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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
biochemistry, genetics and molecular biology
A genomic catalog of Earth’s microbiomes
Nature Biotechnology, Volume 39, No. 4, Year 2021
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Description
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. © 2020, The Author(s).
Authors & Co-Authors
Nayfach, Stephen
United States, Berkeley
U.s. Department of Energy Joint Genome Institute
Roux, Simon
United States, Berkeley
U.s. Department of Energy Joint Genome Institute
Seshadri, Rekha
United States, Berkeley
U.s. Department of Energy Joint Genome Institute
Udwary, Daniel W.
United States, Berkeley
U.s. Department of Energy Joint Genome Institute
Varghese, Neha Jacob
United States, Berkeley
U.s. Department of Energy Joint Genome Institute
Schulz, Frederik
United States, Berkeley
U.s. Department of Energy Joint Genome Institute
Wu, Dongying
United States, Berkeley
U.s. Department of Energy Joint Genome Institute
Páez-Espino, David
United States, Berkeley
U.s. Department of Energy Joint Genome Institute
Chen, I. Min Amy
United States, Berkeley
U.s. Department of Energy Joint Genome Institute
Huntemann, Marcel
United States, Berkeley
U.s. Department of Energy Joint Genome Institute
Palaniappan, Krishna
United States, Berkeley
U.s. Department of Energy Joint Genome Institute
Ladau, Joshua
United States, Berkeley
U.s. Department of Energy Joint Genome Institute
Mukherjee, Supratim
United States, Berkeley
U.s. Department of Energy Joint Genome Institute
Reddy, Tatiparthi B.K.
United States, Berkeley
U.s. Department of Energy Joint Genome Institute
Nielsen, Torben N.
United States, Berkeley
U.s. Department of Energy Joint Genome Institute
Kirton, Edward S.
United States, Berkeley
U.s. Department of Energy Joint Genome Institute
Faria, José P.
United States, Lemont
Argonne National Laboratory
Edirisinghe, Janaka N.
United States, Lemont
Argonne National Laboratory
Henry, Christopher S.
United States, Lemont
Argonne National Laboratory
Jungbluth, Sean P.
United States, Berkeley
U.s. Department of Energy Joint Genome Institute
United States, Berkeley
Lawrence Berkeley National Laboratory
Chivian, Dylan C.
United States, Berkeley
Lawrence Berkeley National Laboratory
Dehal, Paramvir S.
United States, Berkeley
Lawrence Berkeley National Laboratory
Wood-Charlson, Elisha M.
United States, Berkeley
Lawrence Berkeley National Laboratory
Arkin, Adam Paul
United States, Berkeley
Lawrence Berkeley National Laboratory
Tringe, Susannah Green
United States, Berkeley
U.s. Department of Energy Joint Genome Institute
Visel, Axel
United States, Berkeley
U.s. Department of Energy Joint Genome Institute
Abreu, Helena Helena
Portugal, Albergaria-a-velha
Algaplus
Acinas, Silvia G.
Spain, Barcelona
Csic - Instituto de Ciencias Del Mar Icm
Allen, Eric E.
United States, La Jolla
University of California, San Diego
Allen, Michelle A.
Australia, Sydney
Unsw Sydney
Alteio, Lauren V.
Austria, Vienna
Universität Wien
Andersen, Gary L.
United States, Berkeley
Lawrence Berkeley National Laboratory
Anesio, Alexandre Magno
Denmark, Aarhus
Aarhus Universitet
Attwood, Graeme T.
New Zealand, Palmerston North
Agresearch Grasslands
Avila-Magaña, Viridiana
United States, University Park
Pennsylvania State University
Badis, Yacine
United Kingdom, Oban
The Scottish Association for Marine Science
Bailey, Jake V.
United States, Minneapolis
University of Minnesota Twin Cities
Baker, Brett J.
United States, Austin
The University of Texas at Austin
Baldrian, Petr
Czech Republic, Prague
Institute of Microbiology of the Academy of Sciences of the Czech Republic
Barton, Hazel A.
