The human gut consists of both beneficial and pathogenic species, with the most diverse and abundant amounts being found in the colon. Microbiota diversity largely depends on the diet and lifestyle of the host.  Gut microbiota (both beneficial and pathogenic) have specific fuel preferences, and if available, they will flourish. Beneficial microbiota are best fueled by polysaccharides and amino acids.  In return, they help the host maintain a normal glycemic response to food, regulate energy metabolism, and produce acetate, butyrate, and propionate – the small-chain fatty acids that help keep colonocytes healthy (Kårlund et al., 2019).

Athletes have higher protein requirements, and it is very common for them to eat high protein diets (Kårlund et al., 2019).  The World Health Organization recommends 0.83 g/kg body weight per day for the average person. However, for strength and endurance athletes, the American College of Sports Medicine recommends 1.2-2g/kg body weight per day (Moreno-Pérez et al., 2018).  Higher protein is required for the athlete to:

  • maintain protein synthesis (Kårlund et al., 2019)
  • produce energy during exercise (Kårlund et al., 2019)
  • protect the immune system (Kårlund et al., 2019)
  • maintain gut health during intense exercise (stress conditions) (Kårlund et al., 2019)
  • maintain nitrogen balance (Moreno-Pérez et al., 2018)
  • maintain muscle mass maintenance during exercise and/or caloric deficits (Moreno-Pérez et al., 2018)
  • improve athletic performance (Moreno-Pérez et al., 2018)

Because of their higher-than-normal protein requirements, athletes are more likely to consume a high protein diet.  Supplements like whey protein powder are often used to help increase daily protein intake due to its fast absorption and easy digestion. In high-protein diets, however, more undigested protein waste ends up in the colon which causes more bacterial amino acid metabolism. This can either be a positive or negative factor depending on whether the host is capable of processing and using the small-chain fatty acids that are produced. In other words, the health and makeup of the host’s gut determine how effectively protein is digested, absorbed, and used (Kårlund et al., 2019).

Gut microbiota is linked to both health and chronic disease (Bressa et al., 2017). The study of gut microbiota and intestinal health is a quickly developing field.  As a hot topic in the field of functional medicine, new research is being published rapidly. As it relates to athletes, research availability is not as plentiful despite the fact that more athletes now supplement with probiotics and prebiotics in order to experience greater health benefits (Kårlund et al., 2019).  The research that does exist seeks to explain the impact of the athlete’s diet and physical activity on the athlete’s gut microbiota.  It does so by making comparisons between sedentary and active people, by testing fecal specimens of athletes on special diets, and by testing the fecal specimens of athletes involved in intense exercise.

Gut microbiota has the potential to be very helpful to health.  Intestinal microbiota may help boost immune system functioning, digest food, produce nutrients, protect the body from pathogenic microorganisms, produce the small chain fatty acids that colonic cells need in order to flourish (Colbey et al., 2018).  It also helps the body produce compounds like tryptamine, serotonin, phenethylamine, histamine, all of which help with neurological health (Moreno-Pérez et al., 2018).  Additionally, there is two-way communication between muscle fibers and gut microbiota.  Gut microbiota prevents fat accumulation in and around the muscle.  Simultaneously, during exercise, muscle releases myokines that promote microbiota growth (Moreno-Pérez et al., 2018).

On the other hand, problems with intestinal microbiota have the potential to contribute to many health problems, including intestinal diseases, obesity, and metabolic syndrome

Low gut microbiota diversity is linked to low dietary diversity (Colbey et al., 2018).  Problems with intestinal gut microbiota are often referred to as gut dysbiosis – an imbalance of beneficial and pathogenic bacteria.

While it’s unclear whether gut microbiota dysbiosis is a cause of disease or a consequence of disease, gut dysbiosis is associated with many chronic diseases (O’Sullivan et al., 2015).  Fortunately, probiotic and prebiotic interventions have helped resolved some of those chronic diseasesProbiotics and prebiotic supplementation may be an effective strategy in improving levels of beneficial gut microbiotaThe efficacy of probiotics depends on the host’s level of physical activity, the strain of the probiotic, and the form of the supplement (Colbey et al., 2018).   Scientists are still trying to establish a baseline on healthy gut microbe balance (Bressa et al., 2017).

