SMRT Sequencing Enables Characterization of Cavities-Causing Bacteria in Children

We’re told to avoid sugar and refined carbohydrates if we want our teeth to remain strong and cavity-free. But what is the role of microbiota in our oral health?
Cavities – or caries – actually occur as the result of bacterial infection that leads to sustained decalcification of tooth enamel and the layer beneath it, the dentin. Left unchecked, it can reach the tooth’s inner layer, with its soft pulp and sensitive nerve fibers, and, in some cases, can cause serious complications such as phylogenetic osteomyelitis and the life-threatening bacterial endocarditis.
In addition to diet and host factors, the occurrence and development of dental caries seems to be closely related to the imbalance of the oral microbiota. With this in mind, researchers at Zhejiang University in Hangzhou, China, wanted to create a profile of oral microbiota in early childhood caries, and they turned to PacBio SMRT Sequencing to do so.
As detailed in a paper published in the Frontiers in Microbiology, lead author Hui Chen, first author Yuan Wang, and colleagues derived 876 species from 13 known bacterial phyla and 110 genera from saliva samples collected from 41 Chinese preschoolers, aged 3–5 years old (21 with severe early childhood caries, and 20 who were caries-free).
A shift in the oral core microbiota was observed in the two groups, allowing the researchers to identify both protective and destructive bacteria.
“Our findings indicate that dental caries have a microbial component, which might have potential therapeutic implications,” the authors write.
At the species level, 38 species, including Streptococcus spp., Prevotella spp., and Lactobacillus spp., showed higher abundance in the caries group compared to the caries-free group. This suggests these bacteria may be risk factors for dental caries in children, the authors state.
The researchers also collected samples from the same children six months later. New cavities were developing in 5 children who were initially caries-free. Analyzing their microbiota, the researchers found that 6 species of bacteria that were abundant in the caries-free children, including Abiotrophia spp. and Neisseria spp., were much less abundant in these cases. Those bacteria were also less abundant in the initial caries group, leading the researchers to associate the strains with a healthy oral microbial ecosystem.
The authors say they chose single-molecule real-time sequencing because of its richness and resolution. Previous studies have explored the relationship between microorganisms and the development of caries; however, most of the cariogenic bacteria were only identified at the genus level, they noted.
“Species-level and even strain-level resolution is thought to be important for caries prognosis,” the authors state. “PacBio outperformed other sequencers… in terms of the length of reads, and it reconstructed the greatest portion of the 16S rRNA genome when sequencing the oral microbiota.”