Interrogating the viral dark matter of the rumen ecosystem with a global virome database

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Aug. 29, 2023

Abstract The diverse rumen virome can modulate the microbiome, but it remains largely unexplored. Here, we mine 975 published metagenomes for viral sequences, create a global database (RVD), and analyze diversity, virus-host linkages, potential roles in affecting functions. Containing 397,180 species-level operational taxonomic units (vOTUs), RVD substantially increases detection rate of viruses from compared with IMG/VR V3. Most classified vOTUs belong to Caudovirales , differing those found human gut. is predicted infect core including fiber degraders methanogens, carries auxiliary metabolic genes, thus likely impacts ecosystem both top-down bottom-up manner. findings provide useful resources baseline framework future research investigate how may impact digestive physiology.

Language: Английский

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Unravelling viral ecology and evolution over 20 years in a freshwater lake

Nature Microbiology, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 3, 2025

Language: Английский

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Overcoming donor variability and risks associated with fecal microbiota transplants through bacteriophage-mediated treatments

Microbiome, Journal Year: 2024, Volume and Issue: 12(1)

Published: July 1, 2024

Abstract Background Fecal microbiota transplantation (FMT) and fecal virome (FVT, sterile filtrated donor feces) have been effective in treating recurrent Clostridioides difficile infections, possibly through bacteriophage-mediated modulation of the gut microbiome. However, challenges like variability, costly screening, coupled with concerns over pathogen transfer (incl. eukaryotic viruses) FMT or FVT hinder their wider clinical application less acute diseases. Methods To overcome these challenges, we developed methods to broaden FVT’s while maintaining efficacy increasing safety. Specifically, employed following approaches: (1) chemostat-fermentation reproduce bacteriophage component remove viruses (FVT-ChP), (2) solvent-detergent treatment inactivate enveloped (FVT-SDT), (3) pyronin-Y inhibit RNA virus replication (FVT-PyT). We assessed processed FVTs a C. infection mouse model compared them untreated (FVT-UnT), FMT, saline. Results FVT-SDT, FVT-UnT, FVT-ChP reduced incidence mice reaching humane endpoint (0/8, 2/7, 3/8, respectively) FVT-PyT, saline (5/8, 7/8, 5/7, significantly load colonizing cells associated toxin A/B levels. There was potential elimination colonization, seven out eight treated FVT-SDT testing negative qPCR. In contrast, all other treatments exhibited continued presence . Moreover, results were supported by changes microbiome profiles, cecal cytokine levels, histopathological findings. Assessment viral engraftment FMT/FVT host-phage correlations analysis suggested that phages likely an important contributing factor efficacy. Conclusions This proof-of-concept study shows specific modifications hold promise addressing related variability risks. Two strategies lead limiting colonization mice, solvent/detergent chemostat propagation emerging as promising approaches.

Language: Английский

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Prophage-DB: a comprehensive database to explore diversity, distribution, and ecology of prophages

Environmental Microbiome, Journal Year: 2025, Volume and Issue: 20(1)

Published: Jan. 13, 2025

Abstract Background Viruses that infect prokaryotes (phages) constitute the most abundant group of biological agents, playing pivotal roles in microbial systems. They are known to impact community dynamics, ecology, and evolution. Efforts document diversity, host range, infection effects bacteriophage on cell metabolism extremely underexplored. Phages classified as virulent or temperate based their life cycles. Temperate phages adopt lysogenic mode infection, where genome integrates into forming a prophage. Prophages enable viral replication without lysis, often contribute novel beneficial traits genome. Current phage research predominantly focuses lytic phages, leaving significant gap knowledge regarding prophages, including biology, ecological roles. Results Here we develop describe Prophage-DB, database proteins, associated metadata will serve resource for genomics ecology. To create database, identified characterized prophages from genomes three largest publicly available databases. We applied several state-of-the-art tools our pipeline annotate these viruses, cluster them, taxonomically classify detect respective auxiliary metabolic genes. In total, identify characterize over 350,000 35,000 Our prophage is highly representative statistical results contains diverse set archaeal bacterial hosts which show wide environmental distribution. Conclusion Given particularly overlooked merit increased attention due vital implications microbiomes hosts, created Prophage-DB advance understanding through comprehensive characterization genomes. propose valuable advancing research, offering insights taxonomy, relationships, genes,

Language: Английский

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Characterization and genome analysis of lytic Vibrio phage VPK8 with potential in lysing Vibrio parahaemolyticus isolates from clinical and seafood sources

Virology Journal, Journal Year: 2025, Volume and Issue: 22(1)

