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Nature. 2017 Nov 23;551(7681):457-463. doi: 10.1038/nature24621. Epub 2017 Nov 1.

A communal catalogue reveals Earth's multiscale microbial diversity.

Collaborators (261)

Rivera JLA, Al-Moosawi L, Alverdy J, Amato KR, Andras J, Angenent LT, Antonopoulos DA, Apprill A, Armitage D, Ballantine K, Bárta J, Baum JK, Berry A, Bhatnagar A, Bhatnagar M, Biddle JF, Bittner L, Boldgiv B, Bottos E, Boyer DM, Braun J, Brazelton W, Brearley FQ, Campbell AH, Caporaso JG, Cardona C, Carroll J, Cary SC, Casper BB, Charles TC, Chu H, Claar DC, Clark RG, Clayton JB, Clemente JC, Cochran A, Coleman ML, Collins G, Colwell RR, Contreras M, Crary BB, Creer S, Cristol DA, Crump BC, Cui D, Daly SE, Davalos L, Dawson RD, Defazio J, Delsuc F, Dionisi HM, Dominguez-Bello MG, Dowell R, Dubinsky EA, Dunn PO, Ercolini D, Espinoza RE, Ezenwa V, Fenner N, Findlay HS, Fleming ID, Fogliano V, Forsman A, Freeman C, Friedman ES, Galindo G, Garcia L, Garcia-Amado MA, Garshelis D, Gasser RB, Gerdts G, Gibson MK, Gifford I, Gill RT, Giray T, Gittel A, Golyshin P, Gong D, Grossart HP, Guyton K, Haig SJ, Hale V, Hall RS, Hallam SJ, Handley KM, Hasan NA, Haydon SR, Hickman JE, Hidalgo G, Hofmockel KS, Hooker J, Hulth S, Hultman J, Hyde E, Ibáñez-Álamo JD, Jastrow JD, Jex AR, Johnson LS, Johnston ER, Joseph S, Jurburg SD, Jurelevicius D, Karlsson A, Karlsson R, Kauppinen S, Kellogg CTE, Kennedy SJ, Kerkhof LJ, King GM, Kling GW, Koehler AV, Krezalek M, Kueneman J, Lamendella R, Landon EM, Lane-deGraaf K, LaRoche J, Larsen P, Laverock B, Lax S, Lentino M, Levin II, Liancourt P, Liang W, Linz AM, Lipson DA, Liu Y, Lladser ME, Lozada M, Spirito CM, MacCormack WP, MacRae-Crerar A, Magris M, Martín-Platero AM, Martín-Vivaldi M, Martínez LM, Martínez-Bueno M, Marzinelli EM, Mason OU, Mayer GD, McDevitt-Irwin JM, McDonald JE, McGuire KL, McMahon KD, McMinds R, Medina M, Mendelson JR, Metcalf JL, Meyer F, Michelangeli F, Miller K, Mills DA, Minich J, Mocali S, Moitinho-Silva L, Moore A, Morgan-Kiss RM, Munroe P, Myrold D, Neufeld JD, Ni Y, Nicol GW, Nielsen S, Nissimov JI, Niu K, Nolan MJ, Noyce K, O'Brien SL, Okamoto N, Orlando L, Castellano YO, Osuolale O, Oswald W, Parnell J, Peralta-Sánchez JM, Petraitis P, Pfister C, Pilon-Smits E, Piombino P, Pointing SB, Pollock FJ, Potter C, Prithiviraj B, Quince C, Rani A, Ranjan R, Rao S, Rees AP, Richardson M, Riebesell U, Robinson C, Rockne KJ, Rodriguezl SM, Rohwer F, Roundstone W, Safran RJ, Sangwan N, Sanz V, Schrenk M, Schrenzel MD, Scott NM, Seger RL, Seguin-Orlando A, Seldin L, Seyler LM, Shakhsheer B, Sheets GM, Shen C, Shi Y, Shin H, Shogan BD, Shutler D, Siegel J, Simmons S, Sjöling S, Smith DP, Soler JJ, Sperling M, Steinberg PD, Stephens B, Stevens MA, Taghavi S, Tai V, Tait K, Tan CL, Tas N, Taylor DL, Thomas T, Timling I, Turner BL, Urich T, Ursell LK, van der Lelie D, Van Treuren W, van Zwieten L, Vargas-Robles D, Thurber RV, Vitaglione P, Walker DA, Walters WA, Wang S, Wang T, Weaver T, Webster NS, Wehrle B, Weisenhorn P, Weiss S, Werner JJ, West K, Whitehead A, Whitehead SR, Whittingham LA, Willerslev E, Williams AE, Wood SA, Woodhams DC, Yang Y, Zaneveld J, Zarraonaindia I, Zhang Q, Zhao H.

Author information

1
Department of Pediatrics, University of California San Diego, La Jolla, California, USA.
2
Department of Biological Sciences and Northern Gulf Institute, University of Southern Mississippi, Hattiesburg, Mississippi, USA.
3
Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, stationed at Southwest Fisheries Science Center, La Jolla, California, USA.
4
The Gladstone Institutes and University of California San Francisco, San Francisco, California, USA.
5
Department of Biology, Indiana University, Bloomington, Indiana, USA.
6
Industrial and Applied Genomics, IBM Almaden Research Center, San Jose, California, USA.
7
Division of Biological Sciences, University of California San Diego, La Jolla, California, USA.
8
Skaggs School of Pharmacy, University of California San Diego, La Jolla, California, USA.
9
Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
10
The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
11
Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA.
12
Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, California, USA.
13
Department of Family Medicine and Public Health, University of California San Diego, La Jolla, California, USA.
14
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA.
15
Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA.
16
Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.
17
Biosciences Division, Argonne National Laboratory, Argonne, Illinois, USA.
18
Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, USA.
19
BioFrontiers Institute, University of Colorado, Boulder, Colorado, USA.
20
Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA.
21
Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado, USA.
22
Department of Biological Sciences, University of Southern California, Los Angeles, California, USA.
23
Department of Computer Science, University of Colorado, Boulder, Colorado, USA.
24
Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne, Illinois, USA.
25
Department of Computer Science, University of Chicago, Chicago, Illinois, USA.
26
Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA.
27
Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA.
28
Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, Michigan, USA.
29
Department of Surgery, University of Chicago, Chicago, Illinois, USA.
30
Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA.

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.

PMID:
29088705
PMCID:
PMC6192678
DOI:
10.1038/nature24621
[Indexed for MEDLINE]
Free PMC Article

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