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 J. Ryan, Thomas D.S. Sutton, Lorraine A. Draper, Enrique Gonzalez-Tortuero, R. Paul Ross, Colin Hill

Research output: Contribution to journalArticlepeer-review

103 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.

Original languageEnglish
Pages (from-to)653-664.e6
Number of pages18
JournalCell Host and Microbe
Volume24
Issue number5
DOIs
Publication statusPublished - 14 Nov 2018
Externally publishedYes

Keywords

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

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