@article {pmid41508467,
year = {2026},
author = {Chang, H and Zhang, Q and Soro, PL and Zhang, W and Ma, L and Feng, Z and Gu, C},
title = {Integrative metagenomic, metabolomic, and transcriptomic analyses unravel flavor development driven by a defined starter cocktail in cocoa fermentation.},
journal = {Food research international (Ottawa, Ont.)},
volume = {225},
number = {},
pages = {118042},
doi = {10.1016/j.foodres.2025.118042},
pmid = {41508467},
issn = {1873-7145},
mesh = {*Fermentation ; *Cacao/microbiology/metabolism ; *Metabolomics/methods ; *Metagenomics/methods ; Saccharomyces cerevisiae/metabolism/genetics ; Gene Expression Profiling ; Odorants/analysis ; Transcriptome ; Food Microbiology ; Hanseniaspora/metabolism ; Gas Chromatography-Mass Spectrometry ; },
abstract = {This study investigated the impact of a defined starter cocktail (Hanseniaspora uvarum XY23.1, Saccharomyces cerevisiae XY23.2, Lactiplantibacillus plantarum XY23.1, and Gluconobacter oxydans XY23.2) on Trinitario cocoa fermentation in Hainan, China. A multi-omic approach integrating shotgun metagenomics, metabolomics (LC-MS and GC-MS), and transcriptomics was employed to comprehensively assess microbial succession, metabolite dynamics, and functional gene expression. Starter inoculation accelerated cocoa fermentation and stabilized microbial succession, and the four introduced strains remained dominance during the process. Metabolomic analysis revealed that the inoculated group had a remarkable increase in the content of the aromatic volatiles phenylethyl alcohol, 3-methylbutyl acetate, and delta-decalactone, which contributes to fruity and floral aroma characteristics. Shotgun metagenomics revealed enrichment of genes involved in carbohydrate utilization, amino acid catabolism, and acetate ester biosynthesis. Transcriptomics also indicated that S. cerevisiae upregulated Ehrlich pathway and glyoxylate cycle under co-culture conditions, demonstrating its central role in aroma formation and redox balance, while H. uvarum upregulated sugar transporters and stress-response genes, demonstrating a putative regulatory role in nutrient competition and interspecies interaction. Overall, our findings elucidate that defined starter cultures can shape cocoa fermentation toward improved consistency and aroma outcomes, providing a foundation for designing function-driven microbial consortia for controlled fermentation applications.},
}

*Fermentation
*Cacao/microbiology/metabolism
*Metabolomics/methods
*Metagenomics/methods
Saccharomyces cerevisiae/metabolism/genetics
Gene Expression Profiling
Odorants/analysis
Transcriptome
Food Microbiology
Hanseniaspora/metabolism
Gas Chromatography-Mass Spectrometry

@article {pmid41508436,
year = {2026},
author = {Li, C and Yang, F and Han, Y and Yang, C and Qin, X and Zheng, H and Chen, L and Lu, J and Zhang, C and Lu, F and Wang, L},
title = {Corrigendum to "Aldehyde metabolism in Maotai-flavor baijiu: insights from integrated metagenomic and metaproteomic analyses" [Food Res. Int. 221(Part 3) (2025) 117518].},
journal = {Food research international (Ottawa, Ont.)},
volume = {225},
number = {},
pages = {117954},
doi = {10.1016/j.foodres.2025.117954},
pmid = {41508436},
issn = {1873-7145},
}

@article {pmid41508161,
year = {2026},
author = {Villafuerte, AB and Comeau, AM and Soria, R and Ortega, R and Wright, RJ and Miralles, I},
title = {Linking microbial taxonomy and function in N and P metabolism: a study of organic amendments in semiarid restored soils.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-025-00845-9},
pmid = {41508161},
issn = {2524-6372},
support = {FIRESOIL CNS2023-14150//Ministerio de Ciencia e Innovación (Spain), Agencia Estatal de Investigación (Spain) and European Union/ ; BIOQUALIRES-PID2021-1275910B-100//Ministerio de Ciencia e Innovación (Spain), Agencia Estatal de Investigación (Spain) and European Union/ ; P_FORT_GRUPOS_2023/69//Research Plan of the University of Almeria/ ; TECHBIOSOL-PID2024-156189OB- I00//Ministerio de Ciencia, Innovación y Universidades/ ; },
abstract = {BACKGROUND: Arid and semi-arid regions cover approximately 41% of Earth's surface and their soils are highly vulnerable to degradation due to harsh climatic conditions and extractive activities, such as opencast mining. Organic amendments are widely used to restore degraded soils because they improve physical, chemical, and biological properties. However, little is known about how these amendments alter microbial communities and the relationship between microbial taxonomy and function, particularly in nitrogen and phosphorus cycling. To address this knowledge gap, the effects of different organic amendments (gardening compost, greenhouse horticultural compost, sewage sludge and two blends of the above) on soil properties, microbial communities and their contributions to nitrogen metabolism and phosphorus turnover in degraded soils from a limestone quarry in the Gádor Range (Almería, SE-Spain) six months after their application were investigated.

RESULTS: Organic amendments increased nutrient content (total organic carbon, total nitrogen and available phosphorus), microbiological activity, and bacterial biomass compared to unamended soils, with the largest increases in sewage-sludge-treated soils. Shotgun metagenomic assays revealed that organic amendments modified bacterial community composition and differentially influenced potential function pathways, contributing more strongly to nitrogen metabolism than phosphorus turnover, particularly within the phosphonate pathway. Across soils, Pseudomonadota and Actinomycetota were the dominant phyla. Sludge-amended soil showed higher relative abundance of Pseudomonas, associated with denitrification processes (nirK, nosZ, norB) and phosphonate degradation via C-P lyase (phnJ). Genera such as Streptomyces were linked to ammonium assimilation (glnAd, gltBD) and phosphonate synthesis (pmmS), and were more abundant in soil with vegetable-compost and unamended soils. Both nitrogen and phosphorus metabolisms exhibited phylogenetically unrestricted functional patterns, indicating high functional redundancy at phylum and genus levels.

CONCLUSIONS: This research establishes key relationships between taxonomy and function in restored soils and demonstrates how organic amendments rephase microbial communities and their potential roles in nutrient cycling. Although dominant taxa and functions were identified, many microorganisms involved in nitrogen and phosphorus turnover remain insufficiently characterized. Further research across restoration contexts is needed to compare nutrient-cycling responses and to deepen understanding of taxonomy-function linkages in soils amended with organic residues.},
}

@article {pmid41508143,
year = {2026},
author = {Gong, Y and Shen, S and Cao, Z and Zou, X and Zhou, S and Jiang, R and Kang, X and Liu, S and Tian, Y},
title = {Prophylactic impact of cecal fermentation broth against gut microbiota dysbiosis of broiler chickens challenged with Escherichia coli.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-025-00514-9},
pmid = {41508143},
issn = {2524-4671},
support = {2024CXZX009//The Science and Technology Innovation Fund of Henan Agricultural University/ ; 30601985//The Scientific Studio of Zhongyuan Scholars/ ; },
}

@article {pmid41508107,
year = {2026},
author = {Bay, P and Cappy, P and Rodriguez, C and Mongardon, N and Petit, M and Voiriot, G and Sonneville, R and Pineton de Chambrun, M and Urbina, T and Pham, T and Decavèle, M and Benghanem, S and Contou, D and Lepeule, R and Melica, G and de Prost, N and Angebault, C and Mekontso Dessap, A and Woerther, PL and Razazi, K},
title = {Real-life impact of clinical metagenomics in the intensive care unit: a multicenter retrospective study in greater paris area hospitals.},
journal = {Critical care (London, England)},
volume = {30},
number = {1},
pages = {18},
pmid = {41508107},
issn = {1466-609X},
}

@article {pmid41507798,
year = {2026},
author = {Zhao, J and Cai, W and Zhang, X and Fang, H and Zhuge, J and Zhang, L and Wang, J and Sun, L and Hua, Z and Fu, J},
title = {Exploring lung microbiota and clinical application of BALF-mNGS in patients with pulmonary mycobacterial diseases: a multicenter retrospective study.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04707-9},
pmid = {41507798},
issn = {1471-2180},
support = {2020ZZ002,2021ZZ003//Project of Zhejiang Administration of Traditional Chinese Medicine/ ; LZ22H150001//Natural Science Foundation of Zhejiang Province/ ; 82072161//National Natural Science Foundation of China/ ; 2024KY1761//2024 Science and Technology Program for Medicine and Health in Zhejiang Province/ ; 2023K112//Quzhou Science and Technology Program/ ; },
abstract = {BACKGROUND: Pulmonary mycobacterial diseases (PMDs) remain a leading cause of infectious disease-related mortality worldwide, with the majority of cases attributed to the Mycobacterium tuberculosis complex (MTBC). However, non-tuberculous mycobacteria (NTM) can also cause PMDs, and the incidence of non-tuberculous mycobacterial pulmonary disease (NTM-PD) has been increasing in recent years.

OBJECTIVES: This study aimed to explore the lung microbiota and assess the clinical application of bronchoalveolar lavage fluid metagenomic next-generation sequencing (BALF-mNGS) in patients with PMDs caused by MTBC or NTM.

METHODS: This multicenter, retrospective study included patients with suspected PMDs between July 2021 to June 2025. mNGS and conventional diagnostic methods (CDTs), including GeneXpert, BALF culture, acid-fast bacillus (AFB) staining, and T-SPOT, were performed. Based on the microbiological diagnosis, patients were classified into TB and NTM-PD groups. We further analyzed the clinical impact of different MTBC/NTM abundance levels. The relative abundance of MTBC/NTM was represented by reads ten per million (RTPM). Patient clinical characteristics, length of hospital stay (LOHS), laboratory results, and treatment effectiveness were collected from the electronic medical record system.

RESULTS: Compared with the TB group, patients with NTM-PD exhibited a higher prevalence of immunosuppression (34.96% vs. 53.85%, P = 0.013), particularly prolonged corticosteroid or immunosuppressant therapy (8.94% vs. 21.54%, P = 0.016). In the TB group, higher MTBC abundance was associated with increased positivity of CDTs and alterations in pulmonary microbiota, including enrichment of Candida albicans and other opportunistic pathogens. In the NTM-PD group, although CDTs positivity did not significantly differ between high- and low-abundance subgroups (21.21% vs. 20.00%, P = 0.906), higher NTM abundance was linked to distinct microbial community patterns and a markedly higher ineffective treatment rate (66.67% vs. 39.39%, P = 0.043). Notably, in both TB and NTM-PD groups, elevated MTBC or NTM abundance was associated with longer hospital stays and lower treatment effectiveness, indicating that pathogen abundance is significantly associated with clinical outcomes in pulmonary mycobacterial diseases.

CONCLUSION: BALF-mNGS not only provides superior pathogen detection in patients with PMDs but also shows that lower MTBC/NTM abundance is associated with better clinical prognosis, including shorter hospital stay and better treatment effectiveness, highlighting its potential role as a prognostic indicator.},
}

@article {pmid41507780,
year = {2026},
author = {Gaonkar, PP and Santana-Pereira, ALR and Golden, R and Lambert, A and Higgins, C and Adhikari, Y and Bailey, M and Macklin, K and Huber, L},
title = {Microbiome and resistome dynamics in different stages of commercial broiler production with restricted antimicrobial use.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04664-3},
pmid = {41507780},
issn = {1471-2180},
support = {G00017930//United States Department of Agriculture (USDA)/ ; Intramural funding//Alabama Agricultural Experiment Station/ ; },
abstract = {BACKGROUND: Antimicrobial use (AMU) in poultry production is central to curb the Antimicrobial Resistance (AMR) crisis. Institutional and market pressure led many commercial poultry operations to practice distinct levels of AMU restriction. On-farm data remains one of the main bottlenecks in understanding the impacts of AMU restriction at the farm level and across production systems. However, AMR dynamics in company-wide production chains remain largely unexplored, precluding improvement of AMU policies and stewardship.

STUDY AIM: Here, we shotgun sequenced soil and litter samples from 26 poultry farms and carcass rinses from a processing plant to reconstruct the microbiome and resistome of two vertically integrated commercial poultry operations to explore their dynamics under AMU restriction.

RESULTS: Shotgun sequencing revealed that litter microbiome and resistome changed significantly by production stage and company, reflecting management practices and possible effects of historical AMU. Meanwhile, broiler farms had increased detection of potential pathogens and AMR diversity. We found no evidence of farm-to-fork transmission. Effective biosecurity protocols largely maintained the separation between the internal and external environments of the poultry houses, except on two farms where breaches might have led to external spread of pathogens and AMR.

CONCLUSION: Our study highlights that AMR in commercial poultry system reflects the combined effect of production-stage, company practices, and environmental boundaries. Future studies should integrate quantitative AMR data and culture-based techniques with metagenomic findings to strengthen tracking and surveillance of AMR in poultry farm environments.},
}

@article {pmid41507619,
year = {2026},
author = {Mohamad, M and Sergaki, C and Patel, VC},
title = {Enhancing infection diagnostics in advanced chronic liver disease: harnessing clinical metagenomics for rapid pathogen and antimicrobial resistance detection.},
journal = {npj antimicrobials and resistance},
volume = {4},
number = {1},
pages = {3},
pmid = {41507619},
issn = {2731-8745},
abstract = {Patients with advanced chronic liver disease who have underlying cirrhosis are highly susceptible to bacterial infections, which significantly increase the risk of complications and mortality, compounded by escalating antimicrobial resistance. The current gold standard for infection detection and antimicrobial resistance (AMR) profiling remains dependant on traditional microbiological methods. These conventional approaches are slow, labour-intensive, and often fail to deliver timely and accurate results, delaying critical antimicrobial treatment decisions. Clinical metagenomics (CMg) is emerging as a transformative molecular-based tool in infection diagnostics. By enabling the direct sequencing of pathogens from patient-derived samples, CMg offers rapid and comprehensive identification of pathogens and their resistance profiles. Incorporating this technology into the clinical management of patients with cirrhosis has potential to address diagnostic challenges, reduce reliance on broad-spectrum antibiotics and improve outcomes. To effectively incorporate CMg into infection diagnostics, it will be essential to embed of point-of-care sequencing, standardisation of AMR databases, and accessibility to bioinformatics workflows.},
}

@article {pmid41507585,
year = {2026},
author = {Hsu, CL and Shukla, S and Freund, L and Chou, AC and Yang, Y and Bruellman, R and Raya Tonetti, F and Cabré, N and Mayo, S and Lim, HG and Magallan, V and Cordell, BJ and Lang, S and Demir, M and Stärkel, P and Llorente, C and Palsson, BO and Mandyam, C and Boland, BS and Hohmann, E and Schnabl, B},
title = {Gut microbial ethanol metabolism contributes to auto-brewery syndrome in an observational cohort.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41507585},
issn = {2058-5276},
support = {BX004594//Biomedical Laboratory Research and Development, VA Office of Research and Development (VA Biomedical Laboratory Research and Development)/ ; CTORA23-208366//American Association for the Study of Liver Diseases (AASLD)/ ; CTORA23-208366//American Association for the Study of Liver Diseases (AASLD)/ ; K99 AA031328/AA/NIAAA NIH HHS/United States ; R01 AA029106, R21 AA030654, P30 AR073761//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; },
abstract = {Auto-brewery syndrome (ABS) is a rarely diagnosed disorder of alcohol intoxication due to gut microbial ethanol production. Despite case reports and a small cohort study, the microbiological profiles of patients remain poorly understood. Here we conducted an observational study of 22 patients with ABS and 21 unaffected household partners. Faecal samples from individuals with ABS during a flare produced more ethanol in vitro, which could be reduced by antibiotic treatment. Gut microbiome analysis using metagenomics revealed an enrichment of Proteobacteria, including Escherichia coli and Klebsiella pneumoniae. Genes in metabolic pathways associated with ethanol production were enriched, including the mixed-acid fermentation pathway, heterolactic fermentation pathway and ethanolamine utilization pathway. Faecal metabolomics revealed increased acetate levels associated with ABS, which correlated with blood alcohol concentrations. Finally, one patient was treated with faecal microbiota transplantation, with positive correlations between gut microbiota composition and function, and symptoms. These findings can inform future clinical interventions for ABS.},
}

@article {pmid41507173,
year = {2026},
author = {Han, Y and Liao, J and Li, C and Xing, F and Peng, J and Liu, X and Xie, W and Wu, F and Jian, H and Cheng, R and Dong, X},
title = {Co-occurrence of diverse defense systems shapes complex microbe-virus relationships in deep-sea cold seeps.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-68174-6},
pmid = {41507173},
issn = {2041-1723},
abstract = {Cold seeps host diverse microbes and viruses with numerous unexplored defense and anti-defense systems. Analysis of 3813 microbial and 13,336 viral genomes from 191 metagenomes across 17 cold seep sites reveals extensive microbial defense repertoires, with over 60% representing candidate systems. Experimental validation confirms that several candidates protect against viral infection. These defense systems frequently co-occur, suggesting potential synergistic interactions, and are broadly distributed across sediments. In response, viruses have evolved diverse anti-defense genes, and the concurrent presence of multiple viral and microbial systems highlights intricate coevolution. Functionally critical lineages, such as anaerobic methanotrophic archaea, sulfate-reducing bacteria, and diazotrophs, appear to modify their defensive strategies under ecological and environmental pressures; for example, sulfate-reducing bacteria harbor multiple Gabija systems while corresponding viruses carry anti-Gabija genes, illustrating specific coevolutionary adaptations. Overall, these findings underscore the critical role of virus-microbe interactions in shaping microbial metabolic functions and environmental adaptation in deep-sea ecosystems.},
}

@article {pmid41506580,
year = {2026},
author = {Nichols, S and Estandía, A and Young, CM and Knowles, LS and Palinauskas, V and Okamura, B and Clegg, SM},
title = {Host whole genome sequence data represent an untapped resource for characterising affiliated parasite diversity.},
journal = {International journal for parasitology},
volume = {},
number = {},
pages = {104768},
doi = {10.1016/j.ijpara.2025.104768},
pmid = {41506580},
issn = {1879-0135},
abstract = {Parasites are ubiquitous and exert varied ecological and evolutionary pressures on their hosts. Yet, characterising parasite diversity and distributions can be challenging and costly. Leveraging existing data to identify parasites is thus an attractive alternative. High-throughput sequencing (HTS) can generate whole genome sequence (WGS) data which are increasingly freely available in public repositories and represent an untapped resource for characterising parasites affiliated with hosts. In this study, we examine WGS data generated for the silvereye (Zosterops lateralis), to identify endogenous eukaryotic parasites that were inadvertently captured during host sequencing. We compared detection of parasite genera by this approach with detection via 18S metabarcoding. Mining WGS data for parasite DNA revealed the broadest range of genera. Results were verified by traditional microscopy of blood slides and conducting a targeted multiplex Polymerase Chain Reaction (PCR) for haemosporidian parasites. Detection of haemosporidians was largely consistent across microscopy, multiplex PCR and WGS data while 18S metabarcoding entirely failed to detect this group of parasites. Our results demonstrate that existing WGS datasets can be used to estimate endoparasite diversity and provide greater insights on diversity than metabarcoding whilst also avoiding the costs and challenges of direct sampling. We provide a framework outlining opportunities and constraints to consider when mining WGS data to identify parasite sequences. The framework particularly stresses the influences of sequencing depth, database completeness, and methodological biases. Our findings demonstrate how repurposing existing WGS data can provide a cost-effective and informative means of unravelling complex host-parasite interactions in future disease ecology studies.},
}

@article {pmid41506577,
year = {2026},
author = {Sagar, K and Priti, K and Chandra, H},
title = {Artificial intelligence in metagenome-assembled genome reconstruction: Tools, pipelines, and future directions.},
journal = {Journal of microbiological methods},
volume = {},
number = {},
pages = {107390},
doi = {10.1016/j.mimet.2026.107390},
pmid = {41506577},
issn = {1872-8359},
abstract = {Metagenomic sequencing has revolutionised the field of microbial ecology, as it has led to cultivation-independent exploration of complicated microbial communities. The assembly of metagenome-assembled genomes has provided genome-scale information about uncultivated microorganisms, but issues such as sequencing errors, fragmented assemblies, residual redundancy, uneven coverage, recovery of low-abundance taxa, and highly diversified taxa continue to impair the quality of these genomes. The latest achievements in artificial intelligence, particularly in machine learning and deep learning, have played a significant role in overcoming these limitations by enhancing quality control, error correction, assembly, binning, refinement, and annotation procedures. It is demonstrated that representation learning and graph-based binning methods have high strain-level resolution and can reduce contamination in complex microbial communities, whereas artificial intelligence-based assemblers and polishing tools improve base-level precision and assembly contiguity. This review synthesises traditional and artificial intelligence-based workflows involved in the reconstruction of metagenome-assembled genomes, encompassing quality control, assembly, binning, refinement, and annotation, as well as quantitative benchmarking of significant artificial intelligence-based pipelines. As future directions, the focus on emerging trends, such as explainable artificial intelligence, federated learning, cloud-native scalable pipelines, multimodal and multi-omics integration, and large language model-based annotation, is covered. In general, the incorporation of artificial intelligence represents a paradigm shift in the reconstruction of metagenome-assembled genomes, allowing for a more relevant, scalable, and biologically informative search of the microbial dark matter in various ecosystems.},
}

@article {pmid41506454,
year = {2026},
author = {Shi, T and Xu, S and Lin, Y and Zheng, X and Ruan, H and Shi, W and Zhang, R and Chen, H and Chen, T and Chen, H and Wang, H},
title = {The Clinical Application of Metagenomic Next-Generation Sequencing in Pathogen Identification of Postoperative Spinal Implant Infection.},
journal = {The spine journal : official journal of the North American Spine Society},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.spinee.2026.01.004},
pmid = {41506454},
issn = {1878-1632},
abstract = {BACKGROUND CONTEXT: Postoperative spinal implant infection (PSII) poses significant diagnostic challenges and can lead to serious clinical outcomes. Traditional microbial culture methods are limited by prolonged turnaround times and low sensitivity, which have long hindered a comprehensive understanding of the pathogen spectrum in PSII. Metagenomic next-generation sequencing (mNGS) offers rapid, broad-spectrum, and highly sensitive pathogen detection, providing a promising solution to the diagnostic difficulties associated with PSII.

PURPOSE: This study aimed to evaluate the clinical utility of mNGS for the pathogenic diagnosis of PSII.

STUDY DESIGN/SETTING: Retrospective cohort study.

PATIENT SAMPLE: A retrospective analysis was conducted on clinical data from 122 patients with suspected surgical site infection following spinal implant-related surgery between January 2020 and July 2025.

OUTCOME MEASURES: Identification of pathogenic bacteria in patients.

METHODS: According to the National Healthcare Safety Network (NHSN) criteria, patients were classified into the PSII group (n = 89) and the non-PSII group (n = 33). Pathogen spectrum characteristics of PSII detected by mNGS were analyzed, and the diagnostic performance of mNGS was compared with that of traditional microbial culture, laboratory tests, and imaging studies.

RESULTS: The pathogen detection rate of mNGS was significantly higher than that of traditional culture (79.78% vs. 38.20%, P < 0.001). mNGS successfully detected pathogens in 42.70% (38/89) of culture-negative PSII cases. The main pathogens identified by mNGS included Staphylococcus aureus and coagulase-negative staphylococci (20.00% each, 15/75), Mycobacterium tuberculosis (18.67%, 14/75), and anaerobic bacteria (14.67%, 11/75). Among the 33 patients positive by both mNGS and culture, species-level concordance was 69.70%. No significant difference in the distribution of major pathogens was observed between early-onset (≤3 months) and late-onset (>3 months) infection groups. Antibiotic appropriateness evaluation revealed that only 32.58% (29/89) of patients had initial antibiotic regimens that provided complete coverage against the detected pathogens. The overall diagnostic performance of mNGS for PSII was superior to that of culture, with significantly higher sensitivity (79.78% vs. 38.20%), specificity (100.00% vs. 93.94%), positive predictive value (100.00% vs. 94.44%), negative predictive value (64.71% vs. 36.05%), accuracy (85.25% vs. 53.28%), and AUC (0.8989 vs. 0.6607).

CONCLUSION: mNGS significantly improves the detection of difficult-to-culture pathogens such as M. tuberculosis and anaerobic bacteria in PSII. It is recommended to combine mNGS with conventional methods, thereby improving diagnostic accuracy, guiding rational antibiotic use, and enhancing treatment outcomes.},
}

@article {pmid41506449,
year = {2026},
author = {Zhang, S and Li, Q and Peng, Y and Huo, J and Ran, T and Zhang, X and Wang, R and Jiao, J and Jiang, A and Luo, G and Zhang, Z and Qiu, Q and Li, Z and Mao, S and Yu, Z and Tan, Z and Dong, X and Wang, M},
title = {Spatial heterogeneity of viral communities across the gastrointestinal tracts of ruminants.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2026.01.013},
pmid = {41506449},
issn = {2090-1224},
abstract = {INTRODUCTION: Viruses are abundant biological entities within the gastrointestinal tract (GIT) of ruminants. Current understanding is extensive for bacterial and archaeal communities, but limited for viral communities.

OBJECTIVES: The study aimed to investigate viral diversity, virus-host interactions and ecological functions of viruses across GIT regions and ruminant species.

METHODS: We collected 373 short-read and long-read metagenomes from 10 GIT regions of seven ruminant species, combining Illumina, PacBio HiFi, and Nanopore sequencing. Viral contigs were identified using sequence homology, viral hallmark gene and machine learning, and employed to uncover community assembly of spatial heterogeneity by analyzing virus-host linkage, lifestyle, and auxiliary metabolic genes (AMGs).

