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Published (Version of Record)CC BY V4.0, Open Access
Journal article
Exploring the Complexity of the Human Respiratory Virome through an In Silico Analysis of Shotgun Metagenomic Data Retrieved from Public Repositories
Viruses, Vol.16(6), 953
2024
PMCID: PMC11209621
PMID: 38932245
Abstract
Background: Respiratory viruses significantly impact global morbidity and mortality, causing more disease in humans than any other infectious agent. Beyond pathogens, various viruses and bacteria colonize the respiratory tract without causing disease, potentially influencing respiratory diseases’ pathogenesis. Nevertheless, our understanding of respiratory microbiota is limited by technical constraints, predominantly focusing on bacteria and neglecting crucial populations like viruses. Despite recent efforts to improve our understanding of viral diversity in the human body, our knowledge of viral diversity associated with the human respiratory tract remains limited.
Methods: Following a comprehensive search in bibliographic and sequencing data repositories using keyword terms, we retrieved shotgun metagenomic data from public repositories (n = 85). After manual curation, sequencing data files from 43 studies were analyzed using EVEREST (pipEline for Viral assEmbly and chaRactEriSaTion). Complete and high-quality contigs were further assessed for genomic and taxonomic characterization.
Results: Viral contigs were obtained from 194 out of the 868 FASTQ files processed through EVEREST. Of the 1842 contigs that were quality assessed, 8% (n = 146) were classified as complete/high-quality genomes. Most of the identified viral contigs were taxonomically classified as bacteriophages, with taxonomic resolution ranging from the superkingdom level down to the species level. Captured contigs were spread across 25 putative families and varied between RNA and DNA viruses, including previously uncharacterized viral genomes. Of note, airway samples also contained virus(es) characteristic of the human gastrointestinal tract, which have not been previously described as part of the lung virome. Additionally, by performing a meta-analysis of the integrated datasets, ecological trends within viral populations linked to human disease states and their biogeographical distribution along the respiratory tract were observed.
Conclusion: By leveraging publicly available repositories of shotgun metagenomic data, the present study provides new insights into viral genomes associated with specimens from the human respiratory tract across different disease spectra. Further studies are required to validate our findings and evaluate the potential impact of these viral communities on respiratory tract physiology.
Details
- Title
- Exploring the Complexity of the Human Respiratory Virome through an In Silico Analysis of Shotgun Metagenomic Data Retrieved from Public Repositories
- Authors/Creators
- Talya Conradie - The Kids Research Institute AustraliaJose A. Caparros-MartinSiobhon Egan - Murdoch UniversityAnthony Kicic - The Kids Research Institute AustraliaSulev Koks - Murdoch UniversityStephen M. Stick - Princess Margaret Hospital for ChildrenPatricia Agudelo-Romero
- Publication Details
- Viruses, Vol.16(6), 953
- Publisher
- MDPI
- Grant note
- 2021/GR000216 / NHMRC Investigator Award NHMRC 115648 / National Health and Medical Research Council of Australia Google Cloud Education Program grant Telethon Kids Institute Theme Collaboration Award 2023 APP118364 / Australian NHMRC 2020 Synergy grant
- Identifiers
- 991005681250207891
- Copyright
- © 2024 by the authors.
- Murdoch Affiliation
- Centre for Computational and Systems Medicine; Centre for Molecular Medicine and Innovative Therapeutics; School of Agricultural Sciences
- Language
- English
- Resource Type
- Journal article
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- Collaboration types
- Domestic collaboration
- International collaboration
- Citation topics
- 1 Clinical & Life Sciences
- 1.42 Bacteriology
- 1.42.1349 Bacteriophage
- Web Of Science research areas
- Virology
- ESI research areas
- Microbiology