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Obesity is known to be linked with a shift in skeletal muscle fiber type, which plays a role in insulin sensitivity and myokines activity. Here, we investigated whether aerobic exercise training has any effects on skeletal muscle MHC isoforms related to gene expression, irisin, and FNDC5 in obese rats. Thirty-two male SD-rats (3 wks old) were randomly assigned to normal diet (ND, n = 8) and high-fat diet (HFD, n = 24) groups, with specific caloric intake (ND; 11.5%, HFD; 60% of kcals from fat), for 8 weeks. After 8 weeks, HFD-induced obese rats were randomly reassigned to either an obese control (OC, n = 8) or obese exercise (OE, n = 8) group, and provided a normal diet. The OE group was exercised on the rodent treadmill (60 min, 15 m/min, 5 times) for 8 weeks. We investigated FNDC5, slow-twitch muscle gene (miR-499) and fast-twitch muscle gene (SOX6) expression in gastrocnemius muscle, and serum irisin. HFD group showed heavier body weight compared to ND group (p < .05). Blood glucose concentrations, determined by IGTT, were significantly higher in HFD group compared to ND group in 90-minutes and 120-minutes of the recovery phase (p < .05, 43%, 34%). Average body weight for the OE group was significantly lower than the OC group. The level of blood glucose in the OE group was lower than the OC group in 90-minutes and 120-minutes of the recovery phase (p < .05, 11%, 9%). Irisin levels were not significantly different between the HFD and ND groups. However, FNDC5 level was significantly lower in HFD rats than ND (p < .05, 53%). The OE group showed increased expression of irisin and FNDC5 compared to ND, but there was no change in OC (p < .05, 23%, 42%). While the levels of miR-499 and SOX6 were significantly higher in the OE compared to OC group, there was no change in MYH7. Taken together, 8 week regular aerobic exercise has positive effects on body weight, blood irisin concentration, its precursor FNDC5, as well as fiber type promoting genes mi-499 and SOX6.

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