LAUSR

(1) Background: The large intestine of horses is an anaerobic fermentative chamber filled with fibrolytic bacteria that play essential roles in digesting and absorbing nutrients for energy production. Although Jeju horses are a prominent local breed in Korea, few studies have investigated the gut microbiota of Jeju horses; (2) Methods: This study performed sequencing of V3 and V4 hypervariable regions of the partial 16S rRNA genes obtained from horse fecal samples and compared the gut microbiota between Jeju and Thoroughbred horses. Thirty and 24 fecal samples were obtained from Jeju and Thoroughbred horses, respectively; (3) Results: The gut microbiota belonged to 23 phyla and 159 families. Firmicutes and Bacteroidetes were the most abundant and predominant phyla, followed by Verrucomicrobia, Euryachaeota, and Spirochaete. The ratio of Firmicutes to Bacteroidetes (F/B), which is known as a relevant marker of gut dysbiosis, was 1.84 for Jeju horses, whereas it was 1.76 for Thoroughbred horses. Moreover, at the genus level, 21 genera were significantly different between the Jeju and Thoroughbred horses (p < 0.05); (4) Conclusions: The Thoroughbred horse’s gut microbiotas had significantly higher diversity than the Jeju horses (p < 0.05). In addition, beneficial commensal bacteria that produce short-chain fatty acids thus providing a significant source of energy are also more abundant in Thoroughbred horses. These results provide novel information on the horse gut microbiota and insights for further studies related to the horse gut microbiota.