The work of the Eloe-Fadrosh group is focused on developing computational tools and resources to uncover microbial diversity across Earth’s ecosystems.
Our group leverages genome-resolved metagenomics approaches to identify and characterise genomic information from uncultivated microbes. To date, the majority of microorganisms have eluded cultivation and remain accessible only through cultivation-independent molecular approaches. This presents a huge challenge to understanding how diverse microbial communities function and the interactions that impact ecosystem processes. We are addressing this knowledge gap through reconstructing composite genomes from diverse environments, to provide a genome-centric view into evolutionary relationships and the metabolic properties of uncultivated bacteria and archaea.
In close collaboration with the Integrated Microbial Genomes & Microbiomes (IMG/M) platform team, we have developed a scaled workflow to generate metagenomic bins across diverse assembled metagenomes. This work democratises genome-resolved metagenomics for the broader research community to access and analyse data. We have similarly developed comparative analysis tools using average nucleotide identity (ANI) to compare metagenomic bins to each other and to reference isolate genomes, thereby enabling species level grouping. More recently, we have developed a high-throughput ANI screening tool to recruit genomes of interest across thousands of assembled metagenomes for species level genomic tracking.
Beyond using shotgun metagenomics, we are increasingly interested in developing function-driven metagenomic approaches to identify functionally active microbes in the environment. This work leverages stable isotope probing (SIP), which is a powerful approach to link metabolic activity and taxonomic identity of environmental microbes based on enrichment of isotopes (e.g. carbon (13C), nitrogen (15N), oxygen (18O)) incorporated into their DNA. We have developed a standardised laboratory and analysis framework in collaboration with research teams at The University of British Columbia and Lawrence Livermore National Laboratory to explicitly quantify isotopic enrichment on a per-genome basis using synthetic spike-in standards. This new methodological approach to SIP-metagenomics holds the potential to accurately quantify microbial abundance and activity across diverse microbiomes.
Our work at the Department of Energy Joint Genome Institute (DOE JGI) broadly supports the global research community with cutting-edge sequencing and analysis capabilities. Members of the team are also involved in a new initiative, the National Microbiome Data Collaborative (NMDC), funded by the DOE. The NMDC team aims to support a FAIR (making data findable, accessible, interoperable, and reusable) microbiome data sharing network, through infrastructure, data standards, and community building, that addresses pressing challenges in environmental science. The NMDC currently supports data access through three defined Product Initiatives: (1) The NMDC Submission Portal which was designed to lower barriers to capture and adhere to community standards for sample contextual information; (2) the NMDC Data Portal that is designed to enable microbiome data access to integrated multi-omics studies; and (3) the web application NMDC EDGE to provide broad access to the NMDC workflows for all microbiome scientists. In addition to infrastructure development, the NMDC team fosters strong community partnerships, both within and outside of the DOE, as well as developing a set of robust community outreach and training programs including the NMDC Ambassador and Champions programs focusing on early career researchers.
Together, the Eloe-Fadrosh group focuses on computational tool development, research activities to uncover microbial diversity and associated functional capacity, and efforts to democratise microbiome data science to advance microbiome innovation and discovery.