Utilising genomics of novel uncultivable Chlamydiae to further understand chlamydial diversity, pathogenesis and evolution

The phylum Chlamydiae comprises a diverse group of obligate intracellular bacteria that share a unique biphasic developmental cycle. While many of these bacteria are considered pathogens of humans and animals, particularly in the well-described Chlamydiaceae family, other more distantly related members can be detected in the environment. The limiting factor to studying these diverse Chlamydia-related bacteria is their requirement to be cultured in a host cell, which for many novel and/or Candidatus species, is lacking. To gain insight into the biology and epidemiology of novel bacteria in the phylum Chlamydiae, my project aimed to develop a culture-independent genome sequencing (CIGS) work-flow to characterise the genomes of novel uncultivated chlamydiae in clinical samples. I addressed these aims by applying our CIGS method to two examples encompassing the taxonomic and biological diversity within the phylum, including (a) novel species in the genus Chlamydia from reptiles; and (b) deeply rooted chlamydiae that had previously been identified infecting fish.Submitted in the fulfilment of the requirements of the degree of Doctor of Philosophy, University of the Sunshine Coast, 2018