abundance of spermidine synthase (EC 2.5.1.16), a key enzyme in polyamine metabolism with known antihypertensive effects, was significantly higher in normotensive individuals, independent of u-NaCl excretion; and (3) Bacterial species harboring polyamine metabolic enzyme genes, including EC 2.5.1.16, differed significantly between groups, suggesting group-specific microbial metabolic traits. These findings suggest that GM-mediated polyamine metabolism may contribute to the regulation of salt-sensitive blood pressure. While variations in spermidine-producing bacteria and the involvement of EC 2.5.1.16 were observed, these factors alone do not fully account for the intergroup differences related to salt intake. Thus, polyamine metabolism likely plays a part in salt sensitivity, but additional microbial and host factors are also involved. Further studies are needed to validate these findings and to explore microbiota-targeted strategies for the prevention and treatment of hypertension.},
}

@article {pmid41412926,
year = {2025},
author = {Autenrieth, IB and Bury, L and Rooney, AM and Willmann, M and Vehreschild, MJGT and Egli, A},
title = {Paradigms for microbiome analysis in infectious and non-communicable diseases.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.11.016},
pmid = {41412926},
issn = {1878-4380},
abstract = {Next-generation sequencing and bioinformatics paved the way in deciphering the human gut microbiome and challenged fundamental postulates on the causal role of the microbiota for health and pathogenesis of infectious and noncommunicable diseases. To exploit the clinical relevance and potential of microbiome diagnostics and therapy, deep metagenomic sequencing with standardized, validated laboratory procedures, aiming at deciphering the microbiome at strain level and applying index-scores to allow classification of individual microbiomes as dysbiotic (associated with disease) or eubiotic (associated with health) should be implemented. By this means, metagenomically informed therapies with live biotherapeutic products, fecal microbiota transfer, pro-, pre-, or postbiotics might become a standard in personalized prevention and treatment of infectious and non-communicable diseases.},
}

@article {pmid41412727,
year = {2025},
author = {Osswald, A and Wortmann, E and Wylensek, D and Kuhls, S and Coleman, OI and Peuker, K and Strigli, A and Ducarmon, QR and Larralde, M and Liang, W and Treichel, NS and Schumacher, F and Volet, C and Matysik, S and Kleigrewe, K and Gigl, M and Rohn, S and Guo, CJ and Kleuser, B and Liebisch, G and Schnieke, A and Ridlon, JM and Bernier-Latmani, R and Zeller, G and Zeissig, S and Haller, D and Flisikowski, K and Clavel, T and Ocvirk, S},
title = {Secondary bile acid production by gut bacteria promotes Western diet-associated colorectal cancer.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2024-332243},
pmid = {41412727},
issn = {1468-3288},
abstract = {BACKGROUND: Western diet and associated production of secondary bile acids (BAs) have been linked to the development of sporadic colorectal cancer (CRC). Despite observational studies showing that secondary BAs produced by 7α-dehydroxylating (7αDH+) gut bacteria are increased in CRC, a causal proof of their tumour-promoting effects is lacking.

OBJECTIVE: Investigate the causal role of BAs produced by 7αDH+ gut bacteria in CRC.

DESIGN: We performed feeding studies in a porcine model of CRC combined with multi-omics analyses and gnotobiotic mouse models colonised with 7αDH+ bacteria or a genetically modified strain to demonstrate causality.

RESULTS: Western diet exacerbated the CRC phenotype in APC [1311/+] pigs. This was accompanied by increased levels of the secondary BA deoxycholic acid (DCA) and higher colonic epithelial cell proliferation. The latter was counteracted by the BA-scavenging drug colestyramine. Metagenomic analysis across multiple human cohorts revealed higher occurrence of bai (BA inducible) operons from Clostridium scindens and close relatives in faeces of patients with CRC. Addition of these specific 7αDH+ bacteria (C. scindens/Extibacter muris) to defined communities of gut bacteria led to DCA production and increased colon tumour burden in mouse models of chemically or genetically induced CRC. A mutant strain of Faecalicatena contorta lacking 7αDH caused fewer colonic tumours in azoxymethane/dextran sodium sulfate treated mice and triggered less epithelial cell proliferation in human colon organoids compared with wild-type F. contorta.

CONCLUSION: This work provides functional evidence for the causal role of secondary BAs produced by gut bacteria through 7αDH in CRC under adverse dietary conditions, opening avenues for future preventive strategies.},
}

@article {pmid41412669,
year = {2026},
author = {Li, W and Chen, J and Zhang, J and Peng, Z},
title = {Multi-omics insights into the formation mechanism of aging quality in white tea (Bai Mudan) during storage: Integrating sensory evaluation, volatilomics, metabolomics, and metagenomics.},
journal = {Food research international (Ottawa, Ont.)},
volume = {224},
number = {},
pages = {117996},
doi = {10.1016/j.foodres.2025.117996},
pmid = {41412669},
issn = {1873-7145},
mesh = {*Metabolomics/methods ; *Food Storage ; *Tea/chemistry/microbiology ; Volatile Organic Compounds/analysis ; Taste ; *Metagenomics ; Odorants/analysis ; Humans ; *Camellia sinensis/microbiology/chemistry ; Bacteria/genetics ; Multiomics ; },
abstract = {White tea (WT) develops unique aged quality during long-term storage, characterized by progressive changes in sensory properties and chemical composition. However, integrated insights into the sensory, metabolites, and microbial contribution underlying this process remain limited. This study systematically investigated the quality evolution of Bai Mudan tea (a typical WT) over 0 to 11 years of storage using an integrated multi-omics approach. Sensory analysis revealed a flavor transition from fresh (grassy, fruity) to aged (woody, stale) characteristics. Volatilomics identified 72 volatile compounds, with cedrol and isophorone as aged characteristic aroma compounds (rOAV ≥1, VIP ≥ 1, p ≤ 0.05). Metabolomics identified 1146 non-volatile metabolites, showing accumulation of fatty acyls and flavonoids, and a decrease in amino acids. Metagenomic sequencing analysis revealed that bacterial communities (mainly Sphingomonas, Pedobacter, Methylobacterium, and Chryseobacterium) dominated during the first 7 years of storage, followed by a potential shift toward a bacterial-fungal synergy pattern in later stages as the abundances of Monascus and Aspergillus increased. KEGG annotation highlighted the roles of carbohydrate metabolism and amino acid metabolism, and flavonoid biosynthesis was activated during storage. Multi-omics correlation networks demonstrated that fungi positively regulated volatile flavors, while bacteria may be involved in taste balance. Monascus, Sphingomonas, Sphingobium, and Novosphingobium were identified as core functional taxa that may contribute to WT quality formation during storage through aged flavor synthesis, flavonoid accumulation, and lipid degradation. In conclusion, this study provides a multi-dimensional scientific basis for a comprehensive understanding of the formation mechanism of aged quality in white tea during storage.},
}

*Metabolomics/methods
*Food Storage
*Tea/chemistry/microbiology
Volatile Organic Compounds/analysis
Taste
*Metagenomics
Odorants/analysis
Humans
*Camellia sinensis/microbiology/chemistry
Bacteria/genetics
Multiomics

