A genomic catalog of Earth’s microbiomes
Stephen Nayfach(Joint Genome Institute), Simon Roux(Joint Genome Institute), R. Seshadri(Joint Genome Institute), Daniel Udwary(Joint Genome Institute), Neha Varghese(Joint Genome Institute), Frederik Schulz(Joint Genome Institute), Dongying Wu(Joint Genome Institute), David Páez-Espino(Joint Genome Institute), I-Min A. Chen(Joint Genome Institute), Marcel Huntemann(Joint Genome Institute), Krishna Palaniappan(Joint Genome Institute), Joshua Ladau(Joint Genome Institute), Supratim Mukherjee(Joint Genome Institute), T. B. K. Reddy(Joint Genome Institute), Torben Nielsen(Joint Genome Institute), Edward Kirton(Joint Genome Institute), José P. Faria(Argonne National Laboratory), Janaka N. Edirisinghe(Argonne National Laboratory), Christopher S. Henry(Argonne National Laboratory), Sean P. Jungbluth(Lawrence Berkeley National Laboratory), Dylan Chivian(Lawrence Berkeley National Laboratory), Paramvir Dehal(Lawrence Berkeley National Laboratory), Elisha M. Wood‐Charlson(Lawrence Berkeley National Laboratory), Adam P. Arkin(Lawrence Berkeley National Laboratory), Susannah G. Tringe(Joint Genome Institute), Axel Visel(Joint Genome Institute), Helena Abreu(AlgaPlus (Portugal)), Silvia G. Acinas(Institut de Ciències del Mar), Eric Allen(Scripps Institution of Oceanography), Michelle A. Allen(UNSW Sydney), Lauren V. Alteio(University of Vienna), Gary L. Andersen(Lawrence Berkeley National Laboratory), Alexandre M. B. Anesio(Aarhus University), Graeme T. Attwood(AgResearch), Viridiana Avila‐Magaña(Pennsylvania State University), Yacine Badis(Scottish Association For Marine Science), Jake V. Bailey(University of Minnesota), Brett J. Baker(The University of Texas at Austin), Petr Baldrián(Czech Academy of Sciences), Hazel A. Barton(University of Akron), David A. C. Beck(University of Washington), Eric D. Becraft(University of North Alabama), Harry R. Beller(Lawrence Berkeley National Laboratory), J. Michael Beman(University of California, Merced), Rizlan Bernier‐Latmani(École Polytechnique Fédérale de Lausanne), Timothy D. Berry(University of Wisconsin–Madison), Anthony D. Bertagnolli(Georgia Institute of Technology), Stefan Bertilsson(Swedish University of Agricultural Sciences), Jennifer Bhatnagar(Boston University), Jordan T. Bird(University of Arkansas for Medical Sciences), Jeffrey L. Blanchard(Amherst College), Sara E. Blumer‐Schuette(Oakland University), Brendan J. M. Bohannan(University of Oregon), Mikayla A. Borton(Colorado State University), Allyson Brady(McMaster University), Susan H. Brawley(University of Maine), Juliet Brodie(Natural History Museum), Steven D. Brown(AZ Technology (United States)), Jennifer R. Brum(Louisiana State University), Andreas Brune(Max Planck Institute for Terrestrial Microbiology), Donald A. Bryant(Pennsylvania State University), Alison Buchan(University of Tennessee at Knoxville), Daniel H. Buckley(Cornell University), Joy Buongiorno(Maryville College), Hinsby Cadillo‐Quiroz(Arizona State University), Sean M. Caffrey(University of Toronto), Ashley Campbell(Lawrence Livermore National Laboratory), Barbara J. Campbell(Clemson University), Stephanie Carr(Hartwick College), JoLynn Carroll(Akvaplan-niva), S. Craig Cary(University of Waikato), Anna M. Cates(University of Minnesota), Rose Ann Cattolico(University of Washington), Ricardo Cavicchioli(UNSW Sydney), Ludmila Chistoserdova(University of Washington), Maureen L. Coleman(University of Chicago), Philippe Constant(Institut National de la Recherche Scientifique), Jonathan M. Conway(North Carolina State University), Walter P. Mac Cormack(Universidad de Buenos Aires), Sean A. Crowe(University of British Columbia), Byron C. Crump(Oregon State University), Cameron R. Currie(University of Wisconsin–Madison), Rebecca Daly(Colorado State University), Kristen M. DeAngelis(University of Massachusetts Amherst), Vincent J. Denef(University of Michigan), Stuart E. Denman, Adey Feleke Desta(Addis Ababa University), Hebe M. Dionisi(Centro Científico Tecnológico Patagónico), Jeremy A. Dodsworth(California State University, San Bernardino), Nina Dombrowski(Utrecht University), Timothy J. Donohue(University of Wisconsin–Madison), Mark Dopson(Linnaeus