Some of the mouth’s microbial communities may promote good health, while others contribute to cavities, gum disease, and possibly even heart disease. Now, scientists are learning more about how genetic and environmental factors influence the mouth’s microbial makeup, and how these effects may relate to oral health. The findings, reported in Cell Host & Microbe, could inform future tests to predict or diagnose oral disease.

In principle, the oral microbiome is susceptible to both environmental and genetic effects. During birth, babies encounter a rush of microorganisms, which initialize the microbiome throughout the body. Exposure to food, caregivers, and myriad environmental factors continue to modify the oral microbiome throughout life. Genes could play a role, too: although oral bacteria can’t be inherited through DNA, genetic differences can influence mouth chemistry, shaping the resident microbial communities. Previous research, however, has yielded mixed results on the relative importance of the two factors.

To tease apart these influences, researchers led by genomic scientist Karen Nelson, president of the J. Craig Venter Institute, compared 485 pairs of identical and fraternal twins aged 5-11. Identical twins shared the same genetic and environmental conditions, while fraternal twins shared only environmental influences on the oral microbiome. Researchers swabbed the gum surface of each child, and performed high-throughput genetic sequencing to identify the different microorganisms present.

Most of the variation in microbiome composition across children was explained by environmental factors, but the researchers found evidence of heritability as well. Overall, identical twins had more similar oral microbiomes than fraternal twins, and all subjects were more similar to their own twins (regardless of type) than to randomly selected, unrelated participants. Bacteria that showed the strongest heritability tended not to be associated with cavities. Instead, those cavity-linked microbes, including some in the Streptococcus genus, were mostly influenced by environmental factors, such as increased sugar consumption.

The results contrast with previous research, which showed that levels of Streptococcus mutans, a known cavity-causing microbe was roughly equally determined by genetic and environmental factors. Microbiologist Walter Bretz at New York University led the earlier work on Brazilian children of low socioeconomic status—few of whom had ever visited a dentist. He speculates that the relatively good oral health of the subjects of the present study, which took place in Melbourne and Adelaide, Australia, may have obscured some associations between genetic factors and dental disease. Nelson suggests that different methods for isolating and identifying bacteria in past studies, by not capturing the full microbial milieu, could have generated differing conclusions. But she agrees that different populations, including those of different ethnicities, dietary habits, and health status, could yield different results.

Molecular anthropologist Christina Warinner at the Max Planck Institute for the Science of Human History in Jena, Germany, who was not involved in the research, called it “an exciting first step,” noting that the oral microbiome has been historically understudied compared to that of the gut. Now, she says, further studies are needed to detail what these microbes are actually doing—for example, the genes they’re expressing and the proteins they’re producing to influence health. “It may not be the exact species that are present but more their functions that matter,” Warinner says.

Nelson’s team is planning such experiments, and also intends to track how the oral microbiome changes over time in the children. Eventually, she hopes that this work will lead to tests that dentists can use. “Parents can get insight into the appearance of certain organisms even before they see cavities in their kids,” she says. “That’s my hope.”