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Statistical analyses of complex denaturing gradient gel electrophoresis profiles
Gavin P Gafan1, Victoria S Lucas, Graham J Roberts
1Division of Microbial Diseases, Eastman Dental Institute, UCL, 256 Gray's Inn Road, London WC1X 8LD, United Kingdom.
Journal of Clinical Microbiology
|August 6, 2005
Summary
Gingivitis may be linked to reduced bacterial diversity in dental plaque. Molecular analysis using denaturing gradient gel electrophoresis (DGGE) revealed significant differences in microbial communities between children with and without gingivitis.
Area of Science:
- Microbial Ecology
- Oral Microbiology
- Molecular Biology
Background:
- Culture-based methods often underestimate bacterial diversity.
- Molecular techniques like DGGE offer deeper insights into microbial communities.
- Gingivitis is an inflammatory condition of the gums with a complex etiology.
Purpose of the Study:
- To investigate differences in the oral microbiota of plaque between children with and without gingivitis.
- To compare bacterial diversity using molecular techniques.
- To evaluate the utility of logistic regression for DGGE profile analysis.
Main Methods:
- DNA was extracted from gingival margin plaque of 60 children (30 with gingivitis, 30 without).
- PCR amplification of the 16S rRNA gene was performed using universal primers.
- DGGE profiles were analyzed using Shannon-Wiener index, hierarchical cluster analysis, and logistic regression.
Main Results:
- Higher bacterial diversity was observed in plaque from children without gingivitis (Shannon-Wiener index, P = 0.009).
- Cluster analysis revealed distinct microbial community structures (clades) associated with each group.
- Logistic regression identified specific DGGE bands significantly associated with either the presence or absence of gingivitis.
Conclusions:
- Gingivitis development may correlate with a decrease in bacterial diversity in plaque.
- DGGE combined with logistic regression is an effective method for characterizing oral microbiota and identifying disease-associated bacterial signatures.