TY - JOUR
T1 - A genomic catalog of Earth’s microbiomes
AU - Nayfach, Stephen
AU - Roux, Simon
AU - Seshadri, Rekha
AU - Udwary, Daniel
AU - Varghese, Neha
AU - Schulz, Frederik
AU - Wu, Dongying
AU - Paez-espino, David
AU - Chen, I-min
AU - Huntemann, Marcel
AU - Palaniappan, Krishna
AU - Ladau, Joshua
AU - Mukherjee, Supratim
AU - Reddy, T. B. K.
AU - Nielsen, Torben
AU - Kirton, Edward
AU - Faria, José P.
AU - Edirisinghe, Janaka N.
AU - Henry, Christopher S.
AU - Jungbluth, Sean P.
AU - Chivian, Dylan
AU - Dehal, Paramvir
AU - Wood-charlson, Elisha M.
AU - Arkin, Adam P.
AU - Tringe, Susannah G.
AU - Visel, Axel
AU - Woyke, Tanja
AU - Mouncey, Nigel J.
AU - Ivanova, Natalia N.
AU - Kyrpides, Nikos C.
AU - Eloe-fadrosh, Emiley A.
AU - Gachon, Claire
AU - Badis, Yacine
N1 - The Authors 2020
This paper was originally published under standard Springer Nature copyright (© The Author(s), under exclusive licence to Springer Nature America, Inc.). It is now available as an open-access paper under a Creative Commons Attribution 4.0 International license. The error has been corrected in the print, HTML and PDF versions of the article.
Corresponding author Emiley A. Eloe-fadrosh.
Author consortium- IMG/M Data Consortium
PY - 2020/11/9
Y1 - 2020/11/9
N2 - 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.
AB - 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.
U2 - 10.1038/s41587-020-0718-6
DO - 10.1038/s41587-020-0718-6
M3 - Article
SN - 1087-0156
VL - 2020
JO - Nature Biotechnology
JF - Nature Biotechnology
ER -