RESULTS: We constructed a Ruminant Gastrointestinal Virome Catalog (RGVC) comprising 43,981 vOTUs, revealing that viral communities were remarkably diverse and mainly driven by the GIT regions rather than by the ruminant species. Virus-host linkage analysis identified 4603 putative prokaryotic hosts across 34 classes for 5954 host-linked viruses, along with robust correlation (R[2] = 0.91) observed between abundances of prokaryotic hosts and host-linked viruses across GIT regions. The lysogenic lifestyle was a dominant feature, with integrases being the predominant lysogenic-specific genes. We identified 864 high-confidence AMGs in lysogenic viruses that are annotated as key genes for polysaccharide degradation, glycolysis, and the Wood-Ljungdahl pathway, indicating a putative role for the viruses in supporting these host metabolic functions. The metabolic features of host-linked viruses were further verified by genomic context of selected AMGs of GH10, GPI and FHS with target function.

CONCLUSION: These findings suggest that the GIT viral communities exhibit spatial heterogeneity with distinct virus-host interactions, and offer new perspectives on maintenance of complex ecological and nutritional functions in ruminant GIT.},
}

@article {pmid41506424,
year = {2026},
author = {Shi, R and Han, T and Zhang, H and Huang, H and Xiong, L and Liu, Y and Qi, Z},
title = {Response of Sediment Microbial Community Composition and Function to Mangrove Restoration from an Aquaculture Pond in Southern China.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123718},
doi = {10.1016/j.envres.2026.123718},
pmid = {41506424},
issn = {1096-0953},
abstract = {Mangrove ecosystems, as highly sensitive and productive habitats, host diverse microbial communities essential to biogeochemical cycling. In recent years, large-scale mangrove restoration in former aquaculture ponds has expanded rapidly in China. This represents a typical land-use shift that likely reshapes microbial communities. However, despite its increasing implementation, the accompanying changes in microbial composition and function remain insufficiently understood. Therefore, we compared sediment microbial community composition, diversity, and functional potential between mangrove-planted and reference areas. By absolute-quantification sequencing and metagenomics, we aimed to assess how mangrove restoration regulates the microbial dynamics and their metabolic potentials for carbon, sulfur, and nitrogen cycling after two years of restoration. Mangrove restoration induced a marked phylum shift from Chloroflexota to Pseudomonadota and significantly increased microbial β-diversity (p < 0.05), reflecting enhanced phylogenetic niche differentiation. Specialist species in restored sediments were predominantly Pseudomonadota (e.g., Gammaproteobacteria), contrasting with the Chloroflexota- and Actinobacteriota-dominated reference sites. Functional analysis revealed significant up-regulation of genes involved in polysaccharide metabolism (celB/chbC, sacB, treC, fruB; p < 0.05), assimilatory sulfate reduction, sulfur oxidation (soxZ; p < 0.05), nitrogen fixation (nifH; p < 0.05), and assimilatory nitrate reduction. Furthermore, most high-abundance metagenome-assembled genomes (MAGs) from mangrove sediments encoded sulfate reduction genes. Notably, microbial carbon cycling potential correlated with particulate organic nitrogen, while nitrate concentration linked to nitrogen and sulfur cycling genes, highlighting cross-element synergies. These findings demonstrated that two years of mangrove restoration alters sediment microbiomes and their biogeochemical functions potential, thereby may influence carbon sequestration and nutrient cycling in coastal ecosystems.},
}

@article {pmid41505815,
year = {2026},
author = {Liu, F and Sun, S and Zhang, Y and Wang, F and Yang, X and Zhang, B and Fan, S and Jia, H},
title = {Possible tuberculous meningitis presenting with predominant voiding dysfunction in an elderly patient: A case report.},
journal = {Journal of infection and public health},
volume = {19},
number = {3},
pages = {103128},
doi = {10.1016/j.jiph.2025.103128},
pmid = {41505815},
issn = {1876-035X},
abstract = {Tuberculous meningitis (TBM) typically presents with neurological symptoms. Voiding dysfunction in TBM is usually attributed to spinal cord involvement. We report a rare case of possible TBM co-existing with possible prostatic tuberculosis, presenting primarily with urinary symptoms in the absence of spinal pathology. A 69-year-old male presented with a two-year history of progressive urinary retention, urgency, and frequency. Initial management for benign prostatic hyperplasia was ineffective. He subsequently developed fever, headache, and dizziness. Cerebrospinal fluid (CSF) analysis revealed lymphocytic pleocytosis and elevated protein. Despite extensive testing, including CSF culture, Xpert MTB/RIF, and metagenomic next-generation sequencing (mNGS), no pathogen was identified. However, a history of untreated testicular tuberculosis, pulmonary nodules on CT, and a prostatic nodule on MRI raised suspicion of disseminated tuberculosis. A clinical diagnosis of possible TBM was made based on a Marais score of 11. An intensive anti-tuberculosis regimen including moxifloxacin and linezolid led to complete resolution of neurological and urinary symptoms. This case suggests that voiding dysfunction in TBM patients may stem from concurrent genitourinary tuberculosis rather than spinal cord involvement. It highlights the importance of considering hematogenous dissemination from latent genitourinary foci in elderly patients and the utility of the Marais criteria for the diagnosis of TBM when microbiological evidence is elusive.},
}

@article {pmid41505640,
year = {2026},
author = {Du, S and He, L and Sun, L and Shi, X and Xiao, Y and Jia, Y and Ge, G},
title = {Strategy Development for Improving Ensiling Performance of Ceratoides arborescens (Krascheninnikovia arborescens (Losinsk.) Czerep.) Silage Based on Integrated Omics.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c13269},
pmid = {41505640},
issn = {1520-5118},
abstract = {This study investigated the effects of Lactiplantibacillus plantarum (L. plantarum) on the constituent characteristics, in vitro ruminal fermentation properties, bacterial community structure, metagenome profiles, and metabolite compositions of Ceratoides arborescens silage. Fourier transform infrared spectroscopy analysis demonstrated that L. plantarum inoculation significantly altered the chemical composition, fermentation quality, and in vitro digestibility of the silage. The fermentation process was predominantly driven by Lentilactobacillus and Lactiplantibacillus. Metagenomic profiling and metabolic analyses revealed functional shifts and metabolic alterations, with significant differences observed in the absolute abundance of the carbohydrate-active enzymes. In conclusion, L. plantarum fermentation improved the nutritional value and fermentation properties of Ceratoides arborescens silage by modulating the bacterial community structure, functional gene expression, and metabolic activity. These findings provide mechanistic insights into the beneficial effects of L. plantarum during silage fermentation and offer potential strategies for enhancing the silage quality and ruminal fermentation efficiency.},
}

@article {pmid41505541,
year = {2026},
author = {Leung, PM and Jeffrey, LC and Bay, SK and Gomez-Alvarez, P and Hall, M and Johnston, SG and Dittmann, J and Deschaseaux, E and Hopkins, B and Haskell, J and Jirapanjawat, T and Hutchinson, TF and Coleman, NV and Dong, X and Maher, DT and Greening, C},
title = {Bark microbiota modulate climate-active gas fluxes in Australian forests.},
journal = {Science (New York, N.Y.)},
volume = {391},
number = {6781},
pages = {eadu2182},
doi = {10.1126/science.adu2182},
pmid = {41505541},
issn = {1095-9203},
mesh = {*Methane/metabolism ; *Plant Bark/microbiology ; Australia ; *Microbiota ; *Forests ; *Hydrogen/metabolism ; Carbon Monoxide/metabolism ; Metagenomics ; *Trees/microbiology ; *Bacteria/metabolism/genetics/classification ; Anaerobiosis ; },
abstract = {Recent studies suggest that microbes inhabit tree bark, yet little is known about their identities, functions, and environmental roles. Here we reveal, through gene-centric and genome-resolved metagenomics, that the bark of eight common Australian tree species hosts abundant and specialized microbial communities. The predominant bacteria are hydrogen-cycling facultative anaerobes adapted to dynamic redox and substrate conditions. Furthermore, bark-associated methanotrophs are abundant and can coexist with hydrogenotrophic methanogens. Microcosm experiments showed that bark microorganisms aerobically consume methane, hydrogen, and carbon monoxide at in planta concentrations and produce these gases under anoxia. Combined with in situ field measurements, we show that tree-dwelling microbiota metabolize multiple climate-active gases at marked rates within tree stems, highlighting a potentially substantial role in global atmospheric cycles.},
}

*Methane/metabolism
*Plant Bark/microbiology
Australia
*Microbiota
*Forests
*Hydrogen/metabolism
Carbon Monoxide/metabolism
Metagenomics
*Trees/microbiology
*Bacteria/metabolism/genetics/classification
Anaerobiosis

@article {pmid41504847,
year = {2026},
author = {Wang, W and Li, Y and Sun, J and Jiang, C and Hao, J},
title = {Semi-Rational Design of a Deep-Sea Metagenomic Sucrose Phosphorylase for Enhanced α-Arbutin Biosynthesis.},
journal = {Applied biochemistry and biotechnology},
volume = {},
number = {},
pages = {},
pmid = {41504847},
issn = {1559-0291},
support = {2022YFC2805101//National Key Research and Development Program of China/ ; 2022QNLM030003-2//Qingdao Marine Science and Technology Center/ ; 2023TD71//Central Public-interest Scientific Institution Basal Research Fund, Chinese Academy of Fishery Sciences/ ; },
}

@article {pmid41504449,
year = {2026},
author = {Xu, J and Ma, J and Lin, H and Yan, S and Niu, H},
title = {Metagenomic and metabolomic analyses of rumen fiber digestion in Mongolian cattle fed fresh grass versus hay.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0305125},
doi = {10.1128/spectrum.03051-25},
pmid = {41504449},
issn = {2165-0497},
abstract = {Mongolian cattle exhibit exceptional roughage tolerance due to their rumen microbiome's robust fiber-degrading capacity, enabling efficient utilization of low-quality forage under the Mongolian Plateau's seasonal fluctuations. This study compared rumen microbial composition, CAZyme profiles, fermentation parameters, and metabolic pathways in cattle fed fresh grass (FG) versus hay to elucidate microbe-metabolite interactions underlying fiber digestion. Thirty non-pregnant female Mongolian cattle (460 ± 35 kg, 3-4 years old) were randomly divided into two groups (n = 15/group): one grazed on FG, the other housed and fed autumn-harvested hay (HG). Six animals per group were subsampled for rumen fluid collection and multi-omics analyses (n = 6/group, total n = 12). Compared with the FG group, the HG group showed an increased molar proportion of acetate and a higher acetate-to-propionate ratio, along with reduced molar proportions of propionate and butyrate in rumen fermentation parameters. Metagenomic analysis revealed a higher abundance of Bacteroidalesbacteria and anaerobic fungi (including Neocallimastix sp.JGI-2020a and Piromyces sp.E2) in the HG group. Functional annotation further indicated enriched carbohydrate metabolism pathways in the HG group, along with a greater diversity of CAZymes, particularly those involved in hemicellulose and pectin degradation. Metabolomics identified 13 differentially abundant carbohydrate metabolites, with gluconolactone upregulated in the HG group. Additionally, carbohydrate metabolism pathways identified in the metabolome corroborated the reliability of the metagenomic functional annotations. Correlation network analysis revealed positive associations of Bacteroidaceaebacteria, Neocallimastix sp.JGI-2020a, and Piromyces sp.E2 with acetate, hemicellulose-degrading GHs, and carbohydrate metabolic pathways. In conclusion, hay feeding enhanced ruminal fiber degradation in Mongolian cattle through increased Bacteroidales and anaerobic fungi, diversified CAZymes (especially hemicellulases/pectinases), and upregulated carbohydrate metabolism, reflecting microbial adaptation to low-quality forage.IMPORTANCEMongolian cattle's superior roughage tolerance depends on a specialized rumen microbiome that degrades fibrous substrates via diverse CAZymes. However, microbe-metabolite interactions driving fiber digestion in this breed remain poorly understood. This study revealed an increased abundance of bacteria and fungi involved in rumen fiber degradation, which may be responsible for secreting enzymes associated with hemicellulose and pectin breakdown. Furthermore, the upregulation of key metabolites, including gluconolactone, indirectly promotes acetate production through pathways such as glycolysis and the pentose phosphate pathway. These findings reveal microbial adaptations enhancing low-quality forage utilization, offering new strategies for improving ruminant efficiency in seasonal or resource-limited grazing systems.},
}

@article {pmid41504158,
year = {2025},
author = {Chen, T and Guo, Y and Liang, D and Li, D and Xing, S and Li, D and Zhang, C and Wang, F},
title = {Discriminative Gut Microbial Signatures in Hyperuricemia and Overweight Populations Revealed by Metagenomic Sequencing.},
journal = {International journal for vitamin and nutrition research. Internationale Zeitschrift fur Vitamin- und Ernahrungsforschung. Journal international de vitaminologie et de nutrition},
volume = {95},
number = {6},
pages = {42590},
doi = {10.31083/IJVNR42590},
pmid = {41504158},
issn = {0300-9831},
support = {S2023KFKT-12//Ministry of Agriculture and Rural Affairs/ ; 2024YFF1107000//National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Hyperuricemia/microbiology ; Male ; Female ; *Overweight/microbiology ; Middle Aged ; Cross-Sectional Studies ; Feces/microbiology ; Adult ; Metagenomics ; Metagenome ; },
abstract = {BACKGROUND: This cross-sectional study aimed to investigate the relationships between gut microbiota compositional alterations and chronic metabolic disorders by analyzing taxonomic diversity, community structure, and species-level differences in individuals with hyperuricemia (HUA) and a history of being overweight. Our findings offer novel insights into microbiota-targeted therapeutic strategies for managing metabolic diseases. A total of 144 participants were recruited and divided into three diagnostic categories: healthy controls (HL, n = 29), hyperuricemia group (HU, n = 24), and overweight (OW, n = 91).

METHODS: Comprehensive phenotypic profiles and metagenomes were analyzed for fecal samples from the three groups.

RESULTS: Significant differences were observed in psychological states and microbial ecology between the metabolic disorder groups (HU and OW) and the control group (HL) (p < 0.05). Both the overweight individuals and those with HUA presented significant changes in gut microbial composition, with reduced α-diversity indices (Shannon index: HU vs HL Mann-Whitney U = 306; p = 0.462; OW vs HL Mann-Whitney U = 1008; p = 0.040; richness index: HU vs HL Mann-Whitney U = 307; p = 0.469; OW vs HL Mann-Whitney U = 1072; p = 0.092) compared to healthy individuals. Moreover, analysis of the linear discriminant analysis effect size (LEfSe) identified four discriminatory species in the HU group (Alistipes putredinis, Mediterraneibacter faecis, Streptococcus oralis, and Gemella sanguinis), and five in the OW group (Pantoea endophytica, Pantoea vagans, Phocaeicola coprophilus, Ruminococcus SGB4421, and Klebsiella oxytoca), representing potential biomarkers for the progression of chronic metabolic diseases.

CONCLUSION: This study elucidates the characteristics of overweight individuals and those with HUA in terms of phenotypic features and gut microbiota, providing a theoretical reference for gut microbiota-targeted therapies and lifestyle interventions in chronic metabolic diseases.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Hyperuricemia/microbiology
Male
Female
*Overweight/microbiology
Middle Aged
Cross-Sectional Studies
Feces/microbiology
Adult
Metagenomics
Metagenome

@article {pmid41503923,
year = {2026},
author = {Sun, YF and Yang, KY and Li, H and Liang, YS and Cai, LQ and Xie, JY and Zhang, YW and Liang, JY and Mou, Q and Wang, YM and Chen, D and Qi, MX and Aguila, LCR and Hassan, MA and Li, HS and Pang, H},
title = {LadybirdBase: A comprehensive biology, ecology, and omics resource for ladybird beetles (Coccinellidae).},
journal = {Insect science},
volume = {},
number = {},
pages = {},
doi = {10.1111/1744-7917.70231},
pmid = {41503923},
issn = {1744-7917},
support = {32172472//National Natural Science Foundation of China/ ; //Open Fund of Guangdong Key Laboratory of Animal Protection and Resource Utilization/ ; 2023YFD1400600//National Key Research and Development Program of China/ ; },
abstract = {Ladybird beetles (Coleoptera: Coccinellidae) comprise over 6000 species and have been extensively studied in terms of their biology, ecology, omics, and applications in biological control. However, this knowledge is scattered across diverse publications and databases, limiting accessibility and integration. To address this gap, we developed LadybirdBase (http://www.ladybirdbase.com), a comprehensive database that compiles primarily published resources on 6872 ladybird species. It integrates five modules: Biology (taxonomy and species traits), Ecology (diet ranges and geographic distributions), Genomics (genomes, transcriptomes, and related datasets), Microbiomics (microbial amplicon and metagenome sequencing), and Lab Test (laboratory-derived biological parameters). LadybirdBase also provides analytical tools for species identification via morphology or DNA barcodes, gene and primer searches, and transcriptome-based differential expression analysis. Using Cryptolaemus montrouzieri-a representative biological control ladybird-as an example, we show that by centralizing ecological, laboratory, and multi-omics data, LadybirdBase supports efficacy evaluation, rearing and release optimization, and risk assessment, thereby advancing research and applications in evolutionary biology, ecology, and sustainable pest management.},
}

@article {pmid41503791,
year = {2026},
author = {Jin, J and Yao, G and Zhang, X and Zhang, T and Ye, H and Zhou, X and Yu, Y and Zhao, Y and Qin, Z and Chen, H and Bi, Y and Wang, X and Ren, X and Zhang, Y and Wang, Z and Zhang, Q},
title = {Gut virome dysbiosis contributes to premature ovarian insufficiency by modulating gut bacteriome.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2611645},
doi = {10.1080/19490976.2025.2611645},
pmid = {41503791},
issn = {1949-0984},
mesh = {Female ; Animals ; *Dysbiosis/microbiology/virology ; *Primary Ovarian Insufficiency/microbiology/virology/therapy ; *Gastrointestinal Microbiome ; Rats ; Humans ; Adult ; *Virome ; Fecal Microbiota Transplantation ; *Bacteria/genetics/classification/isolation & purification/virology ; Young Adult ; Feces/virology ; Ovary ; Rats, Sprague-Dawley ; },
abstract = {BACKGROUND: Premature ovarian insufficiency (POI) significantly impairs female fertility and poses substantial health risks; however, its pathogenesis is incompletely understood, and effective therapeutic interventions are limited. Although gut bacteriome has been closely associated with ovarian dysfunction, the role and therapeutic potential of gut viruses, which far outnumber bacteria, remain largely unexplored.

RESULTS: Therefore, we recruited 60 healthy reproductive-aged women and recently diagnosed POI patients and investigated these concerns using various techniques, including whole-genome shotgun sequencing of virus-like particle (VLP) and fecal virome transplantation (FVT) in CTX-induced POI rats. We found considerable interindividual variability in the gut virome. The virome of POI patients exhibited significant dysbiosis, characterized by a marked reduction in virulent phage, significant changes in predominant phages, and a notable increase in horizontal gene transfer of resistance genes and virulence factors. Furthermore, gut VLPs from the healthy reproductive-aged women significantly improved the condition of POI rats. Conversely, gut VLPs from POI patients markedly impaired the ovarian function and reproductive capacity of healthy rats. The above regulatory effect is primarily due to modulations of gut bacteriome, specifically the estrobolome, and intestinal barrier integrity, which subsequently affect hypothalamic-pituitary-ovarian axis hormone levels and regulate ovarian oxidative stress and inflammation, thereby influencing ovarian function.

CONCLUSIONS: Our findings demonstrate the critical roles of the gut virome in regulating ovarian function and provide new insights into the pathogenesis of POI. This study also underscores the therapeutic potential of the gut virome in improving ovarian dysfunction and female infertility including POI.},
}

Female
Animals
*Dysbiosis/microbiology/virology
*Primary Ovarian Insufficiency/microbiology/virology/therapy
*Gastrointestinal Microbiome
Rats
Humans
Adult
*Virome
Fecal Microbiota Transplantation
*Bacteria/genetics/classification/isolation & purification/virology
Young Adult
Feces/virology
Ovary
Rats, Sprague-Dawley

@article {pmid41503787,
year = {2026},
author = {Wang, Y and Yu, Y and Xu, N and Zhang, Z and Chen, B and Song, M and Zhang, Q and Wang, T and Ma, Y and Lu, T and Sun, L and Qian, H},
title = {Genes for Vitamin B Synthesis and Their Distribution in Microbial Producers.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c11883},
pmid = {41503787},
issn = {1520-5118},
abstract = {B vitamins (VBs) are essential micronutrients, yet their microbial production across natural habitats remains poorly understood. We analyzed 126,931 metagenome-assembled genomes to map the distribution of VB producers and constructed a database of 87 VB synthesis genes, identifying VB-independent producers and their environmental drivers. Soil and freshwater habitats harbored the greatest diversity of VB1, VB2, VB7, VB9, and VB12 producers, whereas marine systems contained fewer. Biosynthetic capacity was rare for VB5 and was limited for VB3 and VB6. Gammaproteobacteria are prolific producers, synthesizing up to eight VB types. Soil sulfur content and conductivity significantly enhanced VB production potential, linking beneficial microbes to improved soil health. We further validated VB3 and VB7 synthesis in Acinetobacter kookii, supporting our predictive framework. Because the identified producers include both beneficial and pathogenic taxa, careful evaluation is required. This work provides a robust gene database and a foundation for optimizing microbial VB production in agriculture and biotechnology.},
}

@article {pmid41503705,
year = {2026},
author = {Liu, W and Du, Y and Ning, J and Zheng, S and Qiu, W and Wang, Y},
title = {Geogenic Ammonium Enrichment in Alluvial-Lacustrine Aquifer Systems: Coupled Controls of Microbial Pathways and Organic Matter Composition.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c11156},
pmid = {41503705},
issn = {1520-5851},
abstract = {Elevated geogenic ammonium (NH4[+]) reported globally in alluvial-lacustrine aquifer systems is generally attributed to the mineralization of natural organic matter (OM). However, the contribution of microbial nitrogen (N) metabolism remains unclear. This study integrated hydrogeochemical profiling, metagenomic sequencing, and molecular-level OM characterization to elucidate how microbial nitrogen transformation and organic N mineralization could drive geogenic NH4[+] accumulation in groundwater. A distinct shift in microbial N metabolism pathways was identified along the NH4[+] enrichment gradient. Under N-limited and strongly reducing conditions, N fixation and dissimilatory reduction of nitrate to ammonium provided additional NH4[+] sources, whereas nitrification served as the primary sink by oxidizing NH4[+] to nitrate. At low NH4[+] levels, NH4[+] was mainly produced via deamination of simple mono-N compounds (CHO+1N) found in highly unsaturated low-oxygen (O) compounds and low-O polyphenols. In contrast, at high NH4[+] levels, urease-mediated hydrolysis of multi-N compounds (CHO+nN) in highly unsaturated high-O compounds became dominant. Co-occurrence network analysis revealed tight, pathway-specific linkages between functional genes and NH4[+]-associated OM compounds, highlighting the substrate-dependent nature of geogenic NH4[+] production. These findings could advance our understanding of microbially mediated NH4[+] enrichment mechanisms and offer implications for the management of NH4[+] and other geogenic contaminants in organic-rich aquifers.},
}

@article {pmid41503571,
year = {2026},
author = {Bajaj, JS and Fagan, A and Sterling, RK and Sikaroodi, M and Gallagher, ML and Lee, H and Matherly, SC and Bartels, A and Mousel, T and Davis, BC and Puri, P and Fuchs, M and Thacker, LR and McGinley, JP and Khoruts, A and Gillevet, PM},
title = {The multi-omic basis for hepatic encephalopathy recurrence: Analysis of the THEMATIC trial.},
journal = {JHEP reports : innovation in hepatology},
volume = {8},
number = {1},
pages = {101634},
pmid = {41503571},
issn = {2589-5559},
abstract = {BACKGROUND & AIMS: The THEMATIC trial demonstrated that fecal microbiota transplantation (FMT) reduces recurrence of hepatic encephalopathy (HE) in patients already receiving lactulose and rifaximin. The aim of this analysis was to identify multi-omic predictors of HE recurrence among THEMATIC trial participants.

METHODS: The THEMATIC trial enrolled patients with cirrhosis and HE who received oral or enema FMT vs. placebo (1-3 administrations) and were followed for 6 months. Outcomes included safety and HE recurrence. Serum, urine, and stool samples were collected at baseline and post-FMT for all participants. Stool metagenomics, serum and urine metabolomics, inflammatory cytokines, and clinical data were analyzed. Differences between patients with and without HE recurrence were assessed using pathway, random forest, and latent factor analyses.

RESULTS: HE recurred in 10 of 60 patients (17%), with significantly higher recurrence in the placebo vs. the FMT groups (40% vs. 8%; p = 0.005). Due to the low recurrence rate in the FMT arms, all patients with recurrence were combined and compared with those without recurrence. Stool metagenomics showed that the abundance of short-chain fatty acid (SCFA) producers (Faecalibacterium, Eubacterium, Bacteroides, Blautia spp.) was lower, while that of GABA-producing taxa (Lactobacillus, Bifidobacterium spp.) was higher, in patients with recurrence. Urine and serum metabolomes separated HE recurrence groups on PLS-DA, with serum butyrate and isobutyrate being most significantly associated (p = 0.008). Pathway analyses revealed upregulation of GABA and neurotransmitter pathways in patients with HE recurrence. Random forest and latent factor analysis indicated that SCFA producers and secondary bile acids were protective, whereas IL-6, GABA producers, nicotine metabolites, and primary bile acids were associated with HE recurrence.

CONCLUSIONS: Secondary analysis of the THEMATIC randomized controlled trial indicates that HE recurrence in patients on lactulose and rifaximin is associated with distinct microbiome and metabolomic profiles, particularly involving SCFAs, GABA metabolism, bile acids, and IL-6.

IMPACT AND IMPLICATIONS: Fecal microbiota transplantation (FMT) reduced hepatic encephalopathy (HE) recurrence in patients receiving lactulose and rifaximin in the THEMATIC trial, but the multi-omic mechanisms underlying this effect were unclear. In this secondary analysis, we found that HE recurrence - regardless of FMT or placebo assignment - was associated with distinct multi-omic signatures, including reduced short-chain fatty acid-producing and increased pathobiont taxa, lower urinary and serum short-chain fatty acids, secondary bile acids, and acetaminophen derivatives, and higher GABA-related and nicotine metabolites, along with elevated IL-6 levels. Notably, patients with greater donor microbiota engraftment had lower rates of HE recurrence. These findings suggest that HE recurrence after FMT reflects a multifactorial process involving alterations in gut metagenomics, systemic metabolomics, inflammation, and donor engraftment.

