Metagenomic Analysis of the Human Distal Gut Microbiome
Abstract
The human intestinal microbiota is composed of 1013 to 1014 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 16S 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.
Get full access to this article
View all available purchase options and get full access to this article.
Supplementary Material
File (gill.som.pdf)
- Download
- 614.01 KB
References and Notes
1
F. Backhed, R. E. Ley, J. L. Sonnenburg, D. A. Peterson, J. I. Gordon, Science307, 1915 (2005).
2
P. B. Eckburg et al., Science308, 1635 (2005).
3
R. E. Ley et al., Proc. Natl. Acad. Sci. U.S.A.102, 11070 (2005).
4
S. K. Mazmanian, C. H. Liu, A. O. Tzianabos, D. L. Kasper, Cell122, 107 (2005).
5
S. Rakoff-Nahoum, J. Paglino, F. Eslami-Varzaneh, S. Edberg, R. Medzhitov, Cell118, 229 (2004).
6
F. Backhed et al., Proc. Natl. Acad. Sci. U.S.A.101, 15718 (2004).
7
J. K. Nicholson, E. Holmes, I. D. Wilson, Nat. Rev. Microbiol.3, 431 (2005).
8
M. R. Rondon et al., Appl. Environ. Microbiol.66, 2541 (2000).
9
J. C. Venter et al., Science304, 66 (2004).
10
G. W. Tyson et al., Nature428, 25 (2004).
11
Materials and methods are available as supporting material on Science Online.
12
M. A. Schell et al., Proc. Natl. Acad. Sci. U.S.A.99, 14422 (2002).
14
A. L. McOrist, M. Jackson, A. R. Bird, J. Microbiol. Methods50, 131 (2002).
15
M. Kanehisa, S. Goto, S. Kawashima, Y. Okuno, M. Hattori, Nucleic Acids Res.32, D277 (2004).
16
R. L. Tatusov et al., BMC Bioinformatics4, 41 (2003).
17
S. G. Tringe et al., Science308, 554 (2005).
19
Database available as supporting material on Science Online.
20
21
N. I. McNeil, Am. J. Clin. Nutr.39, 338 (1984).
22
D. L. Topping, P. M. Clifton, Physiol. Rev.81, 1031 (2001).
23
A. J. Stams, Antonie Van Leeuwenhoek66, 271 (1994).
24
J. L. Rychlik, T. May, Curr. Microbiol.40, 176 (2000).
25
M. Rodriguez-Concepcion, A. Boronat, Plant Physiol.130, 1079 (2002).
26
J. Pereto, P. Lopez-Garcia, D. Moreira, Trends Biochem. Sci.29, 469 (2004).
27
D. Umeno, A. V. Tobias, F. H. Arnold, Microbiol. Mol. Biol. Rev.69, 51 (2005).
28
K. C. Wang, S. Ohnuma, Biochim. Biophys. Acta1529, 33 (2000).
29
M. Begley et al., FEBS Lett.561, 99 (2004).
30
J. J. Reiners Jr., R. Clift, P. Mathieu, Carcinogenesis20, 1561 (1999).
31
C. A. Rice-Evans, N. J. Miller, G. Paganga, Free Radic. Biol. Med.20, 933 (1996).
32
G. Williamson, G. W. Plumb, Y. Uda, K. R. Price, M. J. Rhodes, Carcinogenesis17, 2385 (1996).
33
H. Schneider, A. Schwiertz, M. D. Collins, M. Blaut, Arch. Microbiol.171, 81 (1999).
34
A. K. Mallett, C. A. Bearne, I. R. Rowland, Appl. Environ. Microbiol.46, 591 (1983).
35
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 16S rDNA sequences were deposited at DDBJ/EMBL/GenBank under the accessions DQ325545 to DQ327606.
(0)eLetters
eLetters is a forum for ongoing peer review. eLetters are not edited, proofread, or indexed, but they are screened. eLetters should provide substantive and scholarly commentary on the article. Embedded figures cannot be submitted, and we discourage the use of figures within eLetters in general. If a figure is essential, please include a link to the figure within the text of the eLetter. Please read our Terms of Service before submitting an eLetter.
Log In to Submit a ResponseNo eLetters have been published for this article yet.
Information & Authors
Information
Published In
Science
Volume 312 | Issue 5778
2 June 2006
2 June 2006
Copyright
American Association for the Advancement of Science.
Submission history
Received: 22 December 2005
Accepted: 5 May 2006
Published in print: 2 June 2006
Notes
Supporting Online Material
www.sciencemag.org/cgi/content/full/312/5778/1355/DC1
Materials and Methods
Figs. S1 and S2
Tables S1 to S8
References
Authors
Metrics & Citations
Metrics
Article Usage
Altmetrics
Citations
Cite as
- Steven R. Gill et al.
Export citation
Select the format you want to export the citation of this publication.
Cited by
- Integrating the gut microbiome and pharmacology, Science Translational Medicine, 16, 732, (2024)./doi/10.1126/scitranslmed.adg8357
- Lectin-Seq: A method to profile lectin-microbe interactions in native communities, Science Advances, 9, 30, (2023)./doi/10.1126/sciadv.add8766
- The microbiome and gut homeostasis, Science, 377, 6601, (2022)./doi/10.1126/science.abp9960
- Gut Check: Testing a Role for the Intestinal Microbiome in Human Obesity, Science Translational Medicine, 1, 6, (6ps7-6ps7), (2021)./doi/10.1126/scitranslmed.3000483
- Kynurenines: Tryptophan’s metabolites in exercise, inflammation, and mental health, Science, 357, 6349, (2021)./doi/10.1126/science.aaf9794
- The ecology of the microbiome: Networks, competition, and stability, Science, 350, 6261, (663-666), (2021)./doi/10.1126/science.aad2602
- Virulence or Competition?, Science, 336, 6086, (1238-1239), (2021)./doi/10.1126/science.1223303
- Widespread Genetic Switches and Toxicity Resistance Proteins for Fluoride, Science, 335, 6065, (233-235), (2021)./doi/10.1126/science.1215063
- Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes, Science, 334, 6052, (105-108), (2021)./doi/10.1126/science.1208344
- The Microbes Made Me Eat It, Science, 328, 5975, (179-180), (2021)./doi/10.1126/science.1188876
- See more
Loading...
View Options
Check Access
Log in to view the full text
AAAS login provides access to Science for AAAS Members, and access to other journals in the Science family to users who have purchased individual subscriptions.
- Become a AAAS Member
- Activate your AAAS ID
- Purchase Access to Other Journals in the Science Family
- Account Help
Log in via OpenAthens.
Log in via Shibboleth.
More options
Purchase digital access to this article
Download and print this article for your personal scholarly, research, and educational use.
Buy a single issue of Science for just $15 USD.