Do Autoimmune Diseases Start in the Gut? Here’s What You Need to Know

Does poor gut health cause autoimmune disease? Can you overcome genetic predispositions to autoimmunity through diet and lifestyle changes—and even probiotics? Keep reading for answers to these questions and more in this post on autoimmunity and the gut.

The prevalence of autoimmune diseases is higher than ever. In fact, according to the Cleveland Clinic, an estimated one in 15 people in the United States have an autoimmune disease, with numbers rising with each successive generation.

And while you may think that autoimmunity is largely influenced by genetics, that’s only one part of the equation. For instance, did you know that there are scientifically proven links between autoimmune disease and gut health?


Of course, it’s essential to be proactive about your health before symptoms arise—as well as at the initial onset of symptoms—so that you can prevent autoimmune diseases from wreaking havoc on your body and overall state of well-being.

In this article, we’ll discuss:

  • what autoimmunity is

  • types of autoimmune diseases

  • the link between autoimmunity and the gut

  • 4 autoimmune triggers and how to fix/manage them

What Is Autoimmunity?

The term autoimmunity applies to diseases caused by antibodies or lymphocytes that attack substances that naturally exist in the body.

Essentially, when autoimmune conditions are present, your body mistakenly thinks that harmless substances are in fact harmful, which creates a state of alert, attack, and inflammation.

Unfortunately, women have a two to one likelihood of developing autoimmune diseases compared to men. Even further, as I mentioned above, autoimmune conditions are becoming more prevalent over time. This trend started around World War II, largely on account of:

  • increased international travel (and the movement/proliferation of pathogens from different parts of the world)

  • greater exposure to toxic chemicals in our daily lives

  • less nutrient-dense diets, including reliance on processed foods

Types of Autoimmune Diseases

According to the National Institute of Allergy and Infectious Diseases, there are over 80 known types of autoimmune diseases, though other resources estimate that the number actually climbs into the triple digits.

Although this list isn’t comprehensive, for reference and familiarity, here’s a short list of common types of autoimmune disease:

  • Digestive: celiac, Chron’s, ulcerative colitis

  • Skin: psoriasis, eczema

  • Endocrine: Hashimoto’s disease (hypothyroidism), Graves’ disease (hyperthyroidism)

  • Joints and muscles: lupus, rheumatoid arthritis

  • Pancreatic: type 1 diabetes

While different types of autoimmune diseases affect different aspects of your health and parts of the body, the general action remains the same: your immune response goes into overdrive and attacks the tissues, organs, or body part specific to the autoimmune condition you have.

Autoimmune Disease and Gut Health

If you’re familiar with my work and expertise as a functional dietitian, you likely know that I tend to tie everything back to gut health—and that’s because it affects nearly every aspect of our entire well-being!

With that said, do autoimmune diseases start in the gut?

When it comes to autoimmunity and the gut, the link is clear. After all, research shows that 70 percent of immune cells are located in the gut. So naturally, it makes sense that a healthier gut promotes stronger immune function—and a healthy gut microbiome is one that’s diverse and balanced.

Further, a normal gut lining has tight junctions that keep cells bound together. However, when inflammation is present, those tight junctions loosen and create spaces between those cells. These new pathways permit pathogens to enter the bloodstream, resulting in an autoimmune response.

Simply put, if you want to reduce the risk of developing autoimmune diseases—or if you’re seeking natural ways to help heal existing autoimmunity symptoms—you’ll want to heal and nurture your gut.

4 Triggers of Autoimmunity and How to Fix Them

If you’re wondering what causes autoimmune diseases in the first place—as well as how to manage and prevent them—you’re in the right place.

Before we begin, it’s worth noting that autoimmune conditions are caused by several triggers, rather than a solo offender. You can think of it as a “group effort” of sorts—but clearly not a good kind. For this reason, it’s important to boost your defenses across all of these causes whenever possible.

Without further ado, here are the four key triggers of autoimmunity and their accompanying fixes.

1. Your Genetics

Genetic variants exist that can predispose humans to multiple autoimmune diseases. For instance, 95 percent of people with celiac disease have the human leukocyte antigen (HLA-DQA1) gene, thus triggering an autoimmune response and symptoms of gluten allergy/sensitivity.

However, while it’s true that some autoimmune diseases are genetic, a family history of them doesn’t guarantee that you’ll get the same condition(s). Historically, many people thought that genetics are the greatest determining factor of health outcomes, yet a growing body of research shows that this isn’t the case. Your health—in terms of immunity and otherwise—is affected by various other factors, as we’ll see below.

Read: your DNA isn’t your destiny.