TRIAL REGISTRATION: www.clinicaltrials.gov: NCT03796598.},
}

@article {pmid41503531,
year = {2026},
author = {Burd, EM},
title = {Metagenomic next-generation sequencing reveals cross-reactivity of lateral flow cryptococcal antigen assay with Trichosporon inkin.},
journal = {ASM case reports},
volume = {1},
number = {2},
pages = {},
pmid = {41503531},
issn = {2996-2684},
abstract = {Metagenomic next-generation sequencing (mNGS) in plasma, cerebrospinal fluid (CSF), and bronchoalveolar lavage fluid is a relatively new technology that offers a means to potentially provide a diagnosis in cases where infection is suspected, but conventional diagnostic testing has not revealed a pathogen. There have been many publications of individual cases and overall appraisals of its utility in detecting bacteria, fungi, and DNA viruses associated with otherwise undiagnosed systemic infections. A recent article by Phillips et al. published in ASM Case Reports (2:e00053-25, 2025, https://doi.org/10.1128/asmcr.00053-25) presents a case of meningitis in an immunosuppressed child that was ultimately determined to be caused by Trichosporon inkin using mNGS. Elevated ß-1,3-D-glucan (BDG) levels in CSF and serum projected a diagnosis of fungal meningitis. Bacterial, fungal, and mycobacterial cultures were negative. Positive lateral flow cryptococcal antigen titers in serum and CSF complicated the anticipated diagnosis since Cryptococcus spp. are thought to not have sufficient cell wall BDG to produce positive test results. Given the ultimate diagnosis of T. inkin meningitis and the known cross-reactivity with Trichosporon asahii per package insert, the unexpected cryptococcal antigen results raised the possibility of additional cross-reactivity. The authors uncovered this possibility by testing three known clinical isolates of T. inkin which generated positive results. This case adds to the growing literature that highlights the utility of mNGS in providing a diagnosis in otherwise unresolved cases and shows that mNGS can be further instructive in elucidating limitations in commonly used diagnostic tests.},
}

@article {pmid41503526,
year = {2026},
author = {Phillips, K and Acker, KP and Han, JY and Salvatore, CM and Permar, SR and Rolón, RM and Marino, J and Dysart, C and Berman, DM and Chiu, CY and Kidd, SE and Westblade, LF and Dubois, MM},
title = {Trichosporon inkin meningitis in a pediatric patient diagnosed via metagenomic sequencing.},
journal = {ASM case reports},
volume = {1},
number = {2},
pages = {},
pmid = {41503526},
issn = {2996-2684},
abstract = {BACKGROUND: Trichosporon has emerged as an important cause of invasive fungal infections in immunocompromised patients. There are limited data on invasive Trichosporon infections in children.

CASE SUMMARY: We report a case of culture-negative Trichosporon inkin meningitis diagnosed via metagenomic next-generation sequencing of plasma and cerebrospinal fluid in an infant with retinoblastoma. In addition, we highlight the role of β-1,3-D-glucan in the diagnosis and therapeutic monitoring of trichosporonosis, and cross-reactivity of the cryptococcal antigen lateral flow assay with T. inkin.

CONCLUSION: This diagnosis, which was challenging to make in the absence of a positive culture, highlights the utility of metagenomic sequencing methods and fungal biomarkers in identifying infectious agents and ensuring timely diagnosis and management of patients with rare fungal infections of the central nervous system.},
}

@article {pmid41503489,
year = {2026},
author = {Goddard, TR and Carlson-Jones, JA and Morton, J and Ooi, CY and Tai, A and Warner, MS and Wong, J and Evans, IE and Hopkins, E and Iredell, JR and Jersmann, HP and Whiteson, KL and Bouras, G and Doane, MP and Falk, NW and Green, R and Grigson, SR and Mallawaarachchi, V and Martin, B and Roach, MJ and Ryan, FJ and Tarasenko, A and Papudeshi, B and Drigo, B and Giles, SK and Harker, CM and Hesse, RD and Hodgson, RJ and Hussnain, A and Hutton, A and Inglis, LK and Keneally, C and Kerr, EN and Liddicoat, C and Peddle, SD and Watson, CD and Yang, Q and Decewicz, P and Speck, PG and Mitchell, JG and Dinsdale, EA and Edwards, RA},
title = {Microbial Ecological Signatures Predict Pathogen Emergence and Multidrug Resistance in Cystic Fibrosis Airways up to a Year in Advance.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2025.12.28.25342520},
pmid = {41503489},
abstract = {Chronic infections in cystic fibrosis (CF) emerge from gradual ecological transitions in the airway microbiome, yet early predictive markers remain poorly defined. We developed a new autoencoder-based framework that outperforms read-based or metagenome-assembled genome-based analyses at capturing the continuum from health-associated commensals to pathogen-dominated, antibiotic-tolerant communities. This improvement is achieved by integrating taxonomic and functional data from 127 sputum and bronchoalveolar lavage metagenomes from 64 people with CF into latent "Clusters of Phylogeny and Functions" (COPFs). Coupled with gradient-boosted random forests, COPFs predicted Pseudomonas aeruginosa colonisation, multidrug resistance, and impending infection up to a year before clinical detection. The multidrug-resistant P. aeruginosa signature showed the same resistance-mechanism evolution as found in laboratory experiments. The inclusion of eukaryotic markers revealed persistent Aspergillus fumigatus signatures even during culture-negative intervals. Applying our South Australian-trained model to over 1,000 global metagenomes from 22 independent CF datasets, we achieved 94% accuracy in predicting P. aeruginosa status across platforms and geographies, validating the model's universal utility. Our results demonstrate that combining datasets with deep learning reveals conserved ecological and metabolic mechanisms in disease progression, transforming metagenomics into a predictive framework for managing chronic infections.},
}

@article {pmid41503361,
year = {2025},
author = {Uddin, MN and Hartog, C and Murray, E and Loveless, JB and Roberson, L and Aslan, A and Cubas, F and Rowles, LS},
title = {Advancing Circular Bioeconomy through a Systems-Level Assessment of Food Waste and Industrial Sludge Codigestion.},
journal = {ACS environmental Au},
volume = {5},
number = {5},
pages = {479-489},
pmid = {41503361},
issn = {2694-2518},
abstract = {Disposal of food waste (FW) in landfills remains an unsustainable practice for organic waste management. Simultaneously, pulp and paper mills produce significant amounts of recalcitrant organic waste that is difficult to decompose due to its high lignocellulosic content. In this study, we developed an innovative approach to improve the digestion of pulp and paper mill sludge (PPMS) by amending FW to produce a low chemical oxygen demand (COD) sludge while recovering methane in the process. This codigestion process was evaluated through lab-scale biogas production experiments coupled with a comprehensive economic and environmental sustainability assessment. Biomethane production results revealed that the FW-PPMS codigestion methane yield was 36% higher on average than the PPMS monodigestion. Additionally, metagenomic analysis revealed that microbial communities for both systems transitioned from highly heterogeneous to more adapted uniform communities after digestion. Improved microbial communities contributed to higher COD removal (92%) in the FW-PPMS system compared to monodigestion (80% removal). The sustainability analysis revealed that the codigestion of FW-PPMS had median costs of 236.64 USD·tonne[-1]·day[-1] and emissions of 228.30 kg CO2 eq·tonne[-1]·day[-1], a significant reduction compared to directly disposing the FW in landfills (median costs of 405.13 USD·tonne[-1]·day[-1] and emissions of 556.27 kg CO2 eq·tonne[-1]·day[-1]). A nationwide contextual analysis revealed that out of six regions, the US Northeast had the lowest median costs and emissions, while the Mountain Plains region had the highest, highlighting the importance of geographical and infrastructural factors in implementation. Overall, codigesting FW with PPMS is revealed to be a sustainable waste management option to decrease landfill disposal of valuable organic waste.},
}

@article {pmid41502951,
year = {2025},
author = {Oliveira, RA and McSpadden, E and Pandey, B and Lee, K and Yousef, M and Chen, RY and Triebold, C and Haro, F and Aksianiuk, V and Patel, R and Shriram, K and Ramanujam, R and Kuehn, S and Raman, AS},
title = {Statistical design of a synthetic microbiome that suppresses diverse gut pathogens.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.02.28.582635},
pmid = {41502951},
issn = {2692-8205},
abstract = {Engineering functional microbiomes is challenging due to complex interactions between bacteria and their environments [1-6] . Using a set of 848 gut commensal strains and clearance of multi-drug resistant Klebsiella pneumoniae (Kp -MH258) as a target function, we engineered a functional 15-member synthetic microbiome-SynCom15-through a statistical approach agnostic to strain phenotype, mechanism of action, bacterial interactions, or composition of natural microbiomes. Our approach involved designing, building, and testing 96 metagenomically diverse consortia, learning a generative model using community strain presence/absence as input, and distilling model constraints through statistical inference. SynCom15 cleared Kp -MH258 across in vitro , ex vivo , and in vivo environments, matching the efficacy of a fecal microbiome transplant in a clinically relevant murine model of infection. The mechanism of suppression by SynCom15 was related to fatty acid production coupled with environmental acidification. SynCom15 also suppressed other pathogens- Clostridioides difficile , Escherichia coli , and other K. pneumoniae strains-but through different mechanisms. Sensitivity analysis revealed models trained on strain presence/absence captured the statistical structure of pathogen suppression, illustrating that community representation was key to our approach succeeding. Our framework, 'Constraint Distillation', could be a general and efficient strategy for building emergent complex systems, offering a path towards synthetic ecology more broadly.},
}

@article {pmid41502900,
year = {2025},
author = {Hou, Y and Xie, W and Duan, J and Li, X and Wu, Z},
title = {Challenge of Cupriavidus gilardii infection in an immunocompromised child: a case report.},
journal = {Translational pediatrics},
volume = {14},
number = {12},
pages = {3498-3503},
pmid = {41502900},
issn = {2224-4344},
abstract = {BACKGROUND: Cupriavidus gilardii is a multidrug-resistant (MDR) pathogen found in soil and water. Human infection is extremely rare, with only two pediatric cases reported to date, and its clinical features and the antimicrobial strategies remain unclear. The pathogen's MDR nature often poses a therapeutic challenge. This case provides valuable clinical evidence regarding the management of C. gilardii infection in immunocompromised pediatric patients.

CASE DESCRIPTION: A 4-year-old boy with acute lymphoblastic leukemia developed severe immunosuppression after reinduction cyclophosphamide, cytarabine (Ara-C), mercaptopurine (CAM) chemotherapy according to the SCCCG-ALL-2023 protocol. The patient initially presented with recurrent fever, septic shock, and progressive respiratory distress. Despite an aggressive empirical antibiotic regimen including meropenem, imipenem, piperacillin-tazobactam, linezolid, and levofloxacin, his condition continued to worsen. Blood cultures and metagenomic next-generation sequencing (mNGS) subsequently confirmed C. gilardii infection. Based on susceptibility testing, therapy was adjusted to a combination of ceftazidime-avibactam (CAZ-AVI) and tigecycline. After this adjustment, the patient showed marked clinical improvement, with decreased inflammatory indicators and nearly completed clearance of the pathogen. Unfortunately, on hospital day 26, he developed sudden massive hemoptysis due to Aspergillus pulmonary artery invasion and died despite emergency treatment.

CONCLUSIONS: This case demonstrates that CAZ-AVI may offer effective antimicrobial control for C. gilardii infection in immunocompromised pediatric patients. Although the patient succumbed to secondary fungal complications, successful microbiological control demonstrates that CAZ-AVI may serve as a potential salvage therapy for rare MDR Gram-negative bacteria and provides clinical insight into the management of uncommon pediatric infections.},
}

@article {pmid41502854,
year = {2025},
author = {Su, JW and Qin, SY and Liu, J and Lei, CC and Zhang, XT and Shi, WH and Xie, LH and Liu, Y and Ni, HB and Yu, MY and Liang, HR and Qin, Y and Jiang, J and Sun, HT and Ma, H and Li, ZY and Zhang, XX},
title = {Blastocystis presence alters gut archaeal communities and metabolic functions in Tibetan antelopes (Pantholops hodgsonii).},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1744013},
pmid = {41502854},
issn = {2297-1769},
abstract = {BACKGROUND: Archaea are vital members of the gut microbiota, yet their diversity and functions in high-altitude wildlife remain poorly understood. Understanding their ecological roles can provide insights into host health and microbial community dynamics.

METHODS: We applied metagenome-assembled genome (MAG)-based approaches to investigate gut archaea in Tibetan antelopes (Pantholops hodgsonii) and assess their shifts in the presence of Blastocystis. A total of 463 non-redundant archaeal MAGs were reconstructed and analyzed for taxonomic diversity and functional potential.

RESULTS: The MAGs encompassed 16,189 protein clusters, with over 70% representing potentially novel species, highlighting substantial unexplored archaeal diversity. Alpha diversity showed no significant differences between healthy and Blastocystis-present groups, but beta diversity analysis revealed marked community restructuring, including decreased Methanobacteriota and increased Halobacteriota and Thermoplasmatota in the Blastocystis-present group. Functional annotation indicated changes in energy and nucleotide metabolism and alterations in carbohydrate-active enzyme composition. Additionally, putative viral sequences were detected within archaeal MAGs, suggesting potential virus-microbe interactions.

CONCLUSION: Our findings provide novel insights into the diversity and ecological functions of gut archaea in Tibetan antelopes, offering a foundation for future research on their contributions to host health and microbial ecology.},
}

@article {pmid41502470,
year = {2026},
author = {Shukla, A and Yadav, M and Malik, MZ and Aditya, AK and Kumar, A and Tandon, R and Shalimar, and Ray, AK},
title = {Soil influences on rural versus urban human gut microbiota and implications on cardio-metabolic health: a comparative pilot study.},
journal = {3 Biotech},
volume = {16},
number = {1},
pages = {62},
pmid = {41502470},
issn = {2190-572X},
abstract = {UNLABELLED: Humans are exposed to surrounding soil environment and this exposure has reduced with growing urbanisation. Limited evidence exists on how rural and urban soils shape human gut microbiome and related functions. Here, we performed metagenomic analysis, functional prediction, gene ontology using QIIME2, PICRUSt, and DAVID by taking human stool and soil samples (n = 20) from rural and urban settings to characterise gut microbiota and their resemblance to their respective soil microbiota and its functional implications. Our findings demonstrated that soil environment affects gut microbial diversity and abundance of its immediate human inhabitants in both groups and observed shared microbial and functional properties in rural- and urban-guts characteristic of their respective soil microbiota. In rural-group, phylum Bacteroidetes, Firmicutes, Proteobacteria, Actinobacteria, class Actinobacteria were major overlapping features, while in the urban-counterpart phylum Proteobacteria, Firmicutes, class Gammaproteobacteria were observed. We also demonstrated implication of this differential composition on human health in both settings, and observed enrichment of cytokines like IL-12, IFN-ϒ, and oxidative phosphorylation pathway in rural group vital to metabolic homeostasis. While enrichment of response to toxic substances, methane metabolism, and potentially low levels of alanine in the urban counterpart, linked to impaired immune response and metabolism, suggests urban group may be prone to the cardio-metabolic disease risk. These observations were consistent with other findings emphasising rural groups have healthy sets of microbiome compared to their urban counterpart. In conclusion, our findings unveil the significance of soil microbiota in evolution and shaping of human gut microbiota, thereby potentially beneficial to human health.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-025-04675-x.},
}

@article {pmid41502282,
year = {2025},
author = {Sheng, YP and Kong, LJ and Chu, PP and Xia, YL and Shen, CT and Sun, JF},
title = {[Clinical Analysis of Torque Teno Virus Infection after Hematopoietic Stem Cell Transplantation in Children].},
journal = {Zhongguo shi yan xue ye xue za zhi},
volume = {33},
number = {6},
pages = {1784-1789},
doi = {10.19746/j.cnki.issn.1009-2137.2025.06.036},
pmid = {41502282},
issn = {1009-2137},
mesh = {Humans ; *Torque teno virus ; *Hematopoietic Stem Cell Transplantation/adverse effects ; *DNA Virus Infections ; Child ; Male ; Female ; Incidence ; Child, Preschool ; Adolescent ; },
abstract = {OBJECTIVE: To investigate the incidence, clinical characteristics, and complications of Torque teno virus (TTV) in children after hematopoietic stem cell transplantation (HSCT).

METHODS: A total of 40 children with hematological diseases who underwent HSCT were selected, and metagenomic next-generation sequencing (mNGS) technology was used to detect the gene sequences of pathogenic microorganisms in the blood. Combined with clinical data, the characteristics of TTV infection were analyzed.

RESULTS: Among the 40 pediatric patients post-HSCT, the TTV positive rate was 42.5% (17/40). There were no statistically significant differences between the TTV-positive group and the TTV-negative group in sex, age, white blood cell count(WBC), red blood cell count(RBC), hemoglobin, platelet count, neutrophil count, lymphocyte count, and high-sensitivity C-reactive protein (all P >0.05). The incidence of TTV infection was significantly higher in children who underwent haploidentical HSCT and in those with bone marrow stem cells (BMSC) as the transplant source (P <0.05). However, there were no significant differences in the TTV infection rate among patients with different disease types, different HLA matching statuses, or different engraftment times of neutrophils and platelets (all P >0.05). Among 17 children infected with TTV, 13(76.5%) had co-infections with other viruses, mainly including cytomegalovirus (58.8%, 10/17), human polyomavirus (41.2%, 7/17), and Epstein-Barr virus (17.6%, 3/17). In children with TTV infection, the most common complications were sepsis (82.4%), graft-versus-host disease (GVHD) (70.6%), pulmonary infection (41.2%), and hemorrhagic cystitis (17.6%). The incidence of GVHD in the TTV-positive group was significantly higher than that in the TTV-negative group (P <0.05).

CONCLUSION: TTV infection is common in children undergoing HSCT, and it is prone to be complicated with cytomegalovirus infection and GVHD, which has an important influence on the clinical outcomes.},
}

Humans
*Torque teno virus
*Hematopoietic Stem Cell Transplantation/adverse effects
*DNA Virus Infections
Child
Male
Female
Incidence
Child, Preschool
Adolescent

@article {pmid41502197,
year = {2025},
author = {Hasan, I},
title = {Short-Chain Fatty Acids in the Gut-Brain-Liver Axis: Implications for Hepatic Encephalopathy.},
journal = {Acta medica Indonesiana},
volume = {57},
number = {4},
pages = {433-435},
pmid = {41502197},
issn = {2338-2732},
mesh = {Humans ; *Hepatic Encephalopathy/metabolism/etiology/epidemiology/microbiology ; *Gastrointestinal Microbiome ; *Fatty Acids, Volatile/metabolism ; *Liver Cirrhosis/complications ; Indonesia/epidemiology ; *Liver/metabolism ; *Brain/metabolism ; Cross-Sectional Studies ; Feces/chemistry ; },
abstract = {Hepatic encephalopathy (HE) is one of the serious complications of liver cirrhosis, characterized by a broad spectrum of neuropsychiatric symptoms, ranging from subtle cognitive impairment to coma, due to brain dysfunction associated with acute or chronic liver failure and/or portosystemic shunting. Globally, the prevalence of hepatic encephalopathy (HE) is reported to range from 20% to 80% in patients with liver cirrhosis, depending on whether the assessment includes minimal (MHE) or overt (OHE) forms. In Indonesia, determining the true prevalence of HE is challenging due to diagnostic difficulties, with estimates ranging from 30% to 84%. At Cipto Mangunkusumo General Hospital, the prevalence of HE in 2009 was 63.2%. In recent years, evidence has highlighted the role of the gut microbiota in the pathogenesis of hepatic encephalopathy (HE), a concept now widely referred to as the "gut-liver-brain axis." Short-chain fatty acids (SCFAs) are gut microbial-derived metabolites that provide numerous health benefits. SCFA has been demonstrated to impact gut barrier function, immunomodulation, and glucose homeostasis. In this issue, Ferdianto et al. conducted a cross-sectional observational study comparing the amount and composition of fecal SCFA in cirrhotic patients with and without HE. The study revealed no significant difference in SFA levels between HE and non-HE groups; however, the HE groups demonstrated higher levels of total SCFA, acetate, and butyrate compared to the non-HE groups. While this study contributes valuable early evidence from an Indonesian cohort, several important limitations should be acknowledged. First, the diagnostic approach for covert or minimal HE requires clarification. The authors did not explicitly state the neuropsychological tools and specific criteria used. Clear definitions are essential, as minimal and covert HE is susceptible to the choice of diagnostic method and can substantially influence group classification. Second, although SCFAs represent key microbial metabolites, the study did not explore the underlying microbiome composition. Without bacterial taxonomy or species-level data, it remains difficult to determine whether differences in SCFA levels truly reflect gut dysbiosis or altered microbial diversity. SCFA concentrations may be influenced by multiple factors, and therefore, inclusion of metagenomic or sequencing data would strengthen the mechanistic interpretation and allow linking specific bacterial taxa with cognitive impairment. Future studies that include larger and more heterogeneous cohorts, alongside integrated analyses of microbiome composition and validated neurocognitive testing, will be crucial to validate the role of SCFAs in HE development.},
}

Humans
*Hepatic Encephalopathy/metabolism/etiology/epidemiology/microbiology
*Gastrointestinal Microbiome
*Fatty Acids, Volatile/metabolism
*Liver Cirrhosis/complications
Indonesia/epidemiology
*Liver/metabolism
*Brain/metabolism
Cross-Sectional Studies
Feces/chemistry

@article {pmid41502165,
year = {2026},
author = {Keller, LM and Colman, DR and Stefánsson, A and Boyd, ES},
title = {Cross-Feeding of Carbon and Nitrogen Between Aquificales and Thermus in Hot Springs.},
journal = {Environmental microbiology},
volume = {28},
number = {1},
pages = {e70225},
doi = {10.1111/1462-2920.70225},
pmid = {41502165},
issn = {1462-2920},
support = {80NSSC19M0150/NASA/NASA/United States ; MSU D19//W. M. Keck Foundation/ ; },
mesh = {*Hot Springs/microbiology ; *Thermus/metabolism/growth & development/genetics ; *Nitrogen/metabolism ; *Carbon/metabolism ; Iceland ; Nitrogen Fixation ; Carbon Dioxide/metabolism ; Metagenomics ; },
abstract = {Acquisition and cycling of carbon and nitrogen among members of hot spring communities are not well understood. Metagenomic analyses of 105 communities inhabiting high temperature hot springs across Yellowstone and Iceland showed a co-distribution pattern of putatively autotrophic and/or diazotrophic (nitrogen-fixing) Aquificales and Thermus populations. Targeted enrichment of autotrophic and diazotrophic populations in an Icelandic hot spring produced a co-culture of Pampinifervens (Aquificales) that encoded carbon dioxide and nitrogen fixation pathways and Thermus (Thermales). Growth experiments revealed Pampinifervens could support the fixed carbon and nitrogen demands of Thermus, enabling growth. Interestingly, growth of Thermus was enhanced in co-cultures when Pampinifervens was forced to fix both carbon and nitrogen versus just carbon (ammonia-amended cultures). Further experimentation with Thermus, when grown in isolation, showed it preferred amino acids over ammonia as a nitrogen source. These findings demonstrate the importance of metabolic interactions among populations that can dictate the co-distribution of taxa in hot springs, drive community assembly, and maintain biodiversity. Further, these results highlight the fundamental role of Aquificales in the functioning of hot spring ecosystems, particularly those limited in organic carbon and fixed nitrogen like those in Iceland and to a lesser extent Yellowstone.},
}

*Hot Springs/microbiology
*Thermus/metabolism/growth & development/genetics
*Nitrogen/metabolism
*Carbon/metabolism
Iceland
Nitrogen Fixation
Carbon Dioxide/metabolism
Metagenomics

@article {pmid41502155,
year = {2026},
author = {Kim, SS and D'Agostino, E and Needham, DM},
title = {Dynamics and Eco-Genomics of Baltic Sea Nitrifiers: Seasonality, Niches, Interactions and Genomic Uniqueness.},
journal = {Environmental microbiology},
volume = {28},
number = {1},
pages = {e70215},
doi = {10.1111/1462-2920.70215},
pmid = {41502155},
issn = {1462-2920},
support = {//Helmholtz Association/ ; NE 2754/1-1//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*Seawater/microbiology/chemistry ; *Nitrification ; *Archaea/genetics/metabolism/classification/isolation & purification ; Seasons ; Metagenomics ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Phylogeny ; Ammonia/metabolism ; Genomics ; Nitrogen/metabolism ; Nitrites/metabolism ; Oceans and Seas ; Nitrates/metabolism ; },
abstract = {Nitrification is widespread across marine systems, yet the ecological and evolutionary drivers shaping nitrifier populations remain largely unknown. The Baltic Sea, a brackish basin with pronounced gradients in salinity, oxygen, nutrients and strong seasonality, is a valuable model environment to investigate these questions. Here, we combined metagenomics and rRNA gene sequencing to characterise the spatiotemporal dynamics and genomic diversity of nitrifiers, alongside physicochemical measurements. Nitrifiers were persistently abundant throughout aphotic waters, with vertical niche partitioning and seasonal peaks in surface waters from late fall to early spring. The seasonal peaks were positively correlated with nitrite, nitrate and diverse other prokaryotes, and negatively correlated with solar radiation and chlorophyll. To probe the genomic basis of these ecological patterns of the numerically dominant nitrifier, we recovered five novel genomes of ammonia-oxidising archaea through metagenomics of bulk samples and selective enrichments, including the dominant taxon from aphotic depths. Comparative genomics showed high gene conservation, with variation largely in genes linked to interactions with the external environment and nitrogen and phosphorus metabolism between central surface and deep types. Together, our study provides insights into niches of Baltic Sea nitrifiers and begins the process of understanding the mechanisms and functional implications of these patterns.},
}

*Seawater/microbiology/chemistry
*Nitrification
*Archaea/genetics/metabolism/classification/isolation & purification
Seasons
Metagenomics
*Bacteria/genetics/metabolism/classification/isolation & purification
Phylogeny
Ammonia/metabolism
Genomics
Nitrogen/metabolism
Nitrites/metabolism
Oceans and Seas
Nitrates/metabolism

@article {pmid41502126,
year = {2026},
author = {Gutierrez, F and Vargas, S and Machado-Perez, F and Wilson, J and García-Maldonado, JQ and Beman, JM},
title = {Microbial Community Metagenomics in the Eastern Tropical North Pacific Oxygen Minimum Zone Reveals Functional Differences Along Biogeochemical Gradients.},
journal = {Environmental microbiology},
volume = {28},
number = {1},
pages = {e70226},
doi = {10.1111/1462-2920.70226},
pmid = {41502126},
issn = {1462-2920},
support = {OCE-1555375//National Science Foundation/ ; //University of California Alianza MX/ ; },
mesh = {*Oxygen/metabolism/analysis ; *Seawater/microbiology/chemistry ; *Metagenomics ; Pacific Ocean ; *Microbiota/genetics ; *Metagenome ; Photosynthesis/genetics ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Chlorophyll/metabolism ; Nitrites/metabolism ; },
abstract = {Oxygen Minimum Zones (OMZs) are pivotal ocean regions defined by low dissolved oxygen concentrations [DO]. However, biogeochemical variations within OMZs-both laterally and with depth-may select for fundamentally different microbial metabolisms important for ocean biogeochemistry. We used metagenome sequencing to investigate potential differences by specifically targeting biogeochemically-important features-including the primary and secondary nitrite maxima (PNM and SNM), the secondary chlorophyll maximum (SCM), and the upper edge of the OMZ (defined by 20 μM [DO]). Read-based analysis identified variations in 5389 functional genes but high similarity among SCM and SNM metagenomes at multiple stations. 690 genes showed significant differences between different features and included key functional genes involved in photosynthesis elevated in the PNM, while carbon fixation, anaerobic nitrogen cycling, and organic sulphur cycling genes increased in the SCM and SNM. Metagenome assembled genomes from a distinct upper OMZ edge sample included multiple Flavobacteriaceae and Rhodobacteraceae, with annotated functions contributing to metabolism of carbohydrates and amino acids, as well as aerobic anoxygenic photosynthesis (in Rhodobacteraceae). Our results identify functional genes and metabolic pathways that are enriched in unique SCM and SNM features, while also demonstrating sharp shifts in functional capacity in the overlying upper water column, within the ocean's largest OMZ.},
}

*Oxygen/metabolism/analysis
*Seawater/microbiology/chemistry
*Metagenomics
Pacific Ocean
*Microbiota/genetics
*Metagenome
Photosynthesis/genetics
*Bacteria/genetics/classification/metabolism/isolation & purification
Chlorophyll/metabolism
Nitrites/metabolism

@article {pmid41501865,
year = {2026},
author = {Sun, J and Meng, Y and Chen, Z and Zhao, T and Yang, C and Chen, S and Wang, J and Tian, L and Song, F and Duan, Y and Cai, W and Zhang, X and Li, H},
title = {Gut microbiome convergence and functional adaptation underlie the evolution of predation in stink bugs (Heteroptera: Pentatomidae).},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02300-w},
pmid = {41501865},
issn = {2049-2618},
support = {31730086//National Natural Science Foundation of China/ ; 110202101046[LS-06]//Pests and Diseases Green Prevention and Control Major Special Project/ ; xinkywdzc-2025001-91//Project of Fund for Stable Support to Agricultural Sci-Tech Renovation/ ; },
abstract = {BACKGROUND: True bugs (Heteroptera) have undergone repeated evolutionary shifts between phytophagous and carnivorous feeding strategies. Although gut microbiomes are recognized for aiding dietary adaptation, their function in mediating these transitions is still unclear, specifically, how microbial communities change during dietary evolution and influence the diversification of feeding traits.

