Gut Health is Immune Health

When I talk with athletes about immune health, their knee-jerk reaction is vitamin C from orange juice or a supplement. But what I’ve noticed surprises athletes is their unawareness of what the immune system is—and what the gastrointestinal (GI) tract’s role.

In this blog, I will review:

• What the immune system is.

• How the gut plays a role in immune health.

• Nutrition beyond supplementation in support of immune health: Fiber, polyphenols, antioxidants, fats, and food-form probiotics.

What is the Immune System?

The immune system doesn’t exist to solely launch attacks against problematic cells, like harmful bacteria or viruses. It must also recognize familiar faces and choose to not react. Examples of this immune surveillance include:

• Recognizing familiarity: Food sensitivity tests incorrectly interpret a high IgG as problematic. However, IgG is the immune system’s way of marking tolerance—something safe to that person.

• Recognizing a threat: Think scary like the flu or measles (get vaccinated!). Unfortunately for those with autoimmune diseases in the food space, gluten is interpreted as a threat for those with Celiac Disease.

Organs of the immune system exist throughout the body (see Table 1), with the GI tract and skin considered the largest of its organs. (1,2)

Dietitians should consider strengthening the immune system like a suit of armour to help reduce the risk of illness. We can’t fully prevent sickness, but once sick a healthful immune system may result in a reduced duration of illness and the severity of symptoms experienced.

Before jumping into the gut, read past blog articles I’ve written on different factors influencing the immune system: alcohol, Ashwagandha, the endocannabinoid system, zinc, food sensitivity tests, melatonin, energy availability, and vitamin D.

The Gut’s Role in Immune Health

Several of those organs listed live along or within the GI tract, functioning as a barrier between the outside world and our bloodstream. Think nostril hairs keeping out debris or the mucus throughout the mouth, throat, lungs, and intestinal linings.

It’s estimated that anywhere from 60-80% of the cells of the immune system are located in the GI tract.  This makes perfect sense, given what the gut is constantly exposed to: food antigens, alcohol, bacteria, and other toxins that we consume from the outside world. These immune cells include:

• Gut-associated lymphoid tissue (GALT) like the Peyer’s patches, isolated lymphoid follicles located along the entirety of the small and large intestines, and the appendix.

• Adaptive immune cells living in the intestinal lamina propria and epithelium. (10) These include antigen-presenting cells (APCs) like dendritic cells, macrophages, and B-cells. (2)

The epithelial cells (or intestinal cells) are covered by bacteria and a thick mucus layer. In the small intestine, there is one mucosal layer and in the large intestine two. (11) Mucosal cells are studded amongst the epithelial cells, producing mucus and creating a nutritious environment for the gut bacteria to thrive. (12) The lamina propria lives beneath the epithelial cells, is composed of connective tissue, and contains immune-rich cells. (11)

The mucus, bacteria, and the intestinal wall’s integrity (the in-between-cell spaces where “leaky gut” or intestinal permeability can occur) is therefore a main priority when considering immune health strategies for athletes.

A Peyer's patch beneath the epithelial cells. Park et al. (2023). (8)

Immune-supportive Nutrition: What Should We Be Adding?

To maintain a healthy gut barrier, you need to consider:

• Contributing to the bacterial population.

• Feeding those bacteria.

• Protecting against oxidation and cell death.

Fiber, Polyphenols, and Antioxidants

Fiber is found in all whole plant foods, makes us feel full, adds roughage to essentially scrub our intestinal linings to keep things clean, and promotes regular bowel movements. Fiber also acts as a food source to gut bacteria. Bacteria of the large intestine ferment the fiber and produce metabolites, like the short-chain fatty acids (SCFAs) butyrate, acetate, and propionate. These SCFAs are then used as energy sources for the mucosal cells, helping to keep the intestinal barrier healthy and replenished. High-fiber diets help promote intestinal bacterial diversity. (13)

Polyphenols are a plant’s own immune system, protecting it against pathogens, bacteria, viruses, and other environmental concerns, like ultraviolet light. When humans eat plants containing polyphenols, we gain those functions. (14) As fiber can influence intestinal health, as can polyphenols via their influence on modulating the type of bacteria present in the gut—both up- and down-regulating certain bacteria. (14,15)

