All ETDs from UAB

Advisory Committee Chair

Stephen Watts A Watts

Advisory Committee Members

Asim K Bej

Casey D Morrow

Thane Wibbels

Document Type


Date of Award


Degree Name by School

Doctor of Philosophy (PhD) College of Arts and Sciences


Like humans, Danio rerio, commonly known as the zebrafish, generally harbor millions of gut microbes, whose commensal microbial organisms aid in digestive physiology, nutrition, and host health. The emergence of high throughput sequencing technology (HTS) enables researchers to sequence collective microbial genomes, providing information on the composition of entire microbial communities, as well as the dynamics across taxa encompassing the overall community. Thus, the advancement of genome sequencing and metagenomic analysis have provided a broader understanding of resident and exogenous microbes across biological model organisms. These technologies have enabled researchers to review a spectrum of endogenous and exogenous factors influencing microbial composition and, consequently, host homeostasis. Notably, nutrition emerged as a significant exogenous determinant in the development and modulation of the microbiome. D. rerio is a widely recognized vertebrate model organism employed in research since the 1960s, which has previously lacked an established reference diet. We have developed an open-source dietary formulation that can serve as a reference diet, with the aim to promote animal health while increasing experimental reproducibility. We demonstrated that changes in protein and lipid macronutrient content in the reference diet-induced changes in weight gain, body composition, fecundity, and apparent health in relation to changes in gut microbial populations. These data will validate the importance of standardizing dietary ingredients and nutrient content in D. rerio and provide insight into understanding nutrient profiles that will affect overall health in the D. rerio, increasing the value and utility of this important model. Finally, we assessed the impact of protein sources derived from bacteria and yeast on the gut microbiome of D. rerio. We suggest that utilizing microbial-based proteins may exert a probiotic or prebiotic influence on the microbiome, thereby fostering increased microbial diversity. These effects, in turn, hold the potential to benefit the health of the host organism. The outcomes of this study could facilitate the creation of new reference diets tailored specifically for D. rerio and offer valuable insights into the potential use of microbial-based protein sources in mammalian nutrition.

Available for download on Thursday, June 27, 2024