RESULTS: Here, we selected a stink bug lineage of the subfamily Asopinae (Pentatomidae), representative of an independent feeding trait transition from phytophagy to carnivory. Their gut microbiomes were analyzed and compared to those of closely related phytophagous species within the Pentatomidae family, as well as predatory assassin bugs from the Reduviidae family, which represent the ancestral heteropteran feeding trait of predation. It was found that Asopinae lack the gammaproteobacterial symbionts and midgut crypts that are conserved in their phytophagous counterparts. Instead, their gut microbiomes converged on a community dominated by Enterococcus (Firmicutes) and select Proteobacteria (Serratia, Yokenella, Proteus), mirroring the microbiome of assassin bugs. This core community persisted despite prey variation, likely maintained through pentatomid ancestral eggshell-piercing behavior, enabling vertical transmission. Metagenomic analysis linked the Asopinae microbiome to functions potentially associated with predation adaptation, including the digestion of chitinous substrates likely sourced from prey's internal body. Through bacterial isolation, genomics, and functional assays, we demonstrated that Serratia mediates chitin degradation, which along with a potential coordination in diet digestion, may also have been involved in an antifungal effect. Meanwhile, an Enterococcus strain exhibits inhibition to multiple pathogens such that may provide protections to the host, potentially via a class III lanthipeptide.

CONCLUSIONS: Our findings reveal a coordinated restructuring of the gut microbiome during dietary shifts. The convergence of Asopinae and Reduviidae microbiomes underscores how microbial communities may have facilitated the ecological adaptation, likely by enabling hosts to exploit new dietary niches and providing defense against bacterial and fungal pathogens. Video Abstract.},
}

@article {pmid41501755,
year = {2026},
author = {Li, JL and Hu, W and Pu, LH and Sun, J and Ortúzar, M and Lv, ZH and Yang, ZF and Zhu, D and Xie, KQ and Yang, LQ and Yin, YR},
title = {Molecular cloning and characterization of a GH10 thermophilic xylanase from hot spring and its potential application in promoting probiotic growth.},
journal = {BMC biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12896-025-01096-9},
pmid = {41501755},
issn = {1472-6750},
support = {202101AU070138 and 202501AT070411//Yunnan Applied Basic Research Projects/ ; 230212528080//the Xingdian Talent Support Program of Yunnan Province/ ; },
}

@article {pmid41501434,
year = {2026},
author = {Zell, R and Groth, M and Selinka, L and Selinka, HC},
title = {A metagenomic analysis of urban river samples reveals high numbers of sequences related to mycoviruses.},
journal = {Archives of virology},
volume = {171},
number = {2},
pages = {46},
pmid = {41501434},
issn = {1432-8798},
mesh = {*Rivers/virology ; Phylogeny ; Genome, Viral ; *Metagenomics ; *Fungal Viruses/genetics/classification/isolation & purification ; Germany ; Open Reading Frames ; },
abstract = {Mycoviruses have been classified into 35 virus families so far. In addition to numerous mycoviruses with proven fungal or oomycetes hosts, many newly discovered viruses from environmental water and soil samples and various animal or plant specimens exhibit significant similarity to classified mycoviruses, thereby expanding the known sequence space of fungal and related viruses. In this study, we searched for mycoviruses in two environmental water samples that had been collected from the Teltow Canal and the Havel River in Berlin, Germany. Viral sequences with similarity to members of 16 virus families were identified. The most common viruses in our samples were botourmia-like viruses with moderate similarity to members of the genus Ourmiavirus. Notably, 58 of the ourmia-like sequences from the Teltow Canal and Havel River and 10 ourmia-like sequences from other sources exhibited a dicistronic genome layout. The second open reading frame (ORF) of these viruses encoded a putative capsid protein with an S domain that showed little similarity to the structural proteins of the classified ourmiaviruses. The second-largest virus group (59 sequences) was assigned to the order Ghabrivirales, and 13 of these sequences exhibited similarity to members of the suborder Alphatotivirineae (families Orthototiviridae, Pseudototiviridae, Botybirnaviridae, and Chrysoviridae). Thirty-three sequences clustered with members of the suborder Betatotivirineae - three of them with members of the family Artiviridae. Fifteen highly divergent toti-like sequences suggest the need to establish a new higher-order taxon within the order Ghabrivirales. Other virus sequences were assigned to the families Mitoviridae (three unuamitoviruses and 10 highly divergent mitovirus-like sequences), Narnaviridae (five "alphanarnavirus"-like sequences), Amalgaviridae (two zybavirus-like sequences), Hypoviridae (one partial RdRP sequence), and Mymonaviridae (one partial RdRP sequence), and one was not classified (Sclerophthora macrospora B-like virus). Notable results include a clade of highly divergent mitovirus-like sequences with a standard translation code, three narnavirus-like sequences with a reverse-frame ORF, and a clade of four Ghabrivirales-like replicase sequences that were found to have numerous termination codons regardless of which translation table was used.},
}

*Rivers/virology
Phylogeny
Genome, Viral
*Metagenomics
*Fungal Viruses/genetics/classification/isolation & purification
Germany
Open Reading Frames

@article {pmid41501250,
year = {2026},
author = {Liu, C and Xing, Y and Su, J and Liu, Y and Dou, Y and Wang, Z and Sha, S and Yan, Q and Xu, M and Zhao, L and Tian, Y and Xing, G and Li, S and Kang, J and Kong, X},
title = {Multi-kingdom gut microbiota characterization in Chinese patients with idiopathic inflammatory myopathies.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-33939-y},
pmid = {41501250},
issn = {2045-2322},
support = {XJ2023001102//The Cultivating Scientific Research Project of the Second Hospital of Dalian Medical University/ ; 2023-MSLH-032//Joint Funds of the National Natural Science Foundation of Liaoning Province/ ; JCH22023017//Dalian Medical University Interdisciplinary Research Cooperation Project Team Funding/ ; 82370563//National Natural Science Foundation of China/ ; },
abstract = {Idiopathic inflammatory myopathies (IIMs) are systemic autoimmune disorders with unknown etiology. Despite the established link between gut microbes and immunity, the roles of gut bacteriome, mycobiome, and virome in IIM are unexplored. We performed shotgun metagenomic sequencing on fecal samples from 34 IIM patients and 37 healthy controls to profile gut microbiota. Taxonomic, functional, network, and machine-learning analyses revealed microbial dysbiosis and its potential for discriminating IIM. All three microbial kingdoms were significantly altered in IIM. Several inflammation-associated bacterial taxa (e.g., Rothia mucilaginosa, Streptococcus parasanguinis, Trueperella pyogenes) and opportunistic fungi (e.g., Aspergillus spp.) were enriched in IIM, while SCFA-producing bacteria and fungi were depleted. Virome analysis revealed substantial shifts, with higher abundance of Siphoviridae in IIM. Altered viral functional gene profiles suggesting enhanced phage-mediated genome integration, recombination, and bacterial stress adaptation. Multi-kingdom network analysis showed extensive rewiring in IIM, characterized by increased network connectivity and a shift toward fungi-centered ecological hubs, contrasting with bacteria/virus-dominated networks in controls. In machine-learning models, the virome demonstrated the strongest discriminatory power, and viral signatures dominated the combined multi-kingdom classifier (AUC = 0.997). This first comprehensive multi-kingdom gut microbiota analysis in IIM provides a foundation for developing diagnostic and therapeutic strategies.},
}

@article {pmid41501123,
year = {2026},
author = {Alexandrino, DAM and Semedo, M and Cao, W and Azevedo, J and Magalhães, C and Osório, H and Jia, Z and Campos, A and Mucha, AP and Almeida, CMR and Carvalho, MF},
title = {Insights into the biodegradation of two persistent fluorinated fungicides by coupling metabolic modelling with metaproteogenomics.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-31941-y},
pmid = {41501123},
issn = {2045-2322},
abstract = {Epoxiconazole (EPO) and fludioxonil (FLU) are fluorinated fungicides known for their extremely high environmental persistence and significant ecotoxicological impact. Given their decades-old use in the agrochemical sector, EPO and FLU became frequent pollutants of terrestrial and aquatic ecosystems. And yet, not much is known regarding how these pesticides biodegrade in the natural environment or how to develop suitable bioremediation approaches capable of tackling their inherent recalcitrance. As such, this work focused on providing new insights into the bacterial degradation of EPO and FLU, by surveying the catabolic activity of a previously obtained EPO-enriched bacterial consortium through chemical and metaproteogenomic analyses guided by different metabolic modelling tools. The bacterial consortium was capable of extensively degrading EPO and FLU in 21 days, with fungicide removals of over 90% and defluorination efficiencies of up to 80%, but none of the subproducts predicted in silico were identified for either pesticide. Despite this, the combination of metabolic modelling tools and metaproteogenomic surveys suggested that EPO and FLU were first attacked in their N-heterocyclic moieties and that the targets of defluorination were the resulting aromatic fluorinated intermediates. This catabolic cascade is consistent with the experimental data gathered in this study and with the existing literature on this topic. Also, the degrading consortium remained stable at the taxonomical and functional levels, highlighting its catabolic plasticity in biodegrading and defluorinating two chemically distinct fluorinated compounds. This work offers a conceptual framework with novel observations that can guide future efforts to further elucidate the pathways of microbial transformation of these pesticides, ultimately contributing to better environmental risk management practices for these pollutants.},
}

@article {pmid41500299,
year = {2026},
author = {Zhang, W and Gu, L and Yan, W and Zhao, D and Liu, J},
title = {Acetochlor and sulfamethoxazole co-selection alter soil microbial nitrogen metabolism and resistome in agroecosystem.},
journal = {Environmental research},
volume = {292},
number = {},
pages = {123688},
doi = {10.1016/j.envres.2026.123688},
pmid = {41500299},
issn = {1096-0953},
abstract = {Agricultural soils increasingly face co-contamination by herbicides and antibiotics, yet the ecological impacts of such multipollutant exposure remain poorly understood. This study employed a soil-plant microcosm combined with metagenomic sequencing to investigate the co-selective effects of acetochlor (ACE) and sulfamethoxazole (SMX) on soil microbiomes and antibiotic resistance genes (ARGs). The results showed that SMX functioned as the dominant ecological filter, significantly reducing microbial diversity and restructuring community composition via suppressing Pseudomonadota while enriching Acidobacteriota. Co-exposure further decreased diversity and shifted nitrogen metabolic pathways: SMX inhibited denitrification and nitrogen fixation, whereas co-combination synergistically enhanced the potential of nitrous oxide emission. Critically, herbicide-antibiotic co-exposure drove the emergence of clinically relevant ARGs (e.g., CMY-80, MCR-2.5) and enhanced their dissemination by increasing network complexity among host microorganisms. Moreover, ACE acted as an 'antibiotic adjuvant', accelerating resistance evolution through stress-induced physiological responses and mobility activation. ACE dose-dependent responses revealed the dual ecological role of agrochemicals: signaling molecules at low concentrations (2.5 mg/kg) and stressors at elevated levels (5.0 mg/kg). Genomic analysis further showed a higher chromosomal than plasmid-borne ARG abundance, reflecting a dynamic equilibrium between persistent and mobile resistance under fluctuating environmental pressures. These findings underscore the necessity of incorporating multipollutant scenarios into risk assessment, as single-contaminant evaluations underestimate the ecological and public health risks in agricultural ecosystems.},
}

@article {pmid41500138,
year = {2026},
author = {Bellekom, B and Troman, C and Fitz, S and Akello, JO and Grassly, NC and Shaw, AG},
title = {Comparison of the sensitivity of targeted and untargeted (metagenomic) methods for the detection of viral pathogens in wastewater.},
journal = {The Science of the total environment},
volume = {1013},
number = {},
pages = {181333},
doi = {10.1016/j.scitotenv.2025.181333},
pmid = {41500138},
issn = {1879-1026},
abstract = {Timely and accurate pathogen detection is critical for the successful implementation of wastewater surveillance and has broad implications for public health. A wide range of surveillance tools are currently available, offering both quantitative and qualitative insights into the wastewater virome. Careful consideration of molecular methodology is required to successfully implement an effective wastewater surveillance scheme. Using SARS-CoV-2 as a model organism, we compared detection success across multiple approaches, including targeted (RT-PCR, qPCR, random priming RT-PCR) and target-agnostic (Rapid SMART-9N metagenomics) methods. We also estimated the copy number required for reliable detection, examined how the ratio of target to off-target genomes in wastewater affects detection and genome coverage using metagenomics, and assessed the efficacy of hybrid capture enrichment of target genomes in improving metagenomic detection. Our results show significant differences between methods, targeted RT-PCR and qPCR were more likely (68 % and 65 % respectively) to detect SARS-CoV-2 than target agnostic approaches. The inclusion of carrier RNA during extraction significantly increased the likelihood of target detection. Our target-agnostic metagenomic approach was consistently unable to detect our target, and, even in the presence of high concentrations that are atypical for wastewater, detection was limited. Target enrichment increased SARS-CoV-2 detection and maximum coverage by metagenomics (SMART-9N), though was outperformed by targeted amplicon sequencing. Overall, our findings support the use of targeted approaches for the routine surveillance of viral pathogens in wastewater. Whilst metagenomics provides broad insights into the virome, enrichment strategies are essential when using it to detect specific viruses, particularly in complex wastewater matrices.},
}

@article {pmid41500047,
year = {2025},
author = {Gutfreund, MC and Callado, GY and Pardo, I and Hsieh, MK and Celeghini, PD and Lopes, GOV and Marra, PS and Cheng, YR and Kobayashi, T and Pinho, JRR and Generoso, JR and Bulgarelli, L and Mendonça, EA and Deliberato, RO and Amgarten, DE and Malta, FM and Edmond, MB and Marra, AR},
title = {Metagenomic next-generation sequencing in pediatric infectious disease diagnosis: A comprehensive systematic literature review and meta-analysis.},
journal = {Diagnostic microbiology and infectious disease},
volume = {114},
number = {4},
pages = {117248},
doi = {10.1016/j.diagmicrobio.2025.117248},
pmid = {41500047},
issn = {1879-0070},
abstract = {BACKGROUND: Diagnosing pediatric infectious diseases is challenging due to nonspecific presentations, small sample volumes, and the limited sensitivity of conventional microbiological tests (CMTs). Metagenomic next-generation sequencing (mNGS) enables broad, hypothesis-free pathogen detection, but its diagnostic performance in children remains insufficiently characterized. This study evaluates the diagnostic accuracy of mNGS in pediatric infectious diseases and compares its performance with CMTs.

METHODS: This systematic review and meta-analysis was registered in PROSPERO (CRD42024542444). Searches were performed using multiple databases through August 2024. Eligible studies evaluated mNGS and CMTs in pediatric patients (≤21 years) with suspected infectious diseases and compared their respective results with clinical diagnosis. Pooled sensitivity, specificity, and diagnostic odds ratios (DORs) were calculated using a bivariate random-effects model.

RESULTS: Thirty-three studies (n = 4,165) met inclusion criteria, and nine were eligible for meta-analysis. Pooled sensitivity and specificity of mNGS versus clinical diagnosis were 0.84 (95% CI: 0.82-0.86) and 0.71 (95% CI: 0.66-0.75), respectively, compared with 0.40 (95% CI: 0.37-0.43) and 0.82 (95% CI: 0.78-0.86) for CMTs. The pooled DOR favored mNGS (18.6 vs. 5.4). Respiratory infections were most frequently investigated, followed by bloodstream and mixed infections. Over two-thirds of studies reported changes in antimicrobial management following mNGS results.

CONCLUSIONS: mNGS demonstrates superior sensitivity and diagnostic accuracy compared with CMTs, enabling comprehensive pathogen detection, including rare and co-infecting organisms, and informing targeted antimicrobial therapy. Despite limitations related to cost, complex interpretation, and methodological standardization, mNGS represents a promising complement to conventional diagnostics in pediatric infectious disease management.},
}

@article {pmid41499937,
year = {2025},
author = {Wu, X and Zhang, T and Feng, J and Park, S},
title = {Herba Patriniae with probiotics targets Escherichia fergusonii and the 5-hydroxytryptophan-trimethylamine N-oxide axis in Parkinson's disease.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {150},
number = {},
pages = {157758},
doi = {10.1016/j.phymed.2025.157758},
pmid = {41499937},
issn = {1618-095X},
abstract = {BACKGROUND: Parkinson's disease (PD) exhibits a distinct gut microbiota and microbial metabolites, with specific enterotypes potentially influencing disease susceptibility. Current research lacks systematic comparisons of different enterotypes in PD susceptibility and targeted intervention efficacy. This study identifies their gut microbiota-metabolite biomarkers and validates a "probiotic plus herbal medicine" intervention in vitro to explore enterotype-stratified precision strategies for PD prevention and treatment.

PURPOSE: This study aimed to identify a high-risk enterotype for PD and its associated microbial and metabolic signatures using public metagenomic data. Furthermore, we evaluated the therapeutic efficacy of a combination therapy, comprising Patrinia scabiosaefolia Fisch (Herba Patriniae; HP) extract and the probiotics, Faecalibacterium prausnitzii and Lactiplantibacillus plantarum (F.l-HP), in a PD-relevant in vitro model.

METHODS: Public metagenomic data from PD patients and healthy controls (HC) were analyzed to characterize enterotypes. An in vitro gut-brain axis (GBA) model was established by co-culturing PC12 neuronal cells and Caco-2 intestinal epithelial cells to validate the pathogenic role of Escherichia fergusonii. The effects of the F.l-HP combination therapy were then assessed on bacterial growth, key metabolites (5-hydroxytryptophan (5-HTP), trimethylamine N-oxide (TMAO), butyrate), neuroinflammation, oxidative stress, mitochondrial function, and gut barrier integrity, with a focus on the underlying p-Akt and p-AMPKα signaling pathways.

RESULTS: The Bacteroidaceae enterotype (ET-B) was identified as a high-risk enterotype for PD, characterized by an enrichment of E. fergusonii. This bacterium was associated with the consumption of neuroprotective 5-HTP and the production of pro-inflammatory TMAO. The F.l-HP combination therapy significantly suppressed the growth of E. fergusonii while promoting the proliferation of beneficial probiotics. This intervention restored metabolic balance by reducing 5-HTP consumption and TMAO production and increasing butyrate levels. Consequently, F.l-HP treatment alleviated neuroinflammation and oxidative stress in neuronal cells, restoring mitochondrial function via the p-Akt pathway. In intestinal cells, it enhanced gut barrier integrity by upregulating zonula occludens-1 expression and activating p-AMPKα signaling.

CONCLUSION: E. fergusonii may participate in a 5-HTP-TMAO metabolic axis potentially linked to PD risk. F.l-HP intervention suppressed E. fergusonii activity, reduced 5-HTP consumption and TMAO production, modulated Akt and AMPKα signaling pathway, and alleviated neuroinflammation while enhancing intestinal barrier integrity.},
}

@article {pmid41499920,
year = {2025},
author = {Vázquez-Bolea, N and Mora-Martínez, C and Cuervo, M and Martinez, JA and Gil-Campos, M and Leis, R and Babio, N and Moreno, LA and Corella, D and Moreira Echeverria, A and Aguilera, CM and Castro-Collado, C and Picáns-Leis, R and Hernández-Cacho, A and Miguel-Berges, ML and Martin-Climent, P and Jurado-Castro, JM and Vázquez-Cobela, R and Plaza-Diaz, J and Rueda-De Torre, I and Pastor-Villaescusa, B and de la Torre-Aguilar, MJ and Salas-Salvadó, J and Sanz, Y and Navas-Carretero, S},
title = {Gut microbiota composition and derived enterotypes are associated with ponderal status in preschool children. Childhood obesity risk assessment longitudinal study (CORALS) cohort.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {57},
number = {},
pages = {106558},
doi = {10.1016/j.clnu.2025.106558},
pmid = {41499920},
issn = {1532-1983},
abstract = {BACKGROUND AND AIMS: Childhood obesity is a growing public health concern increasingly linked to gut microbiota. We analysed associations between microbiota composition, functionality, and weight status in 1134 children aged 3-6 years from the CORALS cohort.

METHODS: The baseline cross-sectional study stratified participants by weight status (underweight, normal weight, overweight, obesity) and performed shotgun metagenomic sequencing of stool samples. Analyses in R assessed alpha/beta diversity, taxonomic composition, enterotypes, and microbial pathways.

RESULTS: Alpha diversity decreased with increasing BMI, particularly in obesity (Shannon adj.P = 0.00301; Simpson adj.P = 0.00158). Beta diversity revealed distinct microbial structures across groups (p = 0.001). Four enterotypes were identified: obesity was associated with Enterotype 3 (Segatella-dominated, p = 0.023), while Enterotype 1 (Alistipes, Akkermansia, Coprococcus) was enriched in underweight/normal weight. Species linked to obesity included higher Phocaeicola dorei (adj.P = 0.003) and Segatella hominis (adj.P = 0.001), and lower Longicatena caecimuris (adj.P = 0.03) and Blautia parvula (adj.P = 0.003). Functional analyses showed downregulation of vitamin and nucleotide biosynthesis pathways and reduced carbohydrate metabolism in overweight/obesity.

CONCLUSIONS: Gut microbiota composition and functionality are strongly associated with weight status in early childhood, suggesting microbial biomarkers and metabolic pathways relevant to understand early obesity development.