United States, Akron
University of Akron
Beck, David A.C.
United States, Seattle
University of Washington
Becraft, Eric Daniel
United States, Florence
University of North Alabama
Beller, Harry R.
United States, Berkeley
Lawrence Berkeley National Laboratory
Beman, J. Michael
United States, Merced
Uc Merced
Bernier-Latmani, Rizlan Bencheikh
Switzerland, Lausanne
École Polytechnique Fédérale de Lausanne
Berry, Timothy D.
United States, Madison
University of Wisconsin-madison
Bertagnolli, Anthony D.
United States, Atlanta
Georgia Institute of Technology
Bertilsson, Stefan A.
Sweden, Uppsala
Sveriges Lantbruksuniversitet
Bhatnagar, Jennifer M.
United States, Boston
Boston University
Bird, Jordan T.
United States, Little Rock
University of Arkansas for Medical Sciences
Blanchard, Jeffrey L.
United States, Amherst
University of Massachusetts Amherst
Blumer-Schuette, Sara E.
United States, Rochester
Oakland University
Bohannan, Brendan J.M.
United States, Eugene
University of Oregon
Borton, Mikayla A.
United States, Fort Collins
Colorado State University
Brady, Allyson L.
Canada, Hamilton
Mcmaster University
Brawley, Susan Howard
United States, Orono
University of Maine
Brodie, Juliet A.
United Kingdom, London
The Natural History Museum, London
Brown, Steven D.
United States, Skokie
Lanzatech, Inc.
Brum, Jennifer R.
United States, Baton Rouge
Louisiana State University
Brune, Andreas
Germany, Marburg
Max Planck Institute for Terrestrial Microbiology
Bryant, Donald A.
United States, University Park
Pennsylvania State University
Buchan, Alison
United States, Knoxville
The University of Tennessee, Knoxville
Buckley, Daniel H.
United States, Ithaca
Cornell University
Buongiorno, Joy
United States, Maryville
Maryville College
Cadillo-Quiroz, Hinsby
United States, Tempe
Arizona State University
Caffrey, Sean M.
Canada, Toronto
University of Toronto
Campbell, Ashley N.
United States, Livermore
Lawrence Livermore National Laboratory
Campbell, Barbara J.
United States, Clemson
Clemson University
Carr, Stephanie A.
United States, Oneonta
Hartwick College
Carroll, Jolynn Lynn
Norway, Oslo
Norsk Institutt for Vannforskning
Cary, Stephen Craig
New Zealand, Hamilton
The University of Waikato
Cates, Anna M.
United States, Minneapolis
University of Minnesota Twin Cities
Cattolico, Rose Ann
United States, Seattle
University of Washington
Cavicchioli, Ricardo
Australia, Sydney
Unsw Sydney
Chistoserdova, L.
United States, Seattle
University of Washington
Coleman, Maureen L.
United States, Chicago
The University of Chicago
Constant, Philippe
Canada, Laval
Centre Armand-frappier Santé Biotechnologie
Conway, Jonathan M.
United States, Raleigh
Nc State University
Mác Cormack, Walter Patricio
Argentina, San Martin
Instituto Antartico Argentino
Crowe, Sean A.
Canada, Vancouver
The University of British Columbia
Crump, Byron C.
United States, Corvallis
Oregon State University
Currie, Cameron R.
United States, Madison
University of Wisconsin-madison
Daly, Rebecca A.
United States, Fort Collins
Colorado State University
DeAngelis, Kristen M.
United States, Amherst
University of Massachusetts Amherst
Denef, Vincent J.
United States, Ann Arbor
University of Michigan, Ann Arbor
Denman, Stuart Edward
Australia, Canberra
Commonwealth Scientific and Industrial Research Organisation
Desta, Adey Feleke
Ethiopia, Addis Ababa
Addis Ababa University
Dionisi, H.
