A Highly Abundant Bacteriophage Discovered in the Unknown Sequences of Human Faecal Metagenomes

Nat Commun. 2014 Jul 24;5:4498. doi: 10.1038/ncomms5498.

Abstract

Metagenomics, or sequencing of the genetic material from a complete microbial community, is a promising tool to discover novel microbes and viruses. Viral metagenomes typically contain many unknown sequences. Here we describe the discovery of a previously unidentified bacteriophage present in the majority of published human faecal metagenomes, which we refer to as crAssphage. Its ~97 kbp genome is six times more abundant in publicly available metagenomes than all other known phages together; it comprises up to 90% and 22% of all reads in virus-like particle (VLP)-derived metagenomes and total community metagenomes, respectively; and it totals 1.68% of all human faecal metagenomic sequencing reads in the public databases. The majority of crAssphage-encoded proteins match no known sequences in the database, which is why it was not detected before. Using a new co-occurrence profiling approach, we predict a Bacteroides host for this phage, consistent with Bacteroides-related protein homologues and a unique carbohydrate-binding domain encoded in the phage genome.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Bacteriophages / genetics
  • Bacteriophages / isolation & purification*
  • Bacteroides / virology
  • Clustered Regularly Interspaced Short Palindromic Repeats
  • Feces / microbiology
  • Feces / virology*
  • Female
  • Humans
  • Metagenome*
  • Molecular Sequence Data
  • Viral Proteins / genetics

Substances

  • Viral Proteins

Associated data

  • GENBANK/JQ995537
  • GENBANK/KM000086
  • GENBANK/KM000087
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  • GENBANK/KM000089
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  • GENBANK/KM000120
  • GENBANK/KM000121