Bio Forum & Bio Expo Japan Sign up for PNAS Online eTocs
Link: Info for AuthorsLink: Editorial BoardLink: AboutLink: SubscribeLink: AdvertiseLink: ContactLink: Sitemap Link: PNAS Home
Proceedings of the National Academy of Sciences
Link: Current Issue "" Link: Archives "" Link: Online Submission ""  Link: Advanced Search

Published online on January 4, 2006, 10.1073/pnas.0506655103
PNAS | January 17, 2006 | vol. 103 | no. 3 | 732-737
OPEN ACCESS ARTICLE


This Article
Free via Open Access: OA
Right arrow Figures Only
Right arrow OA Full Text
Right arrow Full Text (PDF)
Right arrow Supporting Information
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Right arrow Citation Map
Services
Right arrow Email this article to a colleague
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My File Cabinet
Right arrow Download to citation manager
Right arrow Request Copyright Permission
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via CrossRef
Right arrow Citing Articles via ISI Web of Science (46)
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Bik, E. M.
Right arrow Articles by Relman, D. A.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Bik, E. M.
Right arrow Articles by Relman, D. A.
Social Bookmarking
Add to CiteULike   Add to Complore   Add to Connotea   Add to Del.icio.us   Add to Digg  
What's this?

 Previous Article  | Table of Contents |  Next Article 

MICROBIOLOGY
Molecular analysis of the bacterial microbiota in the human stomach

Elisabeth M. Bik *, {dagger}, {ddagger}, Paul B. Eckburg *, {dagger}, §, Steven R. Gill ¶, Karen E. Nelson ¶, Elizabeth A. Purdom ||, Fritz Francois **, {dagger}{dagger}, Guillermo Perez-Perez **, {dagger}{dagger}, Martin J. Blaser **, {dagger}{dagger}, and David A. Relman *, {dagger}, {ddagger}, §

*Department of Microbiology and Immunology, Stanford University School of Medicine, Fairchild Science Building, 299 Campus Drive, Stanford, CA 94305; {dagger}Veterans Affairs Palo Alto Health Care System, 3801 Miranda Avenue, Palo Alto, CA 94304; §Department of Medicine, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305; The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850; ||Department of Statistics, Sequoia Hall, 390 Serra Mall, Stanford University, Stanford, CA 94305; and Departments of **Medicine and {dagger}{dagger}Microbiology, New York University School of Medicine, New York, NY 10016

Edited by Jeffrey I. Gordon, Washington University School of Medicine, St. Louis, MO, and approved November 23, 2005 (received for review August 3, 2005)

The microbiota of the human stomach and the influence of Helicobacter pylori colonization on its composition remain largely unknown. We characterized bacterial diversity within the human gastric mucosa by using a small subunit 16S rDNA clone library approach and analyzed 1,833 sequences generated by broad-range bacterial PCR from 23 gastric endoscopic biopsy samples. A diverse community of 128 phylotypes was identified, featuring diversity at this site greater than previously described. The majority of sequences were assigned to the Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, and Fusobacteria phyla. Ten percent of the phylotypes were previously uncharacterized, including a Deinococcus-related organism, relatives of which have been found in extreme environments but not reported before in humans. The gastric clone libraries from 19 subjects contained H. pylori rDNA; however, only 12 of these subjects tested positive for H. pylori by conventional laboratory methods. Statistical analysis revealed a large degree of intersubject variability of the gastric ecosystem. The presence of H. pylori did not affect the composition of the gastric community. This gastric bacterial rDNA data set was significantly different from sequence collections of the human mouth and esophagus described in other studies, indicating that the human stomach may be home to a distinct microbial eco-system. The gastric microbiota may play important, as-yet-undiscovered roles in human health and disease.

16S ribosomal rRNA clone library | Helicobacter pylori | microbial diversity | human indigenous microbiota

Conflict of interest statement: No conflicts declared.

This paper was submitted directly (Track II) to the PNAS office.

Freely available online through the PNAS open access option.

Abbreviation: DPCoA, double principal coordinate analysis.

Data deposition: The 16S rDNA sequences of clones have been deposited in the GenBank database (accession nos. AY582885–AY582898).

{ddagger} To whom correspondence may be addressed. E-mail: eliesbik{at}stanford.edu or relman{at}stanford.edu.

© 2006 by The National Academy of Sciences of the USA


Add to CiteULike CiteULike   Add to Complore Complore   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us   Add to Digg Digg    What's this?


