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Author ORCID Identifier


Campus-Only Access for Five (5) Years

Document Type


Degree Name

Doctor of Philosophy (PhD)

Degree Program

Molecular and Cellular Biology

Year Degree Awarded


Month Degree Awarded


First Advisor

David A. Sela

Second Advisor

Kristen M. DeAngelis

Third Advisor

Courtney Babbitt

Fourth Advisor

Kathleen Arcaro

Subject Categories

Other Microbiology


The human body is covered in trillions of microbes that interface with our own cells. A majority of these microbes are present within the lower digestive tract. This gut microbial ecosystem, termed the ‘gut microbiome’, is an assemblage of 1014 microbes that play an important role in human health and nutrition. A thorough understanding of the gut microbiome is key to our perception of the digestive system as a whole. The gut microbiome is inhabited by many commensal bacteria that utilize host dietary components as energy sources. One example of this host-microbial interaction is the metabolism of host-indigestible carbohydrates by species of the genus Bifidobacterium. Bifidobacteria are saccharolytic anaerobes known to colonize in the lower digestive tract of humans, non-human primates, other mammals, birds, and social insects. Bifidobacterial utilization of host dietary complex carbohydrates promotes host health via several mechanisms, including the competitive exclusion of potential pathogens (via increased growth) and the production of short-chain fatty acids which can be taken up by host epithelial cells. Bifidobacteria represent an example of host-microbial symbiosis whereby host dietary patterns stimulate the growth of these organisms, which then may increase host health while enjoying an unperturbed environment. The bifidobacterial host-microbial relationship mediated by diet is the primary focus of this dissertation. Chapter 2 is an analysis of two strains belonging to the species Bifidobacterium callitrichos isolated from the feces of a common marmoset (Callithrix jacchus). In Chapter 3, I present the largest pangenomic investigation to date of Bifidobacterium longum, a species with three subspecies associated with the gut microbiome of infants, adults, and other mammals. Finally, in Chapter 4, I demonstrate the conservation of genes associated with the utilization of human milk oligosaccharides among Bifidobacterium species. Overall, the results of my dissertation research represent an in-depth investigation into signatures of host-microbial coevolution between colonic Bifidobacterium species and host dietary carbohydrates.