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

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

@article {pmid41360290,
year = {2025},
author = {Obermeier, PE and Alchikh, M and Ma, X and Reiche, J and Schweiger, B and Rath, BA},
title = {Digital severity scoring and viral metagenomics: A feasibility study on integrated diagnosis of pediatric influenza-like illness.},
journal = {Infectious diseases now},
volume = {},
number = {},
pages = {105223},
doi = {10.1016/j.idnow.2025.105223},
pmid = {41360290},
issn = {2666-9919},
abstract = {INTRODUCTION: Metagenomic next-generation sequencing (mNGS) holds promise for identifying diverse pathogens in complex cases of influenza-like illness (ILI). Interpreting results requires comprehensive clinical context. We aimed to explore the feasibility of an integrated diagnostic approach by linking shotgun viral mNGS with standardized clinical data for unbiased ascertainment and hypothesis generation in pediatric ILI patients.

PATIENTS AND METHODS: We studied a cohort of 6,073 pediatric ILI patients (mean age 3.1 years, range 0-18.8 years), assessed using the VIVI ScoreApp for immediate computation of Disease Severity and Risk Factor Scores. Nasopharyngeal samples were tested for nine respiratory viruses by PCR. In a nested pilot feasibility study, we linked the clinical dataset of 100 ILI patients with neurological complications (mean age 3.9 years, range 0-17.8 years) to additional viral mNGS. PCR and mNGS were compared by agreement rates and Cohen's κ for inter-method reliability.

RESULTS: In the pilot feasibility study, the mean VIVI Disease Severity Score was above the cohort average (>67th percentile, p < 0.0001), with 'age < 2 years' as the most prevalent risk factor (n = 44/100). mNGS identified 15 viruses, expanding the range of viral identifications by six viruses compared to PCR. Linking VIVI Scores with mNGS-discovered viruses suggested high disease severity. Sensitivity of mNGS was relatively low; overall agreement with PCR was 77-98 % and overall reliability was 'moderate' (κ scores of 0.1-0.85).

CONCLUSIONS: Digital surveillance tools can successfully integrate with mNGS to capture complex clinical patterns and generate data-driven hypotheses. Large-scale investigation and technical refinement are warranted.},
}

@article {pmid41359546,
year = {2025},
author = {Provatas, K and Mouratidis, I and Georgakopoulos-Soares, I},
title = {KmerCrypt: private k-mer search with homomorphic encryption.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {6},
pages = {},
doi = {10.1093/bib/bbaf648},
pmid = {41359546},
issn = {1477-4054},
support = {//University of Texas at Austin/ ; },
mesh = {*Computer Security ; Humans ; Cloud Computing ; *Software ; Algorithms ; *Genomics/methods ; Databases, Genetic ; },
abstract = {Outsourcing the storage and analysis of genomic data to third-party servers is often necessary due to the scale of modern datasets, but it introduces significant privacy challenges that must be addressed to ensure secure handling. K-mer-based analyses offer broad applications across genomics research, clinical diagnostics, pathogen surveillance, and metagenomic classification, though implementation requires careful ethical and technical considerations, particularly when processing human genomic data in clinical settings. We present a novel protocol utilizing homomorphic encryption that enables a client to store a fully encrypted version of a genome on an untrusted server and perform private k-mer searches. The protocol ensures the server never gains access to the client's non-encrypted genome sequence, nor does it learn the content of any k-mer query. After a one-time client-side encryption of the genome, the server performs all computations on ciphertext, returning only encrypted results that can be decrypted solely by the data owner. This framework transforms an honest but curious cloud server into a secure storage and computation system, enabling practical and confidential querying of encrypted, client-owned genomic data. The system supports exact k-mer searches on genomic data, as well as position weight matrix searches. Finally, we provide KmerCrypt, a private k-mer search toolkit that implements this protocol, offering researchers an efficient and secure solution for querying encrypted genomic datasets without compromising privacy.},
}

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

@article {pmid41359366,
year = {2025},
author = {Cheah, S and Burke, J and Bruinsma, FJ and Evans, M and Tsimiklis, H and Hodge, AM and Lynch, BM and Giles, GG and Sinha, R and Southey, MC and Milne, RL},
title = {Faecal sample collection for gut microbiome research in a prospective cohort: a pilot study within the Australian Breakthrough Cancer Study.},
journal = {Cancer research communications},
volume = {},
number = {},
pages = {},
doi = {10.1158/2767-9764.CRC-25-0445},
pmid = {41359366},
issn = {2767-9764},
abstract = {Large prospective analyses of human gut microbiome profiles are needed to elucidate the role of microbiome variation in the development of disease. We conducted a pilot study to assess the feasibility of home faecal sample collection within a cohort study. A subset of cohort study participants was randomly selected and randomised into four groups defined by faecal sample collection method and questionnaire components. Of 1,093 invited participants, 610 (56%) opted in and, of those, 88% returned a sample. Of those asked to provide a faecal sample via faecal occult blood test card (FOBT) and complete a short "day of sample" questionnaire (dosQ), 49% returned a sample. Sample return was comparable for participants additionally asked to provide a sample via ethanol tube (51%), complete a food frequency questionnaire (48%), or complete both additional activities (49%). Whole genome sequencing and metagenomic analysis on paired FOBT and ethanol samples showed that both collection methods provided sufficient quality and quantity of DNA for downstream metagenomic analyses and displayed highly concordant microbiome profiles. Home faecal sample collection for microbiome analysis is feasible in a large prospective cohort. Including additional components did not reduce the likelihood of participants completing all requested items.},
}

@article {pmid41359148,
year = {2025},
author = {Rao, PM and Radha, P},
title = {Pioneering approaches to plastic biodegradation and upcycling for sustainability.},
journal = {Environmental monitoring and assessment},
volume = {198},
number = {1},
pages = {23},
pmid = {41359148},
issn = {1573-2959},
mesh = {*Biodegradation, Environmental ; *Plastics/metabolism/analysis ; Waste Management/methods ; },
abstract = {Plastic pollution has become one of the most significant threats to the environment and human health of the twenty-first century, with more than 300 million tons of waste generated annually, and conventional disposal methods are inadequate. To address this challenge, recent research has increasingly shifted toward biodegradation and upcycling as sustainable alternatives. Microbial degradation of synthetic plastics has shown advancement. This includes the introduction of novel strains like Aspergillus niger MG654699 for the 3.6% and 5% degradation of polyethylene terephthalate and polystyrene, respectively. Also, Streptomyces sp., Methylobacterium, Arthrobacter, and Sphingomonas have been studied to be responsible for mulch film degradation. Advances in metagenomics have further revealed the complexity of microbial consortia for driving these processes, whereas kinetic modeling has provided insights into degradation rates and conditions. Building on this foundation, artificial intelligence and machine learning are now expediting enzyme discovery, optimizing degradation pathways, and enabling intelligent waste management systems. Similarly, biosensors based on Vibrio fischeri and Escherichia coli improve monitoring by detecting plastic monomers. Beyond degradation, the integration of microbial and chemical processes has enabled the upcycling of plastic monomers into value-added products such as polyhydroxyalkanoates, vanillin, bacterial nanocellulose, fuels, and biochemicals, promoting a circular bioeconomy. These advances highlight a paradigm shift from waste accumulation to resource recovery, underscoring the potential of biotechnology and engineering innovations to transform plastic management. The review concludes by highlighting the challenges of scalability, environmental variability, and policy support while positioning biodegradation and upcycling as integrated strategies for a sustainable and resilient future.},
}

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

@article {pmid41358839,
year = {2025},
author = {Li, Y and Fu, X and Sun, F and Dong, M and Wang, Y and Wang, Y and Liu, Q},
title = {Metabolomic and metagenomic insights into WFBG-mediated regulation of gut microbiota and metabolism in broilers.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0189025},
doi = {10.1128/aem.01890-25},
pmid = {41358839},
issn = {1098-5336},
abstract = {UNLABELLED: The steady state of gut microbiota is a key factor in regulating the growth of broilers. The regulatory role of wet-fermented brewer's grain (WFBG) in broiler gut development and microbiota is still elusive. In this study, non-targeted metabolomics and 16S rRNA sequencing analysis were used to investigate the effects of WFBG supplementation on serum metabolites and gut microbiota in 42-day-old broilers. Serum metabolomic analysis identified 546 differentially expressed metabolites (DEMs), with GO and KEGG enrichment analyses showing that specific DEMs were enriched in intestinal development-related pathways, including phenylalanine, tyrosine, tryptophan biosynthesis, and alpha-linolenic acid metabolism. 16S rRNA sequencing analysis showed significant intergroup differences in the relative abundances of Ligilactobacillus, Olsenella, Erysipelatoclostridium, and Blautia at the genus level in broiler gut microbiota between the control and WFBG groups. Integrative analysis of 16S rRNA sequencing and non-targeted metabolomics demonstrated that bacterial genera, including Streptococcus and Proteus, were positively correlated with N6,N6-dimethyllysine and quercetin but negatively associated with 18 DEMs, such as 4-methylbenzenesulfonic acid and deoxycholic acid derivatives. Furthermore, we identified potential biomarkers associated with intestinal development induced by 20% WFBG supplementation. Our findings suggest that the maximum recommended inclusion level of WFBG in broiler feed should not exceed 20%. This study provides novel insights into the molecular mechanisms underlying fiber utilization and intestinal maturation in broilers.

IMPORTANCE: This study investigated the regulatory mechanism of wet-fermented brewer's grain (WFBG) on gut development and microbiota in commercial broilers. Through integrated 16S rRNA sequencing and non-targeted metabolomic analysis, the study not only identified differential gut microbiota, serum metabolites, as well as their correlations, but also discovered potential biomarkers associated with intestinal development induced by 20% WFBG and clarified the maximum recommended inclusion level of WFBG (≤20%). This not only filled the gap in the molecular mechanism underlying WFBG-mediated regulation of fiber utilization and intestinal maturation in broilers but also provided a theoretical basis and practical guidance for the resource utilization of agricultural by-products, precision feeding of broilers, and intestinal health monitoring.},
}

@article {pmid41358761,
year = {2025},
author = {Xu, S and Ding, Y and Li, M and Lin, Y and Wang, X and Liu, N and Zhang, L and Xu, T},
title = {Metagenomic next-generation sequencing diagnoses Talaromyces marneffei infections: case report and review.},
journal = {Journal of infection in developing countries},
volume = {19},
number = {11},
pages = {1727-1736},
doi = {10.3855/jidc.20367},
pmid = {41358761},
issn = {1972-2680},
mesh = {Humans ; *Talaromyces/genetics/isolation & purification ; Male ; *High-Throughput Nucleotide Sequencing/methods ; *Mycoses/diagnosis/drug therapy/microbiology ; *Metagenomics/methods ; Antifungal Agents/therapeutic use ; Amphotericin B/therapeutic use ; Adult ; China ; },
abstract = {INTRODUCTION: Talaromyces marneffei is a pathogenic dimorphic fungus known for causing severe opportunistic infections that can be life-threatening. The fungus is most commonly found in Southeast Asia and southern China.

CASE REPORT: This case report describes the case of a young male patient infected with T. marneffei who was neither human immunodeficiency virus (HIV)-positive nor possessed anti-IFN-γ antibodies, and who resided outside the typical endemic regions. The patient developed cough and sputum three months after the removal of the left arm fracture fixator, and was initially misdiagnosed with tuberculosis; however, the response to anti-tuberculosis treatment was not good. The diagnosis of subsequent recurrence was unknown. The condition recurred during the illness, and he was ultimately diagnosed with talaromycosis via metagenomic next-generation sequencing (mNGS). The patient's condition improved after appropriate treatment with liposomal amphotericin B.

CONCLUSIONS: Previous studies have found that T. marneffei infections are concentrated in patients with acquired immunodeficiency syndrome due to HIV infection, and in anti-IFN-γ antibody-positive patients. However, infections are increasing in individuals who are not immunosuppressed and are often misdiagnosed and underdiagnosed during the initial course of the disease. Therefore, clinicians should be aware that mNGS is an effective technique for detecting T. marneffei infection in non-endemic areas where they encounter non-HIV infected patients. This case report aims to raise the awareness of physicians regarding this rare disease in non-endemic areas and non-HIV patients.},
}

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

@article {pmid41358744,
year = {2025},
author = {Li, Y and Lin, W and Li, Z and Tran, T and Metcalf, BJ and Velusamy, S and Gross, A and Snippes Vagnone, P and Lynfield, R and Beall, B and McGee, L and Chochua, S},
title = {Whole-genome sequencing-based pathogen characterization for streptococcal infection directly from positive blood culture samples.},
journal = {Journal of clinical microbiology},
volume = {},
number = {},
pages = {e0112625},
doi = {10.1128/jcm.01126-25},
pmid = {41358744},
issn = {1098-660X},
abstract = {Clinical laboratories are increasingly using diagnostic tests directly on positive blood cultures, which may lead to fewer attempts to recover bacterial isolates. Consequently, public health laboratories can benefit from assays that directly process blood culture samples without requiring submission of clinical isolates to determine additional pathogen features not identified by clinical tests, such as vaccine serotype and bacterial genomic relatedness, for surveillance and outbreak response purposes. In partnership with the Minnesota Active Bacterial Core surveillance (ABCs) site, we identified blood culture samples positive for ABCs streptococcal pathogens and characterized them by a direct whole-genome sequencing from blood culture (dWGS) assay. The dWGS results were compared with the results of a reference method (WGS of isolates from the same cultures) to evaluate concordance in pathogen features and genome assemblies. Of the 97 eligible blood culture samples, 83 (86%) passed dWGS quality control criteria and were subjected to a total of 655 dWGS-based tests, which yielded 651 (99.3%) evaluable results. The percent agreement with reference results was 100% (83/83) for M protein gene (emm)/capsular types and 100% (81/81) for multilocus sequencing types. For genotypic antimicrobial susceptibility testing prediction, the percent prediction agreement was 100% (487/487), false resistant prediction rate was 0% (0/417), and the false susceptible prediction rate was 0% (0/66). Assemblies of pathogen genomes from the same patient differed by 1.08 ± 1.68 (mean ± SD) sites per genome. The dWGS assay can extract high-quality, important streptococcal strain characteristics directly from positive blood culture samples to support evolving public health needs.IMPORTANCEWhole-genome sequencing (WGS) technologies have emerged as a transformative toolkit used by public health microbiology laboratories to detect and characterize pathogens. The surveillance of bacterial diseases often relies on clinical laboratories to submit pathogen isolates to regional or national public health laboratories, which have the capacity to routinely conduct WGS-based strain characterization. Clinical laboratories are increasingly using diagnostic tests directly on positive blood cultures, which may lead to fewer attempts to recover bacterial isolates. The study evaluated a direct whole-genome sequencing from blood culture (dWGS) assay that directly processes blood culture samples. The dWGS assay recovered high quality, important streptococcal strain characteristics, including vaccine serotypes and whole-genome assemblies, without requiring submission of clinical isolates. Thus, the dWGS assay represents a promising tool for addressing the evolving needs of public health laboratories in the metagenomics era.},
}

@article {pmid41358671,
year = {2025},
author = {Ngwese, MM and Adegbite, BR and Zinsou, JF and Fitzstevens, JL and Schmidt, VT and Moure, PAN and Maloum, MN and Tyakht, AV and Huus, KE and Youngblut, ND and Kremsner, PG and Adegnika, AA and Ley, RE},
title = {Infection with gut parasites correlates with gut microbiome diversity across human populations in Africa.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2587966},
doi = {10.1080/19490976.2025.2587966},
pmid = {41358671},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Feces/parasitology/microbiology ; Animals ; Gabon/epidemiology ; Female ; Male ; Child ; *Helminthiasis/parasitology/epidemiology/microbiology ; Metagenomics ; *Helminths/isolation & purification/classification/genetics ; Child, Preschool ; Rural Population ; Bacteria/classification/genetics/isolation & purification ; Metagenome ; Ascaris lumbricoides/isolation & purification ; Strongyloides stercoralis/isolation & purification ; Necator americanus/isolation & purification ; Trichuris/isolation & purification ; Biodiversity ; },
abstract = {Soil-transmitted helminths (STH) are common in (sub)tropical regions and primarily affect impoverished populations. These parasites reside in the gut, where they interact with both the microbiota and host immunity. Clinical STH detection is laborious and often not performed within the context of gut microbiome studies. Here, we present a proof-of-concept study assessing whether fecal metagenome data could be used to assess STH infection, and to relate STH infection to microbiome features. We leveraged 310 gut metagenomes obtained from mother-child pairs in two different locations in Gabon: one rural and one semi-urban, and assessed the presence of four STH species (Ascaris lumbricoides, Strongyloides stercoralis, Trichuris trichiura, and Necator americanus) using qPCR. Sequence data were used to characterize the microbiomes and to detect these parasites. Metagenomic read mapping and genome coverage metrics closely matched qPCR detection patterns. Within-location analyses revealed that parasite species richness was associated with microbiome diversity and taxonomic composition, with the strongest associations observed in children from the rural site. Applying this approach to published data from five additional African cohorts identified context-specific parasite-microbiome associations, as well as a modest but reproducible association between microbiome alpha diversity and parasite infection. These findings highlight the potential of shotgun metagenomics for concurrent parasite detection and microbiome profiling across diverse geographic and demographic contexts.},
}

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

@article {pmid41358536,
year = {2025},
author = {Amornloetwattana, R and Eiamthong, B and Meesawat, P and Bunkum, P and Royer, B and Zeballos, N and Valenzuela-Ortega, M and Robinson, RC and Wallace, S and Uttamapinant, C},
title = {Cellular Upcycling of Polyethylene Terephthalate (PET) With an Engineered Human Saliva Metagenomic PET Hydrolase.},
journal = {ChemSusChem},
volume = {},
number = {},
pages = {e202502560},
doi = {10.1002/cssc.202502560},
pmid = {41358536},
issn = {1864-564X},
support = {B42G670039//National Science Research and Innovation Fund (NSRF) via the Program Management Unit for Human Resources & Institutional Development, Research and Innovation/ ; MR/S033882/1//UK Research and Innovation/ ; BB/Y007972/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
abstract = {Recent advances in biocatalytic recycling of polyethylene terephthalate (PET) using PET hydrolase enzymes have sparked interest in integrating PET degradation capabilities into living systems. Although cell-based strategies are limited by the mesophilic temperature constraints of microbial hosts, they offer a unique opportunity to couple PET depolymerization with biological upcycling into value-added chemicals. Here, a comprehensive approach for the cellular degradation and valorization of PET is reported. The crystal structure of MG8, a PET hydrolase identified from the human saliva metagenome is solved, and molecular dynamics simulations are used to pinpoint loop regions for targeted mutagenesis aimed at enhancing activity under moderate temperatures. Over 1000 MG8 loop variants are evaluated with a high-throughput mass spectrometric screening platform. Two catalytically improved mutants-MG8[G127Y/F250A] and MG8[N125S/G127Y/F250A]-exhibit significantly enhanced PET hydrolysis at 37°C. To enable whole-cell PET valorization, a two-strain Escherichia coli system called PETCAT is constructed: one strain is engineered to secrete MG8[G127Y/F250A] for PET degradation, and the other harbors a synthetic pathway comprising seven heterologous genes for the conversion of terephthalic acid (TPA) into catechol, a versatile intermediate used in pharmaceuticals and fragrances. This study establishes a modular, one-pot microbial platform for PET recycling and upcycling under physiologically relevant conditions.},
}

@article {pmid41358162,
year = {2025},
author = {Nicolas-Asselineau, L and Speth, DR and Zeller, LM and Woodcroft, BJ and Singleton, CM and Liu, L and Dueholm, MKD and Milucka, J},
title = {Occurrence and temporal dynamics of denitrifying protist endosymbionts in the wastewater microbiome.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf209},
pmid = {41358162},
issn = {2730-6151},
abstract = {Effective wastewater treatment is of critical importance for preserving public health and protecting natural environments. Key processes in wastewater treatment, such as denitrification, are performed by a diverse community of prokaryotic and eukaryotic microbes. However, the diversity of the microbiome and the potential role of the different microbial taxa in some wastewater treatment plant setups is not fully understood. We aimed to investigate the presence and diversity of denitrifying bacteria of the candidate family Azoamicaceae that form obligate symbioses with protists in wastewater treatment plants. Our analyses showed that denitrifying endosymbionts belonging to the Ca. Azoamicus genus are present in 20%-50% of wastewater treatment plants worldwide. Time-resolved amplicon data from four Danish WWTPs showed high temporal fluctuations in the abundance and composition of the denitrifying endosymbiont community. Twelve high-quality metagenome-assembled genomes of denitrifying endosymbionts, four of which were circular, were recovered. Genome annotation showed that a newly described, globally widespread species, Ca. Azoamicus parvus, lacked a nitrous oxide reductase, suggesting that its denitrification pathway is incomplete. This observation further expands the diversity of metabolic potentials found in denitrifying endosymbionts and indicates a possible involvement of microbial eukaryote holobionts in wastewater ecosystem dynamics of nitrogen removal and greenhouse gas production.},
}

@article {pmid41357797,
year = {2025},
author = {Yang, C and Li, M and Yang, S and Pan, J and Ding, Y and Yang, J},
title = {Channel selection of metagenomic next-generation sequencing in infants pathogen detection: a multicenter cross-sectional study.},
journal = {Frontiers in pediatrics},
volume = {13},
number = {},
pages = {1632123},
pmid = {41357797},
issn = {2296-2360},
abstract = {In the neonatal period, infectious diseases associated with high morbidity (e.g., neonatal sepsis and meningitis) are preliminarily assessed using indicators like C-reactive protein (CRP) and procalcitonin, but definitive diagnosis relies on pathogen detection through methods such as blood culture, which is time-consuming and has low sensitivity. To improve diagnostic efficiency, metagenomic next-generation sequencing (mNGS) is increasingly utilized, offering three testing modalities: DNA-only, RNA-only, and combined DNA+RNA channels. This retrospective study analyzed 894 clinical samples (peripheral blood, sputum, bronchoalveolar lavage fluid) to compare detection rates across channels. The overall mNGS positivity rate was 51.9% (464/894), with no significant differences among DNA-only (50.8%), RNA-only (55.7%), and combined channels (49.6%) (p > 0.05). Notably, bronchoalveolar lavage fluid samples exhibited the highest positivity rate (84.57%, 148/175), reaching 97.33% (73/75) with dual-channel testing. Sputum samples showed a 53.7% positivity rate (87/172), increasing to 82.35% (14/17) with dual-channel detection. Conversely, peripheral blood had an overall positivity rate of 43.14% (132/306), with the DNA-only channel outperforming RNA-only and dual channels (45.34% 5s. 43.00% and 34.21%). These findings underscore the importance of channel selection based on sample type to optimize diagnostic accuracy and cost-effectiveness.},
}

@article {pmid41357776,
year = {2025},
author = {Yoshino, N and Matsumoto, K and Ishikawa, M and Nishio, J and Matsuzawa, T},
title = {Identity of Carbohydrate-Responsive Genes in a Cultured Microbial Community Using Metagenomic and Metatranscriptomic Approaches.},
journal = {Journal of applied glycoscience},
volume = {72},
number = {4},
pages = {7204201},
pmid = {41357776},
issn = {1880-7291},
abstract = {Metagenomics can be used to obtain sequence information on putative genes in a microbial community. However, it is difficult to identify genes with specific functions among the numerous predicted genes. In this study, we attempted to identify genes induced in cultured microbes by the addition of saccharides using metagenomic and metatranscriptomic analyses. A mixture of arabinoxylan and its derived oligosaccharides was used as the inducer in this study. Some genes were highly induced in the presence of additive saccharides and formed gene clusters for the utilization of additive saccharides, suggesting that metatranscriptomic and metagenomic analyses are useful for analyzing carbohydrate-responsive genes in microbial communities and screening novel carbohydrate-active enzymes.},
}

@article {pmid41357502,
year = {2025},
author = {He, Y and Liang, L and Wei, S},
title = {Giant intracranial Brucella abscess after head trauma: a Case Report of neurobrucellosis in an urban elderly male without exposure history.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1676548},
pmid = {41357502},
issn = {2296-858X},
abstract = {Giant intracranial Brucella abscess is a severe and rare central nervous system infection whose pathogenesis remains incompletely understood. We detail the case of a 75-years-old urban male without Brucella exposure history who presented with fever and headache. Initial attribution of cephalgia to head trauma delayed diagnosis and treatment. Magnetic resonance imaging, metagenomic next-generation sequencing, and cerebrospinal fluid culture confirmed rapid development of a giant Brucella abscess (31 mm × 58 mm) within 2 weeks after head trauma. Head trauma may be potentially associated with the formation of Brucella brain abscess. Consequently, brucellosis patients with recent head trauma may warrant vigilant monitoring for this rare complication. It is imperative to avoid the premature attribution of headache to head trauma in such patients, as such an oversight risks delaying the diagnosis and management of a Brucella brain abscess.},
}

