Structure, function and diversity of the healthy human microbiome

被引：7889

作者：

Huttenhower, Curtis ^{[1
,2
]}

Gevers, Dirk ^{[2
]}

Knight, Rob ^{[3
,4
]}

Abubucker, Sahar ^{[5
]}

Badger, Jonathan H. ^{[6
]}

Chinwalla, Asif T. ^{[5
]}

Creasy, Heather H. ^{[7
]}

Earl, Ashlee M. ^{[2
]}

FitzGerald, Michael G. ^{[2
]}

Fulton, Robert S. ^{[5
]}

Giglio, Michelle G. ^{[7
]}

Hallsworth-Pepin, Kymberlie ^{[5
]}

Lobos, Elizabeth A. ^{[5
]}

Madupu, Ramana ^{[6
]}

Magrini, Vincent ^{[5
]}

Martin, John C. ^{[5
]}

Mitreva, Makedonka ^{[5
]}

Muzny, Donna M. ^{[8
]}

Sodergren, Erica J. ^{[5
]}

Versalovic, James ^{[9
,10
]}

Wollam, Aye M. ^{[5
]}

Worley, Kim C. ^{[8
]}

Wortman, Jennifer R. ^{[7
]}

Young, Sarah K. ^{[2
]}

Zeng, Qiandong ^{[2
]}

Aagaard, Kjersti M. ^{[11
]}

Abolude, Olukemi O. ^{[7
]}

Allen-Vercoe, Emma ^{[12
]}

Alm, Eric J. ^{[2
,13
]}

Alvarado, Lucia ^{[2
]}

Andersen, Gary L. ^{[14
]}

Anderson, Scott ^{[2
]}

Appelbaum, Elizabeth ^{[5
]}

Arachchi, Harindra M. ^{[2
]}

Armitage, Gary ^{[15
]}

Arze, Cesar A. ^{[7
]}

Ayvaz, Tulin

Baker, Carl C. ^{[16
]}

Begg, Lisa ^{[17
]}

Belachew, Tsegahiwot ^{[18
]}

Bhonagiri, Veena ^{[5
]}

Bihan, Monika ^{[6
]}

Blaser, Martin J. ^{[19
]}

Bloom, Toby ^{[2
]}

Bonazzi, Vivien ^{[20
]}

Brooks, J. Paul ^{[21
,22
]}

Buck, Gregory A. ^{[22
,23
]}

Buhay, Christian J. ^{[8
]}

Busam, Dana A. ^{[6
]}

Campbell, Joseph L. ^{[18
,20
]}

机构：

[1] Harvard Univ, Sch Publ Hlth, Boston, MA 02115 USA

[2] Broad Inst MIT & Harvard, Cambridge, MA 02142 USA

[3] Univ Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA

[4] Howard Hughes Med Inst, Boulder, CO 80309 USA

[5] Washington Univ, Sch Med, Genome Inst, St Louis, MO 63108 USA

[6] J Craig Venter Inst, Rockville, MD 20850 USA

[7] Univ Maryland, Sch Med, Inst Genome Sci, Baltimore, MD 21201 USA

[8] Baylor Coll Med, Human Genome Sequencing Ctr, Houston, TX 77030 USA

[9] Baylor Coll Med, Dept Pathol & Immunol, Houston, TX 77030 USA

[10] Texas Childrens Hosp, Dept Pathol, Houston, TX 77030 USA

[11] Baylor Coll Med, Dept Obstet & Gynecol, Div Maternal Fetal Med, Houston, TX 77030 USA

[12] Univ Guelph, Guelph, ON N1G 2W1, Canada

[13] MIT, Dept Civil & Environm Engn, Cambridge, MA 02139 USA

[14] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Ctr Environm Biotechnol, Berkeley, CA 94720 USA

