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Bronze age teeth discovery sheds light on the evolution of the human diet

A team of researchers has recovered remarkably preserved microbiomes from two 4,000-year-old teeth found in an Irish limestone cave. Through genetic analysis, these microbiomes have unveiled significant shifts in the oral microenvironment from the Bronze Age to our current era. 

Historical changes in human oral microbiomes

Both teeth belonged to the same male individual, offering not only a glimpse into his oral health but also into the broader historical changes in human oral microbiomes.

The team, led by Trinity College Dublin, in partnership with archaeologists from the Atlantic Technological University and the University of Edinburgh, identified multiple bacteria associated with gum disease.

In addition, the teeth provided the first high-quality ancient genome of Streptococcus mutans — a bacterium chiefly responsible for tooth decay.

Reconstructing oral microbiomes 

According to experts, while S. mutans is very common in modern mouths, it is exceptionally rare in the ancient genomic record. Its scarcity in ancient samples might be due to its acid-producing nature, with this acid not only leading to tooth decay but also to DNA degradation that is preventing plaque from fossilizing. 

Although most of the ancient oral microbiomes are extracted from fossilized plaque, the researchers now managed to reconstruct it directly from the tooth material.

The scarcity of S. mutans in ancient samples might also be attributed to a historical lack of suitable environments for our sugar-loving species.

The archaeological record shows an increase in dental cavities following the advent of cereal agriculture thousands of years ago, with a more pronounced surge in recent centuries coinciding with the widespread introduction of sugary foods.

What the teeth revealed

The teeth analyzed were discovered within a larger skeletal collection at Killuragh Cave in Limerick County, and were excavated by the late Peter Woodman of University College Cork. Despite evidence of advanced dental decay in other teeth within the cave, the teeth under study showed no visible cavities. 

However, one tooth revealed a significant amount of S. mutans DNA, indicating a drastic imbalance in the oral microbial community.

“We were very surprised to see such a large abundance of S. mutans in this 4,000-year-old tooth. It is a remarkably rare find and suggests this man was at a high risk of developing cavities right before his death,” said study senior author Lara Cassidy, an assistant professor of genetics and microbiology at TCD.

Further analysis revealed the virtual absence of other streptococcal species in the tooth, suggesting a disruption in the natural balance of the oral microbiome, with S. mutans outcompeting other streptococci and leading to a predisposition to disease.

The disappearing microbiome hypothesis 

The study also supports the “disappearing microbiome” hypothesis, which posits that modern microbiomes are less diverse than those of our ancestors, potentially impacting human health.

The researchers discovered highly divergent strains of Tannerella forsythia, a bacterium implicated in gum disease, within the ancient sample. 

“These strains from a single ancient mouth were more genetically different from one another than any pair of modern strains in our dataset, despite the modern samples deriving from Europe, Japan, and the USA,” said lead author Iseult Jackson, a PhD candidate at Trinity. “This represents a major loss in diversity and one that we need to understand better.”

Dramatic changes in the oral microenvironment

The study highlights dramatic changes in the oral microenvironment over centuries, with a single lineage of T. forsythia becoming dominant worldwide over the last 750 years due to natural selection. 

 “Over the last 750 years, a single lineage of T. forsythia has become dominant worldwide. This is the tell-tale sign of natural selection, where one strain rises rapidly in frequency due to some genetic advantage it holds over the others. T. forsythia strains from the industrial era onwards contain many new genes that help the bacteria colonize the mouth and cause disease,” Cassidy explained.

Dramatic evolution of disease-causing bacteria

S. mutans has also 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.” 

These findings highlight the dramatic evolution of disease-causing bacteria from the Bronze Age to the present, influenced significantly by cultural shifts in the industrial era, offering profound insights into the history of oral health and the intricate relationships between diet, microbiomes, and human evolution.

The study is published in the journal Molecular Biology and Evolution.


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