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Microbial ecology

Sorting out viral dark matter

Nature Reviews Microbiology volume 13, pages 526–527 (2015)Cite this article

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VirSorter identifies viruses based on either enrichment in viral genes, or the presence of genes encoding known viral functions and at least one genomic feature characteristic of viruses. From the 14,977 microbial genomes analysed, the authors identified 12,498 viral genomes, including the first known phages present in 13 bacterial phyla, such as Caldiserica, Marinimicrobia and Omnitrophica, which have important ecological roles.

Interestingly, seven short circular sequences that did not match any viral reference genomes were identified as being viral on the basis of their similarity to human gut viromes. Although these sequences contained plasmid replication genes, the authors suggest that they are derived from encapsidated particles and represent a novel order of viruses. Further analysis of 1,756 VirSorter sequences that were either circularized genomes or large genome fragments (>30 kb) demonstrated that these were mainly extrachromosomal. On the basis of the presence of the plasmid partition genes parA and parB within these sequences, the authors estimated that at least 13% of these sequences were extrachromosomal prophages and suggested that the remaining sequences represent carrier-state lytic viruses, chronic infections or extrachromosomal prophages without parA or parB genes.

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References

  1. Roux, S. et al. Viral dark matter and virus-host interactions resolved from publicly available microbial genomes. eLife http://dx.doi.org/10.7554/eLife.08490 (2015)

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Authors
  1. Denise Waldron
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Brum, J. R. & Sullivan, M. B. Rising to the challenge: accelerated pace of discovery transforms marine virology. Nat. Rev. Microbiol. 13, 147–159 (2015)

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Waldron, D. Sorting out viral dark matter. Nat Rev Microbiol 13, 526–527 (2015). https://doi.org/10.1038/nrmicro3541

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