[15] Univ Calif San Francisco, Sch Dent, San Francisco, CA 94143 USA

[16] Natl Inst Arthrit & Musculoskeletal & Skin, NIH, Bethesda, MD 20892 USA

[17] Off Res Womens Hlth, NIH, Bethesda, MD 20892 USA

[18] NIAID, NIH, Bethesda, MD 20892 USA

[19] NYU, Langone Med Ctr, Dept Med, New York, NY 10016 USA

[20] NHGRI, NIH, Bethesda, MD 20892 USA

[21] Virginia Commonwealth Univ, Dept Stat Sci & Operat Res, Richmond, VA 23284 USA

[22] Virginia Commonwealth Univ, Ctr Study Biol Complex, Richmond, VA 23284 USA

[23] Virginia Commonwealth Univ, Dept Biol, Richmond, VA 23284 USA

[24] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Natl Energy Res Sci Comp Ctr, Technol Integrat Grp, Berkeley, CA 94720 USA

[25] Los Alamos Natl Lab, Biosci Div, Genome Sci Grp, Los Alamos, NM 87545 USA

[26] Joint Genome Inst, Walnut Creek, CA 94598 USA

[27] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Computat Res Div, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA

[28] NIDCR, NIH, Bethesda, MD 20892 USA

[29] Procter & Gamble Co, FemCare Prod Safety & Regulatory Affairs, Cincinnati, OH 45224 USA

[30] Second Genome Inc, Bioinformat Dept, San Bruno, CA 94066 USA

[31] Forsyth Inst, Dept Mol Genet, Cambridge, MA 02142 USA

[32] Harvard Univ, Sch Dent Med, Dept Oral Med Infect & Immun, Boston, MA 02115 USA

[33] Washington Univ, Sch Med, Dept Med, Div Gen Med Sci, St Louis, MO 63110 USA

[34] Washington Univ, Sch Med, Dept Pathol & Immunol, St Louis, MO 63110 USA

[35] bioMerieux Inc, Durham, SC 27712 USA

[36] Drive5 Com, Tiburon, CA 94920 USA

[37] Cleveland Clin, Ctr Eth Humanities & Spiritual Care, Cleveland, OH 44195 USA

[38] VIB, Dept Biol Struct, B-1050 Ixelles, Belgium

[39] Vrije Univ Brussel, Dept Appl Biol Sci DBIT, B-1050 Ixelles, Belgium

[40] Univ N Carolina, Dept Bioinformat & Genom, Charlotte, NC 28223 USA

[41] Univ Idaho, Dept Biol Sci, Moscow, ID 83844 USA

[42] St Louis Univ, Ctr Adv Dent Educ, St Louis, MO 63104 USA

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

[44] Univ Calif Los Angeles, Sch Dent, Div Associated Clin Specialties, Los Angeles, CA 90095 USA

[45] Univ Calif Los Angeles, Sch Dent, Dent Res Inst, Los Angeles, CA 90095 USA

[46] Univ Maryland, Francis King Carey Sch Law, Baltimore, MD 21201 USA

[47] Marine Biol Lab, Josephine Bay Paul Ctr, Woods Hole, MA 02543 USA

[48] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Div Earth Sci, Dept Ecol, Berkeley, CA 94720 USA

[49] Univ Texas Hlth Sci Ctr, Sch Dent, Dept Periodont, Houston, TX 77030 USA

[50] San Diego State Univ, Dept Biol, San Diego, CA 92182 USA

来源：

NATURE | 2012年 / 486卷 / 7402期

基金：

美国国家科学基金会; 比利时弗兰德研究基金会; 美国国家卫生研究院;

关键词：

IDENTIFICATION; BACTERIA;

D O I：

10.1038/nature11234

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：

Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far. We found the diversity and abundance of each habitat's signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81-99% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology and translational applications of the human microbiome.

