Viral Genomics Group

While an ever-increasing number of phage and virus genomes have been assembled and reported from metagenomes, our understanding of the impacts of these viruses on microbiome processes is still limited. One key challenge is to complement diversity surveys (Who is there?) with activity measurements (Who is active when/where, and how?). The JGI Viral Genomics group attempts to address this question in natural soil ecosystems by combining metagenomics with other omics approaches, including especially metatranscriptomics, to better highlight and ultimately predict the main viral impacts in these microbiomes.

Multiomics approaches such as metagenomics and metatranscriptomics provide invaluable information on virus diversity and activity in microbial communities, however they can only provide a signal aggregated at the population level. To fully characterize the range of virus-host interactions occurring in microbiomes, these omics data must be complemented with single-cell resolution assays that can be targeted towards specific phages and/or hosts. To that end, the JGI Viral Genomics group is exploring different approaches including laboratory incubations and microfluidics methods to better investigate the host range of phages in nature, as well as the molecular triggers driving phage infection dynamics.

The JGI Viral Genomics group is leading and/or contributing to the development and maintenance of a number of viromics tools and resources. The main focus of these resource development efforts currently include: 

• in silico host prediction for uncultivated phages
• improved annotation and functional prediction for phage proteins
• user-friendly integrated pipelines (MVP) and databases (IMG/VR) for viromics analyses

• Coclet C, Camargo AP, Roux S. (2024) MVP: a modular viromics pipeline to identify, filter, cluster, annotate, and bin viruses from metagenomes. mSystems 9:e00888-24. https://doi.org/10.1128/msystems.00888-24
• Coclet, C., Sorensen, P.O., Karaoz, U. et al. (2023) Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem. Microbiome 11, 237. https://doi.org/10.1186/s40168-023-01666-z
• Neri U., Wolf, Y., Roux S., Camargo A.P., et al. (2022) Expansion of the global RNA virome reveals diverse clades of bacteriophages. Cell 185, 21. https://doi.org/10.1016/j.cell.2022.08.023
• Roux, S., Paul, B.G., Bagby, S.C. et al. (2021) Ecology and molecular targets of hypermutation in the global microbiome. Nat Commun 12, 3076. https://doi.org/10.1038/s41467-021-23402-7
• Roux, S. and Emerson, J. (2022) Diversity in the soil virosphere: to infinity and beyond? Trends in Microbiology. 30, 11. https://doi.org/10.1016/j.tim.2022.05.003
• Berg, M. et al. (2021) Host population diversity as a driver of viral infection cycle in wild populations of green sulfur bacteria with long standing virus-host interactions. ISME J. 15, 1569–1584. https://doi.org/10.1038/s41396-020-00870-1
• Roux, S. et al. (2019) Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth’s biomes. Nature Microbiology. 4, 1895–1906. https://doi.org/10.1038/s41564-019-0510-x
• Roux, S. et al. (2019) Minimum Information about an Uncultivated Virus Genome (MIUViG). Nature Biotech. 37, 29–37. https://doi.org/10.1038/nbt.4306

• Postdocs:
  • Clement Coclet (JGI Postdoc)
• Interns:
  • Delphine Tripp (MIT, SCGSR Program)
  • Tatiana Demina (University of Helsinki)
  • Asier Fernández-Pato (University Medical Center Groningen)
  • Caroline Winther-Have (University of Copenhagen)
  • Dimitri Boeckaerts (Ghent University, Fulbright Program)
  • Thomas Pitot (University Laval)
  • Ellis Torrance (University of North Carolina Greensboro, CSGF Program)
  • Dean Vik (Ohio State University, SCGSR Program)
  • Marina Vila-Nistal (University of Alicante)
  • Gary Trubl (Ohio State University, SCGSR Program)