This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrowReprints and Permissions
Right arrow Copyright Information
Right arrow Books from ASM Press
Right arrow MicrobeWorld
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Gafan, G. P.
Right arrow Articles by Spratt, D. A.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Gafan, G. P.
Right arrow Articles by Spratt, D. A.

 Previous Article  |  Next Article 

Journal of Clinical Microbiology, August 2005, p. 3971-3978, Vol. 43, No. 8
0095-1137/05/$08.00+0     doi:10.1128/JCM.43.8.3971-3978.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

Statistical Analyses of Complex Denaturing Gradient Gel Electrophoresis Profiles

Gavin P. Gafan,1 Victoria S. Lucas,1 Graham J. Roberts,1 Aviva Petrie,2 Michael Wilson,1 and David A. Spratt1*

Division of Microbial Diseases,1 Biostatistics Unit, Eastman Dental Institute, UCL, 256 Gray's Inn Road, London WC1X 8LD, United Kingdom2

Received 1 October 2004/ Returned for modification 29 January 2005/ Accepted 16 May 2005

Studies using molecular techniques have demonstrated that a culture-based approach can severely underestimate the bacterial diversity in most environments. One of the molecular techniques that has been applied in microbial ecology is denaturing gradient gel electrophoresis (DGGE). The purpose of this study was to investigate differences in the microbiota of plaque, using a number of analysis techniques, from children without gingivitis (n = 30) and from those with gingivitis (n = 30). Extracted DNA from gingival margin plaque was subjected to PCR targeting the 16S rRNA gene using universal primers. DGGE profiles were analyzed in three ways. (i) Bacterial diversity was compared between cohorts by using the Shannon-Wiener index (also known as the Shannon-Weaver index). (ii) A hierarchical cluster analysis of the banding patterns was calculated and expressed as a dendrogram. (iii) Individual DGGE bands and their intensities for both cohorts were compared using a logistic regression analysis. The Shannon-Wiener indices demonstrated a greater bacterial diversity associated with no-gingivitis plaque (P = 0.009). Dendrograms demonstrated that seven clades associated with gingivitis and five clades associated with no gingivitis. The logistic regression demonstrated that one band was significantly associated with no gingivitis (P = 0.001), while two bands were significantly associated with gingivitis (P = 0.005 and P = 0.042). In conclusion, this study demonstrates that the development of gingivitis might be accompanied by a decrease in bacterial diversity. Furthermore, we have demonstrated that logistic regression is a good statistical method for analyzing and characterizing DGGE profiles.

* Corresponding author. Mailing address: Division of Microbial Diseases, Eastman Dental Institute, UCL, 256 Gray's Inn Road, London WC1X 8LD, United Kingdom. Phone: 44 20 7915 1107. Fax: 44 20 7915 1127. E-mail: dspratt{at}eastman.ucl.ac.uk.

Journal of Clinical Microbiology, August 2005, p. 3971-3978, Vol. 43, No. 8
0095-1137/05/$08.00+0     doi:10.1128/JCM.43.8.3971-3978.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.



This article has been cited by other articles:

  • Kim, E. J., Huws, S. A., Lee, M. R. F., Wood, J. D., Muetzel, S. M., Wallace, R. J., Scollan, N. D. (2008). Fish Oil Increases the Duodenal Flow of Long Chain Polyunsaturated Fatty Acids and trans-11 18:1 and Decreases 18:0 in Steers via Changes in the Rumen Bacterial Community. J. Nutr. 138: 889-896 [Abstract] [Full Text]  
  • Lee, M. R. F., Huws, S. A., Scollan, N. D., Dewhurst, R. J. (2007). Effects of Fatty Acid Oxidation Products (Green Odor) on Rumen Bacterial Populations and Lipid Metabolism In Vitro. J DAIRY SCI 90: 3874-3882 [Abstract] [Full Text]  
  • Flanagan, J. L., Brodie, E. L., Weng, L., Lynch, S. V., Garcia, O., Brown, R., Hugenholtz, P., DeSantis, T. Z., Andersen, G. L., Wiener-Kronish, J. P., Bristow, J. (2007). Loss of Bacterial Diversity during Antibiotic Treatment of Intubated Patients Colonized with Pseudomonas aeruginosa. J. Clin. Microbiol. 45: 1954-1962 [Abstract] [Full Text]  
  • Ledder, R. G., Gilbert, P., Huws, S. A., Aarons, L., Ashley, M. P., Hull, P. S., McBain, A. J. (2007). Molecular Analysis of the Subgingival Microbiota in Health and Disease. Appl. Environ. Microbiol. 73: 516-523 [Abstract] [Full Text]  


Copyright © 2009 by the American Society for Microbiology.   For an alternate route to Journals.ASM.org, visit: http://intl-journals.asm.org | More Info»