Date of Award


Degree Type


Degree Name

Doctor of Philosophy in Biological and Environmental Sciences


Cell and Molecular Biology (CMB)


Cell & Molecular Biology

First Advisor

Paul S. Cohen


We previously proposed that colonizing strains of E. coli likely occupy specific niches as minimal members of mixed biofilms formed primarily by anaerobic members of the gut flora. These "restaurants" formed by the different community members of the gut provide individual strains of E. coli with various unique binding pockets and locally provided mono- and disaccharides by breaking down polysaccharides which facultative anaerobes, such as E. coli, could not break down on their own. This allows strains of E. coli that cannot grow as efficiently on available sugars to colonize if they are able to occupy niches that other competing strains could not. For example, if the less efficient strain could bind better to specific anaerobic members or had a higher tolerance for bile salts it would be able to co-colonize with a strain that could grow better on available sugars as it would not be in direct competition to occupy the same niche. While the anaerobes in mixed biofilms provide a source of nutrients for minimal members such as E. coli through breakdown of large polysaccharides, the facultative anaerobes may improve the environment for strict anaerobes by reducing the concentration of oxygen within the biofilms. Oxygen diffuses from surrounding tissue into the intestines, oxygen from swallowed air is present in flatus, and at least one predominant anaerobe in the gut microbiome, Bacteroides fragilis, respires oxygen at low concentrations. As such, manuscript I looks at how colonization with specific strains of E. coli can affect the development of the intestinal microbiota. Five representative E. coli strains were used for this study: Nissle 1917, EDL933, MG1655, and two MG1655 mutants selected by the mouse gut (envZ P41L and flhDC). While slight variances were observed between strains, these were likely due to differences between hosts rather than the colonizing E. coli and no significant differences between the communities could be surmised.

In order to better understand the interactions between E. coli and the members of the intestinal microbiota, a novel in vitro method was developed. Manuscript II examines the development of the in vitro system as it was compared to the mouse model. This method was designed to be simple and inexpensive while providing an environment meant to replicate the natural habitat of these organisms: the mammalian gut. The current study examines the development of said in vitro model and its ability to mimic the mouse gut in terms of diversity of organisms, as well as its usefulness in examining the colonizing ability of competing E. coli strains. It is shown that, while still in development, this system is currently able to maintain diversity comparable to what is seen in mice. While the abundance of these diverse organisms is not necessarily at the levels seen in mice, the model is already an effective system for studying the microbial community of the gut in a controlled environment. Furthermore, the system is able to mimic certain colonization experiments of competing E. coli strains done in mice, and with improvements to bolster the growth of the diverse population could be used as a non-invasive method for studying gut microbes.



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