Optimization and evaluation of the 30S-S11 rDNA gene for taxonomic profiling of oral streptococci

Dental caries is a multifactorial disease driven by interactions between the highly complex microbial biofilm community and host factors like diet, socioeconomic status, and age. The oral streptococci are one of the most dominant members of the plaque biofilm and are implicated in disease and maintaining oral health. Current methods used for studying the supragingival plaque community commonly sequence portions of the16S rRNA gene which often cannot taxonomically resolve members of the streptococcal community past genus level due to their sequence similarity. To gain a better understanding of the differing roles the oral streptococci play in dental caries, the goal of this study was to design, evaluate, and apply a new locus for high-throughput amplicon sequencing. This locus provides a reliable and cost-effective method to identify oral streptococci to species level and beyond. The results of our study found that the newly developed single-copy 30S-S11 gene locus resolved multiple ASVs within numerous species providing much improved taxonomic resolution over 16S rRNA V4. Importantly, our results reveal that different ASVs within a species were found to change in abundance at differing stages of caries progression. This suggests that strains of a single species may perform distinct roles along a biochemical spectrum associated with health and disease. The improved identification of oral streptococci species is crucial to the informed design of an oral probiotic for prevention and treatment of dental caries.