Fragments of bacterial DNA, extracted from the teeth of people who lived in times long gone, are revealing how pathogens have evolved alongside us.
Laboratory research scientist Sarah Johnston extracts human and pathogen DNA from ancient teeth in a clean room. Credit: Bethany Lavin.
We’re drawn to the past, imagining the lives that came before. And one area that particularly fascinates historians, scientists and the morbidly curious is the diseases that our ancestors endured.
For a team of DNA detectives at the Crick and UCL, shadows of these diseases are still detectable in ancient teeth. Within their core, frozen in time, are fragments of DNA from disease causing bacteria or viruses, known as pathogens.
Our teeth have a healthy blood supply to their roots, which proves valuable for ancient genomicists. “If pathogens get into a person’s blood before they die, remnants of their DNA are captured inside teeth,” researcher Pooja Swali explains.
For her PhD at the Crick and postdoc at UCL, Pooja studied how bacteria evolve and spread, focusing on Borrelia recurrentis, which causes ‘relapsing fever’, a nasty concoction of high fevers, pain and headaches which has been speculated to be the agent of the ‘yellow plague’ in the sixth century.
Today, B. recurrentis is transmitted from person to person by lice. But has it always spread in this way? To answer this question, Pooja analysed B. recurrentis samples in four ancient teeth from medieval and Iron Age burial sites across the UK.
“When processing these teeth, we wear ‘cleansuits’ and work in a super sterile environment to avoid contamination,” she describes. “We take off the calcified layer covering the root before drilling into the main tissue of the tooth, aiming to take the smallest sample possible.”
Next, the powdered tooth sample is spun quickly to separate any DNA from other biological materials or physical contaminants such as soil. The DNA is then amplified and read using a ‘catch all’ technique called shotgun sequencing. Finally, human DNA is discounted, leaving the suspected pathogen DNA behind.
“This bit is tricky, as parts of the sequence may be damaged or missing, given the tooth has spent hundreds of years underground,” explains Pooja. “We compare the sections we do have with sequences of modern day pathogens, hoping we have enough to make a match.”
Once Pooja had four matches, she could ask further questions. How did the ancient samples differ from ‘modern’ B. recurrentis? And what did those differences reveal about its evolution?
Pontus Skoglund, who leads the Crick’s Ancient Genomics Lab, believes that ancient pathogen evolution helps piece together human history.
“The differences between the ancient and modern B. recurrentis samples show how the pathogen has changed over time,” he says. “It likely diverged from its nearest cousin about 6,000 to 4,000 years ago, picking up genetic changes that helped it switch host from ticks to lice.”
Pontus speculates that the jump in host happened at the transition of the Neolithic period and the Early Bronze Age, when people began domesticating animals and living in dense settlements. Sheep farming for wool may have also given an advantage to louse borne pathogens, as wool has better conditions for laying eggs.
The scientists are continuing this work, hoping that further research into bacterial evolution will improve knowledge of relatively understudied diseases, both at the Crick and UCL, where Pooja is working with Lucy van Dorp, group leader in microbial evolution.
“Teeth act like a time capsule, giving us a glimpse into infections of the past,” Pooja says. “Humans and pathogens evolve alongside each other, so looking back could help us understand the genetic changes behind our shared history."
