Microbiome Associated with Severe Caries in Canadian First Nations Children

Abstract

Young Indigenous children in North America suffer from a higher degree of severe early childhood caries (S-ECC) than the general population, leading to speculation that the etiology and characteristics of the disease may be distinct in this population. To address this knowledge gap, we conducted the first microbiome analysis of an Indigenous population using modern molecular techniques. We investigated the caries-associated microbiome among Canadian First Nations children with S-ECC. Thirty First Nations children <72 mo of age with S-ECC and 20 caries-free children were recruited in Winnipeg, Canada. Parents or caregivers completed a questionnaire on general and dental health, diet, and demographics. The plaque microbiome was investigated by sequencing the 16S rRNA gene. Sequences were clustered into operational taxonomic units and taxonomy assigned via the Human Oral Microbiome Database, then analyzed at the community level with alpha and beta diversity measures. Compared with those who were caries free, children with S-ECC came from households with lower income; they were more likely to live in First Nations communities and were more likely to be bottle-fed; and they were weaned from the bottle at a later age. The microbial communities of the S-ECC and caries-free groups did not differ in terms of species richness or phylogenetic diversity. Beta diversity analysis showed that the samples significantly clustered into groups based on caries status. Twenty-eight species-level operational taxonomic units were significantly different between the groups, including Veillonella HOT 780 and Porphyromonas HOT 284, which were 4.6- and 9-fold higher, respectively, in the S-ECC group, and Streptococcus gordonii and Streptococcus sanguinis, which were 5- and 2-fold higher, respectively, in the caries-free group. Extremely high levels of Streptococcus mutans were detected in the S-ECC group. Overall, First Nations children with S-ECC have a significantly different plaque microbiome than their caries-free counterparts, with the S-ECC group containing higher levels of known cariogenic organisms.

Keywords: Indigenous population; Streptococcus mutans; dental health survey; healthcare disparities; oral health; preschool child.

Figure 1.

Diversity analyses. (A) Rarefaction curves of alpha diversity indices. Left: chao1 (species richness); right, Faith’s phylogenetic diversity index. (B) Beta diversity shown by principal coordinates analysis (PCoA) of unweighted Unifrac distances (left) and weighted Unifrac distances (right). The plaque microbial communities significantly clustered by caries status (P < 0.05, analysis of similarity). S-ECC, severe early childhood caries.

Figure 2.

Relative abundance of Streptococcus mutans in all subjects. Percentage relative abundance of S. mutans is plotted for each subject. S-ECC, severe early childhood caries.

Figure 3.

S-ECC subgroup analysis. Subjects from the S-ECC group were further divided per their residency in a First Nations community. (A) Beta diversity shown by principal coordinates analysis (PCoA) of weighted Unifrac distances. The plaque microbial communities significantly clustered by place of residency (P < 0.05, analysis of similarity). Blue, resides in First Nations community; red, does not reside in a First Nations community. (B) Average of the top 100 most abundant species identified in each group. FN_no = does not reside in a First Nations community (n = 13); FN_yes = resides in a First Nations community (n = 17). *P < 0.05 (Kruskal-Wallis with false discovery rate correction). S-ECC, severe early childhood caries.