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Journal of Dental Research
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Clinical

Survey of Oral Microbial Diversity using PCR-based Denaturing Gradient Gel Electrophoresis

Y. Li1,*, C.Y.S. Ku1, J. Xu2, D. Saxena3 and P.W. Caufield3

1 Department of Basic Science and Craniofacial Biology and
3 Division of Diagnostics, Infectious Disease and Heath Promotion, New York University College of Dentistry, 345 E. 24th Street, New York, NY 10010-4086, USA; and
2 Department of Pediatrics, New York University School of Medicine, New York, NY 10016, USA;

Correspondence: * corresponding author, yihong.li{at}nyu.edu

Polymicrobial biofilms in the human oral cavity exhibit marked diversity. PCR-based denaturing gradient gel electrophoresis (PCR-DGGE) surveys microbial diversity by displaying PCR-generated 16S rDNA fragments that migrate at different distances, reflecting the differences in the base-pair (i.e., % G+C) composition of the fragment. This study examined DGGE-generated diversity profiles of cultivable bacteria from individuals with different caries status. Initially, we developed a set of PCR-DGGE running conditions appropriate to oral bacteria. Next, we assessed migration standards from known oral bacterial reference strains. To test the methods, we profiled 20 bacterial saliva samples cultivated from young adults. The study produced a battery of species-specific 16S rDNA amplicons that could be used as a migration distance standard necessary for computer-assisted profile analysis. From the clinical samples, we found a significantly greater diversity of oral microbes in caries-free individuals compared with caries-active individuals (P = 0.01). These findings suggest thtat a portion of oral microbiota of caries-active individuals may be absent, suppressed, or replaced.

Key Words: microbial diversity • PCR-DGGE • 16S rDNA • dental caries

Journal of Dental Research, Vol. 84, No. 6, 559-564 (2005)
DOI: 10.1177/154405910508400614
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