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Ancient Human Genome, Microbiome Generated From Chewed Birch Pitch Gum

NEW YORK – An international team led by investigators from the University of Copenhagen has successfully sequenced an ancient human genome — and a collection of microbes from her oral microbiome — using DNA isolated from a piece of birch pitch chewing gum believed to be thousands of years old.

"It is amazing to have gotten a complete ancient human genome from anything other than bone," senior corresponding author Hannes Schroeder, a health and medical sciences researcher at the University of Copenhagen, said in a statement. "[W]e also retrieved DNA from oral microbes and several important human pathogens, which makes this a very valuable source of ancient DNA, especially for time periods where we have no human remains."

As they reported online today in Nature Communications, the researchers sequenced a 5,700-year-old piece of birch pitch found at a mud-sealed archeological site called Syltholm in southern Denmark, generating genome sequences for a woman or girl who chewed the pitch — a dark-haired, dark-skinned, blue-eyed female who shared closer genetic ties to western hunter-gatherer groups on the European mainland than to Scandinavian hunter-gatherers, and did not have ancestry corresponding with known Neolithic farming groups.

From the metagenomic sequences generated from pitch sample, the team also got a glimpse at some of the plants and animals she may have eaten, namely, hazelnuts and duck. It also tallied some of the bacteria, viruses, and archaea in her oral microbiome, identifying sequences that coincided with the Epstein-Barr virus (EBV) or with Streptococcus pneumoniae bacteria, for example.

"Our ancestors lived in a different environment and had a different lifestyle and diet, and it is therefore interesting to find out how this is reflected in their microbiome," Schroeder said.

Past studies suggest tacky black birch pitch, obtained by heating the tree's bark, has been used by humans since the Paleolithic period. While there is some debate over how and why it was used at different time points, the team explained, tooth marks found in pitch samples suggest that the sticky substance may have served not only as a prehistoric chewing gum, but also as a glue for putting together tools and, potentially, for cleaning teeth, suppressing hunger, or serving as an antiseptic.

Moreover, a 2019 paper by investigators in Sweden and Norway revealed the extent to which DNA can be preserved in the pitch, pointing to the possibility of using pitch to look into the past.

For the latest analysis, Schroeder and his colleagues sequenced the Syltholm birch pitch sample, generating a genome sequence for the 5,700-year-old women with 2.3-fold coverage, generating 91-fold average coverage of her mitochondrial genome in the process.

Based on more than 593,000 SNPs identified in the genome, the team determined the biological sex of the individual, her ancestry, and some key physical features, while identifying sequences that clustered with those in present-day oral microbial communities.

From these and other findings, the authors concluded that "genomic information preserved in chewed pieces of birch pitch offers a snapshot of people's lives, providing information on genetic ancestry, phenotype, health status, and even subsistence."