Understanding the biology of Clostridium butyricum using comparative genome analysis

With a focus on the use of comparative genome analysis, this thesis explores differences between strains of the highly diverse species Clostridium butyricum. Chapter 1 describes the conserved genome architecture of the species C. butyricum. This includes the identification of a chromid, which appears to be unique to C. butyricum among the species of the genus Clostridium. Chapter 1 also details a set of gene clusters that are found in pathogenic strains of the species, but are absent from non-pathogenic strains. Chapter 2 investigates a hypervariable region of the C. butyricum genome, which resides within the flagellar biosynthesis locus and is predicted to encode genes involved in the O-linked modification of flagellin proteins with nonulosonic acids (NulOs) in pathogenic C. butyricum strains. The wider occurrence of NulO-mediated flagellin modification across the genus Clostridium is also explored. Chapter 3 investigates the metabolic potential of the probiotic C. butyricum strain DSM 10702 in the context of the human gut environment. The findings of this are captured in a genome scale metabolic model, iOA760, which can be used to predict the growth of C. butyricum using gut-relevant carbon and nitrogen sources. By adding a module of reactions to iOA760 to simulate growth using L-fucose as the carbon source, we demonstrate that this model can be used to guide metabolic engineering strategies which may enhance the therapeutic effects of probiotic C. butyricum strains.