Dietary polyphenols. Wang et al. (2022). (14)

Antioxidants scour for free radicals to mitigate their oxidative damage to DNA, cell membranes, and other cellular parts. This damage can ultimately lead to cell death. (15,16) Even healthy bodies produce free radicals, whether it’s the byproducts from normal cellular pathways or from exercise. Examples of antioxidants include polyphenols; vitamins A, C, and E; glutathione; and alpha lipoic acid. (16) Antioxidants are therefore helpful for the immune system throughout the body and at the intestinal barrier to maintain its integrity.

Yes, you can prioritize ORAC for the highest anti-inflammatory options, but given plant diversity improves intestinal bacterial diversity, prioritize variation in the plants consumed, ORAC options included.

Optimizing Omegas from Fatty Fish and Unsaturated Fats from Plants

Unsaturated fatty acids, like omegas and liquid-at-room-temperature plant oils, help gut bacteria adhere to the mucosal lining and play an anti-inflammatory function as noted above. (14,17)

Examples include fatty fish, nuts, seeds, avocado and its oil, olive oil, and seed oils (e.g., canola). (11)

Food-form Probiotics

I specify food-form to avoid simply recommending a probiotic supplement. Probiotic supplements are meant to be provided with a specific strain in mind that targets a specific outcome (e.g., VSL#3 for irritable bowel syndrome and ulcerative colitis). There is no one strain that can be recommended for everyone. The Alliance for Education on Probiotics (AEProbio) offers Canadian and USA guides for products available for different uses, including traveler’s diarrhea.

Using food to expand an athlete’s pallet for probiotic and fermented foods is a great start. Options include:

• Dairy sources: Kefir, yogurt, buttermilk, and cheese.

• Vegetable sources: Sauerkraut, kimchi, pickles, gundruk, and curtido.

• Fruit sources: Tepache, apple cider vinegar, and wine.

• Grain sources: Sourdough bread and boza (wheat); amazake, rice wine, and rice vinegar (rice); injera (teff); and kvass (rye).

• Legume sources: Idli (lentils); and miso, tempeh, soy sauce, and natto (soybeans).

• Sugar sources: Kombucha and water kefir. (18)

I’ve heard some say pasteurization makes products like kombucha not great fermented options. Given the high heat of pasteurization, yes, those fermentation-associated microbes (FAM) will be killed. However, these once fermented, now pasteurized products will still contain post-biotics—inactivated microbial cell components, cells degraded during pasteurization, and fermentation-derived metabolites (FDM). So, there are still benefits to consuming a pasteurized kombucha. (18) However, if you’re aiming to optimize gut health with fermentation, or kombucha is the only fermented option an athlete will consume, then yes, unpasteurized options would be best. You can read more about that here along with a flowchart on how to identify fermented foods.

Key Take-aways

Athletes know they should be consuming more fruits and vegetables (whole foods in general), but often for the reasons of overall health, fiber, and antioxidants—terms that either may not mean much to them or remind them of nagging parents. Our job as dietitians is to provide new or novel reasons to promote athlete buy-in. I’ve noticed the angle of immune health of being helpful.

The beauty of food over supplements as a focus point is to help remind athletes of all the other goals they’re trying to meet. For instance:

• Carbohydrates as fuel source during exercise: A plant-rich diet to prime muscle glycogen.

• Calories for weight gain: Fibre-and-antioxidant-rich nuts and their butters and antioxidant-rich avocados and plant oils.

• Protein for their muscles: Probiotic-rich kefir, fibre-rich beans and legumes, and antioxidant-rich fatty fish.

Foods, rather than isolated supplements, can multitask for the athlete’s performance and immune health.

When designing your proactive and reactive immune health strategies, don’t forget to place a major focus on eating and avoid taking the shortcut to vitamin C pills.

