Neanderthal microbes reveal surprises about what they ate -- and whom they kissed

If it's true that "you are what you eat," then there is perhaps no better way to understand someone than by looking at his or her teeth. Especially if that person has been dead for more than 40,000 years.

This is the philosophy of Keith Dobney, a professor of human paleoecology at the University of Liverpool and a co-author of a new study that draws some remarkable conclusions about the lives of Neanderthals by peering beneath their dental enamel.

Teeth are the hardest parts of the human body, and are more likely than any other tissue to survive centuries of corrosion and decay. And dental calculus – that mineralized plaque you get admonished about at the dentist – is particularly good at preserving the bits of food, bacteria and other organic matter that swirl around inside our mouths.

Teeth, Dobney said, are "this fantastic time capsule of biological information that traps not only direct evidence of the food that goes in your mouth, but these amazingly well preserved ecosystems that have evolved with us."

"Looking at bacteria and pathogens and the evolution of pathogens and the evolution of diets," he continued, "we have a whole new discipline, a whole new field of study that is going to change the way we look at the past."

The new study, led by University of Adelaide paleomicrobiologist Laura Weyrich and published Wednesday in the journal Nature, examines dental calculus from four Neanderthals who lived between 42,000 and 50,000 years ago; two in what is now Belgium, the other two in modern-day Spain. The microbiomes (the population of microbes in a body) they revealed are the first for Neanderthals and the oldest ever analyzed, Weyrich said.

And they contained several surprises. For one thing, the Belgian individuals seemed to have dramatically different diets than their Spanish contemporaries. For another, the scientists were able to sequence the entire genome of a bacterium trapped in the ancient plaque and found that it's a species that still dwells inside human mouths today – a suggestion that humans and Neanderthals shared microbes.

But perhaps the most intriguing find came from the tooth of a pitiful Spanish individual who was suffering from both a tooth abscess and an intestinal parasite when he died. His dental plaque contained the DNA of a tree that produces the painkiller salicyclic acid (the active ingredient in aspirin) and bits of the fungus Penicillium (which produces the antibiotic penicillin).

"Could the Neanderthal have been self-medicating? We don't know," Dobney cautioned. Barring the invention of a time machine that will allow him to visit ancient hominids and interview them about their medical practices, the best way to figure out whether the drugs were ingested intentionally would be to detect them in other ailing Neanderthal individuals.

"If we found it in more than a few individuals and found it in individuals with diseases and painful conditions . . . then I think yes, we'd have potentially good evidence for quite sophisticated medical knowledge," he said.

It wouldn't surprise Dobney if this does turn out to be the case. Though Neanderthals have long existed in the popular imagination as "knuckle-dragging cave men" (his words), there is a growing body of evidence that they were far more advanced than modern humans give them credit for. Recent studies revealed that they wore jewelry, created art and architecture, made complex tools and developed sophisticated big-game hunting strategies. All this suggests that they were capable of symbolic thought and social coordination, intellectual abilities that were once considered exclusively human.

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The sample size of the Nature paper is small, so it is too soon to draw any broad conclusions based on the results. But Weyrich and Dobney hope the study presages a wider effort to understand Neanderthals via the microbes that lived in their mouths.

Already, their results support a more nuanced understanding of our ancient hominid cousins.

Scientists once believed that Neanderthals were scavengers who ate mainly meat, and that these dietary constraints contributed to their extinction. Unlike humans, the thinking went, Neanderthals couldn't adapt as their environment changed.

But the Nature results suggest quite the opposite. By analyzing DNA, Dobney, Weyrich and their colleagues were able to pick out bits of the Neanderthals' diets. The Belgian individuals, which came from Spy cave about 45 miles south of Brussels, contained traces of woolly rhinoceros, sheep and edible mushrooms – a diet that tracks with the animal remains also uncovered at Spy. In contrast, the Spanish Neanderthals, who were found at El Sidron cave in the country's north, didn't seem to be eating any meat. Their teeth instead bore traces of mushrooms, pine nuts and forest moss.

Not only does this suggest that the Neanderthals were well-adapted to their environments, Weyrich said – it reflects an intriguing transition in the hominid lifestyle. The microbiomes of the El Sidron individuals bore a much stronger resemblance to those of chimpanzees and human gatherers than it did to the Spy Neanderthals.

"Maybe a gatherer lifestyle where you're not eating meat was really the core hominid microbiome," she said. "It's only when lifestyles change that microbiomes started to change."

Weyrich, who studies modern as well as ancient microbiomes, said that understanding Neanderthal microbes could be useful for researching the microbes that affect human health.

"Doctors still don't really know why microbiomes change today," she said. "We can really use ancient DNA to study humans as a model system. We can use all these stories of how things happened as a model to understand how things change."

Microbes are also as useful for understanding the past, she continued. The bacteria that share a creature's body offer some of the most intimate insights into its biology. Anthropologists have examined microbes from the teeth of humans to understand how they were affected by environmental changes, like the end of the last ice age, and behavioral ones, like the rise of agriculture and urbanization.

Weyrich pointed to one eyebrow-raising discovery from the new study: a near-complete genome sequence for a strain of Methanobrevibacter oralis, a simple, single-celled organism that is known to thrive in "pockets" between modern humans' gums and our teeth (often with not-so-pleasant results).

Weyrich says this is the oldest microbial genome ever sequenced, and it suggests that humans and Neanderthals were swapping spit as early as 120,000 years ago. The find supports the growing consensus that prehistoric hanky-panky was not uncommon between Neanderthals and ancient humans. But it also suggests that these interactions were intimate, consensual affairs.

"In order to get microorganisms swapped between people you have to be kissing," Weyrich said.

Today, all humans except people from Africa carry a small fraction of Neanderthal DNA in their genes.

"They haven't gone extinct, really," Dobney said. "They're still alive in us."

Apparently, their microbes are too.