Exercise-Driven Remodeling of the Gut Microbiome: Reciprocal Regulation of Structural and Functional Adaptations in Elite Athletes

The gut microbiome plays a critical role in training adaptation and athletic performance. Athletes exhibit elevated gut microbial α-diversity and enrichment of short-chain fatty acid (SCFA)-producing genera, although these associations may be confounded by dietary and lifestyle factors. Exercise regulates the gut microbiota in a non-linear, intensity-dependent manner: moderate-intensity training preserves intestinal barrier integrity, whereas high-intensity exercise exceeding 85% of maximal oxygen uptake may precipitate dysbiosis, although this remains to be directly validated. Periodized training drives sustained microbial remodeling, with adaptive changes persisting for months in ultra-endurance athletes. Mechanistically, exercise enhances SCFA synthesis, remodels bile acid and tryptophan metabolism, and modulates host energy homeostasis and inflammatory status through AMPK, FXR/TGR5, and epigenetic pathways. In turn, the microbiota exerts bidirectional effects on skeletal muscle mitochondrial function, central fatigue, and post-exercise recovery via the gut–muscle, gut–brain, and immune axes. Probiotic and dietary interventions show translational promise, yet their application is constrained by strain-specific efficacy and the absence of standardized protocols. Finally, we propose the Microbiota-Exercise Threshold-Adaptation-Reconsolidation (METAR) hypothesis framework, which stratifies putative microbiota responses into three intensity-defined zones and three athlete subtypes, providing a testable foundation for precision training that awaits empirical validation.