title: Viral dark matter and virus-host interactions resolved from publicly available microbial genomes.
abstract: The ecological importance of viruses is now widely recognized, yet our limited knowledge of viral sequence space and virus-host interactions precludes accurate prediction of their roles and impacts. In this study, we mined publicly available bacterial and archaeal genomic data sets to identify 12,498 high-confidence viral genomes linked to their microbial hosts. These data augment public data sets 10-fold, provide first viral sequences for 13 new bacterial phyla including ecologically abundant phyla, and help taxonomically identify 7-38% of 'unknown' sequence space in viromes. Genome- and network-based classification was largely consistent with accepted viral taxonomy and suggested that (i) 264 new viral genera were identified (doubling known genera) and (ii) cross-taxon genomic recombination is limited. Further analyses provided empirical data on extrachromosomal prophages and coinfection prevalences, as well as evaluation of in silico virus-host linkage predictions. Together these findings illustrate the value of mining viral signal from microbial genomes.
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, United States.
authors.forename: Simon
authors.initials: S
authors.lastname: Roux
authors.affiliation: Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada.
authors.forename: Steven J
authors.initials: SJ
authors.lastname: Hallam
authors.affiliation: U.S Department of Energy Joint Genome Institute, Walnut Creek, United States.
authors.forename: Tanja
authors.initials: T
authors.lastname: Woyke
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, United States.
authors.forename: Matthew B
authors.initials: MB
authors.lastname: Sullivan
mesh_terms: D001105:Archaea / Q000235:genetics* / Q000821:virology*; D001419:Bacteria / Q000235:genetics* / Q000821:virology*; D064349:Genome, Microbial; D054884:Host-Pathogen Interactions; D014780:Viruses / Q000235:genetics*
keywords: ecology; evolutionary biology; genomics; none; phage; prophage; virus; virus-host adaptation