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 | Matthew Kellom, Microbiome Research Scientist | Neha Varghese, Staff Data Scientist |
Juan C. Villada |
| [email protected] (925) 296-5704 |
[email protected] | [email protected] | [email protected] |
| More about Emiley. | Matt is broadly interested in the interactions between microbial life and environment, and using metagenomics to study these complex natural systems. Microbial communities living in hard-to-reach places that are considered to be inhospitable to humans are of particular interest. Matt also supports various CSP and FICUS user projects for the Metagenome Program. | 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. | Juan is interested in understanding the evolution of microbial populations and their metabolism using global-scale metagenomics. He currently works on benchmarking, building, and deploying computational pipelines, at the interface of evolutionary genomics and systems biology, to extract high-quality metagenome-assembled genomes and identify the biochemical roles of microbial communities. |
Selected Publications
- Nayfach S et al. A Genomic Catalog of Earth’s Microbiomes. Nature Biotechnology. 2020 Nov 9.
- Vyshenska, Dariia et al. (2023) A standardized quantitative analysis strategy for stable isotope probing metagenomics. mSystems , e01280-22. 10.1128/msystems.01280-22
- Clum, A. et al. (2021) DOE JGI metagenome workflow. mSystems 6(3). 10.1128/MSYSTEMS.00804-20
- Nayfach S et al. A Genomic Catalog of Earth’s Microbiomes. Nature Biotechnology. 2020 Nov 9. doi: 10.1038/s41587-020-0718-6.
- Ladau, J. et al. (2019) Spatial, Temporal, and Phylogenetic Scales of Microbial Ecology. Trends Microbiol. 10.1016/j.tim.2019.03.003
- Eloe-Fadrosh, Emiley A. et al. (2016) Metagenomics uncovers gaps in amplicon-based detection of microbial diversity. Nature Microbiology , 15032. 10.1038/nmicrobiol.2015.32