The Gut–Autoimmune Connection: How Nutrition Can Heal Inflammation from the Inside Out

As a clinical nutritionist, I work with clients to address a wide range of health concerns by focusing on foundational systems in the body—especially the gut and immune system. I believe that when we support gut integrity, nourish the microbiome, and reduce inflammatory triggers, we help restore balance throughout the entire body. This is especially true in cases of autoimmunity.

Autoimmune conditions are on the rise, but they’re not simply the result of “bad luck” or genetics. Environment, diet, and lifestyle all play a role—and that’s where nutrition becomes a powerful tool.

Autoimmunity on the Rise: What the Numbers Show

There are now over 80 identified autoimmune diseases, including rheumatoid arthritis, lupus, type 1 diabetes, multiple sclerosis, inflammatory bowel disease, and psoriasis (Granados‑Riveron et al., 2023). What’s most concerning is how much more common these conditions have become.

Globally, the incidence of autoimmune diseases such as RA, IBD, MS, and psoriasis has increased dramatically since the 1990s and is projected to rise even more through 2050 (GBD Study, 2023). In the U.S. alone, a recent analysis estimated that nearly 1 in 20 adults has at least one autoimmune disease, with many living with multiple diagnoses (Watad et al., 2023).

This growing burden signals the need to look beyond traditional care and explore deeper root causes—especially gut health.

The Gut–Immune Connection

When I work with clients who have autoimmune conditions, one of the first areas I address is the gut.

Intestinal permeability (also known as “leaky gut”), microbiome imbalance (dysbiosis), and chronic low-grade inflammation can all contribute to immune dysregulation. A disrupted gut lining allows food particles, pathogens, and toxins to enter the bloodstream, potentially triggering immune responses and worsening symptoms (Zhang et al., 2023; Jiang et al., 2023).

Multiple studies have linked gut health to the development or progression of autoimmune conditions like type 1 diabetes, Crohn’s disease, rheumatoid arthritis, and lupus. Fortunately, we also have evidence that targeted nutrition, probiotics, and microbiome-focused interventions can improve symptoms and reduce inflammation (Wang et al., 2024).

The Role of Diet: How the Standard American Diet Harms Gut and Immune Health

It’s no secret that the Standard American Diet (SAD) is packed with ultra-processed foods—refined grains, added sugars, industrial seed oils, additives, and low fiber. These foods disrupt the gut microbiota, weaken intestinal barrier function, and drive systemic inflammation (Lopez‑Munoz et al., 2023; Mena et al., 2020).

Many of my clients don't realize just how profoundly diet influences immune balance. By shifting away from ultra-processed foods and focusing on whole, nutrient-dense options, we can reduce triggers and begin to heal the gut–immune axis from the inside out.

Nutrients I Prioritize When Supporting Clients with Autoimmunity

When creating personalized nutrition plans, I focus on both food quality and key nutrients that support immune regulation and gut health. Here are a few I prioritize:

Vitamin D

Most clients I work with are low or borderline in vitamin D. This nutrient plays a critical role in reducing inflammation, supporting immune tolerance, and strengthening the gut barrier. A major randomized trial (the VITAL study) found that daily vitamin D supplementation reduced autoimmune disease risk by 22% in adults over age 50 (Manson et al., 2020). I often test vitamin D levels and supplement based on lab data.

Zinc

Zinc is essential for immune signaling and gut lining repair. It helps tighten junctions in the intestinal wall and reduce oxidative stress. In autoimmune clients, I monitor for signs of deficiency and recommend foods like pumpkin seeds, lentils, grass-fed beef, or targeted supplementation when appropriate (Sanna et al., 2018; Sturniolo et al., 2001).

Vitamin A

Vitamin A supports mucosal barriers and promotes a balanced immune response—especially in the gut. It plays a role in encouraging regulatory T cells and reducing the hyperactivity seen in autoimmune conditions (Maggini et al., 2020).

Fiber & Prebiotics

Fiber is food for our gut microbes. Soluble fibers (like those found in oats, chia, flax, and legumes) help produce short-chain fatty acids (SCFAs), which support the gut lining and reduce inflammation. I help clients increase a variety of plant-based fiber sources to support microbial diversity and immune resilience (Zhang et al., 2019; Dalile et al., 2019).Note: I often don’t recommend taking a daily probiotic, as I find this can sometimes lead to more issues down the road.

