Ancient “Chewing Gum” Reveals a 5,700-Year-Old Microbiome

Toward the end of the Stone Age, in a small fishing village in southern Denmark, a dark-skinned woman with brown  hair and piercing blue eyes chewed on a sticky piece of hardened birch tar. The village, dubbed Syltholm by modern archaeologists, was near a coastal lagoon that was protected from the Baltic Sea by sandy barrier islands. Behind them, the woman and her kin built weirs to trap fish that they skewered with bone-tipped spears. The woman may have worked the tar until it was pliable enough to repair a piece of pottery or a polished flint tool—birch tar was a common Stone Age adhesive. Or she might have simply been enjoying what amounted to Neolithic chewing gum. In any case, when she discarded the tar, it was sealed away under layers of sand and silt for some 5,700 years until a team of archaeologists found it. Amazingly, they were able to extract the woman’s complete genome from the birch tar, along with her oral microbiome and DNA from food she may have recently eaten.

Although no human remains have been recovered at the dig site, the DNA on the birch tar revealed what the woman looked like, what she ate, what bacteria and viruses she carried with her, where her people could have come from and whether they may have begun to adopt farming. The results, published Tuesday in Nature Communications, highlight the potential of chewed birch pitch as a source of ancient human and microbial DNA, which can be used to shed light on the population histories, health statuses and subsistence strategies of ancient people.

“We have this inconspicuous little lump of birch pitch that someone discarded thousands of years ago, and suddenly we’re able to conjure up this person from it,” says Hannes Schroeder, an archaeologist at the University of Copenhagen and the paper’s corresponding author. “It’s fascinating to be able to do that from this small object.”

Co-lead study author Theis Jensen, a bioarchaeologist at the University of Copenhagen, initially hit upon the idea of extracting genomic data from birch while he was working at a different dig site in Sweden and began to see pieces of tar with teeth imprints in them. At the time, “next-generation sequencing was starting to revolutionize ancient DNA studies,” he says. “I thought these ‘chewing gums’ could be a source of DNA.” Jensen’s colleagues were able to pull the partial DNA of three individuals from lumps of birch tar dated to about 10,000 years ago and published their findings in Communications Biology in May.

The Syltholm birch tar sample—along with the genomic information concealed in it—was likely so well-preserved because it was buried in an oxygen-free environment, says Natalija Kashuba, an archaeologist at Uppsala University in Sweden and lead author of the paper published in May. Kashuba, who was not involved in the new study, says that if archaeologists recover more ancient-microbiome samples, they could begin to piece together the evolutionary history of bacteria and viruses that are connected to human health. “For studies of human health and environment, this type of material is just priceless,” she says.

Schroeder and his colleagues identified a host of microbial taxa from the sample, some of which were part of the community of microbes that live, often harmlessly, in and on humans called the microbiome. Other oral bacteria species the team found in the gum can cause periodontal disease. The researchers also discovered the woman carried Epstein-Barr virus—a very common member of the herpesvirus family—and several strains of virus responsible for pneumonia. Although they successfully identified 26 virulence factors, or molecules that make pathogens more effective at infecting hosts, they were unable to determine the woman’s health status.

The team did determine that she was lactose-intolerant, which would have been common among hunter-gatherers before the adoption of animal husbandry. The gum had traces of DNA from hazelnut (Corylus avellana) and mallard (Anas platyrhynchos), which the woman may have recently eaten and which could have been staples in a hunter-gatherer’s diet. Farming spread to Denmark relatively late—arriving around the time the Syltholm woman lived—but once there, it probably caught on quickly. Archaeologists, however, do not yet know whether hunter-gatherers in the region independently adopted farming or if new arrivals brought it with them. According to Schroeder and his colleagues, the Syltholm woman’s genome indicates she was not related to communities of farmers that did live in Denmark around the same time. She was descended from a genetic group archaeologists refer to as Western hunter-gatherers, who began settling in Scandinavia via a southern route as early as 11,700 years ago.

The advent of agriculture changed human gut and oral microbiomes, because more carbohydrate-rich foods became available. (They changed again during the industrial revolution, when refined sugars and vegetable oils came to dominate the menu.) Laura Weyrich, a paleomicrobiologist at Pennsylvania State University, who was not involved in either study, says it is difficult to draw broad conclusions about the Syltholm woman’s diet—or even the exact composition of her oral microbiome—from a piece of chewed gum. The bacterial populations that colonize a person’s teeth are very different from those found in their saliva or on their tongue, and so a sample pulled from chewing gum “is probably a mixture of all these different types of oral microbiome,” Weyrich says. “It’s very difficult to put that microbiome into context without further analysis of other hunter-gatherers.”

Weyrich says the study could herald a new chapter in studying ancient people’s—and their microbiome’s—evolution. “I think the ancient DNA field, moving forward, has a lot to offer in human genome–human microbiome coevolution,” Weyrich says. Fortunately, no one has yet tried to coin the word gumomics.

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