CLINICALTRIALS: gov ID NCT06317883.},
}

@article {pmid41499832,
year = {2026},
author = {Wang, Y and Yao, C and Zhou, J and Liu, B and Qi, L and Wang, B and Ma, C and Hou, L and Liu, M and Zheng, Y},
title = {Co-occurring aquatic acidification and hypoxia promote methane emissions from estuarine ecosystems.},
journal = {Water research},
volume = {292},
number = {},
pages = {125307},
doi = {10.1016/j.watres.2025.125307},
pmid = {41499832},
issn = {1879-2448},
abstract = {Estuaries worldwide are experiencing intensifying acidification and hypoxia, driven synergistically by anthropogenic activities and global climate change. Nevertheless, their combined impact on the emissions of the potent greenhouse gas methane (CH4) and its underlying regulatory mechanisms remains poorly understood, undermining our ability to project climate feedbacks. Here, we integrated [13]C stable isotope tracing, DNA/mRNA-based qPCR, and amplicon/metagenomic sequencing to unravel how acidification-hypoxia interactions regulate the complex balance between CH4 production and consumption in estuarine sediments. Results showed that aquatic acidification and hypoxia combined to significantly increase CH4 emissions from estuarine sediments (P < 0.05), in a non-additive (antagonistic) manner where oxygen availability was the dominant factor governing this response. Notably, acidification increased CH4 emissions by suppressing methanotrophy more strongly than methanogenesis, whereas hypoxia preferentially stimulated methanogenic activity over CH4 oxidation. These response patterns were further demonstrated by metagenomic sequencing and mRNA-based quantitative PCR analyses, which revealed coordinated shifts in both the relative abundance and transcriptional activity of key functional genes. These findings uncover a previously overlooked mechanism whereby the worldwide co-occurrence of acidification and hypoxia in estuarine ecosystems jointly promote CH4 emissions, providing a scientific basis for improving predictive models of the global CH4 cycle and its climate feedbacks under combined anthropogenic and climatic stressors.},
}

@article {pmid41499829,
year = {2026},
author = {Huang, Z and Liu, H and Wang, C and Wang, J and Tian, C and Feng, J and Shen, J and Wang, X},
title = {Regulation of carbon cycling in plateau lakes by trophic states and seasonal variations: A focus on dissolved organic matter and microbial interactions.},
journal = {Water research},
volume = {292},
number = {},
pages = {125312},
doi = {10.1016/j.watres.2025.125312},
pmid = {41499829},
issn = {1879-2448},
abstract = {Plateau lakes are highly sensitive to climate change and anthropogenic disturbances. The intensification of seasonal variations caused by global warming has complicated the biogeochemical interactions between dissolved organic matter (DOM) and microbial communities. However, how DOM's chemical composition regulates microbial community dynamics and carbon cycling under varying trophic states and seasonal conditions remains unclear. Here, we employed Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and metagenomic sequencing to investigate the seasonal and trophic controls on DOM composition, microbial communities, and carbon cycling in plateau lakes. The results showed that in the dry season, DOM in the eutrophic lake exhibited pronounced aromaticity, with carboxyl-rich alicyclic molecules (CRAMs) constituting 42.80 % of the molecular pool. Conversely, during the wet season, sulfur- and nitrogen-containing compounds like CHOS and CHONS significantly increased, particularly in the eutrophic lake. The oligotrophic lake displayed the highest molecular lability, characterized by hydrogen-to-carbon (H/C) ratios of 1.24 and molecular lability indices (MLB%) of 34.76 %. Eutrophication altered microbial interaction networks, enhancing interspecies interactions and metabolic specialization. This metabolic shift drove preferential utilization of labile sugars in dry seasons and facilitated the degradation of recalcitrant carbon substrates in wet seasons, thereby optimizing carbon source partitioning. Notably, mesotrophic and oligotrophic lakes fostered resource cooperation by reducing network modularity and shaping carbon cycling through the coordinated action of multiple microbial groups. This study elucidates that carbon cycling in plateau lakes is governed by synergistic effects of trophic states and seasonal dynamics, with DOM serving as a critical mediator in microbial-driven carbon cycling dynamics.},
}

@article {pmid41499817,
year = {2026},
author = {Liu, Y and Zhong, L and Zhou, C and Zhang, Y and Zhang, K and Gan, Y and Wang, J and Lin, S and Xie, G and Zhong, W and Ye, X and Linghu, D and Chen, Q and Peng, W and Cao, C and Li, Z},
title = {Di-n-pentyl phthalate exposure alters intestinal structure and gut microbiota composition and characteristics in mice.},
journal = {Ecotoxicology and environmental safety},
volume = {309},
number = {},
pages = {119669},
doi = {10.1016/j.ecoenv.2025.119669},
pmid = {41499817},
issn = {1090-2414},
abstract = {BACKGROUND: Di-n-pentyl phthalate (DnPP), a ubiquitous plasticizer structurally analogous to the gut toxicant di-(2-ethylhexyl) phthalate (DEHP), poses environmental persistence and human exposure risks, yet its gastrointestinal toxicity remains poorly characterized. We hypothesized DnPP disrupts intestinal homeostasis via gut microbiota dysbiosis, mirroring mechanisms of other phthalates.

METHODS: C57BL/6 mice (n = 10 per group) were orally gavaged with DnPP (1-100 mg/kg/d) for 21 days. Intestinal tissues and microbiota were analyzed using histomorphometry and metagenomic sequencing with functional annotation (GO/KEGG/CARD databases). Taxonomic and functional shifts were identified via Metastats and LEfSe (FDR < 0.05).

RESULTS: DnPP exposure induced dose-dependent villus degeneration (100 mg/kg/d, P < 0.05) and colon shortening (P < 0.01), accompanied by upregulated pro-inflammatory cytokines (IL-6, TNF-α) and downregulated tight junction proteins (ZO-1, occludin) in small intestinal and colonic tissues. Metagenomic analysis revealed tissue-specific dysbiosis: colonic samples showed Bacteroidota enrichment and Firmicutes depletion, while the small intestine exhibited increased Bacteroidota and Bifidobacterium. Functional analyses demonstrated reduced glycan/lipid metabolism pathways (P < 0.001) and elevated antibiotic resistance genes (CARD, P < 0.05).

CONCLUSION: DnPP disrupts mouse intestinal structure, triggers inflammation, reduces probiotic abundance, upregulates antibiotic resistance genes, and impairs gut microbiota metabolic capacities, highlighting non-negligible health risks for intestinal and systemic metabolism, as well as potential risks of metabolic and infectious diseases. These findings provide critical evidence for phthalate ester health hazard mechanistic studies.},
}

@article {pmid41499533,
year = {2026},
author = {Liu, T and Song, Z and Zhang, L and Liu, F and Sun, L},
title = {Clinicopathological Features of Orf Virus Infection in the Human: A Rare Case Report of Extensive Skin Infections and Meta-Analysis.},
journal = {Journal of medical virology},
volume = {98},
number = {1},
pages = {e70794},
doi = {10.1002/jmv.70794},
pmid = {41499533},
issn = {1096-9071},
support = {//Beijing Ditan Hospital, Xuzhou Hospital, Capital Medical University, Special Program for Clinical Research and Scientific Innovation Transformation (KCZL202510)./ ; //Training Program for High-level Public Health Technical Talents Construction Project (academic backbone-03-21)/ ; },
mesh = {Humans ; *Orf virus/isolation & purification/genetics ; *Ecthyma, Contagious/pathology/virology/diagnosis ; Male ; Adult ; Animals ; Female ; Sheep ; Middle Aged ; Skin/pathology/virology ; Young Adult ; },
abstract = {The Orf virus is responsible for causing contagious ecthyma in sheep and goats. Humans are primarily infected with Orf virus result in zoonotic skin diseases. We reported a rare case of orf virus infection affecting the face and thoracodorsal regions and performed pathological examination and metagenomic pathogen detection technology(MethPath[TM]) test on the patient. A meta-analysis of the reported cases was also presented. All cases of human infection with orf virus were searched in PubMed and web of science databases. The pathology revealed eosinophilic inclusion bodies visible in the epidermal cells, and the demonstrated orf virus infection by MetaPath™. We identified 99 articles reporting 159 cases of human orf virus infection. The average (±SD) age of all patients was 34.96 ± 16.82 years. Male gender was predominant; hand infections were the most frequent. 81.3% of the patients were infected by contact with sheep. The observed recovery time averaged 42.7 days, with a median of 40 days. The most typical histopathological finding is characterized by the presence of eosinophilic inclusions within vacuolated epidermal cells. When facial nodular lesions are present, obtaining a detailed medical history is essential to aid in considering orf virus infection in the differential diagnosis.},
}

Humans
*Orf virus/isolation & purification/genetics
*Ecthyma, Contagious/pathology/virology/diagnosis
Male
Adult
Animals
Female
Sheep
Middle Aged
Skin/pathology/virology
Young Adult

@article {pmid41499519,
year = {2026},
author = {Ocampo Morales, BN and Hernández Montes, A and Estrada, K and Valadez Moctezuma, E},
title = {Physicochemical and microbiome changes in queso Crema de Chiapas during ripening.},
journal = {PloS one},
volume = {21},
number = {1},
pages = {e0323038},
doi = {10.1371/journal.pone.0323038},
pmid = {41499519},
issn = {1932-6203},
mesh = {*Microbiota ; *Cheese/microbiology/analysis ; Bacteria/genetics/classification/isolation & purification ; Food Microbiology ; },
abstract = {The dynamic changes in the physicochemical, microbiological, and metagenomic profiles of Crema de Chiapas cheese were evaluated across three ripening stages (2, 29, and 58 days). Although the main physicochemical properties -including fat content- remained remarkably stable, salt and protein levels showed noticeable variation throughout ripening. Protein content had the strongest influence on sample differentiation across ripening stages in unsupervised multivariate models, enabling the clustering of microbial diversity according to maturation time. A clear shift in microbial diversity was detected, marked by a reduction in bacterial genera and a concurrent decline in fungal and yeast populations as ripening advanced. The predominant bacterial genera throughout ripening were Streptococcus, Lactobacillus, and Lactococcus. While Streptococcus and Lactobacillus increased over time, Lactococcus exhibited the opposite trend. Metagenomic analysis revealed a decrease in Candida etchellsii and a concomitant increase in Candida tropicalis as ripening progressed. Quantitative PCR (qPCR) confirmed the presence of C. etchellsii at T1 (Ct = 7.22) and C. tropicalis at T3 (Ct = 9.84). The presence of three additional bacterial genera-Chryseobacterium, Aeromonas, and Enterobacter-identified by next-generation sequencing (NGS), was also assessed by qPCR. Chryseobacterium was detected at T2 (Ct = 3.26), whereas Aeromonas and Enterobacter were absent across all stages. Collectively, these findings suggest that potentially pathogenic microorganisms were not present at biologically relevant levels.},
}

*Microbiota
*Cheese/microbiology/analysis
Bacteria/genetics/classification/isolation & purification
Food Microbiology

@article {pmid41499369,
year = {2026},
author = {Chen, K and Luo, S and Jiang, C and Gu, S and Yang, F and Liu, X and Wang, S and Qu, X and Zhang, Q and Zhang, P and Gong, Y and Zeng, H and Qiu, D and Miao, W and Xiong, J},
title = {HiMBar: A High-Fidelity Metagenomic Barcoding Approach for Transkingdom Species Detection and Interaction Analysis in Aquatic Ecosystems.},
journal = {Molecular ecology resources},
volume = {26},
number = {1},
pages = {e70092},
pmid = {41499369},
issn = {1755-0998},
support = {2023S016//Ningbo Public Welfare Science and the Technology Program Project/ ; 2022xjkk0204//Third Xinjiang Scientific Expedition Program/ ; SNJNP2022008//Background Resources Survey in Shennongjia National Park/ ; 2019 QZKK0304//Second Tibetan Plateau Scientific Expedition and Research (STEP) program/ ; SNJGKL2022008//Open Project Fund of Hubei Provincial Key Laboratory for Conservation Biology of Shennongjia Snub-nosed Monkeys/ ; 32122015//National Natural Science Foundation of China/ ; 32300355//National Natural Science Foundation of China/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; *Ecosystem ; *Metagenomics/methods ; *Aquatic Organisms/classification/genetics ; Fungi/genetics/classification ; Computational Biology/methods ; Bacteria/classification/genetics ; },
abstract = {Aquatic ecosystems host diverse organisms across all six life kingdoms, yet their complex interactions remain poorly understood, primarily due to limitations in transkingdom species detection methods. To address this limitation, we developed HiMBar (https://github.com/Xchenkai2019/HIFI_barcoding), a high-fidelity (HiFi) metagenomic barcoding approach that utilises long, highly accurate reads to extract multiple full-length marker genes (such as rRNA genes, COI, rbcL) directly from environmental DNA sequencing reads. These genes are subsequently clustered into operational taxonomic units (OTUs) for species identification, eliminating the need for PCR amplification or sequence assembly. HiMBar outperforms existing DNA-based methods in accuracy, recall and consistency. Applying HiMBar, we identified a stable interaction network among Cyanobacteria, Planctomycetota, Verrucomicrobiota and Fungi. Further analysis revealed that glucose metabolism plays a key role in maintaining these interactions. Our study offers a powerful tool for transkingdom species monitoring and provides a case study for exploring transkingdom interactions and their molecular mechanisms.},
}

*DNA Barcoding, Taxonomic/methods
*Ecosystem
*Metagenomics/methods
*Aquatic Organisms/classification/genetics
Fungi/genetics/classification
Computational Biology/methods
Bacteria/classification/genetics

@article {pmid41499358,
year = {2026},
author = {Cao, A and Lin, Y and Guan, S and Chen, Y and Zhai, W and Zhou, Y and Feng, S and Guan, Y and Zhang, Y and Huang, M and Wang, X and Long, H},
title = {Baseline multi-omics signatures could predict therapeutic response to neoadjuvant anti-PD-1 immunochemotherapy in non-small-cell lung cancer.},
journal = {Clinical and translational medicine},
volume = {16},
number = {1},
pages = {e70579},
pmid = {41499358},
issn = {2001-1326},
support = {82474002//National Natural Science Foundation of China/ ; 82020108031//National Natural Science Foundation of China/ ; 82404752//National Natural Science Foundation of China/ ; 81973398//National Natural Science Foundation of China/ ; WKZX2023CX020006//Development Center for Medical Science & Technology National Health Commission of the People's Republic of China/ ; 2025A1515012521//Natural Science Foundation of Guangdong Province/ ; 2020B1212060034//Guangdong Provincial Key Laboratory of Construction Foundation/ ; 2017B030314030//Guangdong Provincial Key Laboratory of Construction Foundation/ ; 2017YFC0909300//National Key Research and Development Program/ ; B16047//The 111 project/ ; },
mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/drug therapy ; Female ; Male ; *Neoadjuvant Therapy/methods ; Middle Aged ; Aged ; *Lung Neoplasms/drug therapy ; Gastrointestinal Microbiome/drug effects ; Metabolomics/methods ; Multiomics ; },
abstract = {BACKGROUND: Neoadjuvant anti-programmed cell death 1 (PD-1) immunochemotherapy has shown promising efficiency in the treatment of early-stage non-small-cell lung cancer (NSCLC), but it has not consistently yielded durable responses. Biomarkers for the prediction of efficacy are warranted.

METHODS: We performed shotgun metagenomic and plasma/faecal metabolomic studies in 44 NSCLC patients who underwent neoadjuvant tislelizumab plus platinum-based doublet chemotherapy. Samples were collected at baseline and before surgical resection, and the major pathologic response (MPR) was evaluated.

RESULTS: MPR patients showed a significantly higher gut-microbial alpha diversity, an enrichment of Ruminococcaceae, Lachnospiraceae and Clostridiales species, and an increased plasma level of tryptophan metabolites at baseline. On the contrary, non-MPR patients were characterized by enrichment of Prevotella species in faecal samples and higher plasma levels of linoleic acid metabolites. A high predictive accuracy was achieved using a small panel of differential microbial (Clostridium sp. M62/1 and Eisenbergiella tayi) or metabolomic features (linoleic acid, oxindole-3-acetic acid and quinolinic acid) with AUCs > .85.

CONCLUSIONS: The baseline characteristics of the gut microbiota and plasma metabolites could provide early predictions of the response to neoadjuvant anti-PD-1 immunochemotherapy.

TRIAL REGISTRATION: NCT05244837.

KEY POINTS: Baseline metagenomic and metabolomic signatures were significantly associated with the major pathologic response of neoadjuvant anti-PD-1 immunochemotherapy. Integrated microbial model (consists of Clostridium sp. M62/1 and Eisenbergiella tayi) and metabolomic model (consists of linoleic acid, oxindole-3-acetic acid and quinolinic acid) could provide early predictions of the response.},
}

Humans
*Carcinoma, Non-Small-Cell Lung/drug therapy
Female
Male
*Neoadjuvant Therapy/methods
Middle Aged
Aged
*Lung Neoplasms/drug therapy
Gastrointestinal Microbiome/drug effects
Metabolomics/methods
Multiomics

@article {pmid41498995,
year = {2026},
author = {Yan, X and Liao, X and Zhang, L and Li, L and Liu, K and Lyu, Z and Hu, A},
title = {Genome-centric metagenomes unveiling microbial functional potential in a glacier river in the Mount everest.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {1},
pages = {32},
pmid = {41498995},
issn = {1573-0972},
support = {42430404//National Natural Science Foundation of China/ ; },
}

@article {pmid41498484,
year = {2026},
author = {Huang, T and Ge, H and Wu, Z and Zhang, Y and Wang, L and Dang, C and Fu, J},
title = {Resistance of Microbial Community in Activated Sludge to Nano-Ag Stress Through Regulation of N-Acyl Homoserine Lactones-Mediated Quorum Sensing.},
journal = {Biotechnology and bioengineering},
volume = {},
number = {},
pages = {},
doi = {10.1002/bit.70155},
pmid = {41498484},
issn = {1097-0290},
support = {22306068//National Natural Science Foundation of China/ ; 42476142//National Natural Science Foundation of China/ ; //2022 HUST-UTS Key Partnership Research Seed Funding/ ; 2024AFD091//Hubei Provincial Natural Science Foundation of China/ ; },
abstract = {Nano-Ag is increasingly detected in WWTP due to its widespread application, posing a significant threat to microbial communities responsible for wastewater treatment efficiency. Prior studies have demonstrated that quorum sensing (QS) can modulate bacterial tolerance to various environmental stressors in sludge systems. However, the feasibility and mechanisms of N-acyl homoserine lactones (AHLs)-mediated QS regulation to improve the resistance of microorganisms in WWTPs to nano-Ag shocks have been unexplored. Hence, we conducted sequencing batch reactor experiments, and as expected, nano-Ag significantly reduced the treatment performance of bioreactors. However, with the addition of AHLs (C6-HSL, C10-HSL, and C14-HSL) in the bioreactors, the microbial resistance in activated sludge to nano-Ag stress had been evidently enhanced, including the restoration of the sludge morphology, settleability, biomass and extracellular polymeric substances (EPS), as well as the treatment performance of bioreactors on removals of ammonium nitrogen (NH4 [+]-N), chemical oxygen demand (COD), and suspended solids. The joint analysis of metagenomics, metatranscriptomics, and metametabolomics indicated the multifunctional bacteria (e.g., Amaricoccus, Hydrogenophaga, and Brevundimonas) played a very important role during the regulation of AHLs-mediated QS, which harbored functional genes associated with nitrogen metabolism, carbon metabolism, silver resistance, and AHLs response. The upregulation on glutathione-dependent metabolisms (e.g., glutathione-oxidized glutathione redox cycle) and biosynthesis of EPS (e.g., poly-N-acetylglucosamine) were beneficial for the enhancement of microbial resistance to nano-Ag. This study provided a potentially feasible strategy and important theoretical basis to enhance the robustness and restore the function of microorganisms in wastewater treatment systems by using AHLs-mediated QS regulation.},
}

@article {pmid41497396,
year = {2025},
author = {Depuydt, L and Ahmed, OY and Fostier, J and Langmead, B and Gagie, T},
title = {Run-length compressed metagenomic read classification with SMEM-finding and tagging.},
journal = {iScience},
volume = {28},
number = {12},
pages = {114029},
pmid = {41497396},
issn = {2589-0042},
abstract = {Metagenomic read classification is a fundamental task in computational biology but remains challenging due to the scale and diversity of sequencing data. We present a run-length compressed BWT-based index using the move structure for efficient multi-class classification. Our method finds all super-maximal exact matches (SMEMs) of length ≥ L between a read and a reference and associates each SMEM with one class identifier using a sampled tag array. A consensus algorithm then compacts these SMEMs and their class identifiers into a single classification. We are the first to perform run-length compressed read classification using full rather than semi-SMEMs. We evaluated on long and short reads across two datasets: a large bacterial pan-genome with few classes and a smaller 16S rRNA gene database spanning thousands of genera. Our method outperforms SPUMONI 2 in accuracy and runtime while maintaining run-length compressed memory complexity and surpasses Cliffy in memory efficiency with comparable accuracy.},
}

@article {pmid41497123,
year = {2026},
author = {Mehmood, MS and Hajj, F},
title = {Noninvasive early detection of colorectal cancer through gut microbiome-derived biomarkers.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {1},
pages = {997-998},
pmid = {41497123},
issn = {2049-0801},
abstract = {Colorectal cancer (CRC) remains a major global burden, with 1.9 million new cases and 935000 deaths reported in 2024. Despite available screening tools, nearly 45% of cases are still diagnosed at advanced stages, where the 5-year survival rate falls below 14%, compared to >90% in early detection. The limitations of colonoscopy its invasiveness, cost, and poor compliance (<40% globally) demand innovative, noninvasive diagnostic solutions. Gut microbiome profiling has recently emerged as a transformative approach, with specific bacterial signatures such as Fusobacterium nucleatum, Parvimonas micra, and Peptostreptococcus anaerobius showing AUC values between 0.85 and 0.93 for early CRC identification. Integrating metagenomic and metabolomic data enhances diagnostic accuracy to 89% sensitivity and 91% specificity. Moreover, altered microbial metabolites including decreased short-chain fatty acids and elevated secondary bile acids correlate with a 2.3- to 3.1-fold higher risk of carcinogenesis. Novel CRISPR-Cas13a-based assays further allow sub-attomolar detection of microbial RNA transcripts, underscoring a new frontier in microbiome-driven cancer diagnostics. Collectively, gut microbiome-derived biomarkers represent a noninvasive, mechanistically grounded, and highly sensitive platform for early CRC detection with significant translational potential.},
}

@article {pmid41496931,
year = {2026},
author = {Mehmood, MS and Danaf, N},
title = {Helicobacter pylori persists in pancreatic ductal adenocarcinoma despite eradication therapy.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {1},
pages = {955-956},
pmid = {41496931},
issn = {2049-0801},
abstract = {Pancreatic ductal adenocarcinoma (PDAC) remains one of the deadliest malignancies, with global 5-year survival below 12%. Recent molecular analyses have revealed that Helicobacter pylori may persist within the pancreatic ductal microenvironment despite successful gastric eradication. In a 2024 multicenter study, H. pylori DNA was detected in 41.6% of PDAC tissues, including patients with documented eradication. Metagenomic sequencing identified H. pylori 16S rRNA reads comprising up to 2.5% of total microbial DNA, supporting selective intrapancreatic survival. Mechanistically, CagA/VacA-mediated STAT3 and NF-κB activation drives cytokine release, oxidative stress, and mismatch repair suppression, enhancing oncogenic inflammation and genomic instability. Chronic colonization increased pancreatic intraepithelial neoplasia by more than 60% in murine models, underscoring its pathogenic potential. These findings suggest that H. pylori persistence represents a novel microbial co-factor in PDAC, warranting further exploration as a diagnostic biomarker and therapeutic target.},
}

@article {pmid41350554,
year = {2025},
author = {Protic, D and Bascarevic, D and Dimitrijevic, S and Pesovic, J and Nikolic, V and Nikolic, S and Novicevic, V and Markovic, J and Arandjelovic, I and Savic-Pavicevic, D and Diricks, M and Belheouane, M and Merker, M},
title = {Microbiome modulation and behavioural improvements in children with fragile X syndrome following probiotic intake: A pilot study.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {560},
pmid = {41350554},
issn = {2045-2322},
abstract = {UNLABELLED: The gut microbiome (GM) is increasingly recognized as a key modulator of neurodevelopment via the microbiome-gut-brain axis. Fragile X syndrome (FXS), the most common inherited monogenic cause of intellectual disability, shares behavioural and molecular features with other neurodevelopmental disorders (NDDs), yet the role of the GM in FXS remains largely unexplored. In this open-label, single-arm trial, 15 children with genetically confirmed FXS received a daily probiotic formulation containing Lactobacillus casei, Lactobacillus salivarius, and Bifidobacterium breve for 12 weeks. Behavioural analysis and metagenomic sequencing with network and pathway analyses were performed before and after probiotic supplementation. Significant improvements were observed in irritability (-3.9, SD: ± 5.2; p = 0.027), communication (+ 1.7, SD: ± 2.5; p = 0.022), socialization (+ 1.4, SD: ± 2.1; p = 0.033), and adaptive behaviour (+ 1.3, SD: ± 1.4; p = 0.004). While overall microbial diversity remained stable, SparCC network analysis revealed increases in connectivity measures such as edge count and clustering coefficient, indicating denser microbial interactions and greater community coordination after probiotic supplementation. Functional profiling showed trends toward increased microbial activity in fatty acid biosynthesis, NAD salvage, and starch degradation pathways. This pilot study provides initial evidence that probiotics may modulate structural and functional properties of the GM, with potential links to improved behavioural outcomes in children with FXS. Larger, controlled trials are needed to validate the therapeutic potential of GM-targeted interventions in FXS and related NDDs.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-025-29896-1.},
}

@article {pmid41496864,
year = {2025},
author = {Shi, H and Zhang, X and Liu, L and Thompson, F and Li, X and Sun, H and Mi, H and Zhang, XH and Zhang, Y},
title = {Vertically stratified carbon fixation and coupling processes in deep-sea sediment.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf242},
pmid = {41496864},
issn = {2730-6151},
abstract = {Deep-sea sediments represent a vast yet underexplored reservoir of microbial carbon fixation, playing a critical role in global carbon cycling. However, the vertical distribution of carbon-fixing microorganisms, metabolic pathways, and the underlying energy sources and environmental drivers remain poorly understood. In this study, we investigated microbial carbon fixation and associated energy metabolism in South China Sea (SCS) sediment across 0-690 cm depth. Our findings revealed that dissolved inorganic carbon (DIC) and ammonium (NH4[+]) concentrations were key environmental drivers of carbon fixation and linked redox processes. Carbon fixation gene diversity increased with sediment depth, while the network complexity of functional genes and taxa involved in these processes declined. A distinct vertical succession of dominant microbial carbon-fixation pathways and their associated energy metabolisms was observed along the sediment depth: the Calvin-Benson-Bassham (CBB) and reductive glycine (rGLY) pathways dominated surface sediments, driven by nitrite oxidation, whereas the Wood-Ljungdahl (WL) pathway prevailed in deeper anoxic layers, supported by hydrogen and carbon monoxide oxidation. Taxonomically, Gammaproteobacteria and Methylomirabilia were abundant carbon-fixing groups in surface sediments, while Desulfobacterota, Chloroflexota, and Aerophobota became predominant at depth. Most carbon-fixing metagenome-assembled genomes (MAGs) exhibited mixotrophic lifestyles, and representative carbon fixation MAGs from Methylomirabilota, Dehalococcoidia (Chloroflexota) and Aerophobetes exhibited different metabolic features compared to their counterparts from other environments. These findings underscore the carbon fixation potential of deep-sea subsurface microbial communities and advance the understanding of carbon fluxes in deep biosphere.},
}

