GEMs

A genomic catalog of Earth’s microbiomes

Dataset

A catalog of 52,515 metagenome-assembled genomes from over 10,450 metagenomes collected from diverse microbiomes to capture extant microbial metabolic and functional potential. MAGs from the GEMs catalog all meet the medium-quality level of the MIMAG standard (mean completeness = 83%, mean contamination = 1.3%), and include 9,143 assigned as high-quality based on the presence of a near-full complement of rRNAs, tRNAs, and single-copy protein coding genes.

The entire genome catalog and associated data is available at: https://portal.nersc.gov/GEM/

Results

Exploration of the genomic landscape of uncultivated bacteria and archaea has shed light on the ecological and evolutionary principles at play in natural ecosystems. The reconstruction of genomes directly from the environment is a powerful approach enabled by advances in sequencing and computational technologies. Here we present a catalog of 52,515 metagenome-assembled genomes from over 10,000 metagenomes collected from diverse microbiomes to capture extant microbial metabolic and functional potential. We identify 12,556 novel candidate species, spanning 135 phyla, which increase the phylogenetic diversity of bacteria and archaea by 44%. The collection further enables host-viral linkage prediction, and a view into the distribution of lysogenic viruses. This Resource underscores the value of leveraging genome-centric approaches to reveal genomic properties of uncultivated microbes and their impacts on ecosystem processes.

Data Usage Policy

The MAGs contained in the GEM data bundle are free to use. Underlying metagenomes are protected by JGI data release and utilization policies found here, and we encourage contacting PIs for any planned analyses or publications that may overlap with existing project goals.