A genomic catalog of Earth’s microbiomes

Autor: Nayfach, S., Roux, S., Seshadri, R., Udwary, D., Varghese, N., Schulz, F., Wu, D., Paez-Espino, D., Chen, I., Huntemann, M., Palaniappan, K., Ladau, J., Mukherjee, S., Reddy, T., Nielsen, T., Kirton, E., Faria, J., Edirisinghe, J., Henry, C., Jungbluth, S., Chivian, D., Dehal, P., Wood-Charlson, E., Arkin, A., Tringe, S., Visel, A., Abreu, H., Acinas, S., Allen, E., Allen, M., Alteio, L., Andersen, G., Anesio, A., Attwood, G., Avila-Magaña, V., Badis, Y., Bailey, J., Baker, B., Baldrian, P., Barton, H., Beck, D., Becraft, E., Beller, H., Beman, J., Bernier-Latmani, R., Berry, T., Bertagnolli, A., Bertilsson, S., Bhatnagar, J., Bird, J., Blanchard, J., Blumer-Schuette, S., Bohannan, B., Borton, M., Brady, A., Brawley, S., Brodie, J., Brown, S., Brum, J., Brune, A., Bryant, D., Buchan, A., Buckley, D., Buongiorno, J., Cadillo-Quiroz, H., Caffrey, S., Campbell, A., Campbell, B., Carr, S., Carroll, J., Cary, S., Cates, A., Cattolico, R., Cavicchioli, R., Chistoserdova, L., Coleman, M., Constant, P., Conway, J., Mac Cormack, W., Crowe, S., Crump, B., Currie, C., Daly, R., DeAngelis, K., Denef, V., Denman, S., Desta, A., Dionisi, H., Dodsworth, J., Dombrowski, N., Donohue, T., Dopson, M., Driscoll, T., Dunfield, P., Dupont, C., Dynarski, K., Edgcomb, V., Edwards, E., Elshahed, M., Figueroa, I., Flood, B., Fortney, N., Fortunato, C., Francis, C., Gachon, C., Garcia, S., Gazitua, M., Gentry, T., Gerwick, L., Gharechahi, J., Girguis, P., Gladden, J., Gradoville, M., Grasby, S., Gravuer, K., Grettenberger, C., Gruninger, R., Guo, J., Habteselassie, M., Hallam, S., Hatzenpichler, R., Hausmann, B., Hazen, T., Hedlund, B., Henny, C., Herfort, L., Hernandez, M., Hershey, O., Hess, M., Hollister, E., Hug, L., Hunt, D., Jansson, J., Jarett, J., Kadnikov, V., Kelly, C., Kelly, R., Kelly, W., Kerfeld, C., Kimbrel, J., Klassen, J., Konstantinidis, K., Lee, L., Li, W., Loder, A., Loy, A., Lozada, M., MacGregor, B., Magnabosco, C., Maria da Silva, A., McKay, R., McMahon, K., McSweeney, C., Medina, M., Meredith, L., Mizzi, J., Mock, T., Momper, L., Moran, M., Morgan-Lang, C., Moser, D., Muyzer, G., Myrold, D., Nash, M., Nesbø, C., Neumann, A., Neumann, R., Noguera, D., Northen, T., Norton, J., Nowinski, B., Nüsslein, K., O’Malley, M., Oliveira, R., Maia de Oliveira, V., Onstott, T., Osvatic, J., Ouyang, Y., Pachiadaki, M., Parnell, J., Partida-Martinez, L., Peay, K., Pelletier, D., Peng, X., Pester, M., Pett-Ridge, J., Peura, S., Pjevac, P., Plominsky, A., Poehlein, A., Pope, P., Ravin, N., Redmond, M., Reiss, R., Rich, V., Rinke, C., Rodrigues, J., Rodriguez-Reillo, W., Rossmassler, K., Sackett, J., Salekdeh, G., Saleska, S., Scarborough, M., Schachtman, D., Schadt, C., Schrenk, M., Sczyrba, A., Sengupta, A., Setubal, J., Shade, A., Sharp, C., Sherman, D., Shubenkova, O., Sierra-Garcia, I., Simister, R., Simon, H., Sjöling, S., Slonczewski, J., Correa de Souza, R., Spear, J., Stegen, J., Stepanauskas, R., Stewart, F., Suen, G., Sullivan, M., Sumner, D., Swan, B., Swingley, W., Tarn, J., Taylor, G., Teeling, H., Tekere, M., Teske, A., Thomas, T., Thrash, C., Tiedje, J., Ting, C., Tully, B., Tyson, G., Ulloa, O., Valentine, D., Van Goethem, M., VanderGheynst, J., Verbeke, T., Vollmers, J., Vuillemin, A., Waldo, N., Walsh, D., Weimer, B., Whitman, T., van der Wielen, P., Wilkins, M., Williams, T., Woodcroft, B., Woolet, J., Wrighton, K., Ye, J., Young, E., Youssef, N., Yu, F., Zemskaya, T., Ziels, R., Woyke, T., Mouncey, N., Ivanova, N., Kyrpides, N., Eloe-Fadrosh, E., Consortium, I.
Přispěvatelé: Agencia Estatal de Investigación (España)
Jazyk: angličtina
Rok vydání: 2020
Předmět:
Zdroj: CONICET Digital (CONICET)
Consejo Nacional de Investigaciones Científicas y Técnicas
instacron:CONICET
Nature biotechnology, 39, 499–509
Repositório Institucional da USP (Biblioteca Digital da Produção Intelectual)
Universidade de São Paulo (USP)
instacron:USP
Digital.CSIC. Repositorio Institucional del CSIC
instname
Nature Biotechnology
ISSN: 0733-222X
1087-0156
1546-1696
2331-3684
Popis: 13 pages, 5 figures, supplementary information https://doi.org/10.1038/s41587-020-0718-6.-- Data availability: All available metagenomic data, bins and annotations are available through the IMG/M portal (https://img.jgi.doe.gov/). Bulk download for the 52,515 MAGs is available at https://genome.jgi.doe.gov/GEMs and https://portal.nersc.gov/GEM. Genome-scale metabolic models for the nonredundant, high-quality GEMs are summarized at https://doi.org/10.25982/53247.64/1670777 and available in KBase (https://narrative.kbase.us/#org/jgimags). IMG/M identifiers of all metagenomes binned, including detailed information for each metagenome, are available in Supplementary Table 1.-- The pipeline used to generate the metagenome bins is available at https://bitbucket.org/berkeleylab/metabat/src/master/
Publisher Correction: A genomic catalog of Earth’s microbiomes; Nature Biotechnology 39: 520 (2021); https://doi.org/10.1038/s41587-020-00769-4
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
This work was conducted by the US DOE Joint Genome Institute, a DOE Office of Science User Facility (contract no. DE-AC02–05CH11231), and used resources of the National Energy Research Scientific Computing Center, which is supported by the Office of Science of the US DOE (contract no. DE-AC02–05CH11231). This work was also supported as part of the Genomic Sciences Program DOE Systems Biology KBase (award nos. DE-AC02-05CH11231, DE-AC02-06CH11357, DE-AC05-00OR22725, and DE-AC02-98CH10886).-- With the funding support of the ‘Severo Ochoa Centre of Excelle
Databáze: OpenAIRE
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