A genomic catalog of Earth’s microbiomes
Authors: Nayfach Stephen , Roux Simon , Seshadri Rekha , Udwary Daniel , Varghese Neha , Schulz Frederik , Wu Dongying , Paez-Espino David , Chen I-Min , Huntemann Marcel , Palaniappan Krishna , Ladau Joshua , Mukherjee Supratim , Reddy T. B. K. , Nielsen Torben , Kirton Edward , Faria José P. , Edirisinghe Janaka N. , Henry Christopher S. , Jungbluth Sean P. , Chivian Dylan , Dehal Paramvir , Wood-Charlson Elisha M. , Arkin Adam P. , Tringe Susannah G. , Visel Axel ,   IMG/M Data Consortium, Abreu Helena , Acinas Silvia G. , Allen Eric , Allen Michelle A. , Alteio Lauren V. , Andersen Gary , Anesio Alexandre M. , Attwood Graeme , Avila-Magaña Viridiana , Badis Yacine , Bailey Jake , Baker Brett , Baldrian Petr , Barton Hazel A. , Beck David A. C. , Becraft Eric D. , Beller Harry R. , Beman J. Michael , Bernier-Latmani Rizlan , Berry Timothy D. , Bertagnolli Anthony , Bertilsson Stefan , Bhatnagar Jennifer M. , Bird Jordan T. , Blanchard Jeffrey L. , Blumer-Schuette Sara E. , Bohannan Brendan , Borton Mikayla A. , Brady Allyson , Brawley Susan H. , Brodie Juliet , Brown Steven , Brum Jennifer R. , Brune Andreas , Bryant Donald A. , Buchan Alison , Buckley Daniel H. , Buongiorno Joy , Cadillo-Quiroz Hinsby , Caffrey Sean M. , Campbell Ashley N. , Campbell Barbara , Carr Stephanie , Carroll JoLynn , Cary S. Craig , Cates Anna M. , Cattolico Rose Ann , Cavicchioli Ricardo , Chistoserdova Ludmila , Coleman Maureen L. , Constant Philippe , Conway Jonathan M. , Mac Cormack Walter P. , Crowe Sean , Crump Byron , Currie Cameron , Daly Rebecca , DeAngelis Kristen M. , Denef Vincent , Denman Stuart E. , Desta Adey , Dionisi Hebe , Dodsworth Jeremy , Dombrowski Nina , Donohue Timothy , Dopson Mark , Driscoll Timothy , Dunfield Peter , Dupont Christopher L. , Dynarski Katherine A. , Edgcomb Virginia , Edwards Elizabeth A. , Elshahed Mostafa S. , Figueroa Israel , Flood Beverly , Fortney Nathaniel , Fortunato Caroline S. , Francis Christopher , Gachon Claire M. M. , Garcia Sarahi L. , Gazitua Maria C. , Gentry Terry , Gerwick Lena , Gharechahi Javad , Girguis Peter , Gladden John , Gradoville Mary , Grasby Stephen E. , Gravuer Kelly , Grettenberger Christen L. , Gruninger Robert J. , Guo Jiarong , Habteselassie Mussie Y. , Hallam Steven J. , Hatzenpichler Roland , Hausmann Bela , Hazen Terry C. , Hedlund Brian , Henny Cynthia , Herfort Lydie , Hernandez Maria , Hershey Olivia S. , Hess Matthias , Hollister Emily B. , Hug Laura A. , Hunt Dana , Jansson Janet , Jarett Jessica , Kadnikov Vitaly V. , Kelly Charlene , Kelly Robert , Kelly William , Kerfeld Cheryl A. , Kimbrel Jeff , Klassen Jonathan L. , Konstantinidis Konstantinos T. , Lee Laura L. , Li Wen-Jun , Loder Andrew J. , Loy Alexander , Lozada Mariana , MacGregor Barbara , Magnabosco Cara , Maria da Silva Aline , McKay R. Michael , McMahon Katherine , McSweeney Chris S. , Medina Mónica , Meredith Laura , Mizzi Jessica , Mock Thomas , Momper Lily , Moran Mary Ann , Morgan-Lang Connor , Moser Duane , Muyzer Gerard , Myrold David , Nash Maisie , Nesbø Camilla L. , Neumann Anthony P. , Neumann Rebecca B. , Noguera Daniel , Northen Trent , Norton Jeanette , Nowinski Brent , Nüsslein Klaus , O’Malley Michelle A. , Oliveira Rafael S. , Maia de Oliveira Valeria , Onstott Tullis , Osvatic Jay , Ouyang Yang , Pachiadaki Maria , Parnell Jacob , Partida-Martinez Laila P. , Peay Kabir G. , Pelletier Dale , Peng Xuefeng , Pester Michael , Pett-Ridge Jennifer , Peura Sari , Pjevac Petra , Plominsky Alvaro M. , Poehlein Anja , Pope Phillip B. , Ravin Nikolai , Redmond Molly C. , Reiss Rebecca , Rich Virginia , Rinke Christian , Rodrigues Jorge L. Mazza , Rodriguez-Reillo William , Rossmassler Karen , Sackett Joshua , Salekdeh Ghasem Hosseini , Saleska Scott , Scarborough Matthew , Schachtman Daniel , Schadt Christopher W. , Schrenk Matthew , Sczyrba Alexander , Sengupta Aditi , Setubal Joao C. , Shade Ashley , Sharp Christine , Sherman David H. , Shubenkova Olga V. , Sierra-Garcia Isabel Natalia , Simister Rachel , Simon Holly , Sjöling Sara , Slonczewski Joan , Correa de Souza Rafael Soares , Spear John R. , Stegen James C. , Stepanauskas Ramunas , Stewart Frank , Suen Garret , Sullivan Matthew , Sumner Dawn , Swan Brandon K. , Swingley Wesley , Tarn Jonathan , Taylor Gordon T. , Teeling Hanno , Tekere Memory , Teske Andreas , Thomas Torsten , Thrash Cameron , Tiedje James , Ting Claire S. , Tully Benjamin , Tyson Gene , Ulloa Osvlado , Valentine David L. , Van Goethem Marc W. , VanderGheynst Jean , Verbeke Tobin J. , Vollmers John , Vuillemin Aurèle , Waldo Nicholas B. , Walsh David A. , Weimer Bart C. , Whitman Thea , van der Wielen Paul , Wilkins Michael , Williams Timothy J. , Woodcroft Ben , Woolet Jamie , Wrighton Kelly , Ye Jun , Young Erica B. , Youssef Noha H. , Yu Feiqiao Brian , Zemskaya Tamara I. , Ziels Ryan , Woyke Tanja , Mouncey Nigel J. , Ivanova Natalia N. , Kyrpides Nikos C. , Eloe-Fadrosh Emiley A. 
Published: November 2020

AbstractThe 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.