Microarray Analysis of Bacteria in Root Caries

Objectives: We previously determined the bacterial diversity of healthy roots and root caries (RC) in the elderly by sequencing 16S rRNA genes amplified from isolated DNA. The purpose of the present study was to study a larger set of samples using a new 16S rRNA-based microarray.

Methods: Supragingival plaque was collected from 20 healthy subjects (Controls) and from healthy and carious roots and carious dentin from 21 RC subjects (Patients). The samples were analyzed using the Human Oral Microbe Identification Microarray (HOMIM) that detects about 300 oral species in a single hybridization. Half of the Controls and Patients had previously been analyzed by 16S rRNA gene sequencing (PCR with 16S rRNA universal primers). Statistical analyses were performed on the microarray data to test the significance of the differences between subject and sample groups.

Results: Collectively, 179 bacterial species and species groups were detected. A higher bacterial diversity was observed in Controls as compared to Patients. A number of species were significantly more common in Controls, particularly Fusobacterium nucleatum subsp. polymorphum, Gemella morbillorum, Campylobacter concisus and Capnocytophaga sputigena. Conversely, Lactobacillus casei/paracasei/rhamnosus and Pseudoramibacter alactolyticus showed a notable association with the infected dentin. Streptococcus mutans was detected more frequently in the dentinal samples, but the difference was not significant. Actinomyces spp. were found more frequently in Controls.

Conclusions: The microarray results were in general agreement with the results from the previous 16S rRNA gene sequencing analysis. Species other than Actinomyces and S. mutans may play a role as RC pathogens.