@article {pmid41412647,
year = {2026},
author = {Chen, T and Mo, S and Shen, M and Du, W and Yu, Q and Chen, Y and Xie, J},
title = {Therapeutic potential of Ficus pumila L. in chronic obstructive pulmonary disease through modulation of the gut microbiota-SCFA-lung signaling pathway.},
journal = {Food research international (Ottawa, Ont.)},
volume = {224},
number = {},
pages = {117952},
doi = {10.1016/j.foodres.2025.117952},
pmid = {41412647},
issn = {1873-7145},
mesh = {*Pulmonary Disease, Chronic Obstructive/drug therapy/microbiology/metabolism ; *Gastrointestinal Microbiome/drug effects ; Animals ; *Ficus/chemistry ; *Signal Transduction/drug effects ; *Lung/metabolism/drug effects ; Mice ; *Fatty Acids, Volatile/metabolism ; *Plant Extracts/pharmacology ; Male ; Mice, Inbred C57BL ; Disease Models, Animal ; Polysaccharides/pharmacology ; },
abstract = {Ficus pumila L. has been reported to alleviate pulmonary inflammation, its impact on chronic obstructive pulmonary disease (COPD) pathobiology-specifically via modulation of the gut-lung signaling pathway-has yet to be mechanistically defined. This study investigated how Ficus pumila L. polysaccharides (FP-P) and aqueous extracts (FP-E) remodel the gut microbiome-SCFA network and restore microbial metabolic function in a cigarette smoke-induced COPD mouse model. Microbiota composition was profiled by high-resolution 16S rRNA amplicon sequence variant (ASV) analysis, with concomitant quantification of caecal SCFA using targeted gas chromatography-mass spectrometry (GC-MS) and inference of metagenome function by PICRUSt2. Results demonstrated that FP-P and FP-E alleviated pulmonary pathology, reduced inflammatory cytokine secretion, and significantly restored gut microbiota α-diversity in COPD mice. At the family level, FP-P selectively expanded SCFA-producing Clostridiaceae, and Staphylococcaceae, whereas it contracted pro-inflammatory Helicobacteraceae and Campylobacteraceae. Caecal total SCFA concentration increased by 41.90 %, driven primarily by elevations in butyrate (+23.41 %) and propionate (+45.45 %), without significant changes in acetate. PICRUSt2-inferred metagenomes showed up-regulation of butanoate biosynthesis (PWY-5677), metabolism of cofactors and amino acid (P162-PWY and NAD-BIOSYNTHESIS-II), and carbohydrate degradation (P341-PWY), all of which underpin SCFA production. These functional shifts were accompanied by increased abundance of microbial genes encoding ribosomal proteins and ATP-binding cassette transporters, indicating barrier reinforcement. Collectively, FP-P and FP-E mitigate CS-induced COPD pathology through a gut microbiota-SCFA-lung signaling signaling pathway, highlighting the gut-to-lung communication within the broader gut-lung axis. These findings establish a mechanistic link between microbial metabolism and pulmonary inflammation while acknowledging that the reverse lung-to-gut feedback remains to be elucidated. Future studies will investigate this bidirectional crosstalk and the receptor-mediated signaling of SCFAs in lung tissue.},
}

*Pulmonary Disease, Chronic Obstructive/drug therapy/microbiology/metabolism
*Gastrointestinal Microbiome/drug effects
Animals
*Ficus/chemistry
*Signal Transduction/drug effects
*Lung/metabolism/drug effects
Mice
*Fatty Acids, Volatile/metabolism
*Plant Extracts/pharmacology
Male
Mice, Inbred C57BL
Disease Models, Animal
Polysaccharides/pharmacology

@article {pmid41412637,
year = {2026},
author = {Ferrocino, I and Biolcati, F and Giordano, M and Bertolino, M and Zeppa, G and Cocolin, L},
title = {Dairy environment and seasons affect the microbiome of a traditional artisanal cheese.},
journal = {Food research international (Ottawa, Ont.)},
volume = {224},
number = {},
pages = {117927},
doi = {10.1016/j.foodres.2025.117927},
pmid = {41412637},
issn = {1873-7145},
mesh = {*Cheese/microbiology/analysis ; *Seasons ; *Microbiota ; Animals ; *Food Microbiology ; Italy ; Fungi/classification/genetics/isolation & purification ; *Dairying/methods ; Bacteria/classification/genetics ; Milk/microbiology ; Food Handling/methods ; Cattle ; Metagenomics ; },
abstract = {Cheese microbiome is a complex community shaped by raw ingredients and by the production environment that significantly influences final product characteristics. While environmental microbiome can establish stable resident populations, their composition remains susceptible to seasonal shifts, hygienic practices and other external factors. In this study we investigate the interplay of these factors on the bacterial and fungal communities throughout the production of a full-fat semi cooked semi-hard cow's milk cheese produced in the Piedmont region, North-West of Italy, named Maccagno. Amplicon based sequencing was used to characterize bacterial and fungal diversity across environmental surfaces (contact and non-contact) and during the manufacturing and ripening of Maccagno cheeses over three seasons (autumn, winter and summer). Metabolomic profiling and texture analysis of the ripened cheeses allowed for direct correlation with microbial community shifts. The facility environment maintained a remarkably stable core microbiota, including Staphylococcus, Streptococcus thermophilus, Lactococcus lactis, Debaryomyces, Penicillium and Cladosporium. Among the monitored processing plant sampling sites, the metal stirring tool, milk inlet pipe and the ripening room ventilation system emerged as critical points for microbial transfer and persistence. During ripening, core microbial taxa including Lc. lactis, S. thermophilus and Debaryomyces were observed. Shotgun metagenomics was then performed on final cheeses and genome reconstruction highlighted that Lc. lactis genomes showed impressive seasonal genomic adaptability, particularly in autumn, where it contributed to favorable texture and flavor through proteolytic activity and production of aroma-associated metabolites like acetoin and linear ketons. Conversely, summer production exhibiting the highest prevalence of spoilage-associated microbes such as Acinetobacter and Enterobacteriaceae, mainly of facility origin that led to off-flavor profiles inconsistent with the typical Maccagno sensory identity. The fungal communities, mainly composed by Debaryomyces and Penicillium, also varied seasonally, influenced significantly by the ventilation system in the ripening room. Maccagno cheese quality is a direct reflection of these complex microbial dynamics. Seasonal variations in raw milk microbiome and microbial populations established in specific environmental niches significantly affected the final product's sensory and textural attributes. To this end, understanding seasonal influences and the role of resident environmental populations is crucial for optimizing production protocols, mitigating spoilage risks, and ensuring the consistent quality of traditional cheeses.},
}

*Cheese/microbiology/analysis
*Seasons
*Microbiota
Animals
*Food Microbiology
Italy
Fungi/classification/genetics/isolation & purification
*Dairying/methods
Bacteria/classification/genetics
Milk/microbiology
Food Handling/methods
Cattle
Metagenomics

@article {pmid41412435,
year = {2025},
author = {Dolci, M and Frosio, F and Signorini, L and Soggiu, A and Meroni, G and Favi, E and Alavrez, EC and Ferrante, P and Delbue, S},
title = {Human polyomavirus 6 differentially infects healthy and tumor tissue in the colon: A case report.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {},
number = {},
pages = {105865},
doi = {10.1016/j.meegid.2025.105865},
pmid = {41412435},
issn = {1567-7257},
abstract = {INTRODUCTION: Human polyomavirus 6 (HPyV6) is part of the human skin virome. Like other HPyVs, it encodes proteins with oncogenic properties.

MATERIALS AND METHODS: A 73-year-old Italian female patient with stage II right-sided colon adenocarcinoma underwent hemicolectomy; she died one month later because of bacterial sepsis. Colon tumor (T), adjacent healthy (AH) tissue, and serum samples were collected. Total nucleic acids were subjected to next-generation sequencing, followed by metagenomics analysis. HPyV detection was confirmed by real-time PCR and Rolling Circle Amplification (RCA); HPyV6 transcripts and proteins were identified by means of PCR and Western blot/mass spectrometry, respectively.

RESULTS: Viral metagenomics analysis revealed the presence of several viral genomes, mainly belonging to unclassified viruses and phages, in both AH and T tissues. HPyV6 DNA was detected in the T tissue, representing 7 % of the viral sequences, but not in the AH tissue. Subsequent molecular analysis confirmed the presence of the HPyV6 genomes (3.3x10[6]copies/ug) as episomes, infecting 19.8 % of the tumor cells; LT-Ag and VP1 transcripts were expressed in the T tissue, and the LT-Ag protein was expressed twice as highly in the T tissue as in the AH tissue.