Argentina, Buenos Aires
Consejo Nacional de Investigaciones Científicas y Técnicas
Dodsworth, Jeremy A.
United States, San Bernardino
California State University, San Bernardino
Dombrowski, Nina
Netherlands, 't Horntje
Royal Netherlands Institute for Sea Research
Donohue, Timothy J.
United States, Madison
University of Wisconsin-madison
Dopson, Mark
Sweden, Vaxjo
Linnaeus University, Växjö
Driscoll, Timothy P.
United States, Morgantown
West Virginia University
Dunfield, Peter F.
Canada, Calgary
University of Calgary
Dupont, Christopher L.
United States, Rockville
J. Craig Venter Institute
Dynarski, Katherine A.
United States, Missoula
University of Montana
Edgcomb, Virginia P.
United States, Woods Hole
Woods Hole Oceanographic Institution
Edwards, Elizabeth Anne
Canada, Toronto
University of Toronto
Elshahed, Mostafa S.
United States, Stillwater
Oklahoma State University
Figueroa, Israel A.
United States, Hayward
Visolis, Inc
Flood, Beverly E.
United States, Minneapolis
University of Minnesota Twin Cities
Gachon, Claire M.M.
United Kingdom, Oban
The Scottish Association for Marine Science
Gazitúa, María Consuelo
United States, Columbus
The Ohio State University
Gharechahi, Javad
Iran, Tehran
Baqiyatallah University of Medical Sciences
Girguis, Peter R.
United States, Cambridge
Harvard University
Grasby, Stephen E.
Canada, Ottawa
Natural Resources Canada
Guo, Jiarong
United States, East Lansing
Michigan State University
Hazen, Terry C.
United States, Knoxville
The University of Tennessee, Knoxville
Hedlund, Brian P.
United States, Las Vegas
University of Nevada, Las Vegas
Herfort, Lydie
United States, Portland
Oregon Health & Science University
Hess, Matthias
United States, Davis
University of California, Davis
Jansson, Janet K.
United States, Richland
Pacific Northwest National Laboratory
Kadnikov, V. V.
Russian Federation, Moscow
Federal Research Centre “fundamentals of Biotechnology” of the Russian Academy of Sciences
Kelly, William J.
New Zealand, Ashhurst
Donvis Limited
Klassen, Jonathan L.
United States, Storrs
University of Connecticut
Konstantinidis, Konstantinos T.
United States, Atlanta
Georgia Institute of Technology
Li, Wenjun
China, Guangzhou
Sun Yat-sen University
Loy, Alexander
Austria, Vienna
Universität Wien
Lozada, Mariana
Unknown Affiliation
MacGregor, Barbara J.
United States, Minneapolis
University of Minnesota Twin Cities
Magnabosco, Cara
Switzerland, Zurich
Eth Zürich
Da Silva, Aline Maria
Brazil, Sao Paulo
Universidade de São Paulo
McMahon, Katherine D.
United States, Madison
University of Wisconsin-madison
McSweeney, Christopher S.
Australia, Canberra
Commonwealth Scientific and Industrial Research Organisation
Medina, Mónica M.
United States, University Park
Pennsylvania State University
Meredith, Laura K.
United States, Tucson
The University of Arizona
Mizzi, Jessica E.
United States, Davis
University of California, Davis
Mock, Thomas
United Kingdom, Norwich
Norwich Research Park
Moser, Duane P.
United States, Reno
Desert Research Institute
Muyzer, G.
Netherlands, Amsterdam
Universiteit Van Amsterdam
Myrold, David D.
United States, Corvallis
Oregon State University
Neumann, Anthony P.
United States, Madison
University of Wisconsin-madison
Northen, Trent R.
United States, Berkeley
Lawrence Berkeley National Laboratory
O'Malley, Michelle A.
United States, Santa Barbara
University of California, Santa Barbara
Oliveira, Rafael S.
Brazil, Campinas
Universidade Estadual de Campinas
Onstott, Tullis C.
United States, Princeton
Princeton University
Pachiadaki, Maria G.
