Abstract Objectives Type 1 diabetes mellitus is a metabolic disease characterized by dysbiosis. Modulation of the gut microbiota by oligosaccharides and aerobic training are proposed mechanisms that ameliorate the disease through affecting host-microbiota interactions. Methods Seventy-two male Wistar rats were randomly divided into 8 groups – 5 with streptozotocin-induced diabetes and 3 healthy controls. The effect of two oligosaccharides – xylo- and galactooligosaccharides, and of aerobic training on the blood glucose concentration, growth and diversity of the gut microbiota was evaluated in the current study. Results The galactooligosaccharides positively affected the glycemic status of the experimental animals as the diabetic and healthy rats had lower blood glucose concentration after 6 weeks of treatment (diabetic rats: week 4 vs. week 8, p=0.047; healthy rats: week 2,4,6,10 vs. week 8, p=0.001, p=0.000, p=0.025 and p=0.001, respectively). A positive effect of the galactooligosaccharides on body weight was observed when administered to diabetic rats in comparison to the diabetic control (p=0.020). Similar results were observed for the aerobically trained diabetic rats (p=0.004). The identification of bacterial species showed preserved microbiota diversity and indicated Bifidobacterium indicum, Lactobacillus feritoshensis and E. coli as the most abundant species among the analyzed genera. Conclusions Prebiotic treatment beneficially affected the hyperglycemia and growth of type 1 diabetic rats. The most significant effect of the aerobic training was the improvement of the morphological parameters. Oligosaccharide administration and exercise did not affect the diversity of the bacterial species.