Author ORCID Identifier

Date Available


Year of Publication


Degree Name

Master of Science (MS)

Document Type

Master's Thesis


Agriculture, Food and Environment


Veterinary Science

First Advisor

Dr. Emma N. Adam


Though generally regarded as safe, research continues to demonstrate negative side effects of antibiotic administration on the gastrointestinal (GIT) microbiota across species. In horses, antibiotic associated diarrhea (AAD) is a life-threatening side effect linked to the GIT microbiota. This study tested the hypothesis that short term antibiotic administration to healthy horses would negatively impact the fecal microbiota as measured by their ability to digest nutrients and produce short chain fatty acids (SCFAs). Twenty-four horses were assigned to one of four treatments: control (CO); potassium penicillin/gentamicin sulfate (KPG); ceftiofur crystalline free acid (EX); trimethoprim/sulfamethoxazole (SMZ); and treated for 4 days. Fecal samples were collected before treatment began (S0), the day after treatment conclusion (S5), and at 10, 14, 21, and 28 days after beginning treatment. Horses had highly individualized responses to antibiotic treatment, although all horses receiving antibiotics experienced significantly softer stool compared to controls. Lactobacillus spp. were dramatically reduced in all antibiotic treated S5 samples. Horses receiving antibiotics were significantly more likely to test positive for C. difficile or C. perfringens on fecal qPCR. In conclusion, response to antibiotic administration displays high inter-individual variability, but shows changes to the functions of fecal microbiota that may depend on the antibiotic used.

Digital Object Identifier (DOI)

Funding Information

This work was made possible through Gluck Equine Research Center’s Wright-Markey Trust Endowment from 2021 to 2023.