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Solving the Virome

A marine bacteriophage - just one example among the vast, ecologically influential Earth virome. (Image: Sullivan Lab)

By Shelley Littin, CyVerse

CyVerse community members are developing novel tools to help overcome computational challenges faced by the viral ecology community.

“Microbes are recently recognized to be important in the environment as well as human health, behavior and disease. Probably equally important are the viruses that infect such microbes,” said Matthew Sullivan, an assistant professor at The Ohio State University (OSU). “The lack of analysis tools and centralized databases to study viruses has bottlenecked scientific advances.”

Ben Bolduc is a postdoctoral researcher in the Sullivan Lab who is working to alleviate that bottleneck. Bolduc develops tools for viral ecology and creates instructional videos to help provide viral ecologists with the resources they need to manage computational challenges.

Bolduc’s tools, and other resources, will be available through iVirus, a CyVerse-supported web-based platform for viral ecologists to collaborate and share resources and knowledge to spur scientific advances. iVirus was created by Sullivan and colleagues and modeled after iMicrobe, a similar community that serves microbiologists and is led by Bonnie Hurwitz, an assistant professor of biosystems engineering at the University of Arizona. Hurwitz also co-leads iVirus.

“iVirus is a suite of tools designed for viral ecology and metagenomics, contained within CyVerse,” Bolduc said.

To help launch the iVirus community platform, the Sullivan Lab recently hosted a two-and-a-half-day workshop at OSU, co-organized by Bolduc along with Hurwitz, and Simon Roux and Jennifer Brum, who are also postdoctoral researchers in the Sullivan Lab. The workshop was attended by researchers from a dozen U.S.-based institutions, studying ocean, lake, and hot spring viromes, as well as microbial ecology and the human gut, among other fields.

“The first two days involved going through the apps that are available in iVirus and working with the entire suite of functions for each app, as well as how to connect the apps and integrate them to solve a problem using a sample dataset,” Bolduc said. “Some researchers brought their own data that they uploaded to CyVerse, and they were working on their data during the workshop.”

The final half-day of the workshop focused on ecological statistics, and how to conclude an analysis with the iVirus tools. “I think participants were really excited about the possibilities of the iVirus platform. The idea was that participants will bring these new skills to their home institutions and share the knowledge with others.”

Maria Consuelo Gazitua Zavala, a post doctoral researcher at OSU’s department of microbiology, attended the workshop and noted that she appreciated the comprehensive approach. “I will definitely use every tool taught in this workshop for my research in viromics of the oxygen minimum zones.”

“Beyond that,” Zavala added, “there are many apps in CyVerse that can be used for microbial community analyses, and that makes things much easier for people unfamiliar with bioinformatics. I would like to highlight the effort that the developers are doing to achieve this ultimate goal, developing and updating the apps, and quickly responding if issues arise.”

“Having dealt with this kind of data really makes me appreciate what they have put together. I think it will be a very useful tool for the scientific community,” added Maria del Pilar Manrique, a graduate student at Montana State University who attended the workshop.

While successful in its own right, this workshop was intended as a pilot project for a much larger, international workshop to be hosted by the Sullivan Lab at OSU in summer of 2017.

Bolduc speculates that by 2017 the lab will have doubled the number of apps available through iVirus. He is also working on creating animated guides and videos to provide step-by-step instruction on how to use the tools for different research environments.

Partial support for the workshop was provided by the Gordon and Betty Moore Foundation Marine Microbiology Initiative. Participating institutions included Georgia Institute of Technology, the University of Tennessee at Knoxville, the University of South Florida, Woods Hole Oceanographic Institution, the University of Chicago, the University of Illinois, the University of Michigan, Montana State University, and the Ohio State University.