The Gut Microbiome Response to Exercise

The intestinal microbiome plays a vital role in a person’s systemic health and well-being, influencing the balance and performance of multiple organs and systems in the body.^1-5 And lifestyle factors from nutrition⁶ and fasting⁷ to sleep^8,9 and psychological stress¹⁰ impact gut composition and function. What about exercise? How does physical activity impact the gut microbiome and overall intestinal health? What are the known mechanisms, and how might understanding the gut microbiome’s response to different types and levels of exercise help to personalize therapeutic interventions that improve patient outcomes and optimize overall health?

From Sedentary Behavior to Athlete Training: Gut Health Impacts

For optimal health benefits, current guidelines encourage adults to move more and sit less throughout the day and recommend at least 150 to 300 minutes of moderate-intensity aerobic activity per week in addition to two or more days of muscle-strengthening activities per week.¹¹ Recent estimates indicate that only a quarter of US adults meet these exercise recommendations¹² and that people are sitting more often during their days due to a range of factors such as office work and more frequent leisure screen times.^13,14 Increased sedentary behavior (i.e., sitting or lying down for long periods) has consistently shown to be associated with an elevated risk of chronic disease development and rate of all-cause mortality compared to engaging in increased levels of physical activity.^15-17 Recently, more studies have specifically investigated the gut microbiome’s response to exercise in various populations from the extremes of sedentary adults to competitive athletes.

Although study population sizes have been small, results from recent clinical trials suggest that among sedentary adults, low to moderate-intensity exercise training interventions positively impact gut health components. A 2021 clinical trial (n=26 sedentary adults with insulin resistance; median age of 46 years) found that after a two-week intervention of either sprint interval training or moderate-intensity continuous training three times per week, intestinal inflammatory markers significantly decreased, including lipopolysaccharide binding protein (LPS), an indicator of endotoxemia, compared to baseline measurements.¹⁸ In addition, after the training interventions, gut microbiota profiles were significantly modified compared to baseline, with increased amounts of beneficial Bacteroidetes phylum, a decreasing Firmicutes/Bacteroidetes ratio, and decreased amounts of Clostridium genus.¹⁸ A 2021 pilot study (n=22 older sedentary adults; mean age 58 years; 95% male; mean BMI: 27.4) investigated the gut microbiome response to 24 weeks of an exercise regimen that progressed from low to either moderate or high-intensity physical activity routines that included both aerobic and resistance training conducted under supervision three times per week.¹⁹ At the end of treatment, compared to baseline measurements, the gut microbiota profiles indicated significant increases in beneficial Bifidobacterium, Oscillospira, and Anaerostipes and decreases in Prevotella and Oribacterium.¹⁹ Researchers also reported significant increases in the beneficial short-chain fatty acid (SCFA) butyrate after the exercise intervention compared to baseline.¹⁹

Research studies have also explored the gut health impact of training routines often undertaken by athletes. When comparing an athlete’s overall gut microbiome composition and function to that of a healthy non-athlete, a 2022 meta-analysis of metagenomics data found a higher abundance of anti-inflammatory, health-promoting, and SCFA-producing bacteria in athletes.²⁰ Yet, when investigating the acute gut microbiome response to exercise, some studies have also found that high-intensity exercise or endurance training resulted in an increase in intestinal lining damage and permeability.^21,22 Research continues to clarify the factors, from neuroendocrine to microbial to nutritional, that may be involved in any gastrointestinal distress experienced during or following endurance exercise in athlete and non-athlete populations.²³

Mechanisms: Explaining the Gut Microbiome Benefits of Exercise

Reducing intestinal transit and evacuation time,²⁴ influencing the gut-brain axis,²⁵ and increasing SCFA-producing commensal bacteria^26,27 are all suggested mechanisms that could describe how the gut microbiome responds to physical activity. After exercise interventions that have included moderate to vigorous-intensity aerobic exercise, clinical trials have indicated positive changes to the gut microbiota profiles of overweight and obese participants as well as those with type 2 diabetes.^28-30 Research suggests that the improved gut microbial profiles and increased SCFA production noted after some exercise treatments may be associated with improved insulin sensitivity by way of SCFA signaling to the glucose homeostasis mediator, GLP-1.³¹ Specific to obese children, a 2020 randomized controlled trial (n=39 obese children, 7 to 12 years of age) found that after a twelve-week strength and endurance combined training program, plasma glucose levels were reduced, improvements in the gut microbiota profile were noted, including changes in SCFA production, and the obesity-associated NLRP3 signaling pathway was significantly inhibited compared to controls.³² Echoing these results, a 2020 randomized controlled trial with adult participants (n=39 men with prediabetes) found that compared to controls, those who completed 12 weeks of high-intensity exercise training showed an altered gut microbiota profile, improved glucose homeostasis, and improved insulin sensitivity.³³ 

Specific to the gut-brain axis, the underlying details of the communication pathways impacted in response to exercise are not clearly defined; however, the proposed mechanisms center on exercise promoting gut microbiota diversity and increasing SCFA-producing bacteria that may further influence vagus nerve activation, modulation of neurotransmitter metabolism, reduction of intestinal permeability and systemic inflammation, and maintaining the integrity of the blood brain barrier.²⁵ To further this exploration of exercise and the gut-brain axis, research perspectives are also considering the connection between exercise, the gut microbiome, and neurodegenerative diseases and propose that, for example, the benefits of exercise seen in Parkinson’s disease treatments may be due in part to the restoration of the gut microbiota.³⁴

As research around the gut microbiome response to exercise develops, the prominent physiological pathways and molecular mechanisms will continue to be elucidated, and we may learn more about other potential health benefits due to the exercise-gut interaction such as cancer prevention,³⁵ aging,³⁶ and bone homeostasis.³⁷

Personalized Health Strategies & the Collaborative Therapeutic Intervention

As described above, incorporating regular physical activity from low to high intensities may benefit a patient’s gut and overall health, and low to moderate-intensity exercise programs may specifically be important and beneficial for those patients with insulin resistance and those who have low SCFAs. Exercise prescriptions that consider the gut microbiome response are among those functional medicine strategies that may be appropriate for a patient’s treatment or prevention plan. Different movement activities can easily fit into therapeutic interventions, and they can be fun for the patient. Personalizing treatments by aligning exercise programs with a patient’s preferences and goals helps patients achieve sustainable health improvements and positive lifestyle change. As research studies continue to explore the impact of different types, intensities, durations, and timings of exercise trainings on the gut microbiome,^38,39 new details will help to further inform personalized clinical interventions.

Within the functional medicine framework, practitioners collaborate with patients to develop personalized therapeutic strategies that are most beneficial for a patient’s conditions and concerns. The IFM Toolkit, available to IFM members, offers practitioners a wide range of tools and resources, including those specific to exercise, from setting exercise goals and tracking treatment progress to tips for increasing daily movement and sustaining an active lifestyle to resources for wearable fitness devices.

At IFM’s Gastrointestinal (GI) Advanced Practice Module (APM), learn from functional medicine experts about the latest gut microbiome research and how lifestyle-based clinical interventions impact gut health.