Exploring the virus world, inside out
Did you know that your body contains 100-fold more viruses than your own cells? Luckily, majority of these viruses infect only microbes, including archaea, bacteria and fungi. In fact, these natural predators of the microbial world are the most dominant biological entities found on earth and are increasingly recognized as key enablers in soil, ocean and human ecosystems.
Scientists are investigating contributions of microbe associated viruses in modulating microbial community structure, function and evolution, pathogen limitation, mammalian immunity and global biogeochemical cycles.
Viromics: revolutionizing our understanding of viral impact
Viromics leverage high-throughput sequence-based tools to study viral genomic content in an environment and have revolutionized our understanding of the impact of microbial viruses on mammalian health and environment.
Recently, nearly 60 research trainees from across the world attended a viromics workshop hosted by leading marine virologist Prof. Matthew B. Sullivan at Ohio State University to learn about the computational tools available to identify viruses in complex genomic datasets and predict their biological functions.
During this interactive training with instructors Ben Bolduc (OSU), Simon Roux (JGI), Arvind Varsani (ASU), Bonnie Hurwitz (U Arizona), and Ben Temperton (U Exeter), the trainees were exposed to resources like iVirus and IMG/VR.
iVirus: a set of bioinformatics apps geared toward viruses
iVirus, developed by the collaborative efforts of Sullivan and Hurwitz labs, offers diverse bioinformatic applications or “apps” through the CyVerse Discovery Environment cyberinfrastructure, geared to facilitate virus discovery in diverse environmental specimens.
The OSU viromics workshop trainees gained first-hand experience in using iVirus apps to assemble and annotate virus genomes, predict structure, composition and relative abundance of viral communities in metagenomic datasets.
Making bioinformatics friendlier to non-computational biologists
The availability of community-friendly apps in iVirus and accessibility to CyVerse supercomputing nodes allow wet-lab scientists to analyze viral ecological datasets without necessarily learning to write command line codes from scratch or completely rely on computational biologists to analyze high-throughput sequencing data.
Additionally, the workshop participants also learned how use IMG/VR’s interactive virus database to detect viruses in their own data and predict host specificity of those viruses.
Concluding remarks
Together, the OSU viromics mini-symposium provided an exciting opportunity to the next-generation viral ecologists to get well-acquainted with the state-of-the-art tools in viral ecology, inspired them to leverage apps in iVirus to customize their own viromics data analysis pipeline and opened doors for future collaborations to build and improve resources to explore biological functions of environmental viruses.
References
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- Bolduc B, Youens-Clark K, Roux S, Hurwitz BL, Sullivan MB. 2017. iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure. ISME J 11:7-14. https://doi.org/10.1038/ismej.2016.89
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- Paez-Espino D, Pavlopoulos GA, Ivanova NN, Kyrpides NC. 2017. Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data. Nat Protoc 12:1673-1682. https://doi.org/10.1038/nprot.2017.063
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