A genomic catalog of Earth’s microbiomes

著者: Stephen Nayfach, Simon Roux, R. Seshadri, Daniel Udwary, Neha Varghese, Frederik Schulz, Dongying Wu, David Páez-Espino, I-Min A. 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. Jungbluth, Dylan 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 L. Andersen, Alexandre M. B. Anesio, Graeme T. Attwood, Viridiana Avila‐Magaña, Yacine Badis, Jake V. Bailey, Brett J. Baker, Petr Baldrián, Hazel A. Barton, David A. C. Beck, Eric D. Becraft, Harry R. Beller, J. Michael Beman, Rizlan Bernier‐Latmani, Timothy D. Berry, Anthony D. Bertagnolli, Stefan Bertilsson, Jennifer Bhatnagar, Jordan T. Bird, Jeffrey L. Blanchard, Sara E. Blumer‐Schuette, Brendan J. M. Bohannan, Mikayla A. Borton, Allyson Brady, Susan H. Brawley, Juliet Brodie, Steven D. Brown, Jennifer R. Brum, Andreas Brune, Donald A. Bryant, Alison Buchan, Daniel H. Buckley, Joy Buongiorno, Hinsby Cadillo‐Quiroz, Sean M. Caffrey, Ashley Campbell, Barbara J. Campbell, Stephanie Carr, JoLynn 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 A. Crowe, Byron C. Crump, Cameron R. Currie, Rebecca Daly, Kristen M. DeAngelis, Vincent J. Denef, Stuart E. Denman, Adey Feleke Desta, Hebe M. Dionisi, Jeremy A. Dodsworth, Nina Dombrowski, Timothy J. Donohue, Mark Dopson, Timothy Driscoll, Peter F. Dunfield, Christopher L. Dupont, Katherine A. Dynarski, Virginia P. Edgcomb, Elizabeth A. Edwards, Mostafa S. Elshahed, Israel Figueroa, Beverly E. Flood, Nathaniel W. Fortney, Caroline S. Fortunato, Christopher Francis, Claire M. M. Gachon, Sarahi L. Garcia, María Consuelo Gazitúa, Terry J. Gentry, Lena Gerwick, Javad Gharechahi, Peter Girguis, John M. Gladden, Mary R. Gradoville, Stephen E. Grasby, Kelly Gravuer, Christen L. Grettenberger, Robert J. Gruninger, Jiarong Guo, Mussie Y. Habteselassie, Steven Hallam, Roland Hatzenpichler, Bela Hausmann, Terry C. Hazen, Brian P. Hedlund, Cynthia Henny, Lydie Herfort, Maria Hernandez, Olivia S. Hershey, Matthias Hess, Emily B. Hollister, Laura Hug, Dana E. Hunt, Janet Jansson, Jessica Jarett, Vitaly V. Kadnikov, Charlene N. Kelly, Robert M. Kelly, William J. Kelly, Cheryl A. Kerfeld, Jeffrey A. Kimbrel, Jonathan L. Klassen, Konstantinos T. Konstantinidis, Laura L. Lee, Wen‐Jun Li, Andrew J. Loder, Alexander Loy, Mariana Lozada, Barbara J. MacGregor, Cara Magnabosco, Aline Maria da Silva, R. Michael L. McKay, Katherine D. McMahon, Christopher S. McSweeney, Mónica Medina, Laura Meredith, Jessica E. Mizzi, Thomas Möck, Lily Momper, Mary Ann Moran, Connor Morgan‐Lang, Duane P. Moser, Gerard Muyzer, David D. Myrold, Maisie Nash, Camilla Nesbø, Anthony P. Neumann, Rebecca B. Neumann, Daniel R. Noguera, Trent R. Northen, Jeanette M. Norton, Brent Nowinski, Klaus Nüsslein, Michelle O’Malley, Rafael S. Oliveira, Valéria Maia de Oliveira, T. C. Onstott, Jay Osvatic, Yang Ouyang, Maria Pachiadaki, Jacob Parnell, Laila P. Partida‐Martínez, Kabir Peay, Dale A. Pelletier, Xuefeng Peng, Michael Pester, Jennifer Pett‐Ridge, Sari Peura, Petra Pjevac, Alvaro M. Plominsky, Anja Poehlein, Phillip B. Pope, Nikolai V. Ravin, Molly C. Redmond, Rebecca A. Reiss, Virginia I. Rich, Christian Rinke, Jorge L. Mazza Rodrigues, William Rodriguez-Reillo, Karen Rossmassler, Joshua Sackett, Ghasem Hosseini Salekdeh, S. R. Saleska, Matthew Scarborough, Daniel P. Schachtman, Christopher W. Schadt, Matthew Schrenk, Alexander Sczyrba, Aditi Sengupta, João Carlos Setúbal, Ashley Shade, Christine Sharp, David H. Sherman, О. V. Shubenkova, Isabel Natalia Sierra-Garcia, Rachel L. Simister, Holly M. Simon, Sara Sjöling, Joan L. Slonczewski, Rafael Soares Correa de Souza, John R. Spear, James Stegen, Ramūnas Stepanauskas, Frank J. Stewart, Garret Suen, Matthew B. Sullivan, D. Y. Sumner, Brandon K. Swan, Wesley D. Swingley, Jonathan Tarn, Gordon T. Taylor, Hanno Teeling, Memory Tekere, Andreas Teske, Torsten Thomas, Cameron Thrash, James M. Tiedje, Claire S. Ting, Benjamin Tully, Gene W. Tyson, Osvlado Ulloa, David L. Valentine, Marc W. Van Goethem, Jean S. VanderGheynst, Tobin J. Verbeke, John Vollmers, Aurèle Vuillemin, Nicholas B. Waldo, David A. Walsh, Bart C. Weimer, Thea Whitman, Paul W. J. J. van der Wielen, Michael J. Wilkins, Timothy J. Williams, Ben J. Woodcroft, Jamie Woolet, Kelly Wrighton, Jun Ye, Erica B. Young, Noha H. Youssef, Feiqiao Brian Yu, Т. I. Zemskaya, Ryan Ziels, Tanja Woyke, Nigel J. Mouncey, Natalia Ivanova, Nikos C. Kyrpides, Emiley A. Eloe‐Fadrosh - Nature Biotechnology 2020 被引用: 973

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.