@article {pmid41357037,
year = {2025},
author = {Syromyatnikov, MY and Burakova, IY and Smirnova, YD and Morozova, PD and Pogorelova, SV and Chirkin, EA and Tolkacheva, AA},
title = {Study of Akkermansia muciniphila Effect on the Gut Microbiome of Mice Under LPS-Induced Systemic Inflammation.},
journal = {International journal of inflammation},
volume = {2025},
number = {},
pages = {8695182},
pmid = {41357037},
issn = {2090-8040},
abstract = {Probiotics are strains of living bacteria and yeast that play an important role in regulating the gut microbiota and enhancing host immunity. In the last decade, the bacterial species Akkermansia muciniphila has attracted great interest due to its possible probiotic properties, which play an important role in human health. However, the mechanisms of action of A. muciniphila are still poorly understood. The effect of the A. muciniphila on the intestinal microbiome of model animals with systemic inflammation induced by lipopolysaccharide (LPS) is unexplored. This study aims to investigate the impact of A. muciniphila on the microbiological composition of the mouse gut under LPS-induced systemic inflammation using high-throughput sequencing. The study used a new generation sequencing method aimed at genome-wide sequencing of microorganisms, which makes it possible to study changes in the composition of the microbiome at the bacterial species level, as well as to identify the genes of the metabolic pathways of intestinal bacteria in the studied mice. Our analysis revealed statistically significant differences across all studied groups, with a notable predominance of members from the families Muribaculaceae, Rikenellaceae, and Oscillospiraceae. Consumption of A. muciniphila increased the alpha diversity of gut bacteria (Shannon index) in the context of induced inflammation. Evaluation of the effect of LPS and A. muciniphila on metabolic pathways showed statistically significant differences for the pathways of synthesis and degradation of amino acids, transforming folic acid, and synthesis of sugars. Genetic analysis showed that the probiotic bacterium A. muciniphila reduced the degree of negative effects of LPS on the mouse gut microbiome under systemic inflammation.},
}

@article {pmid41356787,
year = {2025},
author = {Chatterjee, T and Roy, M and Almoujahed, MO and Ahmad, S},
title = {Aspergillus calidoustus: An Emerging Cause of Invasive Aspergillosis and the Role of Metagenomic Next-Generation Sequencing Test in Its Diagnosis.},
journal = {Case reports in infectious diseases},
volume = {2025},
number = {},
pages = {3221057},
pmid = {41356787},
issn = {2090-6625},
abstract = {Transplant recipients have a high risk of infection with opportunistic pathogens. The type, dose, and duration of immunosuppression and use of prior broad-spectrum antimicrobials contribute to overall risk of infections. Aspergillosis is a known opportunistic infection that can occur as mid or late infection after visceral transplant. Aspergillus fumigatus is the commonly isolated species, but with the use of prophylactic broad-spectrum antifungals, other species such as Aspergillus calidoustus are emerging. We report a case of invasive sinusitis and brain mass due to this species of Aspergillus that was identified using next-generation sequencing (NGS). Use of NGS early in clinical presentation may help in effective management of opportunistic infections in immunocompromised hosts.},
}

@article {pmid41356481,
year = {2025},
author = {Rao, AV and Ghare, SS and Gautam, V and Hoffman, KL and Petrosino, J and So-Armah, K and Samet, JH and Patts, GJ and Cheng, DM and Blokhina, E and Krupitsky, EM and Lioznov, D and Zvartau, E and McClain, CJ and Tindle, H and Freiberg, MS and Barve, SS},
title = {Sex differences in beneficial and pathogenic bacteria in People With HIV (PWH) with a history of heavy alcohol drinking.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1632949},
pmid = {41356481},
issn = {1664-302X},
abstract = {BACKGROUND: HIV-1 infection and hazardous levels of alcohol consumption have been independently linked to gut dysbiosis affecting beneficial butyrate-producing bacteria. However, sex-based differences in the composition and function of gut microbiome of People With HIV (PWH) with a history of heavy alcohol drinking remain undetermined, which is the focus of this study.

METHODS: Cross-sectional study examining structural and functional features of the gut microbiome in PWH between men and women with a history of hazardous alcohol drinking recruited at St. Petersburg, Russia. 16S rDNA sequencing information was used for metataxonomic, Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) and Linear Discriminant Analysis Effect Size (LEfSe) analyses. Group-wise comparisons were done using Mann-Whitney U-test. Further, linear and logistic regression models were used to evaluate the association between sex and measures of gut microbial dysbiosis and Firmicutes/Bacteroidota (F/B) ratio, respectively. Data were adjusted for confounding covariates particularly, HIV-viral load, Anti-retroviral Therapy (ART) and alcohol usage.

RESULTS: Metataxonomic analysis demonstrated that women depicted significantly higher microbial diversity (Operational Taxonomic Units, OTUs and Shannon Index), higher percent relative abundance (%RA) of Firmicutes, lower %RA of Bacteroidota and higher F/B ratio. Importantly, logistic regression revealed that women had twice the odds of having F/B ratio > 1. Notably, women demonstrated significantly higher %RA of butyrate-producing bacterial families, i.e., Lachnospiraceae, Oscillospiraceae, Rikenellaceae and Marinifilaceae and genera. Correspondingly, significantly greater expression of bacterial genes involved in butyrate synthesis in women was demonstrated by PICRUSt2 analysis. Additionally, women depicted lower %RA of pathobiont, Prevotellaceae particularly, Prevotella_9 genus.

CONCLUSION: Overall, we observed significant sex-based differences in the relative abundances of beneficial bacterial communities such as butyrate producers and potential pathogenic Prevotella community in the gut microbiome of PWH with a history of heavy alcohol consumption. The observed sex-based differences are clinically relevant and could inform therapeutic strategies with evidence-based probiotics.},
}

@article {pmid41356476,
year = {2025},
author = {Chen, Q and Guan, J and Yang, L and Lv, J and Gui, G and Xu, J and Yang, Z and Wang, X and Sun, B},
title = {Exploring the characteristics of gut microbiota in the development and progression of early-stage colorectal cancer based on metagenomic sequencing.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1658160},
pmid = {41356476},
issn = {1664-302X},
abstract = {INTRODUCTION: Colorectal cancer (CRC), a leading cause of cancer-related morbidity and mortality worldwide, often presents asymptomatically, resulting in late diagnosis. Accumulating evidence links gut microbiota dysbiosis to CRC initiation and progression.

OBJECTIVE: This study aimed to investigate the differences in gut microbiota composition and diversity among healthy controls (HC) and patients with colorectal lesions-including common colorectal polyps, small colorectal adenomas (SCRA), large colorectal adenomas (LCRA), and intramucosal carcinoma (IMC)-to identify bacterial species associated with disease progression and provide novel insights into the diagnosis and treatment of CRC based on the "polyp-adenoma-carcinoma" sequence.

METHODS: A total of 250 participants were recruited from the First Affiliated Hospital of Anhui Medical University between July 2023 and June 2024. The cohort included 30 HC, 52 with common colorectal polyps, 58 with SCRA, 56 with LCRA, and 54 with IMC. Fecal samples were collected for bacterial DNA extraction, followed by metagenomic sequencing to analyze microbial diversity. Differential microbiota analysis was performed using the R package microbiomeMarker and LEfSe. Group classification and feature identification were conducted using a random forest model. Functional profiling was performed using DIAMOND against the KEGG and MetaCyc databases.

RESULTS: No significant differences in α-diversity were observed across the groups. β-diversity analysis revealed significant differences in Bray-Curtis and Jaccard distances among the groups. The composition and abundance of gut microbiota at the phylum, class, order, family, genus, and species levels were significantly altered. LEfSe analysis identified specific bacterial species with significant differences in IMC compared to other groups. Furthermore, the random forest model effectively distinguished patients with IMC from other groups based on distinct microbial signatures. Functional profiling revealed that the gut microbiota undergoes metabolic reprogramming from a homeostatic to a pro-tumorigenic phenotype during CRC progression as well as reduced protective pathway abundance and impaired energy/biosynthetic metabolism in CRC-associated microbiota.

CONCLUSION: Gut microbiota profiles varied significantly among HC, polyp, SCRA, LCRA, and IMC groups. Specific microbial signatures were able to effectively differentiate IMC from both HC and non-malignant colorectal lesions, highlighting their potential as diagnostic biomarkers.},
}

@article {pmid41356466,
year = {2025},
author = {Han, X and Sun, QG and Zang, D and Chen, J},
title = {Comprehensive fecal metagenomic and metabolomic analysis reveals the role of gut microbiota and metabolites in detecting brain metastasis of small cell lung cancer.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1673983},
pmid = {41356466},
issn = {1664-302X},
abstract = {BACKGROUND: Brain metastasis (BM) is a common and highly lethal complication in patients with small cell lung cancer (SCLC). People have paid great attention to exploring the relationship between gut microbiota and the occurrence and development of cancer. This study investigated the relationship between brain metastasis, gut microbiota, and their metabolites in SCLC, providing new insights for the prevention and diagnosis of brain metastasis in SCLC.

METHODS: Baseline fecal samples were collected from 45 participants, including 15 patients with BM and 30 patients with no distant metastasis who were newly diagnosed with SCLC. The gut microbiota and metabolite levels were analyzed using metagenomics and untargeted metabolomics, and machine learning models were utilized to identify differences and potential biomarkers.

RESULTS: Gut microbiota composition varied significantly between the two groups. Genus such as Alistipes and Streptococcus were more abundant in the brain metastasis group, while Bacteroides and Prevotella predominated in patients without distant spread. Metabolomic profiling identified several metabolites inversely associated with brain metastasis, including leukotriene F4, benzoic acid, velnacrine, piperidine, and an unidentified compound labeled C20916. KEGG pathway analysis linked multiple key physiological processes, such as aminobenzoate degradation, carbapenem biosynthesis, toluene degradation, dioxin degradation, and benzoate degradation, underscoring the complex role of gut microbial metabolites in cancer progression. Furthermore, machine learning models identified key biomarkers, including the genus Marvinbryantia and the metabolites benzoic acid, which showed strong discriminatory ability for brain metastasis. After robust validation, the model demonstrated good performance with excellent discriminative power (AUC = 0.80).

CONCLUSION: Compared to patients without distant metastasis, SCLC patients with BM exhibit distinctive gut microbial and metabolite profiles. These findings suggest that specific gut microbes and their metabolic products may serve as valuable biomarkers for diagnosing and stratifying treatment in brain metastatic SCLC.},
}

@article {pmid41355980,
year = {2025},
author = {Wu, X and Wang, W and Xu, L and Zhou, W and Zhou, J and Zhou, H},
title = {Value of plasma metagenomic next-generation sequencing for the diagnosis of invasive aspergillosis: a multicenter-center retrospective study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1656233},
pmid = {41355980},
issn = {2235-2988},
mesh = {Humans ; Retrospective Studies ; Male ; Female ; *High-Throughput Nucleotide Sequencing/methods ; Middle Aged ; Aged ; *Metagenomics/methods ; *Aspergillus/genetics/isolation & purification/classification ; Adult ; Risk Factors ; Aged, 80 and over ; Young Adult ; China ; *Aspergillosis/diagnosis/microbiology ; *Plasma/microbiology ; },
abstract = {INTRODUCTION: Invasive aspergillosis (IA) is a severe fungal infection. Metagenomic Next Generation Sequencing (mNGS) is abroad and highly sensitive pathogen detection method that can accurately differentiate fungi to the species, and even subspecies level.

METHODS: To explore the value of plasma mNGSs in the diagnosis of invasive aspergillosis, a retrospective analysis was conducted on the clinical data of 334 patients with findings of Aspergillus spp. From mNGS from plasma at 4 hospitals, Zhejiang, from February 2021 to December 2022. The study analyzed risk factors, clinical manifestations, imaging features, microbiological results, and treatment outcomes of patients with Aspergillus infection.

RESULTS AND DISCUSSION: According to the diagnostic criteria for IA, among the 334 patients, there were 4 confirmed cases, 62 probable cases, 134 possible cases, and 134 false-positive cases. All 196 probable and possible cases exhibited risk factors, clinical manifestations, imaging features, and treatment outcomes consistent with Aspergillus infection. In 18 out of the 62 probable cases, the same Aspergillus nucleic acid was found in 2-4 peripheral blood mNGS samples collected at intervals of 17 days. The remaining 134 patients had detectable Aspergillus in plasma mNGS but lacked high-risk factors and clinical characteristics of Aspergillus infection, and there was a lack of other microbiological evidence, determined as false positives. Among the cases included in this study, the positive predictive value of plasma mNGS for diagnosing invasive aspergillosis was 59.9%. Plasma mNGS detection has significant reference value for diagnosing IA. However, comprehensive judgment should still be made in conjunction with clinical features.},
}

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

@article {pmid41355608,
year = {2026},
author = {Chong, SY and Ilham, Z and Wan-Mohtar, WAAQI and Cheng, A},
title = {The Road to Sustainable Soy Sauce Production and Consumption.},
journal = {Comprehensive reviews in food science and food safety},
volume = {25},
number = {1},
pages = {e70352},
doi = {10.1111/1541-4337.70352},
pmid = {41355608},
issn = {1541-4337},
support = {//Universiti Malaya/ ; },
mesh = {Fermentation ; *Soy Foods/microbiology/analysis ; Food Microbiology ; Humans ; },
abstract = {Soy sauce (SS), a fermented condiment integral to various global cuisines, has undergone considerable technological advancements while preserving its traditional microbiological processes. This systematic review, adhering to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, synthesized findings from 181 peer-reviewed articles to examine trends in SS production and consumption. Our descriptive statistics and thematic analysis revealed five key focus areas: process optimization, microbial fermentation, safety, waste management, and evolving analytical technologies. Advances, such as metagenomics, synthetic biology, and enzyme engineering, have refined fermentation dynamics, improving flavor and production efficiency. Concurrently, sustainability-orientated innovations, including by-product bioconversion, low-sodium formulations, and traceable packaging, support both environmental goals and health-conscious consumption. The integration of multi-omics approaches (e.g., metabolomics, genomics, and transcriptomics) and high-resolution analytical tools (e.g., spectroscopy and sensor-based systems) has further strengthened quality control by enhancing authenticity, safety, and traceability. However, integrating traditional methods with emerging technologies such as precision fermentation, which facilitates targeted microbial control to improve product consistency, remains challenging due to microbial strain incompatibility, scalability issues, and the necessity to maintain cultural authenticity and sensory attributes. It is essential to implement scalable and sustainable solutions that improve microbial function while minimizing hazardous by-products and environmental effects. This review presents an integrated framework connecting five key thematic areas with the core pillars of sustainability: environment, economy, society, technology, and nutrition, offering a foundation for directing future research, policymaking, and industrial practices. Key priorities include the development of salt-tolerant microbial consortia, the valorization of fermentation by-products via circular economy strategies, and the standardization of sustainability certification criteria to facilitate practical implementation.},
}

Fermentation
*Soy Foods/microbiology/analysis
Food Microbiology
Humans

@article {pmid41355553,
year = {2025},
author = {Kim, MJ and Park, JH and Eom, YB},
title = {The Transmissibility of the Human Skin Virome: Potential Forensic Implications.},
journal = {MicrobiologyOpen},
volume = {14},
number = {6},
pages = {e70197},
doi = {10.1002/mbo3.70197},
pmid = {41355553},
issn = {2045-8827},
support = {//Soonchunhyang University (SCH-20130328), Ministry of Science and ICT, South Korea, RS-2023-NR076438 (NRF-2023R1A2C1003486)/ ; //Ministry of Science and ICT, South Korea, RS-2023-NR076438 (NRF-2023R1A2C1003486)/ ; },
mesh = {Humans ; *Virome ; *Skin/virology ; Adult ; *Viruses/classification/genetics/isolation & purification ; Male ; Female ; Young Adult ; Republic of Korea ; Metagenome ; },
abstract = {The objective of this study was to evaluate the temporal stability and object-to-skin transferability of the skin virome in a Korean population. Skin virus metagenomes were collected from the anatomical locations (forehead, left hand, and right hand) of eight healthy adults and monitored over 3 months at intervals of 6 weeks. To assess the potential transfer of virome between skin and objects, subjects were instructed to contact four types of objects (cell phones, door handles, fabric, and plastic). Virome samples were then collected from the surfaces of these objects. Viruses were identified using databases and viral annotation bioinformatics tools. Fifteen viral families were consistently found to be stable and well-transmissible across anatomical locations and four types of objects. Furthermore, the presence/absence profiles of 54 viral species belonging to these 15 viral families exhibited significant individual specificity on both the skin (p < 0.01) and the objects handled by each subject (p < 0.05). We confirmed that these 54 viral markers remain stable over time within individuals and are transferable to contacted surfaces. Additionally, we explored the potential of using the virome as an individual identification marker, which may suggest new approaches for forensic applications.},
}

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

@article {pmid41355481,
year = {2025},
author = {Becerra, D and Rodríguez-Caballero, G and Marhuenda-Egea, FC and Olaya-Abril, A and Moreno-Vivián, C and Sáez, LP and Luque-Almagro, VM and Roldán, MD},
title = {Microbial Diversity of the Surface of Polypropylene and Low Density Polyethylene-Based Materials (Plastisphere) From an Area Subjected to Intensive Agriculture.},
journal = {MicrobiologyOpen},
volume = {14},
number = {6},
pages = {e70121},
doi = {10.1002/mbo3.70121},
pmid = {41355481},
issn = {2045-8827},
support = {//This study was supported by Ministerio de Ciencia e Innovación, Spain (grant PID2021-124174OB-I00)./ ; },
mesh = {*Polypropylenes/metabolism ; *Polyethylene/metabolism ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Soil Microbiology ; RNA, Ribosomal, 16S/genetics ; Agriculture ; *Biodiversity ; Biodegradation, Environmental ; Phylogeny ; },
abstract = {Accumulation of synthetic plastics in the biosphere has led to global pollution, provoking serious consequences for the environment and human health. Uncontrolled agricultural plastic landfills have the risk of becoming a source of agrochemicals and microplastics. Biotechnological approaches to solve plastic pollution include the removal of these polymers through biological degradation, which is a friendly environmental method. The microbial communities colonizing plastic debris (plastisphere) are considered as a potential source of plastic-degrading microorganisms. In this study, a bacterial biodiversity analysis, based on 16S rRNA gene-targeted metagenomic sequencing, was achieved in the plastisphere of low-density polyethylene (LDPE) and polypropylene (PP) polymers from an agricultural landfill. The α-diversity analysis did not show significant differences between LDPE and PP plastispheres and the plastic-free bulk soil, while LDPE and PP bacterial communities clustered close, but separately from the bulk soil in a β-diversity analysis. Although the taxonomic composition of both plastispheres was different, they shared a significantly higher proportion of Cyanobacteria and Deinococcota than the bulk soil. Additional analyses showed different indicator families, genera and species that can be associated with plastispheres. A predictive functional analysis suggests that degradation of plastic additives in both plastispheres is probably occurring. In addition, the existence of degradation processes for specific herbicides in each plastisphere is highlighted, and the possible exposure of LDPE to both physical and biological degradation processes is also described. These results will contribute to characterize the soil plastisphere exposed to different environmental conditions, and to understand the specific biological niches where plastic-degrading microorganisms could survive.},
}

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

@article {pmid41354995,
year = {2025},
author = {Li, J and Jiang, E and Zhang, M and Pan, C and Lei, C and Han, L and Lan, X},
title = {Phloretin inhibits ferroptosis by restoring the antioxidant capacity of bovine adipose and muscle cells via the AMPK-PPAR signaling pathway.},
journal = {Stress biology},
volume = {5},
number = {1},
pages = {74},
pmid = {41354995},
issn = {2731-0450},
support = {No.32372852//National Natural Science Foundation of China/ ; No.32402726//National Natural Science Foundation of China/ ; Innovative Exploration Category//Natural Science Basic Research Program of Shaanxi Province, Key Project on Frontier Exploration/ ; No.2025JC-QYCX-027//Natural Science Basic Research Program of Shaanxi Province, Key Project on Frontier Exploration/ ; No. 2024JC-JCQN-30//Science Fund for Distinguished Young Scholars of Shaanxi Province/ ; No.2023SR205//Shaanxi Provincal Innovation Leadership Program in Sciences and Technologies for Young and Middle-aged Scientists/ ; },
abstract = {Ferroptosis has been increasingly implicated in adipose and muscle dysfunction, systemic metabolic disturbances, and several diseases in livestock, which necessitates effective and side-effect-free inhibition strategies. Phloretin, a dihydrochalcone with excellent antioxidant and anti-inflammatory properties, may have the potential to restrain cell ferroptosis. Herein, phloretin was verified to significantly inhibit (1S,3R)-RSL3-induced ferroptosis by reducing intracellular MDA, Fe[2][+], and ROS levels and restoring cell total antioxidant capacity in bovine and mouse preadipocytes or myoblasts. It also alleviated oxidative stress (OS), a vital inducer of ferroptosis, by restoring antioxidant enzyme activity in the above cells and obese mice. In vivo, phloretin gavage significantly reversed the trend where high-fat diet (HFD)-induced OS promoted the expression of ferroptosis-promoting genes and proteins (e.g., ACSL4 and PTGS2) while inhibiting the expression of ferroptosis-negative regulators (e.g., Fth1 and Gpx4). Unlike most flavonoids that exert anti-inflammatory or antioxidant activities by altering the gut microbiota composition, metagenomic sequencing analysis of cecal contents from phloretin-gavaged and HFD mice revealed that phloretin exerts its antioxidative and ferroptosis-inhibitory effects independent of modulating gut microbiota diversity. Further transcriptomic analyses of mouse adipose tissues revealed that phloretin alleviated ferroptosis in adipocytes by modulating the transcription of genes enriched in AMPK and PPAR signaling pathways, such as Camkk2. Hence, based on multi-omics analysis combined with in vivo and in vitro verification, phloretin effectively alleviated the OS to further inhibit ferroptosis of adipose or muscle cells through the AMPK-PPAR pathway, which can provide new research ideas for ameliorating adipose or myocyte dysfunction induced by ferroptosis in animals.},
}

@article {pmid41354993,
year = {2025},
author = {Zhang, W and Zhang, M and Xie, J and Huang, H and Schmitz-Esser, S and Li, W and Liu, H and Li, D},
title = {Dynamics of the gut microbiome and resistome in response to prophylactic antibiotic treatment in post-surgical giant pandas.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-25645-6},
pmid = {41354993},
issn = {2045-2322},
support = {2023NSFSC0011//Natural Science Foundation of Sichuan Province/ ; 2023NSFSC0011//Natural Science Foundation of Sichuan Province/ ; QD2023A46//Mianyang Teachers' College/ ; QD2023A46//Mianyang Teachers' College/ ; 2022 CPB-B09//the grants from the independent project of Chengdu Research Base of Giant Panda Breeding/ ; },
abstract = {For giant pandas, the ecological impact of prophylactic postoperative antibiotics on their gut microbial communities and resistome is not well characterized. Here, we assessed the impact of intravenous cefotaxime administration by analyzing longitudinal fecal samples from five giant pandas via 16 S rRNA sequencing (n = 304 samples) and shotgun metagenomics (n = 22 samples). 16 S-based analysis revealed that antibiotic exposure significantly altered bacterial community structure, resulting in a pronounced increase in the abundance of Pseudomonadota (from 50% ± 24% to 60% ± 38%; P < 0.001) and a reduction in Shannon diversity (from 2.8 ± 0.4 to 2.4 ± 1.3; P < 0.05). In contrast, metagenomic analysis indicated that cefotaxime exposure did not significantly increase the overall diversity of antimicrobial resistance genes (ARGs) or virulence factor genes (VFGs). However, we observed a marked expansion in the diversity of the CTX-M β-lactamase family (blaCTX-M), which persisted into the recovery phase. We also recovered 10 metagenome-assembled genomes (MAGs) harboring both ARGs and VFGs, identifying them as potential antibiotic-resistant pathogens (ARPs). Their abundance, however, remained unchanged throughout treatment. These findings provide new insights into the effects of short-term antibiotic exposure in giant pandas, highlighting its transient effect on microbial community structure and a limited effect on resistome diversity.},
}