References

(1) The gastrointestinal immune system. (n.d.). Colorado State University. Retrieved February 23, 2026, from https://vivo.colostate.edu/hbooks/pathphys/digestion/basics/gi_immune.html

(2) Parts of the immune system. (2023, May 12). Children’s Hospital of Philadelphia. Retrieved February 25, 2026, from https://www.chop.edu/vaccine-education-center/human-immune-system/parts-immune-system

(3) 6.3 bone structure. (2025). Oregon State University. Retrieved February 23, 2026, from https://open.oregonstate.education/anatomy2e/chapter/bone-structure/

(4) SickKids Staff. (2023, July 20). Bone marrow and the immune system. SickKids. https://www.aboutkidshealth.ca/bone-marrow-and-the-immune-system

(5) Farina, D. [Professor Dave Explains]. (2021, March 22). Structure and immune function of the lymphatic system [Video]. YouTube. https://www.youtube.com/watch?v=DZX5AGST8qE

(6) Hussell, T. (n.d.). Immunity in the lung. British Society for Immunology. https://www.immunology.org/public-information/bitesized-immunology/organs-tissues/immunity-lung

(7) Cleveland Clinic. (2021, April 29). Spleen. https://my.clevelandclinic.org/health/body/21567-spleen

(8) Park, J.I., Cho, S.W., Kang, J.H., & Park, T.-E. (2023). Intestinal Peyer’s patches: structure, function, and in vitro modeling. Tissue Eng Regen Med,20(3):341-353. https://pubmed.ncbi.nlm.nih.gov/37079198/

(9) Cleveland Clinic. (2026, January 18). Appendix. https://my.clevelandclinic.org/health/body/appendix

(10) Mörbe, U.M., Jørgensen, P.B., Fenton, T.M., von Burg, N., Riis, L.B., … & Agace, W.W. (2021). Human gut-associated lymphoid tissue (GALT); diversity, structure, and function. Mucosal Immunol,14(4):793-802. https://pubmed.ncbi.nlm.nih.gov/33753873/ 

(11) Fundaro, G., & Hoffman, J. (2021). The science of gut health: what the research really says about your microbiome. Independently published. https://www.goodreads.com/book/show/59457915-the-science-of-gut-health

(12) Tonetti, F.R., Equileor, A., & Llorente, C. (2024). Goblet cells: guardians of gut immunity and their role in gastrointestinal diseases. eGastroenterology,2(3):e100098. https://pmc.ncbi.nlm.nih.gov/articles/PMC11542612/

(13) Fu, J., Zheng, Y., Gao, Y., & Xu, W. (2022). Dietary fiber intake and gut microbiota in human health. Microorganisms,10(12):2507. https://pmc.ncbi.nlm.nih.gov/articles/PMC9787832/

(14) Wang, X., Qi, Y., & Zheng, H. (2022). Dietary polyphenol, gut microbiota, and health benefits. Antioxidants (Basel),11(6):1212. https://pmc.ncbi.nlm.nih.gov/articles/PMC9220293/

(15) Rajoka, M.S.R., Thirumdas, R., Mehwish, H.M., Umair, M., Khurshi, M., … & Barba, F.J. (2021). Role of food antioxidants in modulating gut microbial communities: novel understandings in intestinal oxidative stress damage and their impact on host health. Antioxidants (Basel),10(10):1563. https://pmc.ncbi.nlm.nih.gov/articles/PMC8533511/

(16) Harvard Health Publishing. (2019, January 31). Understanding antioxidants. Harvard Medical School. https://www.health.harvard.edu/staying-healthy/understanding-antioxidants

(17) Fu, Y., Wang, Y., Gao, H., Li, D., Jiang, R., … & Xu, K. (2021). Associations among dietary omega-3 polyunsaturated fatty acids, the gut microbiota, and intestinal immunity. Mediators Inflamm:8879227. https://pubmed.ncbi.nlm.nih.gov/33488295/

(18) Caffrey, E.B., Perelman, D., Ward, C.P., Sonnenburg, E.D., Gardner, C.D., & Sonnenburg, J.L. (2025). Unpacking food fermentation: clinically relevant tools for fermented food identification and consumption. Adv Nutr,16(5):100412.  https://pubmed.ncbi.nlm.nih.gov/40120687/