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

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.

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
    mbsulli@email.arizona.edu
    Competing interests
    The authors declare that no competing interests exist.

Copyright

© 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.

Metrics

  • 11,579
    views
  • 2,336
    downloads
  • 385
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Simon Roux
  2. Steven J Hallam
  3. Tanja Woyke
  4. Matthew B Sullivan
(2015)
Viral dark matter and virus-host interactions resolved from publicly available microbial genomes
eLife 4:e08490.
https://doi.org/10.7554/eLife.08490

Share this article

https://doi.org/10.7554/eLife.08490

Further reading

    1. Ecology
    Mathilde Delacoux, Fumihiro Kano
    Research Article

    During collective vigilance, it is commonly assumed that individual animals compromise their feeding time to be vigilant against predators, benefiting the entire group. One notable issue with this assumption concerns the unclear nature of predator ‘detection’, particularly in terms of vision. It remains uncertain how a vigilant individual utilizes its high-acuity vision (such as the fovea) to detect a predator cue and subsequently guide individual and collective escape responses. Using fine-scale motion-capture technologies, we tracked the head and body orientations of pigeons (hence reconstructed their visual fields and foveal projections) foraging in a flock during simulated predator attacks. Pigeons used their fovea to inspect predator cues. Earlier foveation on a predator cue was linked to preceding behaviors related to vigilance and feeding, such as head-up or down positions, head-scanning, and food-pecking. Moreover, earlier foveation predicted earlier evasion flights at both the individual and collective levels. However, we also found that relatively long delay between their foveation and escape responses in individuals obscured the relationship between these two responses. While our results largely support the existing assumptions about vigilance, they also underscore the importance of considering vision and addressing the disparity between detection and escape responses in future research.

    1. Ecology
    Elham Nourani, Louise Faure ... Kamran Safi
    Research Article

    The heterogeneity of the physical environment determines the cost of transport for animals, shaping their energy landscape. Animals respond to this energy landscape by adjusting their distribution and movement to maximize gains and reduce costs. Much of our knowledge about energy landscape dynamics focuses on factors external to the animal, particularly the spatio-temporal variations of the environment. However, an animal’s internal state can significantly impact its ability to perceive and utilize available energy, creating a distinction between the ‘fundamental’ and the ‘realized’ energy landscapes. Here, we show that the realized energy landscape varies along the ontogenetic axis. Locomotor and cognitive capabilities of individuals change over time, especially during the early life stages. We investigate the development of the realized energy landscape in the Central European Alpine population of the golden eagle Aquila chrysaetos, a large predator that requires negotiating the atmospheric environment to achieve energy-efficient soaring flight. We quantified weekly energy landscapes using environmental features for 55 juvenile golden eagles, demonstrating that energetic costs of traversing the landscape decreased with age. Consequently, the potentially flyable area within the Alpine region increased 2170-fold during their first three years of independence. Our work contributes to a predictive understanding of animal movement by presenting ontogeny as a mechanism shaping the realized energy landscape.