A genomic catalog of Earth's microbiomes

被引：517

作者：

Nayfach, Stephen ^{[1
]}

Roux, Simon ^{[1
]}

Seshadri, Rekha ^{[1
]}

Udwary, Daniel ^{[1
]}

Varghese, Neha ^{[1
]}

Schulz, Frederik ^{[1
]}

Wu, Dongying ^{[1
]}

Paez-Espino, David ^{[1
]}

Chen, I-Min ^{[1
]}

Huntemann, Marcel ^{[1
]}

Palaniappan, Krishna ^{[1
]}

Ladau, Joshua ^{[1
]}

Mukherjee, Supratim ^{[1
]}

Reddy, T. B. K. ^{[1
]}

Nielsen, Torben ^{[1
]}

Kirton, Edward ^{[1
]}

Faria, Jose P. ^{[2
]}

Edirisinghe, Janaka N. ^{[2
]}

Henry, Christopher S. ^{[2
]}

Jungbluth, Sean P. ^{[1
,3
]}

Chivian, Dylan ^{[3
]}

Dehal, Paramvir ^{[3
]}

Wood-Charlson, Elisha M. ^{[3
]}

Arkin, Adam P. ^{[3
]}

Tringe, Susannah G. ^{[1
]}

Visel, Axel ^{[1
]}

Woyke, Tanja ^{[1
]}

Mouncey, Nigel J. ^{[1
]}

Ivanova, Natalia N. ^{[1
]}

Kyrpides, Nikos C. ^{[1
]}

Eloe-Fadrosh, Emiley A. ^{[1
]}

机构：

[1] US DOE, Berkeley, CA 94720 USA

[2] Argonne Natl Lab, 9700 S Cass Ave, Argonne, IL 60439 USA

[3] Lawrence Berkeley Natl Lab, Berkeley, CA USA

来源：

NATURE BIOTECHNOLOGY | 2021年 / 39卷 / 04期

关键词：

READ ALIGNMENT; METABOLISM; PHYLOGENY; BACTERIAL; ORIGINS; BIOLOGY; TREE;

D O I：

10.1038/s41587-020-0718-6

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

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. Cataloging microbial genomes from Earth's environments expands the known phylogenetic diversity of bacteria and archaea.

引用

页码：499 / 509

页数：11

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