Microbiome associated with severe caries in Canadian First Nations children

Objectives: To determine the caries-associated microbiome among First Nations children with severe early childhood caries (S-ECC).
Methods: First Nations children < 72 months of age with S-ECC or caries-free were recruited in Winnipeg, Canada. Children with S-ECC were recruited on the day of their dental surgery. Caries-free children were recruited from the community. Parents completed a questionnaire on general and dental health, diet, and demographics. Plaque and saliva samples were collected following set protocol. Microbiome analysis was conducted including Human Oral Microbe Identification using Next Generation Sequencing (HOMINGS). This study was approved by the University of Manitoba’s Health Research Ethics Board. Data analysis included descriptive and bivariate analyses (Chi Square and t tests). A p value ≤ 0.05 was significant.
Results: 30 children with S-ECC and 20 caries-free controls participated. The mean age was 40.7±11.7 months and 56% were male. There were no significant differences between the groups with respect to sex or age (p=0.20 and p=0.11, respectively). Children with S-ECC were weaned from the bottle at a later age than those caries-free (25.8±12.0 months vs. 17.9±8.9, p=0.28). There was no difference in daily snacking frequency between the groups (p=0.71). Microbiome analyses revealed no new unique pathogens. However, the abundance of S. mutans rDNA relative to total bacterial rDNA was significantly higher in children with S-ECC (5.99%±7.01% vs. 0.21%±0.28%, p<0.05). Meanwhile, compared to caries-free children, those with S-ECC displayed nearly a 3-fold decrease in Streptococcus sanguinis (a competitor of S. mutans), and a 3-fold increase in Veillonella spp (metabolically dependent on S. mutans) relative abundance. There was an increased abundance of S. mutans, as well as population shifts in oral microbial communities in children with S-ECC.

Conclusions: First Nations children with S-ECC had significantly higher levels of cariogenic microorganisms than their caries-free counterparts, which might explain the high prevalence of S-ECC in Indigenous children.