The aim of the present study was to clarify the influence of inulin and lactulose-fortified prebiotic food intakes on bone metabolism turnover among Japanese female athletes. The participants included 29 female athletes aged 18–25 years. They were requested to consume their habitual foods or drinks with one pack of prebiotic food every day for 12 weeks. Dietary intake, training time, body composition, blood sample, and fecal microbiota were assessed during this intervention period. Body composition, total energy intake, and training time of the participants revealed no significant changes during the intervention period. The occupation ratio of Bifidobacterium spp. was significantly increased at 3 and 4 weeks (18.0 ± 8.3% and 17.6 ± 8.5%, respectively) compared to that of pre-intervention (11.7 ± 7.3%) (p = 0.019 and p = 0.035, respectively). The serum TRACP-5b level was significantly decreased at 12 weeks (363 ± 112 mU/dL) compared to that at baseline (430 ± 154 mU/dL) (p = 0.018). These results suggest that the prebiotic food used in this study might have beneficial effects on bone health and gut microbial environment among female athletes. Further studies are warranted to identify the mechanism of the prebiotics–gut–bone axis.
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