Collaborative Research: ABI Development: VIROME, bioinformatics cyberinfrastructure for the next wave of scientific advancements in microbiome research

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The University of Delaware and the University of Maryland Baltimore are awarded collaborative grants for improvements to a computational tool that will enable a broader community of life scientists, engineers, and geoscientists to access viral metagenomics for the next wave of scientific discoveries in microbiome research. Eight percent of the human genome derives from retroviruses; these viral sequences differentiate the human genome from that of other primates. Within microbial communities, including those living in association with animal hosts, viruses are the most numerically abundant microorganisms, outnumbering all cellular microbes by 10 to 1,000 fold. These natural viral communities are genetically diverse, containing a vast number of novel and unknown genes. In the oceans, viral breakdown of microbial cells contributes to the chemical transformation of carbon and nutrient elements. Ultimately, these transformations impact the productivity of marine ecosystems as well as regional and global climate. While understanding of extant viral diversity and the role of viruses within natural systems is still rudimentary, there is evidence that viruses play critically important roles in the biology, ecology, and evolution of life on earth. This project will enhance a newly developed computational tool, the Viral Informatics Resource for Metagenome Exploration (VIROME) to better facilitate the coming wave of discoveries surrounding the role of viruses in natural systems. In particular, we will pursue three specific developmental goals: 1) leverage sources of long-length DNA sequence data to improve the quality of the information output from the VIROME bioinformatics pipeline; 2) utilize the VIROME gene classification scheme to develop a sustainable database of unknown viral genes, i.e., viral genetic dark matter; and 3) advance the sustainability of the VIROME resource through virtualization of its underlying computational workflow.Given that viruses impact life on earth over evolutionary time and global scales, further development of VIROME will benefit researchers in the life sciences, engineering, and geosciences. The project?s impact will be enhanced by directly training graduate and undergraduate students and by conducting twice yearly workshops on the use of VIROME for the analysis of viral metagenome sequence data. The project will also advance public understanding of the emerging scientific consensus surrounding the nuanced and critical impacts of viruses on cellular life by hosting an informational booth at Ag Day, a public outreach event reaching thousands of residents in the quad state vicinity of the University of Delaware, Newark campus (DE, MD, PA, & NJ). Lastly, the team will reach out to K-12 students by hosting an annual ?Get to know viruses? STEM program at the Delaware Biotechnology Institute for groups of Cub Scouts and Girl Scouts in the Newark, Delaware area.