Omega-3 Fatty Acids & Selenium

I include foods rich in EPA/DHA (like wild-caught salmon or algae oil) to help modulate inflammation. Selenium also supports immune defense and antioxidant capacity—especially in thyroid-related autoimmunity.

My Approach in Practice

Every client is different, but I often use a modified version of the 5-R gut healing approach to guide autoimmune nutrition therapy:

• Remove: Inflammatory foods and potential triggers (e.g., gluten, dairy, additives)

• Replace: Stomach acid, enzymes, or nutrients that may be deficient

• Reinoculate: Introduce prebiotics and probiotics for microbial balance (as needed)

• Repair: Use nutrients like zinc, omega-3s, vitamin D, and glutamine

• Rebalance: Support stress, sleep, and movement—all essential for immune health

  
  

Through this framework, clients feel empowered, informed, and supported in their healing journey.

Autoimmune conditions can feel overwhelming and unpredictable, but they don’t have to be. Nutrition offers a powerful, research-backed approach to calm the immune system, heal the gut, and alleviate symptom flares.

If you’re struggling with an autoimmune diagnosis or feel like something is “off” with your immune health, I’d love to support you with a personalized approach that gets to the root.

For personalized care, you can work with me or build your own team of holistic practitioners! Reach your optimum health in-person or online. Check out our Get Started page to learn how to work with us!

Author: Elena DiPerri CNS, LN

References:

1. Dalile, B., Van Oudenhove, L., Vervliet, B., & Verbeke, K. (2019). The role of short-chain fatty acids in microbiota–gut–brain communication. Nature Reviews Gastroenterology & Hepatology, 16(8), 461–478. https://doi.org/10.1038/s41575-019-0157-3

2. GBD Study. (2023). Global incidence and burden of autoimmune diseases, 1990–2021. The Lancet. https://pubmed.ncbi.nlm.nih.gov/39232989/

3. Granados-Riveron, J. T., et al. (2023). The role of the gut in autoimmune diseases. Frontiers in Immunology. https://pmc.ncbi.nlm.nih.gov/articles/PMC4036413/

4. Jiang, Y., et al. (2023). Intestinal permeability and autoimmune disease pathogenesis. Autoimmunity Reviews, 22(3). https://pmc.ncbi.nlm.nih.gov/articles/PMC10907812/

5. Lopez-Munoz, P., et al. (2023). Ultra-processed foods and the gut–immune axis. Nutrients, 15(7), 1654. https://pubmed.ncbi.nlm.nih.gov/40077728/

6. Maggini, S., Pierre, A., & Calder, P. C. (2020). Immune function and micronutrient requirements. Nutrients, 12(1), 118. https://pubmed.ncbi.nlm.nih.gov/33308613/

7. Manson, J. E., et al. (2020). Vitamin D supplements and prevention of autoimmune disease — VITAL trial. BMJ, 376:e066452. https://pubmed.ncbi.nlm.nih.gov/35075005/

8. Sanna, A., Firinu, D., Zavattari, P., & Valera, P. (2018). Zinc status and autoimmunity: A meta-analysis. Nutrients, 10(1), 68. https://pubmed.ncbi.nlm.nih.gov/29346322/

9. Sturniolo, G. C., et al. (2001). Zinc supplementation tightens “leaky gut” in Crohn’s disease. Inflammatory Bowel Diseases, 7(2), 94–98. https://pubmed.ncbi.nlm.nih.gov/11341629/

10. Wang, H., et al. (2024). Gut microbiota-based interventions in autoimmune diseases: A meta-analysis. Frontiers in Immunology, 15. https://pubmed.ncbi.nlm.nih.gov/38475833/

11. Watad, A., et al. (2023). Prevalence of autoimmune diseases in US adults, 2011–2022. JAMA, 329(20), 1780–1790. https://pubmed.ncbi.nlm.nih.gov/39666393/

    Zhang, Y., et al. (2023). Microbiota dysbiosis and autoimmune conditions. Autoimmunity Reviews, 22(5). https://pmc.ncbi.nlm.nih.gov/articles/PMC9390838/

Disclaimer: This information is generalized and intended for educational purposes only. Due to potential individual contraindications, please see your primary care provider before implementing any strategies in these posts.