Researchers reveal how exercise-driven changes in gut microbes could influence recovery and propose a new “intestinal rehabilitation” approach for people with limited exercise capacity.
Study: The role of gut microbiome in exercise rehabilitation: current status and perspective. Image credit: PeopleImages/Shutterstock.com
A recent NPJ Biofilms and Microbiomes study reviewed the available literature and summarized current understanding of the interaction between exercise rehabilitation and the gut microbiome, examined potential mechanisms underlying exercise-induced microbial adaptation, and proposed microbiome-based interventions for personalized rehabilitation.
Exercise as a therapeutic intervention for non-communicable diseases
The high and growing prevalence of non-communicable diseases, including metabolic, cardiovascular, oncological, and neurodegenerative disorders, demands the development of safe, cost-effective, and integrative therapeutic solutions to improve clinical outcomes. Physical exercise stands out as a robust non-pharmacological intervention in this context.
Exercise-based rehabilitation enhances musculoskeletal function, restores performance post-injury, and improves cognition and mobility in neurological disorders such as spinal cord injury, stroke, multiple sclerosis, and Parkinson’s disease. Additionally, exercise offers notable benefits for obesity, diabetes, metabolic syndrome, cancer, and cardiovascular diseases.
While exercise reshapes the gut microbiota, particularly by increasing short-chain fatty acid-producing bacteria and enhancing microbial diversity, the precise molecular mechanisms linking these changes to clinical benefits remain unclear. This knowledge gap limits the optimization of exercise-based rehabilitation strategies. Addressing these unresolved mechanisms will be critical for advancing targeted interventions and forms the rationale for the present study.
How gut microbiota impact health
Gut microbiota refers to the diverse community of microorganisms residing in the human gastrointestinal tract, including archaea, bacteria, fungi, and viruses. These microbes are vital for physiological stability, pathogen protection, immune regulation, and nutrient metabolism.
The dominant bacterial phyla are Firmicutes and Bacteroidetes, with smaller amounts of Actinobacteria, Proteobacteria, and Verrucomicrobia. The balance of these groups is linked to health. Gut microbes, such as Lactobacilli, Bacteroides, and Bifidobacteria, produce metabolic enzymes essential for nutrient absorption and breakdown. Their metabolites, like short-chain fatty acids (SCFAs) and bile acids, regulate metabolic processes and maintain homeostasis.
Disruptions in the gut microbiota, particularly the overgrowth of Enterobacteriaceae like Escherichia coli, are associated with multi-organ diseases and inflammation. Studies highlight that certain beneficial microbes, especially those involved in fiber fermentation and butyrate production, play a crucial role in health.
Lifestyle, diet, medications, disease, genetics, and immune function influence gut microbiota composition. It changes across the lifespan. For example, previous studies highlight that animal-based diets increase bile-tolerant species and decrease plant polysaccharide-metabolizing Firmicutes, while high-fat diets raise deoxycholic acid levels and disease risk. In obese mice, studies have reported reduced Bacteroidetes and increased Firmicutes.
Plant-based diets, like the Mediterranean diet, promote beneficial gut bacteria, support symbiosis, and strengthen gut homeostasis by increasing short-chain fatty acid production, which supports tissue repair and reduces inflammation.
Effects of exercise on gut microbiota
Exercise supports health and fitness by beneficially shaping the gut microbiome, with both intensity and type of activity playing a central role. Endurance sports such as running, cycling, and swimming increase gut microbial diversity and promote beneficial bacteria like Veillonellaceae, Bacteroides, Prevotella, Methanobrevibacter, and Akkermansia. These microbial shifts have been associated with pathways involved in nutrient metabolism, muscle function, and immune regulation, although the effects of many individual taxa remain poorly characterized.
Moderate- to high-intensity aerobic exercise can produce some of the most pronounced changes in the gut microbiome, raising levels of Bifidobacterium, Akkermansia, and butyrate producers, improving the Bacteroidetes/Firmicutes ratio, and enhancing overall microbial diversity. This is linked to better metabolic control, glucose tolerance, and reduced inflammation. However, very intense exercise may temporarily disrupt gut barrier function and increase inflammation. In mouse studies, voluntary exercise appears more favorable for gut health than forced exercise, which can increase inflammatory responses.