@article {pmid41354859,
year = {2025},
author = {Robas-Mora, M and Fernández-Pastrana, VM and González-Reguero, D and Probanza, A and Jiménez-Gómez, PA},
title = {Effect of PGPB-enriched organic fertilizer ORGAON[®]PK on the rhizospheric microbiota and biomass of Lupinus albus (L.): a sustainable alternative to chemical fertilizer.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-025-00827-x},
pmid = {41354859},
issn = {2524-6372},
support = {TED2021-132285A-I00//European Union NextGenerationEU/PRTR/ ; TED2021-132285A-I00//European Union NextGenerationEU/PRTR/ ; TED2021-132285A-I00//European Union NextGenerationEU/PRTR/ ; TED2021-132285A-I00//European Union NextGenerationEU/PRTR/ ; TED2021-132285A-I00//European Union NextGenerationEU/PRTR/ ; },
abstract = {The intensive use of agrochemicals is essential to maintain crop yields, but it has led to overexploitation of land and environmental deterioration. To promote more sustainable agriculture, this study evaluates the novel effects of biofertilizers enriched with plant growth promoting bacteria, such as Bacillus pretiosus and Pseudomonas agronomica, on Lupinus albus var. Orden Dorado, to improve the rhizospheric soil health and plant biomass as well as reducing dependence on chemical fertilizers. The organic matrix ORGAON[®]PK and its sterilized version, both derived from horticultural waste, were tested compared with a traditional chemical fertilizer and a water control. After three months of treatment, metagenomic analyses (16 S rRNA gene amplicons) indicated that the strains remained in the rhizosphere, increasing metabolic diversity without altering the microbial structure (Shannon index). In addition, a significant reduction in the minimum inhibitory concentration against clinical antibiotics (p < 0.05) was observed, highlighting the potential of biofertilizers to decrease microbial resistance in the soil. Principal component analysis showed clear differences between treated and control groups, and ANCOM-BC revealed changes in non-culturable bacteria. Biometric analyses revealed increases of 70-88% in shoot weight, ~ 80% in total biomass, and up to 36% in shoot elongation compared with the control. Biofertilizers improved nutritional quality and plant biomass, suggesting their potential as a sustainable and efficient alternative to the use of chemical fertilizers.},
}

@article {pmid41354765,
year = {2025},
author = {Su, H and Han, P and Yan, H and Wu, C and Zeng, S and Zhang, P and Wang, Z and Dong, J and Liang, M and Jing, H and Zhang, D and Yang, C and Xie, N and Liu, X and Weng, S and Dong, G and He, J},
title = {Age-dependent patterns of the gut microbiome, antibiotic resistome, and pathogenicity in captive koalas (Phascolarctos cinereus).},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-025-09302-2},
pmid = {41354765},
issn = {2399-3642},
abstract = {Gut microbiome has a profound influence on koalas' health. Yet, the relationships among the gut bacteriome, virome, antibiotic resistome, and pathogenicity throughout different stages in koala's life remain elusive. Here, we presented a metagenome-resolved survey of gut microbiome utilizing 75 fecal samples from three groups of captive koalas. The diversity of bacteriome and virome were age-dependent, predominating in adult koalas. Lytic viruses increased with age as lysogenic viruses and bacterial hosts declined, and virus-to-microbe ratios rose, revealing concomitant age-related shifts in microbial communities, though causality remains unresolved. Antibiotic resistance genes (ARGs) were more prevalent in young koalas, unlike in humans, where they accumulate with age. Two ARG-carrying pathogens, Klebsiella pneumoniae and Escherichia coli, were identified and cultured, with K. pneumoniae and E. coli predominating in young koalas. One age-dependent lytic virus infecting K. pneumoniae only detected in young koalas, and two lysogenic viruses infecting E. coli identified the in young and adult koalas. Analyses showed a positive correlation between mobile genetic elements (MGEs) and virulence factors (VFs), which facilitated the widespread dissemination of VFs and impacted health. Collectively, this study advances the understanding of gut microbiome in health, providing solutions to the treatment and management of captive koalas.},
}

@article {pmid41354674,
year = {2025},
author = {Yang, S and Deng, W and Yang, T and Liu, C and Li, C and Li, G and Wei, R and Li, D and Huang, Y and Zhao, K and Zou, L},
title = {Enriched Streptococcus alactolyticus in non-cub giant panda gut contributes to the regulation of tryptophan and its neuromodulatory derivatives.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-025-00879-4},
pmid = {41354674},
issn = {2055-5008},
support = {031-2222996053//the Scientific Research Foundation from Sichuan Agricultural University/ ; The Giant Panda Microbiome Research and Biobank Establishment//the International Cooperation Funding Project for Giant Pandas/ ; },
abstract = {Despite feeding on a high-lignocellulose bamboo diet, the giant panda (Ailuropoda melanoleuca) retains a typical gut microbiome of Carnivora. We conducted shotgun metagenomic sequencing and functional validation of the giant panda's gut microbiome to elucidate its physiological roles and explore its functional adaptation to the species' specialized diet. Our results revealed that Streptococcus alactolyticus significantly increased in the guts of subadult, adult, and elderly individuals versus that in cubs. The gut microbiome of these non-cub giant pandas was significantly enriched in pathways and modules associated with tryptophan biosynthesis. Whole-genome sequencing and in vitro fermentation of S. alactolyticus demonstrated its ability to biosynthesize tryptophan. Gavage of S. alactolyticus in mice led to the enrichment of aromatic amino acid metabolism pathways in gut microbiome, accompanied by significantly elevated levels of 5-hydroxyindole acetic acid and kynurenine in fecal and/or serum samples (p < 0.05). Transcriptome sequencing of colons from mice revealed that most significant upregulated Gene Ontology (GO) terms mainly were related to spindle checkpoint signaling and chromosome segregation, while most significant downregulated GO terms mainly involved synaptic functional regulation. These findings suggest that S. alactolyticus enriched in the non-cub giant panda gut can regulate tryptophan, influencing host gut physiology via tryptophan metabolites.},
}

@article {pmid41354462,
year = {2025},
author = {Wang, X and Liu, Y and Sun, Z and Li, J and Lu, Z and Huang, J and Hu, S and Cao, P and Cao, X and Li, S and Ruan, J and Liu, J and Xie, J and Sun, H and Chen, T and Li, S and Zhu, Z and Wen, Z and Tuan, RS and Hunter, DJ and Li, ZA and Shi, D and Ding, C},
title = {Multi-Omics Reveal the Dysregulated Gut-Joint Axis in Knee Synovitis: Data from Two Osteoarthritis Studies in China.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e12020},
doi = {10.1002/advs.202512020},
pmid = {41354462},
issn = {2198-3844},
support = {2023YFE0209700//National Key Research and Development Program of China/ ; GZC20231059//Postdoctoral Fellowship Program of CPSF/ ; 2024M761326//China Postdoctoral Science Foundation/ ; 2023A1515110748//Guangdong Basic and Applied Basic Research Foundation/ ; 2024A1515011794//Guangdong Basic and Applied Basic Research Foundation/ ; 82373653//National Science Foundation of China/ ; 82572825//National Science Foundation of China/ ; 2024A04J5169//Science and Technology Projects in Guangzhou/ ; A2401031//Shenzhen Medical Research Funds/ ; 1194737//Arthritis Australia and an NHMRC Investigator Grant Leadership 2/ ; 82325035//National Natural Science Foundation of China for Distinguished Young Scholars/ ; 82530083//Key Project of the National Science Foundation of China/ ; },
abstract = {Gut microbiota dysbiosis and associated host immuno-metabolic disorders may play a role in knee synovitis. Herein, integrated multi-omics analyses of stool and blood samples from subjects from Pearl River Osteoarthritis Cohort (PROC, N = 207) are conducted to explore the potential gut-joint axis. Specifically, gut metagenomics, serum metabolomics and plasma proteomics are carried out. Knee synovitis is identified by magnetic resonance imaging. A total of 87 synovitis cases are identified in PROC, which are characterized by increased Firmicutes/Bacteroidetes (F/B) ratio. Alterations in microbial functions of both leucine and geraniol degradation are closely associated with increased serum 3-hydroxyisovaleric acid and decreased geranic acid. These perturbations are significantly correlated with F/B ratio and down-regulated plasma TWEAK. Building upon these, the potential synovial targets are explored using a synovial single-cell dataset and the Nanjing Osteoarthritis Cohort (NOC, N = 22). Synovial fluid proteomics, histological analysis, and in vitro experiments with human fibroblast-like synoviocytes (FLS) are conducted for NOC subjects with different synovitis grades. An upregulated TWEAK receptor is found in higher grade of synovitis. In vitro, higher TWEAK induced down-regulated TWEAK receptor in FLS. The study for the first time revealed the gut-joint axis in knee synovitis, providing new insight into potential targets for synovitis treatment.},
}

@article {pmid41354223,
year = {2025},
author = {Adhikary, P and Maddheshiya, A and Takkar, B and Das, T and Mukherjee, S},
title = {Differential gut microbiome profiles in diabetic retinopathy: A comparative study across continental populations.},
journal = {Diabetes research and clinical practice},
volume = {},
number = {},
pages = {113043},
doi = {10.1016/j.diabres.2025.113043},
pmid = {41354223},
issn = {1872-8227},
abstract = {Gut dysbiosis damages gut barrier, stimulates inflammation, endotoxemia, and breakdown of blood-retina barrier, promoting diabetic retinopathy (DR). Most microbiome studies on DR relied on 16S rRNA gene sequencing, documenting altered microbial richness, diversity, and shifts in dominant phyla and genera, though these findings remain inconsistent across populations. The only shotgun metagenomic study to date identified species Eubacterium hallii, Firmicutes bacterium and Alistipes finegoldii enriched in DR, with altered metabolic pathways. The β-diversity showed distinct inter-individual variations in diseased individuals compared to healthy controls (HC). The objective of this narrative review is to highlight the key microbial biomarkers, metabolic pathways, and putative microbiota-gut-retina axis integrating both 16S rRNA and shotgun data to compare microbial alterations across HC, T2DM, and DR. The review concludes with a comprehensive understanding of dysbiotic gut taxa associated with DM and DR in different populations showing wide variability in results mostly due to small sample size, geography, antidiabetic medications, lack of demographic and clinical data and limited taxonomic classification by 16S sequencing. This emphasizes the need of a large scale, multi-ethnic shotgun metagenomic sequencing study with systematically collected medical data and dietary information to understand the contributions of gut microbiome in the progression of DR.},
}

@article {pmid41354039,
year = {2025},
author = {Meng, Y and Zhou, JX},
title = {Beyond technical feasibility: addressing practical hurdles for equitable wastewater metagenomic surveillance.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {101311},
doi = {10.1016/j.lanmic.2025.101311},
pmid = {41354039},
issn = {2666-5247},
}

@article {pmid41353953,
year = {2025},
author = {Pan, Y and Tan, T and Meng, J and Guo, H and Dong, Y and Cui, Y and Yu, N and Jin, X and Zhang, Y and Zou, H and Bolan, N and Siddique, KHM},
title = {Biochar and moisture variability shape soil carbon pools via microbial carbon-degrading genes.},
journal = {Journal of environmental management},
volume = {397},
number = {},
pages = {128157},
doi = {10.1016/j.jenvman.2025.128157},
pmid = {41353953},
issn = {1095-8630},
abstract = {Microbially derived organic carbon is a key component of the soil carbon pool. Shifts in microbial communities and their associated functional genes-triggered by moisture variability and biochar addition-can influence the composition and stability of soil organic carbon (SOC). However, the microbial processes involved in SOC formation and degradation under different biochar levels and moisture variability intensities remain clear. To address this, we conducted a 90-day microcosmic incubation using three levels of biochar addition (C0: 0, C1: 1 %, C2: 2 %, w/w) and three moisture regimes (W0: constant moisture, W1: high-intensity variability, W2: low-intensity variability) to analyzed microbial communities, carbohydrase activity, C-degrading genes, and C, N, and P enzyme activities to trace and characterize microbial contributions to SOC formation. The results showed a shift in the dominant soil microbial community from Actinomycetes to Ascomycetes with increasing moisture variability. Microbial biomass carbon increased by 158-900 % relative to C0W0, peaking under C2W1. This stimulation enhanced microbial carbon sequestration under high moisture variability while simultaneously accelerating the decomposition of both plant- and microbial-derived carbon. Biochar addition exerted only a marginal, non-significant inhibitory effect on the decomposition either carbon source (P > 0.05). Functional gene analysis revealed that 62 % of carbohydrate-active enzymes (CAZymes) targeted plant-derived components significantly exceeding the 38 % targeting microbial-derived components, indicating a significantly stronger degradation potential for plant residues under varying moisture conditions. This process was genetically regulated, as shown by the concurrent increase in of carbon-degrading gene abundance and corresponding enzyme activities. Consequently, microbial activity was efficiently modulated, with carbon use efficiency increasing by up to 767 % compared with the C0W0. Moisture variability and its interaction with biochar significantly (P < 0.05) or highly significantly (P < 0.01) affected these microbial indicators. This study reveals a moisture-driven microbial "carbon pump" operating through coordinating gene-enzyme-community regulation. Within this framework, up-regulated carbon-degrading genes align with enzyme activities to channel plant-derived carbon into stable SOC. The C2W1 treatment achieved the highest SOC stabilization, offering a theoretical basis for managing SOC under extreme climate conditions and advancing mechanistic understanding of microbe-mediated carbon dynamics.},
}

@article {pmid41353697,
year = {2025},
author = {Pandey, AK},
title = {Computational approach for identification and characterization of a glucose-tolerant thermostable β-glucosidase from marine metagenome.},
journal = {Molecular diversity},
volume = {},
number = {},
pages = {},
pmid = {41353697},
issn = {1573-501X},
abstract = {Cellulase enzymes comprising endo-1,4-β-glucanase, exo-1,4-β-glucanase, and β-glucosidase mediate the degradation of cellulosic biomass and are frequently used in biofuel production from lignocellulose. β-glucosidases that convert cellobiose to glucose are sensitive to temperature and glucose concentration and thus often show limited catalytic efficiency. Several β-glucosidases having high temperature or glucose tolerance have been evaluated, but a potential candidate having high efficiency along with thermostability and glucose tolerance is yet to be identified. The present study focuses on marine metagenome investigation for the identification of high-potential β-glucosidase. Nine β-glucosidases of the GH 1 family having (β/α)8 barrel domains were observed. Six β-glucosidases were predicted to have a Tm value higher than 65 ℃, including ECV39653.1 β-glucosidase. Molecular docking of all identified β-glucosidases with cellobiose and glucose revealed that ECV39653.1 β-glucosidase has the highest negative binding energy of - 7.4 kcal/mol for cellobiose at the active site, while having insignificant binding of glucose with binding energy of -5.4 kcal/mol at a site different from the active site. The structural analysis showed an effective similarity of ECV39653.1 β-glucosidase with known thermostable and glucose-tolerant β-glucosidases. The prediction of kinetic parameters gave kcat/Km value of 989.08163 sec[-1] mM[-1] for cellobiose. In-depth MD simulation and free binding energy analysis showed highly effective binding of cellobiose over the 100 ns trajectory with an average total binding energy of - 17.45 kcal/mol. The PCA and analysis of free energy landscape showed less variance and conformational changes in ECV39653.1 β-glucosidase cellobiose complex form in comparison to apo-form and disclosed attainment of global minima, thus proving the high ECV39653.1 β-glucosidase-cellobiose complex stability. The analysis of the simulation trajectory revealed that glucose left the binding cavity during simulation, thus disclosing weak binding and, hence, effective glucose tolerance. Therefore, the present in-silico investigation provides a promising high-efficiency, thermostable, and glucose-tolerant ECV39653.1 β-glucosidase. Further studies can provide scope for its utilization in the development of effective technologies for large-scale biofuel production.},
}

@article {pmid41353545,
year = {2025},
author = {Briggs, P and Trimmell, L and Stiemsma, LT and Monzón, J},
title = {Sexual and regional differences in the microbiome and functional metagenome of the lone star tick, Amblyomma americanum.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-025-00498-6},
pmid = {41353545},
issn = {2524-4671},
}

@article {pmid41353522,
year = {2025},
author = {Mugwanya, M and Mpingirika, EZ and AbdelMaksoud, Y and Eissa, RA and Sewilam, H},
title = {Assessment of sediment physiochemical properties, microbial and predicted functional diversity in mangrove eco-restoration sites of Hamata, Mangrove Bay, and Saffaga along the Egyptian Red Sea coast.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {41353522},
issn = {1614-7499},
abstract = {Microbial communities perform important roles in nutrient cycling, degradation of environmental pollutants, and support of various life forms on Earth. Mangroves live in very harsh environments, and if not for the existence of several microbial species in their ecosystems, they would not survive. The Egyptian Red Sea coast is dominated by two mangrove species, Avicennia marina and Rhizophora mucronata, which serve as breeding grounds for marine organisms and aid in carbon sequestration. Despite their ecological significance, comparative studies examining the physiochemical properties and heavy metal concentration of mangrove sediments of two dominant species along the Egyptian Red Sea coast (Hamata, Mangrove Bay, and Saffaga) and their relationship to microbial and functional diversity are scarce. Our findings revealed significant differences in sodium ions, potassium ions, organic carbon, and bulk density at 30-50 cm depth across the locations. Heavy metal analysis revealed significantly lower concentrations of zinc and manganese and high concentrations of copper in sediment samples collected from Mangrove Bay at all sampling depths. Metagenomics analysis revealed that the dominant phyla across the three sites were Pseudomonadota, Bacillota, and Bacteroidota, along with Actenomycetota, and Chloroflexota, and unclassified bacteria. Within the phylum Bacillota, several major classes were identified, including Bacillota_A_368345, Bacillota_I, and Bacillota_C. Functional prediction revealed a higher abundance of microbes involved in energy metabolism and carbon cycle, whereas a lower abundance of microbes involved in sulfur and nitrogen cycles was noted across the sites. In conclusion, the identification of different microbial communities in sediments collected along the Egyptian Red Sea coastal areas suggests the role of different mangrove species and human activities in recruiting unique microbial species involved in promoting their survival under different environmental factors.},
}

@article {pmid41353382,
year = {2025},
author = {Kacnik, S and MacIntyre, C and Guarido, M and Venter, M},
title = {Identification of insect-specific viruses in mosquitoes collected from wildlife and rural areas in north-eastern parts of South Africa using a metagenomic RNA sequencing approach.},
journal = {One health outlook},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42522-025-00185-1},
pmid = {41353382},
issn = {2524-4655},
}

@article {pmid41353361,
year = {2025},
author = {France, MT and Chaudry, I and Rutt, L and Quain, M and Shirtliff, B and McComb, E and Maros, A and Alizadeh, M and Hussain, FA and Elovitz, MA and Relman, DA and Rahman, A and Brotman, RM and Price, JT and Kassaro, MP and Holm, JB and Ma, B and Ravel, J},
title = {VIRGO2: an enhanced gene catalog of the vaginal microbiome provides insights into its functional and ecology complexity.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-67136-2},
pmid = {41353361},
issn = {2041-1723},
support = {UH2AI083264//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; T32AI162579//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; OPP1189217//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; INV048956//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; INV048982//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; },
abstract = {Despite the importance of the cervicovaginal microbiome, the mechanisms that govern its composition and drive its impact on host physiology remain poorly understood. With the aim to expand our understanding of the function and ecology of the vaginal microbiome, we present VIRGO2, an enhanced non-redundant gene catalog comprising over 1.7 million well-annotated genes from body-site specific microbes and viruses. Analyses using VIRGO2 reveal insights such as including the identification of previously uncharacterized vaginal bacteria, features of the vaginal mycobiome and phageome, and differential expression of bacterial carbohydrate catabolic genes. Constructed from over 2500 metagenomes and 4000 bacterial genomes, VIRGO2 broadens geographic representation and microbial diversity compared to its predecessor. This updated catalog enables more precise profiling of taxonomic and functional composition from metagenomic and metatranscriptomic datasets. VIRGO2 is a critical resource for integrative analyses of vaginal microbial communities and their interactions with host tissues, thereby enhancing our mechanistic understanding of vaginal health and disease.},
}

@article {pmid41353034,
year = {2025},
author = {McCone, N and Hosokawa, M},
title = {Recovering genomes from uncultured fungi with single-cell genomics.},
journal = {Journal of bioscience and bioengineering},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jbiosc.2025.11.004},
pmid = {41353034},
issn = {1347-4421},
abstract = {Single-cell genomics (SCG) complements culture-independent metagenomics for accessing fungal genomes, particularly from lineages that remain uncultured. We contrast metagenomics, which excels when profiling community composition and metabolic potential but often underrepresents low-abundance fungi, with SCG, which first isolates individual cells or nuclei to generate single-amplified genomes (SAGs) and can recover rare or microdiverse taxa. We then organize existing fungal SCG applications into three subgroups: spore-level sequencing from host-enriched or environmental material; single-nucleus genomics for multinucleate fungi; and single-spore sequencing of haploid progeny for diploid linkage and chromosome phasing. Across studies, pooling and co-assembly of cognate cells improves completeness; key hurdles persist in wall lysis, whole-genome amplification bias, and contamination control. Practical advances include shallow sequencing for QC triage, nuclei pooling with normalized co-assembly, and hybrid long- and short-read assembly. SCG adds unique value where strain resolution and genotypic context matter, including host-to-mobile-element linkage, recovery of large biosynthetic gene clusters, and karyotype validation against telomere-to-telomere references. Used alongside metagenomics, SCG enables a strain-resolved view of fungal biodiversity and function, with incremental improvements across the SCG pipeline promising routine access to genomes from early-diverging and other environmentally embedded fungi.},
}

@article {pmid41352820,
year = {2026},
author = {Chen, X and Tie, Y and Yang, Q and Wu, Z and Xu, W and Zhang, Z and Ju, F and Takamine, K and Zhang, W},
title = {Temporal metabolomic dynamics and microbial functional mechanisms unravel biomarkers for distinguishing maturation stages and types in medium- and high-temperature daqu.},
journal = {Food research international (Ottawa, Ont.)},
volume = {223},
number = {Pt 1},
pages = {117916},
doi = {10.1016/j.foodres.2025.117916},
pmid = {41352820},
issn = {1873-7145},
mesh = {Biomarkers/analysis ; *Metabolomics/methods ; *Hot Temperature ; *Wine/analysis/microbiology ; *Bacteria/metabolism/classification/genetics ; *Alcoholic Beverages/microbiology/analysis ; },
abstract = {Daqu maturation is essential for developing the characteristic flavor profiles of Chinese Baijiu, yet the underlying microbial metabolic mechanisms remain incompletely understood. This study employed an integrated multi-omics approach to investigate metabolic heterogeneity and identify differential biomarkers during the aging of medium-temperature (MD) and high-temperature (HD) Daqu. Physicochemical analysis revealed MD exhibited higher saccharifying power, whereas HD showed increased esterifying power and dynamic acidity changes. Microbial succession and metagenomic analysis uncovered distinct succession patterns: MD was dominated by Saccharopolyspora and Bacillus, while HD featured thermophilic genera including Kroppenstedtia and Virgibacillus. Co-occurrence network analysis demonstrated higher connectivity and reduced modularity in HD, indicating functional adaptation to high temperatures. Combined VIP and OAV analysis identified key aroma biomarkers that distinctly define both Daqu type and maturation stage. Tetramethylpyrazine and acetic acid characterized MD, while benzaldehyde and methyl hexadecanoate marked HD. Non-targeted metabolomics further indicated MD was enriched in phenylpropanoids and branched-chain amino acid derivatives, whereas HD accumulated peptides and steroid-related compounds. Crucially, integrated analysis demonstrated that these metabolic shifts were directly driven by microbial enzymatic activities (e.g., EC 4.1.1.5, EC 3.1.1.3). These findings establish a causal link between temperature-driven microbial functional specialization and metabolic output, and provide a biomarker framework for precise quality assessment of Daqu.},
}

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

@article {pmid41352612,
year = {2025},
author = {Fishman, JA},
title = {Assuring Microbiological Safety in Clinical Xenotransplantation.},
journal = {American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajt.2025.11.027},
pmid = {41352612},
issn = {1600-6143},
}

@article {pmid41352476,
year = {2025},
author = {Su, J and Zhao, K and Zhou, X and Pan, Z and Xia, C},
title = {Early-life exposure to linezolid caused gut microbiota dysbiosis can be inherited from parents to offspring.},
journal = {Chemico-biological interactions},
volume = {},
number = {},
pages = {111863},
doi = {10.1016/j.cbi.2025.111863},
pmid = {41352476},
issn = {1872-7786},
abstract = {BACKGROUND AND OBJECTIVES: Linezolid is a broad-spectrum antibiotic against Gram-positive bacterial infections. Widespread use of linezolid has brought about significant adverse effects and potential reproductive toxicity, but there is not yet any study regarding to the transgenerational impact.

METHODS: Gut microbiota and metabolites from the 12-weeks old male mice who were treated with one-week linezolid at 4 weeks of age, as well as those from their offsprings, were analyzed by metagenomics and metabolomics, respectively. Reproductivity of the male parents were monitored, including fertility, litter size, survival and weight gain of offsprings.

