Investigating Bacterial Intestinal Colonization Through the Lens of Systems Biology

Abstract

The mammalian gastrointestinal tract is a complex ecosystem shaped by interactions between the host, indigenous gut microbiota, and external world. When colonizing the gut, bacteria must overcome barriers imposed by the intestinal environment, such as host immune responses and microbiota-mediated nutrient limitation. Thus, understanding bacterial colonization requires determining how the gut landscape interacts with microbes attempting to associate with the established community. However, the myriad interactions between elements of the gastrointestinal ecosystem make it difficult to detect emergent properties of the system when studied solely via reductive methods. Therefore, a systems biology approach, which unites biological and computational modeling to investigate complex systems by analyzing the behavior and relationships of all elements of the system, may be the best way to obtain an integrative perspective of the colonization process. This dissertation encompasses multiple projects that collectively follow a systems biology framework to interrogate how the intestinal environment regulates bacterial colonization of the gut.

I first explore the challenges faced by a bacterium as it initially colonizes the gut using human intestinal organoids (HIOs) and germ-free mice. I show that HIOs pose a more restrictive environment to bacteria than the murine gut. These results demonstrate that different experimental systems model unique aspects of host-microbe interactions in the gut, thus underscoring the need to benchmark such systems to inform their incorporation into integrative experimental frameworks. I conclude that the murine gut is best suited for increasingly holistic investigations of the gut ecosystem moving forward.

To that end, I next explore bacterial colonization in a complex intestinal landscape encompassing both host and microbiota elements. I focus on colonization by the enteric pathogen Clostridioides difficile in the setting of inflammatory bowel disease (IBD). While susceptibility to C. difficile infection (CDI) typically follows the administration of antibiotics, patients with IBD exhibit increased incidence of CDI, even in the absence of antibiotic treatment. However, the mechanisms underlying this susceptibility are unclear. To explore these mechanisms, I leverage murine and computational models to demonstrate that IBD-associated intestinal inflammation alters microbiota composition to permit C. difficile colonization. These results advance our understanding of the host-microbiota interface as it relates to C. difficile colonization in the setting of inflammation. More broadly, this dissertation highlights the value of a systems biology paradigm for gaining insights into ecosystem elements regulating the colonization process. Ultimately, such insights could inform the development of strategies to promote or prevent intestinal colonization by symbiotic and pathogenic bacteria, respectively.