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Molecular Biology

Structured exercise alters the gut microbiota in humans with overweight and obesity—A randomized controlled trial



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.


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.


Shannon’s diversity index increased by 5% in VIG (CI95 1–9%, 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.


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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We would like to thank all participants, as well as the technical staff and the students in our lab; in particular we would like to thank Desirée Milling for her invaluable work. Furthermore, we thank Asker Daniel Brejnrod, Christian Theil Have, and Manimozhiyan Arumugam for their assistance and important advice in relation to the microbiome analysis.

Author contributions

TK and MBB contributed equally to this paper. MBB, MR, JSQ, ASG, TH and BS: conception and design of the study. TK, MBB, MR, JSQ, ASG and BS: acquisition of data. TK, MBB, THH and CTE: analysis and interpretation of data. TK and MBB: drafting the manuscript. TK, MBB, THH, MR, JSQ, ASG, CTE, BS and TH: revision of the manuscript. All authors read and approved the final version of the manuscript.


The work is carried out as a part of the research programme ‘Governing Obesity’ funded by the University of Copenhagen's Excellence Programme for Interdisciplinary Research ( Additional funding was provided by the Faculty of Health and Medical Sciences, University of Copenhagen, TrygFonden and Gerda og Aage Haenschs Fond.

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Correspondence to Timo Kern.

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The authors declare that they have no conflict of interest.

Ethical approval

The study was approved by the ethical committee of The Capital Region of Denmark (H-4-2013-108), and is registered at (NCT01962259) and at the Danish Data Protection Agency. The study was performed in accordance with the Helsinki declaration.

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Kern, T., Blond, M.B., Hansen, T.H. et al. Structured exercise alters the gut microbiota in humans with overweight and obesity—A randomized controlled trial. Int J Obes 44, 125–135 (2020).

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