RESULTS: Offsprings survival from the linezolid-treated male parents was obviously decreased, although fertilities, litter size, or weight gain was not affected. The linezolid-induced gut microbiota perturbation in male parents was manifested as lower alpha diversity, distinguishing beta diversity, and the dramatically altered profiles of function genes and metabolites. Especially, linezolid exposure reversed the relationship between Dysosmobacter and butyrogenic species, and that between Dysosmobacter and inflammation-associated species. Interestingly, gut microbiota dysbiosis also existed in both female and male offsprings from the treated male parents. Moreover, it was found that the differential metabolites enriched in ABC transporter pathway were found male parents and offsprings, while those enriched in sphingolipid signaling pathway were only found in offsprings of both sexes CONCLUSIONS: The early-life short-term exposure to linezolid make long-term gut microbiota dysregulation, which was even inherited from parents to offsprings. These findings raised critical concern about the ecological consequences of early-life antibiotic exposure and clinical safety evaluations.},
}

@article {pmid41352467,
year = {2025},
author = {Nalladiyil, A and Khuntia, HK and Chanakya, HN and Babu, GLS},
title = {Treatment of ultra-high-strength compost leachate using an anaerobic biomass biofilm reactor.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133774},
doi = {10.1016/j.biortech.2025.133774},
pmid = {41352467},
issn = {1873-2976},
abstract = {Leachate produced during the composting of the organic fraction of municipal solid waste (OFMSW) is highly concentrated and acidic (chemical oxygen demand (COD) -125 g/L, pH 3-5). Its recalcitrant nature necessitates long hydraulic retention times for effective digestion, which, in turn, leads to high organic loads and, consequently, large reactor footprints. This study evaluated the treatment performance, bioenergy potential, and microbial ecology of the Anaerobic Biomass Biofilm Reactor (ABBR) for ultra-high strength leachate treatment. The reactor employed lignocellulosic wastes such as coir, ridge gourd, and dried acacia leaves as natural biofilm supports. Operated over 180 days with a gradually increasing organic loading rate from 1.1 to 11.2 kg COD/m[3]/d, the reactor achieved 92.9 % COD removal and a methane yield of 0.357 NL/g COD removed at the maximum loading rate. Moreover, the reactor also exhibited exceptionally high space utilization efficiency (3.5-4 L CH4/L/d), highlighting its enhanced volumetric productivity and effectiveness in treating high-strength leachate. Metagenomic analysis revealed a diverse microbial community, with Methanospirillum (3 %) and Methanosaeta (2.6 %) identified as dominant archaea contributing to methanogenesis. The high moisture content of OFMSW, coupled with tropical climatic conditions, leads to rapid fermentation and the generation of large volumes of leachate. Therefore, the ABBR represents a sustainable and high-rate alternative to conventional anaerobic systems, enabling efficient leachate treatment and enhanced bioenergy recovery in windrow composting facilities.},
}

@article {pmid41352466,
year = {2025},
author = {Liu, Z and Gao, Y and Wang, J and Jing, X and Chen, X and Hu, W and Lu, X and Liu, M and He, X and Kumar, G and Zhen, G},
title = {Perfluorooctane sulfonate (PFOS) inhibits methane production during sludge anaerobic digestion by breaking the carbon-transfer bridge between methanogenesis and acidogenesis.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133775},
doi = {10.1016/j.biortech.2025.133775},
pmid = {41352466},
issn = {1873-2976},
abstract = {Per- or polyfluoroalkyl compounds (PFASs) are recognized as emerging contaminant, with perfluorooctane sulfonate (PFOS) being one of the most extensively utilized PFASs due to its great chemical stability. However, knowledge of the bio-chemical behavior, the toxicity of PFOS and its mechanisms of interfacial binding to microorganisms remain inadequately validated. In this study, the biotoxicity of PFOS and its molecular interfacial adsorption mechanism in anaerobic digestion were investigated. The results showed that the tightly bound EPS (TB-EPS) of anaerobic microorganisms could defend against the biotoxicity of PFOS to some extent by physical adsorption and chemical binding, the exposure to PFOS might produce a greater disturbance to methanogenic archaea. With the increase of PFOS, acid-producing bacteria (APB) and methanogenic archaea showed different resistance to PFOS, suppressing cumulative methane production by up to 91.64 %. On the contrary, APBs were more tolerant, and fatty acids accumulated up to 2194.27 mg/L. Metagenomics analysis further confirmed that functional genes associated with fatty acid biosynthesis (fas, FAS2, fabK, etc.) were significantly enriched (approximately 85.29 %) whereas the relative abundance of genes associated with methanogenesis (acs, comA, mcrB, etc.) were decreased (up to 65.96 %). Molecular docking results suggested a potential route for PFOS cellular entry, as it was observed to bind to the substrate-binding protein of the ATP-binding cassette (ABC) transporter and interact with key functional enzymes, which led to the inhibition of methanogens. This study provides novel insights into the molecular blocking mechanism by which PFOS disrupts carbon metabolic flux through the selective inhibition of methanogenic archaea, rather than through a general suppression of acidogenic bacteria.},
}

@article {pmid41352108,
year = {2025},
author = {Zeng, Z and Lei, T and Zhou, M and Wen, H and Li, S},
title = {Ciprofloxacin removal and antibiotic resistance genes response in the EGSB-AnMBR system treating swine wastewater: Performance, mechanism, and metagenomics.},
journal = {Journal of environmental management},
volume = {397},
number = {},
pages = {128233},
doi = {10.1016/j.jenvman.2025.128233},
pmid = {41352108},
issn = {1095-8630},
abstract = {Ciprofloxacin (CIP), a veterinary antibiotic in swine wastewater is an emerging contaminant with low concentration but significant environmental risk. Its inhibitory effects on biological treatment systems and the proliferation of antibiotic resistance genes have raised widespread public concern. An expanded granular sludge bed reactor was coupled with an anaerobic membrane bioreactor (EGSB-AnMBR) to treat swine wastewater containing CIP. During 320 days operation, the EGSB-AnMBR system achieved over 98.6 % chemical oxygen demand (COD) removal efficiency and 61.4 %-100 % CIP removal efficiency. During the initial operation phase, sludge adsorption served as the primary mechanism for CIP removal, whereas biodegradation became dominant in the last operational phase. 16S rRNA gene high-throughput sequencing analysis revealed that under CIP stress, the abundance of CIP-resistant Spirochaetota increased from 4.7 % to 9.5 %, whereas Patescibacteria abundance progressively decreased from 72.7 % to 15.7 %. Metagenomic analysis demonstrated microbes in anaerobic granular sludge (AnGS) achieved "defense-efflux" by activating macB/evgS efflux pumps while suppressing tetA, whereas membrane biofilm (MB) developed a "storage-retention" strategy through synergistic effects of tetA and evgS. This EGSB-AnMBR system exhibits promising application potential for swine wastewater treatment and antibiotic control, providing significant support for livestock pollution management.},
}

@article {pmid41352011,
year = {2025},
author = {Yang, K and Zhang, L and Zhao, K and Liu, W and Tiehm, A and Zhang, X},
title = {Metabolism regulates spatial distribution patterns of different microbial taxonomic groups in chlorinated aliphatic hydrocarbons contaminated soil.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140640},
doi = {10.1016/j.jhazmat.2025.140640},
pmid = {41352011},
issn = {1873-3336},
abstract = {A mechanistic understanding of the distribution and role of subsurface microbial communities is crucial for sustainable environmental management. Bioremediation of chlorinated solvents relies on the bioactivity of organohalide-respiring bacteria and their interaction with syntrophic members. However, the spatial distribution pattern and its influencing factors of these members remain poorly understood. In this study, Distance-decay relationship (DDR) models and Sloan's neutral community models (NCM) were employed to quantify spatial turnover rates and stochastic processes of different taxa in chlorinated aliphatic hydrocarbon-contaminated soil. Incorporating metagenomic analysis and machine learning, this study highlights the contribution of genomic information and reveals how genetic potential for functional mechanisms may relate to distinct spatial distribution patterns. Findings indicate that metabolic potential, rather than environmental preference, primarily governs the heterogeneous distribution of different taxa. Archaeal syntrophic members, Bathyarchaeia, was identified as a potential reliable target for improving bioremediation efficiency. Correlation between parameters of different models suggests that dispersal ability plays an important role in the variation of spatial turnover rate. This was further supported by LASSO regression models in which genomic features relevant to biofilm formation, dormancy, and DNA repair pathways were identified as key predictors of spatial turnover. These findings not only offer actionable insights for enhancing bioremediation strategies at chlorinated solvent-contaminated sites but also demonstrate the potential of incorporating genomic features to understand microbial biogeography.},
}

@article {pmid41351981,
year = {2025},
author = {Li, A and Ju, Z and Zhang, X and Wang, M and Xing, J and Liu, G and Qin, X},
title = {Fangji Huangqi Tang alleviated chronic kidney disease by regulating intestinal bacteria to inhibit the AHR/ROS pathway.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {150},
number = {},
pages = {157610},
doi = {10.1016/j.phymed.2025.157610},
pmid = {41351981},
issn = {1618-095X},
abstract = {BACKGROUND: Fangji Huangqi Tang (FHT) is a traditional Chinese herbal formula that is clinically effective and safe for chronic kidney disease (CKD). However, the mechanism of action of FHT remains unclear.

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

METHOD: A CKD model was established in rats and mice by tail vein injection of doxorubicin, and the rats and mice were administered FHT orally. Metagenomic sequencing analysis was employed to screen and identify FHT-regulated key gut bacteria in CKD model rats and mice. In vitro bacterial co-cultures of these taxa were analyzed for metabolite discovery. Oral supplementation of key bacteria in CKD mice was evaluated the therapeutic effects and validated the metabolic changes observed in vitro. Cellular Aryl Hydrocarbon Receptor (AHR) overexpression was conducted to clarify the mechanistic of the metabolite derived from microbiota.

RESULTS: FHT significantly enriched Corynebacterium stationis (C. stationis) in both CKD rat and mice models. In vitro, C. stationis metabolized tryptophan into Indole-3-Carbinol (I3C) while reducing indole levels. Oral administration of C. stationis in CKD mice attenuated renal dysfunction and elevated systemic I3C. Additionally, it downregulated AHR expression and diminished the expression of ROS-related inflammatory factors, thereby ameliorating CKD. Crucially, AHR overexpression reversed I3C's cytoprotective effects in MPC5 injury models.

CONCLUSIONS: This study reveals that FHT targets the enrichment of the gut bacterium C. stationis, driving tryptophan metabolism toward I3C conversion. This process suppresses AHR expression, reduces ROS levels and inflammatory injury, and ultimately retards the progression of CKD.},
}

@article {pmid41351872,
year = {2025},
author = {Mukherjee, I and Bulzu, PA and Boukheloua, R and Asghar, U and Park, H and Vieira, HH and Chiriac, MC and Kasalický, V and Znachor, P and Rychtecký, P and Šimek, K and Salcher, MM and Haber, M and Ghai, R},
title = {Cultivation, genomics, and giant viruses of a ubiquitous and heterotrophic freshwater cryptomonad.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf271},
pmid = {41351872},
issn = {1751-7370},
abstract = {Heterotrophic nanoflagellates are the chief agents of bacterivory in the aquatic microbial loop but remain underrepresented in culture collections and in genomic databases. We isolated and characterised a representative of the previously uncultured freshwater Cryptomonad Group 1 (CRY1a) lineage using a genome-streamlined, ultrasmall and abundant microbe Planktophila versatilis as a prey and CARD-FISH probe-based screening. This isolate, Tyrannomonas regina, is one of the most dominant ubiquitous heterotrophic cryptomonads in freshwaters. It is a small heterotrophic nanoflagellate (ca. 3-5 μm) and has the smallest genome of any cryptomonad sequenced thus far. The compact genome (ca. 69 Mb) revealed no traces of a photosynthetic lifestyle, consistent with its phylogenomic placement as a sister-clade to cryptophytes that are characterised by the acquisition of a red-algal symbiont. Moreover, in comparison to its photosynthetic counterparts, its genome presents substantially lower repeat content and endogenous viral elements. Genomes of two giant viruses, Tyrannovirus reginensis GV1 and GV2, were also recovered from the same culture and represent a viral genus that has been described so far solely by metagenome-recovered genomes. Collectively, these findings provide insights into genomic ancestry and evolution, widespread ecological impact and interactions of an elusive protist lineage and illustrate the advantages of culture-centric approaches towards unfolding complex tapestries of life in the microbial world.},
}

@article {pmid41351776,
year = {2025},
author = {Hussain, B and Javed, K and Ali, M and Ullah, S and Sun, S and Idris, AM and Singh, S},
title = {Impact of nanoparticles on biogeochemical processes in soil-plant system under heavy metals stress; exploring remediation mechanism and plant health status.},
journal = {Environmental geochemistry and health},
volume = {48},
number = {1},
pages = {31},
pmid = {41351776},
issn = {1573-2983},
mesh = {*Metals, Heavy/toxicity/metabolism ; *Soil Pollutants/toxicity/metabolism/chemistry ; Soil/chemistry ; *Plants/drug effects/metabolism ; *Environmental Restoration and Remediation ; Biodegradation, Environmental ; Stress, Physiological ; *Metal Nanoparticles/chemistry/toxicity ; },
abstract = {Although, NPs have potential to improved plant resistance against abiotic stress, increased nutrient usage efficiency, and sustenance of agricultural production. However, reactions of NPs in soil matrices, particularly their movement, perseverance, and biogeochemical reactions in soil-plant system under heavy metals (HMs) were not well understood. Therefore, this review presents the latest research in order to clarify the molecular interactions, beneficial transformations, and detoxification processes of NPs in plants and evaluates their roles in these processes. It further aims to quantify the benefits and risks, and give future directions for NPs design and applications in environmental remediation and agriculture. NPs significantly enhanced agricultural outcomes through mechanisms such as regulating HMs uptake, boosting antioxidant enzyme activity (up to a 60% increase), altering soil properties, and optimizing physiological metabolism. NPs amendments raised crop output by 20-55% while reducing disease and nutrient leaching to 50% and 30%, respectively, and improving the soil's carbon sink by 15%. Meanwhile, green-synthesized nanomaterials offer eco-friendly alternatives in remediation through processes like adsorption, oxidation, coprecipitation, ion-exchange, photocatalysis, and nanophytoremediation, achieving 100% pollutant removal efficiency for elements like hexavalent chromium using iron NPs. However, challenges such as NPs accumulation in food chains, potential toxicity to non-target species, and physiological disruptions necessitate solutions like microbiome co-delivery and stimuli-responsive systems to balance safety and effectiveness. In order to increase the available resources and address the worldwide food safety issue, the use of NPs in agroecosystems might be a crucial step towards sustainable farming. Therefore, the influence of NPs on soil, and plant antioxidant defense systems and oxidative stress activation under HMs should be studied using molecular, physiological, and biochemical techniques. For this purpose, real-time polymerase chain reaction (RT-PCR) analysis, illumina MiSeq sequencing, pyrosequencing analysis, metagenomics, metabolomics, proteomics, and functional assays etc. could be most useful for NPs risk/benefit evaluation.},
}

*Metals, Heavy/toxicity/metabolism
*Soil Pollutants/toxicity/metabolism/chemistry
Soil/chemistry
*Plants/drug effects/metabolism
*Environmental Restoration and Remediation
Biodegradation, Environmental
Stress, Physiological
*Metal Nanoparticles/chemistry/toxicity

@article {pmid41351708,
year = {2025},
author = {Campbell, KL and Armitage, AR and Labonté, JM},
title = {Microbial Communities Display Key Functional Differences between Reference and Restored Salt Marshes.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02661-7},
pmid = {41351708},
issn = {1432-184X},
abstract = {Salt marshes, despite their ecological importance (i.e., carbon sequestration) and rapid decline due to climate change and sea-level rise. Salt marsh ecosystems provide essential services such as removal of pollutants, carbon sequestration, and protection of coastal lands from storm surges. These services are strongly influenced by plant productivity, which is closely linked to microbial processes such as biogeochemical cycling of carbon, nitrogen, and sulfur. To retain carbon sequestration and other ecological functions, substantial efforts are currently directed towards coastal marsh restoration. Restoration efforts often lack comprehensive assessments of ecosystem functioning. Here, in an effort to assess ecosystem functions, we compared the microbial and viral community composition, as well as the genetic potential between reference and 10-year-old restored marshes in Galveston Bay, TX, USA. Duplicate bulk surface sediment in stands of Spartina alterniflora were sampled for metagenomic analysis. Metagenome assembled genomes analysis showed that while the microbial community composition was largely similar among sites, the overall metabolic potential was dissimilar. Restored sites displayed a higher abundance of carbon and nitrogen cycling functions compared to reference sites, which mainly consisted of sulfur cycling. Although the restored sites developed sediment microbial communities that approached reference microbial composition, the differences in the metabolic functions suggest that even after 10 years, the restored sites were still in a transitional stage of development. The differences between the reference and restored sites were even more differentiated in the viral community's predicted host composition. Additionally, viruses potentially play a variety of roles within the sediment community, including population control and biogeochemical cycles participation through auxiliary metabolic genes. These results highlight the prolonged timeline of functional development in restored salt marshes and highlight the need to develop approaches to boost the development of soil microbial communities in newly created habitats.},
}

@article {pmid41351628,
year = {2025},
author = {Liu, S and Liu, P and Deng, J and He, J and Xiang, Y and Chen, H and Liao, S and Lu, Y and Zhang, Z and Xu, J and Zhang, Z},
title = {C-arm-guided percutaneous biopsy combined with mNGS: a dual-modality strategy for op timizing diagnosis and targeted management of spinal infections.},
journal = {European spine journal : official publication of the European Spine Society, the European Spinal Deformity Society, and the European Section of the Cervical Spine Research Society},
volume = {},
number = {},
pages = {},
pmid = {41351628},
issn = {1432-0932},
support = {2025ZDXM002//Chongqing Science and Health Joint Medical Research(CN)/ ; 2025ZDXM002//Chongqing Science and Health Joint Medical Research(CN)/ ; 2025ZDXM002//Chongqing Science and Health Joint Medical Research(CN)/ ; 2025ZDXM002//Chongqing Science and Health Joint Medical Research(CN)/ ; 2025ZDXM002//Chongqing Science and Health Joint Medical Research(CN)/ ; 2025ZDXM002//Chongqing Science and Health Joint Medical Research(CN)/ ; 2025ZDXM002//Chongqing Science and Health Joint Medical Research(CN)/ ; 2025ZDXM002//Chongqing Science and Health Joint Medical Research(CN)/ ; 2025ZDXM002//Chongqing Science and Health Joint Medical Research(CN)/ ; 2025ZDXM002//Chongqing Science and Health Joint Medical Research(CN)/ ; 2025ZDXM002//Chongqing Science and Health Joint Medical Research(CN)/ ; },
}

@article {pmid41351142,
year = {2025},
author = {Sharko, F and Busova, V and Boulygina, E and Burakova, A and Pankova, S and Nedoluzhko, A},
title = {Ancient DNA sheds light on the historical distribution of the rare and ephemeral plant Coleanthus subtilis in Southern Siberia.},
journal = {BMC genomics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12864-025-12365-4},
pmid = {41351142},
issn = {1471-2164},
abstract = {BACKGROUND: Ancient DNA is a valuable source of information about the distant past of our planet. Reconstructing the past ecosystems is essential for understanding many aspects of life in the steppes of southern Siberia and Central Asia, where numerous human societies representing different archaeological cultures have lived. The remains of their activities, revealed by archaeological excavations, provide a wide range of sources for the cultural and natural/biological history of the region. One of the most enigmatic Iron Age archaeological cultures in southern Siberia is the Tashtyk culture, which dates back to the 1st - 7th centuries AD. The people of this culture inhabited the Minusinsk Basin and practiced different burial rites, including cremation. Thanks to the exceptional preservation of organic remains in individual Tashtyk burials we know of quite an unusual phenomenon: the placement of cremains into the human-like mannequins made from animal skin and filled with herbaceous plants. This study analyses ancient DNA extracted from the grass stuffing of a mannequin found in 2023 at the Oglakhty cemetery, which dates back to 250-300 AD. Our aim is to identify the plant species that were used to stuff the mannequin approximately 1,700 years ago, and to compare their diversity with that of modern-day plant species. This is particularly significant given that the Oglakhty region is part of the Khakassky State Nature Reserve, which was added to the UNESCO Tentative List in 2016 due to its biodiversity and concentration of archaeological sites.

RESULTS: We sequenced the ancient DNA of a dried historical grass mixture in order to reconstruct the nearly complete chloroplast genomes of several apparent Poaceae species. Our analysis showed that, 1,700 years ago, the diversity of plant species in the Oglakhty area was similar to the modern meadow flora of the Minusinsk Basin. These included typical steppe and forest-steppe zone plant genera of Siberia, such as Holcus, Phleum, Poa, and Stipa. Interestingly, alongside the species commonly found in modern southern Siberian steppes and meadows, we discovered the rare, ephemeral, and protected moss grass, Coleanthus subtilis (Tratt.) Seidel ex Roem. et Schult. whose current distribution range spans highly fragmented areas of northern Eurasia and North America but not the Minusinsk Basin.

CONCLUSION: The herbaceous plant C. subtilis, whose DNA fragments were obtained through the metagenomic profiling of the human-like mannequin's stuffing at the Oglakhty cemetery, provides new insights into the cultural and natural history of Siberia. Firstly, we identified several grass taxa in the mannequin's stuffing. Most of them are characteristic for the steppe zone; the only exception is C. subtilis, which usually inhabits riverbanks. Therefore, we assume that, despite being primarily stuffed with the steppe plants, the Oglakhty mannequin was crafted on a riverbank, where C. subtilis might have got inside likely by chance. It is important to note that the stuffing process apparently took place after the vegetation season of C. subtilis in second half of summer and the beginning of autumn. Secondly, our research suggests that a population of C. subtilis, which is currently absent from the documented flora of southern Siberia, previously grew in the Minusinsk Basin wetlands. Our study highlights the need for field expeditions aimed to identify endemic populations of C. subtilis in the Yenisei River valley.},
}

@article {pmid41351056,
year = {2025},
author = {Stach, TL and Starke, J and Bouderka, F and Bornemann, TLV and Soares, AR and Wilkins, MJ and Goldman, AE and Stegen, JC and Borton, MA and Probst, AJ},
title = {Conserved environmental adaptations of stream microbiomes in the hyporheic zone across North America.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02236-1},
pmid = {41351056},
issn = {2049-2618},
support = {426547801//Deutsche Forschungsgemeinschaft/ ; DE-AC05-76RL01830//U.S. Department of Energy/ ; },
abstract = {BACKGROUND: Stream hyporheic zones represent a unique ecosystem at the interface of stream water and surrounding sediments, characterized by high heterogeneity and accelerated biogeochemical activity. These zones-represented by the top sediment layer in this study-are increasingly impacted by anthropogenic stressors and environmental changes at a global scale, directly altering their microbiomes. Despite their importance, the current body of literature lacks a systematic understanding of active nitrogen and sulfur cycling across stream sediment and surface water microbiomes, particularly across geographic locations and in response to environmental factors.

RESULTS: Based on previously published and unpublished datasets, 363 stream metagenomes were combined to build a comprehensive MAG and gene database from stream sediments and surface water including a full-factorial mesocosm experiment which had been deployed to unravel microbial stress response. Metatranscriptomic data from 23 hyporheic sediment samples collected across North America revealed that microbial activity in sediments was distinct from the activity in surface water, contrasting similarly encoded metabolic potential across the two compartments. The expressed energy metabolism of the hyporheic zone was characterized by increased cycling of sulfur and nitrogen compounds, governed by Nitrospirota and Desulfobacterota lineages. While core metabolic functions like energy conservation were conserved across sediments, temperature and stream order change resulted in differential expression of stress response genes previously observed in mesocosm studies.

