Population-based characterisation of child and adolescent oral bacterial microbiomes

The factors influencing the oral microbiome during childhood and adolescence remain under-explored at the population level. Furthermore, details on how the oral microbiome differs with age, varies between individuals of different ethnicities, or is associated with socioeconomic factors and diet in children and adolescents are almost entirely unknown. Saliva samples and detailed demographic, health, diet and socioeconomic data were collected from children and adolescents that attended the Ontario Science Centre (Toronto, Canada) and were enrolled in the Spit for Science cohort. We characterised the bacterial microbiota of 4812 samples using 16S rRNA gene sequencing to make this the largest population cohort of the paediatric oral microbiome to date. Exploration of limited participant genotyping information and more than 50 variables encompassing the demographics, health, diet, socioeconomic status and living environment of participants revealed that almost all of the investigated variables were associated with overall community structure and/or the abundance of specific bacterial genera. However, most of these associations were modest (R 2 < 0.01) and the correlation between genetic relatedness and salivary bacteriome similarity was weak (R 2 = -0.014), while the strongest determinants of oral bacteriome composition were shared family/household environment (R 2 = 0.61 in the subset of participants from multi-child households), age (R 2 = 0.014) and ethnicity (R 2 = 0.01). We show that older children and adolescents have higher richness but lower evenness than younger children, suggesting that their oral bacteriome changes as they are exposed to more influences outside the home, and that the oral bacteriome is more consistent with more core taxa among children and adolescents than adults. We also find that diet variables related to the frequency of sugar consumption have the largest impact on the oral bacteriome of children and adolescents, and that microbial differences attributed to ethnicity and diet are likely intertwined. This study provides an atlas of the demographic, health and lifestyle factors that are associated with the salivary bacteriome of children and adolescents. These findings highlight the complex interplay between social, environmental, and biological factors in shaping the developing oral microbiome and underscore the importance of inclusive, demographically diverse cohorts in microbiome research. This presents a reference for the variables that are important to account for in paediatric oral microbiome studies. Video Abstract