CONCLUSIONS: This is the first report of the differential presence and expression of the HPyV6 genome in colon tumors but not in the AH tissue. These results are indicative of ongoing active replication of the virus, which might play a triggering role in malignant transformation.},
}

@article {pmid41412398,
year = {2025},
author = {Zhang, H and Jing, X and Gong, Y and Zheng, P and Ren, Y and Chen, R and Wu, Y and Liu, S and Zhang, L and Xu, J and Xu, Y},
title = {Single-cell phenotyping and sequencing uncover metabolically active low-abundance yeasts in thermophilic fermentation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133803},
doi = {10.1016/j.biortech.2025.133803},
pmid = {41412398},
issn = {1873-2976},
abstract = {Microbiota-driven fermentation is a global biomanufacturing process that often operates under extreme and fluctuating temperatures. To understand how such systems maintain productivity, this study investigated the Chinese fermentation starter high-temperature Daqu (HTD) as a model system. By combining metagenomics and Raman microspectroscopy, the analysis revealed a drastic decoupling between phylogenetic composition and metabolic activity, with only 10-32 % of yeast species detected by sequencing remaining metabolically active under heat stress. Raman-activated cell sorting and culture (RACS-Culture) recovered three yeasts that consistently maintained viability throughout HTD production: Pichia kudriavzevii, Wickerhamomyces anomalus, and Saccharomycopsis fibuligera. Mono-species and synthetic-community fermentation further revealed a sophisticated mechanism of temporal niche partitioning: in the moderate-temperature early and late stages, S. fibuligera and W. anomalus dominated substrate degradation and flavor precursor biosynthesis, respectively. However, as temperatures rose above 45 °C, both species exhibited low metabolic activity and survival rates. In contrast, only P. kudriavzevii sustained robust growth at this elevated temperature. Genomic analysis revealed a remarkable expansion of heat-resistance and cell-clustering-related genes of wos2 and FLO8 in P. kudriavzevii. These genetic characteristics underpin its enhanced viability, which enables the initially low-abundance species to thrive as a primary ethanol producer and ultimately establish numerical dominance. Thus, temporally overlaying single-cell metabolic vitality profiles onto the corresponding metagenomes can unravel novel functional species and reveal their ecological roles in a complex ecosystem.},
}

@article {pmid41412053,
year = {2025},
author = {Xu, Y and Han, Y and Dong, X and Feng, Y and Wu, F and Xing, F and He, J and Rogers, MJ and Luan, X and Liu, R and He, J and Dang, H and Zhang, D},
title = {Temperature shapes the biogeography of rdhA and reductive dehalogenators in sediment across northwestern Pacific marginal seas.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140847},
doi = {10.1016/j.jhazmat.2025.140847},
pmid = {41412053},
issn = {1873-3336},
abstract = {Dehalogenating microorganisms are crucial in organohalide detoxification in marine sediments. However, the large-scale biogeography and potential environmental adaptability of reductive dehalogenators (RDGs) in marginal sea sediments remain poorly understood. Here, dehalogenating cultures enriched from different marginal sea sediments across northwestern Pacific showed varied dehalogenation patterns, suggesting diverse reductive dehalogenase genes (rdhA). Genome-resolved metagenomic analysis of in situ marginal sea sediments revealed the presence of rdhA-like genes belonging to six distinct categories, with two novel clades more abundant in hypothermal deep-sea sediments (p<0.05). The results of canonical correspondence analysis and distance decay relationship revealed that temperature outweighed geographical contiguity in determining rdhA biogeography and phylogenetic diversity in sediments. A total of 64 putative RDGs were identified across 13 phyla. Low ratios of non-synonymous and synonymous polymorphisms and nucleotide diversity at gene and genome levels indicated the conservation of dehalogenation metabolism in sediment microbiome. RDGs at higher abundance (p<0.05) in mesothermal (≥17.40 ℃) sediments may rely more on sulfate reduction, whereas those with higher abundance (p<0.05) in hypothermal (≤5.5 ℃) sediments (hyp-RDGs) may rely on nitrate utilization. Additionally, hyp-RDGs were prone to external cobalamin acquisition, possibly as an efficient energy-saving strategy. These findings provide insights into the ecological roles of RDGs in marine sediments.},
}

@article {pmid41412046,
year = {2025},
author = {Li, X and Zhang, Y and Zhao, C and Dang, X and Li, B and Hou, S and Gao, X and Hao, J and Lyu, Z and Wang, Y and Hao, L and Zhu, T},
title = {Breaking the cycle of resistance: Hyperthermophilic composting establishes a multi-layered defense against ARG dissemination.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140801},
doi = {10.1016/j.jhazmat.2025.140801},
pmid = {41412046},
issn = {1873-3336},
abstract = {The environmental dissemination of antibiotic residues and antibiotic resistance genes (ARGs) from livestock manure poses major risks to public health. Here, we established a hyperthermophilic composting (HC, >80℃) system alongside conventional composting (CK) to elucidate the mechanisms driving antibiotic and ARG removal. By integrating metagenomics, Quantitative PCR (qPCR), and machine learning, we systematically assessed antibiotic degradation, ARG/MGE dynamics, and microbial functional shifts. HC rapidly reached 87.3 ℃ within 24 h and maintained extreme thermophilic conditions, achieving higher TOC degradation (36.58 % vs. 22.59 % in CK), accelerated humification (HA/FA=2.19 by day 15), and efficient removal of oxytetracycline, enrofloxacin, and sulfamethoxazole (98.44 %, 92.34 %, and 99.63 %, respectively), thereby shortening the selective pressure window. Metagenomics identified 796 ARGs and 128 MGEs; key ARGs (macB, bcrA, tetA(58)) declined markedly in HC, with ARG and MGE abundances strongly correlated and virulence factor genes synchronously reduced. qPCR confirmed rapid ARG/MGE attenuation in HC without the rebound observed in CK. Partial least squares path modeling (GOF=0.858) showed MGEs were the primary driver of ARG dissemination (path coefficient=0.790), while temperature exerted indirect effects by reshaping thermophilic communities, enhancing metabolism, and suppressing antibiotics and MGEs. Random forest further highlighted MGEs (integrase, transposase, IS91/ISCR) and humification indices (HA/FA/HS) as key factors, with Bacillus and Truepera as major contributors under HC. Overall, HC established a multilayered "high temperature-community restructuring-functional metabolism-MGE suppression" barrier, enabling faster, more stable and safer resistance risk control than CK. This provides a scalable pathway for safe manure valorization and ARG mitigation under the One Health framework.},
}

@article {pmid41412032,
year = {2025},
author = {You, F and Yang, S and Ding, Y and Han, J and Xing, D and Jin, C and Zhao, Y and Gao, M and Guo, L},
title = {Comparative insights into denitrification performance and microbial adaptation of heterotrophic, autotrophic, and mixotrophic systems under florfenicol stress for recirculating mariculture wastewater treatment.},
journal = {Water research},
volume = {291},
number = {},
pages = {125172},
doi = {10.1016/j.watres.2025.125172},
pmid = {41412032},
issn = {1879-2448},
abstract = {Wastewater from marine recirculating aquaculture systems (RAS) poses significant treatment challenges due to its high nitrate concentrations and low carbon-to-nitrogen ratio. The additional presence of antibiotic residues such as florfenicol creates mixed pollution that further impairs denitrification and destabilizes microbial communities. This study systematically compared the multi-scale responses of heterotrophic (HDN), sulfur-autotrophic (SADN), and mixotrophic (MDN) denitrification under 4.0 mg L[-1] florfenicol stress in synthetic recirculating mariculture wastewater (salinity = 3.5 %). The MDN system achieved the highest denitrification rate (46.83 mg NOx[-]-N h[-1] g[-1] MLVSS) and maintained nitrate removal efficiency above 98 % with minimal fluctuations under florfenicol stress. Although the HDN system exhibited high NAR/NIR activities and electron transport system activity (ETSA), nitrite accumulation occurred due to functional imbalance. The SADN system, relying on sulfur oxidation, demonstrated limited metabolic flexibility and electron supply capacity under florfenicol stress, resulting in slower nitrate reduction. Metagenomic and KEGG pathway revealed significant differences in microbial community composition and functional potential among HDN, SADN and MDN denitrification systems: HDN was dominated by biofilm-forming Proteobacteria, with broad antibiotic resistance gene (ARG) enrichment and stronger mobile genetic element co-localization; SADN showed enrichment of Campylobacterota, consistent with sulfur oxidation-based pathways, and Mantel tests confirmed tighter ARG-environment coupling; MDN showed the highest microbial diversity with elevated Planctomycetota, functional enrichment in carbohydrate and energy metabolism, and stable quorum sensing-electron transfer coupling with functional redundancy. These findings provide new insights for designing robust treatment strategies for recirculating mariculture wastewater subject to compound pollution from nitrate and antibiotics.},
}

