Microbial Indicators of Rampant Caries

Dental caries is the most common chronic disease of childhood. Objective: Our purpose was to determine the overabundance and underabundance of bacterial species in the primary dentition of caries-active subjects. Methods: Plaque samples were collected from 208 children (4.7+2.6 years old). Caries-free subjects (n=110) had pooled plaque removed from intact surfaces. Caries-active subjects (n=98) contributed with plaque originating from intact surfaces, white-spot, cavitated lesions, and deep dentinal lesions. Using a 16S rDNA-based, reverse capture checkerboard assay, the abundance of 84 bacterial species was determined. Simple univariate methods were used to determine overabundant and underabundant bacteria in caries-active relative to caries-free children. Naïve Bayes classifiers were constructed and evaluated using a machine learning approach (random resampling validation) to calculate significant externally generalizable estimates of classification error. A statistically significant result increases the chances of a discriminative signal in the data. The best performing classifier constructed gave 17.5% test set errors (SN=0.75; SP=0.89). Results: The achieved classification error was statistically significant using a permutation test (PACE analysis) at the 99% level. In using this model, a number of informative species were determined. The overabundant species included Fusobacterium spp., Streptococcus mutans, Actinomyces strain B27SC, Lactobacillus spp., Cardiobacterium sp. A, Cardiobacterium hominis, Porphyromonas clone DS033, Atopobium clone DS033, and Selenomonas clone EY047. The underabundant species included Streptococcus parasanguinis, Abiotrophia defectiva, Gemella haemolysans, Streptococcus mitis/oralis, Streptococcus sanguinis, and Streptococcus cristatus. Conclusions: Several known acidogenic species, e.g., S. mutans and Lactobacillus spp. were overabundant in caries-active children. Other increased species may be involved in initiation of the disease. The underabundant species in caries-active children were those often associated with health. It appears that dental caries is a polymicrobial infection that involves an overabundance of specific species, in addition to S. mutans, in combination with an underabundance of health-related species. Supported by NIH grants DE145428 and DE015351.