Date of Award


Degree Type


Degree Name

Doctor of Philosophy (PhD)


Comparative Pathobiology

Committee Chair

Yava L. Jones-Hall

Committee Co-Chair

Cindy H. Nakatsu

Committee Member 1

Harm HogenEsch

Committee Member 2

Hyonho Chun


Crohn’s Disease (CD) and Ulcerative Colitis (UC) are chronic, inflammatory conditions of the digestive tract that are collectively known as Inflammatory Bowel Disease (IBD). Currently, IBD has no cure and the exact mechanisms of disease development and progression are unknown. The gut microbiome is the collection of microbes that reside in the digestive tracts of humans and animals, and it has been shown to be associated with a variety of diseases, including IBD. Mouse models of colitis are often used to investigate the role of the gut microbiome in IBD. In this work, I investigated the role of tumor necrosis factor (TNF) on the gut microbiome in a mouse model of CD. Tumor necrosis factor is an inflammatory cytokine that plays a critical role in the inflammatory response. A common IBD treatment strategy is the use of TNF inhibitors. However, a subset of patients only responds to anti-TNF treatment for a limited time, while others do not respond at all. It is not fully understood how TNF, or TNF blockade, impacts the microbiome. Therefore, my overall objective was to determine how TNF and host variables impact the mouse gut microbiome during colitis. My hypotheses were that 1) Age, sex, and TNF affect the fecal microbiome of mice, and impact the severity of acute 2,4,6 trinitrobenzenesulfonic acid (TNBS) colitis. 2) TNF, sex and disease severity impact the microbiome in chronic TNBS colitis and the composition of the fecal microbiome will closely correlate with colitis severity. 3) Different mouse strains have a distinct fecal microbiome. To test my hypotheses, I induced acute and chronic TNBS colitis in WT mice and Tnf-/-mice. 16S rRNA gene sequencing, microbiome analysis, and multivariate analyses were used to determine the relationship of host factors to the gut microbiome. I found that TNF, age, and sex impact the gut microbiome in mice before and after colitis. Additionally, I identified specific microbes that are differentially abundant depending on TNF expression, GI site, as well as the mouse age, sex, strain, and vendor. This work highlights the importance of considering host factors in microbiome studies and provides important data to the literature concerning the role of the gut microbiome in IBD pathogenesis.