@article {pmid41411799,
year = {2025},
author = {Chen, M and Meng, S and Guan, R and Dong, Q and Dong, X and Shen, X and Fang, L and Zhao, F},
title = {Lead exposure changes carbohydrate and amino acid metabolism corresponding to a disturbed microbiota-gut-brain axis in mice.},
journal = {Ecotoxicology and environmental safety},
volume = {309},
number = {},
pages = {119554},
doi = {10.1016/j.ecoenv.2025.119554},
pmid = {41411799},
issn = {1090-2414},
abstract = {Chronic lead exposure can cause irreversible neurological damage. The brain-gut axis's involvement in lead-induced neurotoxicity, a key factor in cognitive deficits, requires further exploration. To deepen our understanding of how lead exposure influences the brain-gut connection, we carried out the behavioral and morphological analysis, as well as metabolome and metagenome analysis associated with the gut-brain axis. The study results suggested that Pb exposure resulted in inflammation in both the brain and gut, along with decreased cognitive ability. The metagenomic data indicated that Pb exposure impacted microbial diversity and composition, with a marked increase in genes linked to carbohydrate and amino acid metabolism. Compared to control mice, the metabolic profiles of brain, feces and serum samples from Pb-exposed mice were differed, with higher levels of amino acids in serum and soluble sugars in feces, but lower levels of amino acids in brain. Key enriched microbial (eg: Tenericutes, Thermotogae, Alistipes_putredinis) was significantly negatively correlated with brain amino acid (eg: proline, asparagine, tryptophan) but positively correlated with serum amino acids (eg: valine, leucine, tyrosine). This research uncovers new perspectives on how lead exposure alters metabolites in the brain-gut axis, regulated by gut microbiota, highlighting the need for additional research on lead's health risks.},
}

@article {pmid41410816,
year = {2025},
author = {He, JH and Wang, H and Qiu, E and Qi, Q and Wang, Z},
title = {Gut Microbiota and Atherosclerosis: Integrative Multi-Omics and Mechanistic Insights.},
journal = {Current atherosclerosis reports},
volume = {28},
number = {1},
pages = {1},
pmid = {41410816},
issn = {1534-6242},
support = {R01HL170904/HL/NHLBI NIH HHS/United States ; K01HL169019/HL/NHLBI NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Atherosclerosis/microbiology/metabolism ; Metabolomics/methods ; Metagenomics ; Dysbiosis ; Proteomics ; Multiomics ; },
abstract = {PURPOSE OF REVIEW: This review synthesizes and discusses evidence from metagenomics, metabolomics, and proteomics on gut microbiome alterations in atherosclerotic cardiovascular disease (ACVD), with carotid atherosclerosis (CAS) serving as an example.

RECENT FINDINGS: Evidence on gut microbial α-diversity and β-diversity was mixed and differs by disease status. Pro-inflammatory/pathogenic gut bacterial taxa (e.g., Escherichia coli, Klebsiella spp., Streptococcus spp., and Ruminococcus gnavus) were often enriched in patients with ACVD or CAS, whereas short-chain fatty acid (SCFA) producers (e.g., Faecalibacterium prausnitzii, Roseburia spp., Bacteroides spp., and Eubacterium eligens) were depleted. Targeted and untargeted metabolomics implicated multiple microbial-derived metabolites in relation to ACVD and CAS, including trimethylamine N-oxide, short-chain fatty acids, bile acids, lipopolysaccharides, phenylacetylglutamine, indole-3-propionate and imidazole propionate. Gut dysbiosis contributes to ACVD or CAS possibly via metabolite-mediated effects on endothelial function, inflammation, and lipid metabolism. Future research prioritizing longitudinal and interventional studies integrating microbial metagenomics with host multi-omics are needed to elucidate causal pathways and identify clinically actionable targets.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Atherosclerosis/microbiology/metabolism
Metabolomics/methods
Metagenomics
Dysbiosis
Proteomics
Multiomics

@article {pmid41410786,
year = {2025},
author = {Senel, E and Ramos-Barbero, MD and Santos, F and Villamor, J and Mutlu, MB and Antón, J},
title = {Viral diversity of brine and precipitated halite of Tuz Lake, an inland hypersaline lake in Turkey.},
journal = {Archives of virology},
volume = {171},
number = {1},
pages = {28},
pmid = {41410786},
issn = {1432-8798},
support = {208F135//the Anadolu University Research Foundation No. 1208F135. ES. was an MSc student of the Erasmus program./ ; },
mesh = {*Lakes/virology/chemistry ; Salinity ; Turkey ; Salts/chemistry ; *Viruses/genetics/classification/isolation & purification ; Phylogeny ; *Biodiversity ; Metagenomics ; Genome, Viral ; },
abstract = {The diversity of viral communities in inland hypersaline environments remains largely unexplored. Here, we characterized viral assemblages of the thalassohaline inland hypersaline Tuz Lake (Turkey). To identify viral groups and viral sequences present in multiple samples, brine and precipitated salt samples were analysed using microscopy and metagenomics. Viral assemblages showed an abundance and morphology similar to what is commonly found in hypersaline systems. Despite these similarities, the vast majority of sequences remained unknown with regard to taxonomy and function and could not be characterized, highlighting their novelty. A remarkably high fraction of the viral sequences identified were present in both brine and salt samples, indicating viral stability during salt precipitation and dissolution in the lake, suggesting that Tuz Lake might be of considerable astrobiological interest. Alongside this high level of similarity, read recruitments revealed the presence of some sample-specific viral sequences in the salt sample. Tuz Lake viral assemblages displayed a distinct composition when compared to previously described viral metagenomes and haloviral genomes from hypersaline environments, with the highest similarity to the viral assemblages of the crystallizer ponds in the Bras del Port saltern (Spain).},
}

*Lakes/virology/chemistry
Salinity
Turkey
Salts/chemistry
*Viruses/genetics/classification/isolation & purification
Phylogeny
*Biodiversity
Metagenomics
Genome, Viral

@article {pmid41410736,
year = {2025},
author = {Nath, S},
title = {Advanced microbial engineering approaches for biodegradation of pharmaceutical pollutants.},
journal = {Biodegradation},
volume = {37},
number = {1},
pages = {15},
pmid = {41410736},
issn = {1572-9729},
mesh = {*Biodegradation, Environmental ; *Water Pollutants, Chemical/metabolism ; Pharmaceutical Preparations/metabolism ; *Metabolic Engineering/methods ; *Bacteria/metabolism/genetics ; Bioreactors/microbiology ; },
abstract = {Pharmaceutical pollutants have emerged as pervasive environmental contaminants, entering ecosystems via wastewater effluents, agricultural runoff and improper disposal. These pollutants typically belong to classes such as antiepileptics, antibiotics, analgesics, non-steroidal anti-inflammatory drugs, hormones and antiseptics. Their recalcitrance arises from their stable chemical structures, which resist degradation and pose significant challenges for conventional wastewater treatment processes, leading to their persistence in the environment and potentially harmful effects on ecosystems and human health. This study investigates microbial engineering strategies for the efficient degradation of pharmaceutical pollutants. Recent advancements in CRISPR systems, ALE, metabolic engineering, bioaugmentation and bioreactor designs have significantly improved pollutant breakdown. Additionally, novel approaches to address emerging contaminants and the application of advanced biotechnologies like synthetic biology and metagenomics are crucial for developing more effective and sustainable bioremediation strategies. These insights offer a roadmap for developing more effective and sustainable solutions for the bioremediation of pharmaceutical pollutants.},
}

*Biodegradation, Environmental
*Water Pollutants, Chemical/metabolism
Pharmaceutical Preparations/metabolism
*Metabolic Engineering/methods
*Bacteria/metabolism/genetics
Bioreactors/microbiology

