Gut Bacteria and a Theory for Everything

 In Nutrition

A few years ago my family and I visited the Costa Rican Jungle. While on a nature hike, we observed a lethargic three-toed sloth foraging for food high in the canopy of a Cecropia Tree. My son took particular note of the dark-green algae that had covered the fur on his back. A simple camouflage at first glance, that algae also served a much more benevolent purpose; it serves as the sole feeding ground for several species of moth. The sloth and the moss and the moth interact peacefully in a functioning symbiotic manner. The very important corollary that I discussed with my son, “No sloth, no moss….no moth”—symbiosis.

Such relationships exist throughout nature, including humans. Despite these relationships taking thousands (and perhaps) millions of years to cultivate, we know surprisingly little about one very important one in humans—that is the relationship between the bacteria in our Gastro-Intestinal (GI) Tract and how its existence (or lack there-of) affects us. Researchers have linked gut bacteria to many important facets of human life including immune function, digestion, metabolism, even mental health. It is not a stretch to think that many more links exist. Learning more about the bacteria living rent-free in our GI tract could provide valuable insight into human health and disease, sport and athletic performance, illness, and recovery and so much more. Even more fascinating, is that the food and bacteria you eat can have a direct impact on who’s living in your gastro-intestinal zip-code and from that—we birth the Probiotic industry with its dozens of fancy bacteria’s, varying doses, and spurious health claims.

Your GI tract microbiome is incredibly important to your health. Modifying your dietary intake with consideration for these organisms and their symbiotic relationship with our species may not only make you feel better but train and race better too. To take advantage of the possibility of improved health and athletic performance, we need to delve into the world of bacteria.

My Soapbox

As a consumer and athlete, you exist at the intersection of knowledge, discovery and creative genius paired against dogma, doctrine, and emotion. Human nature prefers a quick fix, we are quickly distracted by neon-lit ideas funded by bitcoins and hyperbole. We must remember to learn from our history, that scientific rigor replaced cardiac-knowledge (listen to what your heart is telling you sans proof). The world is flat; the earth is the center of the universe; vaccines cause autism; we faked the moon landing; and most definitely, you should be eating Keto.

Discovery is a peculiar thing. As a society, we are all too often, quick to reject the results of scientific discovery, on the grounds that it might upset our sensibility of current understanding. If you want real discovery, real invention, truly unique ideas, it requires not that you think “outside the box”…but that you think “without a box.” And thus our story of Gut Microbiota begins.

A Common Language

Words matter. Before we have an informed discussion, we need accurate vocabulary. The gastrointestinal tract refers to the tube that connects your lips to your anus. There’s a lot going on in that tube, but for this discussion, we are interested in the bacteria that live there, and in particular, your small and large intestines. The collection of those bacteria and other living things in your intestines (like a virus, etc.) are referred to as Microbiota or your living gut microbiome. The term Probiotic refers to any live microorganism, taken in adequate amounts, to confer a health benefit to the host.

On the label of many probiotics, you’ll see the term Colony Forming Units or CFUs. CFUs refer to the number of bacteria on a probiotic label, often written as either 1 Billion or equally as 1×109 and this is important to know because recommendations for how much of a probiotic you might want to take can be written as something like “take at least 5 Billion CFUs” or possibly as “consume at least 5×109 colony-forming units.” Both of these statements are equal.

Probiotics and What we Know Today

Probiotic science is fairly new, with numerous scientific studies that offer some incredibly fascinating findings! Some specific probiotic strains have been shown to beneficially impact the GI tract leading to impactful benefits to immune function (think athletes not getting sick!), digestion (such as break down of proteins), and reduction in oxidative stress (think quicker recovery). One interesting but not a well-studied possibility is the difference between males and females when it comes to our microbiome. Stay tuned for more research in this area.

On the cutting edge and not yet well defined are possible beneficial links to Probiotics and chronic fatigue syndrome (CFS), emotional symptoms, anxiety, depression, and even mood. This link between our gut microbiome and our physical and mental health is important enough that every athlete should be paying attention.

