OBJECTIVES: Studies suggest that exercise affects the composition and function of the human gut microbiota, yet this has not been investigated in a randomized controlled trial. The primary aim of this study was to assess if exercise alters the diversity, composition and functional potential of the gut microbiota in free-living humans. A secondary aim was to test whether alpha diversity was associated with phenotypical outcomes. METHODS: Eighty eight participants with overweight or obesity completed a 6-month randomized controlled trial with 4 arms; habitual living (CON), active commuting by bike (BIKE) and leisure-time exercise of moderate (MOD) or vigorous intensity (VIG). Faecal samples for 16 s rRNA gene amplicon sequencing were collected prior to randomization and again after 3 and 6 months, with simultaneous registration of phenotypical outcomes and diet. RESULTS: Shannon's diversity index increased by 5% in VIG (CI95 1 to 9%, p = 0.012) at 3 months compared with CON. No associations were observed between alpha diversity and phenotypical outcomes. Beta diversity changed in all exercise groups compared with CON, particularly the participants in VIG showed decreased heterogeneity. No genera changed significantly. The inferred functional potential of the microbiota in the exercise groups was increased, primarily at 3 months and in MOD. CONCLUSION: Structured exercise induced subtle changes to the human gut microbiota. Cardiorespiratory fitness and fat mass were not associated with alpha diversity.

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