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

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

Author information

1
1] Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud university medical centre, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands [2] Department of Computer Science, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA [3] Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA [4] Department of Marine Biology, Institute of Biology, Federal University of Rio de Janeiro, Av. Carlos Chagas Fo. 373, Prédio Anexo ao Bloco A do Centro de Ciências da Saúde, Ilha do Fundão, CEP 21941-902 Rio de Janeiro, Brazil.
2
1] Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA [2].
3
Department of Computer Science, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA.
4
Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA.
5
Computational Science Research Center, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA.
6
Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
7
1] Department of Computer Science, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA [2] Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, Cairo 11562, Egypt.
8
Department of Mathematics, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA.
9
1] Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA [2] Computational Science Research Center, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA.
10
1] Department of Computer Science, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA [2] Department of Marine Biology, Institute of Biology, Federal University of Rio de Janeiro, Av. Carlos Chagas Fo. 373, Prédio Anexo ao Bloco A do Centro de Ciências da Saúde, Ilha do Fundão, CEP 21941-902 Rio de Janeiro, Brazil [3] Computational Science Research Center, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA [4] Division of Mathematics and Computer Science, Argonne National Laboratory, 9700 S Cass Ave B109, Argonne, Illinois 60439, USA.

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.

PMID:
25058116
PMCID:
PMC4111155
DOI:
10.1038/ncomms5498
[Indexed for MEDLINE]
Free PMC Article

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