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This review examines how exercise influences the gut microbiome and its implications for health and performance.

May 16, 2026Open Access

Exercise and the Gut Microbiome: From Mechanisms to Clinical Applications

Key Points

This review examines how exercise influences the gut microbiome and its implications for health and performance.
Systematic search of PubMed, Scopus, Web of Science, and SID for articles from January 2000 to February 2025.
Included 89 studies (47 human, 42 animal) focusing on exercise and gut microbiome effects.
Critical appraisal of studies to evaluate mechanisms and clinical applications.
Exercise enhances gut microbiome diversity, particularly increasing butyrate-producing taxa such as Faecalibacterium prausnitzii and Roseburia hominis.
High-intensity interval training initially raises intestinal permeability but leads to increased butyrate production post-adaptation.
Causal relationships established in animal models; human trials show individual responses to exercise on gut microbiome.

Abstract

Background/Objectives: The gut microbiome is a critical regulator of host metabolism, immunity, and the gut–brain axis. Exercise is a promising non-pharmacological modulator of microbial ecology, yet human evidence remains heterogeneous and the translational gap persists. This narrative review synthesizes mechanisms, human and animal evidence, and future directions for the exercise–gut microbiome axis. Methods: PubMed, Scopus, Web of Science, and SID were searched for articles published between January 2000 and February 2025. Keywords included exercise, physical activity, gut microbiome, gut microbiota, short-chain fatty acids, and gut–muscle axis. From 218 initial records, 89 original studies (47 human, 42 animal) met inclusion criteria and were critically appraised. Results: Exercise modulates the gut microbiome via splanchnic hypoperfusion, hyperthermia, altered transit time, and immune-mediated barrier regulation. Moderate-intensity continuous training consistently increases alpha diversity and enriches butyrate-producing taxa (Faecalibacterium prausnitzii, Roseburia hominis) and mucin-degrading Akkermansia muciniphila. High-intensity interval training transiently increases intestinal permeability in untrained individuals but, following adaptation, stimulates butyrate production via lactate cross-feeding metabolism—a recent breakthrough. Effects are transient and reversible upon detraining. Animal models establish causality through fecal microbiota transplantation; human randomized controlled trials demonstrate modest, intensity-dependent, and highly individualistic responses. Emerging evidence supports the gut–muscle axis in sarcopenia and personalized exercise prescription guided by microbiome profiling. Conclusion: Exercise shows promise as a low-cost modulator of the gut microbiome for enriching health-associated taxa and improving metabolic outcomes. Definitive evidence linking exercise-induced microbial shifts to enhanced athletic performance in humans remains lacking. Future research requires diet-controlled randomized controlled trials with ≥12-week interventions, shotgun metagenomics, and mechanistic validation of the gut–muscle axis in humans.

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