How Poor Gut Health Can Cause Autoimmune Disorders
- Katie Bailey, MS, RD, LD, FNC

- 2 days ago
- 6 min read
Did you know that about 70 to 80% of your immune system actually lives inside your gut?
That means that the food that you eat, the bacteria in your intestines and the health of your gut lining have a direct impact on how your immune system behaves. When that system gets out of balance, it can sometimes turn against you, and that is how autoimmune disorders can begin.
Today we're diving into how poor gut health can contribute to autoimmune diseases like Hashimoto's, rheumatoid arthritis, lupus, psoriasis, and many more. And most importantly, what you can start doing now to support your gut health and reduce your risk.
[Video Transcript Below Video - it is the same information]
What Is Autoimmunity?
Before we start connecting the dots to the gut, let's quickly go over what autoimmunity actually is. So your immune system's main job is to protect you. So it's like your body's personal security team. Normally it knows how to tell the difference between self and not self, so it fights off infections and bacteria and toxins while leaving your own tissues alone.
Autoimmunity happens when this system gets confused and instead of attacking invaders, it starts attacking your own healthy tissues. That's why there are so many different autoimmune conditions. The immune system can target our joints, like in arthritis, it can target the thyroid like in Hashimoto's, the skin and psoriasis, and also the gut like we see with Crohn's disease or colitis. In other words, autoimmune diseases are not just the immune system being overactive, it's also being misdirected. And one of the biggest questions that we ask is how did the confusion start in the first place? And that's where the gut comes in.
How Poor Gut Health Triggers Autoimmunity
Alright, so how exactly does poor gut health lead to something as serious as autoimmune disorders? Let's break it down step by step.
The Gut Lining: Your First Line of Defense

So let's first talk about your gut lining because that really is the frontline defense of your immune system. Imagine your gut lining like a bouncer in a club so it decides who gets in. So things like nutrients and who stays out, things like toxins and bacteria and undigested food particles.
But here's the problem, things like chronic stress, inflammatory foods, alcohol, certain medications and environmental toxins can all weaken that gut lining. So when that gut lining becomes weak, it becomes permeable, and that's what we call leaky gut. So those particles that should be staying inside the gut start to leak into the bloodstream. Your immune system sees these particles as foreign invaders and launches an attack over time, that constant immune activation can flip the switch toward autoimmunity.
Next, I'm going to explain a few more reasons why poor gut health can contribute to autoimmune disease. But first, I'm Katie Bailey. I'm a gut health dietitian at Oswald Digestive Clinic, where we help individuals improve and resolve their bothersome gut issues. If you're interested in learning more about gut health, I'll link our free guide Five Ways to Improve Your Gut Health here.
The Role of Inflammation in Autoimmune Diseases
Now, once the gut barrier is compromised, the next thing you end up with is inflammation. And this is really where a lot of the damage starts. Now, inflammation is not always a bad thing, it's how our body heals from a cut or fights off an infection. But when your immune system is activated day after day because of a leaky gut, you end up with chronic low grade inflammation simmering in the background.
Now over time, this can confuse your immune system. So for example, proteins and gluten can resemble proteins in your thyroid. So if you already have inflammation and your immune system is on high alert, it may start mistaking your thyroid tissue for gluten and start attacking it. That's one way conditions like Hashimoto's can develop. It's like your immune systems defense radar is so sensitive that it starts shooting at the wrong targets.
Gut Microbiome and Autoimmunity
Now, it's also important to note that the trillions of bacteria in your gut called your gut microbiome are also running the show. So your microbiome acts almost like a teacher for your immune system. From the moment that you're born, the bacteria in your gut are helping your immune system cells learn. This is harmful and this is safe.
When you have a calm and healthy diverse microbiome, your immune system stays calm and balanced. But things like antibiotics, highly processed foods, excess sugars and low fiber diets can wipe out good bacteria, allowing harmful bacteria to overgrow this imbalance, which we call dysbiosis, can push your immune system into an overactive state.
And here's something fascinating. Studies show that individuals with autoimmune disorders often have low diversity in their microbiome. It's not proof that dysbiosis causes autoimmunity, but there is a strong connection.
How Autoimmunity Develops Over Time
Now, I want to point out that autoimmunity does not happen overnight. It builds over years of the immune system being constantly triggered. And if we can identify and remove certain triggers, especially ones in the gut, it can often calm down the autoimmune response and start to help individuals feel dramatically better.
How to Support Gut Health and Prevent Autoimmunity
That being said, what can you do now to help protect and support the gut as well as the immune system?
Eat More Anti-Inflammatory Foods
So the first thing that you can do is to eat more anti-inflammatory foods because this is going to help to calm down inflammation that's going to look like colorful fruits and vegetables, omega fatty fish, olive oil, nuts and seeds, and turmeric.
Remove Potential Triggers
Next, you want to remove potential triggers. So gluten and dairy are common culprits with autoimmune disease, but also excess sugar, processed foods and excess alcohol, even small daily exposures can start to fuel inflammation.
Repair the Gut Lining
Next is to repair the gut lining. So nutrients like L-glutamine, zinc, collagen and alle can be really helpful for starting to repair that gut barrier.
Rebalance the Microbiome
Rebalance the microbiome, so including probiotics, either through food or supplements, and then feeding that bacteria with your prebiotic fibers, garlic, onions, artichokes, asparagus, and a variety of fiber rich foods and resistance starches, including those are going to feed that good bacteria and keep them happy and thriving.
Lifestyle Factors for Gut and Immune Health
And then lastly, don't forget about lifestyle changes. So getting adequate sleep, getting movement in practicing stress management. These are all non-negotiables. The gut brain connection is real, and stress alone can contribute to a leaky gut.
Final Thoughts
So let's pull this all together. Your gut is home to a majority of your immune system. If the gut lining breaks down, if chronic inflammation is left unchecked or if your microbiome falls out of balance, your immune system can start to turn on its own tissues, and that is the root of autoimmune diseases. But the hopeful message is this, your gut health can be influenced through nutrition and lifestyle and targeted supplements. You can give your immune system the support that it needs to protect you and set of turning on you.
That's it for today's video. If you liked this video, please hit the like button and subscribe for more nutrition videos. Let us know in the comments if you have any questions. And if you're interested in working with our clinic, you could click the link here to schedule an appointment. We do take insurance. You can find more information about that on our website.
Thank you for watching. I'll see you next time. Bye.
If you'd like to explore any of this information further or obtain an individualized nutrition plan, you can schedule an initial appointment at our clinic. We also take insurance and some of our clients get full coverage, which is great.
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