University), Timothy Driscoll(West Virginia University), Peter F. Dunfield(University of Calgary), Christopher L. Dupont(J. Craig Venter Institute), Katherine A. Dynarski(University of Montana), Virginia P. Edgcomb(Woods Hole Oceanographic Institution), Elizabeth A. Edwards(University of Toronto), Mostafa S. Elshahed(Oklahoma State University), Israel Figueroa(Visolis (United States)), Beverly E. Flood(University of Minnesota), Nathaniel W. Fortney(University of Wisconsin–Madison), Caroline S. Fortunato(Widener University), Christopher Francis(Stanford University), Claire M. M. Gachon(Scottish Association For Marine Science), Sarahi L. Garcia(Stockholm University), María Consuelo Gazitúa(The Ohio State University), Terry J. Gentry(Texas A&M University), Lena Gerwick(Scripps Institution of Oceanography), Javad Gharechahi(Baqiyatallah University of Medical Sciences), Peter Girguis(Harvard University), John M. Gladden(Sandia National Laboratories California), Mary R. Gradoville(University of California, Santa Cruz), Stephen E. Grasby(Natural Resources Canada), Kelly Gravuer(University of California, Davis), Christen L. Grettenberger(University of California, Davis), Robert J. Gruninger(Agriculture and Agri-Food Canada), Jiarong Guo(Michigan State University), Mussie Y. Habteselassie(University of Georgia), Steven Hallam(University of British Columbia), Roland Hatzenpichler(Montana State University), Bela Hausmann(University of Vienna), Terry C. Hazen(University of Tennessee at Knoxville), Brian P. Hedlund(University of Nevada, Las Vegas), Cynthia Henny(Indonesian Institute of Sciences), Lydie Herfort(Oregon Health & Science University), Maria Hernandez, Olivia S. Hershey(University of Akron), Matthias Hess(University of California, Davis), Emily B. Hollister(Diversitech (United States)), Laura Hug(University of Waterloo), Dana E. Hunt(Duke University), Janet Jansson(Pacific Northwest National Laboratory), Jessica Jarett, Vitaly V. Kadnikov(Russian Academy of Sciences), Charlene N. Kelly(West Virginia University), Robert M. Kelly(North Carolina State University), William J. Kelly, Cheryl A. Kerfeld(Lawrence Berkeley National Laboratory), Jeffrey A. Kimbrel(Lawrence Livermore National Laboratory), Jonathan L. Klassen(University of Connecticut), Konstantinos T. Konstantinidis(Georgia Institute of Technology), Laura L. Lee(North Carolina State University), Wen‐Jun Li(Sun Yat-sen University), Andrew J. Loder(North Carolina State University), Alexander Loy(University of Vienna), Mariana Lozada(Instituto de Biología Subtropical), Barbara J. MacGregor(University of Minnesota), Cara Magnabosco(ETH Zurich), Aline Maria da Silva(Universidade de São Paulo), R. Michael L. McKay(University of Windsor), Katherine D. McMahon(University of Wisconsin–Madison), Christopher S. McSweeney, Mónica Medina(Pennsylvania State University), Laura Meredith(University of Arizona), Jessica E. Mizzi(University of California, Davis), Thomas Möck(University of East Anglia), Lily Momper(Exponent (United States)), Mary Ann Moran(University of Georgia), Connor Morgan‐Lang(University of British Columbia), Duane P. Moser(Desert Research Institute), Gerard Muyzer(University of Amsterdam), David D. Myrold(Oregon State University), Maisie Nash(University of Bristol), Camilla Nesbø(University of Toronto), Anthony P. Neumann(University of Wisconsin–Madison), Rebecca B. Neumann(University of Washington), Daniel R. Noguera(University of Wisconsin–Madison), Trent R. Northen(Lawrence Berkeley National Laboratory), Jeanette M. Norton(Utah State University), Brent Nowinski(University of Georgia), Klaus Nüsslein(University of Massachusetts Amherst), Michelle O’Malley(University of California, Santa Barbara), Rafael S. Oliveira(Universidade Estadual de Campinas (UNICAMP)), Valéria Maia de Oliveira(Universidade Estadual de Campinas (UNICAMP)), T. C. Onstott(Princeton University), Jay Osvatic(University of Vienna), Yang Ouyang(University of Oklahoma), Maria Pachiadaki(Woods Hole Oceanographic Institution), Jacob Parnell(Novozymes (United States)), Laila P. Partida‐Martínez(Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional), Kabir Peay(Stanford University), Dale A. Pelletier(Oak Ridge National Laboratory), Xuefeng