Salivary microbiome diversity in caries-free and caries-affected children

Abstract

OBJECTIVES: Controversies remain in the diversity of bacterial communities of caries-active and healthy individuals. This study aimed to phylogenetically characterize the diversity of bacterial microbiome in saliva of children with and without caries. METHODS: Unstimulated saliva samples (2mL) were collected from 3-4 years old children with (n=20) and without caries (n=20). Total microbial genomic DNA was extracted. DNA amplicons of the v3-v4 hypervariable region of the bacterial 16S rRNA gene were generated and subjected to analysis using the Illumina MiSeq platform. RESULTS: A total of 17 phyla, 26 classes, 40 orders, 80 families, 151 genera and 310 bacterial species were represented in total samples. Overall, there was no significant difference in the diversity of bacterial microbiome between the caries-affected and caries-free children (p>0.05 for both Shannon index and Simpson index). 268 species were identified in caries-affected group, and 244 species were identified in caries-free group. Notably, Prevotella melaninogenica, Prevotella histicola, Streptococcus sanguinis and Actinomyces odontolyticus were the most dominant species in both groups. The relative abundance of several species was higher in caries-affected group than in caries-free group, including Rothia dentocariosa, Actinomyces graevenitzii, Veillonella sp. oral taxon 780, Prevotella salivae and Streptococcus mutans (p<0.05). In contrast, Fusobacterium periodonticum, Leptotrichia sp. oral clone FP036 and Prevotella nanceiensis were more abundant in caries-free children than those with caries (p<0.05). CONCLUSIONS: The salivary microbiome diversity of caries-free and caries-affected children was similar. Salivary counts of certain bacteria such as R. dentocariosa and F. periodonticum may be potentially useful for screening and assessing cariogenic risk in children.