Epigenomic landscape of the human pathogen Clostridium difficile

Clostridium difficile is a leading cause of health care-associated infections. Although significant progress has been made in the understanding of its genome, the epigenome of C. difficile and its functional impact has not been explored. Here, we performed the first DNA methylome analysis of C. difficile using 36 human isolates and observed great epigenomic diversity. Strikingly, we discovered a DNA methyltransferase with a well-defined specificity, highly conserved across our dataset and in all the ~300 global C. difficile genomes we further examined. Inactivation of the methyltransferase negatively impacted sporulation, a key step in C. difficile transmission, consistently supported by multi-omics data and genetic experiments and a mouse infection model. Transcriptomic analysis also suggested that epigenetic regulation is associated with host colonization and biofilm formation. The epigenomic landscape also allowed an integrative analysis of multiple defense systems with respect to their roles in host defense and in regulating gene flux in C. difficile . These findings open up a new epigenetic dimension to characterize medically relevant biological processes in this critical pathogen. This work also provides a set of methods for comparative epigenomics and integrative analysis, which we expect to be broadly applicable to bacterial epigenomics studies.