It’s a good thing that Neanderthals didn’t have tartar-control toothpaste.

What looks to us like unsightly buildup has turned out to be a goldmine for microbiologists who study human evolution. Hardened plaque harvested from Neanderthals is loaded with genetic material from plants and animals these prehistoric hominins ate, as well as remnants of microbes that reveal a surprising amount about how they lived and even what made them sick.

Researchers extracted the ancient DNA and bacteria from the jaws of three Neanderthal individuals from Belgium and Spain, and described the results in a paper published today in the journal Nature.

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The Belgian individuals ate a heavily meat-based diet, indicated by DNA from wooly rhinoceros and wild sheep. Meanwhile, the Spanish Neanderthal seemed to have eaten mostly vegetable material, including moss, pine nuts, and mushrooms.

Perhaps more intriguing, though, were the microbial riches Weyrich’s team found preserved in the calcified plaques: The team recovered DNA from these prehistoric individuals’ microbiomes, communities of bacteria and fungi living on and inside their bodies.

“It gives us a picture of a wide variety of things they were exposed to in their daily lives, including diseases and the medicines they were using to treat them,” says study leader and University of Adelaide microbiologist Laura Weyrich.

For instance, the individual from El Sidrón, Spain, seems to have had some bacterial strains that gave him a hard time, and it’s possible the hominin turned to botanicals to treat them.

The Spanish Neanderthal was suffering from a dental abscess, possibly caused by a subspecies of the bacterium Methanobrevibacter oralis. Poplar found in the sample likely provided salicylic acid—the active ingredient in aspirin—for pain relief. (Read “Neanderthal Gums Relieved by Toothpicks.”)

The individual was also dealing with diarrhea and vomiting caused by a different pathogen, Enterocytozoon bieneusi, and may even have turned to antibiotic-producing molds for treatment. Genetic material from Penicillium rubens was found on plant matter in this Neanderthal’s teeth.

Digesting the Data

The idea of looking at tooth plaques for clues about life in ancient times has been around for decades; study co-author Keith Dobney has been working on some form of the technique since the 1980s.

But it wasn’t until the advent of super high-powered microscopy and precision genetics tools that researchers were able to drill down into prehistoric plaques to really perceive what might be lurking there.

View Images A closeup of the Neandertal teeth shows dental calculus deposits as a rind on the tooth enamel. Photograph by Royal Belgian Institute of Nature Sciences

Worse, says Weyrich, until the last 10 to 15 years, calcified tartar would routinely be cleaned away from new specimens at museums and labs, because scientists then were more interested in growth and wear patterns on the teeth themselves.

The idea that Neanderthals ate both meat and vegetables or self-medicated with plants isn’t strictly new. This study backs up results from earlier examinations of nitrogen isotopes found in tooth enamel and physical plant remains found jammed between their teeth.

What really grabbed Weyrich and her group in the new data was the fact that the meat-eaters’ overall microbiomes differed from the vegetarian’s, and that they differed altogether from the microbial mashups that live inside modern humans.

What the various groups were eating may be the key to these differences. And with this ancient reference point, scientists can now better track the way diet impacts the microbiome over time, and how those effects have shaped our evolution.

“Looking at how dietary changes cause changes in the microbiome is really hard to do with modern medicine—you’d have to get millions of people eating the same thing for months on end,” Weyrich says.

“But using Neanderthals as a model—people who are stuck in one place and limited to the food sources those places provide—we can determine what they were doing that might have caused a change in their microbiome.”

Dobney, an archaeologist with the University of Aberdeen, says he’s hopeful that being able to compare post-agricultural biomes with those of prehistoric people can offer ideas for how to combat modern dietary blights.

“Microbiomes have evolved over millions of years with us, and we can’t live without them,” Dobney says. “Obesity, diabetes—these don’t come out of nowhere. This will give us some serious insight on how changes in migration and diet have impacted human society.”

The work could even offer fresh clues to why Neanderthals ultimately died out.

“The [Belgian] Neanderthals we looked at were some of the last that existed, so if there’s a signal in the changes in their microbiome that contributes to their health, then these are the ones we’d want to look in,” Weyrich says.

Signs of Swapping Spit?

View Images Skeletal remians from one of the Belgian Neanderthals. Photograph by Royal Belgian Institute of Nature Sciences

Weyrich’s group also sequenced the entire genome of the gum-disease causing Methanobrevibacter bacteria—at 48,000 years old, it’s by far the oldest bacterial genome sequenced to date.

They found that the Neanderthal strain originated around 125,000 years ago, at the time when Homo sapiens and Neanderthals are thought to have been interbreeding. The modern form of this bacterium is transmitted from person to person via saliva, so the find raises interesting questions about how humans and Neanderthals may have interacted during such intimate moments.

“Breeding encounters have often been thought of as brash, rough events, but these are oral microorganisms, transferred through kissing or food-sharing,” Weyrich says. “That we’re finding them in the mouths of these Neanderthals tells us more about how they would have potentially gotten along with humans. And that’s just one microorganism in the mouth.”

While there’s more work to be done to determine exactly how the bacterium moved across populations, the concept intrigues Lawrence Straus, a University of New Mexico anthropologist who has studied European Neanderthals for 45 years.

“It would be truly fantastic to see evidence of the passing of specific bacteria from Neanderthals to Homo sapiens,” says Straus.