@article {pmid41409983,
year = {2025},
author = {Hira, J and Mahbub, NB and Ali, J and Ahmad, R},
title = {Low-cost in-house re-formulated brain heart infusion medium for effective planktonic growth and early detection of bloodstream bacterial pathogens.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1680006},
pmid = {41409983},
issn = {1664-302X},
abstract = {Sepsis, a clinically defined life-threatening condition, is a global contributor to high morbidity and mortality rates in humans. It is caused by systemic bloodstream bacterial infections, primarily involving aerobic pathogens such as Escherichia coli, Staphylococcus aureus, and Klebsiella pneumoniae. Rapid and accurate identification of these pathogens is a high-demand task, as prolonged diagnosis may increase the mortality rate among sepsis patients. Globally, commercial blood culture systems like the BD BACTEC™ FX blood culture system, which utilizes BD BACTEC™ PLUS Aerobic/F culture bottles (used in this study), are commonly used to detect aerobic bloodstream infections. However, due to high costs (∼$10.00-$15.00/bottle), limited availability of culture media (especially in low- and middle-income countries, and war zones), and a lack of customization for antibiotic susceptibility assay and epidemiology research, there is a need for secondary alternatives to facilitate the growth and identification of bloodborne pathogens. Therefore, we developed a low-cost (∼$4-$5/bottle) in-house culture medium with a newly improved formulation of Brain Heart Infusion media that enhances bacterial growth from spiked human blood tested on a panel of bacteria (Escherichia coli, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterococcus faecalis). The growth dynamics of these microbes in in-house formulated BHI-Blood+ culture media coincide with those in BACTEC™ Plus Aerobic/F culture vials, which primarily suggests the compatibility of bloodborne pathogens with this media and can be flagged positive <8 h based on cellular growth rate. Additionally, conventional qPCR-based early detection (<24 h) and validation with the Oxford Nanopore MinION NGS platform highlight the value of this in-house culture media as an alternative to commercial culture media in terms of low-cost availability.},
}

@article {pmid41409546,
year = {2025},
author = {Zhao, L and Peng, S and Ge, M and Xing, B and Zhao, X and Yang, T and Yu, S and Zhang, C and Liu, J and Miao, Z and Ma, H},
title = {Gut-to-tumor translocation of multidrug-resistant Klebsiella pneumoniae shapes the microbiome and chemoresistance in pancreatic cancer.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1694479},
pmid = {41409546},
issn = {2235-2988},
mesh = {Humans ; *Pancreatic Neoplasms/microbiology/drug therapy/pathology ; *Klebsiella pneumoniae/drug effects/genetics/isolation & purification ; *Gastrointestinal Microbiome ; Feces/microbiology ; Male ; Female ; Middle Aged ; Aged ; *Drug Resistance, Multiple, Bacterial ; Metagenomics ; Anti-Bacterial Agents/pharmacology ; Whole Genome Sequencing ; Klebsiella Infections/microbiology ; },
abstract = {BACKGROUND: Despite advances and successes in precision oncology, pancreatic cancer (PC) remains a tumor with extremely low survival rates, and many of these cases experienced postoperative recurrence and metastasis. Alterations in the gut microbiota have been linked to the survival rates of PC patients. Nevertheless, the complexity of gut microbiota composition poses significant challenges in identifying definitive clinical biomarkers for PC.

METHODS: Fecal samples were collected from PC patients, half of whom had metastasis, and their matched healthy controls (HCs). A metagenomic analysis was employed to further investigate the functional features of gut microbiota with both PC and metastatic PC. The clinical correlations, microbial metabolic pathways and antibiotic resistome were further assessed. In a follow-up validation, intraoperative tumor tissue and pancreatic fluid were sampled from PC patients and underwent comprehensive microbiological analysis, including bacterial culture, mass spectrometry-based identification, and third-generation whole-genome sequencing of Klebsiella pneumoniae isolates.

RESULTS: We observed a significant alteration of the gut microbiota in PC patients, highlighted by an overall increase in microbial diversity compared to healthy controls (p < 0.05). Comparative abundance analysis identified 59 differentially abundant microbial species in non-metastatic pancreatic cancer (NMPC) (56 increased, 3 decreased) and 21 in metastatic pancreatic cancer (MPC) (19 increased, 2 decreased), alongside 18 significantly altered microbial metabolic pathways (FDR-adjusted p < 0.05). Notably, Klebsiella pneumoniae, Klebsiella oxytoca, and Akkermansia muciniphila were identified as prominent antibiotic resistance gene (ARG) carriers in the gut microbiota of PC patients, with 653 ARG subtypes detected across fecal samples, 38-47% of which were shared among groups. Strong co-occurrence patterns between ARGs (e.g., acrB, mdtC, cpxA, emr, pmrF) and the above species were observed predominantly in MPC samples (p < 0.05). Whole-genome sequencing of 14 isolates obtained from tumor tissue and pancreatic fluid revealed consistent ARG profiles and virulence genes, corroborating the metagenomic findings and supporting the hypothesis of gut-to-tumor translocation and potential intratumoral colonization.

CONCLUSION: This study provides a comprehensive microbiome-based insight into PC and its metastatic subtypes. By integrating microbiome analysis with microbial culture, this study provides direct evidence of gut-derived multidrug-resistant (MDR) K. pneumoniae colonization in PC tissues.},
}

Humans
*Pancreatic Neoplasms/microbiology/drug therapy/pathology
*Klebsiella pneumoniae/drug effects/genetics/isolation & purification
*Gastrointestinal Microbiome
Feces/microbiology
Male
Female
Middle Aged
Aged
*Drug Resistance, Multiple, Bacterial
Metagenomics
Anti-Bacterial Agents/pharmacology
Whole Genome Sequencing
Klebsiella Infections/microbiology

@article {pmid41409544,
year = {2025},
author = {Liu, J and Qin, SY and Lei, CC and Ma, H and Xie, LH and Liu, Y and Li, JH and Ni, HB and Yu, MY and Liang, HR and Shi, WH and Qin, Y and Jiang, J and Yan, WL and Chen, BN and Li, ZY and Sun, HT},
title = {Blastocystis infection in Tibetan antelopes (Pantholops hodgsonii) alters gut microbiota composition and function.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1719025},
pmid = {41409544},
issn = {2235-2988},
mesh = {*Gastrointestinal Microbiome ; *Antelopes/microbiology/parasitology ; Animals ; *Blastocystis ; *Blastocystis Infections/veterinary/parasitology/microbiology ; Tibet ; Metagenome ; Metagenomics ; Bacteria/classification/genetics/isolation & purification ; Feces/microbiology/parasitology ; },
abstract = {INTRODUCTION: The gut microbiota plays an important role in host environmental adaptation, including defense against pathogens. Parasite infections can disrupt gut microbial communities and thus influence host adaptability. However, most current knowledge of Blastocystis-microbiota interactions comes from humans or domestic animals, and data from wild mammals, especially those inhabiting extreme environments, remain scarce.

METHODS: In this study, we analyzed 68 gut metagenomes from Tibetan antelopes (Pantholops hodgsonii) and screened for infections by four intestinal parasites - Blastocystis, Cryptosporidium, Giardia, and Encephalitozoon bieneusi.

RESULTS: Among them, 26 individuals were solely infected with Blastocystis subtype ST31. Compositional analysis revealed 25 differential families, with 12 enriched in infected and 13 in healthy individuals. LEfSe further identified 38 species-level biomarkers (LDA > 2, p < 0.05), indicating a significant shift in gut microbial diversity following Blastocystis ST31 infection. Notably, the relative abundance of Arthrobacter sp. 08Y14, associated with environmental resilience, was markedly reduced in infected individuals. Functional profiling showed a decrease in metabolic diversity, with 18 CAZy families detected in the healthy group but only 2 in the infected group. KEGG analysis showed that the average relative abundance of K07497 was higher in the infected group (5.16) than in the healthy group (1.03).

DISCUSSION: These findings suggest that Blastocystis ST31 infection reshapes the gut microbiota and may impair the high-altitude adaptability of Tibetan antelopes by reducing plateau-adaptive microbes and functional capacity. This study provides the first evidence of Blastocystis-induced gut microbiota changes in Tibetan antelopes and broadens our understanding of parasite-microbiota interactions across hosts.},
}

*Gastrointestinal Microbiome
*Antelopes/microbiology/parasitology
Animals
*Blastocystis
*Blastocystis Infections/veterinary/parasitology/microbiology
Tibet
Metagenome
Metagenomics
Bacteria/classification/genetics/isolation & purification
Feces/microbiology/parasitology