CONCLUSIONS: The hyporheic zone is a microbial hotspot in stream ecosystems, surpassing the activity of overlaying riverine surface waters. Metabolic activity in the form of sulfur and nitrogen cycling in hyporheic sediments is governed by multiple taxa interacting through metabolic handoffs. Despite the spatial heterogeneity of streams, the hyporheic sediment microbiome encodes and expresses conserved stress responses to anthropogenic stressors, e.g., temperature, in streams of separate continents. The high number of uncharacterized differentially expressed genes as a response to tested stressors is a call-to-action to deepen the study of stream systems. Video Abstract.},
}

@article {pmid41350884,
year = {2025},
author = {De Sanctis, B and Mirchandani, C and Dong, H and Macleod, R and Corbett-Detig, R and Wang, Y},
title = {Bamdam: a post-mapping authentication toolkit for ancient metagenomics.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {413},
pmid = {41350884},
issn = {1474-760X},
support = {35GM128932./NH/NIH HHS/United States ; 35GM128932./NH/NIH HHS/United States ; 4198810//National Natural Science Foundation of China-China Academy of General Technology Joint Fund for Basic Research/ ; 4198810//National Natural Science Foundation of China-China Academy of General Technology Joint Fund for Basic Research/ ; G10144//Social Sciences and Humanities Research Council of Canada/ ; },
mesh = {*Metagenomics/methods ; *Software ; Humans ; },
abstract = {Ancient metagenomic studies using capture or shotgun sequencing often perform pairwise alignment of individual reads against large reference databases followed by lowest common ancestor assignment for taxonomic identification. Here, we present bamdam, a lightweight post-mapping, post lowest common ancestor toolkit for eukaryotic or microbial metagenomics. Bamdam can shrink large metagenomics bam files, often by a factor of 10x or more, while retaining all informative reads and alignments, compute a suite of authentication metrics for each taxonomic node including k-mer duplicity, postmortem damage, and mean read complexity, and generate various visualizations including multi-sample deamination plots and damage-colored interactive Krona plots.},
}

*Metagenomics/methods
*Software
Humans

@article {pmid41350579,
year = {2025},
author = {Tarracchini, C and Longhi, G and Gennaioli, E and Muscò, A and Rizzo, SM and Viappiani, A and Vitale, SG and Mancabelli, L and Lugli, GA and Angioni, S and Turroni, F and van Sinderen, D and Milani, C and Ventura, M},
title = {Compiling an early life human gut microbiome atlas and identification of key microbial drivers.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-025-00868-7},
pmid = {41350579},
issn = {2055-5008},
abstract = {During the first year after birth, the infant gut microbiome undergoes a rapid and profound compositional and functional transformation, impelled by an intricate network of intrinsic and extrinsic factors. This process results in increased taxonomic and functional diversification, alongside greater interindividual variability. To better understand this early-life ecosystem, this study assessed the interindividual variability of the infant gut microbiome using a comprehensive infant gut microbiome database of 5288 fecal metagenomic data from healthy, full-term infants across various geographical locations. Our study identified six reference microbial communities, termed Early-Life Community State Types (ELi-CSTs), which not only capture specific compositional profiles and heterogeneity of the infant gut microbiome, but also record the extensive transformation experienced by this developing microbial community during the first year of human life. Indicative Species analysis and Random Forest modeling assisted the precise identification of unique, key taxonomic signatures that are critical to the structure of each ELi-CST, highlighting microbial taxa with pivotal roles in shaping the infant gut microbiota. To complement these findings, we established a bacterial biobank through dedicated cultivation efforts of the infant microbiota, comprising 182 genome-sequenced isolates corresponding to key taxa involved in early life gut microbiota assembly. This biobank provided the basis for co-cultivation experiments combined with transcriptome analyses, thereby enabling in vitro investigations into microbial cross-talk among key modulators, and yielding novel insights into the molecular interactions and cooperative dynamics behind early microbiome development.},
}

@article {pmid41350543,
year = {2025},
author = {Nickodem, CA and Tran, PQ and Neeno-Eckwall, E and Congdon, AG and Sanford, GR and Silva, EM and Hite, JL},
title = {Soil management strategies drive divergent impacts on pathogens and environmental resistomes.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {43215},
pmid = {41350543},
issn = {2045-2322},
support = {AD00001395//U.S. Department of Agriculture/ ; 58-5090-2-035//U.S. Department of Agriculture/ ; AD00001395//U.S. Department of Agriculture/ ; },
mesh = {*Soil Microbiology ; Manure/microbiology ; Fertilizers ; *Soil/chemistry ; Animals ; Agriculture/methods ; Poultry ; Microbiota ; Metagenomics ; *Drug Resistance, Bacterial/genetics ; Humans ; Gene Transfer, Horizontal ; },
abstract = {Antimicrobial resistance (AMR) is a growing global health threat, and the genes that confer drug resistance are increasingly recognized as widespread environmental contaminants. Livestock manure, widely used as a non-synthetic fertilizer, is a potential source of AMR contamination in the environment. Manure fertilizers are well-documented reservoirs of AMR genes (ARGs) and drug-resistant pathogens. However, the role of soil management practices in shaping the persistence and spread of these genes after manure application remains poorly understood. We conducted a large-scale field experiment to evaluate how soil management practices influence the resistome (the genomic content involved in resistance to antimicrobial agents) and the overall microbiome of agricultural soils. Specifically, we ask: Does the use of composted poultry manure in organic soil management practices increase the risk of transmitting ARGs and drug-resistant pathogens? We integrated metagenomic sequencing with risk score analyses to assess the abundance, diversity, and mobility of resistance genes. Contrary to expectations, our results indicate that non-organic practices, despite not applying poultry manure, posed greater risks for transmitting AMR genes and human pathogens - due to significantly higher co-occurrence of ARGs with mobile genetic elements (MGEs), which facilitate horizontal gene transfer. In contrast, organic practices, that applied composted poultry manure, increased overall ARG and metal resistance gene (MRG) abundance, but the genes were less diverse and less mobile. These findings show that focusing solely on ARG and MRG abundance can misrepresent AMR risks and underscore the importance of evaluating gene mobility and management context when assessing AMR hazards. Our study highlights how soil management can be strategically leveraged to mitigate AMR transmission, offering actionable insights for sustainable agriculture, environmental stewardship, and public health protection.},
}

*Soil Microbiology
Manure/microbiology
Fertilizers
*Soil/chemistry
Animals
Agriculture/methods
Poultry
Microbiota
Metagenomics
*Drug Resistance, Bacterial/genetics
Humans
Gene Transfer, Horizontal

@article {pmid41350329,
year = {2025},
author = {Sato, Y and Kumagai, H and Hirooka, H and Yoshida, T},
title = {Differences in prokaryotic and viral community between rumen and feces.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {43232},
pmid = {41350329},
issn = {2045-2322},
mesh = {*Feces/microbiology/virology ; Animals ; *Rumen/microbiology/virology ; Metagenomics/methods ; *Viruses/genetics/classification ; Metagenome ; Bacteria/genetics ; Virome ; *Prokaryotic Cells/virology ; Genome, Viral ; Gastrointestinal Microbiome ; },
abstract = {Ruminants harbor diverse microbial communities, including prokaryotes and viruses, across their digestive tract. Rumen viruses contribute to carbohydrate metabolism; however, their persistence and host interactions in the lower gastrointestinal tract remain unclear. In this study, we investigated the prokaryotic and viral communities in the rumen and feces of the same wethers using whole-metagenomic and virus-like particle metagenomic sequencing. For prokaryotic community analysis, we reconstructed over 300 metagenome-assembled genomes, most of which were novel. These revealed strong site specificity, with distinct prokaryotic community compositions between the rumen and feces. Virome analysis recovered more than 6,000 viral genomes, including many novel viruses. Unlike prokaryotes, several viruses were found to be shared between the rumen and feces. Auxiliary metabolic genes encoding glycoside hydrolases were identified in several rumen-associated viral genomes, whereas fecal-associated viral genomes did not harbor such genes. Host-virus interaction analysis predicted that viruses predominantly infect dominant bacterial taxa and methanogens within each gastrointestinal site, although some viruses may interact with hosts across different sites. These findings highlight the strong site specificity of the prokaryotic communities and the comparatively broader distribution of viruses within the ruminant gastrointestinal tract. These insights advance understanding of virus-prokaryote-host interactions with implications for animal productivity.},
}

*Feces/microbiology/virology
Animals
*Rumen/microbiology/virology
Metagenomics/methods
*Viruses/genetics/classification
Metagenome
Bacteria/genetics
Virome
*Prokaryotic Cells/virology
Genome, Viral
Gastrointestinal Microbiome

@article {pmid40691354,
year = {2026},
author = {Roux, S and Coclet, C},
title = {Viromics approaches for the study of viral diversity and ecology in microbiomes.},
journal = {Nature reviews. Genetics},
volume = {27},
number = {1},
pages = {32-46},
pmid = {40691354},
issn = {1471-0064},
mesh = {*Microbiota/genetics ; *Viruses/genetics/classification ; *Virome/genetics ; Humans ; Metagenomics/methods ; Ecosystem ; Genetic Variation ; Biodiversity ; Animals ; Genome, Viral ; },
abstract = {Viruses are found across all ecosystems and infect every type of organism on Earth. Traditional culture-based methods have proven insufficient to explore this viral diversity at scale, driving the development of viromics, the sequence-based analysis of uncultivated viruses. Viromics approaches have been particularly useful for studying viruses of microorganisms, which can act as crucial regulators of microbiomes across ecosystems. They have already revealed the broad geographic distribution of viral communities and are progressively uncovering the expansive genetic and functional diversity of the global virome. Moving forward, large-scale viral ecogenomics studies combined with new experimental and computational approaches to identify virus activity and host interactions will enable a more complete characterization of global viral diversity and its effects.},
}

*Microbiota/genetics
*Viruses/genetics/classification
*Virome/genetics
Humans
Metagenomics/methods
Ecosystem
Genetic Variation
Biodiversity
Animals
Genome, Viral

@article {pmid41350265,
year = {2025},
author = {Tang, H and Liu, H and Yuan, L and Xie, M and Zheng, J and Wang, J and Zhou, J and Yang, B and Lou, B and Han, D},
title = {Bronchoalveolar lavage fluid metagenomic datasets: a multidimensional clinical biomolecular resource.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1919},
pmid = {41350265},
issn = {2052-4463},
support = {82472371//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Humans ; *Metagenomics ; *Bronchoalveolar Lavage Fluid/microbiology ; High-Throughput Nucleotide Sequencing ; *Metagenome ; DNA Copy Number Variations ; },
abstract = {Metagenomic Next-Generation Sequencing (mNGS) enables simultaneous sequencing of both microbial and host nucleic acids in clinical samples. However, analytical approaches for interpreting complex mNGS datasets are seldom disclosed, limiting advancements in multimodal analysis and omics-driven research models built upon mNGS results. We present 402 high-quality bronchoalveolar lavage fluid mNGS DNA and RNA sequencing datasets for developing combined microbial-host metagenomic diagnostic approaches. Only the microbial (non-host) sequence reads have been deposited. We provide comprehensive descriptions of methods, tools, and pipelines used for mining microbial features (DNA/RNA microbial composition and bacteriophage abundances) and host response features (differential expression genes, transposable elements, cell-type composition, and copy number variation). These data processing pipelines set a standard for future multimodal omics diagnostic research, promoting the adoption of standardized practices in omics-based studies that integrate clinical data.},
}

Humans
*Metagenomics
*Bronchoalveolar Lavage Fluid/microbiology
High-Throughput Nucleotide Sequencing
*Metagenome
DNA Copy Number Variations

@article {pmid41350118,
year = {2025},
author = {Fukase, S and Kouketsu, A and Tamahara, T and Saito, T and Ito, A and Higashi, Y and Kajita, T and Kurobane, T and Miyakoshi, M and Iikubo, M and Shimizu, R and Takahashi, T and Yamauchi, K and Sugiura, T},
title = {Differences in the Oral Microbiome Between Patients With and Without Oral Squamous Cell Carcinoma.},
journal = {Journal of oral pathology & medicine : official publication of the International Association of Oral Pathologists and the American Academy of Oral Pathology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jop.70099},
pmid = {41350118},
issn = {1600-0714},
abstract = {BACKGROUND: Although studies have demonstrated a relationship between pathogenic microorganisms and oral cancer, no study has demonstrated a relationship between changes in bacterial flora and oral squamous cell carcinoma (OSCC). Therefore, we investigated the association between oral microbiota and oral squamous cell carcinoma using metagenomic analysis.

METHODS: Saliva samples from 64 patients with OSCC and 50 healthy controls who visited the Department of Oral Surgery, Tohoku University Hospital, were collected, and bacterial genomic DNA was extracted using polymerase chain reaction amplification. Single-end sequencing was performed using the Illumina MiSeq platform, and sequence data were analyzed using the Quantitative Insights Into Microbial Ecology 2 platform. The Steel-Dwass test was used for between-group comparisons, and Analysis of Compositions of Microbiomes with Bias Correction was used to detect significant differences in microbiome composition.

RESULTS: Significant differences were observed in alpha-diversity indices of bacterial flora (richness, Faith- phylogenetic diversity, Shannon index) in the OSCC group compared to those in the control group. Among the OSCC group, patients with larger tumor diameters and lymph node metastases (T3/T4, N1 or greater) formed independent clusters in the beta diversity analysis of the bacterial flora. Bacteria of the Actinomycetia phylum, such as Actinomyces and Rothia, were significantly reduced in patients with higher stage and pathological grade. Conversely, bacteria of the phylum Spirochaetia and Proteobacteria, particularly those of the genus Treponema, were significantly elevated in advanced cancer cases.

CONCLUSIONS: Our results suggest that changes in the oral microbiota may play a role in OSCC development and progression.},
}

@article {pmid41349993,
year = {2026},
author = {Zepernick, BN and Niknejad, DJ and Chase, EE and Abiodun, BA and Adler, MJ and Houghton, KA and Olavesen, JL and Sarumi, Q and Truchon, AR and Walton, JL and Cheshire, JH and Stanislawczyk, K and Hart, LN and Paerl, HW and Chaffin, JD and Boyer, GL and Castro, HF and Campagna, SR and Bullerjahn, GS and Wilhelm, SW},
title = {The ornithine-arginine cycle supported a toxic, metalimnic Planktothrix rubescens bloom.},
journal = {Harmful algae},
volume = {151},
number = {},
pages = {103008},
doi = {10.1016/j.hal.2025.103008},
pmid = {41349993},
issn = {1878-1470},
mesh = {*Cyanobacteria/metabolism/physiology/genetics ; *Arginine/metabolism ; *Ornithine/metabolism ; *Harmful Algal Bloom ; Metagenomics ; },
abstract = {Planktothrix rubescens is distinct from other cyanobacterial harmful algal bloom (cHAB) genera: the crimson-red cHAB thrives in the cold, low-light, nutrient-limited metalimnion. Studies have attributed this ecological success to buoyancy regulation, low-light adaptations, and the uptake of nitrogen-rich amino acids. Yet, it remains to be mechanistically determined how this cHAB maintains physiological nutrient quotas in the metalimnion due to limited in situ molecular studies. We employed metagenomics and metabolomics to generate hypotheses concerning a toxigenic P. rubescens bloom in Mead's Quarry (Knoxville, TN, USA) observed in two separate years. Our results suggest a perennial, metalimnic P. rubescens population may exist, with spring turnover facilitating seasonal migration to the epilimnion. Although P. rubescens dominated the epilimnion and metalimnion, intracellular metabolite pools grouped by depth and suggested depth-discrete partitioning of the arginine deiminase-mediated ornithine-arginine cycle (OAC, i.e., urea cycle) - while further indicating the presence of the arginine catabolic pathway. Though the arginine influx driving the OAC is unclear, we hypothesize this input is provided via the uptake of urea or nitrogen-rich amino acids. Further, we demonstrate arginine deiminase (agrE/argZ) is broadly distributed in Planktothrix genera and known microcystin producers, suggesting agrE/argZ-mediated arginine metabolism and the OAC may influence the fitness of toxigenic cHAB genera which require ample nitrogen to synthesize microcystins. Cumulatively, our results serve as a case study to provide insight on the metabolic pathways driving the ecological success of metalimnic P. rubescens blooms. On a broader scale, this work strengthens the case that alternative nitrogen metabolism - including urea utilization, amino acid catabolism, and the OAC - is a driver of toxigenic cHABs in fresh waters.},
}

*Cyanobacteria/metabolism/physiology/genetics
*Arginine/metabolism
*Ornithine/metabolism
*Harmful Algal Bloom
Metagenomics

@article {pmid41349311,
year = {2025},
author = {Manfreda, C and Ghidini, S and Fuschi, A and Remondini, D and Guarneri, F and Alborali, GL and Fernández-Trapote, E and Cobo-Dìaz, JF and Alvarez-Ordóñez, A and Ianieri, A},
title = {In-depth characterization of microbiome and resistome of carcasses and processing environments in a swine slaughterhouse.},
journal = {Veterinary microbiology},
volume = {312},
number = {},
pages = {110820},
doi = {10.1016/j.vetmic.2025.110820},
pmid = {41349311},
issn = {1873-2542},
abstract = {Antimicrobial resistance represents a critical global health challenge. Within the swine production chain, all stages have been identified as potential reservoirs for antimicrobial resistance genes. In the present study whole metagenomic sequencing technology was applied in a swine slaughterhouse and pig carcasses to investigate microbial communities and their associated antimicrobial resistance genes. Actinomycetota and Pseudomonadota were the dominant phyla across all samples, while Bacillota, Bacteroidota, and Campylobacteriota were more prevalent in the dirty zone and carcass samples than in the clean zone. Key antimicrobial-resistant bacteria included genera such as Acinetobacter, Aeromonas, and Streptococcus, with Acinetobacter spp., Streptococcus suis, and Aliarcobacter cryaerophilus identified as high-priority species for food safety due to their persistence and antimicrobial resistance genes associations. Several genera showed strong correlations with resistance to macrolides, lincosamides, and beta-lactams. Moreover, the plasmid-borne and lateral gene transfer events were associated with dirty zone and carcass samples in comparison to clean zone samples, suggesting the potential dissemination of antimicrobial resistance genes, especially for macrolides and sulphonamides resistance genes. Tetracycline, beta-lactam, and aminoglycoside resistance genes were the most abundant antimicrobial resistance genes across all samples, consistent with a pig slaughterhouse environment. This study highlights distinct microbiome profiles across environmental zones of a pig slaughterhouse, reflecting the adaptation of bacterial taxa to specific processing conditions. The findings have significant implications for food business operators who have to apply appropriate hygienic measures to reduce the dissemination of bacterial food-borne pathogens and to mitigate the risk of antimicrobial resistance transfer along the food chain.},
}

@article {pmid41348832,
year = {2025},
author = {Cervantes-Echeverría, M and Jimenez-Rico, MA and Manzo, R and Hernández-Reyna, A and Cornejo-Granados, F and Bikel, S and González, V and Hurtado Ramírez, JM and Sánchez-López, F and Salazar-León, J and Pedraza-Alva, G and Perez-Martinez, L and Ochoa-Leyva, A},
title = {Human-derived fecal virome transplantation (FVT) reshapes the murine gut microbiota and virome, enhancing glucose regulation.},
journal = {PloS one},
volume = {20},
number = {12},
pages = {e0337760},
doi = {10.1371/journal.pone.0337760},
pmid = {41348832},
issn = {1932-6203},
mesh = {Animals ; *Gastrointestinal Microbiome ; Humans ; Mice ; *Fecal Microbiota Transplantation/methods ; *Virome ; Male ; Diet, High-Fat/adverse effects ; Obesity/therapy/microbiology ; *Feces/virology ; Mice, Inbred C57BL ; *Glucose/metabolism ; Metabolic Syndrome/therapy/microbiology ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; },
abstract = {The gut microbiome, comprising bacteria, viruses, archaea, fungi, and protists, plays a crucial role in regulating host metabolism and health. This study explored the effects of fecal virome transplantation (FVT) from healthy human donors on metabolic syndrome (MetS) in a diet-induced obesity (DIO) mouse model, without diet change. Mice received a single oral dose of human-derived virus-like particles (VLPs) and continued on a high-fat diet (HFD) for 17 weeks. Despite persistent dietary stress, FVT significantly improved glucose tolerance. Longitudinal profiling by virome shotgun metagenomics and bacterial 16S rRNA sequencing revealed marked, durable shifts in both viral and bacterial community composition. Notable bacterial changes included a decrease in Akkermansia muciniphila and Peptococcaceae and increases in Allobaculum and Coprococcus; A. muciniphila positively correlated with glucose levels and negatively correlated with body weight. Together, these results suggests that human-derived virome can durably reshape gut microbial ecology and improve glucose metabolism in mice with obesity, even without dietary modification, offering a novel avenue for developing phage-based therapies. This proof-of-concept study provides foundational observations for using human-derived VLPs for FVT in standard laboratory mouse models, and provides a foundation for elucidating bacteria-phage interactions and their role in host metabolic health.},
}

Animals
*Gastrointestinal Microbiome
Humans
Mice
*Fecal Microbiota Transplantation/methods
*Virome
Male
Diet, High-Fat/adverse effects
Obesity/therapy/microbiology
*Feces/virology
Mice, Inbred C57BL
*Glucose/metabolism
Metabolic Syndrome/therapy/microbiology
RNA, Ribosomal, 16S/genetics
Bacteria/genetics

@article {pmid41348596,
year = {2025},
author = {Hernández-Velázquez, R and Ziemski, M and Bokulich, NA},
title = {ViromeXplore: integrative workflows for complete and reproducible virome characterization.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {6},
pages = {},
doi = {10.1093/bib/bbaf638},
pmid = {41348596},
issn = {1477-4054},
support = {22.00210//Swiss State Secretariat for Education, Research and Innovation/ ; //European Union nor European Research Executive Agency/ ; },
mesh = {*Virome ; *Workflow ; *Metagenomics/methods ; *Software ; High-Throughput Nucleotide Sequencing ; *Computational Biology/methods ; *Viruses/genetics/classification ; Metagenome ; Microbiota ; Genome, Viral ; Reproducibility of Results ; },
abstract = {Viruses play a crucial role in shaping microbial communities and global biogeochemical cycles, yet their vast genetic diversity remains underexplored. Next-generation sequencing technologies allow untargeted profiling of metagenomes from viral communities (viromes). However, existing workflows often lack modularity, flexibility, and seamless integration with other microbiome analysis platforms. Here, we introduce "ViromeXplore," a set of modular Nextflow workflows designed for efficient virome analysis. ViromeXplore incorporates state-of-the-art tools for contamination estimation, viral sequence identification, taxonomic assignment, functional annotation, and host prediction while optimizing computational resources. The workflows are containerized using Docker and Singularity, ensuring reproducibility and ease of deployment. Additionally, ViromeXplore offers optional integration with QIIME 2 and MOSHPIT, facilitating provenance tracking and interoperability with microbiome bioinformatics pipelines. By providing a scalable, user-friendly, and computationally efficient framework, ViromeXplore enhances viral metagenomic analysis and contributes to a deeper understanding of viral ecology. ViromeXplore is freely available at https://github.com/rhernandvel/ViromeXplore.},
}

*Virome
*Workflow
*Metagenomics/methods
*Software
High-Throughput Nucleotide Sequencing
*Computational Biology/methods
*Viruses/genetics/classification
Metagenome
Microbiota
Genome, Viral
Reproducibility of Results

@article {pmid41348453,
year = {2025},
author = {Li, C and Ge, H and Huang, W and Zilda, DS and Radjasa, OK and Zhao, L and Cong, B and Liu, S and Zhang, Z},
title = {Vertically stratified microbial diversity and keystone species driving element cycling in the Magellan seamount sediments.},
journal = {Microbial genomics},
volume = {11},
number = {12},
pages = {},
doi = {10.1099/mgen.0.001493},
pmid = {41348453},
issn = {2057-5858},
mesh = {*Geologic Sediments/microbiology/chemistry ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/metabolism ; Metagenomics/methods ; Archaea/genetics/classification ; Phylogeny ; Biodiversity ; Microbiota ; },
abstract = {Deep-sea polymetallic nodules, rich in cobalt, nickel and titanium, are valuable for electronics, aerospace and energy industries. However, the vertical distribution and ecological functions of prokaryotic communities in sediments beneath nodules from the Magellan seamounts, a unique microbial habitat characterized by ultra-slow sedimentation rates (0.4-4 mm ky[-1]) and heterogeneous metal gradients, remain poorly characterized. In our research, 16S rRNA gene amplicon sequencing and metagenomic analyses of sediment cores (0-20 cm) from the western Pacific polymetallic nodule province revealed statistically significant decreases in prokaryotic diversity (Shannon index: 9.446 to 2.288; P<0.001). Proteobacteria, Crenarchaeota, Chloroflexi and Bacteroidota were the dominant taxa. The microbial co-occurrence network in the surface layer had a longer mean path length (2.11 vs 1 in the bottom layer) and a larger network diameter (11 vs 1), indicating a loose community structure and greater resistance to disturbance, while the bottom microbial network had a higher density (0.037 vs 0.01) and clustering coefficient (0.32 vs 1), suggesting tight microbial interactions. The concentrations of MnO (6.96-9.41 µg g[-1]) and P2O5 (2.55-3.89 µg g[-1]) gradually decreased with increasing depth. The concentrations of Co and Pb were relatively high in the surface sediments (0-8 cm) but decreased significantly below 8 cm. In contrast, the concentrations of Fe2O3 and As increased with depth. The environmental factors depth, MnO, Fe2O3 and heavy metals (Cr, Zn and Cu) were found to be the main drivers of the microbial community structure. We assembled 122 metagenome-assembled genomes from the metagenomic data. Gene abundance analysis revealed that sox genes (soxB/C/D/X/Y/Z) and assimilatory sulphate reduction genes (cysC and cysH) were highly abundant in the surface sediment, whereas the abundance of dissimilatory sulphate reduction genes (dsrA and dsrB) was enhanced in the bottom layer, reflecting a hierarchical adaptive strategy for sulphur metabolism. Our study expands current knowledge on the vertical variations of microbial diversity and microbially driven biogeochemical cycling in deep-sea settings underneath polymetallic nodules. Characterizing the microbial community underneath those nodules may provide insights into microbial resilience in extreme oligotrophic environments and valuable insights for future deep-sea mining activities.},
}

