Joanne, 43, received a diagnosis of Hashimoto’s hypothyroidism and gluten sensitivity from her functional medicine doctor. Her doctor placed her on a leaky gut diet that eliminated gluten and all grains and prescribed multiple supplements for leaky gut, and high doses of vitamin D and probiotics. The protocol resulted in modest improvements, but she still suffered from symptoms. She always felt fatigued, especially in the afternoon and after meals. Some days, her symptoms returned full force even though she followed her diet and took her supplements.
She started to feel hopeless and confused, partly because her doctor gave her the impression that her autoimmunity would go into remission when she fixed her leaky gut.
Joanne’s story is like many other patients’ stories I have heard over the years. Unfortunately, Joanne’s functional medicine doctor may have been a bit naïve about clinical realities. This happens with practitioners with little experience treating chronically ill patients. Many learn at seminars that if they can cure their patient’s leaky gut, they can cure their autoimmunity. Unfortunately, the leaky gut model of autoimmunity is not as simple as many practitioners and autoimmune patients realize.
The Many Causes of Autoimmunity
When it comes to what causes autoimmunity, the media gives the impression that this terrible mystery strikes without rhyme or reason. Newspaper articles frequently fall back on the “hygiene hypothesis,” the notion that we develop autoimmune diseases because we are too clean. Although that can play a role, it’s much more complex than that, and I’m not sure we can point to any one factor. In exhaustively reading the scientific literature on this topic over the years, I have found that many factors play a role in autoimmune disease. It’s not necessarily that a single factor—gluten, an environmental toxin, infection, leaky gut, genetics, pregnancy, a major life stressor—is the giant hammer that delivers the blow of autoimmunity, but rather that that factor is only the final nudge that sends an already precariously balanced immune system into a downward spiral of self-attack.Managing autoimmunity is not a one-size-fits-all approach. Ten people with the same autoimmune disease, such as Hashimoto’s hypothyroidism, rheumatoid arthritis, or multiple sclerosis, will have acquired it through different circumstances and require different approaches to manage it.
If you understand the various factors that play a role in autoimmunity, you have more knowledge to manage your own case. Everyone may employ a few of the same general strategies, but the key is knowing which applies to you, which ones to use first, and how to fine-tune your care based on your response. If any disease in the world needs a personalized medicine approach, it is an autoimmune disease.
For instance, take a person with Hashimoto’s whose blood sugar is out of control. She swings between symptoms of high blood sugar (falling asleep after meals) to low blood sugar (getting irritable and spaced out between meals), has trouble falling asleep or staying asleep, eats a high-carb diet, and gets crazy sugar cravings. Managing blood sugar might be a good place to begin her journey. Blood sugar surges increase inflammatory immune signalers (interleukin-17) that promote autoimmunity.
A different person with Hashimoto’s may have had a past head injury and has noticed she hasn’t been entirely the same since. She has difficulty swallowing, doesn’t seem to make enough saliva, and struggles with poor digestion and constipation. Communication between the brain and the organs may be poor for this person, perpetuating a leaky gut that promotes her autoimmunity. Brain injury has been shown to cause intestinal permeability by reducing the inputs from the brainstem to the gut. She may improve by stimulating her vagus nerve, which connects the brain to the digestive organs, through daily vagus nerve exercises.
A third person has pale nail beds, chronic fungal nail infections, cold hands and feet, and low blood pressure. His initial focus may be on improving circulation so that his blood, which carries nutrients, oxygen, and immune cells, can better reach the hands, feet, and brain.
And yet another person has multiple food sensitivities, skin rashes, achy joints, and is always bloated and gassy. She may focus first on repairing leaky gut or managing small intestine bacterial overgrowth (SIBO) and loss of oral tolerance.
How Gluten, Leaky Gut, and Autoimmunity Intersect
The functional medicine doctor described above may have been a little too optimistic, but they were on the right track. You should always address the potential for leaky gut and gluten sensitivity because they are so commonly found in autoimmune conditions. Likewise, those with leaky gut or gluten sensitivity should always address the potential for autoimmunity.Gluten Sensitivity and Autoimmunity
Wheat is not the same plant it was when our grandparents ate it. Because of the way it is altered through hybridization, sprayed with pesticides, stored, and processed today, many people’s bodies now recognize it as a new protein (antigen) and have an inflammatory reaction to it. Recent studies have found that gluten sensitivity is much more prevalent than previously thought.In my clinical experience, a gluten-free diet is a cornerstone in managing many cases of autoimmunity.
Because gluten intolerance frequently damages the gut, it often leads to other food sensitivities. As undigested food particles slip through the damaged gut wall and into the bloodstream, the immune system tags them for attack, creating sensitivities to these foods. We often see patients who have developed a sensitivity to other grains, such as rice, amaranth, teff, or millet, which people eat more of when embarking on a gluten-free diet. It’s important to screen for these along with cross-reactive foods or follow the leaky gut diet during a gut repair program. Otherwise simply eliminating gluten alone may not have any effect on helping you manage your autoimmunity.
If you struggle with autoimmunity, I can’t emphasize enough how important an anti-inflammatory diet that does not trigger immune reactions is to your success.





