title: A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes.
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.
authors: 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.
authors: Bas E
authors: BE
authors: Dutilh
authors: 1] Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA [2].
authors: Noriko
authors: N
authors: Cassman
authors: Department of Computer Science, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA.
authors: Katelyn
authors: K
authors: McNair
authors: Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA.
authors: Savannah E
authors: SE
authors: Sanchez
authors: Computational Science Research Center, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA.
authors: Genivaldo G Z
authors: GG
authors: Silva
authors: Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA.
authors: Lance
authors: L
authors: Boling
authors: Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA.
authors: Jeremy J
authors: JJ
authors: Barr
authors: Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
authors: Daan R
authors: DR
authors: Speth
authors: Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA.
authors: Victor
authors: V
authors: Seguritan
authors: 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.
authors: Ramy K
authors: RK
authors: Aziz
authors: Department of Mathematics, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA.
authors: Ben
authors: B
authors: Felts
authors: 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.
authors: Elizabeth A
authors: EA
authors: Dinsdale
authors: Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA.
authors: John L
authors: JL
authors: Mokili
authors: 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.
authors: Robert A
authors: RA
authors: Edwards
mesh_terms: D001435:Bacteriophages / Q000235:genetics / Q000302:isolation & purification*; D001439:Bacteroides / Q000821:virology; D064112:Clustered Regularly Interspaced Short Palindromic Repeats; D005243:Feces / Q000382:microbiology / Q000821:virology*; D005260:Female; D006801:Humans; D054892:Metagenome; D008969:Molecular Sequence Data; D014764:Viral Proteins / Q000235:genetics
chemical_list: D014764:Viral Proteins