Sports nutrition is not just about fueling muscles.

By Rafal Nazarewicz. Ph.D. 

Athletes usually think about the gut in practical terms: absorption, tolerance, and bathroom risk on race day. Calories in, watts out. However, physiology reveals a more complex narrative.

Your gut is not just a digestive tube. It is a metabolic, immune, and signaling organ that directly shapes endurance, recovery, and even injury risk.

For athletes, gut health is the foundation of their performance.

Why gut health matters for athletes

About 70 percent of the immune system is associated with the gut. That matters because intense training already creates controlled stress, inflammation, and immune suppression. When the gut barrier is compromised, inflammatory signals leak into circulation and compete with recovery.

The gut also regulates how efficiently carbohydrates are absorbed and delivered to the muscle. Transporters like SGLT1 and GLUT5 are influenced by diet composition and gut integrity. A healthy gut improves carbohydrate uptake, reduces GI distress during exercise, and stabilizes blood glucose, all of which support sustained output.

There is also the gut-brain axis. Microbial metabolites such as short-chain fatty acids influence neurotransmitters, stress hormones, and fatigue perception. In endurance sports, perceived effort can be as limiting as muscle glycogen.

Ultra-processed foods and the athletic gut

Ultra-processed carbohydrates are often used in sports nutrition for convenience and shelf stability. But the form of carbohydrate matters, especially with repeated use.

Highly refined ingredients like dextrins, corn syrup, and rice syrup are rapidly absorbed glucose polymers with little structural complexity. From a metabolic perspective, they spike blood glucose efficiently. From a gut perspective, they do very little else.

Research shows that diets high in ultra-processed carbohydrates can reduce microbial diversity and lower production of beneficial short-chain fatty acids like butyrate. These fatty acids help maintain the gut barrier and regulate inflammation. Low butyrate levels are associated with increased intestinal permeability, often called leaky gut.

Dextrins are partially hydrolyzed starches. While they are easy to digest, their rapid absorption means minimal interaction with the microbiota. Over time, this can shift the gut ecosystem toward fewer beneficial bacteria and more inflammation-associated species.

Corn syrup and rice syrup are primarily simple sugars with trace micronutrients removed during processing. Studies in both humans and animal models show that frequent intake of refined sugars increases gut permeability and endotoxin translocation, especially when combined with exercise-induced heat and mechanical stress on the intestine.

During long or intense training, blood flow is diverted away from the gut. This makes the intestinal lining more vulnerable. When ultra-processed sugars dominate fueling, the gut receives high osmotic loads without protective compounds like soluble fiber, polyphenols, or natural fats that slow absorption and support the mucosal layer. The result is a higher risk of cramping, bloating, and inflammation during and after exercise.

What the science points to instead

Whole food-based carbohydrate sources contain small amounts of soluble fiber, organic acids, and bioactive compounds that interact with gut microbes and the intestinal lining. These components help moderate absorption speed, support microbial diversity, and maintain barrier function without sacrificing energy availability.

This does not mean athletes should avoid carbohydrates. It means the source and processing level of those carbohydrates matter, especially when used daily.

Performance is not just about fueling muscles. It is about protecting the system that delivers that fuel.

When the gut works with you, not against you, everything else performs better.

Laudisi F, et al. The Food Additive Maltodextrin Promotes Endoplasmic Reticulum Stress-Driven Mucus Depletion and Exacerbates Intestinal Inflammation. Cellular and Molecular Gastroenterology and Hepatology (2019). 

The impact of dietary fructose on gut permeability, microbiota, and endotoxemia-related pathways.Heliyon (2023).

Ultra-processed food intake, gut microbiome, and metabolic inflammation (prediabetes/T2D context).Cell Metabolism (2024)

Liu P, et al.The role of short-chain fatty acids in intestinal barrier function, inflammation, oxidative stress, and metabolic diseases.Pharmacological Research (2021).

van Wijck K, et al.Physiology and pathophysiology of splanchnic hypoperfusion and intestinal injury during exercise.American Journal of Physiology Gastrointestinal and Liver Physiology (2012).