The fix

Okay, so you can’t quite modify your inherited genetics. But with the right dietary and lifestyle habits and modifications (including those shared below), you can avoid and/or fix your symptoms if you have a genetic predisposition to autoimmune conditions.

2. Your Environment

I don’t mean to scare you, but the fact is that our daily lives are full of harmful chemicals and environmental stressors that contribute to toxic load, which can instigate the development of autoimmune diseases.

While such toxins include the likes of common offenders you’re likely already familiar with (think air pollution, cigarette smoke, car exhaust, viruses, bacteria, etc.), others you may be surprised to learn about include:

  • heavy metals, such as those in tap water

  • chemicals in foods, beverages, furniture, household/personal care products

  • medications

  • side effects of stress and a lack of quality sleep

An accumulation of these toxins (and the many more not listed here) on a daily basis contribute to toxic load in the long-term, burdening your immune system and potentially developing an autoimmune condition.

The fix

There are countless ways in which you can limit your exposure to chemicals and pathogens, and thus decrease your toxic load naturally help stave off autoimmunity. Better yet, many of these modifications are simple enough to integrate in your daily life. Plus, they naturally promote other aspects of your well-being.

Some of my top tips to reduce the damaging effects of exposure to toxins and environmental stress include:

  • limiting processed foods (including those packaged in plastic or cans)

  • eating a healthier, more balanced, more nutrient-rich diet (more on that below)

  • using a water purifier or switching to a reverse osmosis filter (I love my Berkey!)

  • purchasing non-toxic products when possible (e.g., clean skincare, makeup, and nail polish; naturally derived cleaning products; non-toxic candles; etc.)

  • practicing stress management practices that you enjoy (e.g., yoga, meditation, breathwork, journaling, reading, low-intensity walks, etc.)

For a more advanced protocol, you may wish to get functional tests to uncover hidden infections such as Lyme, mold, yeast, bacteria, and viruses, which I employ for clients in my functional RD practice.

3. Trauma

Trauma to the mind, body, or both may also trigger autoimmune disease.

Whether caused by physical illness, surgery, or stressful events (particularly PTSD), trauma is associated with autoimmunity since it reduces bacterial diversity in the gut and impedes nutrient absorption.

As we saw above, there’s a clear link between autoimmune diseases and gut health—and since trauma affects your gut microbiome, those who suffer from traumatic life experiences can be more susceptible to autoimmunity.

The fix

People who struggle from trauma can adopt several methods to avoid or help remedy autoimmune conditions, which include:

  • getting physical rehabilitation

  • talking to a psychologist or licensed therapist who specializes in trauma

  • practicing the stress management techniques and dietary modifications shared in the previous section

4. Gut Dysbiosis

Finally, a reduction in microbial diversity and an imbalance of good-to-bad bacteria (aka gut dysbiosis) is another underlying cause of autoimmunity.

While a range of factors can contribute to dysbiosis, the major offenders include:

  • the changing genetic structure of food (corn, wheat, soy, rice) via GMOs

  • pesticides in produce and animal products as well as other chemicals in food

  • high levels of unhealthy fats in the Standard American Diet that feed unhealthy bacteria

Remember when we talked about poor gut health and autoimmune disease earlier? Gut permeability is a key indicator of dysbiosis, as lipopolysaccharides (LPS) put little holes in the gut lining to disrupt tight junctions and allow pathogens to circulate in the bloodstream.

The fix

To prevent or treat dysbiosis, you’ll want to incorporate the tips in the second section above, as well as:

  • regulate inflammation with omega-3 fatty acids

  • get more vitamin D (a major immunity modulator) through sunshine and supplementation

  • add anti-inflammatory curcumin (the active ingredient in turmeric) to your diet

  • integrate antioxidant-rich foods and drinks to your diet to protect against free radical damage

  • prioritize immune-boosting vitamin C and zinc in your diet and supplement routine

  • take probiotic supplements and/or eat foods rich in probiotics, which help to heal your gut and thus serve as a good protection against autoimmune diseases


Final Thoughts

As we can see, there are a few factors that go beyond genetics that contribute to autoimmune diseases.

While autoimmunity is more common than ever before, it’s worth being at least a little optimistic since there are many ways in which you can protect yourself against them—including, of course, boosting your gut health.

I’m blessed to say that, over the years, I’ve helped dozens of clients with autoimmune diseases recover from their symptoms and reclaim their health—all through discovering root causes, implementing functional medicine, and offering individualized protocols for gut restoration.


Whether you currently suffer from an autoimmune disease or want to take proactive measures to help prevent the development of illness, I’d be happy to chat about your options. Get in touch to begin to benefit from your gut health and total well-being yet.

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