Description: The oral microbiota contains billions of microbial cells, which could contribute to diseases in a number of body sites. Challenged by eating, drinking and dental hygiene on a daily basis, the oral microbiota is regarded as highly dynamic. Here, we report significant human genomic associations with the oral metagenome from more than 1,915 individuals, for both the tongue dorsum and saliva. Five genetic loci, APPL2, SLC2A9 and MGST1 associated with tongue dorsum, LOC102723769-OR11H1-POTEH and MTRNR2L1-LOC105371703-MIR4522 associated with salivary microbial features, reached study-wide significance (p < 3.16*10-11). Further analyses confirmed 6 genome-wide significant loci shared between tongue dorsum and saliva. For example, the dental caries pathogen Prevotella melaninogenica associated with MARK2-RCOR2; the periodontis bacteria Treponema associated with CCL26-CCL24 and Porphyromonas associated with CSMD1 at both niches. As many of the human genetic associations lie near RNA genes, we further validated the potential of host miRNAs to modulate growth of specific oral bacteria. Machine learning models showed that polygenetic risk score dominated over oral microbiome in predicting predisposing risk of dental diseases such as dental calculus and gingival bleeding. These findings indicate that human genetic differences are one explanation for a stable or recurrent oral microbiome in each individual. DATA AVAILABILITY : All summary statistics that support the findings of this study including the associations between host genetics and saliva microbiomes, host genetics and tongue microbiomes will be publicly available here. The release of the data was approved by the Ministry of Science and Technology of China (Project ID: 2021BAT1539).

Data type: Metagenome; Other

Sample scope: Multispecies

Relevance: Other

Release date: 2023-09-12

Last updated: 2023-09-13

Data size: 410.46GB