View Images Teosinte (left), corn (right), and a teosinte-corn hybrid (middle). Photo by John Doebley/Wikipedia

We’ve been tinkering with the DNA of other species for thousands of years. We just didn’t know what we were doing.

Starting about ten thousand years ago, humans began to steer the evolution of animals and plants. Our ancestors collected certain seeds instead of others, started to plant them in gardens, and gradually produced domesticated crops. They didn’t know which genetic variants they were choosing, or how those genes helped build new kinds of plants. All they knew was that some plants were better than others. Over thousands of years, for example, an innocuous bush called teosinte turned into tall stalks with gargantuan seeds–otherwise known as corn.

Our ancestors could see the outward changes they were bringing to crops like corn, as well as livestock like cows and pigs. But hidden from view, other species were evolving in response to the dawn of agriculture. Early dairy farmers had no idea that they needed certain bacteria to turn their milk to yogurt or cheese. And they didn’t realize that the bacteria were adapting to this strange new environment that had never existed before.

And it wasn’t just the bacteria in pots of yogurt that were evolving. So were the microbes in our mouths.

The human mouth is home to hundreds of species of bacteria. While some of them keep our mouths healthy, others can cause us trouble. One of the worst offenders is Streptococcus mutans. It lives in the nooks of our teeth, feeding on carbohydrates. It excretes lactic acid as waste, and the acid eats away at the enamel on which it rests. Over time, Streptococcus mutans can dig a hole in a tooth–otherwise known as a cavity.

View Images A drawing by J. Kilian Clarke's 1924 paper on the discovery of S. mutans as the cause of cavities

Streptococcus mutants is not some jack-of-all trades microbe that happens to drop onto our teeth once in a while. For them, human teeth are the world. They are passed down from mothers to their children, and colonize those children for life. Other mammals have closely related Streptococcus strains on their teeth as well, suggesting that these bacteria have been tracking their hosts–and dwelling on their teeth–for tens of millions of years.

Recently Michael Stanhope, a biologist at Cornell, and his colleagues carried out a large-scale study of Streptococcus mutans. a large-scale study of Streptococcus mutans. a large-scale study of Streptococcus mutans. They looked at 57 colonies that had been gathered from the mouths of people in Brazil, Britain, Iceland, Hong Kong, South Africa, Turkey, and the United States. The scientists tallied up the genes that the bacteria had in common, as well as the ones that were only present in some people. (Bacteria sometimes pick up genes from other species.) Then the scientists compared all the human strains of the bacteria to Streptococcus living in rats, hamsters, and monkeys to pinpoint the DNA that is unique to our own passengers. And when they analyzed all these genes, they discovered something remarkable: these bacteria appear to have evolved with resounding success in response to the rise of civilization.

The Streptococcus mutans the scientists found in people’s mouths shared 1490 genes in common–a core genome, as it’s known. These shared genes varied from mouth to mouth, Stanhope found, with minor mutations sprinkled among them. It’s possible to tally up these mutations and use them to reconstruct some of the history of their ancestors. Stanhope and his colleagues found that Streptococcus mutans underwent a population explosion. And that explosion started ten thousand years ago.

It may well be no coincidence that this was also when our ancestors began to farm. Those early farmers shifted to diets dominated by corn and other grains–which turned the human mouth into an endless banquet of carbohydrates.

Stanhope and his colleagues were also able to pinpoint some of the genes that were important for Streptococcus mutans’s adaptation to civilization. Fourteen genes, for example, show signs of having experienced strong natural selection. Some of those evolved genes are essential for breaking down sugar. Others help the bacteria survive in the acidic conditions that arise in the mouth when we eat starches.

Perhaps most intriguing of all the genes in Streptococcus mutans are the 148 that Stanhope and his colleagues found in every human strain, but in none of the related bacteria in the mouths of other animals. The best explanation for this is that Streptococcus mutans picked these 148 genes up from other species in our bodies. Once Streptococcus mutans grabbed these genes, it didn’t let them go.

The function of the genes hints at their value. Some provide additional help at breaking down sugar. Others create more defenses against low pH. Others produce toxins that can kill off other species of bacteria that are competing with Streptococcus mutans for the spoils of civilization.

These adaptations have made Streptococcus mutans spectacularly successful, and they’ve also provided us with a lot of misery. The cavities would be bad enough. Archaeological evidence indicates that cavities went from rare to common with the advent of agriculture. Making matters, worse, however, is the fact that when Streptococcus mutans gets into the bloodstream through the gums, it can make its way to the heart and cause problems there, too.