Integrative analysis of taste genetics and the dental plaque microbiome in early childhood caries

Abstract

Early childhood caries (ECC) is a multifactorial disease mainly caused by the oral microbiome; however, it is also influenced by host genetics and environmental factors. The combinatorial analysis of these multiple factors influencing ECC susceptibility requires further research. This study investigated the interplay between genetic variants in taste-related genes and the microbiome in ECC, targeting taste genes because of their role in taste preference and potential interactions with oral fungi and bacteria. Using a case-control design involving 538 children, we obtained dental plaque microbiome profiles and genetic variants across 55 candidate genes through next-generation sequencing. Our association analysis for taste genetics and ECC outcome used the socioeconomic factor index (SEFI) and rural-urban status as confounders. We observed a few taste gene variants associated with ECC and microbial diversity. However, no specific association was observed between the variants and cariogenic species. Furthermore, our analysis indicated that Streptococcus mutans is a partial mediator between these genetic variants and ECC outcomes. Machine learning models integrating microbiome, genetics, and covariates achieved robust ECC vs. caries-free classification (AUROC = 0.96), with Streptococcus mutans, rural-urban status, a bitter taste receptor variant, Candida dubliniensis, and SEFI as the top ECC-associated factors. Our findings highlight the association between host genetics and the oral microbiome, underscoring the need for multiomics approaches in ECC risk assessment. HighlightsO_LIS. mutans, C. dubliniensis, and taste genetic variants are associated with ECC. C_LIO_LIRural-urban status and SEFI score are among the top social markers for ECC prediction. C_LIO_LITaste-related genetic factors modulate the composition of dental plaque microbiome. C_LI