Exploring bacterial epigenomics in the next-generation sequencing era: a new approach for an emerging frontier

• Genome sequencing projects coupled with bioinformatics tools will aid identification of DNA modification.
• Knowledge of the bacterial epigenome will help understand dynamic changes in gene expression that regulates the bacterial life cycle.
• Integrating NGS and bioinformatics empowers estimation of complex epigenome networks that provides new hypotheses for biological validation.
• Availability of thousands of genomes ushers in a new era for epigenomic discovery to define bacterial regulatory networks with increased precision.

Epigenetics has an important role for the success of foodborne pathogen persistence in diverse host niches. Substantial challenges exist in determining DNA methylation to situation-specific phenotypic traits. DNA modification, mediated by restriction-modification systems, functions as an immune response against antagonistic external DNA, and bacteriophage-acquired methyltransferases (MTase) and orphan MTases – those lacking the cognate restriction endonuclease – facilitate evolution of new phenotypes via gene expression modulation via DNA and RNA modifications, including methylation and phosphorothioation. Recent establishment of large-scale genome sequencing projects will result in a significant increase in genome availability that will lead to new demands for data analysis including new predictive bioinformatics approaches that can be verified with traditional scientific rigor. Sequencing technologies that detect modification coupled with mass spectrometry to discover new adducts is a powerful tactic to study bacterial epigenetics, which is poised to make novel and far-reaching discoveries that link biological significance and the bacterial epigenome.