A genomic catalog of Earth’s microbiomes

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

doi:10.1038/s41587-020-0718-6

A genomic catalog of Earth’s microbiomes

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

Research output: Contribution to journal › Article › peer-review

386 Scopus citations

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.

Original language	English (US)
Pages (from-to)	499-509
Number of pages	11
Journal	Nature biotechnology
Volume	39
Issue number	4
DOIs	https://doi.org/10.1038/s41587-020-0718-6
State	Published - Apr 1 2021
Externally published	Yes

Bibliographical note

Generated from Scopus record by KAUST IRTS on 2023-10-23

Access to Document

10.1038/s41587-020-0718-6

Cite this

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, 39(4), 499-509. https://doi.org/10.1038/s41587-020-0718-6

@article{9ecb8e36fdcb485fa246e49feecd563c,

title = "A genomic catalog of Earth{\textquoteright}s microbiomes",

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{\textquoteright}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.",

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

note = "Generated from Scopus record by KAUST IRTS on 2023-10-23",

year = "2021",

month = apr,

day = "1",

doi = "10.1038/s41587-020-0718-6",

language = "English (US)",

volume = "39",

pages = "499--509",

journal = "Nature biotechnology",

issn = "1546-1696",

publisher = "Nature Publishing Group",

number = "4",

}

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, JL, 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 2021, 'A genomic catalog of Earth’s microbiomes', Nature biotechnology, vol. 39, no. 4, pp. 499-509. https://doi.org/10.1038/s41587-020-0718-6

TY - JOUR

T1 - A genomic catalog of Earth’s microbiomes

AU - Nayfach, Stephen

AU - Roux, Simon

AU - Seshadri, Rekha

AU - Udwary, Daniel

AU - Varghese, Neha

AU - Schulz, Frederik

AU - Wu, Dongying

AU - Paez-Espino, David

AU - Chen, I. Min

AU - Huntemann, Marcel

AU - Palaniappan, Krishna

AU - Ladau, Joshua

AU - Mukherjee, Supratim

AU - Reddy, T. B.K.

AU - Nielsen, Torben

AU - Kirton, Edward

AU - Faria, José P.

AU - Edirisinghe, Janaka N.

AU - Henry, Christopher S.

AU - Jungbluth, Sean P.

AU - Chivian, Dylan

AU - Dehal, Paramvir

AU - Wood-Charlson, Elisha M.

AU - Arkin, Adam P.

AU - Tringe, Susannah G.

AU - Visel, Axel

AU - Abreu, Helena

AU - Acinas, Silvia G.

AU - Allen, Eric

AU - Allen, Michelle A.

AU - Alteio, Lauren V.

AU - Andersen, Gary

AU - Anesio, Alexandre M.

AU - Attwood, Graeme

AU - Avila-Magaña, Viridiana

AU - Badis, Yacine

AU - Bailey, Jake

AU - Baker, Brett

AU - Baldrian, Petr

AU - Barton, Hazel A.

AU - Beck, David A.C.

AU - Becraft, Eric D.

AU - Beller, Harry R.

AU - Beman, J. Michael

AU - Bernier-Latmani, Rizlan

AU - Berry, Timothy D.

AU - Bertagnolli, Anthony

AU - Bertilsson, Stefan

AU - Bhatnagar, Jennifer M.

AU - Bird, Jordan T.

AU - Blanchard, Jeffrey L.

AU - Blumer-Schuette, Sara E.

AU - Bohannan, Brendan

AU - Borton, Mikayla A.

AU - Brady, Allyson

AU - Brawley, Susan H.

AU - Brodie, Juliet

AU - Brown, Steven

AU - Brum, Jennifer R.

AU - Brune, Andreas

AU - Bryant, Donald A.

AU - Buchan, Alison

AU - Buckley, Daniel H.

AU - Buongiorno, Joy

AU - Cadillo-Quiroz, Hinsby

AU - Caffrey, Sean M.

