Athlete Gut Microbiome

What’s Going On Inside Your Gut?

What is your gut microbiome? How does it work? And how does it affect your WOD and systemic health? Here are some answers to those questions and more.

Unit 2 of 7

Your gut microbiome is a vast ecosystem of microorganisms, composed of bacteria, viruses, fungi, and protozoa that call your gastrointestinal system home. This web of life, which has been with you since birth, interacts with your immune system, brain, and many other organs — and those systems interact back with it, too. This all has enormous implications on your systemic health as a human, let alone as a CrossFit athlete.

So if you want to be comprehensive when it comes to your health, it would be wise to ask: How does all of this work, and how can I support it?

What Is The Gut Microbiome?

Your gastrointestinal tract — that’s your mouth, esophagus, stomach, small intestine, large intestine, and anus — is “the most populated organ in your body,” when it comes to microorganisms. Your colon, or large intestine, in particular, is home to a vast ecosystem of microbes, just as rich in specialized organisms as a rainforest. This is your gut microbiome, and it is complex and brimming with life.

Within and around the intestinal crypts (not the burial kind but the space between the microscopic finger-like projections with enormous surface area to absorb and exclude) and mucus layers of your colon, billions of microbes are constantly eating, reproducing, and interacting with each other and your body’s vital systems. A field called microbiology studies these microorganisms, their interrelationships, and their environment. Today, scientists are studying the gut microbiome closer — and in more detail — than ever, giving us exciting answers about why our guts work (and don’t work) the way they do.

Eubiosis, Dysbiosis: Working Hard or Hardly Working?

What does it mean to have a healthy gut? Scientists have come up with a word for this state,  “Eubiosis,” meaning it contains “a great number of microbial species living in balance by adopting mutualistic strategies.” “Mutualistic” in this case means that both humans and microbes benefit. 

When the denizens of your gut are in eubiosis, scientists compare your intestines to an “anaerobic bioreactor,” where armies of microorganisms break down the polysaccharides (those are long chains of carbohydrates made up of sugars) that our body can’t digest — AKA dietary fiber. While the microbiome is diverse, and includes microbes that are not always beneficial to human health, an eubiotic gut microbiome is mostly made up of species that have the potential to be beneficial to human life. Both the microbiome and your gut stay happy and demonstrate something scientists call the “Nash Equilibrium” (originated by Nobel Prize winning mathematician John “Beautiful Mind” Nash) — when none of the components of an ecosystem are advantaged by changing its strategy. (Keep calm and carry on.) Think of a gut in eubiosis as riding smoothly along on rails. Everything is gravy, baby. (Yum.)

That is not the case when your gut microbiome is in dysbiosis — the opposite of eubiosis, when bacteria in your gut no longer live in mutual harmony with each other or your body. The term was coined by Elie Metchnikoff, a 1908 Nobel Prize-winning Russian zoologist and immunologist (some consider him the father of probiotics…) who believed disease began in the digestive tract when “good” bacteria no longer controlled “bad” bacteria. 

We now know it’s more complex than that. A ton of influences — both environmental and genetic — can cause dysbiosis. It’s even true that some microbes seek out and thrive in dysbiotic environments, like the strains of E. coli that promote inflammation in the gut, and prosper in inflamed environments. This means that your body’s reaction to bad microbes can actually make dysbiosis worse — an unhealthy gut spiralling out of control.

The Gut Connection

Your gut is not a vacuum, and an enormous ecosystem of tiny life can’t live inside you without communication and interaction with your body. Studies show your microbiome plays an important role in the health of your gut, particularly by maintaining the integrity of your intestine’s epithelial barrier, to keep you from experiencing the symptoms of “leaky gut,” when increased permeability allows pathogens and pro-inflammatory molecules to enter your bloodstream.

But that’s not all! Many studies suggest that your gut microbiome influences the function (and dysfunction) of major organ systems in the body. These “axes” appear to be a two-way street: your gut microbiome affects your body, and your body affects your gut microbiome.


Take for instance your skin. Numerous studies have linked GI health to the skin’s ability to stay healthy or return to health after dysfunction. Disorders of the GI system are often accompanied by skin problems. A review article from Imam Salem et al. states that “the GI system, particularly the gut microbiome, appears to participate in the pathophysiology of many inflammatory disorders.” And remember “Leaky Gut,” when intestinal bacteria and their fragments escape the GI tract and enter the bloodstream? Scientists have found those microbes and their metabolites may accumulate in the skin, where they disrupt cutaneous homeostasis. Short-chain fatty acids (SCFAs), a byproduct of microbial fermentation of fiber in the gut, are believed to be important in influencing the skin’s immune defense mechanisms. It’s just more proof of that old chestnut: “You are what you eat.”


You’re at the job interview. It’s stressful to wait, and you’re nervous, and then — do you really have to go now? Yep. Your gut microbiome also communicates with your brain, and vice versa, through the “gut-brain axis.” Your central nervous system (brain and spinal cord) and enteric nervous system (a system of neurons in the intestines) link emotional and cognitive centers of your brain with your intestinal functions. Think of those nervous butterflies ascending to your brain, and back. One infamous gut-brain axis link was discovered decades ago, when oral antibiotics delivered to the GI tract were found to dramatically improve the health of patients suffering from hepatic encephalopathy, a disorder of the nervous system, liver, and brain. New research data supports the role of microbiota in anxiety and depressive-like behaviors. And the connection needn’t be caused by systemic or enduring health problems: one study in mice showed being exposed to social stresses for just two hours caused significant changes to the gut microbiome’s community profile.

