Supragingival Biofilm Transcriptomics in Early Childhood Oral Health

Objectives: The supragingival oral microbiome is the fundamental pathogenetic element for dental caries development, including its severe, early-onset form—early childhood caries (ECC). Next-generation sequencing methods can help illuminate functional features that underlie oral health and ECC; however, no functional biofilm data exist from population-based cohorts of early childhood oral health. The purpose of this pilot study was to characterize preschool-age children’s supragingival biofilm transcriptomes according to clinical statuses of dental health and disease.
Methods: The sample comprised 118 children aged 3-5, enrolled in a community-based genetic epidemiologic study in North Carolina. Caries experience was recorded using modified ICDAS criteria and children were classified as caries-free (n=40), restored (n=19) and untreated disease (n=59). Supragingival biofilm samples were collected from facial surfaces of upper-right quadrant teeth using sterile toothpicks, immediately placed in RNAlater TissueProtect tubes and frozen until analyses. Nucleic acids were isolated using a MO BIO PowerBiofilm kit. We used Illumina HiSeq-4000 to carry out pair-ended 150bp read length RNA sequencing. After bioinformatics processing and alignment, rank orders of species, genes and pathways were obtained, overall and by group. Between-group comparisons were done using two-part logistic beta models.
Results: We obtained 378 million reads mapped to 132 bacterial species and 238,693 gene families. The most represented species in healthy biofilm transcriptome were: Streptococcus mitis, S. oralis and S. pneumoniae; and in unrestored disease biofilm: Corynebacterium matruchotii. The top five most represented pathways were common for health, restored and untreated ECC. Beyond these, glycolysis, guanosine and adenosine nucleotide de novo biosynthesis were functions more represented in untreated disease, whereas propanediol, lactose and galactose degradation were more represented in health.
Conclusions: These results provide novel insights into the transcriptional profile of the supragingival biofilm as it relates to states of health, restored and untreated ECC. Upon validation, these data can inform the development of biologically-driven caries risk assessment and disease management.