AU - Campbell, Ashley N.

AU - Campbell, Barbara

AU - Carr, Stephanie

AU - Carroll, Jo Lynn

AU - Cary, S. Craig

AU - Cates, Anna M.

AU - Cattolico, Rose Ann

AU - Cavicchioli, Ricardo

AU - Chistoserdova, Ludmila

AU - Coleman, Maureen L.

AU - Constant, Philippe

AU - Conway, Jonathan M.

AU - Mac Cormack, Walter P.

AU - Crowe, Sean

AU - Crump, Byron

AU - Currie, Cameron

AU - Daly, Rebecca

AU - DeAngelis, Kristen M.

AU - Denef, Vincent

AU - Denman, Stuart E.

AU - Desta, Adey

AU - Dionisi, Hebe

AU - Dodsworth, Jeremy

AU - Dombrowski, Nina

AU - Donohue, Timothy

AU - Dopson, Mark

AU - Driscoll, Timothy

AU - Dunfield, Peter

AU - Dupont, Christopher L.

AU - Dynarski, Katherine A.

AU - Edgcomb, Virginia

AU - Edwards, Elizabeth A.

AU - Elshahed, Mostafa S.

AU - Figueroa, Israel

AU - Flood, Beverly

AU - Fortney, Nathaniel

AU - Fortunato, Caroline S.

AU - Francis, Christopher

AU - Gachon, Claire M.M.

AU - Garcia, Sarahi L.

AU - Gazitua, Maria C.

AU - Gentry, Terry

AU - Gerwick, Lena

AU - Gharechahi, Javad

AU - Girguis, Peter

AU - Gladden, John

AU - Gradoville, Mary

AU - Grasby, Stephen E.

AU - Gravuer, Kelly

AU - Grettenberger, Christen L.

AU - Gruninger, Robert J.

AU - Guo, Jiarong

AU - Habteselassie, Mussie Y.

AU - Hallam, Steven J.

AU - Hatzenpichler, Roland

AU - Hausmann, Bela

AU - Hazen, Terry C.

AU - Hedlund, Brian

AU - Henny, Cynthia

AU - Herfort, Lydie

AU - Hernandez, Maria

AU - Hershey, Olivia S.

AU - Hess, Matthias

AU - Hollister, Emily B.

AU - Hug, Laura A.

AU - Hunt, Dana

AU - Jansson, Janet

AU - Jarett, Jessica

AU - Kadnikov, Vitaly V.

AU - Kelly, Charlene

AU - Kelly, Robert

AU - Kelly, William

AU - Kerfeld, Cheryl A.

AU - Kimbrel, Jeff

AU - Klassen, Jonathan L.

AU - Konstantinidis, Konstantinos T.

AU - Lee, Laura L.

AU - Li, Wen Jun

AU - Loder, Andrew J.

AU - Loy, Alexander

AU - Lozada, Mariana

AU - MacGregor, Barbara

AU - Magnabosco, Cara

AU - Maria da Silva, Aline

AU - McKay, R. Michael

AU - McMahon, Katherine

AU - McSweeney, Chris S.

AU - Medina, Mónica

AU - Meredith, Laura

AU - Mizzi, Jessica

AU - Mock, Thomas

AU - Momper, Lily

AU - Moran, Mary Ann

AU - Morgan-Lang, Connor

AU - Moser, Duane

AU - Muyzer, Gerard

AU - Myrold, David

AU - Nash, Maisie

AU - Nesbø, Camilla L.

AU - Neumann, Anthony P.

AU - Neumann, Rebecca B.

AU - Noguera, Daniel

AU - Northen, Trent

AU - Norton, Jeanette

AU - Nowinski, Brent

AU - Nüsslein, Klaus

AU - O’Malley, Michelle A.

AU - Oliveira, Rafael S.

AU - Maia de Oliveira, Valeria

AU - Onstott, Tullis

AU - Osvatic, Jay

AU - Ouyang, Yang

AU - Pachiadaki, Maria

AU - Parnell, Jacob

AU - Partida-Martinez, Laila P.