United States, Woods Hole
Woods Hole Oceanographic Institution
Partida-Martínez, Laila P.
Mexico, Mexico
Centro de Investigacion y de Estudios Avanzados Del Instituto Politécnico Nacional
Peay, Kabir G.
United States, Palo Alto
Stanford University
Pelletier, Dale A.
United States, Oak Ridge
Oak Ridge National Laboratory
Peng, Xuefeng
United States, Santa Barbara
University of California, Santa Barbara
Poehlein, Anja
Germany, Gottingen
Georg-august-universität Göttingen
Pope, Phillip Byron
Norway, As
Norges Miljø- og Biovitenskapelige Universitet
Ravin, Nikolai V.
Russian Federation, Moscow
Federal Research Centre “fundamentals of Biotechnology” of the Russian Academy of Sciences
Rich, Virginia I.
United States, Columbus
The Ohio State University
Rinke, Christian
Australia, Brisbane
The University of Queensland
Rodrigues, Jorge Luiz Mazza
United States, Missoula
University of Montana
Rossmassler, Karen
United States, Aurora
University of Colorado Anschutz Medical Campus
Sackett, Joshua D.
United States, Cincinnati
University of Cincinnati
Hosseini Salekdeh, Ghasem
Iran, Karaj
Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization Areeo
Schadt, Christopher W.
United States, Oak Ridge
Oak Ridge National Laboratory
Sczyrba, Alexander
Germany, Bielefeld
Universität Bielefeld
Setubal, João Carlos
Brazil, Sao Paulo
Universidade de São Paulo
Shade, Ashley L.
United States, East Lansing
Michigan State University
Sherman, David H.
United States, Ann Arbor
University of Michigan, Ann Arbor
Simister, Rachel L.
Canada, Vancouver
The University of British Columbia
Simon, Holly M.
United States, Oakland
Animalbiome
Sjöling, Sara
Sweden, Huddinge
Södertörn University
Spear, John R.
United States, Golden
Colorado School of Mines
Stegen, James C.
United States, Richland
Pacific Northwest National Laboratory
Stepanauskas, Ramunas
United States, East Boothbay
Bigelow Laboratory for Ocean Sciences
Stewart, Frank J.
United States, Atlanta
Georgia Institute of Technology
Suen, Garret
United States, Madison
University of Wisconsin-madison
Sullivan, Matthew B.
United States, Columbus
The Ohio State University
Tekere, Memory
South Africa, Pretoria
University of South Africa
Thomas, Torsten
Australia, Sydney
Unsw Sydney
Tiedje, James M.
United States, East Lansing
Michigan State University
Tyson, Gene W.
Australia, Brisbane
The University of Queensland
Ulloa, Osvaldo
Chile, Biobio
Universidad de Concepcion
Van Goethem, Marc W.
United States, Berkeley
Lawrence Berkeley National Laboratory
Vollmers, John
Germany, Karlsruhe
Karlsruher Institut Für Technologie
Weimer, Bart C.
United States, Davis
University of California, Davis
Williams, Timothy J.
Australia, Sydney
Unsw Sydney
Woodcroft, Ben J.
Australia, Brisbane
The University of Queensland
Wrighton, Kelly C.
United States, Fort Collins
Colorado State University
Youssef, Noha H.
United States, Stillwater
Oklahoma State University
Woyke, Tanja
United States, Berkeley
U.s. Department of Energy Joint Genome Institute
Ivanova, Natalia N.
United States, Berkeley
U.s. Department of Energy Joint Genome Institute
Kyrpides, Nikos C.
United States, Berkeley
U.s. Department of Energy Joint Genome Institute
Eloe-Fadrosh, Emiley A.
United States, Berkeley
U.s. Department of Energy Joint Genome Institute
Statistics
Citations: 424
Authors: 180
Affiliations: 145
Identifiers
Doi:
10.1038/s41587-020-0718-6
ISSN:
10870156
Research Areas
Noncommunicable Diseases