Viral dark matter and virus-host interactions resolved from publicly available microbial genomes
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
- Richard A Neher, Max Planck Institute for Developmental Biology, Germany
- Received: May 2, 2015
- Accepted: July 22, 2015
- Accepted Manuscript published: July 22, 2015 (version 1)
- Accepted Manuscript updated: August 4, 2015 (version 2)
- 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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