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

Megan Michel; Aida Andrades Valtueña; Murat Akar; Carmen Alonso Fernández; Micaela Álvarez Calmet; Maria Andreadaki-Vlazaki; Gonzalo Aranda Jiménez; Eszter Bánffy; Rodrigo Barquera; María Inés Barreto Romero; Paula Becerra Fuello; Stuart Bedford; Andrey B. Belinskiy; Natalia Berezina; Kamen Boyadzhiev; Yavor Boyadzhiev; Alexandra Buzhilova; Luca Cappuccini; José Enrique Ccencho Huamaní; Eva Celdrán Beltrán; Geoffrey Clark; Mantas Daubaras; María Paz de Miguel Ibáñez; Marta Díaz‐Zorita Bonilla; Miroslav Dobeš; Veit Dresely; Yılmaz Selim Erdal; Michal Ernée; Tiago Ferraz; Levy Figuti

doi:10.64898/2025.12.02.691581

Evolutionary BiologybioRxivDec 4, 2025

Preprint

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

Megan Michel iD, Aida Andrades Valtueña iD, Murat Akar iD, Carmen Alonso Fernández iD, Micaela Álvarez Calmet iD, Maria Andreadaki-Vlazaki, Gonzalo Aranda Jiménez iD, Eszter Bánffy iD, Rodrigo Barquera iD, María Inés Barreto Romero, Paula Becerra Fuello iD, Stuart Bedford iD, Andrey B. Belinskiy, Natalia Berezina iD, Kamen Boyadzhiev iD, Yavor Boyadzhiev iD, Alexandra Buzhilova iD, Luca Cappuccini iD, José Enrique Ccencho Huamaní iD, Eva Celdrán Beltrán iD, Geoffrey Clark iD, Mantas Daubaras iD, María Paz de Miguel Ibáñez iD, Marta Díaz‐Zorita Bonilla iD, Miroslav Dobeš iD, , Cristina Tejedor Rodríguez iD

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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