Abstract
Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.
Original language | English |
---|---|
Pages (from-to) | 457-463 |
Number of pages | 7 |
Journal | Nature |
Volume | 551 |
Issue number | 7681 |
DOIs | |
State | Published - Nov 23 2017 |
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In: Nature, Vol. 551, No. 7681, 23.11.2017, p. 457-463.
Research output: Contribution to journal › Article › peer-review
TY - JOUR
T1 - A communal catalogue reveals Earth's multiscale microbial diversity
AU - Earth Microbiome Project Consortium
AU - Thompson, Luke R.
AU - Sanders, Jon G.
AU - McDonald, Daniel
AU - Amir, Amnon
AU - Ladau, Joshua
AU - Locey, Kenneth J.
AU - Prill, Robert J.
AU - Tripathi, Anupriya
AU - Gibbons, Sean M.
AU - Ackermann, Gail
AU - Navas-Molina, Jose A.
AU - Janssen, Stefan
AU - Kopylova, Evguenia
AU - Vázquez-Baeza, Yoshiki
AU - González, Antonio
AU - Morton, James T.
AU - Mirarab, Siavash
AU - Xu, Zhenjiang Zech
AU - Jiang, Lingjing
AU - Haroon, Mohamed F.
AU - Kanbar, Jad
AU - Zhu, Qiyun
AU - Song, Se Jin
AU - Kosciolek, Tomasz
AU - Bokulich, Nicholas A.
AU - Lefler, Joshua
AU - Brislawn, Colin J.
AU - Humphrey, Gregory
AU - Owens, Sarah M.
AU - Hampton-Marcell, Jarrad
AU - Berg-Lyons, Donna
AU - McKenzie, Valerie
AU - Fierer, Noah
AU - Fuhrman, Jed A.
AU - Clauset, Aaron
AU - Stevens, Rick L.
AU - Shade, Ashley
AU - Pollard, Katherine S.
AU - Goodwin, Kelly D.
AU - Jansson, Janet K.
AU - Gilbert, Jack A.
AU - Knight, Rob
AU - Agosto Rivera, Jose L.
AU - Al-Moosawi, Lisa
AU - Alverdy, John
AU - Amato, Katherine R.
AU - Andras, Jason
AU - Angenent, Largus T.
AU - Antonopoulos, Dionysios A.
AU - Apprill, Amy
AU - Armitage, David
AU - Ballantine, Kate
AU - Bárta, Jiří
AU - Baum, Julia K.
AU - Berry, Allison
AU - Bhatnagar, Ashish
AU - Bhatnagar, Monica
AU - Biddle, Jennifer F.
AU - Bittner, Lucie
AU - Boldgiv, Bazartseren
AU - Bottos, Eric
AU - Boyer, Donal M.
AU - Braun, Josephine
AU - Brazelton, William
AU - Brearley, Francis Q.
AU - Campbell, Alexandra H.
AU - Caporaso, J. Gregory
AU - Cardona, Cesar
AU - Carroll, Jo Lynn
AU - Cary, S. Craig
AU - Casper, Brenda B.
AU - Charles, Trevor C.
AU - Chu, Haiyan
AU - Claar, Danielle C.
AU - Clark, Robert G.
AU - Clayton, Jonathan B.
AU - Clemente, Jose C.
AU - Cochran, Alyssa
AU - Coleman, Maureen L.
AU - Collins, Gavin
AU - Colwell, Rita R.
AU - Contreras, Mónica
AU - Crary, Benjamin B.
AU - Creer, Simon
AU - Cristol, Daniel A.
AU - Crump, Byron C.
AU - Cui, Duoying
AU - Daly, Sarah E.
AU - Davalos, Liliana
AU - Dawson, Russell D.
AU - Defazio, Jennifer
AU - Delsuc, Frédéric
AU - Dionisi, Hebe M.
AU - Dominguez-Bello, Maria Gloria
AU - Dowell, Robin
AU - Dubinsky, Eric A.
AU - Dunn, Peter O.
AU - Ercolini, Danilo
AU - Espinoza, Robert E.
AU - Ezenwa, Vanessa
AU - Fenner, Nathalie
AU - Findlay, Helen S.
AU - Fleming, Irma D.
AU - Fogliano, Vincenzo
AU - Forsman, Anna
AU - Freeman, Chris
AU - Friedman, Elliot S.
AU - Galindo, Giancarlo
AU - Garcia, Liza
AU - Garcia-Amado, Maria Alexandra
AU - Garshelis, David
AU - Gasser, Robin B.
AU - Gerdts, Gunnar
AU - Gibson, Molly K.
AU - Gifford, Isaac
AU - Gill, Ryan T.
AU - Giray, Tugrul
AU - Gittel, Antje
AU - Golyshin, Peter
AU - Gong, Donglai
AU - Grossart, Hans Peter
AU - Guyton, Kristina
AU - Haig, Sarah Jane
AU - Hale, Vanessa
AU - Hall, Ross Stephen
AU - Hallam, Steven J.
AU - Handley, Kim M.
AU - Hasan, Nur A.
AU - Haydon, Shane R.
AU - Hickman, Jonathan E.
AU - Hidalgo, Glida
AU - Hofmockel, Kirsten S.
AU - Hooker, Jeff
AU - Hulth, Stefan
AU - Hultman, Jenni
AU - Hyde, Embriette
AU - Ibáñez-Álamo, Juan Diego
AU - Jastrow, Julie D.
