A communal catalogue reveals Earth's multiscale microbial diversity

被引：1723

作者：

Thompson, Luke R. ^{[1
,2
,3
,4
]}

Sanders, Jon G. ^{[1
]}

McDonald, Daniel ^{[1
]}

Amir, Amnon ^{[1
]}

Ladau, Joshua ^{[5
,6
]}

Locey, Kenneth J. ^{[7
]}

Prill, Robert J. ^{[8
]}

Tripathi, Anupriya ^{[1
,9
,10
]}

Gibbons, Sean M. ^{[11
,12
]}

Ackermann, Gail ^{[1
]}

Navas-Molina, Jose A. ^{[1
,13
]}

Janssen, Stefan ^{[1
]}

Kopylova, Evguenia ^{[1
]}

Vazquez-Baeza, Yoshiki ^{[1
,13
]}

Gonzalez, Antonio ^{[1
]}

Morton, James T. ^{[1
,13
]}

Mirarab, Siavash ^{[14
]}

Xu, Zhenjiang Zech ^{[1
]}

Jiang, Lingjing ^{[1
,15
]}

Haroon, Mohamed F. ^{[16
]}

Kanbar, Jad ^{[1
]}

Zhu, Qiyun ^{[1
]}

Song, Se Jin ^{[1
]}

Kosciolek, Tomasz ^{[1
]}

Bokulich, Nicholas A. ^{[17
]}

Lefler, Joshua ^{[1
]}

Brislawn, Colin J. ^{[18
]}

Humphrey, Gregory ^{[1
]}

Owens, Sarah M. ^{[19
]}

Hampton-Marcell, Jarrad ^{[19
,20
]}

Berg-Lyons, Donna ^{[21
]}

McKenzie, Valerie ^{[22
]}

Fierer, Noah ^{[22
,23
]}

Fuhrman, Jed A. ^{[24
]}

Clauset, Aaron ^{[21
,25
]}

Stevens, Rick L. ^{[26
,27
]}

Shade, Ashley ^{[28
,29
,30
]}

Pollard, Katherine S. ^{[5
,6
]}

Goodwin, Kelly D. ^{[4
]}

Jansson, Janet K. ^{[18
]}

Gilbert, Jack A. ^{[19
,31
]}

Knight, Rob ^{[1
,13
,32
]}

Rivera, Jose L. Agosto ^{[33
]}

Al-Moosawi, Lisa ^{[34
]}

Alverdy, John ^{[35
]}

Amato, Katherine R. ^{[36
]}

Andras, Jason ^{[37
]}

Angenent, Largus T. ^{[38
,39
]}

Antonopoulos, Dionysios A. ^{[40
]}

Apprill, Amy ^{[41
]}

机构：

[1] Univ Calif San Diego, Dept Pediat, La Jolla, CA 92093 USA

[2] Univ Southern Mississippi, Dept Biol Sci, Hattiesburg, MS 39406 USA

[3] Univ Southern Mississippi, Northern Gulf Inst, Hattiesburg, MS 39406 USA

[4] Southwest Fisheries Sci Ctr, Natl Ocean & Atmospher Adm, Atlantic Oceanog & Meteorol Lab, Ocean Chem & Ecosyst Div, La Jolla, CA USA

