Diversity of the Human Intestinal Microbial Flora
Abstract
The human endogenous intestinal microflora is an essential “organ” in providing nourishment, regulating epithelial development, and instructing innate immunity; yet, surprisingly, basic features remain poorly described. We examined 13,355 prokaryotic ribosomal RNA gene sequences from multiple colonic mucosal sites and feces of healthy subjects to improve our understanding of gut microbial diversity. A majority of the bacterial sequences corresponded to uncultivated species and novel microorganisms. We discovered significant intersubject variability and differences between stool and mucosa community composition. Characterization of this immensely diverse ecosystem is the first step in elucidating its role in health and disease.
Footnotes
Supporting Online Material www.sciencemag.org/cgi/content/full/1110591/DC1 Materials and Methods SOM Text Figs. S1 to S8 Tables S1 to S6 References
References and Notes
References
- 1. Hooper LV, Gordon JI. Science. 2001;292:1115.[PubMed]
- 2. Rakoff-Nahoum S, Paglino J, Eslami-Varzaneh F, Edberg S, Medzhitov R. Cell. 2004;118:229.[PubMed]
- 3. Backhed F, et al Proc. Natl. Acad. Sci. U.S.A. 2004;101:15718.[Google Scholar]
- 4. Stappenbeck TS, Hooper LV, Gordon JI. Proc. Natl. Acad. Sci. U.S.A. 2002;99:15451.
- 5. Zoetendal EG, et al Appl. Environ. Microbiol. 2002;68:3401.[Google Scholar]
- 6. Hayashi H, Sakamoto M, Benno Y. Microbiol. Immunol. 2002;46:535.[PubMed]
- 7. Hold GL, Pryde SE, Russell VJ, Furrie E, Flint HJ. FEMS Microbiol. Ecol. 2002;39:33.[PubMed]
- 8. Suau A, et al Appl. Environ. Microbiol. 1999;65:4799.[Google Scholar]
- 9. Wang X, Heazlewood SP, Krause DO, Florin TH. J. Appl. Microbiol. 2003;95:508.[PubMed]
- 10. Horner-Devine MC, Carney KM, Bohannan BJM. Proc. R. Soc. London. 2003;271:113.[PubMed]
- 11. Sonnenburg JL, Angenent LT, Gordon JI. Nat. Immunol. 2004;5:569.[PubMed]
- 12. Materials and methods are available as supporting material on Science Online.
- 13. Pace NR. Science. 1997;276:734.[PubMed]
- 14. Curtis TP, Sloan WT. Curr. Opin. Microbiol. 2004;7:221.[PubMed]
- 15. Barcenilla A, et al Appl. Environ. Microbiol. 2000;66:1654.[Google Scholar]
- 16. Pryde SE, Duncan SH, Hold GL, Stewart CS, Flint HJ. FEMS Microbiol. Lett. 2002;217:133.[PubMed]
- 17. Hooper LV, et al Science. 2001;291:881.[PubMed][Google Scholar]
- 18. Good's coverage estimates were 99.3%, 97.9%, and 98.3% for subjects A, B, and C, respectively.
- 19. Pavoine S, Dufour AB, Chessel D. J. Theor. Biol. 2004;228:523.[PubMed]
- 20. Colwell RK. EstimateS, version 7. 2004. [PubMed]
- 21. Martin AP. Appl. Environ. Microbiol. 2002;68:3673.
- 22. Schloss PD, Larget BR, Handelsman J. Appl. Environ. Microbiol. 2004;70:5485.
- 23. Fargione J, Brown CS, Tilman D. Proc. Natl. Acad. Sci. U.S.A. 2003;100:8916.
- 24. Relman DA, Falkow S. Trends Microbiol. 2001;9:206.[PubMed]
- 25. We thank B. Bohannan, M. B. Omary, and S. Holmes (Stanford University) for helpful comments on the manuscript. This research was supported by grants from the NIH (no. AI51259) and Ellison Medical Foundation (D.A.R.), Canadian Institutes of Health Research and Crohn's and Colitis Foundation of Canada (C.N.B., M.S.), National Science Foundation (E.P.), and Defense Advanced Research Projects Agency (S.R.G., K.E.N.). Representatives of novel phylo-types (AY916135 to AY916390) and all other sequences (AY974810 to AY986384) were deposited in GenBank