Microbiome of Dentinal Caries and Plaque using Next-Generation-Sequencing

Objective:  To investigate the metagenome in dentinal caries and plaque using 16S rRNA Next Generation Sequencing (NGS). The aims of this study were twofold: (i) to determine the predominant bacterial taxa associated in dentinal caries from permanent teeth of healthy adults; and (ii) to describe the similarity of microbial niche from dentinal caries and dental plaque. Method: Four freshly extracted human molars and premolars from healthy adults with proximal or occluso-proximal caries lesion with ICDAS score 5 and 6 were used in this study. Plaque samples were collected from either of any four surface of the carious tooth. The carious biomass was excavated from the infected part of lesion using standardized scales of measurements used in clinics. Total DNA from each sample of dentinal caries and plaque was extracted separately followed by PCR amplification. In the single NGS run, 14.4 M raw reads were resulted, each read was blasted against the updated 16S microbial database in NCBI. With the facilitation of Metagenome Analyzer (MEGAN), the resulted sequences from BLAST were taxonomically assigned down to species level and compared among dental caries and plaque samples. Result:  Our amplicon NGS data identified 10 major phyla: Actinobacteria, Bacteroidetes, Fibrobacteres, Firmicutes, Fusobacteria, Alphaproteobacteria, Proteobacteria, Spirochaetes, Synergistetes and Tenericutes. The predominant bacteria included Chryseobacterium E. meningoseptica sp., Prevotella, P. multisaccharivorax sp., Lactobacillus, L. delbrueckii sp., Capnocytophaga, C. leadbetteri sp., Actinomycineae, A. graevenitzii sp., Coriobacterineae, O. profusa sp.. Among these, Chryseobacterium and its member namely E. meningoseptica sp. was single most abundant bacteria within dentinal caries. The genera Lactobacillus and Prevotella were most commonly found in both dentinal caries and plaque, followed by Capnocytophaga and Actinomycineae. Conclusion: E. meningoseptica sp. was single most abundant bacterium showing within dentinal caries. The predominant genera most commonly found in both dentinal caries and plaque sample were lactobacilli and Prevotella.