A new study in the US has found human genetic factors that influence the oral microbiome and may increase risk of cavities and tooth loss in some people.
The study, led by scientists at the Broad Institute and Mass General Brigham—and published in Nature—found a surprisingly large effect of human genetics on the abundance of microbes in the mouth. The researchers discovered genome-to-genome interactions between human DNA and the DNA of the oral microbiome.
To find human-microbiota associations, the team analysed whole-genome sequences from saliva-derived DNA from more than 12,500 individuals. Typically, the microbial DNA in human samples is tossed aside, but the team found a new purpose for the bacterial data sequenced together with each human genome.
They measured the abundances of 439 common microbial species, and found 11 regions of the human genome associated with differences in the levels of dozens of species of bacteria in the mouth.
“We also found that the same 11 human loci influence natural selection on dozens of different bacterial genes, so it seems like there’s a lot of interaction between human genetics and the oral microbiome,” study first author Nolan Kamitaki said.
Notably, the scientists found the strongest relationship between a genetic variant that breaks the FUT2 gene—which has previously been linked to gut microbiome composition—and the levels of 58 oral bacterial species.
The researchers also leveraged data from the UK Biobank to analyse how human-bacteria interactions relate to oral health. One of the strongest associations they saw involved the AMY1 gene, which encodes a digestive enzyme found in saliva that breaks down starch into sugar. The team uncovered a link between the number of copies of this gene in a person’s genome and a change in the abundances of more than 40 oral bacterial species, many of which feed on sugars and over time build plaque.
Based on their biobank data analysis, they found that this same variation in the AMY1 gene correlated with an increase in denture use, suggesting that having more copies of the gene can lead to higher rates of tooth decay by changing the ecology of the microbiota in the mouth.
