Date of Award


Document Type


Degree Name

Master of Science (MS)



First Advisor

Harrison, Scott H. Dr.


Changes in bacterial genomes due to the integration of prophages have been proposed to be part of a symbiotic relationship. Prophage activity is common for bacterial pathogens in the fluctuating environment of animal hosts. Pathogenic bacteria have been found to have extensive variation of their bacterial cell boundary zone of components, which is the inherent interface for virulence properties of antigenicity, toxicity, and resistance. Prophages are a source of this variation, both through insertion of cargo genes via prophages into bacterial strains, and additional effects due to prophage insertions affecting the overall genomic structure. The latter scenario of genomic reorganization effects has not been well explored. Our hypothesis on genomic reorganization effects was that prophage integration sites would adaptively associate with locations of cell boundary genes occurring outside the prophage insertion sites. Using clusters of orthologous groups (COG) designations, we investigated how prophage insertions collocate with COG-based categories of genes into chromosomes of pathogenic versus nonpathogenic bacteria. Here we study the integration of prophages into the genomes of 49 strains of Escherichia coli. The frequency of genomes containing intact prophages was much higher for pathogenic strains than for non-pathogenic strains. We examined likelihoods of proximity at which prophages integrated near genes of different COG-based categories and found that significant integration occurs near cell boundary genes. This workflow was then implemented as a tool inside the web-based genome analysis system GALAXY to enable further study of other bacterial varieties and overall genomic context.