Genes influence the microbes in our mouths to shape dental health

Q: I brush my teeth twice in a day, floss them, but still I am getting infections. Why is this?

Krishna: Several people ask me this question. Recent research answers this question well.

Genes influence the microbes in our mouths to shape dental health!

No matter how much they brush their teeth, some people still get more cavities than others, in part because of differences in genetics and the make-up of the microbes in their mouths. A new study has found human genetic factors that influence the oral microbiome and may increase risk of cavities and tooth loss in some people.

The abundance of many bacterial species in our mouths is strongly influenced by human genetics. We know that the microbial environment in one person's mouth is going to be quite different from another person's mouth due to many factors, but genetics is a pretty strong one.
Human genetic variation significantly influences the composition of the oral microbiome, affecting susceptibility to cavities and tooth loss. Specific genes, such as AMY1 and FUT2, are linked to changes in the abundance of numerous oral bacterial species. These genome-to-genome interactions shape oral health outcomes, with AMY1 copy number correlating with increased risk of tooth decay and denture use.

The study, led by scientists at the Broad Institute and Mass General Brigham, 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. For example, they found that a human gene, AMY1, was strongly linked to the composition of the oral microbial community, and even to denture use, suggesting that the relationship between this gene and the bacteria in the mouth plays a role in oral health.

The paper, published in Nature, is an analysis of the largest collection of oral microbiome profiles to date.

Image source: iStock

To find human-microbiota associations, the team analyzed 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.

They 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,

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.

Nolan Kamitaki, Human and bacterial genetic variation shape oral microbiomes and health, Nature (2026). DOI: 10.1038/s41586-025-10037-7. www.nature.com/articles/s41586-025-10037-7