Common management practices such as high concentrate diets, low forage quality, meal feeding, and confinement housing have an effect on intestinal function, specifically large intestinal fermentation. The microbiome of the equine large intestine is a complex and diverse ecosystem, and disruption of microflora and their environment can lead to increased incidence of gastrointestinal disorder. Digestion in the horse can be improved through a variety of mechanisms such as feedstuff selection, forage quality, feeding management, and inclusion of digestive aids. These digestive aids such as prebiotics and probiotics have been used to improve digestibility of equine diets and stabilize the microbiome of the large intestine. Probiotics, or direct fed microbials, have been widely used in horses for treatment and prevention of gastrointestinal disease. The introduction of these live, beneficial microorganisms orally into the intestinal tract has yielded variable results. However, it is difficult to compare data due to variations in choice of organism, dosage, and basal diet. While there are still many unanswered questions about the mode of action of successful probiotics, evidence suggests competitive inhibition and enhanced immunity. Lactic acid bacteria such as Lactobacillus, Bifidobacterium, and enterococci and Saccharomyces yeast have all been successfully used in the horse. Use of these products has resulted in improved fiber digestibility in horses offered both high starch and high fiber diets. When high concentrate diets were fed, probiotic supplementation helped maintain cecal pH, decreased lactic acid concentrations, and enhanced populations of cellulolytic bacteria. Similarly, use of prebiotic preparations containing fructooligosaccharide (FOS) or mannanoligosaccharides (MOS) have improved DM, CP, and NDF digestibility when added to high fiber diets. Furthermore, use of FOS in horses reduced disruptions in colonic microbial populations after an abrupt change in diet and altered fecal VFA concentrations toward propionate and butyrate. Potential use of prebiotics and probiotics to create greater stability in the equine microbiome affects not only digestibility but also health of the horse.