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Originally published in Science Express on 14 April 2005
Science 10 June 2005:
Vol. 308. no. 5728, pp. 1635 - 1638
DOI: 10.1126/science.1110591
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Reports

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,5 Karen E. Nelson,5 David A. Relman1,2,6*

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.

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 Veterans Affairs Palo Alto Health Care System, 3801 Miranda Avenue, Palo Alto, CA 94304, USA.

* To whom correspondence should be addressed. E-mail: eckburg1{at}stanford.edu (P.B.E.); relman{at}stanford.edu (D.A.R.)

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Ruminococcus gauvreauii sp. nov., a glycopeptide-resistant species isolated from a human faecal specimen.
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Bacterial-Modulated Signaling Pathways in Gut Homeostasis.
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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.
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Relative Abundance of Bacteroides spp. in Stools and Wastewaters as Determined by Hierarchical Oligonucleotide Primer Extension.
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Systemic Control of Plasmacytoid Dendritic Cells by CD8+ T Cells and Commensal Microbiota.
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J. Immunol. 180, 5843-5852
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Sutterella parvirubra sp. nov. and Megamonas funiformis sp. nov., isolated from human faeces.
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Gut Microbiota and Its Possible Relationship With Obesity.
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Evaluation of alternatives to antibiotics using an Escherichia coli K88+ model of piglet diarrhea: Effects on gut microbial ecology.
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From the Cover: Regulation of surface architecture by symbiotic bacteria mediates host colonization.
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