Preserved in plaque of ancient teeth, a fossilized microbial world

Scientists have discovered the DNA of millions of tiny organisms entombed in the ancient dental plaque of four medieval skeletons.

The findings, published in the journal Nature Genetics, have implications for research into what our ancestors ate, how they interacted, and what diseases they fought, the authors write.

“I feel like we discovered a time capsule that has been right under our noses this whole time,” said Christina Warinner, a molecular anthropologist at the University of Oklahoma and the lead author of the study. “This is a game changer.”

Matthew Collins of the University of York, a coauthor on the paper, put it this way: “What we found is a microbial Pompeii.”

Calcified plaque is the rough, bumpy stuff you might notice coating your teeth if you have skipped too many dental appointments. Today, dentists scrape plaque off our teeth as part of our regular dental cleanings, but before the days of modern oral care, it could grow layer upon layer until sometimes the hard plaque covering a tooth was thicker than the tooth itself.

The layers of calcified plaque entomb the bacteria that also live in our mouths -- turning them into small fossils even when we are alive. And when we die, these dense, calcified micro-fossils remain intact, even as most of the rest of us decomposes.

Throughout most of the history of archaeology, researchers have considered calcified plaque disposable -- often removing it from skeletons in the process of cleaning them. But recently, it has become clear that calcified plaque is a reservoir of information.

“People are realizing that you have this rich bacterial community living on the surface of your teeth, and if your gums are bleeding you have an open vascular network right next door to a microbial community,” said Collins. “There is so much information there. The challenge is how to access it.”

Over the last decade scientists had started to look at ancient plaque samples under a microscope, hoping to find microscopic bits of food stuck in its hard matrix. But Warinner, who has a background in extracting DNA from bones and teeth, wanted to know whether it had also preserved DNA.

To find out, she scraped the mineralized plaque off the teeth of four skeletons from a medieval convent in Dalheim, Germany, and after treating the samples with various chemicals and enzymes, she put them through a machine that separates cell debris from DNA.

The result, she said, was thrilling.

“When you get DNA from bones it is so damaged and there is so little of it left, “ she said. “When we analyzed the dental calculus we got 100 to 1,000 times more DNA fragments than we would have from a bone.”

From those DNA fragments Warinner and an international team of colleagues determined that the bacteria associated with human periodontal disease have not changed much in 1,000 years even as dental hygiene and diet have. They also found that ancient oral bacteria had a gene that could allow it to resist low-level antibiotics, just as some of our oral bacteria has today. And they found bits of plant DNA in the plaque, which provides direct evidence of the ancient diet.

But these results are just scratching the surface of what scientists can learn from ancient plaque.

Anne Stone, a molecular anthropologist at Arizona State University who was not involved in the study, said the findings were significant.

“What is exciting is it looks like the way calculus forms protects the DNA -- almost like it is sealed in concrete -- so it is more protected from the environment,” she said. “People who study respiratory pathogens will be interested in this study, and people who study how periodontal disease has changed over time.”

Warinner notes that every known human population has had dental plaque problems, so this technique could be used to learn more about people from a wide range of time periods.

“Everything was there in an incredible level of detail and it was frozen in time,” said Collins. “You have so much DNA that you can get complete genomes without even trying.”

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