The determination of the composition of the microbial community in the oral cavity is usually based on cultivation methods; however, nearly half of the bacteria in the saliva and the dental plaque are not cultivable. Objectives: To evaluate the difference in oral microbial diversity between children with severe early childhood caries (S-ECC) and caries-free (CF) controls by cultivation-independent methods including denaturing gradient gel electrophoresis (DGGE) and 16S rDNA sequence analysis. Methods: Pooled plaque samples were collected from 20 children (S-ECC=12; CF=8) aged 2 to 8 years. Total microbial genomic DNA was isolated from those children, and a portion of the 16S rDNA locus was PCR amplified using universal primers. Results: The data indicated a clear distribution of the phylotypes between the two groups. The diversity of the bacterial population was greater in the CF children (42±3.7) than in the S-ECC children (35±4.3); the difference was statistically significant (p< 0.01). The average diversity of plaque samples as measured by the Shannon index (H') was 3.5 for the S-ECC group and 3.7 for the CF group (p <0.01). The mean similarity values of the DGGE profiles were 91.3±4.3% within the S-ECC samples and 92.7±3.6% within the CF samples, but it decreased significantly to 89.4±4.7% (p< 0.01, ANOVA) in a comparison between the two groups. Based on sequence analysis and the number of detected DGGE bands, we estimated that the S-ECC group exhibited 95 total phylotypes and that the CF group exhibited 113. Conclusion: These results suggest that the microbial diversity and complexity of the microbial biota in dental plaque is significantly less in S-ECC children than in CF children. This work was supported by NIH grant # DE13937

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