New research has shed light on the evolution of oral health and the impact of dietary changes on the human mouth. A team of scientists has successfully extracted and analyzed microbial DNA from two remarkably well-preserved 4,000-year-old teeth discovered in a limestone cave in Ireland.

Their findings, which include the identification of gum disease-causing bacteria and the first high-quality ancient genome of S. mutans, a primary culprit behind tooth decay, provide a fascinating glimpse into the oral health of our ancestors and how it has changed over time.

By comparing the ancient microbial DNA with modern samples, the researchers were able to trace the effects of significant dietary shifts, such as the rise of agriculture and the increasing popularity of sugar, on the oral microbiome. The study supports the “disappearing microbiome” hypothesis, which suggests that our ancestors’ mouths harbored a more diverse array of bacteria compared to modern populations.

This loss of microbial diversity may have negative implications for both oral and overall human health. One of the most striking discoveries was the exceptionally high abundance of S. mutans in one of the ancient teeth. This finding suggests that the individual was at a high risk of developing tooth decay just before their death, despite the absence of visible cavities.

The researchers believe that the cool, dry, and alkaline conditions within the limestone cave may have contributed to the exceptional preservation of the S. mutans DNA. The study also revealed that two strains of T. forsythia, a bacteria linked to gum disease, found in the ancient teeth were more genetically different from each other than any pair of modern strains, even though the modern samples came from diverse locations such as Europe, Japan, and the United States.

This finding indicates that prehistoric populations likely had much higher levels of strain diversity, further supporting the idea of a more varied oral microbiome in the past. Over the last 750 years, the reconstructed genomes of T. forsythia and S. mutans showed drastic changes in the oral microenvironment.

In recent centuries, a single lineage of T. forsythia has become dominant in global populations, suggesting a selective event where one strain rapidly increased in frequency due to a genetic advantage. Similarly, S. mutans populations have undergone recent lineage expansions and changes in gene content, coinciding with the widespread adoption of sugar in the human diet.

Despite these similarities, the researchers found that modern S. mutans populations have remained more diverse than those of T. forsythia, likely due to differences in the evolutionary mechanisms shaping their genomic diversity. S. mutans is particularly adept at exchanging genetic material between strains, allowing beneficial innovations to spread among lineages rather than one lineage becoming dominant and replacing all others.

The study emphasizes the importance of analyzing ancient microbial DNA to understand the evolution of the oral microbiome and its response to dietary changes throughout human history. The findings suggest that recent cultural transitions, such as the increased consumption of sugar, have had a disproportionate impact on the composition and diversity of the bacteria responsible for tooth decay and gum disease.


Oxford University Press USA | Iseult Jackson, Peter Woodman, Marion Dowd, Linda Fibiger, Lara M Cassidy, Ancient Genomes From Bronze Age Remains Reveal Deep Diversity and Recent Adaptive Episodes for Human Oral Pathobionts, Molecular Biology and Evolution, Volume 41, Issue 3, March 2024, msae017,

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