More than two‑thirds of your immune system sits along your intestinal wall, and the very gels and drinks athletes rely on to finish a marathon can either strengthen that defence or punch holes straight through it. In other words, your immune resilience is inseparable from the microbes you feed.

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Endurance athletes put their bodies through a great deal. Hours of training, travel to races, and exposure to crowds all place stress on the immune system. A growing body of research shows that one of the most powerful levers athletes control is what they eat. Far beyond calories and macros, a diverse plant‑rich diet feeds the trillions of microbes in the gut. These microbes in turn influence the integrity of the intestinal barrier, the development of regulatory immune cells and the inflammatory tone throughout the body. In contrast, high-sugar supplements and ultra-processed foods (UPFs), which dominate much of modern sports nutrition, may undermine both the microbiome and immunity. The interaction between diet and the gut microbiome highlights why taking probiotics alone is insufficient and how common endurance fuels can contribute to “leaky gut” and impaired recovery.

The gut–immune axis: microbes as guardians of the barrier

The gut is lined by a single layer of epithelial cells, covered by a layer of mucus. It is here that the majority of the body’s immune cells sample antigens, learn what is friend and what is foe, and initiate immune responses. Commensal microbes help train this system. When dietary fibres reach the colon, they are fermented into short‑chain fatty acids (SCFAs) such as acetate, propionate and butyrate. These metabolites serve as the main energy source for colonocytes, stimulate mucin production and strengthen tight junctions between cells [1]. Adequate SCFA production fosters a thick mucus layer that keeps microbes at a safe distance and induces regulatory T cells, helping to prevent inappropriate inflammation [1].

When fibre intake is low, however, mucin‑degrading bacteria switch from plant carbohydrates to host glycans. In mouse models, fibre deprivation led to erosion of the mucus layer and increased susceptibility to pathogens [1]. A similar erosion appears to occur in humans consuming Western diets high in saturated fat and simple sugars. These diets favour bile-tolerant bacteria, such as Bilophila wadsworthia, while suppressing fibre-fermenting species, including Roseburia and Eubacterium rectale [3]. The shift in microbial metabolism reduces SCFA production and increases the production of inflammatory bile acids. Chronic exposure to saturated fats and refined carbohydrates also disrupts tight junction proteins, compromising barrier integrity [1]. This sequence, loss of fibres, loss of protective microbes and metabolites, and barrier breakdown- sets the stage for systemic immune activation.

Food shapes the microbiome: fibre, polyphenols and animal products

Research over the past decade has underscored how rapidly dietary changes can alter microbial communities. In a controlled crossover study, participants consumed a plant‑rich diet for several days and then switched to an all‑animal diet comprised of meats, cheeses and eggs. Within 24 hours of the meat diet, the abundance of bile‑tolerant organisms such as Alistipes and Bilophila increased while fibre‑fermenting species diminished [3]. These changes correlated with higher fecal bile acids and markers of inflammation. The authors noted that the Western diet—high in fat and sugar and low in fibre has fundamentally altered the human microbiome and likely contributes to obesity and inflammatory diseases [3].

Fibre is not a single entity but a family of non‑digestible carbohydrates. Soluble fibres from oats, legumes, and psyllium feed butyrate‑producing bacteria, while resistant starches in cooked and cooled potatoes or green bananas support species such as Ruminococcus bromii. Polyphenol‑rich foods, such as berries, cocoa, coffee, and red wine, are metabolised by microbes into bioactive compounds that dampen inflammatory pathways. Traditional diets rich in these substrates support diverse communities dominated by Prevotella and Bacteroidetes, whereas diets dominated by refined grains, sugars, and fats select for pathobionts [3].

Ultra‑processed foods and sports nutrition products: hidden threats to the microbiome

Ultra‑processed foods are formulations of isolated nutrients, added sugars, industrial fats and additives designed for convenience and shelf life. A 2024 narrative review summarised clinical trials in which participants consumed fast‑food diets for as little as four days. The diet dramatically increased bile‑tolerant bacteria like Collinsella, Parabacteroides and Bilophila while reducing fibre‑fermenting Lachnospiraceae and Butyricicoccus [2]. Ready‑to‑eat military rations caused similar shifts and altered the fecal metabolome, increasing saturated fatty acids and decreasing plant‑derived compounds [2]. The same review emphasised that many sports drinks, gels and supplements count as UPFs because they are composed of isolated sugars, flavourings and emulsifiers [2]. Even though they may be fortified with vitamins or electrolytes, their nutrient profile and additive load can induce dysbiosis and increase intestinal permeability.