AU - Jex, Aaron R.
AU - Johnson, L. Scott
AU - Johnston, Eric R.
AU - Joseph, Stephen
AU - Jurburg, Stephanie D.
AU - Jurelevicius, Diogo
AU - Karlsson, Anders
AU - Karlsson, Roger
AU - Kauppinen, Seth
AU - Kellogg, Colleen T.E.
AU - Kennedy, Suzanne J.
AU - Kerkhof, Lee J.
AU - King, Gary M.
AU - Kling, George W.
AU - Koehler, Anson V.
AU - Krezalek, Monika
AU - Kueneman, Jordan
AU - Lamendella, Regina
AU - Landon, Emily M.
AU - Lanede Graaf, Kelly
AU - LaRoche, Julie
AU - Larsen, Peter
AU - Laverock, Bonnie
AU - Lax, Simon
AU - Lentino, Miguel
AU - Levin, Iris I.
AU - Liancourt, Pierre
AU - Liang, Wenju
AU - Linz, Alexandra M.
AU - Lipson, David A.
AU - Liu, Yongqin
AU - Lladser, Manuel E.
AU - Lozada, Mariana
AU - Spirito, Catherine M.
AU - MacCormack, Walter P.
AU - MacRae-Crerar, Aurora
AU - Magris, Magda
AU - Martín-Platero, Antonio M.
AU - Martín-Vivaldi, Manuel
AU - Martínez, L. Margarita
AU - Martínez-Bueno, Manuel
AU - Marzinelli, Ezequiel M.
AU - Mason, Olivia U.
AU - Mayer, Gregory D.
AU - McDevitt-Irwin, Jamie M.
AU - McDonald, James E.
AU - McGuire, Krista L.
AU - McMahon, Katherine D.
AU - McMinds, Ryan
AU - Medina, Mónica
AU - Mendelson, Joseph R.
AU - Metcalf, Jessica L.
AU - Meyer, Folker
AU - Michelangeli, Fabian
AU - Miller, Kim
AU - Mills, David A.
AU - Minich, Jeremiah
AU - Mocali, Stefano
AU - Moitinho-Silva, Lucas
AU - Moore, Anni
AU - Morgan-Kiss, Rachael M.
AU - Shakhsheer, Baddr
N1 - Funding Information: Acknowledgements We thank J. DeReus for management of information systems; J. Huntley and K. Jepsen for management of sequencing facilities; B. Erickson for administrative assistance; J. Lennon for discussions about macroecological theory; S. Peddada for assistance with effect size calculations; P. L. Buttigieg, C. Mungall, and D. Siegele for assistance with ontologies; A. Rose, A.-S. Roy, A. Bearquiver, B. Cohen, C. Tischer, C. Feh, D. Winkler, E. Jones, E. Angert, F. Blackwolf, G. Martin, H. Schunck, K. Hallinger, L. R. McGuinness, M. Mühling, M. Lombardo, R. Madsen, S. Bowatte, S. Romac, S. Garcia-Houchins, V. Harriman, and W. James for assistance with sample and/or metadata collection; and the following individuals for supporting the project’s founding: A. Scyzrba, A. McHardy, A. Teske, A. Wilke, C. T. Brown, C. Brown, D. Huson, D. Field, D. Evers, D. Wendel, E. Glass, E. Kolke, F. Sun, F. O. Glöckner, G. Kowalchuk, H.-P. Klenk, J. Tiedje, J. Gordon, J. Raes, J. Knight, J. Kostka, J. Heidelberg, J. Eisen, K. E. Wommack, K. Docherty, K. Keegan, K. Konstantindis, M. Bailey, M. Sullivan, N. Desai, N. Kyprides, N. Pace, P. Balaji, R. Gallery, R. Mackelprang, R. O’Dor, R. Ley, T. Vogel, T. Chen, and W. Feng. This work was supported by the John Templeton Foundation (grant ID 44000, Convergent Evolution of the Vertebrate Microbiome), the W. M. Keck Foundation (DT061413), Argonne National Laboratory (US Department of Energy contract DE-AC02-06CH11357), the Australian Research Council, the Tula Foundation, the Samuel Lawrence Foundation, and the Extreme Science and Engineering Discovery Environment (XSEDE, project number BIO150043), which is supported by National Science Foundation grant number ACI-1053575. Funding for L.R.T. was provided in part by NOAA’s Atlantic Oceanographic and Meteorological Laboratory (AOML) and the Mississippi State University/NOAA Northern Gulf Institute. We thank MO BIO Laboratories, Luca Technologies, Eppendorf, Boreal Genomics, Illumina, Roche, and Integrated DNA Technologies for in-kind support at various phases of the project. Publisher Copyright: © 2017 Macmillan Publishers Limited, part of Springer Nature. All rights reserved.
PY - 2017/11/23
Y1 - 2017/11/23
N2 - Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.
AB - Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.
UR - http://www.scopus.com/inward/record.url?scp=85034804875&partnerID=8YFLogxK
U2 - 10.1038/nature24621
DO - 10.1038/nature24621
M3 - Article
C2 - 29088705
AN - SCOPUS:85034804875
SN - 0028-0836
VL - 551
SP - 457
EP - 463
JO - Nature
JF - Nature
IS - 7681
ER -