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

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

doi:10.1038/ncomms5498

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

Journal Article · Thu Jul 24 00:00:00 EDT 2014 · Nature Communications

DOI:https://doi.org/10.1038/ncomms5498· OSTI ID:1623951

Dutilh, Bas E. ^[1]; Cassman, Noriko ^[2]; McNair, Katelyn ^[3]; Sanchez, Savannah E. ^[2]; Silva, Genivaldo G. Z. ^[4]; Boling, Lance ^[2]; Barr, Jeremy J. ^[2]; Speth, Daan R. ^[5]; Seguritan, Victor ^[2]; Aziz, Ramy K. ^[6]; Felts, Ben ^[7]; Dinsdale, Elizabeth A. ^[8]; Mokili, John L. ^[2]; Edwards, Robert A. ^[9]

Radboud Univ., Nijmegen (Netherlands). Radboud Univ. Medical Centre. Radboud Inst. for Molecular Life Sciences. Centre for Molecular and Biomolecular Informatics; San Diego State Univ., CA (United States). Dept. of Computer Science; San Diego State Univ., CA (United States). Dept. of Biology; Federal Univ. of Rio de Janeiro (Brazil). Inst. of Biology. Dept. of Marine Biology; DOE/OSTI
San Diego State Univ., CA (United States). Dept. of Biology
San Diego State Univ., CA (United States). Dept. of Computer Science
San Diego State Univ., CA (United States). Computational Science Research Center
Radboud Univ., Nijmegen (Netherlands). Inst. for Water and Wetland Research. Dept. of Microbiology
San Diego State Univ., CA (United States). Dept. of Computer Science; Cairo Univ. (Egypt). Faculty of Pharmacy. Dept. Microbiology and Immunology
San Diego State Univ., CA (United States). Dept. of Mathematics
San Diego State Univ., CA (United States). Dept. of Biology; San Diego State Univ., CA (United States). Computational Science Research Center
San Diego State Univ., CA (United States). Dept. of Computer Science; Federal Univ. of Rio de Janeiro (Brazil). Inst. of Biology. Dept. of Marine Biology; San Diego State Univ., CA (United States). Computational Science Research Center; Argonne National Lab. (ANL), Argonne, IL (United States). Division of Mathematics and Computer Science

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 B97 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 cooccurrence 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.

View Accepted Manuscript (DOE)

Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division; National Institutes of Health (NIH); National Science Foundation (NSF); Netherlands Organization for Scientific Research (NWO); Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES); Dutch Virgo Consortium

Grant/Contract Number:: AC02-06CH11357

OSTI ID:: 1623951

Journal Information:: Nature Communications, Journal Name: Nature Communications Journal Issue: 1 Vol. 5; ISSN 2041-1723

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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