The Gut-Autoimmune Connection: How Your Immune System Starts in the Gut

If you've been diagnosed with an autoimmune condition — or you're experiencing symptoms like joint pain, fatigue, skin flare-ups, or brain fog — it might surprise you to learn that your gut could be at the root of it all.

As both a rheumatologist and a functional medicine doctor, I often explain to my patients that the gut isn't just about digestion. It's a major immune organ. In fact, over 70% of your immune system is housed in the gut wall, and when something disrupts that environment, the ripple effects can be felt throughout the entire body.

What Is the Gut-Immune Connection?

Your gut lining acts like a finely tuned security system: deciding what gets absorbed into the bloodstream and what gets kept out. A healthy gut lining is tightly sealed and supported by trillions of helpful bacteria — your microbiome.

But when that barrier becomes damaged (from stress, poor diet, antibiotics, infections, or environmental toxins), it can become "leaky." This allows particles like undigested food, bacteria, and toxins to escape into the bloodstream, triggering your immune system to attack what it sees as invaders. This is a major driver of chronic inflammation and can lead to the development or worsening of autoimmune disease.

This condition is often called "leaky gut" or intestinal permeability — and while conventional medicine may not always recognise it, the research is growing.

Signs Your Gut May Be Driving Autoimmunity

  • Bloating, gas, or digestive discomfort

  • Food sensitivities (especially gluten, dairy, soy, eggs)

  • Skin conditions like eczema, psoriasis, or acne

  • Brain fog, poor memory, or mood swings

  • Fatigue that worsens after meals

  • Autoimmune conditions that flare with stress or diet changes

How Functional Medicine Heals the Gut

In functional medicine, we use a proven framework called the 5R Approach:

  1. Remove – inflammatory foods, toxins, and gut infections

  2. Replace – digestive support (like enzymes and stomach acid)

  3. Reinoculate – with beneficial bacteria (probiotics and fermented foods)

  4. Repair – the gut lining with nutrients like glutamine, zinc, and omega-3s

  5. Rebalance – the nervous system and lifestyle habits that affect digestion

This is exactly the framework I teach inside my Autoimmune Reset course. It’s a safe, science-based system for helping you calm inflammation, repair your gut lining, and reduce autoimmune symptoms naturally.

Best Foods for Gut & Immune Health

  • Bone broth (rich in glutamine and collagen)

  • Cooked vegetables and fibre-rich foods (like squash, carrots, beetroot, and leeks)

  • Fermented foods (like sauerkraut, kefir, and kimchi)

  • Omega-3-rich fats (like oily fish, flaxseeds, and walnuts)

  • Herbs and spices (like turmeric, ginger, rosemary, and oregano)

Foods to Avoid

  • Gluten, dairy, soy, and processed sugars

  • Alcohol and caffeine (in excess)

  • Deep-fried foods and transfats

  • Artificial sweeteners and additives

If you're unsure where to start, removing gluten alone can be incredibly helpful for many people with autoimmune conditions, as it's been shown to increase gut permeability and inflammation.

You Can Heal

I’ve seen hundreds of patients transform their health by addressing the gut first. When we reduce the immune triggers and rebuild the gut lining, inflammation begins to settle, and symptoms start to fade. This isn’t just about symptom management — it’s about healing at the root.

Ready to go deeper?

My Autoimmune Reset course walks you through every step of gut repair, food reintroduction, and immune system regulation — with recipes, supplements, and support.

🌟 Join the waitlist [here]
📚 Download my e-book: "Autoimmune Reset” — available now in the store

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Can Autoimmune Disease Be Reversed Naturally? A Doctor’s Perspective

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10 Signs Your Symptoms Might Be Autoimmune – And What to Do Next