[5] Gladstone Inst, San Francisco, CA USA

[6] Univ Calif San Francisco, San Francisco, CA 94143 USA

[7] Indiana Univ, Dept Biol, Bloomington, IN USA

[8] IBM Almaden Res Ctr, Ind & Appl Gen, San Jose, CA USA

[9] Univ Calif San Diego, Div Biol Sci, La Jolla, CA 92093 USA

[10] Univ Calif San Diego, Skaggs Sch Pharm, La Jolla, CA 92093 USA

[11] MIT, Dept Biol Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA

[12] Broad Inst, MIT & Harvard, Cambridge, MA USA

[13] Univ Calif San Diego, Dept Comp Sci & Engn, La Jolla, CA 92093 USA

[14] Univ Calif San Diego, Dept Elect & Comp Engn, La Jolla, CA 92093 USA

[15] Univ Calif San Diego, Dept Family Med & Publ Hlth, La Jolla, CA 92093 USA

[16] Harvard Univ, Dept Organism & Evolutionary Biol, Cambridge, MA 02138 USA

[17] No Arizona Univ, Pathogen & Microbiome Inst, Flagstaff, AZ 86011 USA

[18] Pacific Northwest Natl Lab, Earth & Biol Sci Directorate, Richland, WA 99354 USA

[19] Argonne Natl Lab, Biosci Div, 9700 S Cass Ave, Argonne, IL 60439 USA

[20] Univ Illinois, Dept Biol Sci, Chicago, IL 60680 USA

[21] Univ Colorado, BioFrontiers Inst, Boulder, CO 80309 USA

[22] Univ Colorado, Dept Ecol & Evolutionary Biol, Boulder, CO 80309 USA

[23] Univ Colorado, Cooperat Inst Res Environm Sci, Boulder, CO 80309 USA

[24] Univ Southern Calif, Dept Biol Sci, Los Angeles, CA 90089 USA

[25] Univ Colorado, Dept Comp Sci, Boulder, CO 80309 USA

[26] Argonne Natl Lab, Comp Environm & Life Sci, 9700 S Cass Ave, Argonne, IL 60439 USA

[27] Univ Chicago, Dept Comp Sci, Chicago, IL 60637 USA

[28] Michigan State Univ, Dept Microbiol & Mol Genet, E Lansing, MI 48824 USA

[29] Michigan State Univ, Dept Plant Soil & Microbial Sci, E Lansing, MI 48824 USA

[30] Michigan State Univ, Program Ecol Evolutionary Biol & Behav, E Lansing, MI 48824 USA

[31] Univ Chicago, Dept Surg, 5841 S Maryland Ave, Chicago, IL 60637 USA

[32] Univ Calif San Diego, Ctr Microbiome Innovat, La Jolla, CA 92093 USA

[33] Univ Puerto Rico, San Juan, PR 00936 USA

[34] Plymouth Marine Lab, Plymouth, Devon, England

[35] Univ Chicago, Chicago, IL 60637 USA

[36] Northwestern Univ, Evanston, IL USA

[37] Mt Holyoke Coll, S Hadley, MA 01075 USA

[38] Cornell Univ, Ithaca, NY USA

[39] Univ Tubingen, Tubingen, Germany

[40] Argonne Natl Lab, 9700 S Cass Ave, Argonne, IL 60439 USA

[41] Woods Hole Oceanog Inst, Woods Hole, MA 02543 USA

[42] Univ Calif Berkeley, Berkeley, CA 94720 USA

[43] Univ Notre Dame, South Bend, IN USA

[44] Univ South Bohemia, Ceske Budejovice, Czech Republic

[45] Univ Victoria, Victoria, BC, Canada

[46] Univ Calif Davis, Davis, CA 95616 USA

[47] Maharshi Dayanand Saraswati Univ, Ajmer, India

[48] Univ Delaware, Newark, DE USA

[49] Univ Paris 06, Evolut Paris Seine, Paris, France

[50] Natl Univ Mongolia, Ulaanbaatar, Mongolia

来源：

NATURE | 2017年 / 551卷 / 7681期

基金：

美国国家科学基金会; 澳大利亚研究理事会;

关键词：

OPERON COPY NUMBER; BACTERIAL DIVERSITY; MARINE BACTERIAL; GLOBAL PATTERNS; COMMUNITIES; NESTEDNESS; ONTOLOGY; CONSISTENT; EVOLUTION; ARCHAEAL;

D O I：

10.1038/nature24621

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

引用

页码：457 / +

页数：21

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