Intestinal epithelial and microbial interactions at cellular resolution

• Author / Creator

  Willms, Reegan J

• The intestinal epithelium is a complex tissue monolayer composed of regionally and functionally specialized cells. Given epithelial exposure to harsh and varied luminal conditions, epithelial cells continuously regenerate to sustain the barrier against environmental factors, including microbial invaders. Both host factors and microbial input contribute to intestinal epithelial growth, differentiation, and function. However, the epithelium contains a complex mixture of secretory and absorptive cell types, and it is unclear how each of these cell populations responds to microbial signals or contributes to epithelial homeostasis.
  To determine how microbes alter cell type-specific processes in the intestine, I employed a zebrafish model and single-cell RNA sequencing (scRNA-seq) of the intestine to measure microbe-dependent transcriptional changes at the cellular level. First, I describe genetic markers for cell types in the zebrafish gut under conventional conditions in larvae and adults, establishing homeostatic cell profiles of the zebrafish intestine at two developmental stages. Next, I compare these conventional scRNA-seq datasets to respective cell profiles of intestines from fish larvae raised without microbes, or adults exposed to pathogenic Vibrio cholerae, an aquatic bacterium that infects the gastrointestinal tract, and for which zebrafish are natural hosts. Lastly, I employ these single-cell profiles of the zebrafish intestine to identify the receptor activator of nuclear factor kappa light-chain-enhancer of activated B cells (RANK), as a developmental regulator of cells with genetic similarity to microbe-sensing tuft cells in mammals. Taken together, this thesis
  provides a framework for how commensal and pathogenic microbes impact IEC transcriptional programmes, and explores regulatory infrastructure underlying development of a candidate
  microbe-sensing cell type.

• Subjects / Keywords

  • intestine
  • single cell RNA sequencing
  • zebrafish
  • host-microbe interactions

• Graduation date

  Fall 2023

• Type of Item

  Thesis

• Degree

  Doctor of Philosophy

• DOI

  https://doi.org/10.7939/r3-41vj-yy41

• License

  This thesis is made available by the University of Alberta Libraries with permission of the copyright owner solely for non-commercial purposes. This thesis, or any portion thereof, may not otherwise be copied or reproduced without the written consent of the copyright owner, except to the extent permitted by Canadian copyright law.