This article has been cited by other articles in HighWire Press-hosted journals:


Home page
 GutHome page
M. J Blaser, Y. Chen, and J. Reibman
Does Helicobacter pylori protect against asthma and allergy?
Gut, May 1, 2008; 57(5): 561 - 567.
[Full Text] [PDF]

Home page
 Cancer Res.Home page
C.-W. Lee, B. Rickman, A. B. Rogers, Z. Ge, T. C. Wang, and J. G. Fox
Helicobacter pylori Eradication Prevents Progression of Gastric Cancer in Hypergastrinemic INS-GAS Mice
Cancer Res., May 1, 2008; 68(9): 3540 - 3548.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
J. A. Frank, C. I. Reich, S. Sharma, J. S. Weisbaum, B. A. Wilson, and G. J. Olsen
Critical Evaluation of Two Primers Commonly Used for Amplification of Bacterial 16S rRNA Genes
Appl. Envir. Microbiol., April 15, 2008; 74(8): 2461 - 2470.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
C. H. Liu, S. M. Lee, J. M. VanLare, D. L. Kasper, and S. K. Mazmanian
From the Cover: Regulation of surface architecture by symbiotic bacteria mediates host colonization
PNAS, March 11, 2008; 105(10): 3951 - 3956.
[Abstract] [Full Text] [PDF]

Home page
 FASEB J.Home page
S. M. Levine, E. A. Lin, W. Emara, J. Kang, M. DiBenedetto, T. Ando, D. Falush, and M. J. Blaser
Plastic cells and populations: DNA substrate characteristics in Helicobacter pylori transformation define a flexible but conservative system for genomic variation
FASEB J, November 1, 2007; 21(13): 3458 - 3467.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
B. A. Rader, S. R. Campagna, M. F. Semmelhack, B. L. Bassler, and K. Guillemin
The Quorum-Sensing Molecule Autoinducer 2 Regulates Motility and Flagellar Morphogenesis in Helicobacter pylori
J. Bacteriol., September 1, 2007; 189(17): 6109 - 6117.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
S. Fraune and T. C. G. Bosch
Long-term maintenance of species-specific bacterial microbiota in the basal metazoan Hydra
PNAS, August 7, 2007; 104(32): 13146 - 13151.
[Abstract] [Full Text] [PDF]

Home page
 Arch Intern MedHome page
Y. Chen and M. J. Blaser
Inverse Associations of Helicobacter pylori With Asthma and Allergy
Arch Intern Med, April 23, 2007; 167(8): 821 - 827.
[Abstract] [Full Text] [PDF]

Home page
 Int. J. Syst. Evol. Microbiol.Home page
O. O. Glazunova, T. Launay, D. Raoult, and V. Roux
Prevotella timonensis sp. nov., isolated from a human breast abscess
Int J Syst Evol Microbiol, April 1, 2007; 57(4): 883 - 886.
[Abstract] [Full Text] [PDF]

Home page
 Infect. Immun.Home page
C. R. Cox and M. S. Gilmore
Native Microbial Colonization of Drosophila melanogaster and Its Use as a Model of Enterococcus faecalis Pathogenesis
Infect. Immun., April 1, 2007; 75(4): 1565 - 1576.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
Z. Gao, C.-h. Tseng, Z. Pei, and M. J. Blaser
Molecular analysis of human forearm superficial skin bacterial biota
PNAS, February 20, 2007; 104(8): 2927 - 2932.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
L. R. Hoffman, E. Deziel, D. A. D'Argenio, F. Lepine, J. Emerson, S. McNamara, R. L. Gibson, B. W. Ramsey, and S. I. Miller
Selection for Staphylococcus aureus small-colony variants due to growth in the presence of Pseudomonas aeruginosa
PNAS, December 26, 2006; 103(52): 19890 - 19895.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
W.-K. Lee, K. Ogura, J. T. Loh, T. L. Cover, and D. E. Berg
Quantitative Effect of luxS Gene Inactivation on the Fitness of Helicobacter pylori
Appl. Envir. Microbiol., October 1, 2006; 72(10): 6615 - 6622.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
M.-E. Dumas, R. H. Barton, A. Toye, O. Cloarec, C. Blancher, A. Rothwell, J. Fearnside, R. Tatoud, V. Blanc, J. C. Lindon, et al.
Metabolic profiling reveals a contribution of gut microbiota to fatty liver phenotype in insulin-resistant mice
PNAS, August 15, 2006; 103(33): 12511 - 12516.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
J. D. Oh, H. Kling-Backhed, M. Giannakis, J. Xu, R. S. Fulton, L. A. Fulton, H. S. Cordum, C. Wang, G. Elliott, J. Edwards, et al.
The complete genome sequence of a chronic atrophic gastritis Helicobacter pylori strain: Evolution during disease progression
PNAS, June 27, 2006; 103(26): 9999 - 10004.
[Abstract] [Full Text] [PDF]