Document Type

Thesis - Open Access

Award Date


Degree Name

Master of Science (MS)

Department / School

Veterinary and Biomedical Sciences

First Advisor

Joy Scaria


The human intestine encompasses a vast community of microorganisms known as the gut microbiota that play a crucial role in maintaining health. Common perturbations such as changes in the normal diet, antibiotic treatment, and changes in environmental conditions can alter the gut microbiome. This can create dysbiosis in the gut leading to disease conditions. Therefore, it becomes important to determine the forces that influence the gut microbial ecology. In the first study, we focus on antibiotic perturbations on microbial succession and resilience in a synthetic consortium consisting of the most prevalent gut bacteria in humans. In addition, we investigated the ability of the consortium to provide colonization resistance against the gut enteric pathogen Clostridium difficile. The results show that the 14-species synthetic community formed after antibiotic perturbation is able to resist C. difficile, providing us insights for understanding the community effect against the pathogen and the possibility of using the synthetic community as a therapeutic. The bacteria Bacteroides caccae, Bacteroides thetataimicron, and Parabacteroides distanosis appear to increase significantly after antibiotic perturbation, accenting their role in inhibiting C. difficile growth. In the second study, we focus on the effects of supplementing quercetin on the gut microbiome. By using bioinformatic analysis, we predicted a subset of gut bacteria capable of degrading the flavonoid quercetin. From this information, we propose a set of quercetin degraders in the healthy individual that may be capable of producing antiproliferative metabolites through quercetin biotransformation. The bioinformatic analysis showed 64 gut bacteria were predicted to have enzymes capable of degrading quercetin. The abundance of the 64 bacteria was determined by analyzing shotgun metagenomes public datasets of healthy and colorectal cancer (CRC) patients and resulted in 11 bacteria being significantly higher in the healthy population. The two studies lay the groundwork to study the gut communities under different ecological conditions in further depth. Understanding the niche an organism occupies in the gut, its survival strategies, the interactions with other microbes and advantage of certain phenotypes of gut communities under stress can provide the answer to the basic functioning of the human microbiota.

Library of Congress Subject Headings

Intestines -- Microbiology.
Microbial ecology.

Number of Pages



South Dakota State University

Included in

Microbiology Commons



Rights Statement

In Copyright