It has been postulated that physical exercise can modify microbiota density and composition.  Several studies have been published to determine the effects of diet and/or exercise on gut microbiota. 

  • Exercise was induced in lab rats and gut microbiota was assessed post-exercise (Bressa et al., 2017). 
  • 40 premenopausal Caucasian women ages 18-40 years old, were separated into two groups (sedentary versus active), stool was collected, microbiota was analyzed, and participants were classified into enterotype groups (Bressa et al., 2017).
  • Professional rugby players (and a control group) provided stool samples. Metabolic phenotyping and metagenomic analysis of gut bacteria was conducted. (Barton et al., 2018).
  • 18 male endurance athletes ages aged 18-45 who were in training for a race were divided into two groups. Eight were provided a maltodextrin supplement once per day over 10 weeks, and 10 were provided a whey isolate & beef hydrolysate mix supplement once per day over 10 weeks. Then fecal and urine samples were collected to assess gut bacteria, the production of small-chain fatty acids, and levels of ammonia (Moreno-Pérez et al., 2018).
  • 21 male elite race walkers beginning an intense training period were divided into three diet test groups (high carbohydrate, periodized carbohydrate, keto), and baseline and post-diet/training stool samples were collected (Murtaza et al., 2019).
  • 33 cyclists aged 19-49 with no major medical issues, no antibiotic use the previous year, and who all ate high carbohydrate diet provided fecal samples which were assessed (Petersen et al., 2017)
  • The Irish international professional rugby football team provided stool samples while participating in training camp.  These samples were compared to others from two control groupsalow BMI group of non-professional athletes, and a high BMI group of non-professional athletes (O’Sullivan et al., 2015)

Research by Karlund (2019), suggests no changes in the microbiota in a high protein diet unless paired with exercise. Upon pairing, the microbiota is increased. It must be noted that protein digestion capability depends on the age, health, and microbiota diversity of the host, so benefits may not be realized by everyone.  Some may experience side effects of a high protein diet, to include abdominal pain, bloating, foul-smelling gas, and occasional diarrhea.  These side effects are related to excessive protein metabolism and amino acid fermentation in the colon (Kårlund et al., 2019).  

In endurance race runners, 20 grams of protein supplementation (whey & beef) resulted in decreases in beneficial gut bacteria. However, the supplementation did not increase ammonia despite higher protein intake. It also had no effect on the microbiota’s production of small-chain fatty acids (Moreno-Pérez et al., 2018).

21 male elite race walkers were divided into three diet sample groups.  The high carbohydrate group and the periodized carbohydrate group both experienced improved race performance and increased speed.  There were no significant changes in total gut microbiota or diversity of either of those groups.  The low carbohydrate group (followed a ketogenic diet) experienced the highest rates of fat oxidation during exercise.  However, they also had a significant reduction in beneficial fecal bacteria and an increase in pathogenic bacteroides. This may be due to the increase in bile acid secretion into the gut commonly associated with a high-fat diet (Murtaza et al., 2019).

Effects of training on microbiota

In a study of lab rats, wheel running was found to increase gut microbiota (Lactobacillus strains) in healthy rats that had been exposed to environmental toxinsExercise in obese rats with hypertension also increased gut microbiotaIt must be noted that exercise affected the microbiota in younger rats more than older rats (Bressa et al., 2017). 

When the microbiota of professional athletes was compared to sedentary individuals, athletes had increased amounts of microbe-produced short-chain fatty acids in the stool.  This shows a larger number of microbiota in athletes.  The differences between athletes’ and sedentary individuals’ microbiota were attributed to greater muscle synthesis in the athletes (due to exercise) and better overall health than the control group(Barton et al., 2018).  In a similar study that compared active women to sedentary women, there was not an increased number of bacteria among active women, but there was increased biodiversity among active women (Bressa et al., 2017).

Fecal samples were collected from 33 cyclists aged 19-49.  Each followed a relatively high carbohydrate diet.  Samples showed low amounts of pathogenic bacteria and larger levels of bacteria diversity (Petersen et al., 2017).  There is no way to tell whether this is the result of diet or physical activity.