Peng(University of California, Santa Barbara), Michael Pester(Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures), Jennifer Pett‐Ridge(Lawrence Livermore National Laboratory), Sari Peura(Science for Life Laboratory), Petra Pjevac(University of Vienna), Alvaro M. Plominsky(Scripps Institution of Oceanography), Anja Poehlein(University of Göttingen), Phillip B. Pope(Norwegian University of Life Sciences), Nikolai V. Ravin(Russian Academy of Sciences), Molly C. Redmond(University of North Carolina at Charlotte), Rebecca A. Reiss(New Mexico Institute of Mining and Technology), Virginia I. Rich(The Ohio State University), Christian Rinke(The University of Queensland), Jorge L. Mazza Rodrigues(University of Montana), William Rodriguez-Reillo(Harvard University), Karen Rossmassler(University of Colorado Anschutz Medical Campus), Joshua Sackett(University of Cincinnati), Ghasem Hosseini Salekdeh(Agricultural Research & Education Organization), S. R. Saleska(University of Arizona), Matthew Scarborough(University of Vermont), Daniel P. Schachtman(University of Nebraska–Lincoln), Christopher W. Schadt(Oak Ridge National Laboratory), Matthew Schrenk(Michigan State University), Alexander Sczyrba(Bielefeld University), Aditi Sengupta(California Lutheran University), João Carlos Setúbal(Universidade de São Paulo), Ashley Shade(Michigan State University), Christine Sharp(University of Calgary), David H. Sherman(University of Michigan), О. V. Shubenkova(Siberian Branch of the Russian Academy of Sciences), Isabel Natalia Sierra-Garcia(Universidade Estadual de Campinas (UNICAMP)), Rachel L. Simister(University of British Columbia), Holly M. Simon, Sara Sjöling(Södertörn University), Joan L. Slonczewski(Kenyon College), Rafael Soares Correa de Souza(Universidade Estadual de Campinas (UNICAMP)), John R. Spear(Colorado School of Mines), James Stegen(Pacific Northwest National Laboratory), Ramūnas Stepanauskas(Bigelow Laboratory for Ocean Sciences), Frank J. Stewart(Georgia Institute of Technology), Garret Suen(University of Wisconsin–Madison), Matthew B. Sullivan(The Ohio State University), D. Y. Sumner(University of California, Davis), Brandon K. Swan, Wesley D. Swingley(Northern Illinois University), Jonathan Tarn(University of California, Santa Barbara), Gordon T. Taylor(Stony Brook University), Hanno Teeling(Max Planck Institute for Marine Microbiology), Memory Tekere(University of South Africa), Andreas Teske(University of North Carolina at Chapel Hill), Torsten Thomas(UNSW Sydney), Cameron Thrash(University of Southern California), James M. Tiedje(Michigan State University), Claire S. Ting(Williams College), Benjamin Tully(University of Southern California), Gene W. Tyson(The University of Queensland), Osvlado Ulloa(University of Concepción), David L. Valentine(University of California, Santa Barbara), Marc W. Van Goethem(Lawrence Berkeley National Laboratory), Jean S. VanderGheynst(University of Massachusetts Dartmouth), Tobin J. Verbeke(University of Calgary), John Vollmers(Karlsruhe Institute of Technology), Aurèle Vuillemin(Ludwig-Maximilians-Universität München), Nicholas B. Waldo(University of Washington), David A. Walsh(Concordia University), Bart C. Weimer(University of California, Davis), Thea Whitman(University of Wisconsin–Madison), Paul W. J. J. van der Wielen(KWR Water Research Institute), Michael J. Wilkins(Colorado State University), Timothy J. Williams(UNSW Sydney), Ben J. Woodcroft(The University of Queensland), Jamie Woolet(University of Wisconsin–Madison), Kelly Wrighton(Colorado State University), Jun Ye(The University of Queensland), Erica B. Young(University of Wisconsin–Milwaukee), Noha H. Youssef(Oklahoma State University), Feiqiao Brian Yu(Chan Zuckerberg Initiative (United States)), Т. I. Zemskaya(Siberian Branch of the Russian Academy of Sciences), Ryan Ziels(University of British Columbia), Tanja Woyke(Joint Genome Institute), Nigel J. Mouncey(Joint Genome Institute), Natalia Ivanova(Joint Genome Institute), Nikos C. Kyrpides(Joint Genome Institute), Emiley A. Eloe‐Fadrosh(Joint Genome Institute)
Cited by 967Open Access
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.
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