Research in the Eloe-Fadrosh group focuses on using genome-resolved metagenomic approaches to identify and characterize genomic information from uncultivated microbes and viruses. We develop computational approaches to sift through thousands of metagenomes for signatures of viruses and novel microbial lineages, and reconstruct metabolic properties encoded within those genomes. Our aim is to more fully capture microbial and viral diversity, leading to a better understanding of microbial communities and ecosystem function.
Research Team
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| Emiley Eloe-Fadrosh, PI | Simon Roux, Research Scientist | Joshua Ladau, Project Scientist | Sean Jungbluth, Postdoctoral Fellow | Maureen Berg, Postdoctoral Fellow |
| eaeloefadrosh@lbl.gov (925) 296-5704 |
sroux@lbl.gov | JLadau@lbl.gov | sjungbluth@lbl.gov | MBerg@lbl.gov |
| More about Emiley. | Simon’s research interests revolve around viral diversity in the environment and the impacts of virus-host interactions on individual microbes and on ecosystems. His work includes the development of bioinformatics tools for viral datasets, the analysis and meta-analysis of viral genomes assembled from metagenomes, and the design of new approaches to investigate virus-host interactions in nature. | Josh’s research adapts and develops theory and ideas from ecology to Earth’s microbial systems. His research aims to adapt macroecology and biogeography to microbial systems to understand the ecological processes underpinning microbial systems, and to forecast the behavior of microbial systems at microscopic to global scales. | Sean is exploring the phylogenomic diversity of novel microbial lineages with the goal of uncovering major taxonomic “blind spots” in the tree of life. | Maureen is currently developing new high-resolution and high-throughput methods to link uncultivated viruses to their host. With these new methods, she hopes to expand our understanding of the roles that viruses play in their ecosystems, particularly in freshwater ecosystems. |
Selected Publications
Roux S, et al. (2015) Viral dark matter and virus-host interactions resolved from publically available microbial genomes. Elife. 4:e08490.
Roux S, et al. (2016) Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses. Nature. 537:689-93.
Eloe-Fadrosh EA, et al. (2016) Metagenomics uncovers gaps in amplicon-based detection of microbial diversity. Nat Microbiol. 15032
Eloe-Fadrosh EA, et al. (2016) Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs. Nat Commun. 7:10476
Kyrpides NC. et al. (2016) Microbiome Data Science: Understanding Our Microbial Planet. Trends in Microbiology. 24(6):425-7.
Paez-Espino, D. et al. (2016) Uncovering Earth’s virome. Nature. 536:425-30.
Jungbluth SP, et al. (2017) Metagenome sequencing and 98 microbial genomes from Juan de Fuca Ridge flank subsurface fluids. Sci Data. 4:170037.
Nigro OD, et al. (2017) Viruses in the oceanic basement. mBio. 8:e02129-16.
Roux, S. et al. (2017) Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics. Nat. Commun. 8, 858