Streptococcus mutans from ancient dental calculus

Oral streptococci play key roles in oral and systemic health, with acid production of Streptococcus mutans tightly linked to dental caries. Understanding the evolutionary history of S. mutans after the onset of agriculture is critical to understanding the development of this disease. We used hybridization capture targeting S. mutans in dental calculus of ancient individuals from across Europe previously reported to be positive for the species through PCR amplification of the gtfB gene. A total of 851,518 unique baits of length 60 were used. As multiple closely-related Streptococcus species can be found in a single individual, we used a three-part mapping strategy to authenticate the presence of S. mutans in two samples (Bronze_2_8891, ~2100 BCE and Medieval_1_8832, ~1275 CE). We used the enrichments from these two samples to reconstruct draft ancient S. mutans genomes, and these genomes lacked key competition and acidogenic mechanisms common in strains today. Three other oral Streptococcus species were identified to have high values of unique hits in the enrichments: Streptococcus infantis, Streptococcus australis, and Streptococcus sanguinis. Our findings draw attention to an ecologically centered approach to dental caries, where other acidogenic microbes may contribute to caries progression.