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The equine fecal microbiome may vary across horse populations due to the diversity of the habitual diet. The purpose of this study was to assess and compare the microbial population of different horse populations, specifically the differences between feral versus domesticated populations. Samples were collected from 3 different populations of horses: horses from the Shackleford Banks (n = 24), a feral horse population living on the Outer Banks of North Carolina who eat native grasses such as Spartina marsh and island grasses; horses from the NCSU Equine Educational Unit (n = 18) that are predominantly kept on cool season mixed pastures and may be supplemented with hay and concentrates from time to time; and finally, privately owned horses (n = 36) that are fed mixed diets consisting of pasture, hay and concentrates. Horses were monitored and samples were collected immediately following a void …