A genomic catalog of Earth’s microbiomes

TLDR

The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host‑associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth’s continents and oceans, including human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. The catalog contains 52,515 metagenome‑assembled genomes, including 12,556 novel species‑level OTUs across 135 phyla, expanding bacterial and archaeal phylogenetic diversity by 44 % and providing a freely available resource for comparative analyses, interactive exploration, metabolic modeling, and bulk download, while demonstrating its utility for secondary‑metabolite biosynthetic potential, new host–virus linkages, and revealing genomic traits of uncultivated microbes that influence ecosystem processes.

Abstract

Abstract The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth’s continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic diversity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes.