A communal catalogue reveals Earth's multiscale microbial diversity

Luke R. Thompson, Jon G. Sanders, Daniel McDonald, Amnon Amir, Joshua Ladau, Kenneth J. Locey, Robert J. Prill, Anupriya Tripathi, Sean M. Gibbons, Gail Ackermann, Jose A. Navas-Molina, Stefan Janssen, Evguenia Kopylova, Yoshiki Vázquez-Baeza, Antonio González, James T. Morton, Siavash Mirarab, Zhenjiang Zech Xu, Lingjing Jiang, Mohamed F. HaroonJad Kanbar, Qiyun Zhu, Se Jin Song, Tomasz Kosciolek, Nicholas A. Bokulich, Joshua Lefler, Colin J. Brislawn, Gregory Humphrey, Sarah M. Owens, Jarrad Hampton-Marcell, Donna Berg-Lyons, Valerie McKenzie, Noah Fierer, Jed A. Fuhrman, Aaron Clauset, Rick L. Stevens, Ashley Shade, Katherine S. Pollard, Kelly D. Goodwin, Janet K. Jansson, Jack A. Gilbert, Rob Knight, Jose L. Agosto Rivera, Lisa Al-Moosawi, John Alverdy, Katherine R. Amato, Jason Andras, Largus T. Angenent, Dionysios A. Antonopoulos, Jonathan B. Clayton, Earth Microbiome Project Consortium

Research output: Contribution to journalArticlepeer-review

532 Scopus citations

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 languageEnglish (US)
Pages (from-to)457-463
Number of pages7
JournalNature
Volume551
Issue number7681
DOIs
StatePublished - Nov 23 2017

Bibliographical note

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.

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