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Nayfach S, Roux S, Seshadri R, Udwary D, Varghese N, Schulz F, Wu D, Paez-Espino D, Chen IM, Huntemann M, Palaniappan K, Ladau J, Mukherjee S, Reddy TBK, Nielsen T, Kirton E, Faria JP, Edirisinghe JN, Henry CS, Jungbluth SP, Chivian D, Dehal P, Wood-Charlson EM, Arkin AP, Tringe SG, Visel A, Abreu H, Acinas SG, Allen E, Allen MA, Alteio LV, Andersen G, Anesio AM, Attwood G, Avila-Magaña V, Badis Y, Bailey J, Baker B, Baldrian P, Barton HA, Beck DAC, Becraft ED, Beller HR, Beman JM, Bernier-Latmani R, Berry TD, Bertagnolli A, Bertilsson S, Bhatnagar JM, Bird JT, Blanchard JL, Blumer-Schuette SE, Bohannan B, Borton MA, Brady A, Brawley SH, Brodie J, Brown S, Brum JR, Brune A, Bryant DA, Buchan A, Buckley DH, Buongiorno J, Cadillo-Quiroz H, Caffrey SM, Campbell AN, Campbell B, Carr S, Carroll J, Cary SC, Cates AM, Cattolico RA, Cavicchioli R, Chistoserdova L, Coleman ML, Constant P, Conway JM, Mac Cormack WP, Crowe S, Crump B, Currie C, Daly R, DeAngelis KM, Denef V, Denman SE, Desta A, Dionisi H, Dodsworth J, Dombrowski N, Donohue T, Dopson M, Driscoll T, Dunfield P, Dupont CL, Dynarski KA, Edgcomb V, Edwards EA, Elshahed MS, Figueroa I, Flood B, Fortney N, Fortunato CS, Francis C, Gachon CMM, Garcia SL, Gazitua MC, Gentry T, Gerwick L, Gharechahi J, Girguis P, Gladden J, Gradoville M, Grasby SE, Gravuer K, Grettenberger CL, Gruninger RJ, Guo J, Habteselassie MY, Hallam SJ, Hatzenpichler R, Hausmann B, Hazen TC, Hedlund B, Henny C, Herfort L, Hernandez M, Hershey OS, Hess M, Hollister EB, Hug LA, Hunt D, Jansson J, Jarett J, Kadnikov VV, Kelly C, Kelly R, Kelly W, Kerfeld CA, Kimbrel J, Klassen JL, Konstantinidis KT, Lee LL, Li WJ, Loder AJ, Loy A, Lozada M, MacGregor B, Magnabosco C, Maria da Silva A, McKay RM, McMahon K, McSweeney CS, Medina M, Meredith L, Mizzi J, Mock T, Momper L, Moran MA, Morgan-Lang C, Moser D, Muyzer G, Myrold D, Nash M, Nesbø CL, Neumann AP, Neumann RB, Noguera D, Northen T, Norton J, Nowinski B, Nüsslein K, O’Malley MA, Oliveira RS, Maia de Oliveira V, Onstott T, Osvatic J, Ouyang Y, Pachiadaki M, Parnell J, Partida-Martinez LP, Peay KG, Pelletier D, Peng X, Pester M, Pett-Ridge J, Peura S, Pjevac P, Plominsky AM, Poehlein A, Pope PB, Ravin N, Redmond MC, Reiss R, Rich V, Rinke C, Rodrigues JLM, Rodriguez-Reillo W, Rossmassler K, Sackett J, Salekdeh GH, Saleska S, Scarborough M, Schachtman D, Schadt CW, Schrenk M, Sczyrba A, Sengupta A, Setubal JC, Shade A, Sharp C, Sherman DH, Shubenkova OV, Sierra-Garcia IN, Simister R, Simon H, Sjöling S, Slonczewski J, Correa de Souza RS, Spear JR, Stegen JC, Stepanauskas R, Stewart F, Suen G, Sullivan M, Sumner D, Swan BK, Swingley W, Tarn J, Taylor GT, Teeling H, Tekere M, Teske A, Thomas T, Thrash C, Tiedje J, Ting CS, Tully B, Tyson G, Ulloa O, Valentine DL, Van Goethem MW, VanderGheynst J, Verbeke TJ, Vollmers J, Vuillemin A, Waldo NB, Walsh DA, Weimer BC, Whitman T, van der Wielen P, Wilkins M, Williams TJ, Woodcroft B, Woolet J, Wrighton K, Ye J, Young EB, Youssef NH, Yu FB, Zemskaya TI, Ziels R, Woyke T, Mouncey NJ, Ivanova NN, Kyrpides NC, Eloe-Fadrosh EA
Nat Biotechnol 39 (4) 499-509 [2021-04-00; online 2020-11-09]
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.
PubMed 33169036
DOI 10.1038/s41587-020-0718-6
Crossref 10.1038/s41587-020-0718-6
pmc: PMC8041624
pii: 10.1038/s41587-020-0718-6