*Geologic Sediments/microbiology/chemistry
RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification/metabolism
Metagenomics/methods
Archaea/genetics/classification
Phylogeny
Biodiversity
Microbiota

@article {pmid41348443,
year = {2025},
author = {Luu, LDW and Bryant, C and Brown, J and Turner, M and Pham, TH and Mazraani, R and Burke, C and Jury, B and Shrestha, M and Fleming, K and Bateson, D and Russell, D and Bassett, F and Ong, E and Hocking, JS and Sweeney, S and Huston, WM},
title = {Cervicovaginal microbiome composition and absolute quantity are associated with pelvic inflammatory disease.},
journal = {Microbial genomics},
volume = {11},
number = {12},
pages = {},
doi = {10.1099/mgen.0.001574},
pmid = {41348443},
issn = {2057-5858},
mesh = {Humans ; Female ; *Pelvic Inflammatory Disease/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Case-Control Studies ; *Vagina/microbiology ; Adult ; *Cervix Uteri/microbiology ; Vaginosis, Bacterial/microbiology ; Gardnerella vaginalis/genetics ; Metagenomics ; *Bacteria/genetics/classification/isolation & purification ; Young Adult ; },
abstract = {Pelvic inflammatory disease (PID), which involves infection and inflammation of the female reproductive tract, can lead to sequelae including chronic pelvic pain, ectopic pregnancy and tubal factor infertility. A causative pathogen is not identified in many PID cases (idiopathic PID) and does not develop in all women with a sexually transmitted infection or bacterial vaginosis. Therefore, there is a need to better understand the pathogenesis of PID. A case-control study was conducted to explore microbiome, antibiotic resistance and immune gene expression in PID. Microbial profiling using both 16S rRNA gene amplicon and metagenomic approaches revealed that bacterial vaginosis-associated bacteria such as Gardnerella vaginalis, Fannyhessea vaginae, Ureaplasma parvum and members of the Prevotella spp. were significantly enriched in PID cases, while healthy controls were associated with Lactobacillus (L.) crispatus. Quantitative analysis with species-specific quantitative real-time PCR (qPCR) indicated that a high copy number of L. crispatus (measured using calibrated copy estimates by qPCR) was strongly associated with cervical samples from women in the control group, whereas PID cases with this organism had low copies when measured using qPCR. Antibiotic resistance to tetracyclines was more frequently predicted in metagenome-assembled genomes from PID cases, and corresponding isolates cultured from cases were less susceptible to doxycycline (L. iners). Overall, this study supports that PID is associated with cervicovaginal dysbiosis and an absence or low quantity of L. crispatus.},
}

Humans
Female
*Pelvic Inflammatory Disease/microbiology
RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
Case-Control Studies
*Vagina/microbiology
Adult
*Cervix Uteri/microbiology
Vaginosis, Bacterial/microbiology
Gardnerella vaginalis/genetics
Metagenomics
*Bacteria/genetics/classification/isolation & purification
Young Adult

@article {pmid41347789,
year = {2025},
author = {Malina, N and Tollerson, R and Monami, SJ and Rivera, E and Lee, M-K and Bilenker, LD and Ojeda, AS},
title = {Microbial community diversity and geochemistry inform bioremediation of molybdenum-contaminated groundwater.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0098825},
doi = {10.1128/aem.00988-25},
pmid = {41347789},
issn = {1098-5336},
abstract = {In situ remediation of groundwater at coal combustion product (CCP) sites can be challenging for elements such as molybdenum (Mo), which do not respond well to commonly used treatment. This research was initiated to improve the understanding of geochemistry and microbial diversity associated with a Mo plume at a CCP site toward the development of an in situ treatment scheme. Diffusive microbial samplers were designed and deployed at the study site for 9 weeks. Afterward, geochemical and community analyses were used as the basis to understand how microbial communities respond to elevated Mo concentrations within a plume. Our results show that the Mo and other constituents within the plume do not reduce the diversity of the community, in contrast to trends observed at other industrial sites with metals and metalloids in groundwater. Interestingly, bacteria of the order Burkholderiales were higher in abundance in wells where Mo >0.3 mg/L, and several sulfate-reducing bacteria were less abundant but not absent. Molybdenum sequestration experiments were also performed with sulfate-reducing bacteria enriched from groundwater samples collected at the site. The results show that Desulfomicrobium escambiense played a major role in Mo sequestration and activated a detoxification mechanism. This process involved the sequential activation of periplasmic heavy metal sensors, followed by the activation of atpE ATP synthase, which may function as an exporter of Mo to form Mo-S species in the periplasm of the cell. The results provide important considerations for bioremediation potential in groundwater settings impacted by Mo, especially those who seek to stimulate sulfate-reducing bacteria for Mo sequestration in biogenic sulfide solids.IMPORTANCEBioremediation of contaminated sites has become popular for chlorinated hydrocarbons, but it has not been widely applied to inorganic constituents outside of arsenic. Here, we show the potential for the development of geochemistry-informed bioremediation technologies of Mo-contaminated groundwater by leveraging Mo-tolerant communities despite the suppression of sulfate reduction by Mo.},
}

@article {pmid41347294,
year = {2026},
author = {McCaughan, KJ and Kniel, KE},
title = {Current Knowledge and Future Directions for Cyclospora cayetanensis Research and Its Surrogates.},
journal = {Comprehensive reviews in food science and food safety},
volume = {25},
number = {1},
pages = {e70327},
doi = {10.1111/1541-4337.70327},
pmid = {41347294},
issn = {1541-4337},
support = {//National Institute of Food and Agriculture/ ; },
mesh = {*Cyclospora/genetics/isolation & purification/physiology ; *Cyclosporiasis/parasitology/transmission ; Humans ; Animals ; Host-Parasite Interactions ; Oocysts ; Food Parasitology ; Cryptosporidium parvum ; },
abstract = {Cyclospora cayetanensis is a foodborne protozoan parasite that causes cyclosporiasis, a disease transmitted by the consumption of sporulated oocysts, often via contaminated produce. Since 2018, outbreaks traced back to domestically grown produce in the United States have raised growing concern. Despite its public health significance, research is hindered by methodological challenges, including inability to culture in vitro/in vivo and limited genomic characterization. This review examines current knowledge on its occurrence and transmission, detection methods, host-parasite interactions, genetics, and remediation strategies, while also evaluating use of surrogate organisms (Eimeria spp. and Cryptosporidium parvum) to address research gaps. Detection remains challenging due to low oocyst concentrations in environmental and food matrices, requiring highly sensitive molecular assays. Additionally, the lack of standardized sampling methods that are representative of an entire batch of produces further complicates reliable detection and surveillance efforts. The recently implemented Food and Drug Administration (FDA) Bacteriological Analytical Manual (BAM) Chapter 19c method has improved sensitivity but still requires refinement. Although Eimeria spp. offer insight into sporulation and environmental behaviors and C. parvum has supported methodological development, neither fully replicates C. cayetanensis biology; limiting the translatability of surrogate-based research. Remediation strategies are underexplored, though research on related coccidia suggests significant resistances to conventional sanitizers. Genomic advancements, including the identification of distinct C. cayetanensis lineages, provide useful insights, though gaps in genome assemblies limit phylogenetic and functional analyses. Emerging tools, such as metagenomics, single-cell sequencing, and AI-driven bioinformatics, may overcome persistent barriers. Addressing these challenges is essential for improving detection, risk assessment, and guiding policy, all of which will mitigate the public health burden of cyclosporiasis.},
}

*Cyclospora/genetics/isolation & purification/physiology
*Cyclosporiasis/parasitology/transmission
Humans
Animals
Host-Parasite Interactions
Oocysts
Food Parasitology
Cryptosporidium parvum

@article {pmid41346779,
year = {2025},
author = {Orsud, H and Zoughbor, S and AlDhaheri, F and Hajissa, K and Refaey, M and Ajab, S and Alswaider, K and Mohamed, N and Alkaabi, O and Al Rasbi, Z},
title = {Multi-marker comparative analysis of 18S, ITS1, and ITS2 primers for human gut mycobiome profiling.},
journal = {Frontiers in bioinformatics},
volume = {5},
number = {},
pages = {1690766},
pmid = {41346779},
issn = {2673-7647},
abstract = {BACKGROUND: Gut fungi play crucial roles in human health. The profiling of the human gut mycobiome continues to progress. However, adjustments in the selection of ribosomal DNA marker regions can substantially affect the taxonomic resolution of a population. In particular, the impact of using primers' combinations is insufficiently defined. In this study, we investigated the performance of three targeted sequencing regions, ITS1, ITS2 and 18S rRNA, separately and in combination.

METHODS: Eight fecal samples from healthy individuals (n = 4) and cancer patients (n = 4) were selected as proof of principle for amplicon-based sequencing conducted with the DNBSEQ™ sequencing system. Quality-filtered reads were grouped into operational taxonomic units (OTUs) via USEARCH and categorized using the SILVA (18S) and UNITE (ITS) databases. Downstream bioinformatics encompassed diversity analyses, principal component analysis (PCA), and biomarker detection via linear discriminant analysis effect size (LEfSe). To improve taxonomic coverage and compositional understanding, data were examined using ALDEx2 with centered log-ratio (CLR) transformation, facilitating reliable differential abundance and effect size assessment in small sample metagenomic contexts.

RESULTS AND DISCUSSION: Among primers, ITS2 and ITS1 enhanced the coverage of identified taxa, with operational taxonomic unit quantities of 183 and 158, respectively, compared to 58 OTUs of 18S. Accordingly, among primer combinations tested, the triple integration of ITS1-ITS2-18S produced the highest fungal richness, while the dual ITS1-ITS2 combined datasets enhanced group discrimination analysis, showing enrichment of Candida albicans and scarcity of Penicillium sp. in cancer patients. Our findings based on ITS sequencing and the combination of ITS1 and ITS2 provide instructive information on the composition and dynamics of gut fungi in our initial test subjects, enhancing our understanding of their roles in gut homeostasis and the microbial shifts associated with cancer. Despite our approach being conducted with a limited cohort to establish methodological feasibility, it brings attention to multi-marker strategies, demonstrating that integrated primer datasets surpass traditional single-marker methods in both taxonomic coverage and biomarker detection sensitivity in low-biomass fecal samples. Our research provides a reliable starting point for future studies on gut mycobiome in both healthy and diseased individuals, which could lead to better diagnostics and treatments based on microbiome profiles.},
}

@article {pmid41346662,
year = {2025},
author = {Ren, M and Liao, Q},
title = {Diagnosis of Salmonella enterica-induced septic arthritis in a healthy child using metagenomic next-generation sequencing: a case report.},
journal = {Frontiers in pediatrics},
volume = {13},
number = {},
pages = {1704234},
pmid = {41346662},
issn = {2296-2360},
abstract = {Salmonella enterica-induced arthritis frequently manifests in children with malignancies, sickle cell disease, immunodeficiency, or undergoing immunosuppressive therapy; however, its incidence in healthy children is rare. Here, we present a case of septic arthritis resulting from S. enterica infection in a previously healthy child, diagnosed utilizing metagenomic next-generation sequencing (mNGS). This case underscores the utility of mNGS in the clinical identification of S. enterica arthritis. Particularly in scenarios where the causative pathogen remains unidentified, mNGS emerges as a pivotal adjunctive diagnostic modality for uncommon pathogens.},
}

@article {pmid41346360,
year = {2025},
author = {Huang, J and Li, S and Jiang, C and Wang, L and Pan, Z and Zhang, Z and Zhu, J and Chen, W and Hu, X},
title = {Targeted next-generation sequencing for respiratory infections in patients with haematological malignancies.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1678858},
pmid = {41346360},
issn = {2235-2988},
mesh = {Humans ; *Hematologic Neoplasms/complications ; *Respiratory Tract Infections/diagnosis/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; Middle Aged ; Female ; Male ; Adult ; Aged ; Immunocompromised Host ; Sensitivity and Specificity ; Metagenomics/methods ; Young Adult ; Aged, 80 and over ; Adolescent ; Bacteria/genetics/isolation & purification/classification ; },
abstract = {BACKGROUND: Patients with haematological malignancies are immunocompromised and prone to respiratory infections, but identification of causative pathogens is challenging. The aim of this study was to analyse the ability of targeted next-generation sequencing (tNGS) to detect pathogens in immunocompromised patients.

METHODS: tNGS and conventional microbiological tests (CMT) were performed on samples from the respiratory tract of 99 patients with suspected respiratory infections. Metagenomic next-generation sequencing (mNGS) was conducted in parallel in 43 patients. Comparative analysis was conducted using the Pearson χ2 test and Fisher's exact test, as appropriate.

RESULTS: The overall microbial detection rates for tNGS were 100% (23/23) in the upper respiratory tract and 96.1% (99/103) in the lower respiratory tract. Microorganism colonization was detected by tNGS in 80.8% (97/120) of cases. The sensitivity of tNGS was approximately 30% higher than that of CMT (87.7% vs. 52.5%; P < 0.001), but tNGS had a lower specificity (33.3% vs. 83.3%; P = 0.242). tNGS improved the overall treatment success rate by 69.7% (69/99 cases) in CMT true-negative or CMT-partially matched cases. In the paired respiratory tNGS and mNGS cases, tNGS verified 73.3% (11/15) cases of infection, while mNGS only verified 40% (P = 0.139).

CONCLUSIONS: Most immunosuppressed patients are colonized by microorganisms, and require prompt identification of the cause of any infections. tNGS has promising diagnostic potential and offers valuable information for optimizing antibiotic therapy, especially when compared to CMT.},
}

Humans
*Hematologic Neoplasms/complications
*Respiratory Tract Infections/diagnosis/microbiology
*High-Throughput Nucleotide Sequencing/methods
Middle Aged
Female
Male
Adult
Aged
Immunocompromised Host
Sensitivity and Specificity
Metagenomics/methods
Young Adult
Aged, 80 and over
Adolescent
Bacteria/genetics/isolation & purification/classification

@article {pmid41346331,
year = {2025},
author = {Preenanka, R and Sivam, V and Sasikala, R and Koombankallil, R and Raveendran, K and Jacob, J and Devadas, AL and Ravikumar, NK and Anbalakan, M and Chigilipalli, H and Thangaraj, RS and Basha, AK and Joseph, TC and Badireddy, MR and Vaiyapuri, M},
title = {Muscle Microbiome Analysis of Indian Mackerel (Rastrelliger kanagurta) Delineated Classical and Novel Spoilage Bacteria.},
journal = {Journal of food science},
volume = {90},
number = {12},
pages = {e70751},
doi = {10.1111/1750-3841.70751},
pmid = {41346331},
issn = {1750-3841},
support = {BT/PR46349/AAQ/3/1063/2022// Department of Biotechnology/ ; // Department of Biotechnology, Ministry of Science and Technology, India/ ; },
mesh = {Animals ; *Perciformes/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Microbiota ; *Seafood/microbiology ; Food Packaging/methods ; Food Microbiology ; RNA, Ribosomal, 16S/genetics ; *Muscles/microbiology ; Vacuum ; Metagenomics ; Food Storage ; },
abstract = {Metagenomics allows a comprehensive insight into the spoilage-associated muscle microbiome shifts in the air-packed and vacuum-packed Indian mackerel. This study explored the microbial composition and diversity of spoilage flora in air-packed (T1M, T2M, and T3M) and vacuum-packed (T4M, T5M, and T6M) Indian mackerel (Rastrelliger kanagurta) stored at 0 ± 2°C (iced), 5 ± 2°C (chilled), and 30 ± 2°C (abused) temperatures through metagenomics, targeting the V1-V9 region of 16s rRNA. Total Volatile Base Nitrogen and Thiobarbituric Acid were analyzed to confirm the spoilage threshold limit, and accordingly, the fish muscle tissue on the spoilage day was selected for microbiome analysis. Metagenomic analysis revealed distinct variation in the relative abundance and spoilage microbiome between the air-packed and vacuum-packed Indian mackerel stored at iced, chilled, and abused temperatures. The predominant bacterial species responsible for spoilage were Cetobacterium ceti, Clostridium polyendosporum, and Gilliamella apicola in vacuum-packed mackerel, whereas Shewanella arctica, S. aquimarina, S. baltica, Staphylococcus xylosus, and Burkholderia cepacia played a major role in the spoilage of air-packed samples. The observed bacterial population dynamics across different temperatures and packaging significantly influenced the microbiome diversity in Indian mackerel. Summing up, this study emphasizes the unique and diverse microbes contributing to spoilage and provides a valuable guide for the flora that need to be controlled for extending the shelf life of Indian mackerel.},
}

Animals
*Perciformes/microbiology
*Bacteria/classification/genetics/isolation & purification
*Microbiota
*Seafood/microbiology
Food Packaging/methods
Food Microbiology
RNA, Ribosomal, 16S/genetics
*Muscles/microbiology
Vacuum
Metagenomics
Food Storage

@article {pmid41346299,
year = {2025},
author = {Zhang, C and Zhao, Z and Zhou, F and Shi, C and Zhai, X and Sha, Z and Chu, Q and Liu, H and Liu, S and Pan, Z and Wang, X and Pan, X and Fang, M and Rillig, MC and Wang, Z},
title = {Conventional and Biodegradable Microplastics Both Impair Soil Phosphorus Cycling and Availability via Microbial Suppression.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c11806},
pmid = {41346299},
issn = {1520-5851},
abstract = {Microplastics (MPs) are emerging soil pollutants that can disrupt essential biogeochemical processes, yet their effects on phosphorus (P) cycling remain underexplored. Here, we conducted a 150-day incubation experiment using agricultural soil amended with either polyethylene (PE, conventional) or polylactic acid (PLA, biodegradable) MPs to investigate their impact on microbially mediated P cycling. MPs altered soil P cycling and decreased available phosphorus (AP) by ∼15% after 90 days. Fourier transform infrared spectroscopy revealed weakened AP-associated functional groups (P-O-P, P-O, and P═O), most pronounced under PLA treatment. These shifts were accompanied by reduced abundances of key P-cycling taxa (Bacillus, Paenibacillus, and Sphingomonas) and downregulation of phosphatase gene abundance (phoA/D/X: -65.4% in PE, -59.8% in PLA). Correspondingly, the activities of acid, neutral, and alkaline phosphatases were all suppressed, with alkaline phosphatase in PE-treated soil reduced by 34.1%. Together, these results demonstrate that MPs disturb biotic transformation pathways, leading to subsequent alterations in the chemical speciation of soil P and decreased AP content. Notably, significant disruption was observed for both conventional and biodegradable types. Our findings challenge the prevailing assumption of environmental benignity for biodegradable plastics and underscore the urgent need for mechanistic assessments of their byproducts. Such disruption may hinder microbial P mobilization and decrease fertilizer use efficiency, ultimately threatening soil health and agricultural sustainability.},
}

@article {pmid41345980,
year = {2025},
author = {Jiang, Y and Che, L and Li, SC},
title = {Deciphering the personalized functional redundancy hierarchy in the gut microbiome.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02273-w},
pmid = {41345980},
issn = {2049-2618},
support = {JCYJ20220818101201004//Shenzhen Science and Technology Innovation Program/ ; JCYJ20220818101201004//Shenzhen Science and Technology Innovation Program/ ; JCYJ20220818101201004//Shenzhen Science and Technology Innovation Program/ ; },
abstract = {BACKGROUND: Functional redundancy (FR) in the human gut microbiome is crucial for maintaining stability and resilience, exhibiting a hierarchical structure. However, the precise configuration and functional implications of this hierarchy remain elusive and limited by single-metric measurements. We aimed to develop a method that comprehensively characterizes the hierarchical organization of functional redundancy in personalized microbiomes.

RESULTS: We represented functional redundancy as a network and developed a structural entropy (SE)-based approach to elucidate FR hierarchy, revealing functional redundancy clusters (FRCs)-groups of species capable of independently executing specific metabolic pathways. Through controlled simulations and cross-cohort analyses spanning 4912 gut metagenomes across 28 disease cohorts, we established that our approach offers higher resolution, more comprehensive measurement, and greater robustness in detecting disease-associated functional patterns than traditional FR methods. In healthy individuals, we observed FR network polycentric structure, which shifted to monocentric structure in non-alcoholic steatohepatitis patients. Vitamin biosynthesis FRCs correlated with microbiota transplantation efficiency, while FRCs specialized in short-chain fatty acid production predicted immunotherapy response and patient survival. Permutation tests validated the causal relationship between SE differences and disease phenotypes, while perturbation experiments revealed that FR keystone species exert disproportionate influence on the system's resilience.

CONCLUSIONS: Our SE-based approach to functional redundancy analysis provides superior sensitivity compared to conventional metrics by integrating multiple hierarchical levels of functional organization. This methodology establishes a novel perspective for understanding microbiome stability through personalized FR networks, positioning FRCs as promising diagnostic markers and therapeutic targets for microbiome-associated diseases. Video Abstract.},
}

@article {pmid41345979,
year = {2025},
author = {Sakanaka, A and Furuno, M and Ishikawa, A and Katakami, N and Inoue, M and Mayumi, S and Kurita, D and Nishizawa, H and Omori, K and Taya, N and Isomura, ET and Kudoh, M and Takeuchi, H and Amano, A and Shimomura, I and Fukusaki, E and Kuboniwa, M},
title = {Diabetes alters the supragingival microbiome through plasma-to-saliva migration of glucose and fructose.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02256-x},
pmid = {41345979},
issn = {2049-2618},
support = {22H03300, 22H00487, 22K10311, 21K18281//Japan Society for the Promotion of Science/ ; JP16gm0710005//Japan Agency for Medical Research and Development/ ; },
abstract = {BACKGROUND: Dental caries, a dysbiotic biofilm disease driven by polymicrobial acidogenesis, often coexists with type 2 diabetes (T2D). Previous studies suggest covarying relationships between circulating and salivary metabolites in patients with T2D. However, the role of hyperglycemia-induced saccharide migration from plasma to saliva in caries pathogenesis remains unclear. Here, we developed a novel method for untargeted metabolomics profiling of trace saliva from sublingual and submandibular glands, comparing this profile with those of plasma and whole saliva in participants with T2D (n = 31) and those with normoglycemia (n = 30). This comparison aimed to determine how circulating saccharide migration into the oral cavity and its subsequent microbial consumption are linked to dental caries. Additionally, shotgun metagenomic sequencing was combined with this analysis to investigate the cariogenic impact of circulating saccharide migration on the composition and function of supragingival biofilm using MetaPhlAn4 and HUMAnN3 pipelines.

RESULTS: The metabolomics profiles of glandular saliva showed intermediate dissimilarity between plasma and whole saliva, reflecting cardiometabolic traits more sensitively than whole saliva. Glucose and fructose showed a decreasing positive correlation with glycemic parameters in the order of plasma, glandular saliva, and whole saliva, suggesting systemic-to-oral migration and subsequent microbial consumption. Saccharide migration was more pronounced in participants with dental caries and plaque accumulation, coinciding with shifts in supragingival microbiota, including depletion of Streptococcus sanguinis, Corynebacterium durum, and Rothia aeria, and enrichment of Streptococcus mutans, Veillonella parvula, and Actinomyces sp. oral taxon 448. Glycolytic potential increased at the community level. Improved glycemic control reduced fructose migration and mitigated dysbiosis, decreasing fructose phosphotransferase abundance and shifting the S. mutans-S. sanguinis balance. Experimental validation demonstrated that fructose promotes S. mutans dominance over S. sanguinis in dual-species biofilms.

