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February 13, 2022 10 min read

Science only recently begun to appreciate the human gut as a complex ecosystem of bacteria, archaea, eukaryotes, and viruses that have co-evolved with humans over thousands of years. Known collectively as the gut microbiota, these microbes are imperative to host digestion, metabolic function and resistance to infection [1].

It’s really incredible when you think about the metabolic capacity of the human gut microbiota. There are over 1000 different unique bacterial species and over 3 million unique genes [2].

Collectively, the sum of the microbial genes in the gut is called the gut microbiome.

The microbiome eats what you eat, it gets stressed when you do, and now science demonstrates that the composition and functions of your gut bacteria are enhanced by exercise and physical activity.

First, let’s look at some microbiome basics before diving into the exciting findings about physical exercise.

Essentially, your gut bacteria belong in an ecosystem that also includes some yeasts and other microscopic creatures. Many important functions for human health are performed but your gut bacteria such as breaking down food molecules into nutrients that complement the physiological functions of the human body.

Your gut bacteria produce fatty acids, vitamins, and amino acids that have a range of beneficial effects for the body, from promoting healthy immune system function to maintaining gut lining integrity.

The Relationship Between Gut Microbiome and Exercise

When we live a healthy life, we form a symbiotic relationship with our microbes. Essentially, we give these single-celled organisms a home and they in turn work hard alongside us!

A diverse microbiota profile is associated with enhanced vitamin and short-chain fatty acid production, dietary fiber metabolism and even increased disease protection.

The microbiome influences nutrition, metabolic health, and immune system function among other things, including the human brain.

So, it wasn’t much of a stretch when scientists considered the possibility that exercise can also influence our microbiome. Diversity is a key factor for measuring microbiome health, and this ecosystem is made up of hundreds of species. 

On the other hand, dysbiosis is how we describe a poor or imbalanced ecosystem that can’t adequately do its job. When dysbiosis affects the gut, the communities of beneficial and benign bacteria that typically make up the microbiota are altered which leads to digestive symptoms and conditions.

How Your Gut Health Impacts Muscle Growth & Recovery

It’s well established in the scientific community that the gut microbiota influences host health in part due to its co-evolvement with the host to meet mutually beneficial biochemical and biological needs [3].

There are many studies investigating how the gut microbiota influences the liver and intestinal metabolism, immunity, and behavior, however there are not many studies demonstrating how the gut microbiota regulates skeletal muscle, one of the dominant metabolic organs in the body.

It was recently shown that the gut microbiota contributes to skeletal muscle mass and function in mice. Germ-free mice (multi-cellular organisms that have no microorganisms living in or on them) displayed reduced muscle mass and signs of muscle atrophy and reduced muscle strength. Essentially, it was shown that protein degradation exceeded protein synthesis, which in part could contribute to the reduced skeletal muscle mass observed in these germ-free mice [4].

Gut microbes synthesize amino acids and make them available to the host [5].

Analyses of the skeletal muscle, liver, and serum metabolites revealed altered amino acid metabolism in germ-free mice. BCAA catabolism, which is associated with skeletal muscle protein breakdown, correlated with low leucine and valine concentrations in liver tissue and serum of germ-free mice.

BCAAs not only serve as an alternate energy substrate but also improve nitrogen retention and protein synthesis [6].

They represent the major nitrogen source for alanine synthesis in muscle.

Before their use as fuel and being fed into the tricarboxylic acid cycle, BCAAs undergo a series of transamination steps eventually resulting in production of alanine. High quantities of alanine observed in the skeletal muscle of GF mice thus might be a consequence of muscle protein breakdown resulting in increased bioavailability of amino acids to cope with the stress generated by the absence of a gut microbiota.

Many interactions between the host and its gut microbiota are mediated by short-chain fatty acids generated from the bacterial fermentation of dietary polysaccharides. Research indicates that short-chain fatty acids support skeletal muscle function by preventing atrophy and increasing muscular strength.