@article {pmid41496862,
year = {2025},
author = {Rojas-Vargas, J and Samperio-Ramos, G and Camacho-Ibar, VF and Pajares, S},
title = {Taxonomic and functional stability of sedimentary microbial communities in a pristine upwelling-influenced coastal lagoon.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf241},
pmid = {41496862},
issn = {2730-6151},
abstract = {Coastal lagoons are dynamic transitional ecosystems shaped by complex hydrodynamic and biogeochemical processes. Their sediments host diverse microbial communities essential for nutrient cycling, organic matter sequestration, and pollutant degradation. However, the taxonomic and functional profiles of these communities remain poorly understood, especially in pristine systems. Here, shotgun metagenomics was used to investigate microbial diversity and functional potential in a seagrass-dominated coastal lagoon on the Mexican Pacific coast, influenced by seasonal upwelling and with minimal anthropogenic impact. Despite pronounced physicochemical gradients and oceanographic variability, these sediments harbored a diverse and taxonomically conserved microbial community. 60% of genera and 38% of species (with relative abundance >0.1%) were consistently shared across sites and the two upwelling seasons, with Gammaproteobacteria, Deltaproteobacteria, Alphaproteobacteria, Flavobacteria, and Actinobacteria as dominant taxa. Genes associated with nitrogen and sulfur metabolic pathways were consistently detected, suggesting the presence of a conserved functional core supporting key biogeochemical processes. In contrast, genes related to antibiotic resistance and virulence factors exhibited more heterogeneous distributions. Among measured physicochemical variables, only nitrate and ferric iron significantly influenced microbial community structure and its functional repertoire, suggesting that additional factors likely contribute to the broader distribution of these communities. These findings reveal a high degree of taxonomic and functional stability of microbial communities in a minimally impacted lagoon, providing a valuable baseline for understanding microbial dynamics in coastal sediments primarily shaped by oceanographic processes.},
}

@article {pmid41496502,
year = {2026},
author = {Majzoub, ME and Santiago, FS and Raich, SS and Sirigeri, P and Simovic, I and Tedla, N and Kaakoush, NO},
title = {Immunoglobulin A protease from Sutterella wadsworthensis modifies outcome of infection with Campylobacter jejuni and is associated with microbiome diversity.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2611543},
doi = {10.1080/19490976.2025.2611543},
pmid = {41496502},
issn = {1949-0984},
mesh = {Humans ; *Immunoglobulin A/metabolism ; Animals ; Phylogeny ; *Campylobacter jejuni/physiology ; *Campylobacter Infections/microbiology/immunology ; *Gastrointestinal Microbiome ; Mice ; *Clostridiales/enzymology/genetics/classification ; Neutrophils/immunology/microbiology ; *Bacterial Proteins/genetics/metabolism ; China ; Phagocytosis ; Epithelial Cells/microbiology ; Serine Endopeptidases ; },
abstract = {Sutterella wadsworthensis is an enigmatic member of the microbiota, previously reported to be present in healthy humans yet also associated with certain gut diseases and their therapeutic outcomes. Here, we report on S. wadsworthensis classified to S. wadsworthensis_A that encodes an immunoglobulin A (IgA) protease that digests human IgA1 and IgA2 but not mouse IgA. The activity of this IgA protease could influence the trajectory of Campylobacter jejuni infection in human epithelial cells and phagocytosis in primary neutrophils. Comparative genomics and screening of metagenomic samples revealed that the protease shared sequence identity with an IgA protease from a bacterium that colonized other mammals and that S. wadsworthensis harboring IgA protease can be detected in individuals globally. Individuals positive for S. wadsworthensis IgA protease in China and Fiji (detection at >90% similarity) were found to have a different microbiome when compared to individuals where the protease was not detected. Phylogenetic analysis of pathogen IgA proteases along with IgA proteases from members of the microbiota suggested that there may be a unique subset of microbiota-derived IgA proteases. Our results highlight the importance of taxonomic resolution in microbiome studies and identify a subgroup of S. wadsworthensis that may be of potential clinical relevance.},
}

Humans
*Immunoglobulin A/metabolism
Animals
Phylogeny
*Campylobacter jejuni/physiology
*Campylobacter Infections/microbiology/immunology
*Gastrointestinal Microbiome
Mice
*Clostridiales/enzymology/genetics/classification
Neutrophils/immunology/microbiology
*Bacterial Proteins/genetics/metabolism
China
Phagocytosis
Epithelial Cells/microbiology
Serine Endopeptidases

@article {pmid41496335,
year = {2026},
author = {Li, G and Zhao, Z and Machitani, M and Ishikawa, R and Ishikawa, K and Yokota, N and Haba, R and Nakamura, K and Sun, Z and Kurahara, LH and Hirano, K},
title = {Elucidation of mechanisms underlying the therapeutic effects of cordycepin on pulmonary hypertension, with a focus on cell senescence and gut microbiota.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {194},
number = {},
pages = {118923},
doi = {10.1016/j.biopha.2025.118923},
pmid = {41496335},
issn = {1950-6007},
abstract = {INTRODUCTION: Pulmonary hypertension (PH) is a progressive cardiopulmonary disorder characterized by excessive pulmonary vascular remodeling and aberrant proliferation of pulmonary artery smooth muscle cells (PASMCs). Emerging evidence suggests that gut microbiota dysbiosis contributes to PH development. Cordycepin, a natural adenosine analogue derived from Cordyceps militaris, has demonstrated antiproliferative and microbiota-modulating properties; however, its mechanism of action in PH remains unclear.

OBJECTIVE: Elucidate the mechanisms underlying the therapeutic effects of cordycepin on PH, focusing on cellular senescence and gut microbiota.

METHODS: The effects of cordycepin on PH pathology were investigated by transcriptome analysis of PASMCs from patients, and metagenomic analysis of rodent PH models. Cellular senescence was analyzed in lung tissue from p16[Ink4a]-Cre[ERT2] reporter mice and in rat bone marrow-derived macrophages (BMDMs).

RESULTS: RNA sequencing analysis revealed activation of p53 signaling by cordycepin in PASMCs. Cordycepin suppressed CDK1 expression and TERT phosphorylation at threonine 249. It ameliorated vascular and cardiac remodeling in PH rat and mouse models. Cordycepin induced M1-like macrophage senescence in p16 [Ink4a] reporter mice lungs and rat BMDMs. Cordycepin significantly reshaped the gut microbiota, increasing beneficial genera (e.g. Alistipes and Acetatifactor) and reducing proinflammatory taxa (e.g., Ruminococcus), with modulating key metabolic pathways, including short-chain fatty acid, tryptophan, and vitamin K2 metabolism.

CONCLUSION: Cordycepin exerts multi-target therapeutic effects in PH by inhibiting PASMC proliferation via the p53-CDK1/pTERT axis, modulating gut microbiota-linked immunometabolism and induces proinflammatory macrophage senescence. These findings support cordycepin as a promising candidate for PH therapies targeting the vascular, immune, and gut-lung axes.},
}

@article {pmid41496236,
year = {2025},
author = {Huang, C and Huang, P and Zhang, Y and Bartlam, M and Wang, Y},
title = {Ecological filtering enhanced by smaller PBS biodegradable microplastics constrains ARG dynamics in the soil plastisphere.},
journal = {Environment international},
volume = {207},
number = {},
pages = {110030},
doi = {10.1016/j.envint.2025.110030},
pmid = {41496236},
issn = {1873-6750},
abstract = {Microplastics (MPs) are increasingly recognized as hotspots for antibiotic resistance genes (ARGs), yet the combined effects of polymer type and particle size on ARG dynamics in the soil plastisphere remain unclear. Here, we employed metagenomic assembly and binning to explore how MP polymer type and particle size jointly modulate ARG carrying frequencies (ACFs), mobility, and microbial hosts with polyethylene (PE), polystyrene (PS), and biodegradable polybutylene succinate (PBS) MPs across a size gradient (1000, 500, and 106 μm). PBS, PS, and PE plastispheres exhibited different size-related trends in ARG association, with PBS showing the strongest and most consistent decline in ACFs. Only PBS showed a corresponding reduction in ARG-MGE co-localization, suggesting size-dependent constraints on horizontal gene transfer. Distinct ARG combinations in ARG-Carrying Contigs (ACCs) also showed plastic-type selectivity, with complex resistance clusters absent in 106 μm PBS samples, potentially due to environmental constraints that limit the assembly or persistence of multigene resistance structures. Potential pathogens Enterobacter bugandensis and Stutzerimonas urumqiensis were markedly reduced in 106 μm PBS samples, a pattern not observed in PS or PE. Bacterial community analysis revealed that smaller PBS particles were associated with reduced richness, increased evenness, and more competitive interactions within co-occurrence networks. These features, together with the decline in ARG abundance and mobility, suggest that enhanced ecological filtering may occur in smaller biodegradable plastispheres, jointly limiting the persistence of resistance genes and their bacterial hosts. Together, our findings highlight the importance of considering both MP type and particle size in assessing plastisphere-associated ARG risks.},
}

@article {pmid41496069,
year = {2026},
author = {Zhao, Y and Wang, H and Lu, Y and Lou, D},
title = {Evolving landscapes in childhood asthma-gut microbiota research: A bibliometric analysis from 2000 to 2024.},
journal = {Medicine},
volume = {105},
number = {1},
pages = {e46594},
doi = {10.1097/MD.0000000000046594},
pmid = {41496069},
issn = {1536-5964},
support = {ZHGF2024-1//The Key Construction Discipline of Immunology and Pathogen biology in Zhuhai Campus of Zunyi Medical University/ ; NO. QKHRC-CXTDã€"2025〕046//The Program for High level Innovative Talents in the Guizhou Province/ ; },
mesh = {Humans ; *Asthma/microbiology/immunology ; *Bibliometrics ; *Gastrointestinal Microbiome ; Child ; Dysbiosis ; *Biomedical Research/trends ; },
abstract = {BACKGROUND: Pediatric asthma, a chronic inflammatory airway disorder, is increasingly recognized for its association with gut microbiota dysbiosis, mediated through immune dysregulation and systemic inflammation. Recent advancements in multi-omics technologies and the "gut-lung axis" hypothesis have propelled this field into a research frontier. This bibliometric study delineates global research trends, collaborative networks, and emerging directions in pediatric asthma-gut microbiota research.

METHODS: Publications from the Web of Science Core Collection (2000-2024) were systematically retrieved using keywords related to asthma, children, and gut microbiota. Data from 635 articles (392 original studies, 243 reviews) were analyzed via CiteSpace and VOSviewer to map country/institutional contributions, author networks, citation metrics, and keyword clusters. Non-English publications, patents, and conference abstracts were excluded.

RESULTS: Global output demonstrated exponential growth, with 62% of articles published between 2018 to 2022. The United States led in productivity (180 articles, 28.35%) and citations (10,851), while Canada achieved the highest citation impact (121.12 citations/article). Key contributors included Prof Stuart E. Turvey (19 articles, 2463 citations) and Prof B. Brett Finlay (140.07 citations/article). The University of British Columbia dominated institutional contributions (28 articles, 149.11 citations/article). The Journal of Allergy and Clinical Immunology emerged as the top journal (33 articles, 126.48 citations/article). Seminal works highlighted early-life gut dysbiosis (e.g., reduced Lachnospira and Faecalibacterium) and cesarean delivery's role in asthma risk. Keyword clustering revealed 6 themes: disease phenotypes (asthma-allergy comorbidity), microbiota dynamics (dysbiosis, short-chain fatty acids [SCFAs]), immune mechanisms (T helper 17 cells/Treg imbalance, gut-lung axis), developmental exposures (antibiotics, breastfeeding), methodologies (metagenomics), and therapeutic strategies.

CONCLUSION: This study underscores a paradigm shift from descriptive microbial profiling to mechanistic exploration of microbiota-derived metabolites (e.g., SCFAs) and early-life interventions. Future priorities include elucidating causal pathways via longitudinal cohorts, developing microbiota-targeted therapies, and leveraging multi-omics integration. Despite limitations in database scope, this analysis highlights accelerating translation from basic research to clinical applications through global collaboration. Researchers should prioritize interdisciplinary studies to unravel the "microbiome-immune-development" triad and optimize personalized asthma management.},
}

Humans
*Asthma/microbiology/immunology
*Bibliometrics
*Gastrointestinal Microbiome
Child
Dysbiosis
*Biomedical Research/trends

@article {pmid41495893,
year = {2026},
author = {Bouras, G and Grigson, SR and Mirdita, M and Heinzinger, M and Papudeshi, B and Mallawaarachchi, V and Green, R and Kim, RS and Mihalia, V and Psaltis, AJ and Wormald, PJ and Vreugde, S and Steinegger, M and Edwards, RA},
title = {Protein structure-informed bacteriophage genome annotation with Phold.},
journal = {Nucleic acids research},
volume = {54},
number = {1},
pages = {},
doi = {10.1093/nar/gkaf1448},
pmid = {41495893},
issn = {1362-4962},
mesh = {*Genome, Viral ; *Molecular Sequence Annotation/methods ; *Bacteriophages/genetics ; *Viral Proteins/chemistry/genetics ; *Software ; Protein Conformation ; },
abstract = {Bacteriophage (phage) genome annotation is essential for understanding their functional potential and suitability for use as therapeutic agents. Here, we introduce Phold, an annotation framework utilizing protein structural information that combines the ProstT5 protein language model and structural alignment tool Foldseek. Phold assigns annotations using a database of over 1.36 million predicted phage protein structures with high-quality functional labels. Benchmarking reveals that Phold outperforms existing sequence-based homology approaches in functional annotation sensitivity whilst maintaining speed, consistency, and scalability. Applying Phold to diverse cultured and metagenomic phage genomes shows it consistently annotates over 50% of genes on an average phage and 40% on an average archaeal virus. Comparisons of phage protein structures to other protein structures across the tree of life reveal that phage proteins commonly have structural homology to proteins shared across the tree of life, particularly those that have nucleic acid metabolism and enzymatic functions. Phold is available as free and open-source software at https://github.com/gbouras13/phold.},
}

*Genome, Viral
*Molecular Sequence Annotation/methods
*Bacteriophages/genetics
*Viral Proteins/chemistry/genetics
*Software
Protein Conformation

@article {pmid41495863,
year = {2026},
author = {Ali, H and Rafiq, M and Manzoor, M and Gillani, SW and Degen, A and Iqbal, A and Wang, W and Rafiq, MK and Shang, Z},
title = {Seasonal shifts in vegetation, soil properties, and microbial communities in Western Himalayan forests.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-025-00842-y},
pmid = {41495863},
issn = {2524-6372},
support = {31961143012//Natural Science Foundation of China/ ; ANSO-SBA-2023-02//Science-based Advisory Program of The Alliance of National and International Science Organizations for the Belt and Road Regions/ ; },
abstract = {BACKGROUND: The western Himalayan forest ecosystem faces escalating pressures from climate change and anthropogenic activities, demanding improved conservation strategies. Effective management requires understanding the seasonal fluctuations in vegetation, soil properties and microbial communities, but they remain poorly characterized across high altitude forests. We assessed these variables in 10 forest sites during the winter of 2023 and summer of 2024, analysing vegetation diversity, soil parameters, and microbial metagenomics.

RESULTS: We found pronounced seasonal shifts in plant and microbial diversities, and in soil properties. Plant species richness, and Shannon and Simpson diversity indices were higher (p < 0.001) in summer than in winter while the community maturity index was higher (p < 0.02) in winter than in summer. Soil properties exhibited clear seasonal patterns: pH, available phosphorus (AP), microbial biomass carbon (MBC) and cation exchange capacity (CEC) were higher (p < 0.05) in summer, whereas soil moisture (SM) and soil organic carbon (SOC) were higher (p < 0.05) in winter. Microbial alpha diversity indices (Shannon, Chao, and Sobs) were elevated (p < 0.05) in summer, while the Simpson index was elevated in winter, indicating a shift in community dominance. Beta diversity analyses revealed a significant seasonal shift in overall metabolic potential (KEGG orthologs; ANOSIM R = 0.222, p = 0.016), but not in general protein functions (COG), carbohydrate-active enzymes (CAZy), or taxonomic composition (RefSeq). Therefore, despite taxonomic turnover, core metabolic functions were maintained, indicating strong functional redundancy. Structural equation models (SEM) confirmed distinct seasonal dynamics, revealing stronger plant-soil-microbe interactions and a greater proportion of variance explained by the model in summer (R[2]=0.64-0.72 for key paths) than in winter (R[2]=0.52-0.63).

CONCLUSIONS: The findings demonstrate that the western Himalayan ecosystem undergoes a fundamental seasonal reorganization. Summer is characterized by increased biodiversity, distinct soil conditions, and more dynamic microbial-ecosystem interactions, while winter exhibits greater community maturity and functional stability. The resilience of core ecosystem processes is underpinned by microbial functional redundancy, which ensures metabolic continuity despite taxonomic shifts. We recommend that forest management strategies account for these seasonal dynamics and focus on preserving the conditions that support this critical functional redundancy.},
}

@article {pmid41495321,
year = {2026},
author = {Sato, Y and Sato, Y and Deki, O and Tsuji, K and Tsurui-Sato, K},
title = {Estimated predator composition using environmental DNA analyses and color patterns of male guppies in introduced rivers.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-34186-x},
pmid = {41495321},
issn = {2045-2322},
support = {17K19298//Japan Society for the Promotion of Science/ ; 26249024//Japan Society for the Promotion of Science/ ; 19K12419//Japan Society for the Promotion of Science/ ; },
abstract = {Understanding the mechanisms underlying the successful invasion of the guppy, Poecilia reticulata, a globally invasive species, is important in the field of invasion biology. The body color pattern of male guppies is known to influence predation risk; however, the relationship between body color pattern and local predator guilds has been addressed in only a few studies. To investigate this relationship, we analyzed 32 water samples and 305 male guppies from eight introduced populations on the main island of Okinawa, Japan. The environmental DNA metabarcoding analysis of teleosts from the waters identified six potential guppy predator families, Anguillidae, Eleotridae, Gobiidae, Cichlidae, Mugilidae, and Cyprinidae; however, there was no detection of Characiformes, which are one of the major predators of guppies in their original habitat. Using imaging analysis of color spot areas of male guppies, we found that 16 of 18 potential predator × color combinations exhibited a statistically significant association between body color and the presence of predator families. For example, a negative association between orange spots and Anguillidae, and a positive association between blue-green spots and Cichlidae. These results suggest that the guppy in Okinawa was ecologically released from a major predator in its native habitat and adapted to the new environment through color pattern changes.},
}

@article {pmid41495312,
year = {2026},
author = {Kiran, R and Sharma, M and Subramanian, S and Patil, SA},
title = {Halophilic Anaerobic Cultures Enriched with CO2:H2 from Different Saline Environments Reveal Unknown Autotrophic Bacterial Diversity and Modular Carbon Fixation Pathways.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02654-6},
pmid = {41495312},
issn = {1432-184X},
abstract = {The subsurface sediments of saline-aquatic systems host diverse microbes, with unclear ecological roles and challenging lab cultivability. Chemolithotrophic anaerobes involved in CO2-fixation are one of the poorly studied groups. This study focused on understanding these bacteria from subsurface sediments of four representative saline environments, two marine (i.e., Coastal Arabian and Bay of Bengal seas) and two lake (Sambhar and Lonar) systems through enrichment and metagenomics. Enrichment cultures with bicarbonate/CO2 and hydrogen as the carbon and energy sources, respectively, showed CO2 fixation, producing acetic and formic acids as the major organic products. Enriched culture with Sambhar Lake sediment produced more formic acid (391 ± 8 mg/L) than acetic acid (92 ± 20 mg/L); however, other enriched cultures produced considerably higher acetic acid (up to 966 ± 24 mg/L) than formic acid (up to 367 ± 30 mg/L). The organics production was accompanied by unique thread-like (up to 500 μm long) aggregates, harbouring chains of rod and oval-shaped microbes in all cultures. Metagenome sequencing revealed dominance of Vibrio spp. (relative sequence abundance of 91% to 97%) across all cultures, while canonical CO2-fixing taxa were nearly absent (< 0.01%). KEGG analysis revealed partial genes for various CO2 fixation pathways, including Wood-Ljungdahl, reverse-TCA, dicarboxylate-hydroxybutyrate, hydroxypropionate bicycle, hydroxypropionate-hydroxybutyrate, and the reductive-glycine pathway. The presence of a near-complete serine variant of the reductive glycine pathway, which has been demonstrated in engineered systems, suggests that this pathway may play an operational role in natural systems. The consistent production of organic acids and incomplete pathway representation suggests modular CO2 fixation within the Vibrio-dominated enriched mixed cultures.},
}

@article {pmid41494802,
year = {2026},
author = {Mayorga, L and Noguera Segura, A and Campderros, L and Pons-Tarin, M and Soler, Z and Vega-Abellaneda, S and Serrano-Gomez, G and Herrera-deGuise, C and Robles-Alonso, V and Borruel, N and Manichanh, C},
title = {Distinct microbial mediators link diet to inflammation in Crohn's disease and ulcerative colitis.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-337480},
pmid = {41494802},
issn = {1468-3288},
abstract = {BACKGROUND: Inflammatory bowel disease (IBD) arises from complex interactions among diet, host and gut microbiome. Although diet influences intestinal inflammation, the microbial and metabolic pathways involved, and their differences between Crohn's disease (CD) and ulcerative colitis (UC), the two main subtypes of IBD remain unclear.

OBJECTIVE: To investigate how the gut microbiome mediates the effects of habitual diet on inflammatory activity in IBD.

DESIGN: This longitudinal study included 198 adults (100 healthy controls, 49 CD, 49 UC), participants completed a validated food frequency questionnaire. Dietary quality was evaluated using established indices (Alternative Mediterranean Diet, Healthy Eating Index-2015, Índice de Alimentación Saludable, Mean Adequacy Ratio, Plant-Based Dietary Indexes, Healthy Food Diversity). Participants also provided two stool samples (baseline and 6 months). Shotgun metagenomics (n=366) enabled taxonomic and functional profiling. Causal mediation analyses were used to identify microbial features mediating the effect of diet on inflammation.

RESULTS: IBD patients exhibited lower dietary diversity, fibre intake and nutritional adequacy compared with controls. Microbiome diversity was lowest in CD, intermediate in UC and correlated positively with higher intake of fibre, fruit, vegetables and nuts, and negative with processed foods and sugary beverages. Causal mediation analyses revealed that in CD, coffee, whole wheat bread and healthier diets lowered the Harvey-Bradshaw index through specific bacterial species and metabolites. In UC, Mediterranean-like diets, fruits and coffee reduced C reactive protein via greater microbial richness, reduced dysbiosis and short-chain fatty acid-related functions.

