Christina Warinner uncovers ancient tales in dental plaque

In a pitch-black rainforest with fluttering moths and crawling centipedes, Christina Warinner dug up her first skeleton. Well, technically it was a full skeleton plus two headless ones, all seated and draped in ornate jewelry. To deter looters, she excavated through the night while one teammate held up a light and another killed as many bugs as possible.

As Warinner worked, unanswerable questions about the people whose skeletons she was excavating flew through her mind. “There’s only so much you can learn by looking with your own eyes at a skeleton,” she says. “I became increasingly interested in all the things that I could not see — all the stories that these skeletons had to tell that weren’t immediately accessible, but could be accessible through science.”

At age 21, Warinner cut her teeth on that incredibly complex sacrificial burial left behind by the Maya in a Belize rainforest. Today, at age 37, the molecular anthropologist scrapes at not-so-pearly whites to investigate similar questions, splitting her time between the University of Oklahoma in Norman and the Max Planck Institute for the Science of Human History in Jena, Germany.
In 2014, she and colleagues reported a finding that generated enough buzz to renew interest in an archaeological resource many had written off decades ago: fossilized dental plaque, or calculus. Ancient DNA and proteins in the plaque belong to microbes that could spill the secrets of the humans they once inhabited — what the people ate, what ailed them, perhaps even what they did for a living.

Bacteria form plaque that mineralizes into calculus throughout a person’s life. “It’s the only part of your body that fossilizes while you’re still alive,” notes Warinner. “It’s also the last thing to decay.”

Though plaque is prolific in the archaeological record, most researchers viewed calculus as “the crap you scraped off your tooth in order to study it,” says Amanda Henry, an archaeologist at Leiden University in the Netherlands. With some exceptions, molecular biologists saw calculus as a shoddy source of ancient DNA.

But a few researchers, including Henry, had been looking at calculus for remnants of foods as potential clues to ancient diets. Inspired by some of Henry’s images of starch grains preserved in calculus, Warinner wondered if the plaque might yield dead bacterial structures, perhaps even bacteria’s genetic blueprints.

Her timing couldn’t have been better. Warinner began her graduate studies at Harvard in 2004, just after the sequencing of the human genome was completed and by the time she left in 2010, efforts to survey the human microbiome were in full swing. As a postdoc at the University of Zurich, Warinner decided to attempt to extract DNA from the underappreciated dental grime preserved on the teeth of four medieval skeletons from Germany.
At first, the results were dismal. But she kept at it. “Tina has a very interested, curious and driven personality,” Henry notes. Warinner turned to a new instrument that could measure DNA concentrations in skimpy samples, a Qubit fluorometer. A surprising error message appeared: DNA too high. Dental calculus, it turned out, was chock-full of genetic material. “While people were struggling to pull out human DNA from the skeleton itself, there’s 100 to 1,000 times more DNA in the calculus,” Warinner says. “It was sitting there in almost every skeletal collection untouched, unanalyzed.”
To help her interpret the data, Warinner mustered an army of collaborators from fields ranging from immunology to metagenomics. She and her colleagues found a slew of proteins and DNA snippets from bacteria, viruses and fungi, including dozens of oral pathogens, as well as the full genetic blueprint of an ancient strain of Tannerella forsythia, which still infects people’s gums today. In 2014, Warinner’s team revealed a detailed map of a miniature microbial world on the decaying teeth of those German skeletons in Nature Genetics.

Later in 2014, her group found the first direct protein-based evidence of milk consumption in the plaque of Bronze Age skeletons from 3000 B.C. That same study linked milk proteins preserved in the calculus of other ancient human skeletons to specific animals — providing a peek into long-ago lifestyles.

“The fact that you can tell the difference between, say, goat milk and cow milk, that’s kind of mind-blowing,” says Laura Weyrich, a microbiologist at the University of Adelaide in Australia, who also studies calculus.
Since then, Warinner has found all sorts of odds and ends lurking on archaic chompers from poppy seeds to paint pigments. Warinner’s team is still looking at the origins of dairying and its microbial players, but she’s also branching out to the other end of the digestive spectrum. The researchers are looking at ancient DNA in paleofeces, which is exactly what it sounds like — desiccated or semifossilized poop. It doesn’t stay as fresh as plaque in the archaeological record. But she’s managed to find some sites with well-preserved samples. By examining the array of microbes that lived in the excrement and plaque of past humans and their relatives, Warinner hopes to characterize how our microbial communities have changed through time — and how they’ve changed us.

The research has implications for understanding chronic, complex human diseases over time. Warinner’s ancient DNA work “opens up a window on past health,” says Clark Larsen, an anthropologist at Ohio State University.

It’s all part of what Warinner calls “the archaeology of the unseen.”

Editor’s note: This story was corrected on October 4, 2017, to note that the 2014 report on milk consumption was based on protein evidence, not DNA.