The type and amount of bacteria consumed matters. Bacteria differ, so benefits from one type of bacteria may not be seen with another. There are no “agreed upon” dietary recommendations for Probiotics, so shopping for them (like shopping for many supplements) can feel a bit like trying to throw a ring on a bottle at that popular carnival game—toss the ring, who knows what you’ll get or if you’ll win—the only sure thing is it costs you some money.

This is probably a good point to mention that in reality, more than just bacteria live in your gut; viruses, fungi, and others have also taken up residence. Although the microbiome is stable in adults, many factors can affect it, including diet, antibiotics, consumption of probiotics, and exercise/fitness. So what are those little guys doing in your intestines?

They aren’t freeloading—that’s for sure! In fact, many of those bacteria can metabolize food into nutrients and energy for our use. Many specific bacterial strains have demonstrated health benefits like those mentioned previously. You’ve probably heard of a few of them, they include Lactobacillus, Bifidobacterium, Saccharomyces, Enterococcus, Streptococcus, Pediococcus, Leuconostoc, Bacillus, and Escherichia coli (Fijan S, 2014). Lactobacillus is a particularly interesting bacteria as it has been found to be associated with improving Type 2 diabetes mellitus, reducing the incidence of obesity-related metabolic diseases, regulating blood pressure, and exerting anti-inflammatory and anti-oxidation effects (Huang W, 2019).

Speaking of Athletic Performance

Through current research, we understand how a healthy microbiota might affect an athlete and how an athlete can ensure a healthy microbiome. Athletes are different. Recent studies indicate exercise can beneficially alter the gut microbiome, which is associated with increased health parameters and possibly improve athletic performance.

A systematic review on endurance exercise and gut microbiota (Mach N, 2017) illustrated that gut microbiota might have a key role in controlling oxidative stress/inflammatory responses as well as improving metabolism and energy expenditure during intense exercise. Specifically, elite athletes that train and compete for long periods experience physical and emotional stress that is driven by both hormones in the endocrine system and response in the nervous system. This is a particularly interesting area of research and the link between healthy gut bacteria and exercise-induced stress is an area you should keep your eye on.

Another important relationship is that between gut bacteria and mood, fatigue, insomnia, and depression associated with exercise-induced stress. Many athletes are well aware of the vicious cycle of overtraining, competition, fatigue and ultimately decreased performance. Although the possible relationship is complicated and well described by (Clark A, 2016), simply put, the gut microbiota serves as an endocrine organ, facilitating the production and regulation of many hormones and neurotransmitters.

Making a case for diet and a nutrition coach

We know that the food you consume can heavily affect your microbiota composition and function AND we know that a healthy microbiota may improve the stress response in athletes and improve performance. Importantly, the consumption of a mostly animal or mostly plant diet can dramatically change the gut microbiota (David LA, 2014). Vegetarian athletes will appreciate that link.

Fermentation Foods

Fermented foods enriched with Lactobacillus (yogurt, some bread, wine, sauerkraut, etc.) and Bifidobacteria (yogurt, kombucha, sauerkraut, kefir, etc. ) can result in positive changes to the gut microbiome and possible improvements in stress symptoms, depression, mood, and even some digestive disorders. A non-complete list of fermented foods that you might consider consuming to increase your gut health include: yogurt (live culture), sauerkraut, Japanese fermented/pickled vegetables, cocoa, fermented bean paste, fish sauce, kimchi, kombucha, miso, sour cream, Korean traditional soy sauce, Tabasco sauce, and tempeh. A good, qualified nutrition expert can help you determine the most efficient way to add such foods into your nutrition plan. In particular, a board-certified sports dietitian can help you address your microbiome health by increasing the consumption of fermented foods.

Probiotic Supplementation

Probiotic supplementation is highly variable depending on the strain and microbiota composition and there are no established dietary recommendations for either dosages or strains in athletes. In a recent study by Keaney and colleagues, the authors discuss Olympic athlete recommendations and strategies for preventing illness at the 2020 Tokyo Summer Games and provide some excellent evidence-based recommendations (Keaney LC, 2019):

Probiotic: Non-Refrigerated (travel-friendly), multi-strain, combining Lactobacillus and Bifidobacterium.

