The genomic history of Streptococcus mutans from the Mesolithic until modern times

Streptococcus mutans is a member of the human oral microbiota and is considered one of the most important cariogenic organisms. Previous studies have suggested an expansion of S. mutans populations about 10,000 years ago with the onset of agriculture, yet direct molecular evidence of its presence from ancient DNA remains sparse. Here, we present population genomic analyses of 25 ancient S. mutans genomes (average read depth 0.1X – 387X) recovered from archaeological remains across Eurasia spanning ~ 8,000 years of human evolution. Recombination-corrected phylogenomic analyses using Gubbins showed a star-like phylogeny indicative of an early radiation, with the ancient genomes falling within the genomic diversity of modern isolates but restricted to one of the major clades of the phylogeny (D). Analyses of genes encoding present day virulence factors revealed that the presence of the mutanobactin operon involved in oxygen tolerance was restricted to specific subclades (A &B) and absent among the ancient samples. Using the MEGAHIT assembler followed by binning of contigs with CONCOCT, we recovered Metagenome-Assembled Genomes (MAG) of 7 high-coverage ancient S. mutans strains, including a 7,500-year-old sample from an early European Neolithic farmer. Pangenome analysis with modern isolates using the Anv’io’s suite revealed the presence of specific functional genes in the ancient isolates, which were lost through time. Our study demonstrates that Streptococcus mutans DNA is well preserved in tooth samples from archaeological remains and show that it formed part of the human oral microbiota already before the onset of agriculture, consistent with a radiation and population expansion well before 8,000 years ago.