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. Haroon, Jad 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 () and Rob Knight ()
Additional contact information
Luke R. Thompson: University of California San Diego
Jon G. Sanders: University of California San Diego
Daniel McDonald: University of California San Diego
Amnon Amir: University of California San Diego
Joshua Ladau: The Gladstone Institutes and University of California San Francisco
Kenneth J. Locey: Indiana University
Robert J. Prill: Industrial and Applied Genomics, IBM Almaden Research Center
Anupriya Tripathi: University of California San Diego
Sean M. Gibbons: Massachusetts Institute of Technology
Gail Ackermann: University of California San Diego
Jose A. Navas-Molina: University of California San Diego
Stefan Janssen: University of California San Diego
Evguenia Kopylova: University of California San Diego
Yoshiki Vázquez-Baeza: University of California San Diego
Antonio González: University of California San Diego
James T. Morton: University of California San Diego
Siavash Mirarab: University of California San Diego
Zhenjiang Zech Xu: University of California San Diego
Lingjing Jiang: University of California San Diego
Mohamed F. Haroon: Harvard University
Jad Kanbar: University of California San Diego
Qiyun Zhu: University of California San Diego
Se Jin Song: University of California San Diego
Tomasz Kosciolek: University of California San Diego
Nicholas A. Bokulich: Pathogen and Microbiome Institute, Northern Arizona University
Joshua Lefler: University of California San Diego
Colin J. Brislawn: Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory
Gregory Humphrey: University of California San Diego
Sarah M. Owens: Argonne National Laboratory
Jarrad Hampton-Marcell: Argonne National Laboratory
Donna Berg-Lyons: BioFrontiers Institute, University of Colorado
Valerie McKenzie: University of Colorado
Noah Fierer: University of Colorado
Jed A. Fuhrman: University of Southern California
Aaron Clauset: BioFrontiers Institute, University of Colorado
Rick L. Stevens: Computing, Environment and Life Sciences, Argonne National Laboratory
Ashley Shade: Michigan State University
Katherine S. Pollard: The Gladstone Institutes and University of California San Francisco
Kelly D. Goodwin: Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, stationed at Southwest Fisheries Science Center
Janet K. Jansson: Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory
Jack A. Gilbert: Argonne National Laboratory
Rob Knight: University of California San Diego

Nature, 2017, vol. 551, issue 7681, 457-463

Abstract: 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.

Date: 2017
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DOI: 10.1038/nature24621

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