A genomic catalog of Earth’s microbiomes

Stephen Nayfach, Simon Roux, Rekha Seshadri, Daniel Udwary, Neha Varghese, Frederik Schulz, Dongying Wu, David Paez-Espino, I. Min Chen, Marcel Huntemann, Krishna Palaniappan, Joshua Ladau, Supratim Mukherjee, T. B.K. Reddy, Torben Nielsen, Edward Kirton, José P. Faria, Janaka N. Edirisinghe, Christopher S. Henry, Sean P. JungbluthDylan Chivian, Paramvir Dehal, Elisha M. Wood-Charlson, Adam P. Arkin, Susannah G. Tringe, Axel Visel, Helena Abreu, Silvia G. Acinas, Eric Allen, Michelle A. Allen, Lauren V. Alteio, Gary Andersen, Alexandre M. Anesio, Graeme Attwood, Viridiana Avila-Magaña, Yacine Badis, Jake Bailey, Brett Baker, Petr Baldrian, Hazel A. Barton, David A.C. Beck, Eric D. Becraft, Harry R. Beller, J. Michael Beman, Rizlan Bernier-Latmani, Timothy D. Berry, Anthony Bertagnolli, Stefan Bertilsson, Jennifer M. Bhatnagar, Jordan T. Bird, Jeffrey L. Blanchard, Sara E. Blumer-Schuette, Brendan Bohannan, Mikayla A. Borton, Allyson Brady, Susan H. Brawley, Juliet Brodie, Steven Brown, Jennifer R. Brum, Andreas Brune, Donald A. Bryant, Alison Buchan, Daniel H. Buckley, Joy Buongiorno, Hinsby Cadillo-Quiroz, Sean M. Caffrey, Ashley N. Campbell, Barbara Campbell, Stephanie Carr, Jo Lynn Carroll, S. Craig Cary, Anna M. Cates, Rose Ann Cattolico, Ricardo Cavicchioli, Ludmila Chistoserdova, Maureen L. Coleman, Philippe Constant, Jonathan M. Conway, Walter P. Mac Cormack, Sean Crowe, Byron Crump, Cameron Currie, Rebecca Daly, Kristen M. DeAngelis, Vincent Denef, Stuart E. Denman, Adey Desta, Hebe Dionisi, Jeremy Dodsworth, Nina Dombrowski, Timothy Donohue, Mark Dopson, Timothy Driscoll, Peter Dunfield, Christopher L. Dupont, Katherine A. Dynarski, Virginia Edgcomb, Elizabeth A. Edwards, Mostafa S. Elshahed, Israel Figueroa, Beverly Flood, Nathaniel Fortney, Caroline S. Fortunato, Christopher Francis, Claire M.M. Gachon, Sarahi L. Garcia, Maria C. Gazitua, Terry Gentry, Lena Gerwick, Javad Gharechahi, Peter Girguis, John Gladden, Mary Gradoville, Stephen E. Grasby, Kelly Gravuer, Christen L. Grettenberger, Robert J. Gruninger, Jiarong Guo, Mussie Y. Habteselassie, Steven J. Hallam, Roland Hatzenpichler, Bela Hausmann, Terry C. Hazen, Brian Hedlund, Cynthia Henny, Lydie Herfort, Maria Hernandez, Olivia S. Hershey, Matthias Hess, Emily B. Hollister, Laura A. Hug, Dana Hunt, Janet Jansson, Jessica Jarett, Vitaly V. Kadnikov, Charlene Kelly, Robert Kelly, William Kelly, Cheryl A. Kerfeld, Jeff Kimbrel, Jonathan L. Klassen, Konstantinos T. Konstantinidis, Laura L. Lee, Wen Jun Li, Andrew J. Loder, Alexander Loy, Mariana Lozada, Barbara MacGregor, Cara Magnabosco, Aline Maria da Silva, R. Michael McKay, Katherine McMahon, Chris S. McSweeney, Mónica Medina, Laura Meredith, Jessica Mizzi, Thomas Mock, Lily Momper, Mary Ann Moran, Connor Morgan-Lang, Duane Moser, Gerard Muyzer, David Myrold, Maisie Nash, Camilla L. Nesbø, Anthony P. Neumann, Rebecca B. Neumann, Daniel Noguera, Trent Northen, Jeanette Norton, Brent Nowinski, Klaus Nüsslein, Michelle A. O’Malley, Rafael S. Oliveira, Valeria Maia de Oliveira, Tullis Onstott, Jay Osvatic, Yang Ouyang, Maria Pachiadaki, Jacob Parnell, Laila P. Partida-Martinez, Kabir G. Peay, Dale Pelletier, Xuefeng Peng, Michael Pester, Jennifer Pett-Ridge, Sari Peura, Petra Pjevac, Alvaro M. Plominsky, Anja Poehlein, Phillip B. Pope, Nikolai Ravin, Molly C. Redmond, Rebecca Reiss, Virginia Rich, Christian Rinke, Jorge L.Mazza Rodrigues, William Rodriguez-Reillo, Karen Rossmassler, Joshua Sackett, Ghasem Hosseini Salekdeh, Scott Saleska, Matthew Scarborough, Daniel Schachtman, Christopher W. Schadt, Matthew Schrenk, Alexander Sczyrba, Aditi Sengupta, Joao C. Setubal, Ashley Shade, Christine Sharp, David H. Sherman, Olga V. Shubenkova, Isabel Natalia Sierra-Garcia, Rachel Simister, Holly Simon, Sara Sjöling, Joan Slonczewski, Rafael Soares Correa de Souza, John R. Spear, James C. Stegen, Ramunas Stepanauskas, Frank Stewart, Garret Suen, Matthew Sullivan, Dawn Sumner, Brandon K. Swan, Wesley Swingley, Jonathan Tarn, Gordon T. Taylor, Hanno Teeling, Memory Tekere, Andreas Teske, Torsten Thomas, Cameron Thrash, James Tiedje, Claire S. Ting, Benjamin Tully, Gene Tyson, Osvlado Ulloa, David L. Valentine, Marc W. Van Goethem, Jean VanderGheynst, Tobin J. Verbeke, John Vollmers, Aurèle Vuillemin, Nicholas B. Waldo, David A. Walsh, Bart C. Weimer, Thea Whitman, Paul van der Wielen, Michael Wilkins, Timothy J. Williams, Ben Woodcroft, Jamie Woolet, Kelly Wrighton, Jun Ye, Erica B. Young, Noha H. Youssef, Feiqiao Brian Yu, Tamara I. Zemskaya, Ryan Ziels, Tanja Woyke, Nigel J. Mouncey, Natalia N. Ivanova, Nikos C. Kyrpides, Emiley A. Eloe-Fadrosh

Research output: Contribution to journalArticlepeer-review

417 Scopus citations

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.
Original languageEnglish (US)
Pages (from-to)499-509
Number of pages11
JournalNature biotechnology
Volume39
Issue number4
DOIs
StatePublished - Apr 1 2021
Externally publishedYes

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