Metagenomic Analysis of the Human Distal Gut Microbiome

American Association for the Advancement of Science (AAAS) - Tập 312 Số 5778 - Trang 1355-1359 - 2006
Steven R. Gill1,2,3,4,5, Mihai Pop1,2,3,4,5, Robert T. DeBoy1,2,3,4,5, Paul B. Eckburg1,2,3,5, Peter J. Turnbaugh1,2,3,5, Buck S. Samuel1,2,3,5, Jeffrey I. Gordon1,2,3,5, David A. Relman1,2,3,5, Claire M. Fraser1,3,6,4,5, William Nelson1,2,3,4,5
1Center for Genome Sciences, Washington University School of Medicine, St. Louis, MO 63108, USA
2Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305 (USA)
3Department of Microbiology and Immunology, 299 Campus Drive, Stanford University, Stanford, CA 94305, USA.
4The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
5Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304, USA
6Departments of Pharmacology and Physiology and Microbiology and Tropical Diseases, George Washington University School of Medicine, Washington, DC 20037, USA.

Tóm tắt

The human intestinal microbiota is composed of 10 13 to 10 14 microorganisms whose collective genome (“microbiome”) contains at least 100 times as many genes as our own genome. We analyzed ∼78 million base pairs of unique DNA sequence and 2062 polymerase chain reaction–amplified 16 S ribosomal DNA sequences obtained from the fecal DNAs of two healthy adults. Using metabolic function analyses of identified genes, we compared our human genome with the average content of previously sequenced microbial genomes. Our microbiome has significantly enriched metabolism of glycans, amino acids, and xenobiotics; methanogenesis; and 2-methyl- d -erythritol 4-phosphate pathway–mediated biosynthesis of vitamins and isoprenoids. Thus, humans are superorganisms whose metabolism represents an amalgamation of microbial and human attributes.

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Tài liệu tham khảo

10.1126/science.1104816

10.1126/science.1110591

10.1073/pnas.0504978102

S. K. Mazmanian, C. H. Liu, A. O. Tzianabos, D. L. Kasper, Cell122, 107 (2005).

10.1016/j.cell.2004.07.002

10.1073/pnas.0407076101

J. K. Nicholson, E. Holmes, I. D. Wilson, Nat. Rev. Microbiol.3, 431 (2005).

10.1128/AEM.66.6.2541-2547.2000

10.1126/science.1093857

G. W. Tyson et al., Nature428, 25 (2004).

Materials and methods are available as supporting material on Science Online.

M. A. Schell et al., Proc. Natl. Acad. Sci. U.S.A.99, 14422 (2002).

(http://gordonlab.wustl.edu/supplemental/Gill/Msmithii/draftgenome/).

A. L. McOrist, M. Jackson, A. R. Bird, J. Microbiol. Methods50, 131 (2002).

10.1093/nar/gkh063

10.1186/1471-2105-4-41

10.1126/science.1107851

(http://gordonlab.wustl.edu/supplemental/Gill).

Database available as supporting material on Science Online.

URL (http://afmb.cnrs-mrs.fr/CAZY/).

10.1093/ajcn/39.2.338

D. L. Topping, P. M. Clifton, Physiol. Rev.81, 1031 (2001).

10.1007/BF00871644

J. L. Rychlik, T. May, Curr. Microbiol.40, 176 (2000).

10.1104/pp.007138

J. Pereto, P. Lopez-Garcia, D. Moreira, Trends Biochem. Sci.29, 469 (2004).

D. Umeno, A. V. Tobias, F. H. Arnold, Microbiol. Mol. Biol. Rev.69, 51 (2005).

K. C. Wang, S. Ohnuma, Biochim. Biophys. Acta1529, 33 (2000).

M. Begley et al., FEBS Lett.561, 99 (2004).

J. J. Reiners Jr., R. Clift, P. Mathieu, Carcinogenesis20, 1561 (1999).

C. A. Rice-Evans, N. J. Miller, G. Paganga, Free Radic. Biol. Med.20, 933 (1996).

G. Williamson, G. W. Plumb, Y. Uda, K. R. Price, M. J. Rhodes, Carcinogenesis17, 2385 (1996).

H. Schneider, A. Schwiertz, M. D. Collins, M. Blaut, Arch. Microbiol.171, 81 (1999).

A. K. Mallett, C. A. Bearne, I. R. Rowland, Appl. Environ. Microbiol.46, 591 (1983).

We thank W. Nelson and I. Hance (The Institute for Genomic Research) L. Dethlefsen and E. Bik (Stanford) and D. Leip (Washington University) for their valuable assistance. This work was supported by Defense Advanced Research Projects Agency (DARPA) and the Office of Naval Research grant no. ONR-N00014-02-1-1002 (S.R.G. K.E.N.) the W. M. Keck Foundation (J.I.G.) the Ellison Medical Foundation (D.A.R. J.I.G.) and NIH grants AI51259 (D.A.R.) and DK70977 (J.I.G.). B.S.S. is a recipient of a graduate research fellowship from the NSF (DGE-0202737). This whole-genome shotgun project has been deposited at the DNA Data Bank of Japan (DDBJ) European Molecular Biology Laboratory (EMBL) and GenBank under the project accession AAQK00000000 (subject 7) and AAQL00000000 (subject 8). The version described in this paper is the first version AAQK01000000 and AAQL01000000. All near–full-length 16 S rDNA sequences were deposited at DDBJ/EMBL/GenBank under the accessions DQ325545 to DQ327606.

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American Association for the Advancement of Science (AAAS)

Tập 312 Số 5778

1355-1359

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