Published: Jan. 30, 2025

Abstract Background Vibrio parahaemolyticus is a marine bacterium causing seafood-associated gastrointestinal illness in humans and acute hepatopancreatic necrosis disease (AHPND) shrimp. Bacteriophages have emerged as promising biocontrol agents against V. . This study characterizes phage VPK8, focusing on host specificity, efficiency of plating (EOP) variability across isolates from diverse sources other species, morphology, genomic features, bacteriolytic potential. Methods VPK8 was isolated blood cockles Thailand using mixed-host approach purified via the double-layer agar method. Host specificity evaluated spot assays EOP measurements 120 strains, including AHPND-associated, clinical, seafood isolates. Phage morphology characterized by transmission electron microscopy (TEM), while features were analyzed next-generation sequencing. Lytic characteristics, latent period burst size, determined through one-step growth curves, bacterial reduction over 24-h. Results lytic with 42,866 bp linear double-stranded genome, G + C content 49.4%, 48 coding sequences. Phylogenetic analysis grouped it within Autographiviridae family, showing 95.96% similarity to vB_VpaP_MGD1. Viral proteomic placed Pseudomonadota group. Spot indicated broad activity, but revealed high infectivity clinical isolates, well some cholerae mimicus strains. TEM an icosahedral head (~ 60 nm) short tail. At multiplicity infection 0.01, exhibited 25 min, size 115, effectively inhibited reference PSU5124 6 h, maintaining its activity stability for 24 h. Conclusions provides detailed characterization which exhibits targeted selected species. Its stable performance, rapid replication, safety suggest potential phage-based applications. Further studies should explore vivo efficacy genetic contributing resistance mechanisms, enhancing applicability managing -related diseases.

Language: Английский

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Transfer of modified gut viromes improves symptoms associated with metabolic syndrome in obese male mice

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: June 3, 2024

Abstract Metabolic syndrome encompasses amongst other conditions like obesity and type-2 diabetes is associated with gut microbiome (GM) dysbiosis. Fecal microbiota transplantation (FMT) has been explored to treat metabolic by restoring the GM; however, concerns on accidentally transferring pathogenic microbes remain. As a safer alternative, fecal virome (FVT, sterile-filtrated feces) advantage over FMT in that mainly bacteriophages are transferred. FVT from lean male donors have shown promise alleviating effects of high-fat diet preclinical mouse study. However, still carries risk eukaryotic viral infections. To address this, recently developed methods applied for removing or inactivating viruses component FVT. Modified FVTs compared unmodified saline diet-induced model C57BL/6 N mice. Contrasted obese control, mice administered modified (nearly depleted viruses) exhibits enhanced blood glucose clearance but not weight loss. The improves liver pathology reduces proportions immune cells adipose tissue non-uniform response. GM analysis suggests bacteriophage-mediated modulation influences outcomes. Optimizing these approaches could lead development safe bacteriophage-based therapies targeting through restoration.

Language: Английский

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Metagenome sequence data mining for viral interaction studies: Review on progress and prospects

Virus Research, Journal Year: 2024, Volume and Issue: 349, P. 199450 - 199450

Published: Aug. 22, 2024

• Examining integrative bioinformatics methods used in viral interaction research, this study highlights metagenomic data from various contexts. Accurate identification depends on high-purity genetic material extraction, appropriate NGS platform selection, and sophisticated tools like VirPipe VirFinder. The diversity dynamics of communities are demonstrated by case studies a variety environments. In addition to speeding up the discovery new viruses, metagenomics offers thorough understanding virus-host interactions their ecological effects. Metagenomics has been greatly accelerated development next-generation sequencing (NGS) technologies, which allow scientists discover describe novel microorganisms without need for conventional culture techniques. efficiency precision analysis further improved with advent AI-based environments, emphasizing seasonal geographical variations that influence populations. This review provides promising framework comprehending complexity hosts, highlighting transformational potential research.

Language: Английский

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Prophage-encoded chitinase gene supports growth of its bacterial host isolated from deep-sea sediments

The ISME Journal, Journal Year: 2025, Volume and Issue: 19(1)

Published: Jan. 1, 2025

Language: Английский

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Uncovering soil amendment-induced genomic and functional divergence in soybean rhizosphere microbiomes during cadmium-contaminated soil remediation: Novel insights from field multi-omics

Environmental Pollution, Journal Year: 2025, Volume and Issue: 368, P. 125787 - 125787

Published: Feb. 3, 2025

Language: Английский

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Microbial ecosystems and ecological driving forces in the deepest ocean sediments

Cell, Journal Year: 2025, Volume and Issue: 188(5), P. 1363 - 1377.e9

Published: March 1, 2025

Systematic exploration of the hadal zone, Earth's deepest oceanic realm, has historically faced technical limitations. Here, we collected 1,648 sediment samples at 6-11 km in Mariana Trench, Yap and Philippine Basin for Trench Environment Ecology Research (MEER) project. Metagenomic 16S rRNA gene amplicon sequencing generated 92-Tbp MEER dataset, comprising 7,564 species (89.4% unreported), indicating high taxonomic novelty. Unlike reported environments, neutral drift played a minimal role, while homogeneous selection (HoS, 50.5%) dispersal limitation (DL, 43.8%) emerged as dominant ecological drivers. HoS favored streamlined genomes with key functions adaptation, e.g., aromatic compound utilization (oligotrophic adaptation) antioxidation (high-pressure adaptation). Conversely, DL promoted versatile metabolism larger genomes. These findings indicated that environmental factors drive novelty advancing our understanding mechanisms governing microbial ecosystems such an extreme environment.

Language: Английский

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