Viral dark matter and virus-host interactions resolved from publicly available microbial genomes

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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. Here we mined publicly available bacterial and archaeal genomic datasets to identify 12,498 high‑confidence viral genomes linked to their microbial hosts. These data augment public datasets 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 co‑infection 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.

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Simon Roux

Department of Microbiology, The Ohio State University, Columbus, United States

Competing interests
The authors declare that no competing interests exist.
Steven J Hallam

Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada

Competing interests
The authors declare that no competing interests exist.
Tanja Woyke

U.S Department of Energy Joint Genome Institute, Walnut Creek, United States

Competing interests
The authors declare that no competing interests exist.
Matthew B Sullivan

Department of Microbiology, The Ohio State University, Columbus, United States

For correspondence
mbsulli@email.arizona.edu

Competing interests
The authors declare that no competing interests exist.

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This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.