Megan MichelAida Andrades ValtueñaMurat AkarCarmen Alonso FernándezMicaela Álvarez CalmetMaria Andreadaki-VlazakiGonzalo Aranda JiménezEszter BánffyRodrigo BarqueraMaría Inés Barreto Romero2026-03-222026-03-22202510.64898/2025.12.02.691581https://doi.org/10.64898/2025.12.02.691581https://andeanlibrary.org/handle/123456789/78568ABSTRACT 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.Ancient DNASubsistence agricultureAdaptation (eye)BiologyEvolutionary biologyBiological evolutionHominidaeHuman evolutionary geneticsPhylogeneticsHuman evolutionarticle