Biology and Taxonomy of crAss-like Bacteriophages, the Most Abundant Virus in the Human Gut

Emma Guerin, Andrey Shkoporov, Stephen R. Stockdale, Adam G. Clooney, Feargal Ryan, Thomas D.S. Sutton, Lorraine A. Draper, Enrique Gonzalez-Tortuero, R. Paul Ross, Colin Hill

Research output: Contribution to journalArticlepeer-review

113 Citations (Scopus)

Abstract

CrAssphages represent the most abundant virus in the human gut microbiota, but the lack of available genome sequences for comparison has kept them enigmatic. Recently, sequence-based classification of distantly related crAss-like phages from multiple environments was reported, leading to a proposed familial-level taxonomic group. Here, we assembled the metagenomic sequencing reads from 702 human fecal virome/phageome samples and analyzed 99 complete circular crAss-like phage genomes and 150 contigs ≥70 kb. In silico comparative genomics and taxonomic analysis enabled a classification scheme of crAss-like phages from human fecal microbiomes into four candidate subfamilies composed of ten candidate genera. Laboratory analysis was performed on fecal samples from an individual harboring seven distinct crAss-like phages. We achieved crAss-like phage propagation in ex vivo human fecal fermentations and visualized short-tailed podoviruses by electron microscopy. Mass spectrometry of a crAss-like phage capsid protein could be linked to metagenomic sequencing data, confirming crAss-like phage structural annotations. CrAssphage is the most abundant human gut-associated virus. Guerin et al. identify 249 crAss-like phage genomes and classify them into four subfamilies and ten candidate genera that differ among human populations. These in silico predictions are combined with ex vivo propagations, electron microscopy imaging, and mass spectrometry detection.

Original languageEnglish
Pages (from-to)653-664.e6
JournalCell Host and Microbe
Volume24
Issue number5
DOIs
Publication statusPublished or Issued - 14 Nov 2018

Keywords

  • bacteriophages
  • crAssphage
  • gut microbiota
  • human microbiome
  • phage characterization
  • phage taxonomy

ASJC Scopus subject areas

  • Parasitology
  • Microbiology
  • Virology

Cite this