title: Classification and quantification of bacteriophage taxa in human gut metagenomes.
abstract: Bacteriophages have key roles in microbial communities, to a large extent shaping the taxonomic and functional composition of the microbiome, but data on the connections between phage diversity and the composition of communities are scarce. Using taxon-specific marker genes, we identified and monitored 20 viral taxa in 252 human gut metagenomic samples, mostly at the level of genera. On average, five phage taxa were identified in each sample, with up to three of these being highly abundant. The abundances of most phage taxa vary by up to four orders of magnitude between the samples, and several taxa that are highly abundant in some samples are absent in others. Significant correlations exist between the abundances of some phage taxa and human host metadata: for example, 'Group 936 lactococcal phages' are more prevalent and abundant in Danish samples than in samples from Spain or the United States of America. Quantification of phages that exist as integrated prophages revealed that the abundance profiles of prophages are highly individual-specific and remain unique to an individual over a 1-year time period, and prediction of prophage lysis across the samples identified hundreds of prophages that are apparently active in the gut and vary across the samples, in terms of presence and lytic state. Finally, a prophage-host network of the human gut was established and includes numerous novel host-phage associations.
authors.affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
authors.forename: Alison S
authors.initials: AS
authors.lastname: Waller
authors.affiliation: Department of Biological Information, Tokyo Institute of Technology, Graduate School of Bioscience and Biotechnology, Yokohama, Japan.
authors.forename: Takuji
authors.initials: T
authors.lastname: Yamada
authors.affiliation: National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, MD, USA.
authors.forename: David M
authors.initials: DM
authors.lastname: Kristensen
authors.affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
authors.forename: Jens Roat
authors.initials: JR
authors.lastname: Kultima
authors.affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
authors.forename: Shinichi
authors.initials: S
authors.lastname: Sunagawa
authors.affiliation: National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, MD, USA.
authors.forename: Eugene V
authors.initials: EV
authors.lastname: Koonin
authors.affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
authors.forename: Peer
authors.initials: P
authors.lastname: Bork
mesh_terms: D001419:Bacteria / Q000821:virology; D001435:Bacteriophages / Q000145:classification* / Q000235:genetics; D005060:Europe; D041981:Gastrointestinal Tract / Q000821:virology*; D005819:Genetic Markers; D014644:Genetic Variation; D054884:Host-Pathogen Interactions; D006801:Humans; D054892:Metagenome; D010802:Phylogeny; D039002:Prophages / Q000145:classification / Q000235:genetics
chemical_list: D005819:Genetic Markers