Evolutionary and population genomics of the cavity causing bacteria Streptococcus mutans

Area of Science:

• Microbiology
• Genomics
• Evolutionary Biology

Background:

• Streptococcus mutans is a primary cause of human dental caries.
• Knowledge of S. mutans gene variability and adaptation is limited.
• Demographic history estimates for S. mutans are unavailable.

Purpose of the Study:

• To analyze gene content variability and adaptive features in S. mutans.
• To understand the demographic history and selection pressures on S. mutans.
• To identify genes contributing to S. mutans adaptation.

Main Methods:

• Genome sequencing of 57 S. mutans isolates and related species.
• Population genetic analyses of the core genome.
• Analysis of synonymous and replacement site frequency spectra.

Main Results:

• S. mutans gene content divergence ranges from 5-23%.
• Core genome has 1,490 genes; pan-genome has 3,296 genes.
• Population expansion began ~10,000 years ago, coinciding with agriculture.
• 14 genes under positive selection, linked to sugar metabolism and acid tolerance.
• 73 core genes unique to S. mutans may facilitate adaptation to the human niche.

Conclusions:

• S. mutans gene content is variable, with a significant core genome.
• The species underwent population expansion linked to human agricultural practices.
• Positive selection on specific genes, particularly those for sugar metabolism and acid tolerance, has driven adaptation.
• Unique metabolic genes likely contributed to S. mutans' success in the human oral environment.