Profiling of Oral Microbiota in Early Childhood Caries Using Single-Molecule Real-Time Sequencing

Abstract

<b>Background:</b> Alterations of oral microbiota are the main cause of the progression of caries. The goal of this study was to characterize the oral microbiota in childhood caries based on single-molecule real-time sequencing. <b>Methods:</b> A total of 21 preschoolers, aged 3-5 years old with severe early childhood caries, and 20 age-matched, caries-free children as controls were recruited. Saliva samples were collected, followed by DNA extraction, Pacbio sequencing, and phylogenetic analyses of the oral microbial communities. <b>Results:</b> Eight hundred and seventy six species derived from 13 known bacterial phyla and 110 genera were detected from 41 children using Pacbio sequencing. At the species level, 38 species, including <i>Veillonella</i> spp., <i>Streptococcus</i> spp., <i>Prevotella</i> spp., and <i>Lactobacillus</i> spp., showed higher abundance in the caries group compared to the caries-free group (<i>p</i> < 0.05). The core microbiota at the genus and species levels was more stable in the caries-free micro-ecological niche. At follow-up, oral examinations 6 months after sample collection, development of new dental caries was observed in 5 children (the transitional group) among the 21 caries free children. Compared with the caries-free children, in the transitional and caries groups, 6 species, which were more abundant in the caries-free group, exhibited a relatively low abundance in both the caries group and the transitional group (<i>p</i> < 0.05). We conclude that <i>Abiotrophia</i> spp., <i>Neisseria</i> spp., and <i>Veillonella</i> spp., might be associated with healthy oral microbial ecosystem. <i>Prevotella</i> spp., <i>Lactobacillus</i> spp., <i>Dialister</i> spp., and <i>Filifactor</i> spp. may be related to the pathogenesis and progression of dental caries.