Food additives appear to be particularly problematic. Emulsifiers (such as polysorbate 80 and carboxymethylcellulose), artificial sweeteners and synthetic colourings are common in convenience foods and sports nutrition. Animal and human studies show that these compounds thin the mucus layer, promote growth of mucin‑degrading microbes and increase inflammatory responses [2]. Mice fed these emulsifiers develop low-grade inflammation and metabolic syndrome, effects that are abolished in germ-free animals, indicating that the microbiome mediates the damage. For athletes who rely on processed sports bars and gels, frequent exposure to these additives may compromise gut health over time.

Why probiotics are not a panacea

Given the marketing around probiotic supplements, it is tempting to think that swallowing a capsule can fix diet‑induced dysbiosis. However, most commercial strains belong to the genera Lactobacillus and Bifidobacterium, which transiently pass through the gut. A 2014 review highlighted that probiotic supplementation increases the abundance of these taxa in the short term, but the overall composition of the microbiota remains largely unchanged and often returns to baseline after supplementation stops [5]. While specific strains have documented benefits—such as reducing antibiotic‑associated diarrhea or improving lactose digestion—there is scant evidence that generic mixtures substantially alter an athlete’s microbiome.

Feeding the indigenous microbes appears to be far more powerful than trying to seed new ones. Prebiotics such as inulin, fructo‑oligosaccharides and resistant starch selectively stimulate beneficial bacteria and increase SCFA production. Fermented foods like kefir, sauerkraut and kimchi deliver live cultures along with substrates and bioactive compounds. But even these foods cannot compensate for a diet devoid of fibre and rich in refined sugars. The principle is simple: probiotics need groceries. Without ample fermentable carbohydrates and polyphenols, introduced microbes struggle to survive and the existing community shifts towards pathobionts.

Training, gut permeability and “leaky gut”

Endurance exercise itself imposes stress on the gastrointestinal tract. During prolonged running or cycling, blood flow is diverted toward working muscles and skin, leading to ischemia in the gut. Core temperature rises and the epithelial barrier becomes stressed. A review on endurance exercise and the gut noted that strenuous exercise increases intestinal permeability, reduces mucus thickness and allows endotoxins from Gram‑negative bacteria to enter circulation, a phenomenon often called “leaky gut” [6]. These endotoxins trigger systemic inflammatory responses that can impair recovery and increase susceptibility to infections.

Nutrition plays a pivotal role in exacerbating or mitigating exercise‑induced gastrointestinal symptoms (GIS). High‑osmolality carbohydrate drinks and gels, typically containing >10 % simple sugars, slow gastric emptying and draw water into the intestinal lumen. In a clinical study of endurance athletes, beverages with osmolality greater than 500 mOsm kg⁻¹ were strongly associated with nausea, cramping and diarrhea [7]. High intake of concentrated carbohydrate gels correlated with flatulence and abdominal discomfort. These symptoms not only hamper performance but may further disrupt the mucosal barrier. Athletes often reduce fibre and fat intake before competition to minimise GIS [4]; however, chronically restricting fibre deprives microbes of their substrates and can exacerbate barrier dysfunction.

High‑sugar sports products may also directly feed opportunistic microbes. When large amounts of simple sugars reach the distal small intestine and colon, they can fuel growth of Proteobacteria and Candida species. Combined with additive‑induced thinning of the mucus layer and exercise‑induced ischemia, this can create a perfect storm of dysbiosis and leaky gut. The resulting endotoxemia elevates pro‑inflammatory cytokines, suppresses mucosal immunity and increases the risk of upper respiratory tract infections—common complaints among endurance athletes during heavy training blocks.

Practical strategies for athletes

1. Prioritise whole plant foods every day. Aim for 30 or more different plant foods per week, including vegetables, fruits, whole grains, legumes, nuts and seeds. Diversity provides a range of fibres and polyphenols that support a diverse microbiome and robust SCFA production.

2. Train your gut with low‑glycemic carbohydrates. Instead of relying exclusively on highly concentrated gels, incorporate sources of complex carbohydrates such as ripe bananas, cooked potatoes, rice balls or low‑FODMAP whole‑food bars during long training sessions. Practice fueling strategies during training to increase the gut’s carbohydrate absorption capacity while minimising osmolality. Hydrate with lower‑sugar electrolyte drinks (<6 % carbohydrate) to reduce GI distress [7].