CONCLUSION: Diet quality influences inflammation in IBD through distinct microbiome pathways: specific taxa and metabolites mediate effects in CD, whereas microbial richness and global composition drive protection in UC.},
}

@article {pmid41494342,
year = {2026},
author = {Hu, P and Chen, S and Qian, Y and Hong, Y and Lin, JG and He, B and Gu, JD},
title = {Efficient nitrogen removal by coupling with methane metabolism in three landfill leachate wastewater treatment systems.},
journal = {Journal of hazardous materials},
volume = {502},
number = {},
pages = {141035},
doi = {10.1016/j.jhazmat.2026.141035},
pmid = {41494342},
issn = {1873-3336},
abstract = {High concentration of ammonium-nitrogen (NH4[+]-N) is a widley known characteristic of landfill leachate, and therefore, a thorough understanding of the active nitrogen-related microorganisms is essential for designing an efficient landfill leachate treatment system. Here, we analyze the microbial nitrogen cycling and metabolic interactions at three full-scale landfill leachate treatment plants. Specifically, using metagenomics and metatranscriptomics techniques, we elucidate the mechanisms underlying high NH4[+]-N removal rates achieved through distinct N removal strategies (nitrification-denitrification system at Jilong (JL), denitrification-ammonia oxidation-partial nitrification system at Xinfeng (XF), and simultaneous nitrification-denitrification-ammonia oxidation system at Wenshan (WS)), all three plants achieved efficient NH4[+]-N removal of 96 %, 97.96 % and 97.33 % for JL, XF, and WS, respectively. Highly active methane (CH4)-associated microorganisms, particularly CH4-catabolizing bacteria, exhibited strong interactions with denitrifying bacteria in all three treatment plants, promoting effective nitrogen removal in the landfill treatment systems. In addition, enhanced anammox activity in WS treatment plant in 2023 and 2015 was compared using nitrogen-15 isotope labeling and in situ transcriptome analysis. By comparing microbial metabolic activity, strong interactions were observed between anammox bacteria and other nitrogen-transforming microbes. Meanwhile, detailed physicochemical parameter analysis revealed that optimal Fe[3] [+] concentrations significantly promote the enrichment and enhanced activity of anammox bacteria. Collectively, this study highlights strategies for microbial-mediated high-efficiency ammonia nitrogen removal in full-scale landfill leachate and explains the underlying mechanisms that may lead to increased abundance and activity of anammox bacteria.},
}

@article {pmid41494287,
year = {2026},
author = {Feng, N and Fu, C and You, J and Wang, D and Feng, X and Su, Y},
title = {Controlled release of coated antioxidants inhibits Citrobacter rodentium colonization in the colon of rats by reducing gut redox potential.},
journal = {Redox biology},
volume = {89},
number = {},
pages = {104005},
doi = {10.1016/j.redox.2026.104005},
pmid = {41494287},
issn = {2213-2317},
abstract = {Intestinal redox potential serves as a critical parameter reflecting the dynamic characteristics of the gut microenvironment. To precisely modulate the intestinal redox potential and evaluate its inhibition of pathogenic colonization, this study built a controlled release system and further investigated its role in gut health under a lower redox potential. The results demonstrated that the controlled release formulation significantly reduced fecal redox potential more effectively than uncoated antioxidants. By optimizing the hydrodynamic size and zeta potential of ethoxyquin (EQ) and ferulic acid (FA), the coated FA formulation maintained high efficiency in reducing redox potential and reversed body weight loss induced by pathogenic infection. Both coated EQ (EQC) and FA (FAC) selectively enriched beneficial genera, such as Lactobacillus and Limosilactobacillus, while suppressing opportunistic pathogens like Klebsiella. Notably, coated FA demonstrated enhanced efficacy in alleviating Citrobacter rodentium (C. rodentium)-induced weight loss and reducing pathogens burden compared to uncoated FA. Mechanistically, coated FA promoted the enrichment of Lactobacillus reuteri (L. reuteri), suppressed the proliferation of Enterobacteriaceae, and enhanced intestinal Muc2 gene expression. Functional metagenomic analysis revealed that FAC significantly downregulated ABC transporter activity in Enterobacteriaceae, thereby impairing biofilm formation and synergizing with mucus secretion to inhibit pathogen colonization. Further in vitro co-culture trials confirmed that under a lower redox system, L. reuteri had a stronger inhibitory effect on C. rodentium as well as the expression of their virulence genes ((tir, ler). Collectively, these findings suggest that precise modulation of colonic redox potential through controlled release strategies represents a promising approach to enhance host defense against enteric pathogens via microbiota reprogramming.},
}

@article {pmid41494246,
year = {2026},
author = {Ding, J and Guo, T and Xia, H and Huang, K and Li, M and Li, F},
title = {Earthworm mediated microbial quorum sensing accelerates organic matter transformation during vermicomposting of dewatered sludge.},
journal = {Waste management (New York, N.Y.)},
volume = {212},
number = {},
pages = {115332},
doi = {10.1016/j.wasman.2026.115332},
pmid = {41494246},
issn = {1879-2456},
abstract = {Vermicomposting (VC) relies on the synergistic interaction between earthworms and microorganisms to drive the degradation of organic matter (OM). Quorum sensing (QS), which governs earthworm-microorganism interactions, may influence dissolved organic matter (DOM) transformation during VC. However, the presence of QS and the functional roles of signaling molecules during VC remain unclear. This study investigated earthworm mediated microbial QS in driving microbial community succession and accelerating DOM transformation during VC, by contrasting the process without earthworms. The results showed that VC exhibited a distinct decomposition pathway, achieving significantly faster DOM degradation and mineralization (P < 0.01), compared to the control. Additionally, earthworms markedly facilitated the transformation of protein-like compounds into humic-like substances over a shorter period. Their presence also modified acyl-homoserine lactone (AHL) synthesis patterns and suppressed AHLs hydrolysis, resulting in a 96.14 % increase (P < 0.01) in short-chain AHLs. Metagenomic analysis revealed that earthworm in VC significantly altered the bacterial diversity (P < 0.05), enriching modularity coefficient and deterministic processes by 18.75 % and 87.03 %, respectively. Finally, AHL-responsive microorganisms significantly influencing physicochemical and DOM transformation during the VC. This study suggests that earthworms enhance AHL-type QS regulation in microbial communities, improving their metabolic functions and accelerating DOM transformation.},
}

@article {pmid41493405,
year = {2025},
author = {Seidel, F and Nygren, TM and Opgen-Rhein, B and Hecht, T and Boehne, M and Weickmann, J and Anderheiden, F and Reineker, K and Böcker, D and Rentzsch, A and Wiegand, G and Fischer, M and Kiski, D and Frede, W and Ruf, B and Tarusinov, G and Papakostas, K and Logeswaran, T and Schiebel, A and Voges, I and Kaestner, M and Kramp, J and Kerst, G and Khedim, M and Gatzweiler, E and Wannenmacher, B and Knirsch, W and Meyer-Dobkowitz, L and Donner, B and Klingner, J and Rau, C and Haller, S and Brinkmann, A and Nitsche, A and Noldt, M and Schmoock, G and Herzmann, C and Degenhardt, U and Bühler, S and Enders, M and Hermes, J and Rolfs, N and Manuylova, T and Schwarzkopf, E and Beudt, J and Siffczyk, C and Schubert, S and Sandfort, M and Klingel, K},
title = {Severe Myocarditis Increase in Children Associated With Parvovirus B19 Infection: MYKKE Registry and German Surveillance Data.},
journal = {JACC. Heart failure},
volume = {},
number = {},
pages = {102854},
doi = {10.1016/j.jchf.2025.102854},
pmid = {41493405},
issn = {2213-1787},
abstract = {BACKGROUND: Following a surge in myocarditis in Germany since August 2023, many with parvovirus B19 (B19V) detection, concerns arose about causes and countermeasures.

OBJECTIVES: The authors aimed to verify the association among B19V, myocarditis increase, and severity.

METHODS: Data from the pediatric multicenter registry (MYKKE) from 27 centers were analyzed. B19V myocarditis cases were defined by polymerase chain reaction (PCR) positivity in blood or myocardium with clinical or histopathologic myocarditis evidence. Comprehensive clinical, histopathologic, and epidemiologic analyses were conducted. Past patients were hospitalized from 2013 to July 2023, current from August 2023 to November 2024. Registry data were compared with surveillance and consultant laboratory data. Specimens of current cases underwent metagenomic analysis and B19V sequencing.

RESULTS: Since 2013, 922 myocarditis patients including 126 (13.6%) with B19V myocarditis were enrolled. With 57 of 126 (45.2%) current cases, B19V myocarditis increased, compared with other myocarditis causes. Most current cases were patients who were <2 years of age (64.9%), 56.1% were female. The ratio of B19V myocarditis to incidence did not increase compared with the earlier period. Current cases presented with more reduced ejection fraction (29.0% vs 34.5%; P = 0.007), linked to severe cardiac T-cell infiltration and high numbers of B19V copies. Increased severity was associated with younger age. Phylogenetic analysis identified B19V genotype 1A, without sequence variants indicating increased virulence.

CONCLUSIONS: The increase in pediatric myocarditis since August 2023 was associated with B19V, more likely explained by disproportionately young current cases and young children's vulnerability than a virulent strain. Raising clinicians' awareness and proactive, interdisciplinary approaches are essential for improving prevention of B19V infection, management of myocarditis, and treatment strategies in this vulnerable cohort. (Myocarditis Registry for Children and Adolescents [MYKKE]; NCT02590341).},
}

@article {pmid41493389,
year = {2026},
author = {Buchheister, S and Bolsega, S and Rösel-Birk, S and Smoczek, A and Scheele, T and Bleich, A and Basic, M},
title = {Unraveling potential bacterial contamination in germ-free husbandry using bacterial viability staining.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag001},
pmid = {41493389},
issn = {1365-2672},
abstract = {AIMS: Hygienic monitoring (HM) of germ-free (GF) mouse colonies is exceptionally challenging. The test accuracy of the applied diagnostic methodology has to be outstanding to provide proof of absence of all living microorganisms confirming the GF status. In this context, microscopy of native intestinal content serves as a highly sensitive diagnostic tool for the detection of bacterial contaminants. However, with this method residual microorganisms may be detected. To overcome this risk of false-positive results, we complemented our analyses with a bacterial viability staining of the intestinal content of GF mice.

METHODS AND RESULTS: Intestinal contents of GF mice (n=13) from five isolators were analyzed by bacterial culture and phase-contrast microscopy. Additionally, 16S rRNA gene PCR analysis and metagenomic sequencing were performed. To distinguish between live and dead bacteria, intestinal content was stained by a Bacterial Viability Kit and analyzed by fluorescence microscopy.While culture medium proved sterility of a sample material, increased amounts of scattered bacterial structures were detected during microscopic analysis, indicating potential contamination. Molecular techniques pointed to a presence of environmental bacteria. However, viability staining revealed the presence of only dead (double-stained) bacteria in all samples. Likewise, non-viable bacteria have been identified in samples obtained from irradiated feed, probably being the source of bacterial structures found in GF mice.

CONCLUSIONS: Altogether, detected bacterial structures were proven to be non-viable and therefore should not be interpreted as isolator contaminants. Thus, in our hands, with the herein described report of suspected contamination we prove, that bacterial viability staining served as a highly valuable screening tool, enhancing diagnostic quality of the HM of GF colonies.},
}

@article {pmid41493379,
year = {2026},
author = {Forry, SP and Servetas, SL and Kralj, JG and Hunter, ME and Dootz, JN and Jackson, SA},
title = {A mathematical framework to correct for compositionality in microbiome data sets.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0112625},
doi = {10.1128/aem.01126-25},
pmid = {41493379},
issn = {1098-5336},
abstract = {The increasing use of metagenomic sequencing (MGS) for microbiome analysis has significantly advanced our understanding of microbial communities and their roles in various biological processes, including human health, environmental cycling, and disease. However, the inherent compositionality of MGS data, where the relative abundance of each taxon depends on the abundance of all other taxa, complicates the measurement of individual taxa and the interpretation of microbiome data. Here, we describe an experimental design that incorporates exogenous internal standards in routine MGS analyses to correct for compositional distortions. A mathematical framework was developed for using the observed internal standard relative abundance to calculate "Scaled Abundances" for native taxa that were (i) independent of sample composition and (ii) directly proportional to actual biological abundances. Through analysis of mock community and human gut microbiome samples, we demonstrate that Scaled Abundances outperformed traditional relative abundance measurements in both precision and accuracy and enabled reliable, quantitative comparisons of individual microbiome taxa across varied sample compositions and across a wide range of taxon abundances. By providing a pathway to accurate taxon quantification, this approach holds significant potential for advancing microbiome research, particularly in clinical and environmental health applications where precise microbial profiling is critical.IMPORTANCEMetagenomic sequencing (MGS) analysis has become central to modern characterizations of microbiome samples. However, the inherent compositionality of these analyses, where the relative abundance of each taxon depends on the abundance of all other taxa, often complicates interpretations of results. We present here an experimental design and corresponding mathematical framework that uses internal standards with routine MGS methods to correct for compositional distortions. We validate this approach for both amplicon and shotgun MGS analysis of mock communities and human gut microbiome (fecal) samples. By using internal standards to remove compositionality, we demonstrate significantly improved measurement accuracy and precision for quantification of taxon abundances. This approach is broadly applicable across a wide range of microbiome research applications.},
}

@article {pmid41493376,
year = {2026},
author = {Shklyar, AA and Mesentsev, YS and Smirnov, AV and Nassonova, ES},
title = {Nucleophaga amutiana, sp. nov.-a novel intranuclear parasite of amoebae from the Far East of Russia expands the diversity and biogeography of microsporidia-like organisms.},
journal = {Mycologia},
volume = {},
number = {},
pages = {1-15},
doi = {10.1080/00275514.2025.2586430},
pmid = {41493376},
issn = {1557-2536},
abstract = {The genus Nucleophaga comprises poorly studied intranuclear parasites that infect amoebae. Currently classified within the phylum Rozellomycota, this genus belongs among numerous lineages with unresolved taxonomic positions, primarily identified through metagenomic studies. Three species of Nucleophaga were described at the morphological and molecular levels-N. amoebae, N. terricolae, and N. striatae, all isolated in Europe. Here, we report the discovery of a fourth species of the genus, isolated from the Far East of Russia, infecting nuclei of Thecamoeba sp. A detailed light microscopic study revealed several remarkable morphological features of this organism. For the first time, the division of Nucleophaga plasmodium was illustrated. Experimental infections demonstrated that Thecamoeba quadrilineata and T. foliovenanda can support the development of the parasite, whereas Nucleophaga showed abnormal development in T. onigiri and was unable to survive in T. vumurta. Phylogenetic analysis, based on the nuc 18S rRNA gene sequences, placed the new isolate as a distinct lineage within the genus Nucleophaga. Based on its molecular characteristics, the studied isolate was described as a new species, Nucleophaga amutiana.},
}

@article {pmid41493186,
year = {2026},
author = {Queiroz, VF and Jivaji, AM and Aylward, FO},
title = {Tiny giants in a big ocean.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0299225},
doi = {10.1128/spectrum.02992-25},
pmid = {41493186},
issn = {2165-0497},
abstract = {Prasinoviruses infect some of the most abundant photosynthetic eukaryotes in the ocean, shaping microbial dynamics and playing a major role in nutrient cycling. Despite their ecological significance, they have only been explored in a few marine systems. In a recent study, A. B. de Silva, S. W. Polson, C. R. Schvarcz, G. F. Steward, and K. F. Edwards (Microbiol Spectr 13:e02583-24, 2025, https://doi.org/10.1128/spectrum.02583-24) describe four new prasinoviruses isolated from the tropical North Pacific. The comparative analyses highlighted the placement of these viruses within known prasinovirus lineages while also revealing novel genetic features. To assess their ecological reach, the authors mapped metagenomic reads from global data sets, demonstrating that these viruses are not confined to the Pacific but are globally distributed. These findings expand our understanding of prasinovirus diversity and evolution and highlight their widespread occurrence across oceanic regions.},
}

@article {pmid41492995,
year = {2026},
author = {Sathaye, SB and Sharma, N and Bhaumik, J and Sahoo, D and Rai, AK and Singh, SP},
title = {Novel Glutamate Decarboxylase from Ethnic Food Metagenome: A Potential Biocatalyst to Produce a Nonproteinaceous Amino Acid, γ-Aminobutyric Acid.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c11421},
pmid = {41492995},
issn = {1520-5118},
abstract = {This study reports the biochemical characterization of a novel variant of glutamate decarboxylase (mtGAD), identified from an ethnic food, Kinema. The mtgad gene was cloned from the Kinema metagenome and expressed in a heterologous host, Escherichia coli. The enzyme mtGAD was extracted and purified for biochemical characterization. The enzyme showed optimal activity for γ-aminobutyric acid (GABA) synthesis at 50 °C and pH 4.5. The kinetic parameters of mtGAD were computed to be 29.2 mM Km, 561.8 s[-1] kcat, and 23.2 mM[-1] s[-1] kcat/Km. The in silico protein structure analysis, followed by molecular docking and molecular dynamics simulation, revealed that the binding with pyridoxal-5'-phosphate (PLP; a cofactor for mtGAD) reduces the fluctuations in the structure at high temperatures, contributing to the thermal stability of mtGAD. Furthermore, the conversion of about 60% monosodium glutamate (MSG) into GABA was achieved in approximately 3 h of catalytic reaction with 200 mM MSG, treated with 6.67 U mtGAD. A high turnover number with moderate thermal and pH stability makes mtGAD a potential biocatalyst for GABA production.},
}

@article {pmid41492410,
year = {2025},
author = {Wallau, GDL and Barbier, E and Machado, LC and da Silva, AF and Dias, YJM and Dezordi, FZ and Tomazatos, A and Horváth, B and Lins, RD and Bernard, E and Cadar, D},
title = {Ambecovirus, a novel Betacoronavirus subgenus circulating in neotropical bats, sheds new light on bat-borne coronaviruses evolution.},
journal = {Virus evolution},
volume = {11},
number = {1},
pages = {veaf094},
pmid = {41492410},
issn = {2057-1577},
abstract = {Understanding the viral diversity harboured by wildlife is essential for effective mapping and prevention of future zoonotic outbreaks. Bats, in particular, are recognized as natural reservoirs for several high-impact zoonotic viral pathogens, including coronaviruses responsible for Severe Acute Respiratory Syndrome (SARS), the rabies virus, diverse paramyxoviruses, Marburg, Ebola, Nipah, and Hendra viruses. However, a large extent of bat viruses remains unexplored, especially in highly biodiverse regions of the Neotropics such as Brazilian ecosystems. We used a meta-transcriptomic approach to characterize new virus genomes found in blood, oral, and anal samples collected from cave- and noncave bats from Northeast Brazil, Caatinga, and Atlantic Forest biomes. From a total of 19 coronavirus-positive bats, we have assembled two complete genomes of a new Betacoronavirus subgenus, named Ambecovirus (American betacoronavirus). The subgenus herein described is phylogenetically placed between the Sarbeco-/Hibeco-/Nobecovirus and the Merbeco-/Embecovirus clades, being basal to the former. While the conserved S2 region of the spike protein retained hallmark domains, including HR1 and HR2, the S1/S2 cleavage site and the furin cleavage site, the S1 region consistently displayed only the N-terminal domain. The receptor-binding domain from the C-terminal domai (CTD) region could not be identified due to high dissimilarity relative to known congeners. The detection of Ambercovirus in sympatric Pteronotus gymnonotus and Carollia perspicillata bats suggests potential interspecies transmission. Longitudinal sampling confirmed persistent Ambecovirus infection in P. gymnonotus over multiple years and virus dispersion at a minimum distance of 270 km between caves. The present study confirms that viral diversity in neotropical hosts remains largely unknown, not just in Brazil but likely in the other countries of the region, supporting the need for a systematic approach to virome exploration and analysis followed by in vitro experimentation to assess zoonotic potential.},
}

@article {pmid41492364,
year = {2025},
author = {Solly, EF and Jaeger, ACH and Barthel, M and Six, J and Mueller, RC and Hartmann, M},
title = {Soil water limitation intensity alters nitrogen cycling at the plant-soil interface in Scots pine mesocosms.},
journal = {Plant and soil},
volume = {516},
number = {1},
pages = {705-723},
pmid = {41492364},
issn = {0032-079X},
abstract = {BACKGROUND AND AIM: More intense episodes of drought are expected to affect terrestrial nitrogen (N) cycling by altering N transformation rates, the functioning of soil microorganisms, and plant N uptake. However, there is limited empirical evidence of how progressive water loss affects N cycling at the plant-soil interface.

METHODS: We adopted [15]N tracing techniques and metagenomic analyzes of microbial genes involved in N cycling to assess how different levels of soil water availability influenced the fate of N derived from decomposing litter in mesocosms with Scots pine saplings.

RESULTS: With increasing water limitation, the release of N from decomposing litter into the soil declined rapidly. However, moderate levels of water limitation barely affected the microbial metagenome associated with N cycling and the uptake of N by the saplings. Comparatively, severe levels of water limitation impaired plant N uptake, and increased the prevalence of microbial N-cycling genes potentially involved in mechanisms that protect against water stress. Genes associated with the uptake and release of N during mineralization and nitrification declined under low soil water contents.

CONCLUSIONS: When soil water becomes largely unavailable, the cycling of N at the plant-soil interface is slowed down, and microbial and plant tolerance mechanisms may prevail over N uptake and microbial decomposition.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11104-025-07758-z.},
}

@article {pmid41492358,
year = {2026},
author = {Pan, D and Jiang, M and Wang, Y and He, J and Tang, J and Liu, S and Li, M and Jiang, X and Xu, Q},
title = {Multi-omics reveals associations between the microbiota-gut-brain axis and antidepressant effects of vagus nerve stimulation.},
journal = {Neurobiology of stress},
volume = {40},
number = {},
pages = {100777},
pmid = {41492358},
issn = {2352-2895},
abstract = {BACKGROUND: Major depressive disorder is a severe mental health condition characterized by persistent depressed mood and loss of interest. Current first-line pharmacotherapies often exhibit limited therapeutic performance and adverse side effects. Transcutaneous auricular vagus nerve stimulation (taVNS) is a promising, safe, and noninvasive alternative intervention with demonstrated neuromodulatory efficacy. Nevertheless, its mechanisms remain unclear. This study investigated whether the antidepressant properties of taVNS are associated with the microbiota-gut-brain axis, focusing on the potential crosstalk between differentially expressed hippocampal proteins and the gut microbiota.

METHODS: A chronic unpredictable mild stress (CUMS) rat model of depression was established, and taVNS was administered for 14 days. Hippocampal proteomic profiling was performed using data-independent acquisition. Fecal metagenomic sequencing was conducted to characterize alterations in gut microbial communities. Key signaling pathways were validated using Western blot, qRT-PCR, HE staining, and transmission electron microscopy, all of which were employed to systematically assess behavioral, proteomic, microbial, and molecular changes.

RESULTS: Proteomics and molecular analyses revealed that taVNS upregulated hippocampal expression of glutamate ionotropic receptor N-methyl-D-aspartate type subunit 1 (GluN1) and brain-derived neurotrophic factor (BDNF), while simultaneously restoring mitogen-activated protein kinase (MAPK) signaling activity. Metagenomic profiling demonstrated that taVNS increased the abundance of Akkermansia muciniphila and reduced Ligilactobacillus reuteri. Ligilactobacillus levels were positively correlated with synaptogyrin-1 (Syngr1), indicating their potential association in enhancing the antidepressant effects mediated by the GluN1/MAPK/BDNF signaling cascade.

CONCLUSION: TaVNS significantly alleviated depression-like behaviors in CUMS-exposed rats. The underlying mechanism may involve the restoration of synaptic function of glutamatergic neurons by regulating the GluN1/MAPK/BDNF signaling pathway. In addition, taVNS reshaped the gut microbiota, markedly increasing the abundance of Akkermansia muciniphila and Ligilactobacillus murinus while reducing Limosilactobacillus reuteri and Lactobacillus johnsonii. The positive correlation between Syngr1 protein level and Ligilactobacillus abundance in the hippocampus suggests that the microbiota-gut-brain axis may play a key role in the antidepressant effects of taVNS.},
}

@article {pmid41492297,
year = {2025},
author = {Cordeiro, NF and Coppola, N and Ferreira, F and Vignoli, R and Bado, I},
title = {What are we eating?. Detection of antibiotic resistance mechanisms in frozen chicken nuggets imported from Brazil.},
journal = {One health (Amsterdam, Netherlands)},
volume = {21},
number = {},
pages = {101171},
pmid = {41492297},
issn = {2352-7714},
abstract = {The rise of antibiotic resistance is a growing challenge, affecting humans, the environment, and animals. Under the One Health framework, this study investigated resistance mechanisms to critically important antibiotics in frozen chicken nuggets imported from Brazil. Eighty nugget samples were cultured on selective media containing ceftriaxone, ciprofloxacin, or colistin. Isolates were identified using MALDI-TOF, and antibiotic susceptibility was assessed by disk diffusion. Eight samples were also analyzed using shotgun metagenomic sequencing processed through the SqueezeMeta pipeline. Nineteen Enterobacterales resistant mainly to β-lactams and to a lesser extent, to quinolones and aminoglycosides, were identified. Eight Pseudomonas spp. were recovered, including one P. fulva resistant to colistin. Metagenomics revealed predominant Firmicutes, (Bacillaceae, Lactobacillaceae, and Paenibacillaceae) with low γ-Proteobacteria levels. Additionally, we detected resistance genes against several antibiotics. This study highlights the role of imported food in spreading AMR and the value of combining metagenomics with conventional microbiology to strengthen One Health surveillance.},
}

@article {pmid41491791,
year = {2026},
author = {Seo, J and Araneta, RP and Lee, JH and Montecillo, JA and Yoo, HJ and Lee, YY and Park, CM and Cho, A and Lee, H and Yoon, HY and Kim, MJ and Kim, JM and Lee, YH and Lee, NY and Park, NJ and Han, HS and Seo, I and Chong, GO},
title = {Standardizing vaginal microbial profiling: evaluating swab materials, storage conditions, and host DNA depletion strategies.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {2},
pmid = {41491791},
issn = {1471-2180},
support = {RS-2023-KH135444//Ministry of Health and Welfare/ ; },
abstract = {BACKGROUND: Studies on understanding female health from a microbial perspective have proliferated in recent years; however, validated protocols for swab materials, storage conditions, and host DNA depletion remain limited for vaginal microbiome studies. This study investigates these critical aspects to enhance microbial profiling accuracy.

RESULTS: Three swab materials were evaluated, with minimal variations in bacterial composition observed across different swab materials. The DNA yield and host DNA contamination remained comparable. Mock samples, used to assess the effects of storage conditions (without freezing, -20 °C, and -80 °C), revealed no significant impact on microbial composition. Additionally, the NEBNext® Microbiome DNA Enrichment Kit demonstrated effective performance in host DNA removal and bacterial community recovery, even with reduced reagent volumes.

CONCLUSIONS: These findings underscore the importance of optimizing swab selection and host DNA depletion strategies to enhance microbiome profiling in clinical samples.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-025-04523-1.},
}

@article {pmid41491699,
year = {2026},
author = {Wang, R and Zhang, W and He, Z and Zhou, Y and Chen, C and Song, K and Shang, Q and Wu, Y and Gu, P and Shu, D and Zhao, L},
title = {Core microbiota recruited by healthy grapevines enhance resistance against root rot disease.},
journal = {Genome biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13059-025-03905-y},
pmid = {41491699},
issn = {1474-760X},
support = {2023BCF01026//Key Research and Development Program of Ningxia/ ; 2025NC-YBXM-068//Key Research and Development Projects of Shaanxi Province/ ; 32372501//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Root rot disease caused by fungal pathogens of wine grapevines poses a serious threat to their growth and results in a substantial economic impact on grape industry. The rhizosphere microbiome recruited to plants is critical for mitigating soil-borne pathogens. However, how beneficial microbes influence disease resistance remains unclear.

RESULTS: We investigate the composition and gene functions of microorganisms in wine grapevines with root rot disease and healthy controls by amplicon and metagenomic sequencing. We use culturomics and in vivo experiments to verify the pathogen and beneficial strains to improve plant health. We find that root rot disease in grapevines significantly affects rhizosphere microbiome diversity and composition. The microbial interkingdom network indicates that the disease destabilizes the bacteria-fungi co-occurrence network. We find that plants recruit the potentially beneficial bacteria Pseudomonas, Bacillus and Streptomyces in healthy rhizosphere soil. By culturomics, we confirm that Fusarium solani is the main pathogen causing root rot disease. We further observe that these three key beneficial bacteria from the co-occurrence networks enhance the resistance of grapevines to pathogens. Furthermore, metagenomic analysis reveals that beneficial bacterial strains suppress pathogens by enriching potential functional genes in pathways involved in disease resistance.

