The chlamydiae are a family of obligate intracellular bacteria that have a unique bi-phasic developmental cycle, unique cellular properties, and a unique set of challenges to studying its biology. While genetic manipulation is becoming routine in Chlamydia, there are significant challenges to working with this intracellular parasite. The body of this work focuses on the chlamydiae in context to comparative analysis of genome structure, organization, population dynamics, and recombination. This approach presents its own challenges, and this work includes the development of tools and methods for improving the comparative genomic research.
Next generation sequencing approaches have led to completion of several dozen chlamydial genome sequences, most of which are from Chlamydia trachomatis. Analysis of these genomes has shown that chlamydiae, like other obligate intracellular bacteria, have a much reduced genome structure that implies dependence on the host for much of its metabolic capability. Certain groups of genes, including those encoding inclusion membrane proteins and the family of polymorphic membrane proteins, have been significantly expanded against this general reductive evolutionary strategy. Pregenomic and postgenomic sequence analysis of C. trachomatis has led to considerable understanding of nucleotide polymorphisms, insertions and deletions that are associated with certain clinical presentations.
While widespread recombination in the human pathogen, Chlamydia trachomatis, is revealed in previous studies, the development of novel culture-independent sequencing tools in this work have added and expanded upon our knowledge of the extent and diversity of recombination in Chlamydia spp.. These methods are then adapted and applied to a large-scale comparative study of the ruminant pathogen, Chlamydia abortus, illuminating a closely related group of genomes using an interesting form of pre-transcriptional gene regulation for diversifying the permutations of membrane proteins on its cell surface. Finally, the protocols are modified to vastly improve methods for genome sequencing clonal isolates that have been grown in minimal cell culture.
Future research will address chlamydial genome structure in the context of the system in which they live, and will include data on the host microbiome and host genetic background. We anticipate that integrating these areas of research will lead to significant progress in our understanding of the nature of chlamydial infection and disease.