Undergraduate Honors Thesis Projects

Date of Award


Document Type

Honors Paper

Degree Name

Zoo and Conservation Science-BS


Biology & Earth Science


Dr. Jennifer Bennett & Dr. Steffanie Burk

First Committee Member

Dr. Andrew Calinger-Yoak

Second Committee Member

Dr. Cynthia Laurie-Rose


Microbiome, Equine, Gut, Parasites, 18S rRNA, 16S rRNA

Subject Categories

Other Animal Sciences | Other Microbiology


The gut microbiome of domestic horses (Equus ferus caballus) can be broken down into two primary divisions of interest: (1) prokaryotic composition, consisting of bacteria and archaea and (2) fungal composition. Within the gut, there are also eukaryotic parasite communities that may interact with the microbiome. While each has been the subject of various scientific explorations, in this study we analyze the potential interconnectedness of these categories. To determine the extent to which each component of the gut microbiome/parasitic communities influences the other, DNA was extracted and amplified from the fecal samples of eight horses. A combination of 16S and 18S rRNA Illumina Sequencing was used to illustrate the bacterial/archaeal and fungal compositions taxonomically with the assistance of QIIME2 software. The 16S and 18S sequencing data were compared to the fecal egg counts of each sample which had been calculated using the modified Stoll method. Minimal 18S fungal data was acquired, though two phyla were identified. The 16S data showed some separation in beta diversity groupings between individuals of higher and lower egg count numbers; this observation may indicate a possible connection between parasitic load and the beta diversity of the horses’ gut bacterial communities. Additionally, six phyla were identified from the sequencing of the 16S data, which were classified down to a total of roughly twenty genera.