This thesis contributes significantly to the understanding of phase-variable gene expression in Haemophilus influenzae and phasevarions in Streptococcus pneumoniae, and to the broader fields of bacterial genetics and epigenetics. This thesis has: (i) demonstrated that particular forms of lipooligosaccharide (LOS) are selected for during NTHi invasive infection; (ii) described the autotransporter Lav in NTHi, demonstrating that this protein is phase-variable, is an important virulence factor, and is a potential NTHi vaccine candidate; (iii) informed vaccine development by characterising the prevalence of Hgps across Haemophilus influenzae, while identifying expression in an invasive NTHi isolate collection; (iv) effectively doubled publicly available genomes for Haemophilus influenzae biogroup aegyptius isolates; and (v) carried out a detailed analysis of the pathobiology of the SpnIII system of S. pneumoniae. As the body of work that constitutes each Chapter of this thesis is in manuscript format, abstracts can be found in these Chapters.