CONCLUSIONS: This study establishes saccharide migration as a metabolic driver of supragingival dysbiosis in T2D. The findings highlight the role of both glucose and fructose in caries pathogenesis and suggest that glycemic control could serve as an effective strategy as part of caries control. Video Abstract.},
}

@article {pmid41345977,
year = {2025},
author = {Saati-Santamaría, Z and González-Dominici, LI and Jiménez-Gómez, A and Morais, D and Tláskal, V and Frontela, I and Benada, O and Qi, L and Sheng, Y and Rivas, R and Baldrian, P and García-Fraile, P},
title = {Transcriptome-guided discovery of novel plant-associated genes in a rhizosphere Pseudomonas.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02277-6},
pmid = {41345977},
issn = {2049-2618},
support = {101090267//HORIZON-TMA-MSCA-PF-EF/ ; PID2023-150384NB-I00//European Union NextGenerationEU/PRTR/ ; TED2021-129157B-100//MICIU/AEI/10.1309/501100011033/ ; CLU-2025-2-04//Escalera de Excelencia - Consejería de Educación de Castilla y León - ERDF/ ; RYC2023-045204-I//MCIU/AEI/10.13039/501100011033 and ESF+/ ; 750795//EUROPEAN UNION'S HORIZON 2020/ ; },
abstract = {BACKGROUND: Microorganisms play important ecological roles during interactions with plants, with some strains promoting plant performance. However, the molecular basis of bacterial adaptation to the plant environment remains poorly understood. Microbial plant growth promotion is a complex process that likely involves numerous bacterial genes, many of which remain uncharacterized. In this study, we aimed to identify genes tightly associated with the bacterial adaptation to plant hosts by integrating transcriptomic data from bacteria colonizing roots with comparative genomic and metagenomic analyses.

RESULTS: Here, we identified a set of bacterial genes that were significantly upregulated during root colonization and are more abundant in rhizosphere communities than in bulk soils. Many of these genes had not been previously linked to plant-bacteria interactions. Comparative genomic analyses revealed some of these genes as more prevalent in plant-associated Pseudomonas genomes than in genomes from other environments. We argue that these genes may play relevant biological roles in this host, although only a few have been previously associated with plant colonization. Among them, we focused on a gene homologous to yafL, which encodes a cysteine peptidase of the NlpC/P60 family, known for its role in peptidoglycan remodelling. This gene is more abundant in rhizosphere microbiomes than in bulk soils, and it showed induced expression on the root surface, supporting its ecological relevance in root-associated environments. Functional validation using a knockout mutant confirmed its contribution to plant-bacteria interactions by affecting root architecture and plant growth.

CONCLUSIONS: This study provides new insights into the genetic basis of bacterial adaptation to the plant root environment. By integrating transcriptomic and comparative genomic analyses, we identified numerous genes upregulated during root colonization that are enriched in plant-associated Pseudomonas genomes. Our findings highlight previously overlooked bacterial functions with potential roles in plant-microbe interactions. The functional validation of a protein of the NlpC/P60 family supports its involvement in plant-bacteria interactions and underscores the importance of uncharacterized genes in shaping beneficial associations in the rhizosphere. Video Abstract.},
}

@article {pmid41345889,
year = {2025},
author = {Bessière, P and Hayes, B and Fusade-Boyer, M and Sécula, A and Rous, G and Brun, J and Marchand, A and Croville, G and Cadiergues, MC and Guérin, JL},
title = {Seroprevalence and genetic diversity of feline immunodeficiency virus in outdoor cats in France.},
journal = {Veterinary research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13567-025-01672-z},
pmid = {41345889},
issn = {1297-9716},
abstract = {Feline immunodeficiency virus (FIV) is a retrovirus that causes lifelong infections in cats and may lead to immune dysfunction. Despite its importance for feline health, there is limited FIV data from France. This study investigated samples collected from stray and owned cats with outdoor access across France between December 2023 and January 2025 to estimate FIV seroprevalence, identify seropositivity predictors and analyse the genetic diversity of circulating strains. Serological screening was performed using a commercial ELISA. Polymerase chain reaction (PCR) was conducted on ELISA-positive sera, with selected samples analysed by Sanger sequencing for phylogenetic inference. One sample underwent metagenomic shotgun sequencing using Oxford Nanopore technology. The national seroprevalence, estimated using a Bayesian hierarchical model, was 16% (95% credible interval: 8.4-20%) overall, then 31% (21-42%) among intact male cats, 18% (CrI: 10.6-25.2%) among neutered male cats and 8.4% (CrI: 1.8-14%) among female cats. Outdoor exposure, sex and neuter status were strong predictors of seropositivity. Among strays, predicted probability of seropositivity exceeded 50% by 5 years of age. All sequenced viruses were classified as subtype A. However, the phylogenetic analysis revealed notable genetic variability, indicating at least two independent introductions of FIV into France. While related to other European strains, several isolates appeared to share distinct ancestral lineages. The metagenomic dataset yielded approximately 100,000 FIV reads among 2 million total reads, enabling full genome recovery. These findings highlight the ongoing circulation of FIV in France and provide valuable data for veterinary practitioners and future surveillance efforts in Europe.},
}

@article {pmid41345831,
year = {2025},
author = {Bu, Y and Sun, F and Liu, L and He, X and Wang, H and Chen, Z and He, T and Xu, S and Zhao, X and Meng, X},
title = {Comparative study on the rumen microbial communities and functions between Wagyu and Holstein calves.},
journal = {BMC genomics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12864-025-12392-1},
pmid = {41345831},
issn = {1471-2164},
support = {CX23YQ31//Heilongjiang Agricultural Science and Technology Innovation Leapfrog Project/ ; CARS-37//Supported by China Agriculture Research System of MOF and MARA/ ; },
abstract = {BACKGROUND: Understanding the rumen microbiota's development in calves is essential for optimizing breed-specific feeding strategies. This study aimed to comparatively investigate the dynamic changes in the rumen microbial community structure and function in Wagyu and Holstein calves.

METHODS: Five 3-month-old Wagyu calves and five age-matched Holstein calves were selected. All animals received the same diet consisting of concentrate and hay, with free access to feed and water. Rumen fluid samples were collected monthly from 3 to 6 months of age. Metagenomic sequencing was performed to assess microbial composition (phylum and genus levels), alpha diversity (Shannon, Simpson, ACE, and Chao1 indices), and functional pathway (KEGG-based).

RESULTS: The cumulative relative abundance of dominant taxa at both phylum and genus levels declined with age in both breeds, more markedly in Wagyu calves than in Holsteins. From 3 to 6 months of age, the top five phyla combined dropped by 3.25% in Wagyu and 0.87% in Holstein calves, whereas the top ten genera combined decreased by 1.63% and 0.63%, respectively. Alpha diversity in Wagyu calves increased significantly with age. At 5 and 6 months, the Shannon, ACE, and Chao1 indices were significantly higher than those at 3 months (P < 0.05). Moreover, from 4 to 6 months, Wagyu calves consistently exhibited significantly higher diversity indices than Holsteins (P < 0.05). At 6 months, Wagyu calves showed a significant reduction in metabolism-related microbial genes and an increase in genes related to cellular processes and genetic information processing compared to earlier ages and Holstein calves (P < 0.05).

CONCLUSIONS: These findings suggest potential breed-specific differences in the succession and functional maturation of rumen microbiota. Holstein calves developed earlier and more stable metabolic functions, while Wagyu calves underwent a more dynamic microbial selection process.

CLINICAL TRIAL NUMBER: Not applicable.},
}

@article {pmid41345737,
year = {2025},
author = {Li, F and Yan, M and Su, D and Peng, J and Wang, X and Hao, J and Ma, T and Lin, Y and Shi, H},
title = {Integrated meta-omics reveals AFB1 dose-dependent remodeling of the rumen microbiome-virome-metabolome axis driving metabolic impairment in goats.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02291-8},
pmid = {41345737},
issn = {2049-2618},
support = {grant no. 31902187//National Natural Science Foundation of China/ ; SCCXTD-2024-14//Innovation Team Development Funds for Sichuan Meat Goat and Sheep/ ; },
abstract = {BACKGROUND: Aflatoxin B1 (AFB1), a highly carcinogenic and hepatotoxic mycotoxin frequently contaminating animal feed, presents serious health risks to both humans and livestock. Although AFB1's hepatotoxicity and other organ damage are extensively characterized, how this mycotoxin influences ruminal microbiota dynamics and functional activities in ruminants remains underexplored. Although some studies suggest that AFB1 reduces nutrient digestibility and performance in ruminants, the underlying mechanisms are unclear. To aid in developing effective mitigation strategies for aflatoxicosis in ruminants, this study randomly divided Saanen goats into three groups. The CON group received the standard ration without additives, whereas LD and HD groups were provided identical basal diets fortified with 50 or 500 μg/kg AFB1. Throughout the study, alterations in ruminal fermentation parameters, microbiome, and metabolome profiles were analyzed.

RESULTS: With increasing AFB1 levels, ruminal pH, the concentration of total volatile fatty acids (VFA), acetate, and propionate decreased quadratically, while butyrate decreased linearly. Metagenomic profiling indicated suppressed populations of Pelagibacter and Flavobacterium following AFB1 exposure, contrasting with promoted growth of Cryptobacteroides. Additionally, seven carbohydrate-active enzymes (CAZymes), specifically GT92, GT20, CE7, GT32, GT35, GT57, and GT50, were found to be more prevalent in the rumen of the CON group. Statistically higher viral loads characterized the HD group when benchmarked against CON group. Metabolomics analysis identified 1197 differential metabolites among the CON, LD, and HD groups, including cytochalasin Ppho and chrysophanol, both known for their teratogenic properties and their ability to induce cell death.

CONCLUSIONS: This study indicates that dietary AFB1 exposure can alter the ruminal microbial and metabolomic profiles, induce prophage activation, and impact carbohydrate degradation and microbial protein turnover. These alterations may contribute to reductions in ruminal pH and volatile fatty acid concentrations, thereby impairing feed digestibility and animal performance. The findings provide valuable insights into AFB1's effects on rumen health, and further investigations of these metabolic pathways may help develop precision interventions to mitigate AFB1-induced rumen dysfunction and productivity losses. Video Abstract.},
}

@article {pmid41345617,
year = {2025},
author = {Franco-Duarte, R and Saati-Santamaría, Z and Choowong, P and Dharmarathne, G and Menéndez, E and Soares, P and Rito, T and Cheung, W and Spahr, A and Eberhard, J and Jayasinghe, TN},
title = {Oral-associated bacteria in the gut microbiome of individuals with type 2 diabetes: a secondary analysis of metagenomic data.},
journal = {BMC oral health},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12903-025-07285-4},
pmid = {41345617},
issn = {1472-6831},
}

@article {pmid41345487,
year = {2025},
author = {Karnachuk, OV and Panova, IA and Rusanov, II and Avakyan, MR and Lukina, AP and Ikkert, OP and Kijar, N and Kadnikov, VV and Beletsky, AV and Danilova, EV and Kopitsyn, DS and Pimenov, NV and Shcherbakova, VA and Ravin, NV},
title = {Thermophilic and mesophilic sulfate reduction by rare biosphere bacteria in acidic metal-bearing mine wastes from the temperate climate zone.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-28271-4},
pmid = {41345487},
issn = {2045-2322},
support = {24-14-00396//Russian Science Foundation/ ; 24-14-00396//Russian Science Foundation/ ; 24-14-00396//Russian Science Foundation/ ; 24-14-00396//Russian Science Foundation/ ; 24-14-00396//Russian Science Foundation/ ; 24-14-00396//Russian Science Foundation/ ; 22-14-00178-Р//Russian Science Foundation/ ; 22-14-00178-Р//Russian Science Foundation/ ; 22-14-00178-Р//Russian Science Foundation/ ; },
abstract = {Dissimilatory sulfate reduction is the main microbial process that detoxifies metals and increases pH in acid mine drainage. Acidophilic, copper-resistant Desulfosporosinus sp. BG and Desulfosporosinus sp. OT were previously isolated from acidic metalliferous tailings of the Bom-Gorkhon mine in Transbaikalia and Norilsk, respectively. To understand the role of sulfate-reducing bacteria (SRB) in mine tailings, we returned to the Bom-Gorkhon site to measure sulfate-reduction rate (SRR) with radioactive tracer and to estimate the proportion of SRB in the microbial community using 16 SrRNA gene profiling and metagenomic analysis. The SRR measured under ambient temperature conditions was high, reaching 9.86 ± 0.89 µmol SO4 cm[- 3] day[- 1]. Unexpectedly for a temperate biotope, SRR values of the same order of magnitude were recorded at 60 °C. Thermophilic spore-forming Desulfotomaculum and Desulfofundulus are likely involved in the thermophilic process. The spores of thermophilic Desulfofundulus germinating at 20 °C may input into sulfate reduction at in-situ temperature conditions. Metagenomic analysis by dsr gene mapping and 16 S rRNA gene profiling revealed low abundance of Desulfosporosinus and other SRBs, indicating that geochemically important active sulfate reduction in acidic wetland sediments is carried out by a "rare biosphere" consortium. The cultivated BG[T] and OT strains are described as Desulfosporosinus cupriresistens sp. nov.},
}

@article {pmid41345261,
year = {2025},
author = {Ma, J and Kim, N and Cha, JH and Kim, W and Kim, CY and Lee, YH and Kim, HS and Han, YD and Yong, D and Han, E and Yang, S and Beck, S and Lee, I},
title = {A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41345261},
issn = {2058-5276},
support = {2022M3A9F3016364//National Research Foundation of Korea (NRF)/ ; 2022R1A2C1092062//National Research Foundation of Korea (NRF)/ ; },
abstract = {Understanding the human gut microbiome requires comprehensive genomic catalogues, yet many lack geographic diversity and contain medium-quality metagenome-assembled genomes (MAGs) missing up to 50% of genomic regions, potentially distorting functional insights. Here we describe an enhanced Human Reference Gut Microbiome (HRGM2) resource, a catalogue of near-complete MAGs (≥90% completeness, ≤5% contamination) and isolate genomes. HRGM2 comprises 155,211 non-redundant near-complete genomes from 4,824 prokaryotic species across 41 countries, representing a 66% increase in genome count and a 50% boost in species diversity compared to the Unified Human Gastrointestinal Genome catalogue. It enabled improved DNA-based species profiling, resolution of strain heterogeneity and survey of the human gut resistome. The exclusive use of these genomes improved metabolic capacity assessment, enabling high-confidence, automated genome-scale metabolic models of the entire microbiota and revealing disease-associated microbial metabolic interactions. This resource will facilitate reliable functional insights into gut microbiomes.},
}

@article {pmid41345243,
year = {2025},
author = {Ste Marie, J and Mays, C and Guo, B and Radniecki, TS and Waite-Cusic, J and Navab-Daneshmand, T},
title = {Longitudinal replicated metagenomic analysis of biosolids-amended soils reveals enrichment of ARGs, virulence factors, and ESKAPE pathogens.},
journal = {npj antimicrobials and resistance},
volume = {3},
number = {1},
pages = {96},
pmid = {41345243},
issn = {2731-8745},
support = {2018-67017-27631//USDA National Institute of Food and Agriculture, Agricultural and Food Research Initiative Competitive Program, Agriculture Economics and Rural Communities/ ; },
abstract = {Biosolids land application introduces antibiotic resistance genes (ARGs) and clinically relevant pathogens into agricultural soils, raising concerns about long-term environmental and public health impacts. Despite growing interest in biosolids reuse, there remains a critical need for replicated, longitudinal studies to assess how biosolids amendments shape soil microbiomes and resistomes during crop cultivation. In this replicated longitudinal greenhouse study, we used shotgun metagenomics to characterize the impact of biosolids amendment on the soil microbiome, resistome, virulence factors, and ESKAPE pathogens during carrot cultivation. Biosolids-amended soils exhibited increased richness of microbial genera (e.g., Rhodanobacter, Dyella, and Thermomonas), ARG subtypes (resistance to sulfonamide, tetracycline, fosmidomycin, and macrolides), and virulence factors compared to pristine controls. Notably, all six ESKAPE pathogens, including Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp., were detected at elevated relative abundances (1.4- and 3.4-fold) in biosolids-amended soils and remained detectable throughout the 11-week cultivation period. Network analysis revealed statistically supported co-occurrences between microbial taxa and ARGs (with resistance to tetracyclines, beta-lactams, chloramphenicol, and multidrugs), suggesting possible host associations. These findings underscore the ecological and clinical relevance of biosolids amendment and highlight the need for integrated surveillance frameworks to mitigate antimicrobial resistance dissemination in agricultural environments.},
}

@article {pmid41345146,
year = {2025},
author = {Kar, S and Reddy, MK and Asthana, R and Srivastava, P and Dhaarani, R and Reddy, KVNS and Meghamala, V and Koduru, JR and Karri, RR},
title = {Synergistic effects of syzygium cumini sawdust biochar and poultry manure on soil quality enhancement, nitrogen, organic carbon dynamics, and Amaranthus cruentus growth.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-25003-6},
pmid = {41345146},
issn = {2045-2322},
support = {Ref. No-2022/0149//GITAM Research Seed Grants/ ; },
abstract = {The study aimed to evaluate the potential of incorporating biochar with poultry manure to address the constant challenges of sandy, loam soils due to poor water retention and low soil fertility, and their influence on the growth and yield of Amaranthus cruentus during the Rabi and Kharif seasons. The combined effect of manures on soil health over different seasons was unexplored, so the current research has been taken up to understand the impact of different treatments on physical, chemical, and microbial dynamics in the Rabi and Kharif seasons. Advanced statistical analysis was used to measure the soil and plant factor variations across seasons. Pre- and post-harvest results showed substantial progress in the soil bulk density, water-holding capacity (WHC), and nutrient retention in KR5 (biochar + poultry manure) treatment, where WHC displayed a strong positive correlation with organic matter (r > 0.82). Even chemical analysis indicated increased soil nitrogen, phosphorus, potassium, and carbon levels. Metagenomic analysis implied microbial diversity and abundance promoting nitrogen fixation and decomposition of organic matter. FTIR and SEM also revealed structural improvements that are beneficial for microbial colonization and nutrient retention. The combination of biochar and poultry manure showed higher growth, increasing plant height by 40 cm and yielding over 550 g/m[2] during the Kharif season. The results have revealed that the combination of biochar and poultry manure has improved soil fertility, microbial diversity, and yield of Amaranthus cruentus grown in sandy loam soils.},
}

@article {pmid41345123,
year = {2025},
author = {Tucker, SJ and Füssel, J and Freel, KC and Kiefl, E and Freel, EB and Ramfelt, O and Sullivan, CES and Gajigan, AP and Mochimaru, H and de Souza, MR and Quinn, M and Ratum, C and Tran, LL and Sobczyk, M and Miller, SE and Trigodet, F and Lolans, K and Morrison, HG and Fallon, B and Huettel, B and Pan, T and Rappé, MS and Eren, AM},
title = {A high-resolution diel survey of surface ocean metagenomes, metatranscriptomes, and transfer RNA transcripts.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1913},
pmid = {41345123},
issn = {2052-4463},
support = {687269//Simons Foundation/ ; 989028//Simons Foundation/ ; 989028//Simons Foundation/ ; 2019589//NSF | GEO | Division of Ocean Sciences (OCE)/ ; },
mesh = {*Metagenome ; Pacific Ocean ; *Transcriptome ; *RNA, Transfer/genetics ; *Seawater/microbiology ; Ecosystem ; Microbiota ; },
abstract = {The roles of marine microbes in ecosystem processes are inherently linked to their ability to sense, respond, and ultimately adapt to environmental change. Capturing the nuances of this perpetual dialogue and its long-term implications requires insight into the subtle drivers of microbial responses to environmental change that are most accessible at the shortest scales of time. Here, we present a multi-omics dataset comprising surface ocean metagenomes, metatranscriptomes, tRNA transcripts, and biogeochemical measurements, collected every 1.5 hours for 48 hours at two stations within coastal and adjacent offshore waters of the tropical Pacific Ocean. We expect that this integrated dataset of multiple sequence types and environmental parameters will facilitate novel insights into microbial ecology, microbial physiology, and ocean biogeochemistry and help investigate the different mechanisms of adaptation that drive microbial responses to environmental change.},
}

*Metagenome
Pacific Ocean
*Transcriptome
*RNA, Transfer/genetics
*Seawater/microbiology
Ecosystem
Microbiota

@article {pmid41345120,
year = {2025},
author = {Abad-Recio, IL and Rubel, V and Filker, S and Garate, L and Stoeck, T and Logares, R and Lanzén, A},
title = {The Basque Coast Estuarine Sediment Gene Catalogue.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1909},
pmid = {41345120},
issn = {2052-4463},
support = {Fi 2089/3-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; STO 414/19-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {*Estuaries ; *Geologic Sediments/microbiology ; Archaea/genetics ; Metagenomics ; Bacteria/genetics ; Biodiversity ; Ecosystem ; Eukaryota/genetics ; Viruses/genetics ; },
abstract = {Estuaries are critical transition zones that link marine, riverine, and terrestrial ecosystems, including habitats like intertidal mudflats and tidal marshes. These ecosystems are biodiversity hotspots providing essential ecological functions such as nutrient cycling and pollutant removal. Despite their importance, there is a significant knowledge gap regarding the ecological functioning of these habitats and how they are impacted by anthropogenic pressures. From intertidal estuarine benthos along the Basque Coast 92 microbial metagenomic assemblies were retrieved that allowed us to reconstruct 390 medium plus 81 high quality MAGs, along with 108 million putative genes from bacteria, archaea, eukaryotes, and viruses. This unique dataset will enhance our understanding of ecosystem functioning, biodiversity, and be useful to reveal biogeochemical processes and the role of unculturable biomass.},
}

*Estuaries
*Geologic Sediments/microbiology
Archaea/genetics
Metagenomics
Bacteria/genetics
Biodiversity
Ecosystem
Eukaryota/genetics
Viruses/genetics

@article {pmid41345102,
year = {2025},
author = {Pope, R and Visconti, A and Zhang, X and Louca, P and Baleanu, AF and Lin, Y and Asnicar, F and Bermingham, K and Wong, KE and Michelotti, GA and Wolf, J and Segata, N and Berry, SE and Spector, TD and Leeming, ER and Gibson, R and Menni, C and Falchi, M},
title = {Faecal metabolites as a readout of habitual diet capture dietary interactions with the gut microbiome.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10051},
pmid = {41345102},
issn = {2041-1723},
support = {27/2023//Chronic Disease Research Foundation (CDRF)/ ; },
mesh = {Humans ; *Feces/chemistry/microbiology ; *Gastrointestinal Microbiome/physiology ; *Diet ; Male ; Female ; Metabolome ; Middle Aged ; Metabolomics/methods ; Aged ; Metagenomics ; Adult ; Machine Learning ; },
abstract = {The interplay between diet and gut microbiome composition is complex. Faecal metabolites, the end products of human and microbial metabolism, provide insights into these interactions. Here, we integrate faecal metabolomics, metagenomics, and habitual dietary data from 1810 individuals from the TwinsUK and 837 from the ZOE PREDICT1 cohorts. Using machine learning models, we find that faecal metabolites accurately predict reported intakes of 20 food groups (area under the curve (AUC) > 0.80 for meat, nuts and seeds, wholegrains, tea and coffee, and alcohol) and adherence to seven dietary patterns (AUC from 0.71 for the Plant-based Diet Index to 0.83 for the Dietary Approaches to Stop Hypertension score). Notably, the faecal metabolome is a stronger predictor of atherosclerotic cardiovascular disease risk (AUC = 0.86) than the Dietary Approaches to Stop Hypertension score (AUC = 0.66). We identify 414 associations between 19 food groups and 211 metabolites, that significantly correlate with microbial α-diversity and 217 species. Our findings reveal that faecal metabolites capture mediations between diet and the gut microbiome, advancing our understanding of diet-related disease risk and informing metabolite-based interventions.},
}

Humans
*Feces/chemistry/microbiology
*Gastrointestinal Microbiome/physiology
*Diet
Male
Female
Metabolome
Middle Aged
Metabolomics/methods
Aged
Metagenomics
Adult
Machine Learning

@article {pmid41344778,
year = {2026},
author = {Li, Z and Zhao, C and Mao, Z and Zhao, L and Penttinen, P and Zhang, S},
title = {Metagenomics insights into bacterial community, viral diversity and community-scale functions in fermented red pepper.},
journal = {Food microbiology},
volume = {135},
number = {},
pages = {104986},
doi = {10.1016/j.fm.2025.104986},
pmid = {41344778},
issn = {1095-9998},
mesh = {Fermentation ; *Capsicum/microbiology/virology ; Metagenomics ; *Bacteria/genetics/classification/isolation & purification/metabolism/virology ; *Fermented Foods/microbiology/virology ; Gene Transfer, Horizontal ; *Viruses/genetics/classification/isolation & purification ; Bacteriophages/genetics/classification/isolation & purification ; *Microbiota ; Food Microbiology ; },
abstract = {Fermented red peppers (FRPs) provide distinct flavor and possible health benefits, but understanding of their microbial functions, viral diversity, pathogenicity, and horizontal gene transfer (HGT) patterns remains limited. Integrated multi-method analysis revealed FRP's bacterial community was dominated by Bacillus (21.52 %), Lactobacillus sensu lato (14.27 %), and Pantoea (13.60 %). Bacillus drove core fermentation with an over 40 % contribution to carbon degradation and iron reduction. The virome was dominated by Caudoviricetes phages, yet 25.5 % of the functions of viral genes remained unknown. Critically, multidrug resistance genes were the most abundant ARGs, and beneficial bacteria served as major reservoirs for ARGs, co-occurring with potential opportunistic pathogens. Despite inhibitory conditions, these last dominated key metabolic nodes hydrogen generation and acetate oxidation. Counterintuitively, ARG profiles correlated with bacterial composition but not with mobile genetic elements or detected HGT events, challenging HGT as the primary ARG driver. These findings necessitate dual strategies: leveraging key microbes for fermentation efficiency while implementing stringent monitoring to mitigate pathogen and ARG related risks.},
}

