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 and Robert A. Edwards
Additional contact information
Bas E. Dutilh: Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud university medical centre, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands
Noriko Cassman: San Diego State University, 5500 Campanile Drive
Katelyn McNair: San Diego State University, 5500 Campanile Drive
Savannah E. Sanchez: San Diego State University, 5500 Campanile Drive
Genivaldo G. Z. Silva: Computational Science Research Center, San Diego State University, 5500 Campanile Drive
Lance Boling: San Diego State University, 5500 Campanile Drive
Jeremy J. Barr: San Diego State University, 5500 Campanile Drive
Daan R. Speth: Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135
Victor Seguritan: San Diego State University, 5500 Campanile Drive
Ramy K. Aziz: San Diego State University, 5500 Campanile Drive
Ben Felts: San Diego State University, 5500 Campanile Drive
Elizabeth A. Dinsdale: San Diego State University, 5500 Campanile Drive
John L. Mokili: San Diego State University, 5500 Campanile Drive
Robert A. Edwards: San Diego State University, 5500 Campanile Drive

Nature Communications, 2014, vol. 5, issue 1, 1-11

Abstract: 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.

Date: 2014
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DOI: 10.1038/ncomms5498

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