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Improving Gut Health With Exercise

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Improving Gut Health With Exercise

In recent years we've seen evidence that alterations in the gut microbiome (the trillions of microorganisms that live in the gut) impact the risk for chronic health conditions. Physical inactivity is another factor contributing to health risk, with research showing inactivity to be associated with the development of 40 chronic diseases.

We know exercise is a healthy lifestyle practice, along with a healthy diet, that supports our overall health and well-being, reducing the risk of chronic disease. One potential mechanism by which exercise may benefit our health is its impact on the gut microbiome.

With 70 million Americans suffering from gastrointestinal disorders, gut health has our attention. In this article, we'll explore what kind of impact exercise has on the gut microbiome and overall gut health.


What is a Healthy Gut?

From the mouth to the bowel, gut health covers the well-being of the entire gastrointestinal system. This system's health largely depends upon the gut microbiome or the trillions of microorganisms that reside there.

Your gut is responsible for the digestion of food, absorption of nutrients, and various vitamins and nutrients produced by the gut microbiome. The gut contains 70-80% of the body's immune cells, it offers a mode of elimination of toxins and waste products, it communicates with and modulates aspects of the nervous system, and it has a very significant impact on our overall health.

From a Functional Medicine perspective, a healthy gut doesn't just mean the absence of disease. It means optimal structure and function. In this light, a healthy gut would include an intact mucus barrier and intestinal lining, normal immune and neurologic responses, normal digestive and absorptive processes, normal elimination, low inflammation, and a healthy microbiome.

A healthy microbiome includes diversity (a plethora of different types of beneficial strains of microorganisms) and consists of a higher abundance of these beneficial strains of microorganisms and less of the pathogenic strains of microorganisms. A healthy microbiome also shows signs of resistance and resilience. Resistance includes the ability to resist disruption by pathogenic strains of microorganisms, and resilience is the ability to return to a healthy state after experiencing disruption.

The microbiome is considered a key element not only regarding gut health but in regulating our overall health. So, taking actions that lead to a healthy gut will also have a positive impact on overall health.

Dysbiosis Signs & Symptoms

Dysbiosis is the term for a disruption in the microbiome. This occurs when an imbalance exists between the gut's beneficial and pathogenic (harmful) microorganisms.

Characteristics of dysbiosis include a decrease in the abundance of beneficial microbes, overgrowth of pathogenic microbes, and decreased microbiome diversity. Dysbiosis is also associated with increased gut lining permeability, often called "leaky gut." This increase in intestinal permeability produces an inflammatory response as microbes enter into circulation. Dysbiosis can lead to many signs and symptoms.

Gastrointestinal symptoms may include:

  • Gas
  • Cramping
  • Bloating
  • Diarrhea
  • Constipation
  • Belching
  • Bad breath (halitosis)
  • Nausea
  • Acid reflux
  • Vomiting
  • Abdominal pain
  • Food allergies or sensitivities
  • Mucus in the stool

Dysbiosis can also produce symptoms outside of the gastrointestinal tract. Some people experience symptoms like:

How Does Exercise Improve Gut Health?

The big question is, how does exercise improve gut health? The short answer is that exercise benefits gut health by increasing good bacteria, improving microbiome diversity, reducing inflammation, supporting the integrity of the gut lining, and improving gut function. We'll dive into the evidence below.  

Microbiome Diversity & Abundance

Exercise increases the abundance of the beneficial strains of bacteria in the gut. Women who exercised 3 hours per week had higher levels of health-promoting bacterial species, including Faecalibacterium prausnitzii, Roseburia hominis, and Akkermansia muciniphila. Two of these bacterial species (F. prausnitzii and R. hominis) are known to produce a short-chain fatty acid (SCFA) called butyrate. Butyrate is the primary source of fuel for the cells in the colon and has anti-inflammatory actions in the gut. A. muciniphila is a beneficial strain of bacteria that resides in the mucus layer of the gut and has been shown to positively impact metabolism, regulate immune function, and protect gut health.

This increase in beneficial strains of bacteria that result from moderate exercise represents an increase in microbiome diversity. This finding is confirmed by studies that found microbiome diversity to be higher in athletes than in sedentary individuals.

Inflammation & Bowel Function

Exercise reduces both systemic and intestinal inflammatory markers, reducing inflammation not just in the gut but throughout the entire body. Exercise also improves bowel function by improving colon transit time in women.

What Type of Exercise Improves Gut Health

Aerobic exercise is shown to increase the diversity and abundance of Firmcutes and Actinobacteria phyla, which contains the Lactobacillus and Bifidobacterium genera of bacteria, respectively, known to be vital to gut health.

A moderate amount and intensity of exercise, such as 3 hours per week, appears to provide the best results for gut health. As the intensity of exercise increases, the prevalence of gastrointestinal symptoms also increases, and exercise training to exhaustion is even associated with dysbiosis.

High-intensity exercise is associated with increased levels of stress hormones, such as cortisol, and a transient increase in gut permeability. This may explain the increase in gastrointestinal symptoms associated with higher-intensity bouts of exercise.

It should be noted, however, that individuals that exercise regularly (trained athletes) are shown to have lower levels of circulating bacterial endotoxin lipopolysaccharide, an inflammatory marker associated with increased gut permeability. This indicates that, when performed regularly, exercise acts as a beneficial stressor on the gut, which triggers beneficial adaptations that improve the long-term resilience of the integrity of the gut lining.

Research shows that when exercise is discontinued, changes in the microbiome revert back to baseline, indicating that exercise would need to be maintained as a lifestyle habit in order to have continued benefits for gut health.

How to Test Your Gut Health

Your Functional Medicine practitioner may order functional lab tests to understand the health of your gut microbiome and your overall gut health.

Comprehensive Stool Analysis

Comprehensive stool analysis testing provides an in-depth overview of the structure and function of the gastrointestinal system by providing information about digestion and absorption, inflammation, and microbiome analysis. The GI-MAP + Zonulin test by Diagnostic Solutions and the GI Effects® Comprehensive Profile from Genova Diagnostics both offer comprehensive stool analysis.

This article compares the top 4 comprehensive stool analysis tests to evaluate the gut microbiome and overall gut health.

Intestinal Permeability Testing

Testing for an increase in a protein called zonulin indicates whether there is an increase in the permeability of the gut lining. This increase in permeability of the gut lining is often referred to as "leaky gut." Zonulin can be measured in a comprehensive stool test or evaluated with a blood test. The Advanced Intestinal Barrier Assessment, or Advanced IBA, is a blood test that measures several markers associated with intestinal permeability, including zonulin.

SIBO Breath Test

A breath test may be ordered when disruption in the microbiome is suspected further up in the GI tract, in the small intestine. This test evaluates for small intestine bacterial overgrowth (SIBO). It is performed by drinking a sugar solution and measuring methane and hydrogen levels in the breath, collected in tubes at specified timing.


Regular physical exercise isn't only an excellent lifestyle practice for improving overall health and reducing risk for chronic disease. Exercise offers an exciting, attainable option for improving the gut microbiome and overall gut health.

Regular, moderate physical exercise supports beneficial changes in gut health by improving microbiome diversity, increasing the abundance of beneficial microbes, reducing inflammation, improving gut function, and even supporting the resilience of the integrity of the gut lining.

If you're looking for a way to support your gut health, talk to your healthcare practitioner about how you can make moderate physical activity part of your lifestyle!

The information provided is not intended to be a substitute for professional medical advice. Always consult with your doctor or other qualified healthcare provider before taking any dietary supplement or making any changes to your diet or exercise routine.
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Lab Tests in This Article


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