Dosage: 1×109 colony forming units (CFUs) per day.

Additional recommendations are provided in the paper available at: and in the World Gastroenterology Organization (WHO) guidelines on Probiotic use (Table 8) available at:

Probiotic Selection and Use

For individuals with compromised immune function or other serious underlying diseases, the World Gastroenterology Organization (WGO) advises restricting probiotic use to the strains and indications that have proven efficacy. Other than the WGO, no other expert organizations of health professionals have made specific and detailed recommendations for or against probiotic use by healthy individuals. For athletes and people with various health conditions, published studies and reviews provide some guidance on probiotic species and doses that might alleviate symptoms and promote health benefits.

Probiotic supplement users should check the labels of probiotic supplements for recommended storage conditions; for example, some require refrigeration, whereas others can be stored at room temperature The International Scientific Association for Probiotics and Prebiotics advises manufacturers to list the total number of CFUs—ideally for each strain—on the “expiration” or “use by” date on the product label. The association also suggests that consumers of these supplements avoid products that list the number of CFUs “at the time of manufacture” because this information does not account for declines in CFUs over a product’s lifespan.

Wrapping it all up

Your GI tract microbiome is incredibly important to human health. In particular, the relationship between the microbiome and immune modulation, GI tract disorders, overtraining symptoms, and exercise-induced stress are of particular interest to athletes. You can positively affect your gut microbiota by regular consumption of fermented foods, so drink up that Kombucha and enjoy some Kimchi the next time you eat Korean food, add life-culture yogurt to your snacks, and consider some good sauerkraut. Supplementing with probiotics is a more complicated area since no recommendations have been made and the actual type of bacteria matters. As with most nutrition-related dietary interventions, your best bet as an athlete or consumer is to ask an expert for assistance and the best expert in nutrition is a credentialed dietitian, and in this case, perhaps one board-certified in sports dietetics.

References for Further Reading

Barton, W., Penney, N., Cronin, O., Garcia-Perez, I., Molloy, M., Holmes, E., . . . O’Sullivan, O. (2017). The microbiome of professional athletes differs from that of more sedentary subjects in composition and particularly at the functional metabolic level. Gut, 67;625-633.

Clark A, M. N. (2016). Exercise-induced stress behavior, gut-microbiota-brain axis and diet: a systematic review for athletes. J Int Soc Sports Nutr, 13:43.

Clarke, S., Murphy, E., O’Sullivan, O., Lucey, A., Humphreys, M., Hogan, A., . . . al., e. (2014). Exercise and associated dietary extremes impact on gut microbial diversity. Gut, 63; 1913-1920.

David LA, M. C. (2014). Diet rapidly and reproducibly alters the human gut microbiome. Nature, Jan 23; 505(7484):559-63.

Fijan S. (2014). Microorganisms with Claimed Probiotic Properties: An Overview of Recent Literature. Int. J. Environ. Res. Public Health, 11:4745–4767.

Guarner F, M. J. (2003). gut flora in health and disease. Lancet, 361(9356):512-519.

Huang W, W. C. (2019). The Beneficial Effects of Lactobacillus Plantarum PS128 on High-Intensity, Exercise-Induced Oxidative Stress, Inflammation, and Performance in Triathletes. Nutrients, 11(2):353.

Keaney LC, K. A. (2019). Keeping Athletes Healthy at the 2020 Tokyo Summer Games: Considerations and Illness Prevention Strategies. Front Physiol, 10:426.

Mach N, F.-B. D. (2017). Endurance exercise and gut microbiota: A review. J Sport Health Sci, Jun; 6(2):179-197.

Petersen, L., Bautista, E., Nguyen, H., Hanson, B., Chen, L., Lek, S., . . . Weinstock, G. (2017). Community characteristics of the gut microbiomes of competitive cyclists. Microbiome, 5;98.

Wosinska L, C. P. (2019). The Potential Impact of Probiotics on the Gut Microbiome of Athletes. Nutrients, 11(10); 2270.

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