Other lifestyle factors like stress, sleep, and environmental toxins impact gut health.  In the research included in this review, the only researchers that included other lifestyle factors were those involved in the Barton study of professional rugby players (2018). 

It appears that athletes tend to have a better developed and more diverse gut microbiome than non-athletes (O’Sullivan et al., 2015). It also appears that endurance athletes tend to have less developed gut microbiota than strength and power athletes (Bressa et al., 2017).  It cannot be determined if the differences are a result of training, a result of the high protein/high carbohydrate diets commonly consumed by athletes, a combination of diet and training, or some other factors. There are some controlled trials and observational studies, but none specific enough to draw definitive conclusions.  More research is needed to determine the effects of exercise on the health and diversity of the athlete’s gut microbiota.


Barton, W., Penney, N. C., Cronin, O., Garcia-Perez, I., Molloy, M. G., Holmes, E., … O’Sullivan, O. (2018). The microbiome of professional athletes differs from that of more sedentary subjects in composition and particularly at the functional metabolic level. Gut, 67(4), 625–633.

Bressa, C., Bailén-Andrino, M., Pérez-Santiago, J., González-Soltero, R., Pérez, M., Montalvo-Lominchar, M. G., … Larrosa, M. (2017). Differences in gut microbiota profile between women with active lifestyle and sedentary women. PloS one12(2), e0171352. doi:10.1371/journal.pone.0171352

Colbey, C., Cox, A. J., Pyne, D. B., Zhang, P., Cripps, A. W., & West, N. P. (2018). Upper Respiratory Symptoms, Gut Health and Mucosal Immunity in Athletes. Sports medicine (Auckland, N.Z.)48(Suppl 1), 65–77. doi:10.1007/s40279-017-0846-4

Kårlund, A., Gómez-Gallego, C., Turpeinen, A. M., Palo-Oja, O. M., El-Nezami, H., & Kolehmainen, M. (2019). Protein Supplements and Their Relation with Nutrition, Microbiota Composition and Health: Is More Protein Always Better for Sportspeople? Nutrients11(4), 829. doi:10.3390/nu11040829

Moreno-Pérez, D., Bressa, C., Bailén, M., Hamed-Bousdar, S., Naclerio, F., Carmona, M., … Larrosa, M. (2018). Effect of a Protein Supplement on the Gut Microbiota of Endurance Athletes: A Randomized, Controlled, Double-Blind Pilot Study. Nutrients10(3), 337. doi:10.3390/nu10030337

Murtaza, N., Burke, L. M., Vlahovich, N., Charlesson, B., O’ Neill, H., Ross, M. L., … Morrison, M. (2019). The Effects of Dietary Pattern during Intensified Training on Stool Microbiota of Elite Race Walkers. Nutrients11(2), 261. doi:10.3390/nu11020261

O’Sullivan, O., Cronin, O., Clarke, S. F., Murphy, E. F., Molloy, M. G., Shanahan, F., & Cotter, P. D. (2015). Exercise and the microbiota. Gut microbes6(2), 131–136. doi:10.1080/19490976.2015.1011875

Petersen, L. M., Bautista, E. J., Nguyen, H., Hanson, B. M., Chen, L., Lek, S. H., … Weinstock, G. M. (2017). Community characteristics of the gut microbiomes of competitive cyclists. Microbiome5(1), 98. doi:10.1186/s40168-017-0320-4

Explore More

Is There Really a Such Thing as “Leaky Gut?”

July 1, 2017 0 Comments 0 tags

Is there such a thing as increased intestinal permeability as a pathophysiological state (aka “leaky gut”)? Based on my research, I must conclude that there is indeed such a thing

Therapeutic Benefits of Cinnamon

May 27, 2017 0 Comments 0 tags

The cinnamon tree can be traced to origins in China and India and has unique characteristics. The tree can grow to be over 25 feet tall, with trunks growing up

Why do people with IBS do well on the low FODMAP diet?

July 12, 2018 0 Comments 0 tags

FODMAPs (an acronym for “fermentable oligosaccharides, disaccharides, monosaccharides, and polyols) are short-chain carbohydrates.   They are difficult for the small intestines to absorb, so they are fermented by the microbiota in