3. Include fermented foods and prebiotics, not just probiotics. Regularly consume unsweetened yogurt, kefir, sauerkraut, kimchi or tempeh. Supplement with prebiotic fibres like inulin or partially hydrolysed guar gum under the guidance of a sports dietitian. Recognise that probiotic capsules alone are unlikely to overhaul your gut; they work best when paired with a fibre‑rich diet [5].

4. Limit ultra‑processed sports products. Use gels and drink powders strategically for high‑intensity efforts or races, but do not base everyday fueling on UPFs. Read labels for emulsifiers, artificial sweeteners and synthetic colouring agents. Where possible, opt for real foods and homemade alternatives.

5. Support recovery and immunity with rest and nutrient timing. Consume carbohydrate and protein within an hour after hard sessions to replenish glycogen and support muscle repair. Include sources of omega‑3 fatty acids (fatty fish, walnuts, flaxseeds) and micronutrients (vitamin C from citrus and peppers, zinc from beans and shellfish) that support immune function. Adequate sleep, stress management and periodisation of training are equally important for maintaining gut integrity.

Conclusion

The gut microbiome sits at the intersection of nutrition, immunity and performance. When athletes feed their microbes with a varied, plant‑rich diet, the microbes reward them with SCFAs, a strong mucosal barrier and balanced immune responses. Conversely, excessive consumption of ultra‑processed foods and high‑sugar sports products can degrade the microbiome, compromise barrier function and contribute to the fatigue and illness that plague many endurance athletes. Probiotics can be useful adjuncts but are no substitute for a diet that consistently delivers fibre and polyphenols. By aligning fuelling strategies with microbiome health—both during training and at the dinner table—athletes can support their immune system and performance for the long run.

References

1. Falchi, A., Rossi, M., et al. Influence of foods and nutrition on the gut microbiome. Nutrients 2022, 14, 4414. This review explains how short‑chain fatty acids derived from fermentable fibres increase mucin production and strengthen tight junctions, whereas simple sugars and emulsifiers thin the mucus layer and promote dysbiosispmc.ncbi.nlm.nih.gov.

2. Monteiro, C. A., Martinez-Steele, E., et al. Ultra‑processed foods: A narrative review. Nutrients 2024, 16, 1024. Clinical trials summarised here show that fast‑food diets rapidly increase bile‑tolerant bacteria and reduce fibre‑fermenting speciespmc.ncbi.nlm.nih.gov; the review notes that sports nutrition supplements are considered ultra‑processed and may cause dysbiosis and leaky gutpmc.ncbi.nlm.nih.gov. It also highlights that emulsifiers and artificial sweeteners degrade mucus and increase inflammatory responsespmc.ncbi.nlm.nih.gov.

3. David, L. A., et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature 2014, 505, 559–563. In a crossover study, switching from a plant‑based to an animal‑based diet increased bile‑tolerant bacteria like Bilophila and decreased fibre‑fermenting species within dayspmc.ncbi.nlm.nih.gov, illustrating how a Western diet alters the microbiomepmc.ncbi.nlm.nih.gov.

4. Jäger, R., Purpura, M., et al. The athletic gut microbiota. Journal of the International Society of Sports Nutrition 2020, 17, 24. This review notes that athletes often consume high amounts of simple carbohydrates and avoid fibre to minimise gastrointestinal symptoms; such habits can reduce microbial diversity and SCFA production, highlighting the importance of fibre for athletic gut healthjissn.biomedcentral.com.

5. O’Keefe, S. J. D., et al. Impact of diet and lifestyle on the gut microbiota and human health. Clinics in Nutrition 2014, 33, 253–260. The authors explain that probiotic supplementation usually leads to only small, transient changes in microbiota composition and that long‑term dietary patterns are the dominant factor shaping microbial communitiespmc.ncbi.nlm.nih.gov.

6. Clark, A., et al. Endurance exercise and gut microbiota: A review. Gut Microbes 2017, 8, 577–592. This review describes how strenuous exercise increases intestinal permeability, reduces mucus thickness and promotes endotoxemia, thereby activating systemic inflammationpmc.ncbi.nlm.nih.gov.

7. de Oliveira, E. P., et al. Gastrointestinal complaints during exercise: A clinical approach for treatment strategies. Current Opinion in Clinical Nutrition and Metabolic Care 2014, 17, 1–8. The authors report that high‑osmolality carbohydrate solutions (>500 mOsm kg⁻¹) are associated with nausea, cramps and diarrhea during endurance exercise and that high carbohydrate intake correlates with GI distresspmc.ncbi.nlm.nih.gov.