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The effects of travel stress on the equine cecal microbiota are poorly understood. We hypothesized that travel would affect the equine cecal microbiota. Cecally-cannulated horses (n = 6) were randomly assigned to one of two groups, travel (n = 3) and control (n = 3). Horses received a basal diet (Strategy, Purina Animal Nutrition) with 1.2% body weight mixed grass/alfalfa. Travel horses were transported to an unfamiliar location, stalled to simulate weekend horse show conditions, and then returned to the Southern Illinois University Equine Center. Control horses remained at the equine center for the entire study. Cecal fluid was collected on a 6-hour rotating schedule, four times daily throughout the 6-day study. Data were analyzed using mixed models in SAS with P < .05. Cecal bacterial DNA was extracted, followed by 16S RNA sequencing and then analyzed using QIIME 1.8.0. Averages of sequence data were reported by phase (baseline, transportation, post-travel). Although there were no effects of travel associated with β-diversity (P > .05), analysis of α-diversity measures indicated an effect within the travel group during the transportation phase as compared with baseline (P < .05). Interestingly, α-diversity was also affected for control horses in the return phase when compared to baseline. This may be due to the disruption of the return of the travel group. In addition, we identified multiple taxa affected by travel at both the genus and phylum level. Continued profiling of equine gastrointestinal microbiota is necessary to improve our understanding of equine microbial dysbiosis.The effect of travel stress on equine cecal microbiota has not been well defined.Travel affects the cecal microbiota of horses.Travel affects the blood chemistry of horses.