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. The Environmental Genomics group also hosts the Viral Genomics group.
Research Team
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| Emiley Eloe-Fadrosh, PI | Neha Varghese, Staff Data Scientist |
Dariia Vyshenska, Postdoctoral Fellow |
| eaeloefadrosh@lbl.gov (925) 296-5704 |
njvarghese@lbl.gov | dariiavyshenska@lbl.gov |
| More about Emiley. | 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. | 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