ViWrap: A modular pipeline to identify, bin, classify, and predict viral–host relationships for viruses from metagenomes

iMeta, Journal Year: 2023, Volume and Issue: 2(3)

Published: June 7, 2023

Abstract Viruses are increasingly being recognized as important components of human and environmental microbiomes. However, viruses in microbiomes remain difficult to study because the difficulty culturing them lack sufficient model systems. As a result, computational methods for identifying analyzing uncultivated viral genomes from metagenomes have attracted significant attention. Such bioinformatics approaches facilitate screening enormous sequencing data sets originating various environments. Although many tools databases been developed advancing metagenomes, there is integrated enabling comprehensive workflow analysis platform encompassing all diverse segments virus studies. Here, we ViWrap, modular pipeline written Python. ViWrap combines power multiple into single enable steps analyses, including identification, annotation, genome binning, species‐ genus‐level clustering, assignment taxonomy, prediction hosts, characterization quality, summaries, intuitive visualization results. Overall, enables standardized reproducible both extensive stringent viromes, microbial genomes. Our approach has flexibility using options applications scenarios, its structure can be easily amended with additional functions necessary. designed widely used publicly available via GitHub ( https://github.com/AnantharamanLab/ViWrap ). A detailed description software, usage, interpretation results found on website.

Language: Английский

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Viromes vs. mixed community metagenomes: choice of method dictates interpretation of viral community ecology

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

Published: Oct. 7, 2024

Viruses, the majority of which are uncultivated, among most abundant biological entities on Earth. From altering microbial physiology to driving community dynamics, viruses fundamental members microbiomes. While number studies leveraging viral metagenomics (viromics) for studying uncultivated is growing, standards viromics research lacking. Viromics can utilize computational discovery from total metagenomes all (hereafter metagenomes) or use physical separation virus-specific fractions viromes). However, differences in recovery and interpretation viromes obtained same samples remain understudied.

Language: Английский

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Phages in different habitats and their ability to carry antibiotic resistance genes

Journal of Hazardous Materials, Journal Year: 2024, Volume and Issue: 469, P. 133941 - 133941

Published: March 2, 2024

Language: Английский

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Virion-Associated Nucleic Acid-Based Metagenomics: A Decade of Advances in Molecular Characterization of Plant Viruses

Phytopathology, Journal Year: 2022, Volume and Issue: 112(11), P. 2253 - 2272

Published: June 20, 2022

Over the last decade, viral metagenomic studies have resulted in discovery of thousands previously unknown viruses. These are likely to play a pivotal role obtaining an accurate and robust understanding how viruses affect stability productivity ecosystems. Among metagenomics-based approaches that been developed since beginning 21st century, shotgun metagenomics applied specifically virion-associated nucleic acids (VANA) has used disentangle diversity world. We summarize herein results 24 VANA-based studies, focusing on plant insect samples conducted over decade (2010 2020). Collectively, from 85 different families were reliably detected these including capsidless RNA replicate fungi, oomycetes, plants. Finally, strengths weaknesses VANA approach summarized perspectives applications detection, epidemiological surveillance, environmental monitoring, ecology provided. [Formula: see text] Copyright © 2022 The Author(s). This is open access article distributed under CC BY-NC-ND 4.0 International license .

Language: Английский

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Diversity and Ecology of Caudoviricetes Phages with Genome Terminal Repeats in Fecal Metagenomes from Four Dutch Cohorts

Viruses, Journal Year: 2022, Volume and Issue: 14(10), P. 2305 - 2305

Published: Oct. 20, 2022

The human gut harbors numerous viruses infecting the host, microbes, and other inhabitants of gastrointestinal tract. Most these remain undiscovered, their influence on health is unknown. Here, we characterize viral genomes in metagenomic data from 1950 individuals four population patient cohorts. We focus a subset that highly abundant gut, remains largely uncharacterized, allows confident complete genome identification—phages belong to class Caudoviricetes possess terminal repeats. detect 1899 species-level units belonging this subset, 19% which do not have representative major public virome databases. These display diverse genomic features, are predicted infect wide range microbial hosts, average account for <1% reads. Analysis longitudinal 338 shows composition fraction remained relatively stable over period 4 years. also demonstrate 54 prevalent (detected >5% cohort). Finally, find 34 associations between phages phenotypes, 24 can be explained by relative abundance potential hosts.

Language: Английский

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Hecatomb: an integrated software platform for viral metagenomics

GigaScience, Journal Year: 2024, Volume and Issue: 13

Published: Jan. 1, 2024

Abstract Background Modern sequencing technologies offer extraordinary opportunities for virus discovery and virome analysis. Annotation of viral sequences from metagenomic data requires a complex series steps to ensure accurate annotation individual reads assembled contigs. In addition, varying study designs will require project-specific statistical analyses. Findings Here we introduce Hecatomb, bioinformatic platform coordinating commonly used tasks required Hecatomb means “a great sacrifice.” this setting, is “sacrificing” false-positive annotations using extensive quality control tiered-database searches. processes obtained both short- long-read technologies, providing Results are provided in formats useful downstream demonstrate the functionality through reanalysis primate enteric novel coral reef virome. Conclusion provides an integrated manage many characterization, including rigorous control, host removal, read- contig-based Each step managed Snakemake workflow manager with dependency management Conda. outputs several tables properly formatted immediate use within popular analysis visualization tools, enabling effective interpretation variety designs. hosted on GitHub (github.com/shandley/hecatomb) available installation Bioconda PyPI.

