A genomic catalog of Earth’s microbiomes

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.

doi:10.1038/s41587-020-0718-6

Cited by 865

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A genomic catalog of Earth’s microbiomes

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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.·2021·Nature Biotechnology

DOI 10.1038/s41587-020-0718-6

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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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Authors: Nayfach, S., Roux, S., Seshadri, R., Udwary, D., Varghese, N., Schulz, F., Wu, D., Paez-Espino, D., Chen, I.-M., Huntemann, M., Palaniappan, K., Ladau, J., Mukherjee, S., Reddy, T. B. K., Nielsen, T., Kirton, E., Faria, J. P., Edirisinghe, J. N., Henry, C. S., Jungbluth, S. P., Chivian, D., Dehal, P., Wood-Charlson, E. M., Arkin, A. P., Tringe, S. G., Visel, A., IMG/M Data Consortium, Abreu, H., Acinas, S. G., Allen, E., Allen, M. A., Alteio, L. V., Andersen, G., Anesio, A. M., Attwood, G., Avila-Magaña, V., Badis, Y., Bailey, J., Baker, B., Baldrian, P., Barton, H. A., Beck, D. A. C., Becraft, E. D., Beller, H. R., Beman, J. M., Bernier-Latmani, R., Berry, T. D., Bertagnolli, A., Bertilsson, S., Bhatnagar, J. M., Bird, J. T., Blanchard, J. L., Blumer-Schuette, S. E., Bohannan, B., Borton, M. A., Brady, A., Brawley, S. H., Brodie, J., Brown, S., Brum, J. R., Brune, A., Bryant, D. A., Buchan, A., Buckley, D. H., Buongiorno, J., Cadillo-Quiroz, H., Caffrey, S. M., Campbell, A. N., Campbell, B., Carr, S., Carroll, J., Cary, S. C., Cates, A. M., Cattolico, R. A., Cavicchioli, R., Chistoserdova, L., Coleman, M. L., Constant, P., Conway, J. M., Mac Cormack, W. P., Crowe, S., Crump, B., Currie, C., Daly, R., DeAngelis, K. M., Denef, V., Denman, S. E., Desta, A., Dionisi, H., Dodsworth, J., Dombrowski, N., Donohue, T., Dopson, M., Driscoll, T., Dunfield, P., Dupont, C. L., Dynarski, K. A., Edgcomb, V., Edwards, E. A., Elshahed, M. S., Figueroa, I., Flood, B., Fortney, N., Fortunato, C. S., Francis, C., Gachon, C. M. M., Garcia, S. L., Gazitua, M. C., Gentry, T., Gerwick, L., Gharechahi, J., Girguis, P., Gladden, J., Gradoville, M., Grasby, S. E., Gravuer, K., Grettenberger, C. L., Gruninger, R. J., Guo, J., Habteselassie, M. Y., Hallam, S. J., Hatzenpichler, R., Hausmann, B., Hazen, T. C., Hedlund, B., Henny, C., Herfort, L., Hernandez, M., Hershey, O. S., Hess, M., Hollister, E. B., Hug, L. A., Hunt, D., Jansson, J., Jarett, J., Kadnikov, V. V., Kelly, C., Kelly, R., Kelly, W., Kerfeld, C. A., Kimbrel, J., Klassen, J. L., Konstantinidis, K. T., Lee, L. L., Li, W.-J., Loder, A. J., Loy, A., Lozada, M., MacGregor, B., Magnabosco, C., Maria da Silva, A., McKay, R. M., McMahon, K., McSweeney, C. S., Medina, M., Meredith, L., Mizzi, J., Mock, T., Momper, L., Moran, M. A., Morgan-Lang, C., Moser, D., Muyzer, G., Myrold, D., Nash, M., Nesbø, C. L., Neumann, A. P., Neumann, R. B., Noguera, D., Northen, T., Norton, J., Nowinski, B., Nüsslein, K., O’Malley, M. A., Oliveira, R. S., Maia de Oliveira, V., Onstott, T., Osvatic, J., Ouyang, Y., Pachiadaki, M., Parnell, J., Partida-Martinez, L. P., Peay, K. G., Pelletier, D., Peng, X., Pester, M., Pett-Ridge, J., Peura, S., Pjevac, P., Plominsky, A. M., Poehlein, A., Pope, P. B., Ravin, N., Redmond, M. C., Reiss, R., Rich, V., Rinke, C., Rodrigues, J. L. M., Rodriguez-Reillo, W., Rossmassler, K., Sackett, J., Salekdeh, G. H., Saleska, S., Scarborough, M., Schachtman, D., Schadt, C. W., Schrenk, M., Sczyrba, A., Sengupta, A., Setubal, J. C., Shade, A., Sharp, C., Sherman, D. H., Shubenkova, O. V., Sierra-Garcia, I. N., Simister, R., Simon, H., Sjöling, S., Slonczewski, J., Correa de Souza, R. S., Spear, J. R., Stegen, J. C., Stepanauskas, R., Stewart, F., Suen, G., Sullivan, M., Sumner, D., Swan, B. K., Swingley, W., Tarn, J., Taylor, G. T., Teeling, H., Tekere, M., Teske, A., Thomas, T., Thrash, C., Tiedje, J., Ting, C. S., Tully, B., Tyson, G., Ulloa, O., Valentine, D. L., Van Goethem, M. W., VanderGheynst, J., Verbeke, T. J., Vollmers, J., Vuillemin, A., Waldo, N. B., Walsh, D. A., Weimer, B. C., Whitman, T., van der Wielen, P., Wilkins, M., Williams, T. J., Woodcroft, B., Woolet, J., Wrighton, K., Ye, J., Young, E. B., Youssef, N. H., Yu, F. B., Zemskaya, T. I., Ziels, R., Woyke, T., Mouncey, N. J., Ivanova, N. N., Kyrpides, N. C., & Eloe-Fadrosh, E. A.
Venue: Nature Biotechnology
Publisher: Springer Science and Business Media LLC
Published: 2020-11-09
Volume: 39
Issue: 4
Pages: 499-509
ISSN: 0733-222X (ISSN-L)
1087-0156
1546-1696
DOI: 10.1038/s41587-020-0718-6
OpenAlex: W3104596207
Cited by: 865
References: 17
FWCI: 29.18
Type: journal article
Language: en
Open access: hybrid

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This page: CoChat. (2026). Citation check: A genomic catalog of Earth’s microbiomes. https://app.cochat.ai/papers/10.1038/s41587-020-0718-6
The paper: Nayfach, S., Roux, S., Seshadri, R., Udwary, D., Varghese, N., Schulz, F., Wu, D., Paez-Espino, D., Chen, I.-M., Huntemann, M., Palaniappan, K., Ladau, J., Mukherjee, S., Reddy, T. B. K., Nielsen, T., Kirton, E., Faria, J. P., Edirisinghe, J. N., Henry, C. S., . . . Eloe-Fadrosh, E. A. (2021). A genomic catalog of Earth’s microbiomes. Nature Biotechnology. https://doi.org/10.1038/s41587-020-0718-6

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A genomic catalog of Earth’s microbiomes

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