However, the diverse biosynthetic activity of the gut microbiota beyond providing short-chain fatty acids to be used by the host as an energy source may explain why short-chain fatty acids supplementation alone could not fully rescue the impaired muscle phenotype in germ-free mice. Microbes and their metabolites are likely to engage multiple pathways to regulate muscle growth and function. Microbial products other than short-chain fatty acids might also be involved in skeletal muscle growth and function

Additional research is needed to identify specific bacterially produced metabolites or other microbial products that influence skeletal muscle growth and function. In summary, this research has demonstrated the existence of a gut microbiota–skeletal muscle axis that opens the way for further mechanistic and physiological studies that will lead to a better understanding of mechanisms regulating this important metabolic organ.

How Exercise Can Impact Gut Microbiome

Emerging research indicates that exercise influences gut microbiota.  Multiple animal studies show that exercise training independently alters the composition and functional capacity of the gut microbiota [7].

Early research demonstrated that exercise training increased the bacterial metabolite butyrate.

Since then, several other studies replicated this finding. Butyrate is a short-chain fatty acid produced from the bacterial fermentation of dietary fiber. Butyrate is the main source of fuel for the cells of the gut lining, helping to maintain its integrity, reduce inflammation, and prevent organic compounds from foods, toxins, and metabolites from crossing into the bloodstream. It also helps regulate the host immune system [8].

Longitudinal studies (i.e., a research design that involves repeated observations of the same variables over short and/or long periods of time) in humans show that several taxa were differentially altered by exercise depending on body mass index status.

For instance, Bacterioides species decreased in the lean subjects and increased in obese subjects. Six weeks of exercise increased the abundance of butyrate-producing taxa and fecal acetate and butyrate concentrations, but only in lean subjects. Interestingly, most bacterial taxa and short-chain fatty acids that increased with exercise subsequently decreased during the 6-wk sedentary washout period that followed. This tells us that the effects of exercise on the microbiota are both transient and reversible.

Another study investigated whether endurance exercise could affect the gut metagenome in previously sedentary overweight women. Six weeks of moderate intensity cycling increased the relative abundance of A. muciniphila and a decrease in Proteobacteria (a major category of Gram-negative bacteria).

Together, this evidence indicates that exercise has independent effects on the gut microbiota, but longer duration or higher intensity aerobic training may be required to induce significant taxonomic and metagenomic changes. Furthermore, the microbiota of lean individuals may be more responsive to an exercise intervention than that of overweight or obese individuals.

How Gut Health Impacts Mental Health

The gut microbiota also has been implicated in mental health and cognition, and the existence of a gut-brain axis is well established [9].

Metabolites of the gut-microbiota have been sown to activate receptors on the enteric nervous system (i.e., the system of neurons that governs the function of the gastrointestinal tract), and certain microbes also are capable of producing neurotransmitters. For example, Lactobacilllus species can produce both serotonin and gamma-aminobutyric acid (GABA) [10].

Serotonin is thought to play a role in emotion and cognitive functions, and low levels have been linked to depression. GABA is the chief inhibitory neurotransmitter in the central nervous system and typically has anti-anxiety and relaxant effects.

Gut dysbiosis may also contribute to impaired mental health.

Patients with major depression have an altered gut microbiota, characterized by changes in the relative abundance of Firmicutes, Bacteroidetes, and Actinobacteria [11]. 

Interestingly, transferring fecal material from these patients into germ-free rodents presents depression-like behavior in the recipient rodent model [11].

Research has demonstrated that patients with a depressive or anxiety disorder had a unique predicted gut metagenomic profile and increased levels of plasma markers of intestinal permeability.

It's well known that exercise has benefits for mental and neurological health and it is plausible that some of these benefits of exercise on the brain are mediated by the gut microbiota.  For example, an hour of daily exercise increased the relative abundance of Lachnospraceae, a family of known butyrate-producing microbes, which was negatively correlated with anxiety-like behavior [7]. 

Butyrate itself has been shown to upregulate brain-derived neurotrophic factor expression in the brain of mice, which helps to support the survival of existing neurons and encourage the formation of new neurons and synapses. Butyrate also has been shown to regulate the activation of microglial cells, a specialized population of immune cells in the brain [12].

