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Published Online April 14, 2005
Science DOI: 10.1126/science.1110591

Reports

Submitted on February 2, 2005
Accepted on April 5, 2005

Diversity of the Human Intestinal Microbial Flora

Paul B. Eckburg 1*, Elisabeth M. Bik 2, Charles N. Bernstein 3, Elizabeth Purdom 4, Les Dethlefsen 2, Michael Sargent 3, Steven R. Gill , Karen E. Nelson 5, David A. Relman 6

1 Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Room S-169, 300 Pasteur Drive, Stanford CA 94305-5107, USA.
2 Department of Microbiology and Immunology, 299 Campus Drive, Room D300, Fairchild Science Building, Stanford CA 94305-5124, USA.
3 Section of Gastroenterology, Department of Medicine, University of Manitoba, MS 779-820 Sherbrook Street, Winnipeg, Manitoba R3A 1R9, Canada.
4 Department of Statistics, Sequoia Hall, 390 Serra Mall, Stanford University, Stanford CA 94305, USA.
5 The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA.
6 Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Room S-169, 300 Pasteur Drive, Stanford CA 94305-5107, USA; Department of Microbiology and Immunology, 299 Campus Drive, Room D300, Fairchild Science Building, Stanford CA 94305-5124, USA; Veterans Affairs Palo Alto Health Care System, 3801 Miranda Avenue, Palo Alto, CA 94304, USA.

* To whom correspondence should be addressed.
Paul B. Eckburg , E-mail: eckburg1{at}stanford.edu

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 in order 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.


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R. E. Ley, M. Hamady, C. Lozupone, P. J. Turnbaugh, R. R. Ramey, J. S. Bircher, M. L. Schlegel, T. A. Tucker, M. D. Schrenzel, R. Knight, et al. (2008)
Science 320, 1647-1651
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Ruminococcus gauvreauii sp. nov., a glycopeptide-resistant species isolated from a human faecal specimen.
M.-C. Domingo, A. Huletsky, M. Boissinot, K. A. Bernard, F. J. Picard, and M. G. Bergeron (2008)
Int J Syst Evol Microbiol 58, 1393-1397
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Bacterial-Modulated Signaling Pathways in Gut Homeostasis.
W.-J. Lee (2008)
Science Signaling 1, pe24
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Role of Intestinal Microbiota in Transformation of Bismuth and Other Metals and Metalloids into Volatile Methyl and Hydride Derivatives in Humans and Mice.
K. Michalke, A. Schmidt, B. Huber, J. Meyer, M. Sulkowski, A. V. Hirner, J. Boertz, F. Mosel, P. Dammann, G. Hilken, et al. (2008)
Appl. Envir. Microbiol. 74, 3069-3075
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Relative Abundance of Bacteroides spp. in Stools and Wastewaters as Determined by Hierarchical Oligonucleotide Primer Extension.
P.-Y. Hong, J.-H. Wu, and W.-T. Liu (2008)
Appl. Envir. Microbiol. 74, 2882-2893
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Systemic Control of Plasmacytoid Dendritic Cells by CD8+ T Cells and Commensal Microbiota.
D. Fujiwara, B. Wei, L. L. Presley, S. Brewer, M. McPherson, M. A. Lewinski, J. Borneman, and J. Braun (2008)
J. Immunol. 180, 5843-5852
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Sutterella parvirubra sp. nov. and Megamonas funiformis sp. nov., isolated from human faeces.
H. Sakon, F. Nagai, M. Morotomi, and R. Tanaka (2008)
Int J Syst Evol Microbiol 58, 970-975
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Gut Microbiota and Its Possible Relationship With Obesity.
J. K. DiBaise, H. Zhang, M. D. Crowell, R. Krajmalnik-Brown, G. A. Decker, and B. E. Rittmann (2008)
Mayo Clin. Proc. 83, 460-469
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Evaluation of alternatives to antibiotics using an Escherichia coli K88+ model of piglet diarrhea: Effects on gut microbial ecology.
S. K. Bhandari, B. Xu, C. M. Nyachoti, D. W. Giesting, and D. O. Krause (2008)
J Anim Sci 86, 836-847
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From the Cover: Regulation of surface architecture by symbiotic bacteria mediates host colonization.
C. H. Liu, S. M. Lee, J. M. VanLare, D. L. Kasper, and S. K. Mazmanian (2008)
PNAS 105, 3951-3956
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Enteric Salmonellosis Disrupts the Microbial Ecology of the Murine Gastrointestinal Tract.
M. Barman, D. Unold, K. Shifley, E. Amir, K. Hung, N. Bos, and N. Salzman (2008)
Infect. Immun. 76, 907-915
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