Skeletal Muscle

And new findings about how skeletal muscle mass also appears affected by the gut microbiome are important for CrossFit athletes. Previous studies using germ-free (lacking a gut microbiome) mice appeared to show that upon being administered with gut microbes, they decreased in whole-body lean mass (not what the gut-conscious CrossFit athlete wants to hear) — preliminary evidence that gut microbes may shape body composition. More recently, animal studies suggest that several important species of microbes found in the gut appear to benefit building skeletal muscle mass and performance. In one, Lactobacillus casei or Bifidobacterium longum supplementation increased the mass of select leg muscle groups, swimming endurance, and grip strength in older mice without affecting body weight. SCFAs—those important acids produced by gut microbes as they ferment fiber—appear to play a role. And seven separate studies in 2019 connected the gut microbiome and physical functioning, including muscle strength and endurance. In short: It might not have been spinach that made Popeye’s muscles pop — it might’ve been the microbes doing the digesting.

What Impacts My Gut Microbiome Health?

A long list of different environmental and lifestyle factors impact your gut. (Genetics, by the way,   play a role in your microbiome’s makeup, too.) Here are a few to consider:

Drug Metabolism & Gut Health

Your gut microbiome has emerged as an enormous factor in the metabolism of “xenobiotic compounds” (chemical substances that are foreign to animal life), for instance therapeutic drugs. The mechanisms of microbial drug metabolism remain unclear, but some recent studies have focused in on specific human gut bacteria to study the drug-metabolizing enzymes they produce, and their wider effect on the body. One important drug-microbiome interaction is that of NSAIDs and your gut: studies have shown that these non-steroidal anti-inflammatory drugs, beyond just punching holes in the lining of your physical gut, can directly influence the makeup and function of an individual’s gut microbiome, precipitating dysbiosis. 

Exercise & Gut Health 

A single high-intensity workout can disrupt your gut. Studies like this one show that 60 minutes of endurance exercise, or just 30 minutes of resistance exercise, can cause damage to the epithelial lining that covers more than 4,000 feet of your small intestine’s surface area and, unsurprisingly, plays an important role in digestion. That’s partly why athletes who work out longer and harder have an increased risk of symptoms like cramps, diarrhea, bloating, nausea, and intestinal bleeding. 

Sleep and Recovery & Gut Health 

Simply waiting a little longer to consume carbs and protein after a workout might help your gut digest and absorb more important nutrients. A healthier gut microbiome may produce more lactate, an SCFA that, contrary to long-held belief, is an important part of your body’s fueling/recovery process during and after workouts. And sleep studies like this one show that how much rest you get can directly affect the makeup and function of your gut microbiome — no surprise, given the strength of the gut-brain axis.

Probiotics and Prebiotic & Gut Health

It makes perfect sense that probiotics — live microorganisms that, when administered in adequate amounts, confer a health benefit on the host — and prebiotics — a substrate that is selectively utilized by host microorganisms, conferring a health benefit — could make your gut microbiome happier. That, after all, is what makes them probiotics and/or prebiotics. A number of studies show this, and we’ll dig into their science in our next units.

Food & Gut Health 

You are what you eat, right? A number of studies have examined the effect of diet on the gut microbiome. (It’s worth noting that the vast majority of human studies have measured only fecal microbiota, to use as a presumed surrogate of the microbe makeup that was very recently in your intestines and colon; this means that when scientists say “gut microbiota,” they are almost always referring to fecal microbiota.)  Both your long-term diet and short-term changes in that diet appear to affect the structure and activity of your gut microbiome. This study showed that switching to a plant-based or animal-based diet (and associated increases in fiber, and protein and fat, respectively) can broadly and uniformly alter the gut microbiota within a few days. That makes sense, because many microbes living in our gut ferment non-digestible fiber to use as fuel. So next time you’re buying groceries, remember that you’re cooking for trillions of dinner guests.

Curiosity is rewarded.

If you are reading this, we have a challenge for you—take this quiz. Correct answers may earn you (what we call at Seed) magic.

Also Check Out…

The Microbiome and Your WOD (Unit 1)

Podcast: Planting the Seed for a Healthy Microbiome 


About the Author:

Anthony L. Almada, MSc, FISSN is a member of the research and development team at Seed, which develops probiotics to impact human and planetary health. He is trained as a nutritional and exercise biochemist (UC Berkeley). He has been a co-investigator on over 50 university-based clinical trials exploring the effects of diet, dietary supplements, and therapeutic interventions upon muscle performance, body composition, whole body metabolism, and joint function in health and disease. In 1990 he created the “thermogenic” category. In 1993 he co- founded the first company to introduce creatine monohydrate to North America. He has worked with CF Games and Regional athletes, top Olympic gold medal swimmers, professional cyclists, physique athletes, and NFL teams. He has been part of Seed’s R&D division since late 2018.