A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes

Bas E. Dutilh, Noriko Cassman, Katelyn McNair, Savannah E. Sanchez, Genivaldo G.Z. Silva, Lance Boling, Jeremy J. Barr, Daan R. Speth, Victor Seguritan, Ramy K. Aziz, Ben Felts, Elizabeth A. Dinsdale, John L. Mokili, Robert A. Edwards

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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 ∼97kbp 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.

Original languageEnglish
Article number4498
Number of pages11
JournalNature Communications
Publication statusPublished - 24 Jul 2014
Externally publishedYes

Bibliographical note

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  • metagenomics
  • faecal metagenomes
  • bacteriophage
  • metagenomic sequencing


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