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

  1. Simon Roux
  2. Steven J Hallam
  3. Tanja Woyke
  4. Matthew B Sullivan  Is a corresponding author
  1. The Ohio State University, United States
  2. University of British Columbia, Canada
  3. U.S Department of Energy Joint Genome Institute, United States
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Cite this article as: eLife 2015;4:e08490 doi: 10.7554/eLife.08490


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.

Article and author information

Author details

  1. Simon Roux

    Department of Microbiology, The Ohio State University, Columbus, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Steven J Hallam

    Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
    Competing interests
    The authors declare that no competing interests exist.
  3. Tanja Woyke

    U.S Department of Energy Joint Genome Institute, Walnut Creek, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Matthew B Sullivan

    Department of Microbiology, The Ohio State University, Columbus, United States
    For correspondence
    Competing interests
    The authors declare that no competing interests exist.

Reviewing Editor

  1. Richard A Neher, Max Planck Institute for Developmental Biology, Germany

Publication history

  1. Received: May 2, 2015
  2. Accepted: July 22, 2015
  3. Accepted Manuscript published: July 22, 2015 (version 1)
  4. Accepted Manuscript updated: August 4, 2015 (version 2)
  5. Version of Record published: August 12, 2015 (version 3)


© 2015, Roux et al.

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.


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