Campylobacter jejuni is an important zoonotic agent that is the leading cause of both human foodborne bacterial gastroenteritis worldwide, as well as ovine abortion in the United States. In particular, a single C. jejuni sheep abortion clone, of which IA 3902 is a prototypical isolate, has recently emerged as the dominant causative agent of sheep abortion due to Campylobacter sp. in the U.S. and has been increasingly identified in human outbreaks of disease. Multi-omics approaches to studying this hypervirulent strain have shown that it is remarkably similar to other common strains of C. jejuni such as 11168 that do not show the same ability to cause systemic clinical disease. Further work to elucidate the molecular mechanisms that allow for small changes in genomic structure to lead to large changes in virulence ability in this important zoonotic agent is warranted. A number of studies have demonstrated that the gallbladder of ruminants, as well as other domestic animal species, is often positive on culture for Campylobacter sp. following oral exposure, suggesting that this environment may serve as a chronic nidus of infection for maintenance of disease within populations. By utilizing a unique in vivo model of gallbladder infection, the work conducted within this dissertation has allowed identification of the preferred location of C. jejuni IA 3902 within the gallbladder host environment as well as demonstrated putative host factors that may play a role in its localization to that site. In addition, by utilizing emerging RNA sequencing technology, we were able to determine numerous protein coding genes and non-coding RNAs that were differentially expressed following exposure to the in vivo gallbladder host environment. One of these identified non-coding RNAs, CjNC110, was selected for further study. Inactivation of the CjNC110 non-coding RNA in IA 3902 allowed us for the first time to identify transcriptomic and phenotypic changes associated with loss of function of a small RNA in any species of Campylobacter. The collective results of these experiments provide additional evidence to begin to elucidate the role of gallbladder colonization and small RNAs in the pathobiology of the important zoonotic pathogen, C. jejuni IA 3902.