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Publication Date


Document Type

Masters Thesis

Degree Name

Master of Science


Biological Sciences


Metagenomics, Horses-Parasites, Horses-Diseases-Treatment, Anthelmintics, Gastrointestinal system, Equine, GI tract


There have been many studies that have been performed on the equine microbiome (O’Donnell, 2013; Costa, 2012; Lyon, 2008; Mathee, 2002), however what constitutes a healthy microbiome of the horse has yet to be established. The objective of this study is to identify the difference between the gut microbiomes through fecal sampling of horses with or without intestinal parasites and when treated with antihelmintics. Change in relative abundance between certain bacterial phyla have been noted following treatment with the drug Zimecterin Gold®. This data was generated with high throughput sequencing of metagenomic DNA obtained from fecal sampling. Total DNA was isolated from horse fecal samples (N=6) and assessed for purity and quality. PCR was executed using a modified protocol for 16s V4 amplification. Each horse had two representative examples that corresponded to the pre‐treatment and post treatment dates. The 16s amplicons were sequenced using the Illumina Miseq to assess the bacterial diversity and abundance. Analysis of this data set was done using the software QIIME. The GreenGenes database was used as references for the classifications of sequences into operational taxonomic units. QIIME generates bar charts to illustrate this data, breaking down the represented diversity of each sample by phylum, class, order, family, and genus level. Only one of the horses was infected and treated for parasites. This horse is the test subject that the changing results were noted. The results from these charts showed the most change between the phyla Actinobacteria, Bacteroidetes, and Verrucomicrobia.

There were 14 phyla that were produced from the analysis with Bacteriodetes, Actinobacteria, and Firmicutes being the most prevalent of all the phyla. The difference of a specific phyla post treatment vs pre‐treatment was not determined based on our research since the relative abundance between these phyla did not appear to be insignificant. We hope that this data will offer more insight into the gut microbiota of horses and aid in maintenance of a healthy gut microbiome for horses.




93 pages : color illustrations. Includes bibliographical references (pages 70-77)