An example of a tooth prior to ancient DNA sampling. Note: this was not the tooth sampled in the study. Credit: Lara Cassidy, Trinity
Genetic analysis of microbiomes extracted from 4,000-year-old teeth show both similarities to today’s oral microenvironment as well as major differences and changes that seemingly coincide with the popularization of sugar and industrialization.
For example, the researchers identified several bacteria linked to gum disease, including Streptococcus mutans, which is the major culprit behind tooth decay today. They also discovered a second bacteria implicated in gum disease—Tannerella forsythia. However, the Bronze Age teeth had highly divergent strains of this bacteria, genetically different from any known modern strains.
The sampled teeth were among a large assemblage of skeletal remains excavated from a limestone cave at Killuragh, County Limerick (Ireland) by the late Peter Woodman of University College Cork. The teeth belonged to the same male individual. While other teeth recovered from the cave showed advanced dental decay, there was no evidence of cavities on the sampled teeth. Nevertheless, one tooth root yielded an unprecedented quantity of mutans sequences.
“We were very surprised to see such a large abundance of S. mutans in this 4,000-year-old tooth,” said senior author of the study Lara Cassidy, an assistant professor at Trinity College Dublin. “It is a remarkably rare find and suggests this man was at a high risk of developing cavities right before his death.”
While S. mutans is very common in modern mouths, it is exceptionally rare in the ancient genomic record. There are most likely two reasons for this: the bacteria are acid-producing and sugar-loving. The acidic nature of the species decays teeth and destroys DNA—stopping plaque from fossilizing. Additionally, the scarcity of S. mutans may be due to the lack of sugar in the ancient diet. According to the research team, an increase in dental cavities is seen in the archaeological record after the adoption of cereal agriculture thousands of years ago. Then, a far more dramatic increase occurred the past few hundred years when sugary foods were introduced to the masses.
“S. mutans has undergone recent lineage expansions and changes in gene content related to pathogenicity. These coincide with humanity’s mass consumption of sugar, although we did find that modern S. mutans populations have remained more diverse, with deep splits in the S. mutans evolutionary tree pre-dating the Killuragh genome,” said Cassidy. “S. mutans is very adept at swapping genetic material between strains. This ability to easily share may explain why this species retains many diverse lineages without one becoming dominant and replacing all the others.”
That is the opposite of the trajectory of Tannerella forsythia—a second bacteria implicated in gum disease and also detected in the 4,000-year-old teeth. The two sampled teeth contained quite divergent strains of T. forsythia.
In recent centuries, one lineage of T. forsythia has become dominant in global populations. The study authors say this is the tell-tale sign of a selective episode—where one strain rises rapidly in frequency due to some genetic advantage. The researchers found that post-industrial T. forsythia genomes have acquired many new genes that help the bacteria colonize the oral environment and cause disease.
“These strains from a single ancient mouth were more genetically different from one another than any pair of modern strains in our dataset, despite these modern samples deriving from Europe, Japan, and the U.S.,” said first author of the study Iseult Jackson.
While S. mutans DNA was plentiful, other streptococcal species were virtually absent from the tooth sample. This implies that the natural balance of the oral biofilm had been upset—mutans had outcompeted the other species, leading to a pre-disease state.
“This is interesting because a loss of biodiversity can have negative impacts on the oral environment and overall human health,” said Jackson.
Ultimately, while both disease-causing bacteria have changed dramatically from the Bronze Age to today, the researchers say very recent cultural transitions in the industrial era have had an “inordinate impact.”