Epigenetics refers to heritable changes in the genome that alter gene expression and chromosome structure without altering the underlying DNA sequence. These changes can come in the form of DNA methylation, which are small chemical additions to the DNA, or in chromosome-associated proteins which package the DNA into organized structures. While the role of epigenetics in organisms such as plants, animals, and fungi is well established, its evolutionary significance in bacteria remains poorly understood. Recent observations suggest that the proteins bacteria use to organize their DNA and respond to stress may interact with DNA methylation, pointing to a previously unrecognized link between epigenetics and adaptation. By examining the interplay between these molecular processes over time, this research will advance foundational knowledge of genome evolution and the principles governing how bacteria respond to environmental challenges. This project utilizes cutting-edge DNA sequencing technologies, machine learning algorithms, and high-performance computing to identify methylation targets and will contribute to the progress of science by developing new experimental and computational approaches for studying genome structure and evolution in microbes. It also integrates research and education by engaging undergraduate students in discovery-driven learning at the intersection of microbiology, genomics, and data science, helping to build a skilled workforce in bioinformatics and biotechnology. DNA methylation is a widespread but poorly understood feature of bacterial genomes, with potential to influence gene regulation, phenotypic plasticity, and evolutionary dynamics. Despite its prevalence, the role of epigenetic modifications in bacterial evolution remains largely unexplored. This project seeks to investigate the bidirectional relationship between DNA methylation and evolutionary change by combining experimental evolution, synthetic biology, and genomic analyses. Spec