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 |
Neha Varghese, Staff Data Scientist |
Maureen Berg, Postdoctoral Fellow | Dariia Vyshenska, Postdoctoral Fellow |
| eaeloefadrosh@lbl.gov (925) 296-5704 |
sroux@lbl.gov | njvarghese@lbl.gov | MBerg@lbl.gov | dariiavyshenska@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. | Neha’s key role is to design, benchmark, and apply bioinformatics software to enable analysis and interpretation of genomic and metagenomic data for JGI’s user community. She also provides support for user science and projects through implementation of advanced analysis pipelines and tools as well as development and implementation of microservices in conjunction with the IMG platform. | 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. | Dariia’s research centers on developing a scalable framework for the analysis of DNA stable isotope probing metagenomics data, allowing culture-independent identification of microbial populations performing specific metabolic functions. Her second project is focused on how microbial metabolic pathways can be used to characterize and compare diverse microbial communities. |
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.
Roux, S. et al. (2017) Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics. Nat. Commun. 8, 858
Schulz, F. et al. (2017) Towards a balanced view of the bacterial tree of life. Microbiome 5(1), 140.
Roux, S. et al. (2019) Minimum Information about an Uncultivated Virus Genome (MIUViG). Nature Biotech. 37, 29–37