@article {pmid41409502,
year = {2025},
author = {Pico-Tomàs, A and Sanchís, A and Mejías-Molina, C and Comas-Cufí, M and Balcázar, JL and Bofill-Mas, S and Torrell, H and Canela, N and Borrego, CM and Corominas, L},
title = {Tracking Age-Linked Antibiotic Resistance Patterns through Building-Level Wastewater Analysis.},
journal = {ACS ES&T water},
volume = {5},
number = {12},
pages = {7141-7151},
pmid = {41409502},
issn = {2690-0637},
abstract = {Antimicrobial resistance (AMR) is a global health challenge, and monitoring different demographic populations can improve our understanding of its spread and prevalence in urban settlements. This study applies building-level wastewater-based epidemiology (WBE) to analyze the resistome and mobilome of age-segregated populations from an elementary school (School), a university residence (UnivRes), and an elderly care facility (ElderlyRes) all located in Girona (Catalonia, Spain). Metagenomic analyses were subsequently conducted to investigate differences in bacterial communities, antibiotic resistance genes (ARGs), and mobile genetic elements (MGEs). The results revealed age-linked variations in the relative abundance and diversity of ARGs. The wastewater collected at the School exhibited the highest abundance of ARGs, while the ElderlyRes showed the highest diversity. Furthermore, sequences affiliated with bacterial pathogens were more prevalent in samples from both the School and the ElderlyRes, emphasizing potential public health implications. Among the 12 bacterial genera most strongly correlated with ARGs (Pearson R > 0.7), 11 were identified as members of the gut microbiota, underscoring their predominant role as reservoirs of resistance compared to bacteria of environmental origin. By integrating localized wastewater sampling with metagenomics, our study uncovers demographic-specific resistome patterns, delivering actionable evidence to strengthen AMR surveillance and intervention strategies in urban populations.},
}

@article {pmid41409175,
year = {2025},
author = {Ng, DZW and Low, A and Khairul Sani, KRB and Liu, L and Zhang, Z and Koh, XQ and Zhu, M and Mitra, K and Muthiah, M and Dan, YY and Lee, JWJ and Chan, ECY},
title = {Dysbiosis-Driven Reprogramming of Secondary Bile Acid Metabolism in Metabolic Dysfunction-Associated Steatotic Liver Disease: Insights from an Ex Vivo Human Fecal Microbiota Model.},
journal = {ACS pharmacology & translational science},
volume = {8},
number = {12},
pages = {4335-4344},
pmid = {41409175},
issn = {2575-9108},
abstract = {Gut microbial dysbiosis-induced perturbations in bile acid (BA) metabolism are implicated in metabolic dysfunction-associated steatotic liver disease (MASLD), yet evidence remains largely associative. Using an optimized ex vivo fecal microbiota model, we modeled the metabolism kinetics of conjugated- and primary-BA between MASLD and healthy donors. Enzymes for known BA metabolic reactions were inferred using functional metagenomics. MASLD cultures exhibited impaired deconjugation capacity but preserved downstream primary-BA clearance and demonstrated a substrate-independent shift that favored oxidative metabolism over 7α-dehydroxylation. This was marked by increased formation clearance of 7-keto-deoxycholic acid (175%) and 3-oxo-cholic acid (51.7%) from cholic acid (CA) and 7-keto-lithocholic acid (77.9%) from chenodeoxycholic acid (CDCA). C7-oxidized BA constituted the major proportion of total BA clearance (CA = 56.0%, CDCA = 72.3%) in MASLD cultures. Enrichment of C3- and C7-hydroxysteroid dehydrogenases in MASLD compared to control corroborated the differential secondary BA profiles. Together, microbes catalyzing C7-oxidation warrants further investigation as potential pharmacological targets of MASLD.},
}

@article {pmid41408693,
year = {2025},
author = {Esener, N},
title = {Omics technologies in mastitis: text mining and topic modelling analysis of global research trends.},
journal = {The Journal of dairy research},
volume = {},
number = {},
pages = {1-11},
doi = {10.1017/S0022029925101830},
pmid = {41408693},
issn = {1469-7629},
abstract = {Mastitis, an inflammation of the mammary gland, is a disease of significant clinical and economic importance. In recent years, advances in omics technologies have provided powerful tools to unravel the complex biological mechanisms underlying mastitis. These approaches encompass diverse fields such as genomics, proteomics, transcriptomics, metagenomics, metabolomics, epigenomics, lipidomics, glycomics, pharmacogenomics, foodomics, interactomics and exposomics. However, despite the rapid growth of omics research, the thematic structure of this literature has not been systematically examined. In this study, latent dirichlet allocation (LDA) was employed to perform topic modelling on publications related to omics and mastitis retrieved from Scopus and Web of Science. The LDA analysis revealed ten distinct topics, labelled according to the most frequent terms within each cluster: 'proteomics', 'pathogen genomics', 'differential expression', 'metabolism', 'genetic selection', 'disease economy', 'molecular diagnostics', 'microbiome', 'antimicrobial resistance' and 'genetic variation.' Among these, the topics of 'genomics', 'differential expression' and 'antimicrobial resistance' accounted for the highest number of publications, while 'metabolism' emerged more recently. All topics exhibited an increasing trend in publication volume over time, likely driven by the declining costs and greater accessibility of high-throughput omics technologies. This study provides a comprehensive thematic overview of omics research on mastitis, identifies key areas of emphasis and emerging directions, and highlights knowledge gaps that may inform future investigations and the development of targeted strategies for disease control and prevention.},
}

@article {pmid41408356,
year = {2025},
author = {Yao, QC and Zhang, DY and Du, YP and Chen, C and Lv, YT and Li, D and Xing, YX and Xu, XY and Lin, QQ and Tan, WF and Bai, FH},
title = {Gut microbiome-metabolome dysregulation in systemic sclerosis: a multi-omics study.},
journal = {Rheumatology (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/rheumatology/keaf668},
pmid = {41408356},
issn = {1462-0332},
abstract = {OBJECTIVES: The interplay between the gut microbiome (GM), plasma metabolites, and systemic sclerosis (SSc) has not been systematically studied. We hypothesized that disruption at the GM-metabolome interface contributes to the pathogenesis of SSc. This study aims to investigate the faecal microbiome composition and plasma metabolite profiles in SSc patients.

METHODS: To evaluate the interactions, deep shotgun metagenomic sequencing was conducted on faecal samples from 15 SSc patients and 33 healthy controls. Simultaneously, untargeted Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) metabolomic profiling was performed on plasma samples from 14 SSc patients and 30 controls.

RESULTS: The analysis revealed significant alterations in 11 microbial species and 266 MS2-identified metabolites in SSc patients vs controls. In SSc, elevated levels of Escherichia coli, Lactobacillus mucosae, and Parabacteroides distasonis were noticed. Conversely, P. plebeius, B. hansenii, and Agathobaculum butyriciproducens were enriched in the control group. Functional predictions indicated a depletion of amino acid biosynthesis pathways, including L-isoleucine and L-methionine, in SSc patients. The metabolomic analysis demonstrated a significant reduction in lipid-like molecules and amino acid levels in SSc patients. Dysregulated pathways, such as alanine, aspartate, and glutamate metabolism, arginine and proline metabolism, and glycine, serine, and threonine metabolism, were associated with the development of SSc. Striking microbiota-metabolite correlations (168 significant associations) were identified, with disease-enriched species showing specific metabolic linkages.

CONCLUSIONS: This study offers a comprehensive characterization of the disrupted GM-metabolite interface in SSc patients, providing new perspectives on SSc pathogenesis and potential therapeutic targets.},
}

@article {pmid41408316,
year = {2025},
author = {Wang, L and Remue, L and Adriaens, N and Soto, A and Verwimp, S and van Bree, J and Trappeniers, K and Delang, L},
title = {Identification of a culturable fungal species and endosymbiotic bacteria in saliva of Aedes aegypti and Culex pipiens and their impact on arbovirus infection in vitro.},
journal = {Parasites & vectors},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13071-025-07158-3},
pmid = {41408316},
issn = {1756-3305},
support = {C22/18/007//KU Leuven/ ; C14/20/108//KU Leuven/ ; STG/19/008//KU Leuven/ ; },
abstract = {BACKGROUND: Mosquito saliva plays a key role in arbovirus transmission and pathogenesis. It was shown that saliva contains several molecules that are essential for blood feeding. Recently, bacteria were also reported to be present in the saliva of Aedes albopictus and Anopheles mosquitoes. Nevertheless, information on the bacterial communities in Aedes and Culex saliva is still scarce.

METHODS: This study isolated and identified culturable fungal and bacterial colonies from saliva harvested from Aedes aegypti (laboratory strain) and Culex pipiens (field-collected) mosquitoes. 16S metagenomic sequencing was performed to identify bacterial communities in saliva and mosquito organs. Furthermore, it was assessed how these microbial communities were affected upon blood feeding and upon oral treatment with antibiotics and an antifungal drug.

