Abstract Antibiotics are commonly given to horses to treat known bacterial infections or as prophylaxis against the development of infection. Diarrhea is a recognized adverse effect of antimicrobial administration in horses (antimicrobial associated diarrhea, AAD). In veterinary referral centers, AAD has a reported incidence of 22 to 94% (McGorum, 2010), while horses with AAD are 4.5 times more likely to die compared with horses with other types of colitis (Woods and Cohen, 1999). Although all antibiotics have potential to induce diarrhea, some have increased risk due to low oral absorption, biliary excretion, or enterohepatic recycling. The role of dysbiosis in the gut microbiota is a key feature in the pathogenesis of AAD. Disruption of commensal bacteria of the hindgut allows for pathogen overgrowth and alteration in microbial metabolic function. To date, 16S rRNA sequencing has been used to characterize the effects of penicillin, trimethoprim sulfa, doxycycline, erythromycin, ceftiofur, enrofloxacin, oxytetracycline and metronidazole on the fecal microbiome in healthy horses (Costa et al., 2015; Arnold et al., 2020; Liepman, 2022). Regardless of mechanism of action, antibiotics typically reduce diversity (species richness and evenness) and alter the bacterial community structure of the fecal microbiome, even when animals maintain normal health status and fecal character (Arnold et al., 2021). These effects typically require at least 30 days before the microbiome returns to baseline (Gomez et al, 2023). In horses with colitis, changes in the microbiome are often significant. Horses with AAD demonstrate the most severe disruption of the fecal microbiome compared with horses with Salmonella or undifferentiated colitis. These changes are evident from the phylum to species level, and include important phyla such as Bacteroidetes, Firmicutes, Fibrobacter and Verrucomicrobia (Arnold et al., 2020; Liepman, 2022; Costa et al., 2015). Alterations in the microbiota result in functional metabolic changes that are clinically manifested by diarrhea. Potential changes include alterations in the metabolism of bile acids, carbohydrates including short chain fatty acids, amino acids, lipids and proteins. There is also evidence that antimicrobials increase intestinal permeability via effects on tight junction proteins and by compromising the barrier function provided by the mucus layer between the enterocytes and gut lumen. Recent work comparing horses on antimicrobials that did and did not develop diarrhea confirm that horses with diarrhea have depletion of Verrocomicrobia and metabolites related to gastrointestinal barrier function (Arnold et al., 2021).