Theses and Dissertations

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Open Access
Characterizing the microbiota and profiling small non-coding RNAs in the compartments of the equine hindgut
(Colorado State University. Libraries, 2018) Reed, Kailee Janelle, author; Coleman, Stephen J., advisor; Bruemmer, Jason, committee member; Turk, Phillp, committee member; Bouma, Gerrit, committee member
Gastrointestinal homeostasis is a complex relationship that encompasses the host's immune response, physiology, gut structure and the microbes residing within the host. Each one of these has pathways of communication in order to keep the host in a 'healthy state' or homeostasis. While each category has been extensively researched independently, interactions that occur between host and microbe are largely still unknown, especially within the equine species. Because horses are extremely prone to various gastrointestinal diseases, understanding the microbial populations and how the horse might communicate with those populations will provide more insight on equine gut homeostasis. The main objectives were to delineate the microbial structures residing within compartment of the hindgut and to begin to profile gene expression patterns of small RNAs within the same areas. Two different populations of animal subjects were used for the two projects in this thesis: a herd from the University of Kentucky (n=6) and a herd from Colorado State University (n=3). The herd from Kentucky was used for the microbiota data set in order to determine the microbial population structure within the cecum, right ventral colon, right dorsal colon and feces. First, we characterized microbial communities present in each of these anatomical sites and then completed a multivariate model to determine similarities of compartments and compared those to the fecal sample. The population of microorganisms observed in the proximal hindgut appeared similar between cecum and ventral colon, while the dorsal colon and fecal samples appeared to be more alike. Interestingly, there is an anatomical structure separating ventral and dorsal portions of the colon called the pelvic flexure. This could possibly be an indication of the host's contribution of determining the microbial communities in each anatomical region. We also demonstrated that while some microbial signatures from the proximal gut were identified in the feces, the distal gut seemed to be more represented in the fecal sample. The herd from Colorado was used to produce the gene expression data for the second project and the main focus was to profile microRNA (miRNA) expression along the hindgut. These small non-coding RNAs have been identified to be involved in gastrointestinal homeostasis within the intestinal epithelium and are host derived molecules. We demonstrated that each tissue (n=8 for each horse) had unique miRNA expression profiles and these miRNAs identified were used to complete a target pathway analysis which shows possible pathways that could be associated with the biological function of each intestinal site. While each project had different objectives, they are both key players of gastrointestinal homeostasis. For future research, we plan to combine these two areas of study by knowing which miRNA could target specific bacteria residing in the gut, which may further the knowledge of how the host contributes to the population structure of the microbes within their gastrointestinal tracts.
Open Access
Equine fecal microbiota changes associated with anthelmintic administration
(Colorado State University. Libraries, 2018) Kunz, Isabelle, author; Coleman, Stephen, advisor; Hess, Tanja, committee member; Hassel, Diana, committee member; Metcalf, Jessica, committee member
The equine gastrointestinal tract contains a complex ecosystem comprised of microorganisms and intestinal helminth parasites. Increasing evidence suggests that horses rely on their gastrointestinal microbial populations for many aspects of metabolic and immune function. Furthermore, interactions between the microbes, helminths, and their host may impact these functions, which are vital to maintaining gastrointestinal homeostasis. The use of anthelmintic drugs is a common practice of intestinal helminth parasite control in domestic horse health management. The use of anthelmintic drugs is very effective for controlling the burden of parasitic infection and associated clinical signs, however anthelmintic administration has also been associated with gastrointestinal disturbances in the horse. The potential effects of anthelmintic drug administration on the equine gastrointestinal microbiota and its' role in homeostasis is not yet understood. The objective of research presented in this thesis is to investigate the impact of anthelmintic administration on the equine gastrointestinal microbiota. This goal was addressed in two main studies, which used 16S rRNA amplicon sequencing to identify and describe the microbial populations present in equine fecal samples. The first study described is a pilot project which aimed to characterize the impact of anthelmintic treatment on the fecal microbiota of horses without an observable helminth infection. The results of this study indicated that subtle differences in the microbial community composition and structure are detectable between samples collected before and after anthelmintic treatment. A second study was then conducted as a follow-up to the pilot which included horses with varying detectable levels of helminth infection as determined by fecal egg counts. Results of the second study further demonstrated microbiota changes following anthelmintic treatment, while also suggesting that the most notable effects of anthelmintic treatment may be observed in fecal samples between 48 and 72 hours post-treatment. The results of these studies suggest that anthelmintic treatment may be associated with changes in the equine fecal microbiota.

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