Identification of the Microbiota in Carious Dentin Lesions Using 16S rRNA Gene Sequencing

<div><p>While mutans streptococci have long been assumed to be the specific pathogen responsible for human dental caries, the concept of a complex dental caries-associated microbiota has received significant attention in recent years. Molecular analyses revealed the complexity of the microbiota with the predominance of <i>Lactobacillus</i> and <i>Prevotella</i> in carious dentine lesions. However, characterization of the dentin caries-associated microbiota has not been extensively explored in different ethnicities and races. In the present study, the bacterial communities in the carious dentin of Japanese subjects were analyzed comprehensively with molecular approaches using the16S rRNA gene. Carious dentin lesion samples were collected from 32 subjects aged 4–76 years, and the 16S rRNA genes, amplified from the extracted DNA with universal primers, were sequenced with a pyrosequencer. The bacterial composition was classified into clusters I, II, and III according to the relative abundance (high, middle, low) of <i>Lactobacillus</i>. The bacterial composition in cluster II was composed of relatively high proportions of <i>Olsenella</i> and <i>Propionibacterium</i> or subdominated by heterogeneous genera. The bacterial communities in cluster III were characterized by the predominance of <i>Atopobium</i>, <i>Prevotella</i>, or <i>Propionibacterium</i> with <i>Streptococcus</i> or <i>Actinomyces</i>. Some samples in clusters II and III, mainly related to <i>Atopobium</i> and <i>Propionibacterium</i>, were novel combinations of microbiota in carious dentin lesions and may be characteristic of the Japanese population. Clone library analysis revealed that <i>Atopobium</i> sp. HOT-416 and <i>P. acidifaciens</i> were specific species associated with dentinal caries among these genera in a Japanese population. We summarized the bacterial composition of dentinal carious lesions in a Japanese population using next-generation sequencing and found typical Japanese types with <i>Atopobium</i> or <i>Propionibacterium</i> predominating.</p>