引用

页码：207 / 214

页数：8

共 26 条

[1] Defining the normal bacterial flora of the oral cavity
Aas, JA
Paster, BJ
Stokes, LN
Olsen, I
Dewhirst, FE
[J]. JOURNAL OF CLINICAL MICROBIOLOGY, 2005, 43 (11) : 5721 - 5732
[2] Abubucker S., PLoS Comput Biol
[3] QIIME allows analysis of high-throughput community sequencing data
Caporaso, J. Gregory
Kuczynski, Justin
Stombaugh, Jesse
Bittinger, Kyle
Bushman, Frederic D.
Costello, Elizabeth K.
Fierer, Noah
Pena, Antonio Gonzalez
Goodrich, Julia K.
Gordon, Jeffrey I.
Huttley, Gavin A.
Kelley, Scott T.
Knights, Dan
Koenig, Jeremy E.
Ley, Ruth E.
Lozupone, Catherine A.
McDonald, Daniel
Muegge, Brian D.
Pirrung, Meg
Reeder, Jens
Sevinsky, Joel R.
Tumbaugh, Peter J.
Walters, William A.
Widmann, Jeremy
Yatsunenko, Tanya
Zaneveld, Jesse
Knight, Rob
[J]. NATURE METHODS, 2010, 7 (05) : 335 - 336
[4] Bacterial Community Variation in Human Body Habitats Across Space and Time
Costello, Elizabeth K.
Lauber, Christian L.
Hamady, Micah
Fierer, Noah
Gordon, Jeffrey I.
Knight, Rob
[J]. SCIENCE, 2009, 326 (5960) : 1694 - 1697
[5] Faust K., PLOS COMPUT IN PRESS
[6] Molecular identification of bacteria associated with bacterial vaginosis
Fredricks, DN
Fiedler, TL
Marrazzo, JM
[J]. NEW ENGLAND JOURNAL OF MEDICINE, 2005, 353 (18) : 1899 - 1911
[7] Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes
Giannoukos, Georgia
Ciulla, Dawn M.
Huang, Katherine
Haas, Brian J.
Izard, Jacques
Levin, Joshua Z.
Livny, Jonathan
Earl, Ashlee M.
Gevers, Dirk
Ward, Doyle V.
Nusbaum, Chad
Birren, Bruce W.
Gnirke, Andreas
[J]. GENOME BIOLOGY, 2012, 13 (03):
[8] PATRIC: the Comprehensive Bacterial Bioinformatics Resource with a Focus on Human Pathogenic Species
Gillespie, Joseph J.
Wattam, Alice R.
Cammer, Stephen A.
Gabbard, Joseph L.
Shukla, Maulik P.
Dalay, Oral
Driscoll, Timothy
Hix, Deborah
Mane, Shrinivasrao P.
Mao, Chunhong
Nordberg, Eric K.
Scott, Mark
Schulman, Julie R.
Snyder, Eric E.
Sullivan, Daniel E.
Wang, Chunxia
Warren, Andrew
Williams, Kelly P.
Xue, Tian
Yoo, Hyun Seung
Zhang, Chengdong
Zhang, Yan
Will, Rebecca
Kenyon, Ronald W.
Sobral, Bruno W.
[J]. INFECTION AND IMMUNITY, 2011, 79 (11) : 4286 - 4298
[9] Identifying Genetic Determinants Needed to Establish a Human Gut Symbiont in Its Habitat
Goodman, Andrew L.
McNulty, Nathan P.
Zhao, Yue
Leip, Douglas
Mitra, Robi D.
Lozupone, Catherine A.
Knight, Rob
Gordon, Jeffrey I.
[J]. CELL HOST & MICROBE, 2009, 6 (03) : 279 - 289
[10] Topographical and Temporal Diversity of the Human Skin Microbiome
Grice, Elizabeth A.
Kong, Heidi H.
Conlan, Sean
Deming, Clayton B.
Davis, Joie
Young, Alice C.
Bouffard, Gerard G.
Blakesley, Robert W.
Murray, Patrick R.
Green, Eric D.
Turner, Maria L.
Segre, Julia A.
[J]. SCIENCE, 2009, 324 (5931) : 1190 - 1192

← 1 2 3 →