AU - Peay, Kabir G.

AU - Pelletier, Dale

AU - Peng, Xuefeng

AU - Pester, Michael

AU - Pett-Ridge, Jennifer

AU - Peura, Sari

AU - Pjevac, Petra

AU - Plominsky, Alvaro M.

AU - Poehlein, Anja

AU - Pope, Phillip B.

AU - Ravin, Nikolai

AU - Redmond, Molly C.

AU - Reiss, Rebecca

AU - Rich, Virginia

AU - Rinke, Christian

AU - Rodrigues, Jorge L.Mazza

AU - Rodriguez-Reillo, William

AU - Rossmassler, Karen

AU - Sackett, Joshua

AU - Salekdeh, Ghasem Hosseini

AU - Saleska, Scott

AU - Scarborough, Matthew

AU - Schachtman, Daniel

AU - Schadt, Christopher W.

AU - Schrenk, Matthew

AU - Sczyrba, Alexander

AU - Sengupta, Aditi

AU - Setubal, Joao C.

AU - Shade, Ashley

AU - Sharp, Christine

AU - Sherman, David H.

AU - Shubenkova, Olga V.

AU - Sierra-Garcia, Isabel Natalia

AU - Simister, Rachel

AU - Simon, Holly

AU - Sjöling, Sara

AU - Slonczewski, Joan

AU - Correa de Souza, Rafael Soares

AU - Spear, John R.

AU - Stegen, James C.

AU - Stepanauskas, Ramunas

AU - Stewart, Frank

AU - Suen, Garret

AU - Sullivan, Matthew

AU - Sumner, Dawn

AU - Swan, Brandon K.

AU - Swingley, Wesley

AU - Tarn, Jonathan

AU - Taylor, Gordon T.

AU - Teeling, Hanno

AU - Tekere, Memory

AU - Teske, Andreas

AU - Thomas, Torsten

AU - Thrash, Cameron

AU - Tiedje, James

AU - Ting, Claire S.

AU - Tully, Benjamin

AU - Tyson, Gene

AU - Ulloa, Osvlado

AU - Valentine, David L.

AU - Van Goethem, Marc W.

AU - VanderGheynst, Jean

AU - Verbeke, Tobin J.

AU - Vollmers, John

AU - Vuillemin, Aurèle

AU - Waldo, Nicholas B.

AU - Walsh, David A.

AU - Weimer, Bart C.

AU - Whitman, Thea

AU - van der Wielen, Paul

AU - Wilkins, Michael

AU - Williams, Timothy J.

AU - Woodcroft, Ben

AU - Woolet, Jamie

AU - Wrighton, Kelly

AU - Ye, Jun

AU - Young, Erica B.

AU - Youssef, Noha H.

AU - Yu, Feiqiao Brian

AU - Zemskaya, Tamara I.

AU - Ziels, Ryan

AU - Woyke, Tanja

AU - Mouncey, Nigel J.

AU - Ivanova, Natalia N.

AU - Kyrpides, Nikos C.

AU - Eloe-Fadrosh, Emiley A.

N1 - Generated from Scopus record by KAUST IRTS on 2023-10-23

PY - 2021/4/1

Y1 - 2021/4/1

N2 - 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.

AB - 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.

UR - https://www.nature.com/articles/s41587-020-0718-6

UR - http://www.scopus.com/inward/record.url?scp=85095709328&partnerID=8YFLogxK

U2 - 10.1038/s41587-020-0718-6

DO - 10.1038/s41587-020-0718-6

M3 - Article

SN - 1546-1696

VL - 39

SP - 499

EP - 509

JO - Nature biotechnology

JF - Nature biotechnology

IS - 4

ER -

A genomic catalog of Earth’s microbiomes

Abstract

Bibliographical note

Access to Document

Other files and links

Fingerprint

Cite this