Exploring the Evolution of the Cariogenic Oral Pathobiont Streptococcus mutans Using Ancient DNA

Michel, M.; Valuena, A. A.; Akar, M.; Alonso-Fernandez, C.; Calmet, M. A.; Andreadaki-Vlazaki, M.; Jimenez, G. A.; Banffy, E.; Barquera, R.; Barreto-Romero, M.; Fuello, P. B.; Bedford, S.; Belinkskiy, A. B.; Berezina, N.; Boyadzhiev, K.; Boyadzhiev, Y.; Buzhilova, A.; Cappuccini, L.; Huamani, J. E. C.; Beltran, E. C.; Clark, G.; Daubaras, M.; Ibanez, P. d. M.; Bonilla, M. D.-Z.; Dobes, M.; Dresely, V.; Erdal, Y. S.; Ernee, M.; Ferraz, T.; Figuti, L.; Farre, J. F.; Flexner, J. L.; Friederich, S.; Gaffney, D.; Atienzar, G. G.; Pena, R. G.; Gomez-Valdes, J. A.; Gradoli, M. G.; Guardia i Llorens,

doi:10.64898/2025.12.02.691581

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bioRxiv · 10.64898/2025.12.02.691581

Exploring the Evolution of the Cariogenic Oral Pathobiont Streptococcus mutans Using Ancient DNA

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Abstract

The oral pathobiont Streptococcus mutans can contribute to dental caries development through metabolism of dietary carbohydrates. Adoption of carbohydrate-rich agricultural diets is associated with increased prevalence of dental caries in archaeological populations; however, the evolutionary impact of changing subsistence strategies on cariogenic microbes like S. mutans remains to be explored. Here, we use a novel hybridization capture reagent to generate genome-wide ancient DNA data from a global set of 75 S. mutans strains spanning the last 8,000 years. Most virulence-associated genes predate the origins of agriculture; however, we highlight loci regulating genetic competence, bacteriocin production, and biofilm formation which are absent in 5 strains from pre-agricultural ancient hunter-gatherers, suggesting that their acquisition may have been associated with adaptation to carbohydrate-rich agricultural diets. Together, our study highlights ancient DNA as a promising tool for exploring the dynamic interplay between subsistence strategy, microbes, and dental pathology in human populations through time.

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Michel, M., Valuena, A. A., Akar, M., Alonso-Fernandez, C., Calmet, M. A., Andreadaki-Vlazaki, M., Jimenez, G. A., Banffy, E., Barquera, R., Barreto-Romero, M., Fuello, P. B., Bedford, S., Belinkskiy, A. B., Berezina, N., Boyadzhiev, K., Boyadzhiev, Y., Buzhilova, A., Cappuccini, L., Huamani, J. E. C., Beltran, E. C., Clark, G., Daubaras, M., Ibanez, P. d. M., Bonilla, M. D.-Z., Dobes, M., Dresely, V., Erdal, Y. S., Ernee, M., Ferraz, T., Figuti, L., Farre, J. F., Flexner, J. L., Friederich, S., Gaffney, D., Atienzar, G. G., Pena, R. G., Gomez-Valdes, J. A., Gradoli, M. G., Guardia i Llorens,. 2025-12-04. Exploring the Evolution of the Cariogenic Oral Pathobiont Streptococcus mutans Using Ancient DNA. https://doi.org/10.64898/2025.12.02.691581

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