Background The effects of physical activity and sedentary behavior on human health are well known, however, the molecular mechanisms are poorly understood. Growing evidence points to physical activity as an important modulator of the microbial composition, while evidence of sedentary behavior is scarce. We aimed to synthesize and meta-analyze the current evidence about the effects of physical activity and sedentary behavior on microbiome across different body sites and in different populations.

Methods A systematic search in PubMed, Web of Science, Scopus and Cochrane databases was conducted until September 2022. Random-effects meta-analyses including cross-sectional studies (active vs. inactive / athletes vs. non-athletes) or trials reporting the chronic effect of physical activity interventions on gut microbiome alpha-diversity in healthy individuals were performed.

Results Ninety-one studies were included in this systematic review. Our meta-analyses of 2632 participants indicated no consistent effect of physical activity on microbial alpha-diversity, although there seems to be a trend toward a higher microbial richness in athletes compared to non-athletes. We observed an increase in short-chain fatty acids-producing bacteria such as Akkermansia, Faecalibacterium, Veillonella or Roseburia in active individuals and after physical activity interventions.

Conclusions Physical activity levels were positively associated with the relative abundance of short-chain fatty acids-producing bacteria. Athletes seem to have a richer microbiome compared to non-athletes. However, high heterogeneity between studies avoids to obtain conclusive information on the role of physical activity in microbial composition. Future multi-omics studies would enhance our understanding of the molecular effects of physical activity and sedentary behavior on the microbiome.

The authors have declared no competing interest.

Projects SAF201787526R, PID2021127280OBI00 and PID2020120249RB100 funded by MCIN/AEI/10.13039/501100011033/FEDER Una manera de hacer Europa; Project ACTS614UGR20 funded by FEDER/Junta de Andalucia-Consejeria de Economia y Conocimiento; Projects P2000158 and P2000124 funded by Junta de Andalucia; Unidad de excelencia SOMM17/6107/UGR funded by Plan Propio de Investigacion/Universidad de Granada; I.P.P is supported by grant FPU19/05561, funded by MCIN/AEI/10.13039/501100011033 and FSE El FSE invierte en tu futuro. A.P.F contribution was funded in part by NIH grant #: U01 TR002004 (REACH project). E.U.G is supported by the Maria Zambrano fellowship by the Ministerio de Universidades and the Union Europea NextGenerationEU. This work is part of a Ph.D. thesis conducted in the Biomedicine Doctoral Studies of the University of Granada, Spain.

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