CONCLUSIONS: Our findings highlight the critical role of disease resistance pathways of potentially beneficial microorganisms in fighting disease and supporting plant health, offering new insight for the exploration of beneficial microbial resources and providing a basis for the development of biological control of grape root rot disease.},
}

@article {pmid41491676,
year = {2026},
author = {Long, Y and Guo, J and Dai, L and Jiang, J},
title = {Interactions between phytoplankton and bacterioplankton communities in Caohai plateau lake, revealed by environmental DNA metagenomics.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {4},
pmid = {41491676},
issn = {1471-2180},
support = {QKHJC-ZK[2023]YB233//Guizhou Provincial Science and Technology Projects, China/ ; 32360036//National Natural science Foundation of china/ ; QSS2024001//Talent Team Proiect of Guizhou lnstitute of Biology,china/ ; QKHPT[2025]015//Guizhou Provincial science and Technology Projects, China/ ; },
mesh = {*Phytoplankton/genetics/classification/physiology ; *Lakes/microbiology ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation & purification ; China ; *DNA, Environmental/genetics ; *Plankton/genetics/classification ; Ecosystem ; *Microbial Interactions ; },
abstract = {Phytoplankton-bacterioplankton interactions critically influence aquatic ecosystem stability, yet their dynamics remain poorly understood in eutrophic plateau lakes. This study employed environmental DNA (eDNA) metagenomics to investigate these cross-kingdom relationships in Caohai Plateau Lake, a vulnerable wetland undergoing macrophyte-to-algae regime shifts, integrating correlation analysis, niche overlap, redundancy analysis (RDA), co-occurrence networks, and neutral community model (NCM). A total of 331 phytoplankton species across 10 phyla were characterized in the phytoplankton community, dominated by Cyanophyta with Microcystis as the representative genus, while bacterioplankton communities were primarily structured by Proteobacteria and Sphingomonas. The assembly of phytoplankton community was primarily driven by stochastic processes (R[2]>0.90). Co-occurrence network analysis showed phytoplankton interactions were dominated by positive effects (84.25%), whereas bacterioplankton networks exhibited balanced positive and negative effects. Metabolic specialization emerged through LEfSe analysis: phytoplankton specialized in photosynthesis and carbon storage, while bacterioplankton dominated anaerobic respiration (propanoate metabolism). The positive interactions were more prevalent than negative ones; combined with the metabolic complementarity of phytoplankton and bacterioplankton, this suggests that mutualism is more dominant than competition in cross-kingdom interactions. High niche overlap under sufficient nutrients (TP) facilitated species coexistence of phytoplankton and bacterioplankton by minimizing resource competition, thereby promoting stochastic community assembly, while keystone taxa (Cyanothece, Sphingobium) mediated ecosystem stability. This work demonstrates that nutrient enrichment promote stochastic assembly in eutrophic plateau lakes.},
}

*Phytoplankton/genetics/classification/physiology
*Lakes/microbiology
*Metagenomics/methods
*Bacteria/genetics/classification/isolation & purification
China
*DNA, Environmental/genetics
*Plankton/genetics/classification
Ecosystem
*Microbial Interactions

@article {pmid41491168,
year = {2026},
author = {Zhao, Y and Dai, L and Wang, L and Wang, L},
title = {Case report: a case of neonatal Candida osteomyelitis with septic arthritis and literature review.},
journal = {BMC pediatrics},
volume = {26},
number = {1},
pages = {9},
pmid = {41491168},
issn = {1471-2431},
abstract = {A preterm infant who previously experienced Candida septicemia at 18 days of life and was treated with standard antifungal therapy presented one month later with signs of multifocal osteomyelitis and arthritis. Causative Candida albicans was detected by metagenomic next-generation sequencing (mNGS). Since the symptoms of neonatal candidal osteomyelitis are typically insidious, early diagnosis and appropriate treatment are crucial. Moreover, incision and drainage of the affected joint are essential for a favorable prognosis.},
}

@article {pmid41491581,
year = {2026},
author = {Chen, T and Yu, S and Li, K and Huang, K and Shi, W and Chen, H and Hong, Q and Zhang, Y and Wang, J and Yu, Z and Wang, J},
title = {Rumen microbiota inoculation indicates collaborative mechanisms enhancing propionate supply to alleviate weaning stress in lambs.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02283-8},
pmid = {41491581},
issn = {2049-2618},
support = {2023YFD1300901//the Ministry of Science and Technology of the People's Republic of China/ ; D21C170001//the Natural Science Foundation of Zhejiang Province/ ; 31622056//the National Natural Science Foundation of China/ ; 226-2025-00026//Fundamental Research Funds for the Central Universities/ ; },
abstract = {BACKGROUND: The transition from milk to solid feed during weaning often imposes metabolic stress on young ruminants due to energy deficits. Previous studies suggest that ruminal microbiota transplantation from adults to juveniles can alleviate weaning stress, but the underlying mechanisms remain poorly defined.

RESULTS: In this study, 48 Hu lambs were randomly assigned to two groups (n = 24 each): an inoculated group (Inoc) that received lyophilized ruminal microbiota and a control group (Ctrl) that received no inoculation. We evaluated rumen fermentation characteristics, blood metabolites, hepatic glycogen levels, expression of hepatic gluconeogenic genes, and shifts in the rumen microbiome at three key time points-the end of weaning, 1 and 2 weeks post-weaning. Oral inoculation significantly elevated rumen propionate concentration, upregulated the gene expression of hepatic pyruvate carboxylase (EC 6.4.1.1) and glucose-6-phosphatase (EC 3.1.3.9), and increased hepatic glucose production. Microbiome analysis revealed increased colonization by lactic acid-producing bacteria (e.g., Olsenella and Sharpea) and propionate producers, such as Megasphaera elsdenii, alongside enriched families associated with propionate production, including Prevotellaceae, Succinivibrionaceae, and Erysipelotrichaceae. Genome-resolved metagenomics further demonstrated an increased abundance of metagenome-assembled genomes (MAGs) carrying polysaccharide utilization loci (PULs) and genes involved in lactate-to-propionate conversion. Notably, the inoculation promoted co-occurrence of functionally complementary MAGs-such as s_Megasphaera elsdenii (MAG98), s_Bilifractor sp902797025 (MAG125), s_Prevotella sp002391185 (MAG342), and s_Prevotella sp900540375 (MAG298)-that carry a wide repertoire of genes involved in polysaccharide degradation and lactate-to-propionate fermentation. In vitro co-culture experiments with Megasphaera elsdenii and Bilifractor porci confirmed their synergistic role in promoting propionate production.

CONCLUSIONS: This study demonstrates that oral inoculation of pre-weaned lambs with starter feed-adapted adult rumen microbiota facilitates the establishment of a microbial consortium capable of enhanced lactate and propionate production, thereby enhancing hepatic gluconeogenesis and energy homeostasis, which ultimately mitigates weaning stress. This approach may offer a promising strategy to facilitate dietary transition and enhance metabolic resilience in young ruminants during weaning by modulating rumen microbial composition toward a propionate-producing community. Video Abstract.},
}

@article {pmid41491235,
year = {2026},
author = {Huang, J and Feng, Z and Fu, J and Zou, J and Xiang, Q and Liu, X and Li, L and Yu, R},
title = {Amelioration of acute lung injury by Salvia miltiorrhiza-derived extracellular vesicles: through repair of the vascular barrier and modulation of lung microbiota.},
journal = {Chinese medicine},
volume = {21},
number = {1},
pages = {6},
pmid = {41491235},
issn = {1749-8546},
support = {2025JJ80078//Natural Science Foundation of Hunan Province/ ; 23B0379//Education Department of Hunan Province/ ; A2024010//Health Commission of Hunan Province/ ; kq2402183//Science and Technology Bureau, Changsha/ ; 22JBZ002//Hunan University of Chinese Medicine/ ; 24YS003//Hunan University of Chinese Medicine/ ; },
abstract = {BACKGROUND: Acute lung injury (ALI) is a severe respiratory disease characterized by diffuse lung injury, vascular barrier dysfunction, and inflammatory responses. Its current treatments such as corticosteroids often involve adverse effects, highlighting the need for alternative therapies. Salvia miltiorrhiza-derived extracellular vesicles (SMEVs) have shown a potential therapeutic value for ALI due to their anti-inflammatory and barrier-protective properties, but the specific mechanisms remain unclear.

METHODS: SMEVs were extracted and purified through differential centrifugation coupled with sucrose density gradient centrifugation, and were analyzed by transmission electron microscopy (TEM) and nanoparticle tracking analysis (NTA). Biosafety assessment was then conducted in zebrafish embryos, mouse organs, and human umbilical vein endothelial cells (HUVEC). Subsequently, the treatment efficacy of SMEV on LPS-induced HUVEC inflammation was evaluated in vitro. LPS-induced ALI mice were then treated with SMEVs to further evaluate the posttreatment lung histopathology, vascular barrier markers, and microbial composition using metagenomics in vivo.

RESULTS: SMEVs exhibited a typical bilayer structure (average size: 177.7 nm) and excellent biosafety properties. In vitro, SMEVs effectively reduced LPS-induced inflammation (IL-1β, IL-6, TNF-α) and promoted wound healing in HUVEC, while in vivo, SMEVs ameliorated pulmonary edema and inflammation, and restored the VE-cadherin expression. Metagenomic analysis revealed that SMEVs were capable of regulating lung microbiota and reducing the pathogenic bacterial (e.g., g-Listeria, g-Streptococcus) and microbial diversity and richness after LPS stimulation.

CONCLUSION: SMEVs can ameliorate ALI by repairing the vascular barrier and modulating lung microbiota, offering a novel therapeutic strategy for this disease. Future research may focus on the SMEV-microbiota-immune interaction targeting ALI treatment.},
}

@article {pmid41491053,
year = {2026},
author = {Manirakiza, B and Zhang, S and Addo, FG and Ifon, BE and James, N and Kiribou, R and Nadine, NIA and Nyandwi, V and Sebaziga, JN and Mukasekuru, R and de Dieu Uwizelimana, J},
title = {Untapped Microbial Diversity, Assemblages, and Interactions in Rwandan Geothermal Spring Mats, Africa.},
journal = {Current microbiology},
volume = {83},
number = {2},
pages = {123},
pmid = {41491053},
issn = {1432-0991},
support = {E51879084//National Natural Science Foundation of China/ ; E51579075//National Natural Science Foundation of China/ ; },
mesh = {*Hot Springs/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Rwanda ; *Biodiversity ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; RNA, Ribosomal, 18S/genetics ; *Eukaryota/classification/genetics/isolation & purification ; Phylogeny ; },
abstract = {Research on prokaryotes living in geothermal ecosystems have broadened our understanding of their compositions and response to extreme environmental stresses, especially for plankton bacterial communities in hot spring water. However, the comprehensive exploration of microbial diversity, assemblages, and interactions in geothermal spring mats in Africa, particularly in Rwanda, remain underexplored. This study explored the bacterial and eukaryotic communities' biodiversity, assemblages, and interactions within microbial mats from the Bugarama hot pool (BHP; 40-47 °C) and Gisenyi hot springs (GHS; 58-71.4 °C) in Rwanda, using high-throughput sequencing of the 16S rRNA gene and 18S rRNA gene, complemented by null and neutral community models and physicochemical analytical methods. Interestingly, the bacterial Shannon, Evenness, and Simpson indices were significantly different (P < 0.05) among geothermal spring mats. In BHP and GHS, the abundances of Chloroflexota, Proteobacteria, Firmicutes, and Acidobacteriota were significantly higher in BHP (P < 0.05) than in GHS, whereas Cyanobacteria, Bacteroidota, Planctomycetota, Verrucomicrobiota, and Spirochaetota were significantly more abundant in GHS (P < 0.01). Conversely, Chloroplastida, Mucoromycota, Arthropoda, and Cryptomycota were significantly more prevalent in BHP (P < 0.05), while the SAR supergroup, Ascomycota, Nematoda, and Amoebozoa dominated in GHS (P < 0.05). Through null and neutral modeling, stochastic processes exerted greater influence on bacterial and eukaryotic community assembly in fine-scale variations within geothermal spring mats. Despite this stochastic predominance, abiotic environmental factors (deterministic processes) such as temperature, pH, salinity (EC and TDS), and nitrate cannot be entirely ruled out. Moreover, Co-occurrence network analysis (|r|> 0.7, P < 0.05) revealed more complex and stable microbial interactions at higher temperatures (GHS). These findings highlight the rich underexplored microbial diversity and interactions in Rwandan geothermal spring mats through metagenomic analysis, shedding light on ecological processes and dynamics in extreme environments. Despite being ignored in metagenomic studies, eukaryotic communities highlight novel temperature-tolerant taxa: Echinamoeba and Tubulinea in phylum Amoebozoa, Monhysterida in phylum Nematoda, and Novel_Clade_Gran-5 in phylum Cercozoa, which are both pathogens and fierce predators thriving in geothermal habitats.},
}

*Hot Springs/microbiology
*Bacteria/classification/genetics/isolation & purification
Rwanda
*Biodiversity
RNA, Ribosomal, 16S/genetics
*Microbiota
RNA, Ribosomal, 18S/genetics
*Eukaryota/classification/genetics/isolation & purification
Phylogeny

@article {pmid41490675,
year = {2026},
author = {Li, Y and Cao, L and Li, W and Yan, Y and Zuo, W and Xi, B and Huang, C},
title = {Unveiling nitrogen and sulfur cycling mechanisms of odor reduction in kitchen waste composting driven by exogenous bacterial consortia.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133923},
doi = {10.1016/j.biortech.2026.133923},
pmid = {41490675},
issn = {1873-2976},
abstract = {Odor emissions, primarily ammonia (NH3) and hydrogen sulfide (H2S) restrict the application of kitchen waste (KW) composting. Microbial inoculation is a promising strategy, yet mechanisms underlying odor mitigation remain unclear. KW composting with and without an immobilized bacterial consortium (IBC) was compared by monitoring physicochemical conditions, odor emissions, and microbial and functional profiles. IBC extended the thermophilic phase, improved composting efficiency, and reduced cumulative H2S (-44 %) and NH3 (-18 %). IBC reshaped bacterial, fungal and archaeal communities and strengthened microbial network connectivity. Metagenomic analysis showed IBC enriched nitrogen-fixation genes and suppressed ammonification, nitrification, denitrification, and nitrate reduction. IBC also enhanced thiosulfate and sulfite oxidation while inhibited reductive pathways linked to H2S formation. Partial least squares path model confirmed odor mitigation resulting from coordinated shifts in environmental conditions, microbial structure, and metabolic pathways. Overall, microbial inoculation effectively reduces odor emissions and enhances composting performance by redirecting nitrogen and sulfur transformations.},
}

@article {pmid41490674,
year = {2026},
author = {Hao, X and Zeng, W and Gong, Q and Zhan, M and Miao, H and Yuan, C and Peng, Y},
title = {Biochar derived from waste iron-rich biosludge promotes iron-nitrogen coupled nitrogen removal in wastewater treatment.},
journal = {Bioresource technology},
volume = {444},
number = {},
pages = {133935},
doi = {10.1016/j.biortech.2026.133935},
pmid = {41490674},
issn = {1873-2976},
abstract = {Traditional biological nitrogen removal faces sustainability challenges due to high energy consumption and chemical demands. This study developed a novel autotrophic process leveraging the Fe-N cycle, enhanced by biochar derived from waste iron-rich biosludge (BC-Fe). During 150-day operation, adding 1 g/L BC-Fe (450 °C) achieved a total nitrogen removal efficiency of 94 ± 1 %, reducing aeration energy by 68 % and eliminating the need for external carbon sources compared to conventional nitrification-denitrification. BC-Fe served as a substrate and electron shuttle, facilitating Fe(III) reduction coupled with anaerobic ammonium oxidation (Feammox), nitrate-dependent Fe(II) oxidation, and denitrification, thereby supplying nitrite for Anammox. It enhanced iron bioavailability and established integrated carbon, nitrogen, and iron cycles, promoting microbial metabolism and system resilience. Metagenomics revealed Candidatus Brocadia fulgida performing Feammox via hao, compensating for hzs/hdh deficiency, while Saprospiraceae utilized biochar-derived organics for denitrification. This work provides a scalable solution to promote circular economy principles in wastewater treatment.},
}

@article {pmid41490614,
year = {2026},
author = {Campos-Silva, R and Rahimi, F and Joshi, J and Voiniciuc, C and Zhou, J and Hanson, AD},
title = {Mining bacterial (meta)genomes for enzymes active in aerobic, mesophilic conditions.},
journal = {Analytical biochemistry},
volume = {},
number = {},
pages = {116045},
doi = {10.1016/j.ab.2026.116045},
pmid = {41490614},
issn = {1096-0309},
abstract = {Enzyme biochemistry can now draw on hundreds of thousands of prokaryotic genomes and metagenomes to identify orthologous genes for research, biocatalysis, and metabolic engineering. In many applications, adaptation to O2 and mild temperatures are essential. But as organism lifestyle information can be poor or absent (especially for metagenomes), it is challenging to avoid orthologous genes from anaerobes and extremophiles. Taking bacterial sulfide-dependent THI4 thiazole synthases as test-cases, we built computational pipelines that use only DNA sequence inputs to explore (i) the average oxidation state of carbon (ZC) in orthologous enzymes and (ii) the presence of O2-metabolism genes in the corresponding (meta)genomes. ZC has been proposed to be highest (least negative) in proteins of organisms from O2-rich, mesophilic environments. We found that ZC values of 2,300 THI4s ranged from -0.107 (relatively oxidized) to -0.302 (strongly reduced). As predicted, genes specifying cytochrome c or o oxidases (supporting respiration at relatively high O2 levels) and, to a lesser extent, cytochrome bd oxidases (which can function to scavenge O2) were more frequent in genomes encoding THI4s with high ZC values. Eight THI4s with ZC values in the top 5% and from (meta)genomes having cytochrome oxidases were tested for ability to complement a THI4Δ yeast strain in aerobic conditions. Three THI4 genes from a metagenome with cytochrome c/o oxidase (but without cytochrome bd) were active. These results support the feasibility of combining ZC and cytochrome oxidase profiles to identify bacterial orthologous enzymes that work in aerobic, mild temperature conditions.},
}

@article {pmid41490375,
year = {2025},
author = {Hou, S and Xie, E and Si, B and Xiao, Y and Ding, J and Yan, Z and Zhou, H and Cheng, H and Shen, Y and Li, Y},
title = {Nanobubble aeration accelerates manure wastewater sanitisation and enhances nitrogen retention while reduces greenhouse gas emissions.},
journal = {Water research},
volume = {292},
number = {},
pages = {125267},
doi = {10.1016/j.watres.2025.125267},
pmid = {41490375},
issn = {1879-2448},
abstract = {Manure wastewater is an organic effluent rich in nitrogen and is often regarded as a valuable recycled nutrient source for crop production; however, it also contains high concentrations of organic pollutants and pathogenic microorganisms, and inadequate treatment can lead to serious environmental and public health risks. Nanobubbles (NBs) aeration is an emerging high-efficiency gas-liquid mass-transfer technology, but its role in nitrogen conservation and hygienic stabilisation of nutrient-rich manure wastewater remains unclear. Here, a 180-day experiment with piggery wastewater compared four NBs and conventional aeration regimes against natural storage. We quantified sanitisation performance, nitrogen transformation, greenhouse-gas emissions, microbial communities and virulence factors, and determined oxygen transfer rate (OTR), oxygen transfer efficiency (OTE) and volumetric mass-transfer coefficient (kLa) under identical airflow. NBs aeration markedly increased dissolved oxygen and ·OH generation, thereby enhancing COD, BOD5 and Escherichia coliremoval and shortening the time to reach hygienic standards by 60 and 150 days compared with conventional aeration and natural storage, respectively.Although TN decreased in all treatments, the shorter sanitisation period under NBs aeration led to higher residual TN at compliance. The TN loss rate was 13.96% and 15.39% lower than under CA and CK, and cumulative N2O emissions were 30.21% lower than under conventional aeration. Network and metagenomic analyses showed that NBs aeration reshaped bacterial, fungal and archaeal communities, weakened virulence-factor connectivity, and strengthened the coupling between nitrogen-cycling microbes and gaseous nitrogen pathways. Quantification of OTR, OTE and kLa demonstrated that these benefits arise from the intrinsic mass-transfer properties of nanobubbles rather than an increased oxygen supply rate. Overall, this work provides new mechanistic insight and engineering evidence that NBs aeration can simultaneously accelerate manure wastewater sanitisation and improve nitrogen management for subsequent fertiliser reuse.},
}

@article {pmid41489359,
year = {2026},
author = {Yancey, CE and Hart, LN and Dick, GJ},
title = {Secondary metabolism of Microcystis: current understanding and recent advances in unlocking genomic and chemical diversity.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0163425},
doi = {10.1128/aem.01634-25},
pmid = {41489359},
issn = {1098-5336},
abstract = {The cyanobacterial genus Microcystis is globally distributed and known for its ability to produce microcystins, a structurally diverse group of cyanotoxins. However, the biosynthetic capacity of Microcystis is vast; its diverse genomes contain a variety of biosynthetic gene clusters (BGCs) encoding the synthesis of metabolites that may be toxic, have important ecological function, or have applications for biotechnology or drug discovery. Recent studies illustrate that these BGCs vary significantly across Microcystis strains, can be highly expressed in environmental conditions, and may play key roles in cellular physiology, grazer deterrence, and microbial interactions. However, many of these BGCs and metabolites remain poorly characterized or completely uncharacterized, having been identified only through genome sequencing or mass spectrometry, respectively, leaving no knowledge of their structure, bioactivity, or physiological or ecological functions. Here, we synthesize the current body of knowledge regarding the secondary metabolism of Microcystis in terms of genetic and chemical diversity, potential drivers of synthesis, and physiological and ecological functions. This review highlights the need for further research to characterize the largely unexplored genetic and chemical diversity of Microcystis in communities in the environment and discusses the challenges and opportunities of integrating high-throughput multiomic approaches to link uncharacterized gene clusters with their corresponding metabolites. Microcystis will continue to be a rich source for secondary metabolite research as its genetic and chemical potential likely plays a critical role in the persistence and observed dynamics of harmful algal blooms and may harbor uncharacterized toxins and metabolites.},
}

@article {pmid41489358,
year = {2026},
author = {Surgenor, K and McCormick, C},
title = {Diving into the hidden viral world of marine protists.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {e0126225},
doi = {10.1128/jvi.01262-25},
pmid = {41489358},
issn = {1098-5514},
abstract = {As the most abundant biological entities in the ocean, viruses of microbes play important roles in regulating host population dynamics and influencing biogeochemical cycles. Metagenomic surveys have revealed an astounding reservoir of viral genetic diversity in single-celled marine eukaryotes known as protists, but the vast majority of these viruses have not been directly observed, and information about their protist hosts remains fragmentary. The 2023 discovery of mirusviruses provides a striking example, whereby metagenomic surveys of samples collected by the Tara Oceans expedition led to the discovery of a new phylum of viruses, the Mirusviricota, with remarkable chimeric genomes encoding structural proteins from herpesviruses and enzymes from giant eukaryotic viruses. However, because mirusviruses were detected indirectly by metagenomics, their host range remained unclear, and their biological properties unexplored. Here, we provide new insights into research approaches to identify bona fide protist hosts for marine viruses and characterize virus-host interactions. A greater understanding of these viruses and their natural hosts will unlock opportunities to understand the roles that they play in regulating biogeochemical processes in marine habitats.},
}

@article {pmid41489025,
year = {2026},
author = {Pace, R and Monti, MM and Cuomo, S and Affinito, A and Ruocco, M},
title = {Machine Learning Approaches to Assess Soil Microbiome Dynamics and Bio-Sustainability.},
journal = {Physiologia plantarum},
volume = {178},
number = {1},
pages = {e70719},
pmid = {41489025},
issn = {1399-3054},
mesh = {*Soil Microbiology ; *Machine Learning ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; Fungi/genetics ; Soil/chemistry ; Agriculture ; Principal Component Analysis ; },
abstract = {Understanding soil microbiota dynamics is essential for enhancing bio-sustainability in agriculture, yet the complexity of microbial communities hampers the prediction of their functional roles. Artificial intelligence (AI) and machine learning (ML) offer powerful tools to analyse high-dimensional microbiome data generated by high-throughput sequencing. Here, we apply unsupervised AI-based algorithms to uncover microbial patterns that are not immediately recognisable but are crucial for characterising the biological status of agricultural soils. Soil samples were collected from a site in Northern Italy managed under four strategies: conventional farming without organic matter (C), with organic matter (C + O), with beneficial microorganisms but without organic matter (M), and with both beneficial microorganisms and organic matter (M + O). Metagenomic amplicon sequencing of the 16S ribosomal RNA (rRNA) gene and the internal transcribed spacer (ITS) region was used to profile bacterial and fungal communities. Principal component analysis (PCA), k-means clustering, and t-distributed stochastic neighbour embedding (t-SNE) revealed coherent temporal trajectories in both datasets, with sampling time and crop presence emerging as dominant drivers of community assembly and only subtle compositional shifts attributable to treatments. Fungal communities exhibited higher plasticity and a stronger response to management than bacterial communities, which converged towards a stable oligotrophic core. Our findings highlight the complementary roles of fungal and bacterial guilds and show that unsupervised ML-based workflows provide an effective framework to disentangle temporal and treatment effects in complex microbiome datasets. This exploratory study lays the groundwork for future predictive models aimed at identifying microbial indicators of soil biological status and supporting bio-sustainable agronomic decisions.},
}

*Soil Microbiology
*Machine Learning
*Microbiota/genetics
RNA, Ribosomal, 16S/genetics
Bacteria/genetics
Fungi/genetics
Soil/chemistry
Agriculture
Principal Component Analysis