At the DOE Joint Genome Institute, I lead the Viral Genomics group where we explore viruses of microbes and their impacts on ecosystems using (mostly) fancy ‘omics tools. Our current projects include the study of viral diversity and virus:host interactions in soil and freshwater environments, along with the development of new bioinformatics tools and experimental protocols to probe and characterize uncultivated viruses. We also assist users of the JGI Metagenome Program with their analysis, including identification of viral sequences, functional annotation, taxonomic classification, etc.
The long-term goal of my research is to understand the ecological and evolutionary drivers of virus:host dynamics in natural microbial communities. This research involves a mix of experimental and computational approaches spanning from the molecular to the ecosystem scale, trying to address fundamental questions like “how do viruses spread and adapt across environments ?”, “how do viruses take over and reprogram microbial cells ?”, and “how do viral infections alter ecosystem processes ?”.
PhD in Microbial Ecology, 2013
Université Blaise Pascal, Clermont-Ferrand II (now Université Clermont Auvergne)
MSc in Data Analysis and Modeling for Life Sciences, 2010
Université Blaise Pascal, Clermont-Ferrand II (now Université Clermont Auvergne)
BSc in Microbiology, 2008
Université Blaise Pascal, Clermont-Ferrand II (now Université Clermont Auvergne)
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Virus-driven alterations of microbial metabolism in soil
We plan to study viral diversity and virus:host interactions in two model systems (East River hillslopes and Green Butte biocrusts) from the single-cell to the ecosystem level. Project goals include (i) characterizing new mechanisms by which viruses transform microbial cells, (ii) investigating how how virus:host interactions are transformed by changes in local environmental conditions, (iii) developing innovative methods to measure viral presence and activity in natural soil systems. 5-year project funded by the
DOE Early Career Research Program, in collaboration with the
Brodie Lab and the
Northen Lab. More information in our latest pre-print -
https://doi.org/10.1101/2023.03.06.531389 (Pictures courtesy of Tamy Swenson & Brodie Lab)
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Computational prediction of virus:host interactions
To help with viromics analysis, we have now developed a tool (iPHoP) to integrate multiple signals of virus-host interactions and enable robust prediction of host genus for many uncultivated phages. Now available on bioconda , and described in the following pre-print:
https://doi.org/10.1101/2022.07.28.501908 .
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Virus:host dynamics in Yellowstone National Park biofilms
We study virus:host dynamics across diel cycles in Octopus and Mushroom springs based on coupled metagenomics, metatranscriptomics, and viral metagenomics, to better understand phage infection triggers and synchronization in natural communities. In collaboration with the
Bhaya Lab. (Picture: USGS / Thomas Brock)
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IMG/VR - Large-scale exploration of uncultivated viral diversity
We routinely mine public genomes, metagenomes, and metatranscriptomes for new viral sequences to progressively build a large and comprehensive genomic catalog of the virosphere. IMG/VR v4 now released ! More into in the
tools section (Viral capsids drawing from Leah Pantea /
http://leahpantea.com)
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Towards a user-friendly viral ecogenomics toolkit
Developing tools to identify, clean, compare, and annotate uncultivated viral genomes (mostly) assembled from metagenomes. Currently gathered in the
MVP pipeline, developed by Clement Coclet. See also the
tools section
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Establishing the foundations of a high-throughput phage foundry
Analyzing and modeling phage diversity and phage:host interactions to better understand how microbiomes can be altered and manipulated through the addition of (engineered) phages. Project led by
Vivek Mutalik