RESULTS: The fungal species Penicillium crustosum was identified in mosquito saliva. Culturable bacteria detected in mosquito saliva included Serratia marcescens, Serratia nematodiphila, Enterobacter spp., and Klebsiella spp., which were previously identified as mosquito or insect endosymbionts in the midgut or other organs. Analysis with 16S metagenomics showed that bacterial communities in saliva were more diverse than those in the midgut. Blood feeding did not affect the fungal or bacterial load in mosquito saliva. Oral treatment of adult mosquitoes with antibiotics or an antifungal drug resulted in a significant reduction of bacteria or fungi present in the mosquito saliva. Notably, co-incubation of the mosquito-borne Semliki Forest virus with saliva from antibiotic- or antifungal-treated mosquitoes triggered a decrease in viral infection in human skin fibroblasts compared with nontreated saliva.

CONCLUSIONS: These findings indicate that bacteria and fungi can be present in mosquito saliva and provide a foundation for further exploration of the impact of salivary fungi and bacteria on both vector competence and arbovirus infection in the mammalian host.},
}

@article {pmid41408188,
year = {2025},
author = {Halimi, H and Hesami, Z and Asri, N and Khorsand, B and Rostami-Nejad, M and Houri, H},
title = {Exploring the biliary microbiome in hepatopancreatobiliary disorders: a comprehensive systematic review of microbial signatures and diagnostic potential.},
journal = {BMC gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12876-025-04551-1},
pmid = {41408188},
issn = {1471-230X},
support = {NO. IR.SBMU.RIGLD.REC.1404.036//Shahid Beheshti University of Medical Sciences/ ; },
abstract = {BACKGROUND: Hepatopancreatobiliary (HPB) diseases, encompassing hepatobiliary and pancreatic disorders, pose substantial global health challenges due to their high morbidity and mortality rates. Recent research highlights the crucial role of the biliary microbiome in the development of these diseases.

METHODS: This study provides a comprehensive systematic review of the biliary microbiome's characteristics across various HPB disorders, including cholangiocarcinoma (CCA), pancreatic cancer (PC), primary sclerosing cholangitis (PSC), and gallstone disease (GSD). Following Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, we screened articles from multiple databases, focusing on original research utilizing 16 S rRNA gene sequencing or metagenomics.

RESULTS: Our review included 24 studies that met stringent inclusion criteria. The results indicate distinct alterations in bacterial diversity and composition associated with different HPB conditions, highlighting potential pathogenic mechanisms and candidate taxa as potential microbial indicators. In lithiasis conditions, elevated levels of Pyramidobacter and Citrobacter were associated with recurrent and giant common bile duct (CBD) stones. Proteobacteria were prevalent in PSC and CCA, potentially contributing to these diseases by promoting chronic inflammation. Sphingomonas was associated with both CCA and PSC, with potential implications for lymph node metastasis in PC.

CONCLUSIONS: These findings suggest the potential of the biliary microbiome as a diagnostic tool, offering insights into the pathophysiology and possible therapeutic targets for HPB diseases. However, given the heterogeneity in methodologies and the limited number of studies including healthy controls, these observations remain preliminary; further prospective validation is required before clinical translation.},
}

@article {pmid41408023,
year = {2025},
author = {Wang, H and Zhang, M and Hua, B and He, J and Yang, Y and Wu, W and Zhang, Y and Wei, F and Cai, Y and Wang, Q},
title = {Exploring the gut microbiome in systemic lupus erythematosus: metagenomic and metabolomic insights into a new pro-inflammatory bacteria Clostridium scindens.},
journal = {Clinical rheumatology},
volume = {},
number = {},
pages = {},
pmid = {41408023},
issn = {1434-9949},
support = {C2301008，C2404002//Shenzhen Medical Research Fund/ ; 2023B1515230002//Guangdong Basic and Applied Basic Research Foundation/ ; 2023A1515010294//Guangdong Basic and Applied Basic Research Foundation/ ; 0102018-2019-YBXM-1499-01-0414//Treatment and Prevention Integration Project of Shenzhen Municipal Health Commission/ ; SZSM202311030//Sanming Project of Medicine in Shenzhen/ ; No. NSFC 82302037//The National Natural Science Foundation of China/ ; KYQD2024355//Shenzhen High-level Hospital Construction Fund and Peking University Shenzhen Hospital Scientific Research Fund/ ; },
abstract = {OBJECTIVES: Systemic lupus erythematosus (SLE) is a complex autoimmune disease with unclear pathogenesis. Emerging evidence indicates that the gut microbiome may play a critical role in immune regulation. This study aimed to investigate gut microbiome and metabolome alterations in SLE patients, with a focus on the pro-inflammatory bacterium Clostridium scindens (C. scindens), and explore its potential contribution to disease pathogenesis.

METHOD: We performed metagenomic sequencing to analyze gut microbial composition in SLE patients and healthy controls, alongside untargeted metabolomic profiling of peripheral blood to assess systemic metabolic changes. We examined species diversity, taxonomic differences at both phylum and species levels, and metabolic alterations. Statistical analyses identified significant associations and potential diagnostic markers.

RESULTS: SLE patients did not show a consistent reduction in species diversity, but exhibited significant microbial compositional differences compared to healthy controls. These patterns suggest potential diagnostic utility. Metabolomic analysis revealed systemic metabolic disturbances linked to gut dysbiosis. Ruminococcus gnavus was associated with altered amino acid, lactose, and sphingolipid metabolism, potentially affecting host immunity. Notably, C. scindens appeared to contribute to immune dysregulation via bile acid metabolism.

CONCLUSIONS: This study reveals distinct microbial and metabolic profiles in SLE, identifying C. scindens as a potential driver of immune imbalance. The findings suggest that targeting the gut microbiome could offer novel strategies for diagnosis and therapeutic intervention in SLE. Key Points • Gut microbial composition is significantly altered in SLE patients compared to healthy controls. • Metabolomic profiling reveals systemic disturbances linked to gut dysbiosis. • Clostridium scindens is associated with bile acid metabolism and immune dysregulation in SLE. • The gut microbiome may serve as a potential target for diagnosis and treatment in SLE.},
}

@article {pmid41407999,
year = {2025},
author = {Li, Z and Yang, S and Li, C and Zhang, L and Xi, N and Li, D and Li, L},
title = {Metagenomic next-generation sequencing for the diagnosis of suspected spinal infections from biopsy samples: a novel biopsy toolkit design and real-life diagnostic value.},
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 = {41407999},
issn = {1432-0932},
}

@article {pmid41407459,
year = {2025},
author = {Lin, QX and Wei, JJ and Lian, TT and Lin, BQ and Ren, JH and Zheng, XY and Wu, XQ and Li, J and Chen, H and Xie, SJ and Yang, T},
title = {[Diagnostic value of intestinal tissue metagenomic next-generation sequencing in severe diarrhea following haploidentical hematopoietic stem cell transplantation].},
journal = {Zhonghua xue ye xue za zhi = Zhonghua xueyexue zazhi},
volume = {46},
number = {11},
pages = {1020-1025},
doi = {10.3760/cma.j.cn121090-20241206-00540},
pmid = {41407459},
issn = {0253-2727},
support = {YJRC4415//Hospital talent scientific research project/ ; },
mesh = {Humans ; *Hematopoietic Stem Cell Transplantation/adverse effects ; Male ; Female ; Adult ; Middle Aged ; *High-Throughput Nucleotide Sequencing ; Child, Preschool ; Adolescent ; *Diarrhea/diagnosis/etiology/microbiology ; Child ; *Metagenomics ; Young Adult ; Transplantation, Haploidentical/adverse effects ; },
abstract = {Objective: To evaluate the diagnostic value of intestinal tissue metagenomic next-generation sequencing (mNGS) in severe diarrhea following haploidentical allogeneic hematopoietic stem cell transplantation (allo-HSCT) . Methods: Sixteen patients who developed severe diarrhea or hematochezia after haploidentical allo-HSCT at the First Affiliated Hospital of Fujian Medical University (June 2023-August 2024) were enrolled. All underwent gastrointestinal endoscopy and mNGS for microbial detection. Clinical, endoscopic, pathological, and microbiological data were analyzed to evaluate the diagnostic value of mNGS and treatment outcomes following targeted therapy. Results: The study included 16 patients (12 males, 4 females; median age 32.5 years, range 3-60 years). Diarrhea occurred a median of 3.93 months post-transplant (range 1.63-10.40 months). Stool cultures were negative except for one case with Candida. One patient tested positive for Clostridium difficile antigen. Endoscopy revealed mucosal congestion, edema, erosion, and bleeding, with focal inflammation on pathology. mNGS detected pathogens in 87.5% (14/16) of cases, including mixed infections in 78.5% (11/14). Common pathogens were Klebsiella pneumoniae, Enterococcus faecium, Escherichia coli, Rhizopus microsporus, EBV, and CMV. Targeted treatment adjustments led to symptom improvement in 87.5% of patients. Conclusion: Allo-HSCT patients are prone to infectious diarrhea due to immunosuppression. Molecular analysis of endoscopic biopsy tissues using mNGS can accurately identify pathogens, guide targeted therapy, and improve clinical outcomes.},
}