The benefits of exercise-induced shifts in the gut microbiota extend across multiple health conditions. For example, in obesity, exercise lowers harmful Proteobacteria and increases beneficial Blautia and Roseburia, improving metabolism. Clinical studies show that exercise programs in obese children increase beneficial bacteria and lead to healthier metabolic profiles, while animal studies suggest a causal role: microbiota transplantation from exercised mice has been associated with reduced body weight in one model and improved insulin resistance in another.
Endurance exercise also promotes SCFA producers that may help reduce atherosclerosis and support cardiovascular health. Furthermore, regular physical activity protects against intestinal inflammation, cancer, and neurodegenerative diseases, with evidence for milder colitis, reduced cancer risk, and improved cognitive function: all associated with favorable changes in gut microbial communities. Collectively, these findings suggest that gut microbiome changes may contribute to exercise's wide-ranging health effects across several diseases.
Optimizing recovery through intestinal rehabilitation
Intestinal rehabilitation highlights the gut microbiota's essential role in achieving the full benefits of exercise-based recovery. A healthy and diverse gut microbiome helps regulate systemic inflammation, metabolic health, and disease outcomes, making its restoration a key rehabilitation goal, especially for patients with impaired gut or systemic health.
The authors propose that this approach could involve structured exercise, either alone or combined with dietary and microbiome-targeted strategies, to restore gut microbial balance, reinforce epithelial barrier function, and promote the production of beneficial metabolites such as SCFAs. Their proposed implementation begins with a baseline assessment, followed by interventions stratified by exercise capacity and ongoing monitoring for individualized adjustment.
The framework encompasses two main categories. First, intestinal rehabilitation could enhance standard exercise programs. In people with obesity, type 2 diabetes, fatty liver disease, or metabolic syndrome, adding microbiome-targeted strategies to physical activity may improve glucose control, lipid profiles, and vascular function. For patients with neurological disease or cancer, preclinical and emerging evidence suggests such approaches could potentially support cognitive health or anti-tumor responses. Second, for those with restricted mobility, such as post-surgical patients, the frail elderly, or those with advanced heart, lung, or neurological conditions, the proposed framework includes gut-targeted strategies such as dietary and probiotic interventions aimed at mitigating dysbiosis, inflammation, and frailty.
The authors identify several candidate biomarkers that could be used to assess intestinal rehabilitation. Improvements in alpha and beta diversity, changes in the Firmicutes/Bacteroidetes ratio, and increases in beneficial bacteria such as Akkermansia muciniphila may indicate microbiome resilience. Functional markers such as higher SCFA levels, reduced trimethylamine N-oxide (TMAO), and favorable tryptophan metabolites reflect organ-specific benefits. Additional markers, including zonulin, calprotectin, and secretory IgA, assess intestinal barrier integrity, while lower TNF-α, IL-6, and CRP, along with improved homeostasis model assessment of insulin resistance (HOMA-IR) and lipid profiles, indicate systemic benefit.
Personalized intervention is key. The proposed framework emphasizes moderate regular exercise, a high-fiber, low-saturated-fat diet, and adequate hydration. Combining diet and exercise, especially with Mediterranean or fiber- and polyphenol-rich eating patterns, may yield synergistic effects. Probiotic supplementation may support gut health in some settings, but benefits are not universal, and interventions should be individualized and closely monitored.
By broadening the scope of traditional rehabilitation, the authors propose intestinal rehabilitation as a potentially adaptable and tailored strategy for a wide range of patients, including those unable to engage in standard exercise. Continued research will help refine these strategies, identify optimal biomarker panels, and evaluate long-term safety and efficacy in diverse populations.
Conclusions
The current scientific evidence suggests that the gut microbiota may play an important role in mediating the health benefits of exercise, suggesting that “intestinal rehabilitation” may be a promising preventive and therapeutic approach. Exercise-induced changes in the gut microbial ecosystem have been linked to improved disease outcomes and overall health, reinforcing the importance of considering the microbiota in exercise-based interventions.
However, several limitations constrain the strength and applicability of these findings. Most studies focus on healthy, active individuals, with limited data for patients with chronic diseases or mobility impairments. Methodological heterogeneity, difficulty isolating exercise effects from confounding factors, and reliance on observational data further limit causal inference and generalizability.
Future research should prioritize standardized protocols, rigorous control of confounding variables, and inclusion of diverse populations. Integrating multi-omics technologies and exploring personalized approaches could enable targeted exercise prescriptions and combined interventions.
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