The gut microbiome has become a popular topic of interest in recent years as scientists are beginning to understand the vast impact it can have on overall health and development in both humans and animals. A microbiome is defined as the collection of genomes of the microorganisms that reside in a specific environment [1]. In regards to the gut microbiome, it is comprised of the genetic material of the microbes that inhabit an organism’s gastrointestinal system. In the horse, this microbiome includes bacteria, yeast, fungi and protozoa where the most functionally important microorganism is thought to be bacteria. Researchers have studied how this microbial community can affect not only the digestive tract, but also the immune response, endocrine system, behavior and even cognitive function.