DNA and RNA-based amplicon sequencing of paired supragingival and dentin lesion plaque in children with severe early childhood caries

Early childhood caries is a form of tooth decay in children under the age of 6 and impacts more than 514 million children worldwide. Severe early childhood caries (S-ECC) represents the most advanced and aggressive form of early childhood caries, defined by an age-dependent number of cavitated, missing, or filled smooth surfaces in the primary maxillary anterior teeth, or an overall count of decayed, missing, or filled tooth surfaces. To advance our understanding of the microbiological differences between different types of dental caries, we sought to investigate deep dentin caries isolated from 13 children with S-ECC and compare it with supragingival plaque isolated from the same site to identify differentially abundant species. Co-extraction methods allowed species identification by both the 16S gene and transcript sequences. By sequencing and analyzing reverse transcribed 16S rRNA in parallel to DNA, we were able to identify bacteria with higher metabolic potential within dentin plaque, allowing the detection of potentially active oral bacterial species that may be driving and/or contributing to this most severe form of dental caries. Here, we highlight that Lactobacillus casei and Oribacterium sp. HMT-078 are significantly differentially enriched in dentin plaque and has an increased RNA/DNA ratio, indicating activity within dentin plaque samples from S-ECC patients. These species may therefore play a significant role in the progression and severity of S-ECC within deep dentin plaque, in addition to other well-established cariogenic species associated with S-ECC, like Prevotella denticola, Dialister invicus, and Streptococcus mutans.