Similar to exercise, butyrate also seems to increase neuroplasticity and has anti-depressant activity, boosting brain serotonin levels [13].

How to Improve Gut Health (Diet & Exercise Tips)

Diet Tips

It is clear that our dietary habits strongly impact our gut microbiota composition. Therefore, diets characterized by a high content of sugars and fats and low content of fiber, have been linked with a decrease in community diversity, permanent loss of bacteria and dysbiosis [14].

Conversely, high fiber diets, including fruits, vegetables, legumes, and whole grain products, can increase microbial diversity [15].

Shifts in the microbial community in response to different factors impair the symbiotic relationship between pathogenic and nonpathogenic bacteria, potentially causing the onset of a proinflammatory state, and gut dysbiosis, with health implications [16], such as autoimmune and allergic conditions, colorectal cancer, metabolic diseases [17].

The best advice for diet is to eat whole foods that contain a lot of fiber along with fruits, vegetables, legumes and whole grain type carbohydrates.

Probiotics influence on gut microbiome

Probiotics are defined as “a preparation of or a product containing viable, defined microorganisms in sufficient numbers, which alter the microbiota (by implantation or colonization) in a compartment of the host and by that exert beneficial health effects in this host” [18].

Until recently, the beneficial effects demonstrated after probiotic consumption were immune modulation and strengthening of the gut mucosal barrier.

The mechanisms included:

  • Modifications of gut microbial composition
  • Dietary protein modifications by the microbiota
  • Modification of bacterial enzyme capacity
  • Physical adherence to the intestinal mucosa that may outcompete a Pathogen or inhibit its activation
  • Influence on gut mucosal permeability [19]

Probiotic use has been tested for different potential health effects on athletes. The figure below summarizes the reported effects of probiotic ingestion by athletes or individuals practicing moderate physical exercise.

Fig: Reported effects of probiotic ingestion by athletes or subjects practicing moderate physical exercise. [20]

Altogether, these results show that probiotics may improve oxidative or inflammatory markers but have no proven effect on performance. Potential new generation probiotics, first identified in elite athletes' microbiome undergoing exercise, have recently shown promising results in mouse performance models [21].

These bacteria belonging to the Veillonella genus feed on lactic acid and produce propionate, which may potentially increase endurance capacity.

Exercise Tips

Several studies indicate a relationship between microbiota composition and cardiorespiratory fitness that can account for more than 20% of the variation in “taxonomic richness” which is the diversity of bacteria identified in the microbiome.

Cardio is about going long and steady, ensuring the supply of oxygen to your muscles so they can create fuel (ATP). This includes any exercise that gets your heart rate up and keeps it up for a prolonged period of time. It’s recommended to get the World Health Organization’s for cardiovascular exercise and enhance your microbiome.

These recommendations are:

  • Should do at least 150–300 minutes of moderate-intensity aerobic physical activity


  • At least 75–150 minutes of vigorous-intensity aerobic physical activity; or an equivalent combination of moderate- and vigorous-intensity activity throughout the week.

There’s much more to learn in order to extend our knowledge on the exercise-microbiome connection.

One crucial area in need of further research consists in assessing the possible effects of exercise-induced gut microbiota alterations on skeletal muscle parameters, including muscle structure, mass, strength and function, and muscle metabolism that ultimately affect both skeletal muscle health and physical performance. 

We know that several diet-derived compounds produced or modified by gut microbes can enter the systemic circulation and ultimately influence skeletal muscle cells, such as short-chain fatty acids, amino acids, secondary bile acids, polyphenols and vitamins [22]. 

In recent years, studies in animals and humans have confirmed a positive role of exercise in shaping a healthy gut microbiota, possibly contributing to enhanced human health and, also, physical performance.


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Dr. Paul Henning

About Dr. Paul

I'm currently an Army officer on active duty with over 15 years of experience and also run my own health and wellness business. The majority of my career in the military has focused on enhancing Warfighter health and performance. I am passionate about helping people enhance all aspects of their lives through health and wellness. Learn more about me