This Is AuburnElectronic Theses and Dissertations

The Inflamed Gut: An Integrative Approach to Understanding the Impact of Inflammation on Bacteriophage-Host Dynamics.




Higgins, Keah

Type of Degree

PhD Dissertation


Biological Sciences


The intestinal microbiome is a diverse and dynamic microbial ecosystem residing within the gastrointestinal tract. The mammalian intestine is home to both commensal and opportunistic pathogenic microorganisms. The immune system within the intestine has a unique challenge in maintaining homeostasis while providing protection from invading pathogens. The intestinal microbiome consists primarily of organisms from the domain Bacteria, with smaller populations of Archaea, Eukaryota, and Viruses. The healthy bacteriome profile is dominated by the phylum Bacteroidetes. Members of the Firmicutes, Proteobacteria and Actinobacteria phyla are also major components of the bacteriome. This intestinal microbiota in the ‘healthy state’ contributes to the healthy functionality of metabolic, digestive, endocrine, immune, and neurological function of the host. Inversely, the microbiota can negatively impact the host when the relative abundance of these consortia becomes altered, a condition generally known as dysbiosis. For example, the dysbiotic profile of intestinal microbiota in obesity consistently reflects an increased abundance of Firmicutes, altering the Bacteroidetes:Firmicutes ratio. Dysbiotic bacteriome profiles have also been linked to increased susceptibility of development of intestinal inflammation, colitis. Within the last 10 years, researchers have grown a respect for the intestinal bacteriome, but there are other components within the intestinal microbiome that could contribute, directly or indirectly, to the homeostasis of the intestinal microbiome. Namely, the bacteriophage within the intestinal microbiome, phageome, have recently been shown to display modulation in response to both environmental influences (diet) and internal influences (immune system induced stress). The phageome has been described as more diverse in people who have Inflammatory Bowel Disease (IBD). While the field has made progress towards understanding bacteriophage role in microecosystems, it is not well understood how these changes occur in an established microbiome or how the abundance dynamics of the phageome progress overtime following external or internal influence. The goal of this study was to understand the longitudinal impact of dietary intervention and intestinal inflammation and how these influences affect bacteriophage abundance and functionality in the microbiome. To do this, intestinal bacteria and bacteriophage abundance changes were monitored following high-fat western diet (WD) feeding using shotgun metagenomic sequencing. Additionally, an in vitro study was conducted using a fecal bacterial and bacteriophage isolate to understand the role the mammalian host plays on bacteriophage infectivity rates. These isolates were used in modified adsorption constant kinetic assays and one-step growth curves both in the presence and absence of inflammatory derived products. Overall, components of the phageome are affected by the diet in various ways. The phageome of WD-fed mice display rapid shifts in abundance profiles of bacteriophage genera which appeared to proceed apparent abundance changes of the host. We found that most bacteriophage display abundance patterns that coincide with predicted bacteriophage behavior. For example, temperate bacteriophage displayed a rise in abundance alongside their putative host which is likely explained by replication of host genome containing prophage. Interestingly, the abundance dynamics of bacteriophage do not always follow the abundance dynamics of their host. The in vitro experiments conducted showed that reactive oxygen and chlorine species led to delayed adsorption, delays in time to burst and reduction of progeny produced. At the conclusion of this work, we have shown that bacteriophage are affected in a similar manner to bacteria to external and internal influences on the intestinal microbiome. The abundance dynamics experienced by the phageome could play a role in development of dysbiosis and perpetuation of disease.