National Geographic

The Evolution of Cavities

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.

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. 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.

Appreciating how Streptococcus mutans evolved into such a successful burden might offer a way to fight it. Stanhope’s study provides a veritable catalog of adaptations that the germ relies on to transform the agricultural revolution into trillions of new bacteria. It might be possible to target one of those adaptations and attack Streptococcus mutans with pinpoint accuracy, leaving the rest of the residents of our mouths unharmed. We may have unwittingly made Streptococcus mutans what it is today, but we can wittingly do something about it now.

[Top image: Amy Dame/Flickr via Creative Commons]

There are 19 Comments. Add Yours.

  1. Jack C. Schultz
    December 21, 2012

    It should be possible to design an antibiotic targeting S. mutans. But then that would hurt the dentist industry.

  2. Melissa
    December 21, 2012

    What do you think of the rice exception to the cariogenic grains hypothesis, as laid out in “Agriculture and dental caries? The case of rice in prehistoric Southeast Asia”?

    Some wild plants are also known to be highly cariogenic – “Prehistoric Dental Disease
    and the Dietary Shift from Cactus
    to Cultigens in Northwest Mexico”

  3. Jeff
    December 22, 2012

    Why should we be concerned with “hurting the dental industry” Mr Shultz? The dental industy that keeps us in pain and in debt.
    The dental industy that offers modern tooth implants and technically proficient dentistry practice methods to the rich but keeps the poor in the barbaric driling root canal filling ritual that is rarely a cure.
    A cure would mean no follow up.
    The dental industry it would seem only seeks to keep us in that endless loop as cavities filled further rot they eventually get to charge our insurance to re-drill and fill the same cavities and cause us the same pain over and over!

  4. S.sidhu
    December 22, 2012

    1:jack was being sarcastic about helping dentists
    And two, you seem a bit angry.

  5. Marcus
    December 22, 2012

    The connection between systemic illness and oral bacteria is fascinating… Check this recent article if interested

  6. Ed
    December 22, 2012

    Sure Jeff, let’s get rid of all those evil dentists who are just there to inflict pain and charge your insurance company.The dental profession is one of the few that really stresses prevention. Flouride, sealants, home care instruction and patient education put it at the forefront of eliminating problems before they occur.
    Hope the next time you have a tooth problem your dentist reads your post!

  7. Jc
    December 22, 2012

    The fear I would have about killing off this bacteria is what bacteria might take its place, and might it not be worse? Other than that I can’t fathom why you people are arguing over the dental industry – this was a great article and you’re all missing the point. Schulz comment was obviously toy ur in cheek if you’ll forgive the pun. I don’t see how it could be misconstrued.

  8. David Bofinger
    December 23, 2012

    Antibiotics is a possibility. How about a tailored bacteriophage, or an antidote for the toxins so other species have a better chance?

  9. Jim Jozwiak
    December 23, 2012

    No mention of Vitamin K2?

  10. Miki Ben-Dor
    December 25, 2012

    How about just reducing carbs in the diet? Works like magic (together with D and K2) to secure healthy teeth.

  11. Mc
    December 26, 2012


    What do suggest everyone do? Avoid the dentist and develop infections and die like the Middle Ages. Dentistry is one of the health professions that actually stresses prevention. I for one am thankful that dentists can relieve our pain.

  12. David
    December 28, 2012

    I recall a while back there was an attempt to make a “vaccine” to S. mutans. It wold produce a mucosal antibody response and wipe out tooth decay. Anybody know what happened?

  13. Chris Lindsay
    December 31, 2012

    With the concern of overusing antibiotics that create antibiotic-resistant bacteria, it’s surprising that cavity-fighting compounds like flouride and whatever else comes in toothpaste haven’t created flouride-resistant bacteria.

  14. Jacob W
    December 31, 2012

    Third year dental student here. S. mutans is only an instigator of caries, there are over 100 other species involved in the decay process and they work together as a biofilm. S. mutans is already easily killed by several anti microbiall agents we use, but the problem is that it, along many other biofilm members, is part of your normal flora. If we began the scorched earth campaign required against these bugs, it would leave us with much worse alternatives taking there place in our mouths.
    Do yourself a favor and buy a good electric toothbrush, because not even dentists brush their teeth correctly 100% of the time. Go to your regular cleanings (they save you a ton of money, and trust me your teeth are gross after 6 months anyway).

  15. Hugh
    January 6, 2013

    Great article–but a bit simplified. Strep mutans is a key contributor to tooth decay. Just as important is controlling the pH in the mouth so that the biofilm in the mouth will be less cariogenic and remineralization with Calcium, Phosphate, and Fluoride can occur That. Is critical!

    Furthermore , decay is caused by cracks in teeth from stress and poor eating habits

    The dental profession could use some help. They are not bad guys in general If we could have enough leverage to convince drink companies to tell the truth about the low pH levels in their products, people could control much what occurs
    Lastly, if each patient ( and their parents!!) would truly learn the risk factors less early tooth decay. AND decrease break down of teeth would occur. Let’s stop playing the blame game and fix the problem

  16. Laura
    January 22, 2013

    Jack, I take more pride in my work than most. I am sorry you have been scorned by the dentsits that you have chosen. Do some research in your area, look on the AACD website, FIND A BETTER DENTIST. Because you are right, there are some bad professionals out there, not only in dentistry. Choose one that can get eye to eye with you and talk truthfully. Giving you facts that you can understand and make a decision on the care you want/need. I made a choice to always treat my patients like they were in my living room. Talk with them like they were my family. Find someone you can start building a trustworthy relationship with that is good at what he/she does. Ed, your not helping the problem. Hugh, in order to learn the risk factors early, the teacher needs to know them and be willing to share at an early stage. Im sure you can count the proper teachers on your hands. Besides my boss, I personally know of 2. Agreed, go out and buy a GOOD electric tooth brush. As much as it sucks, floss once a day. Disrupting the bacteria that hides between the tooth and the gum kills it. It grows back every 24 hours. That bacteria that you leave in there eats bone. And yes, go to your cleanings. Listen to your hyg dept and whether it is 3 months, 4 months, 6 months. Go. if your nervous, there is always an upside. N2O. :)

  17. majkinetor
    February 1, 2013

    Yeah, low carb, K2, yogurt and fish oil work like magic.

    Nothing more is required, not even tootbrush.

  18. s.karikalan
    May 28, 2014

    i am also know about this species but i don’t know about detailed information. the major causative agent in oral cavity for dental caries. till this minute we don’t have any evidence of a full cellular structure and also nobody didn’t detect the suitable microscope to identify this bacteria. if any body have a clear structure of s.mutans images please send me to my email id – , i am also a microbiology researcher in tamilnadu ,india is my country. if you have a recent edition last year or before previous year of bergey’s manual please send me.

  19. juan
    June 21, 2014

    If S. mutans lives in 7,000 million mouths over the planet how is it that some people have no tooth decay while others are thoothless? If your answer is because of the diet, the next question is: Why do we have dentists drilling and filling and cashing instead of good, sound and honest nutritionists that will teach us what to eat and what to avoid to save our natural teeth?

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