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A communal catalogue reveals Earth’s multiscale microbial diversity

Author

Listed:
  • Luke R. Thompson

    (University of California San Diego
    University of Southern Mississippi
    Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, stationed at Southwest Fisheries Science Center)

  • 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
    University of California San Diego
    Skaggs School of Pharmacy, University of California San Diego)

  • Sean M. Gibbons

    (Massachusetts Institute of Technology
    The Broad Institute of MIT and Harvard)

  • Gail Ackermann

    (University of California San Diego)

  • Jose A. Navas-Molina

    (University of California San Diego
    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
    University of California San Diego)

  • Antonio González

    (University of California San Diego)

  • James T. Morton

    (University of California San Diego
    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
    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
    University of Illinois at Chicago)

  • Donna Berg-Lyons

    (BioFrontiers Institute, University of Colorado)

  • Valerie McKenzie

    (University of Colorado)

  • Noah Fierer

    (University of Colorado
    Cooperative Institute for Research in Environmental Sciences, University of Colorado)

  • Jed A. Fuhrman

    (University of Southern California)

  • Aaron Clauset

    (BioFrontiers Institute, University of Colorado
    University of Colorado)

  • Rick L. Stevens

    (Computing, Environment and Life Sciences, Argonne National Laboratory
    University of Chicago)

  • Ashley Shade

    (Michigan State University
    Soil and Microbial Sciences, Michigan State University
    Program in Ecology, Evolutionary Biology and Behavior, 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
    University of Chicago)

  • Rob Knight

    (University of California San Diego
    University of California San Diego
    Center for Microbiome Innovation, University of California San Diego)

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.

Suggested Citation

  • 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 & Ste, 2017. "A communal catalogue reveals Earth’s multiscale microbial diversity," Nature, Nature, vol. 551(7681), pages 457-463, November.
    • Handle: RePEc:nat:nature:v:551:y:2017:i:7681:d:10.1038_nature24621
    DOI: 10.1038/nature24621
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    Cited by:

    1. Mishra, Aditya & Müller, Christian L., 2022. "Robust regression with compositional covariates," Computational Statistics & Data Analysis, Elsevier, vol. 165(C).
    2. Gertrude Ecklu-Mensah & Candice Choo-Kang & Maria Gjerstad Maseng & Sonya Donato & Pascal Bovet & Bharathi Viswanathan & Kweku Bedu-Addo & Jacob Plange-Rhule & Prince Oti Boateng & Terrence E. Forrest, 2023. "Gut microbiota and fecal short chain fatty acids differ with adiposity and country of origin: the METS-microbiome study," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    3. Joe J. Lim & Christian Diener & James Wilson & Jacob J. Valenzuela & Nitin S. Baliga & Sean M. Gibbons, 2023. "Growth phase estimation for abundant bacterial populations sampled longitudinally from human stool metagenomes," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    4. Giuseppe Malgioglio & Giulio Flavio Rizzo & Sebastian Nigro & Vincent Lefebvre du Prey & Joelle Herforth-Rahmé & Vittoria Catara & Ferdinando Branca, 2022. "Plant-Microbe Interaction in Sustainable Agriculture: The Factors That May Influence the Efficacy of PGPM Application," Sustainability, MDPI, vol. 14(4), pages 1-28, February.

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