For centuries, archaeologists have studied the teeth of ancient human skulls to glean details about how they lived and what they ate. To get at these valuable remains, they would typically scrape off and dispose of the plaque that coated the teeth.

It turns out they may have been discarding scientific treasure. Scientists are learning that fossilized dental plaque can tell us quite a lot about our ancestors—from how eating meat changed our oral health, to how Neanderthals used medicinal plants and even how they interacted with their human cousins.

While scientists have been able to recover DNA from within bones for decades, that genetic material can’t tell us about the microbiome—or community of bacteria—that the ancient person lived with. It’s only thanks to recent advances in genetic sequencing and a new appreciation for the excretions we leave behind that we’ve started to find clues in things like dental plaque and fossilized feces, says Laura Weyrich, a paleomicrobiologist at the Australian Center for Ancient DNA.

Looking for microbiome DNA in dental plaque “is a brand new research field," Weyrich says. Four years ago, she and her team published one of the first studies that drew on fossilized dental plaque to examine how the oral microbiomes of humans changed after two major events in human history: the rise of agriculture 10,000 years ago, and the advent of the Industrial Revolution in the 19th century.

After sequencing the DNA of bacteria in the plaque, they found that the shift to agriculture appeared to have changed the oral microbiome to make it more receptive to disease-causing microbes. Meanwhile the Industrial Revolution decreased the diversity of the oral microbiome. Both of these shifts, the authors say, may have contributed to the many oral diseases we live with now.

"It worked really well, so we said 'where can we go with this?'" Weyrich says. "The obvious answer was Neanderthals—let's go big."

Since then, the researchers have tracked down two pairs of Neanderthal skeletons ranging in age from 42,000 years old to 50,000 years old, from two separate places: central Belgium and northern Spain. Based on genetic analysis, they found that the two communities' microbiomes differed drastically depending on where they lived, and more importantly, what they ate. The results were published yesterday in the journal Nature.

The Belgian Neanderthals appeared to eat a "classic" meat-heavy Neanderthal diet, based on the DNA of sheep, woolly mammoth and other animals found in their plaque, Weyrich says. This made their oral microbiome look very distinct from the Neanderthals living in Spain, who appeared to eat a much more vegetarian, hunter-gatherer type diet of pine nuts and mushrooms.

"It really contradicts the classical view of the club-toting, meat-eating caveman," Weyrich says. "It suggests that Neanderthals were much more tuned into the environment and their ecology"—that is, that they were able to adapt to a variety of different surroundings and available foodstuffs, much like modern humans.

Interestingly, Weyrich says, the oral microbiomes of the Spanish Neanderthals appear to be much closer to that of chimpanzees, our hunter-gatherer genetic ancestors. This suggests that this microbiome caused by a hunter-gatherer, mostly vegetarian diet was possibly the "core" microbiome for hominids, from which modern human microbiomes have since evolved.

"It's really eating meat that changes the microbiome in humans for the first time," Weyrich says.

Weyrich says that overall these Neanderthals had excellent oral health, despite never having used a toothbrush. "They're immaculate," Weyrich says of the teeth she examined. "They would have been very healthy." While that might sound surprising, Weyrich says the results were similar to what the team found in 2013.

An exception was one of the Spanish Neanderthals. This man suffered from a dental abscess and some kind of diarrhea, Weyrich says, which provided the team an opportunity to find out what was causing him pain and discomfort. After extensively sequencing his microbiome, the team found evidence that the Neanderthal was using medication, including the fungus that creates penicillin and the main ingredient of aspirin, in an attempt to treat himself.

"It's really quite remarkable to think about what a Neanderthal knew about his environment and how he could use the things around him," Weyrich says.

After sequencing the abscess-suffering Neanderthal, Weyrich and her team also ended up with the oldest microbe genome found to date. By comparing the 48,000-year-old genome of the microbe Methanobrevibacter oralis to its genome today, the researchers were able to trace back when this archaea strain diverged from the strain found in humans, and found that it was only roughly 125,000 years ago, long after humans and Neanderthals began to split about 600,000 years ago.

Not only does this suggest that Neanderthals got this microbe from humans, Weyrich says. it also implies something surprising about the nature of interactions between them. While scientists are now certain that humans and Neanderthals interbred at some point, the fact that they were apparently sharing spit suggests that their interactions were friendlier than some have theorized.

For future research, Weyrich plans to turn to the fossils of other ancient humans and human ancestors to see what more can be gleaned. "This is the first time that anybody has ever been able to sequence a microbiome in an extinct species," Weyrich says. "I think we'll be doing this study over and over again but with different sets of [human ancestors]."

Moreover, Weyrich says that these ancient dental insights might help modern humans confront our own health. Particularly, she hopes researchers will think harder about why humans struggle with so many health issues that for Neanderthals would have been unheard of.

"It is really bizarre to think that modern humans have their teeth rot out of their face," Weyrich says. "If you think about wolves or anything else, they wouldn't survive if their teeth couldn't stay in their mouth. … We shouldn't expect that to be normal."