Humans
*Hematopoietic Stem Cell Transplantation/adverse effects
Male
Female
Adult
Middle Aged
*High-Throughput Nucleotide Sequencing
Child, Preschool
Adolescent
*Diarrhea/diagnosis/etiology/microbiology
Child
*Metagenomics
Young Adult
Transplantation, Haploidentical/adverse effects

@article {pmid41407286,
year = {2025},
author = {Herbst, R and Ibrahim, A and Hübner, A and Knüpfer, U and Regestein, L and Wiedemann, C and Hellmich, UA and Warinner, C and Stallforth, P},
title = {Actifensin Evolution in the Human Oral Cavity over the Past 100,000 Years.},
journal = {Journal of the American Chemical Society},
volume = {},
number = {},
pages = {},
doi = {10.1021/jacs.5c14335},
pmid = {41407286},
issn = {1520-5126},
abstract = {Bacterially produced antimicrobial peptides (AMPs), or bacteriocins, play key roles in shaping microbial communities via interspecies competition. Unlike the more temporally dynamic gut microbiome, the oral microbiome exhibits long-term stability and is preserved into deep time in dental calculus, enabling evolutionary analysis across time. Here, we combine metagenomics, structural modeling, and experimental validation to investigate AMP diversity in ancient and modern dental biofilms from humans, Neanderthals, and nonhuman primates spanning 100,000 years. Using our newly developed platform, AMPcombi, we uncover evolutionary trajectories of bacteriocins and elucidate their ecological functions. Among these, we identify a conserved family of Actinomyces-derived defensin-like peptides, termed actifensins, present across all time periods. Phylogenetic, structural, and functional analyses revealed shared ancestry and adaptive diversification between ancient (paleo-) and modern actifensins, with evidence of positive selection and maintained antimicrobial activity. Our findings position the oral microbiome as a valuable reservoir for natural product discovery. In the face of rising antimicrobial resistance, evolutionary insights into AMP function open a door to next-generation therapeutics. AMPcombi streamlines this process, linking ancient biomolecules with biotechnology.},
}

@article {pmid41407095,
year = {2025},
author = {Chen, M and Cai, Y and Shi, Q and Xu, A and Tang, T and Qian, J and Yu, S and Zhu, H and Xu, J and Li, J and Shen, B},
title = {Antimicrobial management and infection outcomes of Elizabethkingia spp. co-detection in lower respiratory tract: a real-world mNGS-based observational study.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108316},
doi = {10.1016/j.ijid.2025.108316},
pmid = {41407095},
issn = {1878-3511},
abstract = {OBJECTIVES: Elizabethkingia spp. infections pose a major threat to human health with high mortality. This study aimed to further understand its detection status, co-detection patterns, pathogenicity, and antimicrobial resistance in lower respiratory tract infections (LRTI) through metagenomic high throughput sequencing (mNGS)-based real-world research.

DESIGN AND METHODS: We retrospectively analyzed 105 LRTI patients positive for Elizabethkingia spp. by mNGS from July 2021 to February 2025. Pathogen profiles, antimicrobial management, and outcomes were reviewed via electronic medical records.

RESULTS: mNGS detection rates for Elizabethkingia spp. in respiratory samples were 21.5% in General Intensive Care Unit (GICU) and 11.1% in Emergency Intensive Care Unit (EICU), more sensitive than culture. Polymicrobial co-detection was ubiquitous (99%), indicating a diverse polymicrobial community. Clinical isolates exhibited variable susceptibility (74%-100%) to trimethoprim-sulfamethoxazole, ciprofloxacin, levofloxacin, doxycycline, minocycline, rifampicin, and azithromycin. Patients receiving targeted antimicrobial therapy based on mNGS indicators (Stringent Map Read Number (SMRN) rank ≤2, normalized SMRN (nSMRN) ≥1000, or SMRN percentage ≥25%) had significantly higher effective treatment rates.

CONCLUSIONS: Elizabethkingia spp. detection rates in ICU respiratory samples are high, frequently complicated by polymicrobial co-detection. Lack of targeted therapy is a key factor in treatment failure. mNGS-derived indicators and local susceptibility databases are essential for guiding effective intervention.},
}

@article {pmid41407051,
year = {2025},
author = {Yuan, Z and Zeng, W and Zhan, M and Peng, Y},
title = {Static magnetic field enhances respiratory dissimilatory nitrate reduction to ammonium over denitrification in sulfide-based autotrophic systems.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133796},
doi = {10.1016/j.biortech.2025.133796},
pmid = {41407051},
issn = {1873-2976},
abstract = {Dissimilatory nitrate reduction to ammonium (DNRA) represents a sustainable strategy for nitrogen resource recovery from wastewater, yet selectively enhancing DNRA over denitrification in sulfide-based autotrophic systems remains challenging. This study investigates the impact of static magnetic field (SMF, 0-100mT) on nitrate reduction pathways in sulfide-rich wastewater. SMF elevated DNRA efficiency to 41.8 % with an influent sulfide concentration of 200 mgS/L (S/N ratio of 3:1) under 30 mT, supported by nrfA upregulation (7.6 × 10[10] vs. 4.0 × 10[7] copies/g SS in control). [15]N isotope labeling and enhanced direct extracellular electron transfer via cytochrome c and conductive pili confirmed that SMF preferentially drove nitrate flux toward DNRA. Metagenomics revealed that SMF enriched DNRA taxa (Aeromonas, Shewanella) and enhanced their synergy with Thiobacillus, improving metabolic flexibility. This work unveils microbial competition mechanisms between denitrification and DNRA in sulfide-based systems and proposes an innovative SMF-assisted ammonium recovery approach, advancing the understanding of sulfide-based nitrogen removal technologies.},
}

@article {pmid41406967,
year = {2025},
author = {Liu, J and Glukhov, E and De Clerck, O and Gerwick, WH and Donia, MS},
title = {Environmentally controlled production of pagoamide A in marine macroalgae by an intracellular bacterial symbiont.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.11.023},
pmid = {41406967},
issn = {1879-0445},
abstract = {Marine algae are a rich source of diverse molecules, most of which are thought to be produced by the alga itself. We recently reported the discovery of pagoamide A from a cultured marine macroalga collected from American Samoa. Here, we found that the production of pagoamide A is conditional upon environmental temperature. Using comparative metagenomic, metatranscriptomic, and metabolomic analyses of algal cultures, we identified a nonribosomal peptide synthetase biosynthetic gene cluster (NRPS BGC) in the algal microbiome that varies in abundance between producing and non-producing conditions and whose architecture and biosynthetic logic match pagoamide A (named pag). pag belongs to a bacterium that we named "Candidatus Bryopsidiphilus pagoamidifaciens BP1," a new genus in the family Amoebophilaceae and a relative of amoeba, arthropod, and nematode endosymbionts. Ca. B. pagoamidifaciens lives intracellularly in its Bryopsis sp. algal host, harbors a reduced genome (1.7 Mbp), has lost most genes essential for free living, and is enriched in genes containing eukaryotic domains. By quantitatively monitoring longitudinal algal cultures under varying conditions for 9 weeks, we found that the abundance of both Ca. B. pagoamidifaciens and pagoamide A undergoes dramatic fluctuations in response to temperature changes. Finally, we discovered three additional strains of Ca. B. pagoamidifaciens that vary in their NRPS BGCs and eukaryotic domain-containing genes from algal samples of diverse geographical origins. Our findings suggest that symbiont-derived production of algal molecules is more common than previously anticipated and provide a unique case of environmental control of both symbiont and chemical levels in marine algae.},
}