Fermentation
*Capsicum/microbiology/virology
Metagenomics
*Bacteria/genetics/classification/isolation & purification/metabolism/virology
*Fermented Foods/microbiology/virology
Gene Transfer, Horizontal
*Viruses/genetics/classification/isolation & purification
Bacteriophages/genetics/classification/isolation & purification
*Microbiota
Food Microbiology

@article {pmid41344758,
year = {2026},
author = {Okoye, CO and Ezenwanne, BC and Olalowo, OO and Ajanwachukwu, OJ and Chukwudozie, KI},
title = {Microbial-mycotoxin interactions in food: A review of ecotoxicological implications and omics approaches for understanding detoxification mechanisms.},
journal = {Food microbiology},
volume = {135},
number = {},
pages = {104955},
doi = {10.1016/j.fm.2025.104955},
pmid = {41344758},
issn = {1095-9998},
mesh = {*Mycotoxins/metabolism/toxicity ; *Food Contamination/analysis ; *Fungi/metabolism/genetics ; *Food Microbiology ; Ecotoxicology ; Inactivation, Metabolic ; Animals ; Humans ; Genomics ; },
abstract = {Mycotoxins, toxic secondary metabolites produced by fungi such as Aspergillus, Fusarium, and Penicillium, frequently contaminate food supplies, posing risks to human health, animal welfare, and ecosystem stability. Mycotoxins like aflatoxins, ochratoxin A, fumonisins, trichothecenes, and zearalenone disrupt microbial communities, food chains, and environmental matrices, with synergistic interactions amplifying their toxicity. This review explores microbial-mycotoxin interactions in food systems, focusing on ecotoxicological implications and omics approaches for elucidating detoxification mechanisms. Microbial detoxification, through adsorption by cell wall components (e.g., β-glucans) or enzymatic biodegradation (e.g., lactonases, oxidoreductases), offers a sustainable alternative to physical and chemical methods. However, challenges include variable detoxification efficiency, mechanistic uncertainties, regulatory hurdles, and the detection of masked mycotoxins in complex food matrices. Omics technologies such as metagenomics, genomics, transcriptomics, and their integration provide comprehensive insights into microbial diversity, gene expression, enzyme activity, and metabolite transformations. In addition, omics integration enhances understanding of microbial-mycotoxin dynamics, supporting targeted biocontrol strategies. Future prospects include leveraging synthetic biology, CRISPR-based gene editing, and machine learning-assisted bioinformatics to optimize microbial strains and predict detoxification outcomes. By addressing these challenges, omics-driven approaches can mitigate mycotoxin contamination, ensure food safety, and reduce ecotoxicological impacts across global food systems.},
}

*Mycotoxins/metabolism/toxicity
*Food Contamination/analysis
*Fungi/metabolism/genetics
*Food Microbiology
Ecotoxicology
Inactivation, Metabolic
Animals
Humans
Genomics

@article {pmid41344333,
year = {2025},
author = {Cao, Y and Bowker, MA and Feng, Y and Delgado-Baquerizo, M and Xiao, B},
title = {The Great Wall of China harbors a diverse and protective biocrust microbiome.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.10.087},
pmid = {41344333},
issn = {1879-0445},
abstract = {The Great Wall of China, one of the most emblematic human heritage sites ever built, is largely covered by a living skin that has a potentially distinct microbiome compared with bare wall surfaces. However, the structure and function of this microbiome remain virtually unknown, which hampers any effort to understand the impacts of this microbiome on the long-term conservation of the Great Wall. Here, we investigated the microbiome of the Great Wall at six sampling sites along a 600-km section, which stretches across arid and semiarid climates and is covered by a mosaic of biological soil crusts (biocrusts) and exposed wall surfaces. We hypothesized that these biocrusts could establish a unique microhabitat and support a microbiome with a community structure and function potentially distinct from those on bare walls, thereby modulating the biodeterioration processes affecting the Great Wall. Our findings revealed that biocrust-covered sections exhibited a 12%-62% increase in abundance, diversity, and co-occurrence network complexity for bacterial and fungal communities compared with bare walls. Further metagenomic analyses indicated that the biocrust cover enhanced the abundance of overall functional genes and stress-resistance pathways within the microbiome by 4%-15%, while decreasing the metabolic pathways linked to heritage biodeterioration. Aridity was an additional determinant of the microbiome. Our work serves as a critical step toward understanding the microbiome of the Great Wall, which contributes to conserving this unparalleled human monument for future generations.},
}

@article {pmid41344255,
year = {2025},
author = {Chen, X and Wu, Y and Xue, B and You, Y and Yin, L and Wang, S and Zheng, J},
title = {Mechanism of flavor formation in Suansun fermented by Lactiplantibacillus plantarum during a three-stage flavor formation model.},
journal = {Food chemistry},
volume = {499},
number = {},
pages = {147316},
doi = {10.1016/j.foodchem.2025.147316},
pmid = {41344255},
issn = {1873-7072},
abstract = {This study employed an integrated multi-omics approach-metagenomics, metatranscriptomics, and metabolomics-to elucidate the flavor formation mechanism in Suansun, leading to the proposal of a three-stage flavor formation model. In the initial stage, Lactiplantibacillus plantarum dominates pyruvate metabolism, rapidly producing lactic acid and creating an acidic environment that drives microbial succession. This pH shift initiates the key flavor-forming stage, during which peak levels of Weissella cibaria align with linalool biosynthesis, suggesting strong temporal coordination. During the mid-to-late stages, the abundance of Clostridium species was strongly correlated with p-cresol generation via tyrosine catabolism, while Lactococcus and related taxa produce nonanal and ketones through fatty acid β-oxidation. Overall, the starter culture actively restructures the fermentation niche, sequentially activating metabolic pathways in successive microbial communities to shape a stable flavor profile. This staged model of flavor evolution provides a scientific foundation for optimizing and controlling Suansun fermentation quality.},
}

@article {pmid41344131,
year = {2025},
author = {Liu, T and Li, L and Chen, J and Cai, G and Meng, F and Jiao, Y and Mao, Y and Wang, Z and Zuo, W and Tian, Y and Sun, H},
title = {Real-world aged microplastics exacerbate antibiotic resistance genes dissemination in anaerobic sludge digestion via enhancing microbial metabolite communication-driven pilus conjugative transfer.},
journal = {Water research},
volume = {290},
number = {},
pages = {125056},
doi = {10.1016/j.watres.2025.125056},
pmid = {41344131},
issn = {1879-2448},
abstract = {The dissemination of antibiotic resistance genes (ARGs) facilitated by coexisting microplastics (MPs) in the "source-sink" hotspots of waste activated sludge (WAS) raises great concern. Despite real-world MPs undergoing aging, whether and how naturally aged microplastics (AMPs) affect ARG dissemination during sludge treatment remains largely unknown. Herein, we systematically explored the evolved effects and underlying mechanisms of environmentally relevant MPs (0, 3, and 30 mg/kg TS) aging on ARG propagation in anaerobic sludge digestion via multi-omics analyses. Specifically, microplastic exposure increased total ARG abundance by 2.59-15.31 % with enriched mobile genetic elements (MGEs, 0.22-16.71 %). These effects were escalated at higher microplastic dosages and aging degrees. Mechanistically, metagenomic and metaproteomic analyses revealed the drivers for ARG amplification in the sludge digester evolved from the pristine microplastics (PMPs)-induced higher oxidative stress and membrane permeability to AMPs-induced higher multidrug efflux coupled with pilus-mediated conjugation. Subsequently, metagenomic binning identified key multidrug-resistant hosts of Sedimentibacter, Alicycliphilus, and Sulfuricurvum genera. Moreover, high-resolution metabolomics and reactomics network analysis uncovered that AMPs stimulated microbial metabolite turnover, particularly of nitrogenous and sulfurous compounds, and enhanced the complexity and communication frequency of molecular transformation networks centered on lignin and protein nodes, thereby promoting ARG exchange. Finally, Mantel tests reconfirmed that reactive oxygen species level (Mantel's r = 0.93, p = 0.04) and metabolite network connectivity (Mantel's r = 0.82, p = 0.04) are paramount drivers of ARG spread. These findings offer novel insights into the ARG amplification risk driven by MPs aging, guiding targeted strategies to mitigate ARG spread and improve resource recovery in sludge bioengineering systems.},
}

@article {pmid41344128,
year = {2025},
author = {Xie, X and Li, E and Jiang, H and Pi, K and Yan, L and Shen, S},
title = {Methane biogeochemical turnover constrains arsenic transformation in groundwater systems: Organic molecular signatures and microbial functional networks.},
journal = {Water research},
volume = {290},
number = {},
pages = {125083},
doi = {10.1016/j.watres.2025.125083},
pmid = {41344128},
issn = {1879-2448},
abstract = {Arsenic (As) contamination of groundwater is primarily driven by microbially mediated redox processes and the dynamic evolution of dissolved organic matter (DOM). The influence of cycled methanogenesis and methane oxidation processes on As species transformation in geogenic As-contaminated groundwater, however, remain mechanistically elusive. In this study, quantitative relationships among DOM molecular characteristics, microbial functional networks, and As speciation were established using sediment microcosm experiments, Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), and metagenomic sequencing. The results indicate that rates of methanogenesis and methane oxidation are regulated by thermodynamic properties of DOM. Labile DOM promoted As(III) mobilization at a rate of 1.04 μg kg[-1] d[-1] through methyl-related metabolism. Remarkably, enhanced methane oxidation further elevated the As(III) generation rate to 3.30 μg kg[-1] d[-1], underscoring the accelerating effect of methane cycling on As release. In contrast, humified DOM decoupled the geochemical linkage between iron and As. Microbial succession governed the redox transitions, as the proliferation of methanogens substantially increased methane production (up to 7.23 mg kg[-1] d[-1]), while methanotrophs enhanced oxidation rates from 94.99 to 190.76 mg kg[-1] d[-1]. This microbial progression coupled sulfate and As(V) reduction through the up-regulation of key functional genes (dsrAB, arsC). Energy conversion during DOM biodegradation governs As migration stages. These findings highlight the interactive constraints on As speciation dynamics by molecular characteristics of DOM and microbial functional networks during methane biotransformation processes in groundwater systems. This research provides new mechanistic insights into As biogeochemical cycling in geogenic contaminated groundwater.},
}

@article {pmid41342600,
year = {2025},
author = {Bauchinger, F and Berry, D},
title = {Metatranscriptomic-driven insights into mucosal glycan degradation by the human gut microbiota.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf118},
pmid = {41342600},
issn = {1574-6941},
abstract = {The secreted mucus layer in the human gastrointestinal tract constitutes both a protective boundary between gut lumen and epithelium as well as an important nutrient source for members of the gut microbiota. While many gut microbes possess the genetic potential to degrade mucin it is still unclear which species transcribe the respective genes. Here, we systematically analyzed publicly available metagenome and metatranscriptome datasets to characterize the gut microbial community involved in mucosal glycan degradation. We utilized co-occurrence network analysis and linear regression to elucidate the ecological strategies of, and relationship between, mucus degraders. We found that although approximately 60% of species carrying genes encoding for mucosal-glycan-degrading enzymes have detectable transcription of these genes, only 21 species prevalently transcribe more than 1 gene. Furthermore, the transcription of individual genes was frequently dominated by single species in individual samples. Transcription patterns suggested the presence of competitive mucosal glycan degraders characterized by abundance-driven transcription that were negative predictors for the transcription of other degraders as well as opportunistic species with decoupled abundance and transcription profiles. These findings provide insights into the ecology of the mucosal glycan degradation niche in the human gut microbiota.},
}

@article {pmid41341964,
year = {2025},
author = {Yao, J and Zhang, J and Zheng, L and Fang, W and Lang, Y},
title = {Coxiella burnetii Should Not Be Ignored: Two Cases of Q Fever Pneumonia Diagnosed by Metagenomic Next-Generation Sequencing.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {6227-6239},
pmid = {41341964},
issn = {1178-6973},
abstract = {BACKGROUND: Q fever is a globally distributed zoonotic disease caused by Coxiella burnetii (C. burnetii). As an obligate intracellular bacterium, C. burnetii is primarily transmitted from domestic animals to humans, with ticks also serving as potential vectors. The clinical manifestations of Q fever are often nonspecific and highly variable, making its diagnosis particularly challenging.

CASE PRESENTATION: Two male pneumonia patients were hospitalized in Deqing People's Hospital, one was 73 years old, and the other one was 30 years old, both of them presented with hyperpyrexia without a clear epidemiological history. However, initial empirical treatment was ineffective and microbiological cultures were all negative, then bronchoscopy was conducted for them and bronchoalveolar lavage fluid (BALF) was sent for metagenomic next-generation sequencing (mNGS) test. Ultimately, two patients were diagnosed with Q fever pneumonia, and the symptoms of patients were significantly improved after timely treatment with the special drug doxycycline and moxifloxacin, and lung inflammation in both patients were effectively absorbed in the subsequent follow-up examination.

CONCLUSION: Two cases of Q fever pneumonia were diagnosed through mNGS. As a new detection method, mNGS has advantages in the diagnosis of unknown infectious pathogens. As a zoonotic pathogen, C. burnetii should not be ignored. The One Health approach may be suitable for Q fever prevention and control.},
}

@article {pmid41341958,
year = {2025},
author = {Chaves, M and Hashish, A and Goraichuk, IV and Casserta, LC and Mears, MC and Gadu, E and Bakre, A and Alexander Morris, ER and Shelkamy, MMS and Nadendla, S and Perez, DR and El-Gazzar, M},
title = {Nanopore sequencing in veterinary medicine: from concepts to clinical applications.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1701570},
pmid = {41341958},
issn = {2235-2988},
mesh = {*Nanopore Sequencing/methods/veterinary ; Animals ; *Veterinary Medicine/methods ; Computational Biology/methods ; *High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; Nanopores ; Genomics/methods ; },
abstract = {Oxford Nanopore Technologies (ONT) stands at the forefront of third-generation sequencing, utilizing a nanopore sequencing approach to achieve high-throughput DNA and RNA sequencing. This technology offers several key advantages, including real-time data generation, portability, and long-read capabilities, making it an increasingly valuable tool for a wide range of applications. This review will focus on the use of ONT in veterinary diagnostics exploring the evolving applications of ONT in veterinary medicine and its use in detecting viral and bacterial pathogens, antimicrobial resistance profiling, foodborne disease surveillance, and metagenomic analysis. We provide an overview of the diverse sequencing workflows available, from sample preparation to bioinformatics analysis, and highlight their advantages over traditional sequencing methods. While powerful, nanopore sequencing does present challenges such as error rates, barcode crosstalk, and workflow complexities. This review will address these issues and discuss potential future developments, as well as the long-term impact of ONT on the field of genomics. As nanopore sequencing technology continues to advance, its role in veterinary diagnostics is expected to expand significantly, leading to improvements in disease surveillance, outbreak response, and contributions to crucial One Health initiatives.},
}

*Nanopore Sequencing/methods/veterinary
Animals
*Veterinary Medicine/methods
Computational Biology/methods
*High-Throughput Nucleotide Sequencing/methods
Metagenomics/methods
Nanopores
Genomics/methods

@article {pmid41341954,
year = {2025},
author = {Fang, XZ and Liu, ZH and Duan, LM and Yao, L and Xu, JQ and Yang, XB and Ren, LH and Jiang, YX and Sun, SW and Shang, Y and Yuan, Y},
title = {Clinical features, pathogens, and prognosis of immunocompromised host pneumonia in patients with malignancies.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1646513},
pmid = {41341954},
issn = {2235-2988},
mesh = {Humans ; *Immunocompromised Host ; Male ; *Neoplasms/complications ; Female ; Middle Aged ; Prospective Studies ; Aged ; Prognosis ; Bronchoalveolar Lavage Fluid/microbiology/virology ; *Pneumonia/microbiology/mortality/diagnosis ; Coinfection/microbiology ; Adult ; Bacteria/isolation & purification/classification ; Metagenomics ; COVID-19 ; Aged, 80 and over ; SARS-CoV-2 ; },
abstract = {BACKGROUND: Cancer patients face elevated risks of severe pulmonary infections due to malignancy-related immunosuppression and anti-neoplastic therapy. Comprehensive data on the etiology and prognostic factors remain limited.

METHODS: This prospective cohort study enrolled 115 patients with malignancies and immunocompromised host pneumonia (ICHP) from July 2023 to July 2024. Pathogens were identified using clinical metagenomics of bronchoalveolar lavage fluid (BALF), supported by CT imaging and clinical evaluation.

RESULTS: Pathogens were detected in 92 patients (80.0%), with 158 potential pathogens detected. Etiologic diagnoses were established by BALF mNGS alone in 68 (73.9%), by combined mNGS plus standard microbiologic testing (SMT) in 24 (26.1%), and by SMT alone in 1 (1.1%). Pneumocystis jirovecii (32, 20.3%), SARS-CoV-2 (14, 8.9%), Aspergillus fumigatus (13, 8.2%), Klebsiella pneumoniae (12, 7.6%) and Haemophilus influenzae (10, 6.3%) were the five most common pathogens. Coinfections occurred in 36.5% of all enrolled patients. Death at 28 days, ICU admission, Death at ICU was more frequent among patients with polymicrobial infections than single pathogen infection, though this difference was not statistically significant. Use rate of vasoactive drugs was significantly higher in patients with coinfection than in patients with single-pathogen infection (39.1% vs. 16.0%). invasive mechanical ventilation (IMV) (OR = 22.86, p=0.047), vasopressor use (OR = 72.69, p=0.039), and higher Acute Physiology and Chronic Health Evaluation II (APACHE II) scores (OR = 1.46, p=0.016) were associated with increased 28-day all-cause mortality.

CONCLUSION: Patients with malignancies and evaluated for pulmonary infection were found to have unique microbiological profiles detected by BAL metagenomic sequencing. Co-detection of potential pathogens was high, and associated with high 28-day all-cause mortality.},
}

Humans
*Immunocompromised Host
Male
*Neoplasms/complications
Female
Middle Aged
Prospective Studies
Aged
Prognosis
Bronchoalveolar Lavage Fluid/microbiology/virology
*Pneumonia/microbiology/mortality/diagnosis
Coinfection/microbiology
Adult
Bacteria/isolation & purification/classification
Metagenomics
COVID-19
Aged, 80 and over
SARS-CoV-2

@article {pmid41341823,
year = {2025},
author = {Huang, W and Lai, HP and Yu, L and Jin, L and Lei, W},
title = {Case Report: Chronic Q fever mimicking malignancy and tuberculosis in a hemodialysis patient: multidisciplinary diagnosis guided by metagenomic next-generation sequencing.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1656891},
pmid = {41341823},
issn = {2296-858X},
abstract = {BACKGROUND: Q fever, caused by Coxiella burnetii, is a rare zoonosis whose clinical presentation is highly heterogeneous. Chronic Q fever can present with atypical systemic masses, creating significant diagnostic challenges as it lacks distinctive imaging features, often leading to misdiagnosis.

CASE PRESENTATION: We report a case of a 50-year-old woman on maintenance hemodialysis who presented with a one-month history of generalized myalgia and abdominal discomfort. Initial PET-CT imaging revealed multiple hypermetabolic abdominal lesions (SUV∼max∼ 7.1), mimicking metastatic malignancy. Histopathology of abdominal biopsies showed granulomatous inflammation with necrosis but lacked definitive microbiological evidence. Empirical anti-tuberculosis therapy was initiated based on clinical suspicion. Despite initial clinical improvement, the patient experienced recurrence of symptoms and radiological progression after 1 year. Re-evaluation with transesophageal echocardiography suggested the possibility of infective endocarditis. Crucially, metagenomic next-generation sequencing (mNGS) of a repeat biopsy identified Coxiella burnetii, confirming chronic Q fever. Targeted doxycycline therapy resulted in sustained clinical and radiological improvement, with lesion resolution confirmed at the 14-month follow-up.

CONCLUSION: This case underscores the diagnostic difficulty of chronic Q fever due to its non-specific presentation and imaging characteristics. PET-CT may suggest malignancy, but incorporating advanced molecular diagnostics such as mNGS is critical for accurate pathogen identification. Recognizing atypical manifestations and utilizing integrative diagnostic approaches can facilitate timely, targeted therapy, improving clinical outcomes in rare infectious diseases like Q fever.},
}

@article {pmid41341819,
year = {2025},
author = {Kong, M and Sun, J},
title = {Case Report: A case of Nocardia otitidiscaviarum pneumonia diagnosed by application of metagenome next-generation sequencing and a narrow literature review.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1646940},
pmid = {41341819},
issn = {2296-858X},
abstract = {Nocardia is an opportunistic pathogen with relatively low incidence but high mortality. Recently, reports of Nocardia infections have increased; however, infections caused by Nocardia otitidiscaviarum (N. otitidiscaviarum) remain relatively rare. Due to its non-specific clinical manifestations and imaging features, N. ototidiscaviarum infections are frequently misdiagnosed or underdiagnosed, and no standardized guidelines currently exist for their diagnosis and treatment. In this study, we report a case of pulmonary infection caused by N. otitidiscaviarum, which was diagnosed using a combination of traditional microbial morphology and second-generation sequencing, and subsequently showed improvement following treatment with trimethoprim-sulfamethoxazole (TMP-SMZ) and linezolid. Additionally, we conducted a comprehensive literature review using PubMed to provide insights for improving the diagnosis and treatment of N. otitidiscaviarum infections.},
}

@article {pmid41341716,
year = {2025},
author = {Leutert, A and Zeckanovic, A and Huber, M and Meyer Sauteur, PM and Morscher, RJ},
title = {Recurrent vaccine-strain varicella zoster virus reactivation in a child with acute lymphatic leukemia.},
journal = {IDCases},
volume = {42},
number = {},
pages = {e02422},
pmid = {41341716},
issn = {2214-2509},
abstract = {This case illustrates recurrent herpes zoster (HZ) in a child with acute lymphatic leukemia. Interestingly, vaccine-strain HZ was confirmed by identifying the live-attenuated Oka vaccine strain (vOka) using metagenomic sequencing and sequence comparison at three loci that distinguish vOka from wild-type varicella zoster virus (VZV). Although vaccine-strain HZ is generally milder than HZ caused by wild-type VZV, prompt recognition and initiation of antiviral treatment is essential in immunocompromised patients, as fatal varicella due to disseminated vaccine-strain VZV has been reported in this high risk group.},
}

@article {pmid41341658,
year = {2025},
author = {Kriem, LS and King, N and Niemann, S and Vainshtein, Y and Sonntag, M},
title = {Molecular Identification of Human and Plant Pathogens in Municipal Domestic Wastewater for Hydroponic System Applications.},
journal = {International journal of microbiology},
volume = {2025},
number = {},
pages = {6958575},
pmid = {41341658},
issn = {1687-918X},
abstract = {Water is essential for human survival and socioeconomic development, yet its overconsumption threatens global food security and ecosystem integrity. This necessitates a 60% increase in food production, further straining water resources. Hydroponic systems represent a promising solution, utilizing up to 90% less water than traditional methods while providing optimal growing conditions for crops. This study was aimed at developing a PCR-based detection system for main human and plant pathogens in hydroponic systems using treated domestic wastewater. Metagenomic analysis of wastewater samples revealed significant microbial diversity, identifying human pathogens such as Pseudomonas aeruginosa and Yersinia enterocolitica, alongside plant pathogens including Rhodococcus fascians. Specific primer pairs for the most abundant species found in a domestic municipal wastewater sample of target pathogens (Streptococcus mutans, P. aeruginosa, Acinetobacter baumannii, Y. enterocolitica, Enterococcus faecalis, Pseudomonas viridiflava, R. fascians, Xanthomonas vesicatoria, and Pseudomonas syringae) were designed and validated, ensuring high specificity and efficiency. Future research should focus on enhancing detection methods and optimizing DNA extraction techniques to improve pathogen quantification and management in hydroponic systems. This approach is crucial for sustainable agricultural practices that minimize water usage while ensuring food safety and environmental health.},
}