The Human Gut Virome Is Highly Diverse, Stable, and Individual Specific

Andrey N. Shkoporov, Adam G. Clooney, Thomas D.S. Sutton, Feargal J. Ryan, Karen M. Daly, James A. Nolan, Siobhan A. McDonnell, Ekaterina V. Khokhlova, Lorraine A. Draper, Amanda Forde, Emma Guerin, Vimalkumar Velayudhan, R. Paul Ross, Colin Hill

Research output: Contribution to journalArticlepeer-review

196 Citations (Scopus)

Abstract

The human gut contains a vast array of viruses, mostly bacteriophages. The majority remain uncharacterized, and their roles in shaping the gut microbiome and in impacting on human health remain poorly understood. We performed longitudinal metagenomic analysis of fecal viruses in healthy adults that reveal high temporal stability, individual specificity, and correlation with the bacterial microbiome. Using a database-independent approach that uses most of the sequencing data, we uncovered the existence of a stable, numerically predominant individual-specific persistent personal virome. Clustering of viral genomes and de novo taxonomic annotation identified several groups of crAss-like and Microviridae bacteriophages as the most stable colonizers of the human gut. CRISPR-based host prediction highlighted connections between these stable viral communities and highly predominant gut bacterial taxa such as Bacteroides, Prevotella, and Faecalibacterium. This study provides insights into the structure of the human gut virome and serves as an important baseline for hypothesis-driven research.

Original languageEnglish
Pages (from-to)527-541.e5
Number of pages21
JournalCell Host and Microbe
Volume26
Issue number4
DOIs
Publication statusPublished - 9 Oct 2019
Externally publishedYes

Keywords

  • bacteriophages
  • crAss-like phages
  • crAssphage
  • CRISPR
  • human microbiome
  • longitudinal study
  • Microviridae
  • persistent personal virome
  • phageome
  • virome

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