Year of Award


Document Type


Degree Type

Doctor of Philosophy (PhD)

Degree Name

Cellular, Molecular and Microbial Biology

Department or School/College

Division of Biological Sciences

Committee Chair

William E. Holben

Committee Co-chair

Douglas W. Raiford

Commitee Members

Creagh W. Breuner, Scott R. Miller, L. Scott Mills


University of Montana


Host associated systems are of particular interest to many microbiologists because invasion of these systems can lead to disease. One important host-associated systems is the intestinal microbiome, but in many studies, including those on pathogenesis, this system is represented by samples from one location (generally the feces or cecum). This body of work was initiated in part because I wondered why a large and diverse ecosystem was being was being represented by samples from only one habitat.

The biogeography of living organisms has an impact on landscape ecology studies, including those in the field of invasion ecology. Despite several studies that specifically investigate the biogeography of the intestinal microbiome, there has been a general failure to describe the luminal biogeography of the lower intestinal tract, primarily due to “noise” introduced by inter-subject variation. Herein, the biogeography of the mouse lower intestinal tract was mapped using novel techniques to overcome problems caused by inter-subject variance. These techniques were then used to reveal nuances of invasion in the lower intestine by Clostridium difficile.

C. difficile is an invader of the intestinal microbiome that is well-known for its ability to cause disease following antibiotic treatment. I observed large changes with the introduction of antibiotics to this system, resulting in a series of “blooms” of various taxa, most likely an indication of successional changes due to the effects of antibiotics. I also found that without antibiotic treatment, C. difficile, is still associated with changes in the intestinal microbiome. This is an important development, as it suggests that small changes associated with normal colonization by introduced species may be compared with range expansion by the same species.

This body of work was primarily done in order to apply ecological theory to microbiome studies and in doing so gave rise to new techniques and new methods of looking at systems. It is my hope that these advances will result in contributions both to investigations of the intestinal microbiome as an ecological system as well as how as it relates to disease.



© Copyright 2015 Ellen Lark