Language: Английский

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Exploring the Complexity of the Human Respiratory Virome through an In Silico Analysis of Shotgun Metagenomic Data Retrieved from Public Repositories

Viruses, Journal Year: 2024, Volume and Issue: 16(6), P. 953 - 953

Published: June 13, 2024

Background: Respiratory viruses significantly impact global morbidity and mortality, causing more disease in humans than any other infectious agent. Beyond pathogens, various bacteria colonize the respiratory tract without disease, potentially influencing diseases’ pathogenesis. Nevertheless, our understanding of microbiota is limited by technical constraints, predominantly focusing on neglecting crucial populations like viruses. Despite recent efforts to improve viral diversity human body, knowledge associated with remains limited. Methods: Following a comprehensive search bibliographic sequencing data repositories using keyword terms, we retrieved shotgun metagenomic from public (n = 85). After manual curation, files 43 studies were analyzed EVEREST (pipEline for Viral assEmbly chaRactEriSaTion). Complete high-quality contigs further assessed genomic taxonomic characterization. Results: obtained 194 out 868 FASTQ processed through EVEREST. Of 1842 that quality assessed, 8% 146) classified as complete/high-quality genomes. Most identified taxonomically bacteriophages, resolution ranging superkingdom level down species level. Captured spread across 25 putative families varied between RNA DNA viruses, including previously uncharacterized note, airway samples also contained virus(es) characteristic gastrointestinal tract, which have not been described part lung virome. Additionally, performing meta-analysis integrated datasets, ecological trends within linked states their biogeographical distribution along observed. Conclusion: By leveraging publicly available data, present study provides new insights into genomes specimens different spectra. Further are required validate findings evaluate potential these communities physiology.

Language: Английский

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First Discovery of Phenuiviruses within Diverse RNA Viromes of Asiatic Toad (Bufo gargarizans) by Metagenomics Sequencing

Viruses, Journal Year: 2023, Volume and Issue: 15(3), P. 750 - 750

Published: March 14, 2023

Most zoonotic pathogens originate from mammals and avians, but viral diversity related biosafety risk assessment in lower vertebrates also need to be explored. Amphibians are an important group of that played a momentous role animal evolution. To elucidate the RNA viruses one species amphibians, Asiatic toad (Bufo gargarizans), we obtained 44 samples including lung, gut, liver, kidney tissues toads Sichuan Jilin provinces, China, for metagenomics sequencing. More than 20 novel derived order Bunyavirales 7 families Astroviridae, Dicistroviridae, Leviviridae, Partitiviridae, Picornaviridae, Rhabdoviridae, Virgaviridae were discovered, which distinct previously described formed new clusters, as revealed by phylogenetic analyses. Notably, bastrovirus, AtBastV/GCCDC11/2022, family Astroviridae was identified gut library, genome contains three open reading frames, with RNA-dependent polymerase (RdRp) coded ORF1 closely hepeviruses, ORF2 encoding astrovirus-related capsid protein. phenuiviruses discovered first time amphibians. AtPhenV1/GCCDC12/2022 AtPhenV2/GCCDC13/2022 clustered together clade rodents. Picornaviruses several invertebrate detected. These findings improve our understanding high provide insights evolution

Language: Английский

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Synthesis and Antiviral Efficacy of Pyrimidine Analogs Targeting Viral Pathways

ChemistrySelect, Journal Year: 2023, Volume and Issue: 8(19)

Published: May 16, 2023

Abstract To date, viruses are known to cause chronic acute pathogenesis. Nevertheless, antiviral drugs have been for their medicinal applications the last few decades treat infections caused by these pathogens. Despite advancements in field of vaccination and drugs, there is a need molecule that can eradicate or control viral infection without getting resistance from pathogens will be real challenge. This review covers possible ways with pyrimidine its mimics compared drugs. A comprehensive study report accomplished synthetic routes analogs target‐specific potential. The present article literature 2018 2022.

Language: Английский

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Functional biology and biotechnology of thermophilic viruses

Essays in Biochemistry, Journal Year: 2023, Volume and Issue: 67(4), P. 671 - 684

Published: May 24, 2023

Abstract Viruses have developed sophisticated biochemical and genetic mechanisms to manipulate exploit their hosts. Enzymes derived from viruses been essential research tools since the first days of molecular biology. However, most viral enzymes that commercialized are a small number cultivated viruses, which is remarkable considering extraordinary diversity abundance revealed by metagenomic analysis. Given explosion new enzymatic reagents thermophilic prokaryotes over past 40 years, those obtained should be equally potent tools. This review discusses still-limited state art regarding functional biology biotechnology with focus on DNA polymerases, ligases, endolysins, coat proteins. Functional analysis polymerases primase-polymerases phages infecting Thermus, Aquificaceae, Nitratiruptor has clades strong proofreading reverse transcriptase capabilities. Thermophilic RNA ligase 1 homologs characterized Rhodothermus Thermus phages, both for circularization single-stranded templates. Endolysins Meiothermus, Geobacillus shown high stability unusually broad lytic activity against Gram-negative Gram-positive bacteria, making them targets commercialization as antimicrobials. Coat proteins Sulfolobales strains characterized, diverse potential applications shuttles. To gauge scale untapped resources these proteins, we also document 20,000 genes encoded uncultivated genomes high-temperature environments encode polymerase, ligase, endolysin, or protein domains.

Language: Английский

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