Today, the U.S. Department of Energy Joint Genome Institute announced a new project, the Genomes from Earth’s Microbiomes, that pulled together the research of more than 200 scientists and researchers to increase the known bacteria and archaea by 44%.
Among those researches was UMass Dartmouth Dean of the College of Engineering and interim Dean of the School for Marine Science & Technology Jean VanderGheynst.
Despite advances in sequencing technologies and computational methods in the past decade, researchers have uncovered genomes for just a small fraction of Earth's microbial diversity. Because most microbes cannot be cultivated under laboratory conditions, their genomes cannot be sequenced using traditional approaches. Identifying and characterizing the planet’s microbial diversity is key to understanding the roles of microorganisms in regulating nutrient cycles, as well as gaining insights into potential applications they may have in a wide range of research fields.
A public repository of 52,515 microbial draft genomes generated from environmental samples around the world, expanding the known diversity of bacteria and archaea by 44%, is now available in Nature Biotechnology. Known as the GEM (Genomes from Earth’s Microbiomes) catalog, this work results from a collaboration involving more than 200 scientists, researchers at the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a DOE Office of Science User Facility located at Lawrence Berkeley National Laboratory (Berkeley Lab), and the DOE Systems Biology Knowledgebase (KBase).
VanderGheynst’s contributions are related to her research on the discovery of industrial enzymes from compost microbiomes for the conversion of plant biomass to biofuels.
Metagenomics is the study of the microbial communities in the environmental samples without needing to isolate individual organisms, using various methods for processing, sequencing, and analysis. "Using a technique called metagenome binning, we were able to reconstruct thousands of metagenome-assembled genomes (MAGs) directly from sequenced environmental samples without needing to cultivate the microbes in the lab," noted Stephen Nayfach, the study's first author and research scientist in Nikos Kyrpides' Microbiome Data Science group. “What makes this study really stand out from previous efforts is the remarkable environmental diversity of the samples we analyzed.”
Emiley Eloe-Fadrosh, head of the JGI Metagenome Program and senior author on the study elaborated on Nayfach’s comments. “This study was designed to encompass the broadest and most diverse range of samples and environments, including natural and agricultural soils, human- and animal-host associated, and ocean and other aquatic environments - that's pretty remarkable.”