What Bronze Age teeth say about the evolution of the human diet

A new paper in Molecular Biology and Evolution, published by Oxford Univeristy Press, uncovers well-preserved microbiomes from two 4,000 year old teeth in a limestone cave in Ireland. These contained bacteria that cause gum disease, as well as the first high quality ancient genome from S. mutans, an oral bacterium that is one of the major causes of tooth decay.

These discoveries allowed the researchers to assess the impact of past dietary changes on the oral microbiome across millennia, including major changes coinciding with the popularization of sugar and industrialization. The teeth, both derived from the same Bronze Age man, also provided a snapshot of oral health in the past, with one tooth showing evidence of microbiome dysbiosis.

Microbial DNA extracted from ancient human teeth can provide information on the evolution of the oral microbiome. How did our ancestors’ mouths differ from our own and why? The excellent preservation of DNA in fossilized dental plaque has made the oral cavity one of the best studied aspects of the ancient human body. However, scientists have retrieved very few full genomes from oral bacteria from prior to the Medieval era. Researchers have limited knowledge about prehistoric bacterial diversity and the relative impact of recent dietary changes compared to ancient ones, such as the spread of farming starting about ten thousand years ago.

S. mutans is the primary cause of dental cavities and very common in oral microbiomes. However, it is exceptionally rare in the ancient genomic record. One reason for its rarity could be its acid-producing nature – this acid causes the tooth to decay but also degrades DNA and prevents plaque from mineralizing. The absence of S. mutans DNA in ancient mouths could also reflect less favorable habitats for the species across most of human history. Archaeologists have observed an uptick in dental cavities in skeletal remains following the adoption of cereal agriculture, but cavities become much more common in the Early Modern period, beginning about 1500 AD.

The sampled teeth were among a large assemblage of skeletal remains excavated from a limestone cave at Killuragh, County Limerick, by the late Peter Woodman of University College Cork. While other teeth in the cave showed advanced dental decay there was no evidence of caries 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 mutans in this 4,000 year old tooth” said Lara Cassidy, an assistant professor at Trinity College Dublin and senior author of the study. “It is a remarkably rare find and suggests this man was at high risk of developing cavities right before his death.”

The cool, dry, and alkaline conditions of the cave may have contributed to the exceptional preservation of S. mutans DNA, but its high abundance also points to dysbiosis. The researchers found that 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.

The study lends support to the “disappearing microbiome” hypothesis, which proposes the microbiomes of our ancestors were more diverse than our own today. Alongside the S. mutans genome, the authors reconstructed two genomes for T. forsythia – a bacteria involved in gum disease – and found them to be highly divergent from one another, implying much higher levels of strain diversity in prehistoric populations.

“The two sampled teeth contained quite divergent strains of T. forsythia” explained Iseult Jackson, a PhD candidate and first author of the study. “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 USA. This is interesting because a loss of biodiversity can have negative impacts on the oral environment and human health.”

The reconstructed T. forsythia and S. mutans genomes revealed dramatic changes in the oral microenvironment over the last 750 years. In recent centuries, one lineage of T. forsythia has become dominant in global populations. 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.

S. mutans also showed evidence of recent lineage expansions and changes in gene content, which coincide with the popularization of sugar. However, the investigators found that modern S. mutans populations have remained more diverse than T. forsythia, with deep splits in the mutans evolutionary tree pre-dating the Killuragh genome.  They believe this is driven by differences in the evolutionary mechanisms that shape genome diversity in these species.

“S. mutans is very adept at swapping genetic material across strains.” said Cassidy “This allows an advantageous innovation to be spread across mutans lineages, rather than one lineage becoming dominant and replacing all others.”

In effect, both these disease-causing bacteria have changed dramatically from the Bronze Age to today, but it appears that very recent cultural transitions, such as the consumption of sugar, have had an inordinate impact.

The paper, “Ancient genomes from Bronze Age remains reveal deep diversity and recent adaptive episodes for human oral pathobionts,” is available (at midnight on March 27^th) at https://academic.oup.com/mbe/article-lookup/doi/10.1093/molbev/msae017.

Direct correspondence to: 
Lara Cassidy
Smurfit Institute of Genetics
Trinity College Dublin
Dublin 2, IRELAND
cassidl4@tcd.ie

To request a copy of the study, please contact:
Daniel Luzer 
daniel.luzer@oup.com